bluuebunny/crossref_metadata_2025_split huggingface dataset:
A theoretical study on toluene oxidization by OH radical
Authors: Mao Yumin , Yang Lijuan , Liu Siqi , Song Yunchang , Luo Mengchao , Guo Yongxue 
Published: April 2024

AbstractToluene, a prominent member of volatile organic compounds (VOCs), exerts a substantial adverse influence on both human life and the environment. In the context of advanced oxidation processes, the ·OH radical emerges as a highly efficient oxidant, pivotal in the elimination of VOCs. This study employs computational quantum chemistry methods (G4MP2//B3LYP/6-311++G(d,p)) to systematically investigate the degradation of toluene by ·OH radicals in an implicit solvent model, and validates the rationale of choosing a single-reference method using T1 diagnostics. Our results suggest three possible reaction mechanisms for the oxidation of toluene by ·OH: firstly, the phenyl ring undergoes a hydrogen abstraction reaction followed by direct combination with ·OH to form cresol; secondly, ·OH directly adds to the phenyl ring, leading to ring opening; thirdly, oxidation of sidechain to benzoic acid followed by further addition and ring opening. The last two oxidation pathways involve the ring opening of toluene via the addition of ·OH, significantly facilitating the process. Therefore, both pathways are considered feasible for the degradation of toluene. Subsequently, the UV-H2O2 system was designed to induce the formation of ·OH for toluene degradation and to identify the optimal reaction conditions. It was demonstrated that ·OH and 1O2 are the primary active species for degrading toluene, with their contribution ranking as ·OH > 1O2. The intermediates in the mixture solution after reactions were characterized using GC–MS, demonstrating the validity of theoretical predictions. A comparative study of the toluene consumption rate revealed an experimental comprehensive activation energy of 10.33 kJ/mol, which is consistent with the preliminary activation energies obtained via theoretical analysis of these three mechanisms (0.56 kJ/mol to 13.66 kJ/mol), indicating that this theoretical method can provide a theoretical basis for experimental studies on the oxidation of toluene by ·OH.
Integrative analysis of single-cell and bulk transcriptome data reveal the significant role of macrophages in lupus nephritis
Authors: Wei Shuping , Shen Haiyun , Zhang Yidan , Liu Chunrui , Li Shoushan , Yao Jing , Jin Zhibin , Yu Hongliang 
Published: April 2024

Abstract
Objective
We attempted to identify abnormal immune cell components and signaling pathways in lupus nephritis (LN) and to identify potential therapeutic targets.

Methods
Differentially expressed genes (DEGs) between LN and normal kidney tissues were identified from bulk transcriptome data, and functional annotation was performed. The phenotypic changes in macrophages and aberrant intercellular signaling communications within immune cells were imputed from LN scRNA-seq data using trajectory analysis and verified using immunofluorescence staining. Finally, lentivirus-mediated overexpression of LGALS9, the gene encoding Galectin 9, in THP-1 cells was used to study the functional effect of this gene on monocytic cells.

Results
From bulk transcriptome data, a significant activation of interferon (IFN) signaling was observed, and its intensity showed a significantly positive correlation with the abundance of infiltrating macrophages in LN. Analysis of scRNA-seq data revealed 17 immune cell clusters, with macrophages showing the highest enrichment of intercellular signal communication in LN. Trajectory analysis revealed macrophages in LN undergo a phenotypic change from inflammatory patrolling macrophages to phagocytic and then to antigen-presenting macrophages, and secrete various pro-inflammatory factors and complement components. LGALS9 was found significantly upregulated in macrophages in LN, which was confirmed by the immunofluorescence assay. Gene functional study showed that LGALS9 overexpression in THP-1 cells significantly elicited pro-inflammatory activation, releasing multiple immune cell chemoattractants.

Conclusion
Our results present an important pathophysiological role for macrophages in LN, and our preliminary results demonstrate significant pro-inflammatory effects of LGALS9 gene in LN macrophages.
Deregulation in adult IgA vasculitis skin as the basis for the discovery of novel serum biomarkers
Authors: Bajželj Matija , Hladnik Matjaž , Blagus Rok , Jurčić Vesna , Markež Ana , Toluay Tanya Deniz , Sodin-Šemrl Snežna , Hočevar Alojzija , Lakota Katja 
Published: April 2024

Abstract
Introduction
Immunoglobulin A vasculitis (IgAV) in adults has a variable disease course, with patients often developing gastrointestinal and renal involvement and thus contributing to higher mortality. Due to understudied molecular mechanisms in IgAV currently used biomarkers for IgAV visceral involvement are largely lacking. Our aim was to search for potential serum biomarkers based on the skin transcriptomic signature.

Methods
RNA sequencing analysis was conducted on skin biopsies collected from 6 treatment-naïve patients (3 skin only and 3 renal involvement) and 3 healthy controls (HC) to get insight into deregulated processes at the transcriptomic level. 15 analytes were selected and measured based on the transcriptome analysis (adiponectin, lipopolysaccharide binding protein (LBP), matrix metalloproteinase-1 (MMP1), C-C motif chemokine ligand (CCL) 19, kallikrein-5, CCL3, leptin, C-X-C motif chemokine ligand (CXCL) 5, osteopontin, interleukin (IL)-15, CXCL10, angiopoietin-like 4 (ANGPTL4), SERPIN A12/vaspin, IL-18 and fatty acid-binding protein 4 (FABP4)) in sera of 59 IgAV and 22 HC. Machine learning was used to assess the ability of the analytes to predict IgAV and its organ involvement.

Results
Based on the gene expression levels in the skin, we were able to differentiate between IgAV patients and HC using principal component analysis (PCA) and a sample-to-sample distance matrix. Differential expression analysis revealed 49 differentially expressed genes (DEGs) in all IgAV patient’s vs. HC. Patients with renal involvement had more DEGs than patients with skin involvement only (507 vs. 46 DEGs) as compared to HC, suggesting different skin signatures. Major dysregulated processes in patients with renal involvement were lipid metabolism, acute inflammatory response, and extracellular matrix (ECM)-related processes. 11 of 15 analytes selected based on affected processes in IgAV skin (osteopontin, LBP, ANGPTL4, IL-15, FABP4, CCL19, kallikrein-5, CCL3, leptin, IL-18 and MMP1) were significantly higher (p-adj < 0.05) in IgAV serum as compared to HC. Prediction models utilizing measured analytes showed high potential for predicting adult IgAV.

Conclusion
Skin transcriptomic data revealed deregulations in lipid metabolism and acute inflammatory response, reflected also in serum analyte measurements. LBP, among others, could serve as a potential biomarker of renal complications, while adiponectin and CXCL10 could indicate gastrointestinal involvement.
Cancer survivorship: understanding the patients’ journey and perspectives on post-treatment needs
Authors: Hussey Conor , Hanbridge Moira , Dowling Maura , Gupta Ananya 
Published: April 2024

Abstract
Background
Cancer treatments have many adverse effects on patient’s health leading to poor cardiorespiratory capacity, muscular- degeneration, fatigue, loss of strength and physical function, altered body-composition, compromised immune-function, peripheral neuropathy, and reduced quality of life (QOL). Exercise programs can significantly increase functional capacity when tailored to individual needs, thus improving health. Exercise interventions in cancer rehabilitation, when supported by appropriate nutrition can be effective in attaining a healthy weight and body-composition. The successful rehabilitation program should also include psycho-social education aimed to reduce anxiety and improve motivation.

Methods
The current study aimed to collect information on the post-treatment needs of cancer patients including barriers and expectations facing them, their caregivers and their families through consultation in focus group interviews. Cancer survivors living in the Republic of Ireland were recruited from the University Hospital Galway, community-based cancer centres, cancer support groups and social media platforms to participate in the study and attend a focus group interview. The focus group discussions were designed to obtain information on the collective views of cancer survivors on relevant topics selected. The topics were developed in consultation with a patient and public involvement (PPI) group supporting the study. The topics list was circulated to all participants prior to the focus group. The interviews were audio recorded and transcribed verbatim. Focus group transcripts were analysed subjected to a thematic framework analysis using NVivo.

Results
Thirty-six participants took part in 9 focus groups. Our analysis uncovered two main themes. The first theme ‘cast adrift with no direction’ was grouped into three sub-themes: everything revolves around treatment; panic and fear; and what exercise should I be doing? The second theme ‘everybody is different’ was clustered into two sub-themes: side effects get in the way; and personalised exercise program.

Conclusion
The study highlighted the lack of information and support needed by patients living with and beyond cancer. The study also highlighted the need for a personalised exercise programme designed to target the individual patient symptoms that would be ideal for the mitigation of long term symptoms and in improving QOL.
Pseudomonas fluorescens CRBSI outbreak: complying with the standardization of invasive procedures is a step ahead in the fight against antimicrobial resistance
Authors: Volkow Patricia , Chávez-Chávez Tania Guadalupe , García-Pineda Bertha , Velázquez-Acosta Consuelo , Carpio-Guadarrama Daniel , Vilar-Compte Diana , Ibanes-Gutiérrez Cyntia 
Published: April 2024

AbstractIn the healthcare sector, the implementation of standardized procedures, such as those commonly employed in franchises to ensure consistent quality, remains underprioritized. Within this framework, we focus on the importance of standardized central venous catheter (CVC) insertion procedures to prevent healthcare-associated outbreaks. While antimicrobial resistance (AMR) may still not be the most prevalent problem in some institutions, its increasing significance certainly underlines the urgency of infection prevention.We aim to highlight this issue by describing and discussing an outbreak scenario of carbapenem-resistant (CR) Pseudomonas fluorescens bloodstream infections resulting from a deviation from the standardized CVC insertion procedure. This outbreak led to six episodes of catheter related bloodstream infection (CRBSI) in patients with hematologic malignancies, delaying their primary treatment. Nineteen patients were exposed, leading to an attack rate of 31.6%.
Dysregulation of neuroprotective lipoxin pathway in astrocytes in response to cytokines and ocular hypertension​
Authors: Karnam Shruthi , Maurya Shubham , Ng Elainna , Choudhary Amodini , Thobani Arzin , Flanagan John G , Gronert Karsten 
Published: April 2024

AbstractGlaucoma leads to vision loss due to retinal ganglion cell death. Astrocyte reactivity contributes to neurodegeneration. Our recent study found that lipoxin B4 (LXB4), produced by retinal astrocytes, has direct neuroprotective actions on retinal ganglion cells. In this study, we aimed to investigate how the autacoid LXB4 influences astrocyte reactivity in the retina under inflammatory cytokine-induced activation and during ocular hypertension. The protective activity of LXB4 was investigated in vivo using the mouse silicone-oil model of chronic ocular hypertension. By employing a range of analytical techniques, including bulk RNA-seq, RNAscope in-situ hybridization, qPCR, and lipidomic analyses, we discovered the formation of lipoxins and expression of the lipoxin pathway in rodents (including the retina and optic nerve), primates (optic nerve), and human brain astrocytes, indicating the presence of this neuroprotective pathway across various species. Findings in the mouse retina identified significant dysregulation of the lipoxin pathway in response to chronic ocular hypertension, leading to an increase in 5-lipoxygenase (5-LOX) activity and a decrease in 15-LOX activity. This dysregulation was coincident with a marked upregulation of astrocyte reactivity. Reactive human brain astrocytes also showed a significant increase in 5-LOX. Treatment with LXB4 amplified the lipoxin biosynthetic pathway by restoring and amplifying the generation of another member of the lipoxin family, LXA4, and mitigated astrocyte reactivity in mouse retinas and human brain astrocytes. In conclusion, the lipoxin pathway is functionally expressed in rodents, primates, and human astrocytes, and is a resident neuroprotective pathway that is downregulated in reactive astrocytes. Novel cellular targets for LXB4’s neuroprotective action are inhibition of astrocyte reactivity and restoration of lipoxin generation. Amplifying the lipoxin pathway is a potential target to disrupt or prevent astrocyte reactivity in neurodegenerative diseases, including retinal ganglion cell death in glaucoma.
Development and validation of a Context-sensitive Positive Health Questionnaire (CPHQ): A factor analysis and multivariate regression study
Authors: Doornenbal Brian M. , van Zutphen Tim , Beumeler Lise F. E. , Vos Rimke C. , Derks Mark , Haisma Hinke , van den Akker-van Marle M. Elske , Kiefte-de Jong Jessica C. 
Published: April 2024

Abstract
Background
The concept of Positive Health (PH) has gained increasing attention as a way of measuring individuals’ ability to adapt in the face of contextual challenges. However, a suitable measurement instrument for PH that encompasses contextual factors has not yet been developed. This paper responds to this need by developing a Context-specific Positive Health (CPH) measurement instrument that aligns with the Capability Approach (CA).

Methods
The measurement instrument was developed and tested among a representative sample of 1002 Dutch internet survey panel members with diverse sociodemographic backgrounds. The instrument was developed in two stages: a preparation phase consisting of focus groups and expert consultations, and a validation among a representative panel of Dutch citizens. The goal of the preparation phase, was to pilot test and refine previously proposed Positive Health questionnaires into an initial version of the CPHQ. The validation phase aimed to examine the initial CPHQ’s factorial validity using Factor Analysis, and its concurrent validity using Multivariate Regression Analysis.

Results
The developed questionnaire demonstrated adequate factorial and concurrent validity. Furthermore, it explicitly includes an assessment of resilience, this being a key component of PH.

Conclusions
The introduced measurement tool, the CPHQ, comprises 11 dimensions that we have labeled as follows: relaxation, autonomy, fitness, perceived environmental safety, exclusion, social support, financial resources, political representation, health literacy, resilience, and enjoyment. In this article, we present four major contributions. Firstly, we embedded the measurement in a theoretical framework. Secondly, we focused the questionnaire on a key concept of Positive Health - the “ability to adapt.” Thirdly, we addressed issues of health inequality by considering contextual factors. Finally, we facilitated the development of more understandable measurement items.
Advances in laser-based diagnostic modalities for intraoperative tissue diagnosis in neurosurgery: current practices and future perspectives
Authors: Pierre Kevin , McCann U. George , Razavi Seyedeh Mehrsa Sadat , Patel Anjali , Acevedo Amanda , Cerillo John , Raviprasad Abheek , Zhou Joseph , Rashdan Dean , Lucke-Wold Brandon 
Published: April 2024

AbstractThis review assesses laser-based diagnostic modalities for intraoperative tissue diagnosis in neurosurgical oncology, emphasizing their utility in delineating tumor margins. Technologies such as optical coherence tomography, photoacoustic imaging, and confocal microscopy are scrutinized for their capability to enhance intraoperative discernment of neoplastic versus healthy tissue. We discuss the technical advancements, limitations related to depth penetration and resolution, and innovative approaches to mitigate these challenges. Economic and regulatory considerations pertinent to the clinical adoption of these technologies are also examined. The review highlights current clinical trials and research initiatives aiming to validate and standardize these applications. It concludes by highlighting the importance of ongoing research, cross-disciplinary cooperation, and professional training to integrate laser-based diagnostics into neurosurgical practice, with the ultimate goal of optimizing patient outcomes in brain tumor resection.
Role of interim positron emission tomography/computed tomography in assessment of lymphoma treatment response
Authors: Borg Salma M. , Saleh Gehad A. , Batouty Nihal M. , Mousa Amani Ezzat 
Published: April 2024

Abstract
Background
Lymphoma is the most common primary hematological malignancy. FDG PET/CT has recently become the standard imaging modality for clinical management owing to its ability to provide precise, non-invasive anatomical and functional data. The purpose of this study was to highlight the role of 18F FDG-PET/CT in the management of lymphoma by monitoring treatment response, providing a guide for response-adapted therapy, and predicting the final therapeutic outcome.

Methods
This was a prospective monocentric cohort observational study in which thirty-three patients with histopathologically proved lymphoma of different types performed FDG-PET/CT scanning several times throughout the 24-month duration of the study. Early-stage interim SUVmax of the most active lesion (both nodal and/or extra-nodal) was measured and statistically analyzed together with data of the international prognostic index parameters and score.

Results
Among the included 33 patients of lymphoma, international prognostic index parameters and score together with the early-stage interim SUVmax of the predominant nodal and extra-nodal sites showed statistical significance in predicting the initial as well as the final treatment response after 24 months. Using ROC analysis, we could obtain cutoff values of SUVmax of the predominant nodal lesion of 2.75 (AUC 72%, 95% CI 0.42–1.0) and SUVmax of the predominant extra-nodal lesion of 3 (AUC 70.8% and 95% CI 0.23–1.0); therefore, SUVmax of higher than these values was related to stable or progressive disease, and lower levels than these values were related to complete or partial metabolic response based on Deauville 5-point scale and Lugano response criteria.

Conclusions
Early-stage interim PET-CT SUVmax of the predominant nodal and extra-nodal lesion could be a reliable parameter in predicting initial and final therapeutic outcome in lymphoma patients.
Design and Implementation of an Opt-Out, End-to-End, Preemptive DPYD Testing Program for Patients Planned for a Systemic Fluoropyrimidine
Authors: Jacobson Joseph O. , Rompelman Garrett , Chen Angela , Morrison-Ma Samantha , Murray Lindsay , Ferzoco Maria , Bunnell Craig , Wagner Andrew J. , Roberts Daniel , Chan Jennifer , Block Caroline , Rubinson Douglas 
Published: April 2024

PURPOSE Several allelic variants of the gene DPYD encoding dihydropyrimidine dehydrogenase (DPD) are associated with impaired metabolism of the systemic fluoropyrimidine fluorouracil (5FU) and its oral prodrug, capecitabine, which elevates the risk for severe toxicity. Following a patient death related to capecitabine toxicity in which DPD deficiency was suspected, a multidisciplinary advisory panel was convened to develop an institution-wide approach to future patients planned for a systemic fluoropyrimidine. METHODS The panel selected an opt-out testing strategy which focused on developing reliable processes to collect and report test results and targeted education. An electronic health record–based automated reminder was designed to activate when a 5FU- or capecitabine-containing chemotherapy regimen was ordered for a patient without prior exposure to either agent and without a prior DPYD sequencing test result. DPYD testing was standardized across all sites of care, and a closed loop reporting system for abnormal test results was created. Before implementation, targeted education was provided to providers, pharmacists, and nurses, and a failure mode and effects analysis was performed. Program rollout was staged over a 6-month period. RESULTS At 10 months, the rate of preemptive testing increased from a baseline of 26% to a sustained rate of >90%. In the six network sites, the testing rate increased from 9% to 96%. A total of 1,043 patients have been tested preemptively; allelic variants have been identified in 43 (4.1%). Among 25 evaluable patients, dose reduction or change to a non–fluoropyrimidine-based regimen was accomplished in 96%. CONCLUSION Preemptive DPYD testing is feasible, and high rates of testing can be achieved using an opt-out, reminder-based program. We provide the details of the implementation and encourage others to emulate it.