bluuebunny/crossref_metadata_2025_split huggingface dataset:
BMI mediates the association of serum uric acid with bone health: a cross-sectional study of the National Health and Nutrition Examination Survey (NHANES)
Authors: Tu Jiayuan , Mo Xiaoqiao , Zhang Xiangda , Chen Zihao , Xi Lijuan , Wu Chunhui , Zeng Xiangchan , Xie Tian 
Published: June 2024

Abstract
Background
The associations between serum uric acid and osteoporosis or osteopenia remain controversial, and few studies have explored whether BMI acts as a mediators in the association between the SUA and OP/ osteopenia.

Objective
To explore the relationship between serum uric acid and osteoporosis or osteopenia among US adults.

Methods
A cross-sectional study was conducted to examine the association between serum uric acid and osteoporosis or osteopenia from four cycles of NHANES. Binary logistic regression models and restricted cubic spline models were used to evaluate the association between serum uric acid and osteoporosis or osteopenia, and interaction analysis was used to test the differences between subgroups. Mediation analysis was utilized to investigate whether BMI acts as a mediator in the association between SUA and OP/ osteopenia.

Results
12581 participants aged ≥ 18 years were included. A U-shape nonlinear relationship between SUA and osteoporosis or osteopenia in all people was found (P < 0.0001, P for nonlinear = 0.0287). There were significant interactions in age subgroups (P for interaction = 0.044), sex subgroups (P for interaction = 0.005), and BMI subgroups (P for interaction = 0.017). We further assessed the subgroups and found the optimal range of serum uric acid levels with a lower risk of osteoporosis or osteopenia was 357–535 µmol/L in males, 327–417 µmol/L in people aged ≥ 50 years, above 309 µmol/L in people aged < 50 years, 344–445 µmol/L in people with BMI ≥ 30, and above 308 µmol/L in people with BMI < 30. BMI fully mediated the association of SUA and OP/osteopenia, with a value of -0.0024(-0.0026–-0.0021). These results were robust in sensitivity analyses.

Conclusions
A complicated relationship between SUA and bone health in different populations was observed. Maintaining SUA within a specific range may be beneficial to bone health. In addition, BMI may play an important role in the association between SUA and bone health, but considering the limitations of this study, further prospective research is required.
The association between dietary inflammatory index with some cardio-metabolic risk indices among the patients with type 2 diabetes from Hoveyzeh cohort study: a cross-sectional study
Authors: Rahimlou Mehran , Ahmadi Amirhossein Ramezani , Cheraghian Bahman , Baghdadi Ghazal , Ghalishourani Samira Sadat , Nozarian Shadi , Hashemi Seyed Jalal , Rahimi Zahra , Jahromi Nasrin Banaei , Hosseini Seyed Ahmad 
Published: June 2024

Abstract
Background
The dietary inflammatory index (DII) serves as a tool to assess the inflammatory impact of an individual’s diet. This study aimed to investigate the association between DII and some cardio-metabolic risk indices among patients with T2DM.

Methods
Data from the Hoveyzeh Cohort Study, encompassing 2045 adults with T2DM, were analyzed. DII scores were calculated based on food frequency questionnaires. Anthropometric measurements and biochemical tests were performed to assess cardio-metabolic risk factors.

Results
Higher DII scores were positively associated with elevated triglyceride levels, triglyceride-glucose (TyG) index, lipid accumulation product (LAP), anthropometric indices including a body shape index (ABSI), body roundness index (BRI), body mass index (BMI), hip, waist circumferences (WC), and waist-to-height ratio (all Ptrend < 0.05). Notably, no significant association was observed between DII and fasting blood sugar (FBS) levels (Ptrend > 0.05). Additionally, dietary intake analysis revealed a negative correlation between DII scores and intake of fiber, fruits, vegetables, legumes, fish, seafood, dairy products, magnesium, and vitamins A, C, D, and E (all Ptrend < 0.05). Conversely, higher DII scores were associated with increased consumption of red meat, processed meat, refined cereals, potatoes, and soft drinks (all Ptrend < 0.05).

Conclusion
This study underscores the critical link between dietary inflammation, assessed by the DII score, and a multitude of cardio-metabolic risk factors in patients with T2DM. Notably, while the study did not find a significant association between DII and fasting blood sugar levels, it identified robust associations with novel anthropometric and biochemical indices indicative of cardio-metabolic risk. These findings highlight the potential of dietary interventions as a cornerstone strategy for managing T2DM and mitigating its associated complications.
Hematoma expansion prediction based on SMOTE and XGBoost algorithm
Authors: Li Yan , Du Chaonan , Ge Sikai , Zhang Ruonan , Shao Yiming , Chen Keyu , Li Zhepeng , Ma Fei 
Published: June 2024

AbstractHematoma expansion (HE) is a high risky symptom with high rate of occurrence for patients who have undergone spontaneous intracerebral hemorrhage (ICH) after a major accident or illness. Correct prediction of the occurrence of HE in advance is critical to help the doctors to determine the next step medical treatment. Most existing studies focus only on the occurrence of HE within 6 h after the occurrence of ICH, while in reality a considerable number of patients have HE after the first 6 h but within 24 h. In this study, based on the medical doctors recommendation, we focus on prediction of the occurrence of HE within 24 h, as well as the occurrence of HE every 6 h within 24 h. Based on the demographics and computer tomography (CT) image extraction information, we used the XGBoost method to predict the occurrence of HE within 24 h. In this study, to solve the issue of highly imbalanced data set, which is a frequent case in medical data analysis, we used the SMOTE algorithm for data augmentation. To evaluate our method, we used a data set consisting of 582 patients records, and compared the results of proposed method as well as few machine learning methods. Our experiments show that XGBoost achieved the best prediction performance on the balanced dataset processed by the SMOTE algorithm with an accuracy of 0.82 and F1-score of 0.82. Moreover, our proposed method predicts the occurrence of HE within 6, 12, 18 and 24 h at the accuracy of 0.89, 0.82, 0.87 and 0.94, indicating that the HE occurrence within 24 h can be predicted accurately by the proposed method.
Cartilage progenitor cells derived extracellular vesicles-based cell-free strategy for osteoarthritis treatment by efficient inflammation inhibition and extracellular matrix homeostasis restoration
Authors: Feng Kai , Wang Feng , Chen Hongfang , Zhang Rui , Liu Jiashuo , Li Xiaodong , Xie Xuetao , Kang Qinglin 
Published: June 2024

AbstractOsteoarthritis (OA) is a common degenerative joint disease which currently lacks of effective agents. It is therefore urgent and necessary to seek an effective approach that can inhibit inflammation and promote cartilage matrix homeostasis. Cartilage progenitor cells (CPCs) are identified as a cell population of superficial zone in articular cartilage which possess strong migration ability, proliferative capacity, and chondrogenic potential. Recently, the application of CPCs may represent a novel cell therapy strategy for OA treatment. There is growing evidence that extracellular vesicles (EVs) are primary mediators of the benefits of stem cell-based therapy. In this study, we explored the protective effects of CPCs-derived EVs (CPCs-EVs) on IL-1β-induced chondrocytes. We found CPCs-EVs exhibited chondro-protective effects in vitro. Furthermore, our study demonstrated that CPCs-EVs promoted matrix anabolism and inhibited inflammatory response at least partially via blocking STAT3 activation. In addition, liquid chromatography-tandem mass spectrometry analysis identified 991 proteins encapsulated in CPCs-EVs. By bioinformatics analysis, we showed that STAT3 regulatory proteins were enriched in CPCs-EVs and could be transported to chondrocytes. To promoting the protective function of CPCs-EVs in vivo, CPCs-EVs were modified with cationic peptide ε-polylysine-polyethylene-distearyl phosphatidylethanolamine (PPD) for surface charge reverse. In posttraumatic OA mice, our results showed PPD modified CPCs-EVs (PPD-EVs) effectively inhibited extracellular matrix catabolism and attenuated cartilage degeneration. Moreover, PPD-EVs down-regulated inflammatory factors expressions and reduced OA-related pain in OA mice. In ex-vivo cultured OA cartilage explants, PPD-EVs successfully promoted matrix anabolism and inhibited inflammation. Collectively, CPCs-EVs-based cell-free therapy is a promising strategy for OA treatment.
Mechanisms, combination therapy, and biomarkers in cancer immunotherapy resistance
Authors: Yang Manshi , Cui Mengying , Sun Yang , Liu Shui , Jiang Weibo 
Published: June 2024

AbstractAnti-programmed death 1/programmed death ligand 1 (anti-PD-1/PD-L1) antibodies exert significant antitumor effects by overcoming tumor cell immune evasion and reversing T-cell exhaustion. However, the emergence of drug resistance causes most patients to respond poorly to these immune checkpoint inhibitors (ICIs). Studies have shown that insufficient T-cell infiltration, lack of PD-1 expression, deficient interferon signaling, loss of tumor antigen presentation, and abnormal lipid metabolism are all considered to be closely associated with immunotherapy resistance. To address drug resistance in tumor immunotherapy, a lot of research has concentrated on developing combination therapy strategies. Currently, ICIs such as anti-PD-1 /PD-L1 antibody combined with chemotherapy and targeted therapy have been approved for clinical treatment. In this review, we analyze the mechanisms of resistance to anti-PD-1/PD-L1 therapy in terms of the tumor microenvironment, gut microbiota, epigenetic regulation, and co-inhibitory immune checkpoint receptors. We also discuss various promising combination therapeutic strategies to address resistance to anti-PD-1/PD-L1 drugs, including combining these therapies with traditional Chinese medicine, non-coding RNAs, targeted therapy, other ICIs, and personalized cancer vaccines. Moreover, we focus on biomarkers that predict resistance to anti-PD-1/PD-L1 therapy as well as combination therapy efficacy. Finally, we suggest ways to further expand the application of immunotherapy through personalized combination strategies using biomarker systems.
Comparative analysis of retroviral Gag-host cell interactions: focus on the nuclear interactome
Authors: Lambert Gregory S. , Rice Breanna L. , Maldonado Rebecca J. Kaddis , Chang Jordan , Parent Leslie J. 
Published: June 2024

AbstractRetroviruses exploit host proteins to assemble and release virions from infected cells. Previously, most studies focused on interacting partners of retroviral Gag proteins that localize to the cytoplasm or plasma membrane. Given that several full-length Gag proteins have been found in the nucleus, identifying the Gag-nuclear interactome has high potential for novel findings involving previously unknown host processes. Here we systematically compared nuclear factors identified in published HIV-1 proteomic studies and performed our own mass spectrometry analysis using affinity-tagged HIV-1 and RSV Gag proteins mixed with nuclear extracts. We identified 57 nuclear proteins in common between HIV-1 and RSV Gag, and a set of nuclear proteins present in our analysis and ≥ 1 of the published HIV-1 datasets. Many proteins were associated with nuclear processes which could have functional consequences for viral replication, including transcription initiation/elongation/termination, RNA processing, splicing, and chromatin remodeling. Examples include facilitating chromatin remodeling to expose the integrated provirus, promoting expression of viral genes, repressing the transcription of antagonistic cellular genes, preventing splicing of viral RNA, altering splicing of cellular RNAs, or influencing viral or host RNA folding or RNA nuclear export. Many proteins in our pulldowns common to RSV and HIV-1 Gag are critical for transcription, including PolR2B, the second largest subunit of RNA polymerase II (RNAPII), and LEO1, a PAF1C complex member that regulates transcriptional elongation, supporting the possibility that Gag influences the host transcription profile to aid the virus. Through the interaction of RSV and HIV-1 Gag with splicing-related proteins CBLL1, HNRNPH3, TRA2B, PTBP1 and U2AF1, we speculate that Gag could enhance unspliced viral RNA production for translation and packaging. To validate one putative hit, we demonstrated an interaction of RSV Gag with Mediator complex member Med26, required for RNA polymerase II-mediated transcription. Although 57 host proteins interacted with both Gag proteins, unique host proteins belonging to each interactome dataset were identified. These results provide a strong premise for future functional studies to investigate roles for these nuclear host factors that may have shared functions in the biology of both retroviruses, as well as functions specific to RSV and HIV-1, given their distinctive hosts and molecular pathology.
Graphical Abstract
Identification of novel therapeutic targets for chronic kidney disease and kidney function by integrating multi-omics proteome with transcriptome
Authors: Si Shucheng , Liu Hongyan , Xu Lu , Zhan Siyan 
Published: June 2024

Abstract
Background
Chronic kidney disease (CKD) is a progressive disease for which there is no effective cure. We aimed to identify potential drug targets for CKD and kidney function by integrating plasma proteome and transcriptome.

Methods
We designed a comprehensive analysis pipeline involving two-sample Mendelian randomization (MR) (for proteins), summary-based MR (SMR) (for mRNA), and colocalization (for coding genes) to identify potential multi-omics biomarkers for CKD and combined the protein–protein interaction, Gene Ontology (GO), and single-cell annotation to explore the potential biological roles. The outcomes included CKD, extensive kidney function phenotypes, and different CKD clinical types (IgA nephropathy, chronic glomerulonephritis, chronic tubulointerstitial nephritis, membranous nephropathy, nephrotic syndrome, and diabetic nephropathy).

Results
Leveraging pQTLs of 3032 proteins from 3 large-scale GWASs and corresponding blood- and tissue-specific eQTLs, we identified 32 proteins associated with CKD, which were validated across diverse CKD datasets, kidney function indicators, and clinical types. Notably, 12 proteins with prior MR support, including fibroblast growth factor 5 (FGF5), isopentenyl-diphosphate delta-isomerase 2 (IDI2), inhibin beta C chain (INHBC), butyrophilin subfamily 3 member A2 (BTN3A2), BTN3A3, uromodulin (UMOD), complement component 4A (C4a), C4b, centrosomal protein of 170 kDa (CEP170), serologically defined colon cancer antigen 8 (SDCCAG8), MHC class I polypeptide-related sequence B (MICB), and liver-expressed antimicrobial peptide 2 (LEAP2), were confirmed. To our knowledge, 20 novel causal proteins have not been previously reported. Five novel proteins, namely, GCKR (OR 1.17, 95% CI 1.10–1.24), IGFBP-5 (OR 0.43, 95% CI 0.29–0.62), sRAGE (OR 1.14, 95% CI 1.07–1.22), GNPTG (OR 0.90, 95% CI 0.86–0.95), and YOD1 (OR 1.39, 95% CI 1.18–1.64,) passed the MR, SMR, and colocalization analysis. The other 15 proteins were also candidate targets (GATM, AIF1L, DQA2, PFKFB2, NFATC1, activin AC, Apo A-IV, MFAP4, DJC10, C2CD2L, TCEA2, HLA-E, PLD3, AIF1, and GMPR1). These proteins interact with each other, and their coding genes were mainly enrichment in immunity-related pathways or presented specificity across tissues, kidney-related tissue cells, and kidney single cells.

Conclusions
Our integrated analysis of plasma proteome and transcriptome data identifies 32 potential therapeutic targets for CKD, kidney function, and specific CKD clinical types, offering potential targets for the development of novel immunotherapies, combination therapies, or targeted interventions.
Using action research and a community-academic partnership to understand clinical trial participation: a patient-centered perspective
Authors: Santarossa Sara , Baber Michele , Hussein Janine , Oley Chrystal , Slangerup Kristen , Murphy Dana , Kippen Karen E. 
Published: June 2024

Abstract
Background
Clinical trials that are patient-centered appear to be more successful (e.g., clinical outcomes, improved communication, mutual empowerment, changed attitudes), thus, action research may be a field of importance. The current study explores the Formation and Execution of Activities phases of a community-academic partnership (CAP).

Methods
Members consisted of industry stakeholders, a healthcare/academic institution, and patients/families with lived experiences as cancer survivors and/or caregivers. Retrospectively, CAP members described the facilitating and/or hindering factors present in the partnership development. A document review process was used. Field notes from three CAP meetings, which focused on understanding clinical trial participation, were analyzed using a thematic approach.

Results
Seven facilitating and three hindering factors were present. Interpersonal (vs. operational) processes were referenced as influential facilitating factors more often. Themes that emerged included ‘trials as a treatment option’, ‘leaving a legacy’, and ‘timing is critical.’

Conclusion
This study provides a patient-centered perspective on barriers/challenges of clinical trial participation and how to improve future perceptions.
Dietary inflammatory index and its association with risk of metabolic syndrome and its components: a systematic review and Meta-analysis of Observational studies
Authors: Bakhshimoghaddam Farnush , Chaharlang Rezvan , Mansoori Anahita , Dehghanseresht Narges 
Published: June 2024

Abstract
Background
It is believed that the progression and development of metabolic syndrome (MetS) are associated with low-grade systemic inflammation. Several studies have suggested that the Dietary Inflammatory Index (DII), which estimates the inflammatory potential of diets, is associated with MetS. This systematic review and meta-analysis aimed to determine the relationships between DII and the MetS and its components.

Methods
Relevant articles published in English from inception to May 2024 were identified by searching electronic databases including PubMed, Scopus, and Web of Science. We included studies that reported the odds ratio (OR), relative risk (RR), or hazard ratio for the association of DII with the MetS and its components. Effect sizes were pooled using a random effects model.

Results
A total of three prospective studies and 22 cross-sectional studies were included in this meta-analysis. The results showed that pro-inflammatory diets were significantly associated with an increased risk of MetS in cohort studies (RR: 1.33; 95% confidence interval [CI]: 1.19–1.48) and cross-sectional studies (OR:1.24; 95% CI: 1.11–1.38). Meta-analysis of cross-sectional studies showed that a higher DII score was significantly associated with higher odds of hypertension (OR = 1.19; 95% CI = 1.10–1.28) and hyperglycemia (OR = 1.18; CI = 1.06–1.32). The pooled OR comparing the highest versus lowest category of DII with the odds of abdominal obesity and hypertriglyceridemia was significant only after adjustment for covariates.

Conclusions
In general, higher DII is associated with a higher risk of MetS and some of its components. Based on the findings, dietary interventions should be considered for preventing MetS from the inflammatory perspective.
Exploring the structural and electronic characteristics of phenethylamine derivatives: a density functional theory approach
Authors: Bhaskarapillai Arya , Parayil Sachidanandan , Santhamma Jayasudha , Mangalam Deepa , Anandakumar Velupillai Madhavan Thampi 
Published: June 2024

AbstractAccurate structure elucidation of biologically active molecules is crucial for designing and developing new drugs, as well as for analyzing their pharmacological activity. In this study, density functional theory calculations are applied to explore the electronic structure and properties of phenethylamine derivatives, including Amphetamine, Methamphetamine, and Methylene Dioxy Methamphetamine(MDMA). The investigation encompasses various aspects such as geometry optimization, vibrational analysis, electronic properties, Molecular Electrostatic Potential analysis, and local and global descriptor analysis. Additionally, the study utilizes Natural Bond Orbital analysis and Quantum Theory of Atoms in Molecules to investigate the chemical bonding and charge density distributions of these compounds. Experimental techniques such as Fourier transform infrared (FT-IR) and Raman spectroscopic analysis are employed in the range of 4000-400 $$cm^{-1}$$

c

m

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1

and 4000-50 $$cm^{-1}$$

c

m

-
1

, respectively. Theoretical vibrational analysis with Potential Energy Distribution(PED) assignments is conducted, and the resulting frequencies are compared to experimental spectral data, revealing good agreement. By correlating various structural parameters with the pharmacological activity of each derivative, computational structure elucidation aids in understanding the unique actions of phenethylamine derivatives. The obtained results offer a comprehensive understanding of the molecular behavior and properties of these drugs, facilitating the development of new drugs and therapies for addiction and related disorders.
Specification and survival of post-metamorphic branchiomeric neurons in a non-vertebrate chordate
Authors: Gigante Eduardo D. , Piekarz Katarzyna M. , Gurgis Alexandra , Cohen Leslie , Razy-Krajka Florian , Popsuj Sydney , Johnson Christopher J. , Ali Hussan S. , Mohana Sundaram Shruthi , Stolfi Alberto 
Published: June 2024

ABSTRACT
Tunicates are the sister group to the vertebrates, yet most species have a life cycle split between swimming larva and sedentary adult phases. During metamorphosis, larval neurons are replaced by adult-specific ones. The regulatory mechanisms underlying this replacement remain largely unknown. Using tissue-specific CRISPR/Cas9-mediated mutagenesis in the tunicate Ciona, we show that orthologs of conserved hindbrain and branchiomeric neuron regulatory factors Pax2/5/8 and Phox2 are required to specify the ‘neck’, a cellular compartment set aside in the larva to give rise to cranial motor neuron-like neurons post-metamorphosis. Using bulk and single-cell RNA-sequencing analyses, we characterize the transcriptome of the neck downstream of Pax2/5/8. We present evidence that neck-derived adult ciliomotor neurons begin to differentiate in the larva and persist through metamorphosis, contrary to the assumption that the adult nervous system is formed after settlement and the death of larval neurons during metamorphosis. Finally, we show that FGF signaling during the larval phase alters the patterning of the neck and its derivatives. Suppression of FGF converts neck cells into larval neurons that fail to survive metamorphosis, whereas prolonged FGF signaling promotes an adult neural stem cell-like fate.
Dens invaginatus: a review of its aetiology, diagnosis and clinical management
Authors: Hook Hannah , Power Gavin 
Published: June 2024

Dens invaginatus is a developmental anomaly predominantly occurring in maxillary lateral incisors, resulting in the invagination of the enamel into the dentine. This infolded area creates a void enabling the stagnation of bacteria and development of dental caries. If left untreated the caries may progress and ultimately result in pulpal necrosis. The treatment of these teeth can be challenging due to the potential complexity of the lesion. It is essential that teeth with dens invaginatus are diagnosed early allowing prophylactic treatment and prevention of pulpal necrosis. This article aims to review the aetiology, prevalence, classification, diagnosis, treatment and orthodontic considerations of teeth affected by dens invaginatus. CPD/Clinical Relevance: Knowledge of dens invaginatus enables early diagnosis, effective management and, therefore, the best treatment outcomes.