bluuebunny/crossref_metadata_2025_split huggingface dataset:
‘The illness isn’t the end of the road’ - Patient perspectives on the initiation of and early participation in a multi-disease, community-based exercise programme
Authors: Regan-Moriarty Joanne , Hardcastle Sarah , McCallion Maire , Youell Azura , Collery Audrey , McCarren Andrew , Moyna Niall , Kehoe Brona 
Published: September 2023

AbstractBackgroundExercise is the cornerstone of cardiac rehabilitation (CR). Hospital-based CR exercise programmes are a routine part of clinical care and are typically 6-12 weeks in duration. Following completion, physical activity levels of patients decline. Multi-disease, community-based exercise programmes (MCEP) are an efficient model that could play an important role in the long-term maintenance of positive health behaviours in individuals with cardiovascular disease (CVD) following their medically supervised programme.AimTo explore patients experiences of the initiation and early participation in a MCEP programme and the dimensions that facilitate and hinder physical activity engagement.MethodsIndividuals with established CVD who had completed hospital-based CR were referred to a MCEP. The programme consisted of twice weekly group exercise classes supervised by clinical exercise professionals. Those that completed (n=31) an initial 10 weeks of the programme were invited to attend a focus group to discuss their experience. Focus groups were transcribed and analysed using reflexive thematic analysis.ResultsTwenty-four (63% male, 65.5±6.12yrs) patients attended one of four focus groups. The main themes identified were ‘Moving from Fear to Confidence’, ‘Drivers of Engagement,’ and ‘Challenges to Keeping it (Exercise) Up’.ConclusionParticipation in a MCEP by individuals with CVD could be viewed as a double-edged sword. Whilst the programme clearly provided an important transition from the clinical to the community setting, there were signs it may breed dependency and not effectively promote independent exercise. Another novel finding was the use of social comparison that provided favourable valuations of performance and increased exercise confidence.
Macrophage-fibroblast crosstalk drives Arg1-dependent lung fibrosis via ornithine loading
Authors: Yadav Preeti , Ortega Javier Gómez , Tamaki Whitney , Chien Charles , Chang Kai-chun , Biswas Nivedita , Pan Sixuan , Nilsson Julia , Yin Xiaoyang , Bhattacharyya Aritra , Boostanpour Kaveh , Jujaray Tanay , Wang Jasper , Tsukui Tatsuya , Sheppard Dean , Li Baosheng , Maishan Mazharul , Taenaka Hiroki , Matthay Michael A. , Muramatsu Rieko , Maliskova Lenka , Ghosh Arnab , Eckalbar Walter L. , Molofsky Ari B. , Wolters Paul J. , Tamaki Stanley J. , Bivona Trever , Abate Adam R. , Wagner Allon , Tharp Kevin M. , Bhattacharya Mallar 
Published: September 2023

AbstractMonocyte-derived macrophages recruited to injured tissues induce a maladaptive fibrotic response characterized by excessive production of collagen by local fibroblasts. Macrophages initiate this programming via paracrine factors, but it is unknown whether reciprocal responses from fibroblasts enhance profibrotic polarization of macrophages. We identify macrophage-fibroblast crosstalk necessary for injury-associated fibrosis, in which macrophages induced interleukin 6 (IL-6) expression in fibroblasts via purinergic receptor P2rx4 signaling, and IL-6, in turn, induced arginase 1 (Arg1) expression in macrophages. Arg1 contributed to fibrotic responses by metabolizing arginine to ornithine, which fibroblasts used as a substrate to synthesize proline, a uniquely abundant constituent of collagen. Imaging of idiopathic pulmonary fibrosis (IPF) lung samples confirmed expression ofARG1in myeloid cells, and arginase inhibition suppressed collagen expression in cultured precision-cut IPF lung slices. Taken together, we define a circuit between macrophages and fibroblasts that facilitates cross-feeding metabolism necessary for injury-associated fibrosis.
Explainable Machine Learning Reveals the Role of the Breast Tumor Microenvironment in Neoadjuvant Chemotherapy Outcome
Authors: Azimzade Youness , Haugen Mads Haugland , Tekpli Xavier , Steen Chloé B. , Fleischer Thomas , Kilburn David , Ma Hongli , Egeland Eivind Valen , Mills Gordon , Engebraaten Olav , Kristensen Vessela N. , Frigessi Arnoldo , Köhn-Luque Alvaro 
Published: September 2023

AbstractRecent advancements in single-cell RNA sequencing (scRNA-seq) have enabled the identification of phenotypic diversity within breast tumor tissues. However, the contribution of these cell phenotypes to tumor biology and treatment response has remained less understood. This is primarily due to the limited number of available samples and the inherent heterogeneity of breast tumors. To address this limitation, we leverage a state-of-the-art scRNA-seq atlas and employ CIBER-SORTx to estimate cell phenotype fractions by de-convolving bulk expression profiles in more than 2000 samples from patients who have undergone Neoad-juvant Chemotherapy (NAC). We introduce a pipeline based on explainable Machine Learning (XML) to robustly explore the associations between different cell phenotype fractions and the response to NAC in the general population as well as different subtypes of breast tumors. By comparing tumor subtypes, we observe that multiple cell types exhibit a distinct association with pCR within each subtype. Specifically, Dendritic cells (DCs) exhibit a negative association with pathological Complete Response (pCR) in Estrogen Receptor positive, ER+, (Luminal A/B) tumors, while showing a positive association with pCR in ER-(Basal-like/HER2-enriched) tumors. Analysis of new spatial cyclic immunoflu-orescence data and publicly available imaging mass cytometry data showed significant differences in the spatial distribution of DCs between ER subtypes. These variations underscore disparities in the engagement of DCs within the tumor microenvironment (TME), potentially driving their divergent associations with pCR across tumor subtypes. Overall, our findings on 28 different cell types provide a comprehensive understanding of the role played by cellular compo-nents of the TME in NAC outcomes. They also highlight directions for further experimental investigations at a mechanistic level.
Clinically relevant orthotopic pancreatic cancer models for adoptive T cell therapy
Authors: Horvat Natalie K. , Karpovsky Isaac , Phillips Maggie , Wyatt Megan , Hall Margaret A. , Herting Cameron , Hammons Jacklyn , Mahdi Zaid , Moffitt Richard A. , Paulos Chrystal M. , Lesinski Gregory B. 
Published: September 2023

AbstractPancreatic ductal adenocarcinoma (PDAC) is an aggressive tumor. Prognosis is poor and survival is low in patients diagnosed with this disease; ∼12% at 5 years. Immunotherapy, including adoptive T cell transfer therapy, has not impacted outcomes in PDAC patients, due in part to the hostile tumor microenvironment (TME) which limits T cell trafficking and persistence. We posit that murine models serve as useful tools to study the fate of T cell therapy. Currently, genetically engineered mouse models (GEMM) for PDAC are considered a “gold-standard” as they recapitulate many aspects of human disease. However, these models have limitations, including marked tumor variability across individual mice and cost of colony maintenance. We characterized the immunologic features and trafficking patterns of adoptively transferred T cells in orthotopic PDAC models using two mouse cell lines, KPC-Luc and MT-5, isolated from KPC-GEMM mouse models (KrasLSL-G12D/+p53-/-and KrasLSL-G12D/+p53LSL-R172H/+, respectively). The MT-5 orthotopic model best recapitulates the cellular and stromal features of the TME in the PDAC GEMM. In contrast, far more host immune cells infiltrate KPC-Luc tumors, which have less stroma. Albeit CD4+ T cells were similarly detected in MT-5 tumors compared to KPC-GEMM in mice. Interestingly, we found that CAR T cells redirected to recognize mesothelin on these tumors that signal via CD3σ and 41BB (Meso-41BBσ-CAR T cells) post antigen recognition infiltrated the tumors of mice bearing stroma-devoid KPC-Luc orthotopic tumors, but not MT-5 tumors. Our data establish for the first time a reproducible and realistic clinical system useful for modeling stroma-rich and stroma-devoid PDAC tumors. These models shall serve in-depth study of how to overcome barriers that limit anti-tumor activity of adoptively transferred T cells.
Neutrophil-fibroblast crosstalk drives immunofibrosis in Crohn’s disease through IFNα pathway
Authors: Gavriilidis Efstratios , Divolis Georgios , Natsi Anastasia-Maria , Kafalis Nikolaos , Kogias Dionysios , Antoniadou Christina , Synolaki Evgenia , Pavlos Evgenios , Koutsi Marianna A. , Didaskalou Stylianos , Tsironidou Victoria , Gavriil Ariana , Papadopoulos Vasileios , Agelopoulos Marios , Tsilingiris Dimitrios , Koffa Maria , Giatromanolaki Alexandra , Kouklakis Georgios , Ritis Konstantinos , Skendros Panagiotis 
Published: September 2023

AbstractThis study investigated the interaction between neutrophils and intestinal fibroblasts in Crohn’s disease (CD) immunofibrosis. Peripheral neutrophils, enriched-neutrophil extracellular traps (eNETs), serum, primary intestinal fibroblasts (PIFs) and intestinal biopsies were studied. Neutrophils’ RNA-sequencing, multi-cytokine profiling and cell-based functional assays at mRNA/protein level were performed. Compared to ulcerative colitis (UC), PIFs from CD patients displayed a distinct fibrotic phenotype characterized by negative Krüppel-like Factor-2 (KLF2) and increased cellular communication network factor-2 (CCN2) expression leading to collagen production. PIFs-derived IL-8 appears as a culprit chemoattractant of neutrophils in the intestine, where CD neutrophils were accumulated close to fibrotic lesions. Functionally, only CD neutrophilsviaeNETs can induce a CD-like phenotype in HI PIFs. High serum IFNα and IFΝ-responsive signature in neutrophils were observed in CD, distinguishing it from UC. Moreover, CD serum can stimulate the release of fibrogenic eNETs in an IFNα-dependent manner, suggesting the priming role of IFNα in circulating neutrophils. Inhibition of eNETs or JAK signaling in neutrophils or PIFs prevented the neutrophil-mediated fibrotic effect on PIFs. Furthermore, serum IFNα and transcripts of key IFN-signaling components in neutrophils were well-correlated with CD severity. This study reveals the role of IFNα/neutrophil/fibroblast axis in CD immunofibrosis, suggesting candidate biomarkers and therapeutic targets.
Molecular Landscape and Contemporary Prognostic Signatures of Gliomas
Authors: Ghosh Hia S. , Patel Ruchit V. , Woodward Eleanor , Greenwald Noah F. , Bhave Varun M. , Maury Eduardo A. , Cello Gregory , Hoffman Samantha E. , Li Yvonne , Gupta Hersh , Spurr Liam F. , Vogelzang Jayne , Touat Mehdi , Dubois Frank , Cherniack Andrew D. , Guo Xiaopeng , Tavakol Sherwin , Cioffi Gino , Lindeman Neal I. , Ligon Azra H. , Chiocca E. Antonio , Reardon David A. , Wen Patrick Y. , Meredith David , Santagata Sandro , Barnholtz-Sloan Jill S. , Ligon Keith L. , Beroukhim Rameen , Bi Wenya Linda 
Published: September 2023

AbstractMolecularly-driven treatments are expanding options for patients with gliomas, driving a need for molecularly-informed prognostic information. To characterize the genomic landscape and contemporary outcomes of gliomas, we analyzed 4,400 gliomas from multi-institutional datasets and The Cancer Genome Atlas (TCGA): 2,195 glioblastoma, 1,198IDH1/2-mutant astrocytoma, 531 oligodendroglioma, 271 otherIDH1/2-wildtype glioma, and 205 pediatric-type glioma. Molecular classification updated 27.4% of gliomas from their original histopathologic diagnosis. Canonical alterations helped categorize glioma subtypes, revealing mutually exclusive alterations within tumorigenic pathways. Across each glioma subtype, non-TCGA patients had longer survival compared to TCGA patients. Several novel prognostic alterations emerged, includingNF1alteration and 21q loss in glioblastoma, andEGFRamplification and 22q loss inIDH1/2-mutant astrocytoma. Certain prognostic features varied across age, with decreasing prevalence ofIDH1/2-mutation over time whileMGMT-methylation remained steady. Our findings provide a framework for further exploration and validation of glioma prognostic indicators in clinically representative cohorts and trials.
The non–muscle actinopathy–associated mutation E334Q in cytoskeletal γ– actin perturbs interaction of actin filaments with myosin and ADF/cofilin family proteins
Authors: Greve Johannes N. , Marquardt Anja , Heiringhoff Robin , Reindl Theresia , Thiel Claudia , Donato Nataliya Di , Taft Manuel H. , Manstein Dietmar J. 
Published: September 2023

AbstractVarious heterozygous cytoskeletal γ–actin mutations have been shown to cause Baraitser–Winter cerebrofrontofacial syndrome, non–syndromic hearing loss, or isolated eye coloboma. Here, we report the biochemical characterization of human cytoskeletal γ–actin carrying mutation E334Q, a mutation that leads to a hitherto unspecified non–muscle actinopathy. Following expression, purification, and removal of linker and thymosin β4 tag sequences, the p.E334Q monomers show normal integration into linear and branched actin filaments. The mutation does not affect thermal stability, actin filament nucleation, elongation and turnover. Model building and normal mode analysis predict significant differences in the interaction of p.E334Q–filaments with myosin motors and members of the ADF/cofilin family of actin–binding proteins. Assays probing the interactions of p.E334Q–filaments with human class 2 and class 5 myosin motor constructs show significant reductions in sliding velocity and actin–affinity. E334Q differentially affects cofilin-mediated actin dynamics by increasing the rate of cofilin-mediatedde novonucleation of actin filaments and decreasing the efficiency of cofilin-mediated filament severing. Thus, it is likely that p.E334Q-mediated changes in myosin motor activity, as well as filament turnover contribute to the observed disease phenotype.
PI-(3,5)P2-mediated oligomerization of the endosomal sodium/proton exchanger NHE9
Authors: Kokane Surabhi , Meier Pascal F. , Gulati Ashutosh , Matsuoka Rei , Pipatpolkai Tanadet , Albano Giuseppe , Delemotte Lucie , Fuster Daniel , Drew David 
Published: September 2023

AbstractNa+/H+exchangers are found in all cells to regulate intracellular pH, sodium levels and cell volume. Na+/H+exchangers are physiological homodimers that operate by an elevator alternating-access mechanism. While the structure of the core ion translocation domain is fairly conserved, the scaffold domain and oligomerization show larger structural variation. The Na+/H+exchanger NhaA fromE. colihas a weak oligomerization interface mediated by a β-hairpin domain and homodimerization was shown to be dependent of the lipid cardiolipin. Organellar Na+/H+exchangers NHE6, NHE7 and NHE9 are likewise predicted to contain β-hairpin domains and a recent analysis ofhorseNHE9 indicated that the lipid PIP2binds at the dimerization interface. Despite predicted lipid-mediated oligomerization, their structural validation has been lacking. Here, we report cryo-EM structures ofE. coliNhaA andhorseNHE9 with the coordination of cardiolipin and PI(3,5)P2binding at the dimer interface, respectively. Cell based assays confirms that NHE9 is inactive at the plasma membrane and thermal-shift assays, solid-supported membrane (SSM) electrophysiology and MD simulations, corroborates that NHE9 specifically binds the endosomal PI(3,5)P2lipid, which stabilizes the homodimer and enhances activity. Taken together, we propose specific lipids regulate Na+/H+exchange activity by stabilizing oligomerization and stimulating Na+binding under lipid-specific cues.
Friction forge riveting of AA7075-T6 sheets with large diameter 2117-T3 rivets
Authors: Soylak Mustafa , Erturun Veysel 
Published: September 2023

Purpose
The purpose of this paper is to examine the effect of changing some riveting parameters on the riveting quality of a riveted aircraft structure. In this study, riveting was performed by applying friction under pressure.

Design/methodology/approach
During this friction riveting process, a feed of 3 mm/min was applied in the axial direction. Rotation speed values of 2,000, 2,200 and 2,400 rpm were selected. A 3-axis die milling machine was used to achieve the required positioning, pressing force and friction effect. 1.27 mm-thick Al 7075-T6 sheets and 2117-T3 forged rivets were used. The feed rate was applied at 1 mm/min in both tensile shear and cross-tensile tests.

Findings
The feasibility of friction riveting in 2117-T3 rivets was examined, it was shown that it could be done, and the most suitable rotation value for this process was determined.

Originality/value
Clamping force is one of the most important parameters for riveting quality. This study will contribute to a better understanding of the friction-forging riveting process along with the effects of riveting parameters. At the same time, it will lead to more research and expand the application of friction forging riveting to more structural connections.
Eddy current losses in power voltage transformer open-type cores
Authors: Frljić Stjepan , Trkulja Bojan , Drandić Ana 
Published: September 2023

Purpose
The purpose of this paper is to present a methodology for calculating eddy current losses in the core of a single-phase power voltage transformer, which, unlike a standard power transformer, has an open-type core (I-type core). In those apparatus, reduction of core losses is achieved by using a multipart open-type core that is created by merging a larger number of leaner cores.

Design/methodology/approach
3D FEM approach for calculation of eddy current losses in open-type cores based on a weak AλA formulation is presented. Method in which redundant degrees of freedom are eliminated is shown. This enables faster convergence of the simulation. The results are benchmarked using simulations with standard AVA formulation.

Findings
Results using weak AλA formulation with elimination of redundant degrees of freedom are in agreement with both simulation using only weak AλA formulation and with simulation based on AVA formulation.

Research limitations/implications
The presented methodology is valid in linear cases, whereas the nonlinear case will be part of future work.

Practical implications
Presented procedure can be used for the optimization when designing the open-type core of apparatus like power voltage transformers.

Originality/value
The presented method is specifically adapted for calculating eddy currents in the open-type core. The method is based on a weak formulation for the magnetic vector potential A and the current vector potential λ, incorporating numerical homogenization and a straightforward elimination of redundant degrees of freedom, resulting in faster convergence of the simulation.
The relation between intellectual capital and digital transformation: a bibliometric analysis
Authors: Yilmaz Ayse Asli , Tuzlukaya Sule Erdem 
Published: September 2023

Purpose
The purpose of this study is to depict the value added by digital transformation to intellectual capital (IC) by virtue of the studies reached by the literature review on different databases are examined.

Design/methodology/approach
Journal of Intellectual Capital, which has the highest number of records from the resources included in the “Web of Science” content and covering the title of “intellectual capital” has been selected in this study. Research using bibliometric analysis has been conducted and it has been determined that the terms “digital transformation” and “intellectual capital” should be searched for simultaneously in each and every article published in the journal between the years 1975 and 2022.

Findings
A bibliometric analysis and citation mapping process are carried out considering all dimensions to reach the results and interpretation of findings. VOSviewer is used to visualize the bibliometric networks of results and findings in the form of scientific mapping, as well as to visualize the co-authorship analysis of keywords, co-authorship analysis and citation networks.

Research limitations/implications
Bibliometric analysis is a method that can be used to evaluate the performance of a single journal. However, it is important to note that bibliometric analysis has some limitations when it comes to assessing the validity of a single journal. This circumstance is elaborately described as a limitation of this study. Bibliometric analysis is a method that can be used to evaluate the performance of a single journal. However, it is important to note that bibliometric analysis has some limitations when it comes to assessing the validity of a single journal. One limitation is that bibliometric analysis is based on quantitative metrics, such as citation counts, which do not take into account the quality of the research. Therefore, bibliometric analysis alone may not provide a complete picture of the validity of a single journal. In addition, bibliometric analysis is based on the number of times a paper is cited, which can be influenced by factors such as the prestige of the journal, the field of research and the time since the publication. In conclusion, bibliometric analysis can be used to evaluate the performance of a single journal, but it is important to consider its limitations.

Originality/value
This study identified contributions, gaps and limits based on the results of a bibliometric analysis. Italy is the most influential country and the issue is structured around four clusters: IC; digital transformation; human capital; and knowledge management. As previously unexplored issues are addressed in an innovative manner, it is acceptable to underline the paper’s originality.
Causes of disputes in the construction industry – a systematic literature review
Authors: Silva Pramod Malaka , Domingo Niluka , Ameer Ali Noushad Ali Naseem 
Published: September 2023

Purpose
The construction industry is complex, human-intensive and driven by monetary values. Hence, disputes are widespread. Initial conflicts among parties may develop into a disastrous dispute that costs the project success and good relationships and affects stakeholders' expectations. There has been a focus on causes of construction-related disputes, and studies over the past three decades have attempted to identify a more comprehensive list of reasons for disputes. Some of these studies' limitations were geographical, project delivery methods and project types. The purpose of this study is to identify the most recent and conclusive list of causes of disputes based on current literature by undertaking a systematic literature review (SLR).

Design/methodology/approach
Considering the large number of studies that focused on causes of disputes, this study aims to develop a comprehensive list of causes, using a SLR, as it ensures that all previous articles in multiple databases are reviewed to produce a comprehensive outcome. A six-stage SLR was followed from background study to analysis and reporting.

Findings
Not surprisingly, the number of publications has increased over time, most from the Middle East region. The interconnected nature of the causes was widely emphasised. The SLR has produced eight common core causes of disputes. They are: poor contractual arrangements, employer-initiated scope changes, unforeseen site changes, poor contract understanding and administration, contractor’s quality of works, the inability of the contractor to achieve time targets, non- or delayed payments and poor quality of design. The majority of previous authors realised that disputes could be avoided by parties’ involvement during the early stages, avoiding being opportunistic and acting collaboratively.

Originality/value
Even though numerous studies have been carried out to identify the causes of disputes in the construction industry, none did a SLR. This study aggregates all the previous studies that focused on construction-related disputes systematically. Categorising causes based on the party primarily responsible help various stakeholders by providing a distinct list of factors to avoid that contribute to disputes.