bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the potential role of palladin in modulating human CAF/ECM functional units
Authors: Dolskii Aleksandr , Alcantara dos Santos Sérgio A. , Andrake Mark , Franco‐Barraza Janusz , Dunbrack Roland L. , Cukierman Edna 
Published: September 2024

AbstractFibroblasts, crucial for maintaining tissue homeostasis, significantly shape the tumor microenvironment (TME). In pancreatic cancer, a highly aggressive malignancy, cancer‐associated fibroblast (CAF)/extracellular matrix (ECM) units dominate the TME, influencing tumor initiation, progression, and treatment responses. Palladin, an actin‐associated protein, is vital for fibroblast structural integrity and activation, playing a key role in CAF/ECM functionality. Palladin interacts with cytoskeletal proteins such as alpha‐actinin (α‐Act) and can therefore regulate other proteins like syndecans, modulating cytoskeletal features, cell adhesion, integrin recycling, and signaling. In this review, we propose that targeting the palladin/α‐Act/syndecan interaction network could modulate CAF/ECM units, potentially shifting the TME from a tumor‐promoting to a tumor‐suppressive state. In silico data and reported studies to suggest that stabilizing palladin‐α‐Act interactions, via excess palladin, influences syndecan functions; potentially modulating integrin endocytosis via syndecan engagement with protein kinase C alpha as opposed to syndecan binding to α‐Act. This mechanism can then affect the distribution of active α5β1‐integrin between the plasma membrane and known intracellular vesicular compartments, thereby influencing the tumor‐suppressive versus tumor‐promoting functions of CAF/ECM units. Understanding these interactions offers likely future therapeutic avenues for stroma normalization in pancreatic and other cancers, aiming to inhibit tumor progression and improve future treatment outcomes.
Imatinib adherence prediction using machine learning approach in patients with gastrointestinal stromal tumor
Authors: Liu Li , Yu Ze , Chen Hefen , Gong Zhujun , Huang Xiao , Chen Linhua , Fan Ziying , Zhang Jinyuan , Yan Jiannan , Tian Hongkun , Zeng Xiangyu , Chen Zhiliang , Zhang Peng , Zhou Hong 
Published: September 2024

AbstractBackgroundNonadherence to imatinib is common in patients with gastrointestinal stromal tumor (GIST), which is associated with poor prognosis and financial burden. The primary aim of this study was to investigate the adherence rate in patients with GIST and subsequently develop a model based on machine learning (ML) and deep learning (DL) techniques to identify the associated factors and predict the risk of imatinib nonadherence.MethodsAll eligible patients completed four sections of questionnaires. After the data set was preprocessed, statistically significance variables were identified and further processed to modeling. Six ML and four DL algorithms were applied for modeling, including eXtreme gradient boosting, light gradient boosting machine (LGBM), categorical boosting, random forest, support vector machine, artificial neural network, multilayer perceptron, NaiveBayes, TabNet, and Wide&Deep. The optimal ML model was used to identify potential factors for predicting adherence.ResultsA total of 397 GIST patients were recruited. Nonadherence was observed in 185 patients (53.4%). LGBM exhibited superior performance, achieving a mean f1_score of 0.65 and standard deviation of 0.12. The predominant indicators for nonadherent prediction of imatinib were cognitive functioning, whether to perform therapeutic drug monitoring (if_TDM), global health status score, social support, and gender.ConclusionsThis study represents the first real‐world investigation using ML techniques to predict risk factors associated with imatinib nonadherence in patients with GIST. By highlighting the potential factors and identifying high‐risk patients, the multidisciplinary medical team can devise targeted strategies to effectively address the daily challenges of treatment adherence.
Lung Mechanics: Material Characterization of Pulmonary Constituents for an Experimentally Informed Computational Pipeline
Authors: Nelson Talyah M. , Mariano Crystal A. , Ramirez Gustavo O. , Badrou Arif , Quiros Kathrine A. M. , Shankel Matthew , Eskandari Mona 
Published: September 2024

AbstractThe lung comprises multiple components including the parenchyma, airways, and visceral pleura, where each constituent displays specific material properties that together govern the whole organ's properties. The structural and mechanical complexity of the lung has historically undermined its comprehensive characterization, especially compared to other biological organs, such as the heart or bones. This knowledge void is particularly remarkable when considering that pulmonary disease is one of the leading causes of morbidity and mortality across the globe. Establishing the mechanical properties of the lung is central to formulating a baseline understanding of its operation, which can facilitate investigations of diseased states and how the lung will potentially respond to clinical interventions. Here, we present established and widely accepted experimental protocols for pulmonary material quantification, specifying how to extract, prepare, and test each type of lung constituent under planar biaxial tensile loading to investigate the mechanical properties, such as physiological stress–strain profiles, anisotropy, and viscoelasticity. These methods are presented across an array of commonly studied species (murine, rat, and porcine). Additionally, we highlight how such material properties may inform the construction of an inverse finite element model, which is central to implementing predictive computational tools for accurate disease diagnostics and optimized medical treatments. These presented methodologies are aimed at supporting research advancements in the field of pulmonary biomechanics and to help inaugurate future novel studies. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: General procedures in lung biaxial testingAlternate Protocol 1: Parenchymal‐specific preparation and loading proceduresAlternate Protocol 2: Airway‐specific preparation and loading proceduresAlternate Protocol 3: Visceral pleura–specific preparation and loading proceduresBasic Protocol 2: Computational analysis
Genetic Manipulation of Candida glabrata
Authors: Usher Jane 
Published: September 2024

AbstractCandida glabrata (Nakaseomyces glabratus) is an opportunistic fungal pathogen that has become a significant concern in clinical settings due to its increasing resistance to antifungal treatments. Understanding the genetic basis of its pathogenicity and resistance mechanisms is crucial for developing new therapeutic strategies. One powerful method of studying gene function is through targeted gene deletion. This paper outlines a comprehensive protocol for the deletion of genes in C. glabrata, encompassing primer design, preparation of electrocompetent cells, transformation, and finally confirmation of the gene deletion. The protocol begins with the identification and design of primers necessary for generating deletion constructs, involving the precise targeting of up‐ and downstream regions flanking the gene of interest to ensure high specificity and efficiency of homologous recombination. Followed is the preparation of electrocompetent cells, a critical step for successful transformation. Transformation of the competent cells is achieved through electroporation, facilitating the introduction of exogenous DNA into the cells. This is followed by the selection and confirmation of successfully transformed colonies. Confirmation involves the use of colony PCR to verify the correct integration of the NAT resistance cassette and deletion of the target gene. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Primer design for gene deletion in C. glabrataBasic Protocol 2: Preparing competent C. glabrata cellsBasic Protocol 3: Transforming C. glabrata using electroporationBasic Protocol 4: Confirming deletion strains with colony PCR
Highly Selective Conversion of Carbon Dioxide to Methane by Copper Single Atom Electrocatalysts
Authors: Liu Yixian , Zhang Mengling , Bao Kaili , Huang Hui , Kang Zhenhui 
Published: September 2024

AbstractElectrocatalytic carbon dioxide reduction into high‐value chemicals is one of the important solutions to the greenhouse effect and energy crisis. However, the slow kinetic process of eight electrons requires the development of efficient catalysts to improve the yields. Single atom catalysts (SACs) with high activity and selectivity have become an emerging research frontier in the field of heterogeneous catalysis. Herein, a catalyst comprised of Cu single atoms loaded on carbon substrate (Cu‐NC) is developed for highly selective electrocatalytic reduction of CO2 to methane (CH4). The optimal catalyst (Cu‐NC‐1‐4) exhibits a faradaic efficiency (FE) of over 50 % for CH4 within a wide potential window from −1.3 V to −1.8 V (vs. RHE) and the highest FE of CH4 is up to 67.22 % at −1.6 V (vs. RHE). Meanwhile, the product selectivity of CH4 among all the carbon products reaches 93.00 %, and the activity decay can be negligible via the 70‐hour‐stability‐test. The existence of atomic dispersed Cu−N3 sites was verified by high‐angle annular dark field scanning transmission electron microscopy (HAADF‐STEM) and X‐ray absorption near edge structure (XANES). Density functional theory (DFT) calculations show that the effective adsorption of the key intermediate *CO on Cu−N3 sites prompts the generation of CH4.
Effects of check dam construction on sediment production and topographic changes in a gully in the Loess Plateau: A rainfall simulation experiment
Authors: Xue Shaobo , Li Peng , Cui Zhiwei , Li Zhanbin , Shen Zhenzhou 
Published: September 2024

AbstractTo maintain a reasonable sediment regulation system in the Loess Plateau, it is critical to determine the effects of check dam construction on sediment production and topographic changes. An indoor simulation experiment was conducted to investigate sediment production at the outlet section of the gully and micro‐topographic changes within the channel before and after dam construction. The results showed that check dam significantly affected the run‐off and sediment transport processes in the watershed. Specifically, the cross‐sectional morphology index (η) and the width‐depth ratio increased by 10.23% and 40.44%, respectively, while sediment content and particle size decreased by 39.29% and 18.58%, respectively. Additionally, the relative importance of section parameters and micro‐topographic parameters that affect sediment production rate and particle size was ranked using the random forest algorithm. The roughness after check dam construction was identified as a relatively important topographic factor affecting sediment production and particle selection by erosion. These findings provide valuable information for future check dam construction and development in the Loess Plateau region.
A computational mechanistic study on the formation of aryl sulfonyl fluorides via Bi(III) redox‐neutral catalysis and further rational design
Authors: Zhang Zhaoyin , Ma Qin , Yang Xing , Zhang Shuqi , Guo Kai , Zhao Lili 
Published: September 2024

AbstractSulfonyl fluorides hold significant importance as highly valued intermediates in chemical biology due to their optimal balance of biocompatibility with both aqueous stability and protein reactivity. The Cornella group introduced a one‐pot strategy for synthesizing aryl sulfonyl fluorides via Bi(III) redox‐neutral catalysis, which facilitates the transmetallation and direct insertion of SO2 into the BiC(sp2) bond giving the aryl sulfonyl fluorides. We report herein a comprehensive computational investigation of the redox‐neutral Bi(III) catalytic mechanism, disclose the critical role of the Bi(III) catalyst and base (i.e., K3PO4), and uncover the origin of SO2 insertion into the Bi(III)C(sp2) bond. The entire catalysis can be characterized via three stages: (i) transmetallation generating the Bi(III)‐phenyl intermediate IM3 facilitated by K3PO4. (ii) SO2 insertion into IM3 leading to the formation of Bi(III)‐OSOAr intermediate IM5. (iii) IM5 undergoes S(IV)‐oxidation yielding the aryl sulfonyl fluoride product 4 and liberating the Bi(III) catalyst for the next catalytic cycle. Each stage is kinetically and thermodynamically feasible. Moreover, we explored other some small molecules (NO2, CO2, H2O, N2O, etc.) insertion reactions mediated by the Bi(III)‐complex, and found that NO2 insertions could be easily achieved due to the low insertion barriers (i.e., 17.5 kcal/mol). Based on the detailed mechanistic study, we further rationally designed additional Bi(III) and Sb(III) catalysts, and found that some of which exhibit promising potential for experimental realization due to their low barriers (<16.4 kcal/mol). In this regard, our study contributes significantly to enhancing current Bi(III)‐catalytic systems and paving the way for novel Bi(III)‐catalyzed aryl sulfonyl fluoride formation reactions.
Longitudinal Multiparametric QuantitativeMRIEvaluation of Acute and Chronic Multiple Sclerosis Paramagnetic Rim Lesions
Authors: Elkady Ahmed M. , Elliott Colm , Fetco Dumitru , Araujo David , Karimaghaloo Zahra , Ganzetti Marco , Clayton David , Craveiro Licinio , Kazlauskaite Agne , Narayanan Sridar , Arnold Douglas L. , Rudko David A. 
Published: September 2024

BackgroundMultiple sclerosis (MS) paramagnetic rim lesions (PRLs) are markers of chronic active biology and exhibit complex iron and myelin changes that may complicate quantification when using conventional MRI approaches.PurposeTo conduct a multiparametric MRI analysis of PRLs.Study TypeRetrospective/longitudinal.SubjectsNinety‐five progressive MS subjects with at least one persistent PRL who were enrolled in the CONSONANCE trial.Field Strength/Sequence3‐T/Susceptibility‐weighted, T1‐weighted, T2‐weighted, and fluid‐attenuated inversion recovery.AssessmentAcute/chronic PRLs and non‐PRLs were measured at screening, 24, 48, and 96 weeks using quantitative magnetic susceptibility (QS), R2*, and standardized T1w/T2w ratio (sT1w/T2w). PRL analyses were performed for whole lesion, core, and rim. The correlations between PRL core and rim sT1w/T2w, QS, and R2* were assessed.Statistical TestsLinear mixed models. AP‐value <0.05 was considered significant.ResultsThere was a significant decrease in sT1w/T2w (−0.24 ± −5.3 × 10−3) and R2* (−3.6 ± 2.2 Hz) but a significant increase in QS (+21 ± 1.3 ppb) using whole‐lesion analysis of chronic PRLs compared to non‐PRLs at screening. Tissue damage accumulated at the 96‐week time point was more evident in acute/chronic PRLs compared to acute/chronic non‐PRLs (ΔsT1w/T2w = −0.21/−0.24 ± 0.033/0.0053; ΔR2* = −4.4/−3.6 ± 1.4/2.2 Hz). New, acute PRL sT1w/T2w significantly increased in lesion core (+4.3 × 10−3 ± 1.2 × 10−4) and rim (+5.6 × 10−3 ± 1.2 × 10−4) 24 weeks post lesion inception, suggestive of partial recovery. Chronic PRLs, contrastingly, showed significant decreases in sT1w/T2w over the initial 24 weeks for both core (−2.1 × 10−4 ± 2.0 × 10−5) and rim (−2.4 × 10−4 ± 2.0 × 10−5), indicative of irreversible tissue damage. Significant positive correlations between PRL core and rim sT1w/T2w (R2 = 0.53), R2* (R2 = 0.69) and QS (R2 = 0.52) were observed.Data ConclusionMultiparametric assessment of PRLs has the potential to be a valuable tool for assessing complex iron and myelin changes in chronic active PRLs of progressive MS patients.Level of Evidence2Technical EfficacyStage 3
ADAR1 Promotes Invasion and Migration and Inhibits Ferroptosis via the FAK/AKT Pathway in Colorectal Cancer
Authors: He Dongsheng , Niu Chao , Bai Rilan , Chen Naifei , Cui Jiuwei 
Published: September 2024

ABSTRACTThe role of adenosine deaminase acting on RNA1 (ADAR1) in colorectal cancer (CRC) is poorly understood. This study investigated the roles and underlying molecular mechanisms of ADAR1 and its isoforms, explored the correlations between ADAR1 expression and the immune microenvironment and anticancer drug sensitivity, and examined the potential synergy of using ADAR1 expression and clinical parameters to determine the prognosis of CRC patients. CRC samples showed significant upregulation of ADAR1, and high ADAR1 expression was correlated with poor prognosis. Silencing ADAR1 inhibited the proliferation, invasion, and migration of CRC cells and induced ferroptosis by suppressing FAK/AKT activation, and the results of rescue assays were consistent with these mechanisms. Both ADAR1‐p110 and ADAR1‐p150 were demonstrated to regulate the FAK/AKT pathway, with ADAR1‐p110 playing a particularly substantial role. In evaluating the prognosis of CRC patients, combining ADAR1 expression with clinical parameters produced a substantial synergistic effect. The in vivo tumorigenesis of CRC was significantly inhibited by silencing ADAR1. Furthermore, ADAR1 expression was positively correlated with tumor mutational burden (TMB) and microsatellite status (p < 0.05), indicating that ADAR1 plays a complex role in CRC immunotherapy. In conclusion, ADAR1 plays oncogenic roles in CRC both in vitro and in vivo, potentially by inhibiting ferroptosis via downregulation of the FAK/AKT pathway. Thus, ADAR1 serves as a potential prognostic biomarker and a promising target for CRC therapy.
Multicenter, multivendor validation of liver quantitative susceptibility mapping in patients with iron overload at 1.5 T and 3 T
Authors: Buelo Collin J. , Velikina Julia , Mao Lu , Zhao Ruiyang , Yuan Qing , Ghasabeh Mounes Aliyari , Ruschke Stefan , Karampinos Dimitrios C. , Harris David T. , Mattison Ryan J. , Jeng Michael R. , Pedrosa Ivan , Kamel Ihab R. , Vasanawala Shreyas , Yokoo Takeshi , Reeder Scott B. , Hernando Diego 
Published: September 2024

AbstractPurposeTo evaluate the repeatability and reproducibility of QSM of the liver via single breath‐hold chemical shift–encoded MRI at both 1.5 T and 3 T in a multicenter, multivendor study in subjects with iron overload.MethodsThis prospective study included four academic medical centers with three different MRI vendors at 1.5 T and 3 T. Subjects with known or suspected liver iron overload underwent multi‐echo spoiled gradient‐recalled‐echo scans at each field strength. A subset received repeatability testing at either 1.5 T or 3 T. Susceptibility and maps were reconstructed from the multi‐echo images and analyzed at a single center. QSM‐measured susceptibility was compared with and a commercial R2‐based liver iron concentration method across centers and field strengths using linear regression and F‐tests on the intercept and slope. Field‐strength reproducibility and test/retest repeatability were evaluated using Bland–Altman analysis.ResultsA total of 155/80 data sets (test/retest) were available at 1.5 T, and 159/70 data sets (test/retest) were available at 3 T. Calibrations across sites were reproducible, with some variability (e.g., susceptibility slope with liver iron concentration ranged from 0.102 to 0.123 g/[mgppm] across centers at 1.5 T). Field strength reproducibility was good (concordance correlation coefficient = 0.862), and test/retest repeatability was excellent (intraclass correlation coefficient = 0.951).ConclusionQSM as an imaging biomarker of liver iron overload is feasible and repeatable across centers and MR vendors. It may be complementary with as they are obtained from the same acquisition. Although good reproducibility was observed, liver QSM may benefit from standardization of acquisition parameters. Overall, QSM is a promising method for liver iron quantification.
Clinical practice guideline‐inconsistent chemotherapy‐induced vomiting prophylaxis in pediatric cancer patients in community settings: A Children's Oncology Group study
Authors: Sugalski Aaron J. , Grimes Allison C. , Nuño Michelle M. , Ramakrishnan Subhash , Beauchemin Melissa P. , Robinson Paula D. , Santesso Nancy , Walsh Alexandra M. , Wrightson Andrea R. , Yu Lolie C. , Parsons Susan K. , Sung Lillian , Dupuis L. Lee 
Published: September 2024

AbstractBackgroundThis study aimed to determine the proportion of patients receiving clinical practice guideline (CPG)‐inconsistent care related to chemotherapy‐induced vomiting (CIV) prophylaxis, and to describe the association between CPG‐inconsistent care and site size. The association between delivery of CPG‐inconsistent care and patient outcomes (CIV control, admission prolongation, and unplanned healthcare visits) was also described.MethodsThis was a retrospective study conducted at Children's Oncology Group (COG) National Cancer Institute Community Oncology Research Program (NCORP) sites. Eligible patients received highly (HEC) or moderately emetogenic chemotherapy (MEC) as inpatients from January 2014 through December 2015, and were previously enrolled in a COG study. The COG generated a patient list from which patients were randomly selected for chart review by participating sites. A central panel adjudicated CIV prophylaxis received as CPG‐consistent or ‐inconsistent.ResultsTwenty‐four sites participated. Over half of patients received CPG‐inconsistent CIV prophylaxis (HEC: 59/112, 52.6%; MEC: 119/215, 55.3%). The most common reasons for CPG‐inconsistency were shortened duration of antiemetic administration or omission of dexamethasone. Site size was not found to be associated with CPG‐inconsistent care delivery (HEC: adjusted odds ratio [OR]: 0.96, 95% confidence interval [CI]: 0.76–1.23; MEC: adjusted OR: 1.07; 95% CI: 0.92–1.24). Additionally, there was no statistically significant association between receipt of CPG‐inconsistent care and patient outcomes.ConclusionsPatients receiving MEC or HEC often received CPG‐inconsistent CIV prophylaxis. Site size was not associated with receipt of CPG‐inconsistent care. Future studies should evaluate strategies to improve CIV control among pediatric oncology patients including those aimed at improving CPG adherence.
Polycaprolactone/MSMA composites for magnetic refrigeration applications
Authors: Sánchez‐Alarcos V. , Khanna D. L. R. , La Roca P. , Recarte V. , Lambri F. D. , Bonifacich F. G. , Lambri O. A. , Royo‐Silvestre I. , Urbina A. , Pérez‐Landazábal J. I. 
Published: September 2024

AbstractA high filling load (62% weight) printable magnetic composite has been elaborated from the dispersion of magnetocaloric Ni45Mn36.7In13.3Co5 metamagnetic shape memory alloy microparticles into a PCL polymer matrix. The composite material has been prepared by solution method, resulting in a very homogeneous particles dispersion into the matrix. The structural transitions in the polymer are not affected by the addition of the metallic microparticles, which in turn results in a significant increase of the mechanical consistency. The good ductility of the elaborated composite allows its extrusion in flexible printable filaments, from which 3D pieces with complex geometries have been grown. The heat transfer of the composite material has been assessed from finite element simulation. In spite of the achievable magnetocaloric values are moderated with respect to the bulk, numerical simulations confirm that, in terms of heat transference, a PCL/Ni‐Mn‐In‐Co wire is more efficient than a bulk Ni‐Mn‐In‐Co cubic piece containing the same amount of magnetic active material. The quite good magnetocaloric response of the composite and the possibility to print high surface/volume ratio geometries make this material a promising candidate for the development of heat exchangers for clean and efficient magnetic refrigeration applications.Highlights
3D printable magnetic composites developed from dispersion of MSMA in PCL.
High filling factor and uniform dispersion characterized by SEM.
Inclusion of microparticles does not affect polymeric structural transitions.
Metallic fillers improve DMA response of 3D printed pieces.
FEM simulations endorse PCL/MSMA composites for magnetic refrigeration.