bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced expressions of apoptosis-related proteins TRAIL, Bcl-2, and TNFR1 in NK cells of juvenile-onset systemic lupus erythematosus patients: relations with disease activity, nephritis, and neuropsychiatric involvement
Authors: Liphaus Bernadete L. , Silva Simone C. , Palmeira Patrícia , Silva Clovis A. , Goldenstein-Schainberg Claudia , Carneiro-Sampaio Magda 
Published: March 2024

BackgroundLupus pathogenesis is mainly ascribed to increased production and/or impaired clearance of dead cell debris. Although self-reactive T and B lymphocytes are critically linked to lupus development, neutrophils, monocytes, and natural killer (NK) cells have also been implicated. This study assessed apoptosis-related protein expressions in NK cells of patients with juvenile-onset systemic lupus erythematosus (jSLE) and relations to disease activity parameters, nephritis, and neuropsychiatric involvement.MethodsThirty-six patients with jSLE, 13 juvenile dermatomyositis (JDM) inflammatory controls, and nine healthy controls had Fas, FasL, TRAIL, TNFR1, Bcl-2, Bax, Bim, and caspase-3 expressions in NK cells (CD3−CD16+CD56+) simultaneously determined by flow cytometry. Disease activity parameters included Systemic Lupus Erythematosus Disease Activity Index 2000 (SLEDAI-2K) score, erythrocyte sedimentation rate, C-reactive protein level, anti-double strain DNA antibody level, complement fractions C3 and C4 levels.ResultsPatients with jSLE had a profile of significantly reduced expression of TRAIL, Bcl-2, and TNFR1 proteins in NK cells when compared to healthy controls. Similar profile was observed in patients with jSLE with active disease, positive anti-dsDNA, nephritis, and without neuropsychiatric involvement. Patients with jSLE with positive anti-dsDNA also had reduced expression of Bax in NK cells when compared healthy controls and to those with negative anti-dsDNA. Yet, patients with jSLE with negative anti-dsDNA had reduced mean fluorescence intensity (MFI) of Bim in NK cells compared to healthy controls. Patients with jSLE with nephritis also had reduced MFI of Fas in NK cells when compared to those without nephritis. In addition, in patients with jSLE, the proportion of FasL-expressing NK cells directly correlated with the SLEDAI-2K score (rs = 0.6, p = 0.002) and inversely correlated with the C3 levels (rs = −0.5, p = 0.007). Moreover, patients with jSLE had increased NK cell percentage and caspase-3 protein expression in NK cells when compared to JDM controls.ConclusionThis study extends to NK cells an altered profile of TRAIL, Bcl-2, TNFR1, Fas, FasL, Bax, Bim, and caspase-3 proteins in patients with jSLE, particularly in those with active disease, positive anti-dsDNA, nephritis, and without neuropsychiatric involvement. This change in apoptosis-related protein expressions may contribute to the defective functions of NK cells and, consequently, to lupus development. The full clarification of the role of NK cells in jSLE pathogenesis may pave the way for new therapies like those of NK cell–based.
Immune cell phenotype and function patterns across the life course in individuals from rural Uganda
Authors: Nalwoga Angela , Nakibuule Marjorie , Roshan Romin , Kwizera Mbonye Moses , Miley Wendell , Whitby Denise , Newton Robert , Rochford Rosemary , Cose Stephen 
Published: March 2024

BackgroundTo determine the pattern of immune cell subsets across the life span in rural sub-Saharan Africa (SSA), and to set a reference standard for cell subsets amongst Africans, we characterised the major immune cell subsets in peripheral blood including T cells, B cells, monocytes, NK cells, neutrophils and eosinophils, in individuals aged 3 to 89 years from Uganda.MethodsImmune phenotypes were measured using both conventional flow cytometry in 72 individuals, and full spectrum flow cytometry in 80 individuals. Epstein-Barr virus (EBV) IFN-γ T cell responses were quantified in 332 individuals using an ELISpot assay. Full blood counts of all study participants were also obtained.ResultsThe percentages of central memory (TCM) and senescent CD4+ and CD8+ T cell subsets, effector memory (TEM) CD8+ T cells and neutrophils increased with increasing age. On the other hand, the percentages of naïve T (TN) and B (BN) cells, atypical B cells (BA), total lymphocytes, eosinophils and basophils decreased with increasing age. There was no change in CD4+ or CD8+ T effector memory RA (TEMRA) cells, exhausted T cells, NK cells and monocytes with age. Higher eosinophil and basophil percentages were observed in males compared to females. T cell function as measured by IFN-γ responses to EBV increased with increasing age, peaking at 31-55 years.ConclusionThe percentages of cell subsets differ between individuals from SSA compared to those elsewhere, perhaps reflecting a different antigenic milieu. These results serve as a reference for normal values in this population.
Lactiplantibacillus plantarum-encapsulated microcapsules prepared from okra polysaccharides improved intestinal microbiota in Alzheimer’s disease mice
Authors: Hsiao Yao-Kun , Lee Bao-Hong , Wu She-Ching 
Published: March 2024

BackgroundOkra contains a viscous substance rich in water-soluble material, including fibers, pectin, proteoglycans, gum, and polysaccharides. This study explored the use of okra polysaccharides by microorganisms and their potential to improve microbiota.MethodsThe regulation of microcapsules prepared from okra polysaccharides with or without L. plantarum encapsulation on intestinal microbiota was assessed through 16S metagenomic analysis and short-chain fatty acids (SCFAs) in AppNL-G-F/NL-G-F mice (Alzheimer’s disease; AD model).ResultsWe found that Lactobacillaceae and Lactobacillus were majorly regulated by microcapsules prepared from okra polysaccharides in AD mice. Similarly, microcapsules prepared from okra polysaccharides with L. plantarum encapsulation markedly elevated the abundance of Lactobacillaceae and Lactobacillus and increased SCFAs in AD mice.ConclusionOur results suggest that microcapsules prepared from okra polysaccharides with or without L. plantarum encapsulation may improve intestinal microbiota by elevating Lactobacillus levels in AD mice.
Opsin expression varies across larval development and taxa in pteriomorphian bivalves
Authors: Hasan Md Shazid , McElroy Kyle E. , Audino Jorge A. , Serb Jeanne M. 
Published: March 2024

IntroductionMany marine organisms have a biphasic life cycle that transitions between a swimming larva with a more sedentary adult form. At the end of the first phase, larvae must identify suitable sites to settle and undergo a dramatic morphological change. Environmental factors, including photic and chemical cues, appear to influence settlement, but the sensory receptors involved are largely unknown. We targeted the protein receptor, opsin, which belongs to large superfamily of transmembrane receptors that detects environmental stimuli, hormones, and neurotransmitters. While opsins are well-known for light-sensing, including vision, a growing number of studies have demonstrated light-independent functions. We therefore examined opsin expression in the Pteriomorphia, a large, diverse clade of marine bivalves, that includes commercially important species, such as oysters, mussels, and scallops.MethodsGenomic annotations combined with phylogenetic analysis show great variation of opsin abundance among pteriomorphian bivalves, including surprisingly high genomic abundance in many species that are eyeless as adults, such as mussels. Therefore, we investigated the diversity of opsin expression from the perspective of larval development. We collected opsin gene expression in four families of Pteriomorphia, across three distinct larval stages, i.e., trochophore, veliger, and pediveliger, and compared those to adult tissues.ResultsWe found larvae express all opsin types in these bivalves, but opsin expression patterns are largely species-specific across development. Few opsins are expressed in the adult mantle, but many are highly expressed in adult eyes. Intriguingly, opsin genes such as retinochrome, xenopsins, and Go-opsins have higher levels of expression in the later larval stages when substrates for settlement are being tested, such as the pediveliger.ConclusionInvestigating opsin gene expression during larval development provides crucial insights into their intricate interactions with the surroundings, which may shed light on how opsin receptors of these organisms respond to various environmental cues that play a pivotal role in their settlement process.
Explainable machine learning radiomics model for Primary Progressive Aphasia classification
Authors: Tafuri Benedetta , De Blasi Roberto , Nigro Salvatore , Logroscino Giancarlo 
Published: March 2024

IntroductionPrimary Progressive Aphasia (PPA) is a neurodegenerative disease characterized by linguistic impairment. The two main clinical subtypes are semantic (svPPA) and non-fluent/agrammatic (nfvPPA) variants. Diagnosing and classifying PPA patients represents a complex challenge that requires the integration of multimodal information, including clinical, biological, and radiological features. Structural neuroimaging can play a crucial role in aiding the differential diagnosis of PPA and constructing diagnostic support systems.MethodsIn this study, we conducted a white matter texture analysis on T1-weighted images, including 56 patients with PPA (31 svPPA and 25 nfvPPA), and 53 age- and sex-matched controls. We trained a tree-based algorithm over combined clinical/radiomics measures and used Shapley Additive Explanations (SHAP) model to extract the greater impactful measures in distinguishing svPPA and nfvPPA patients from controls and each other.ResultsRadiomics-integrated classification models demonstrated an accuracy of 95% in distinguishing svPPA patients from controls and of 93.7% in distinguishing svPPA from nfvPPA. An accuracy of 93.7% was observed in differentiating nfvPPA patients from controls. Moreover, Shapley values showed the strong involvement of the white matter near left entorhinal cortex in patients classification models.DiscussionOur study provides new evidence for the usefulness of radiomics features in classifying patients with svPPA and nfvPPA, demonstrating the effectiveness of an explainable machine learning approach in extracting the most impactful features for assessing PPA.
Oral rehabilitation and associated quality of life following mandibular reconstruction with free fibula flap: a cross-sectional study
Authors: Ritschl Lucas M. , Singer Hannes , Clasen Franz-Carl , Haller Bernhard , Fichter Andreas M. , Deppe Herbert , Wolff Klaus-Dietrich , Weitz Jochen 
Published: March 2024

IntroductionMandibular reconstruction with the free fibula flap (FFF) has become a standardized procedure. The situation is different with oral rehabilitation, so the purpose of this study was to investigate the frequency of implant placement and prosthetic restoration. Additionally, the patients’ situation, motivation, and treatment course were structurally assessed.Materials and methodsAll cases between January 2013 and December 2018 that underwent mandibular reconstruction in our department with a free fibula flap and gave written informed consent to participate were interviewed with two structured questionnaires about their restoration and quality of life. Additionally, medical records, general information, status of implants and therapy, and metric analyses of the inserted implants were performed.ResultsIn total 59 patients were enrolled and analyzed in this monocentric study. Overall, oral rehabilitation was achieved in 23.7% at the time of investigation. In detail, implants were inserted in 37.3% of patients and showed an 83.3% survival of dental implants. Of these implanted patients, dental implants were successfully restored with a prosthetic restoration in 63.6. Within this subgroup, satisfaction with the postoperative aesthetic and functional result was 79.9% and with the oral rehabilitation process was 68.2%. Satisfaction with the implant-borne prosthesis was 87.5%, with non-oral-squamous-cell-carcinoma patients being statistically significantly more content with the handling (p=0.046) and care (p=0.031) of the prosthesis.DiscussionDespite the well-reconstructed bony structures, there is a need to increase the effort of achieving oral rehabilitation, especially looking at the patient’s persistent motivation for the procedure.
Application of machine learning combined with population pharmacokinetics to improve individual prediction of vancomycin clearance in simulated adult patients
Authors: Li Guodong , Sun Yubo , Zhu Liping 
Published: March 2024

Background and aim:Vancomycin, a glycopeptide antimicrobial drug. PPK has problems such as difficulty in accurately reflecting inter-individual differences, and the PPK model may not be accurate enough to predict individual pharmacokinetic parameters. Therefore, the aim of this study is to investigate whether the application of machine learning combined with the PPK method can improve the prediction of vancomycin CL in adult Chinese patients.Methods:In the first step, a vancomycin CL prediction model for Chinese adult patients is given by PPK and Hamilton Monte Carlo sampling is used to obtain the reference CL of 1,000 patients; the second step is to obtain the final prediction model by machine learning using an appropriate model for the predictive factor and the reference CL; and the third step is to randomly select, in the simulated data, a total of 250 patients for prediction effect evaluation.Results:XGBoost model is selected as final machine learning model. More than four-fifths of the subjects’ predictive values regarding vancomycin CL are improved by machine learning combined with PPK. Machine learning combined with PPK models is more stable in performance than the PPK method alone for predicting models.Conclusion:The first combination of PPK and machine learning for predictive modeling of vancomycin clearance in adult patients. It provides a reference for clinical pharmacists or clinicians to optimize the initial dosage given to ensure the effectiveness and safety of drug therapy for each patient.
Combined miRNA and mRNA sequencing reveals the defensive strategies of resistant YHY15 rice against differentially virulent brown planthoppers
Authors: Yu Bin , Geng Mengjia , Xue Yu , Yu Qingqing , Lu Bojie , Liu Miao , Shao Yuhan , Li Chenxi , Xu Jingang , Li Jintao , Hu Wei , Tang Hengmin , Li Peng , Liu Qingsong , Jing Shengli 
Published: March 2024

IntroductionThe brown planthopper (BPH) poses a significant threat to rice production in Asia. The use of resistant rice varieties has been effective in managing this pest. However, the adaptability of BPH to resistant rice varieties has led to the emergence of virulent populations, such as biotype Y BPH. YHY15 rice, which carries the BPH resistance gene Bph15, exhibits notable resistance to biotype 1 BPH but is susceptible to biotype Y BPH. Limited information exists regarding how resistant rice plants defend against BPH populations with varying levels of virulence.MethodsIn this study, we integrated miRNA and mRNA expression profiling analyses to study the differential responses of YHY15 rice to both avirulent (biotype 1) and virulent (biotype Y) BPH.ResultsYHY15 rice demonstrated a rapid response to biotype Y BPH infestation, with significant transcriptional changes occurring within 6 hours. The biotype Y-responsive genes were notably enriched in photosynthetic processes. Accordingly, biotype Y BPH infestation induced more intense transcriptional responses, affecting miRNA expression, defenserelated metabolic pathways, phytohormone signaling, and multiple transcription factors. Additionally, callose deposition was enhanced in biotype Y BPH-infested rice seedlings.DiscussionThese findings provide comprehensive insights into the defense mechanisms of resistant rice plants against virulent BPH, and may potentially guide the development of insect-resistant rice varieties.
Higher serum chromium level may be associated with the presentation of depression in patients with metabolic dysfunction-associated fatty liver disease: evidence from NHANES survey
Authors: Li Xiuhua , Xia Xuezhong , Jiang Bolin , Yao Yao , Ding Fengjiao , Qin Shanyu 
Published: March 2024

BackgroundDepressive symptoms are frequently observed in patients with Metabolic Dysfunction-Associated Fatty Liver Disease (MAFLD), a prevalent metabolic disorder that affects many individuals. It is not yet clear whether there is an association between serum chromium levels and depression.ObjectiveThe purpose of this research was to explore the association between serum chromium level and the manifestation of depression among patients with MAFLD.MethodsThe selection of 1837 patients diagnosed with MAFLD was based on data obtained from the 2017-2018 National Health and Nutrition Examination Survey (NHANES) database in this research. The Patient Health Questionnaire-9 (PHQ-9) was employed to evaluate the severity of depression. The researchers utilized logistic regression models that were weighted for multiple variables to investigate the association between depression and serum chromium levels.ResultsIn our study, we found that 8.98% of US adults with MAFLD were suffering from depression at the time of evaluation. In the logistic regression model, serum chromium levels showed an inverse association with depression (OR=0.82, 95%CI: 0.69-0.96; p=0.016), this relationship remained after adjusting for fully confounding factors (OR=0.83, 95%CI: 0.71-0.97; p=0.021), subgroup analyses showed that the association between serum chromium levels and depression existed in relatively high-prevalence of depression groups.ConclusionPatients diagnosed with MAFLD have a greater likelihood of experiencing depression, whereas individuals with higher levels of serum chromium are less likely to suffer from depression, and this association persists even after adjusting for other factors. These findings indicate supplementing chromium may be a viable treatment for their depressive symptoms.
The meaningfulness of exploring one's own limits through interactions and enjoyment in outdoor high-intensity physiotherapy for people with multiple sclerosis: a qualitative study
Authors: Dahl Stine Susanne Haakonsen , Arntzen Ellen Christin , Normann Britt 
Published: March 2024

Background and purposePhysical activity (PA) is often reduced in people with MS (pwMS), even when disability is low. Understanding the perspectives of pwMS on interventions aiming to improve PA is important to inform the development of such services. The aim of this study was to explore the experiences of pwMS participating in an outdoor, high-intensity and balance exercise group intervention.MethodsThis qualitative study was nested within an RCT exploring a novel intervention integrating sensorimotor exercises with high-intensity intervals of running/walking. Individual, in-depth interviews with the intervention group (n = 15; 12 women, 3 men; age 38–66; EDSS score 0–3.5) were conducted postintervention (mean days = 14), analyzed using a phenomenological-inspired approach with systematic text condensation, and interpreted based on enactive theory.ResultsFour categories were generated: (1) Exploration of one's own physical abilities: Challenging one's own limits was perceived by all participants to improve movement performance and/or intensity level. Such bodily changes engendered strong positive feelings. Some negative consequences of high-intensity training were described, increasing a feeling of loss. (2) New insights and beliefs: Participants experienced enhanced beliefs in their own capabilities, which they integrated in activities outside the intervention. (3) An engaging environment: The group setting was perceived as supportive, and the outdoor environment was perceived as stimulating activity. (4) Professional leadership, tailoring and co-creation of enjoyment: Physiotherapist-led, individualized interactions were regarded as necessary to safely revisit prior activities, such as running. Co-creating enjoyment facilitated high-intensity training and intervention adherence.DiscussionHigh-intensity training combined with detailed exercises in a physiotherapy outdoor group was perceived to create meaningful bodily changes and enhance PA and prospects for both PA and life. Importantly, however, some negative experiences were also reported from the high-intensity training. Enactive theory allowed for the illumination of new perspectives: the importance of embodiment for self-efficacy and of tailored physiotherapy and an outdoor-group environment for exploring one's own limits to physical capabilities. These aspects should inform future exercise interventions in pwMS with low disability.
Comprehensive identification, localization, and validation of innovation measurement indices at the farm level in Iran
Authors: Farsani Elahe Davoodi , Choobchian Shahla , Naghani Moslem Shirvani 
Published: March 2024

IntroductionInnovation is a fundamental component of agricultural infrastructure, fostering the sector’s development and productivity. Innovation indices tailored to the farm level are benchmarks for assessing innovation within this agricultural context. Therefore, this study aims to discover, localize, and validate comprehensive innovation measurement indices at the farm level. A distinguishing feature of this research is its endeavor to discover and validate a comprehensive tool for measuring innovation at the farm level. Notably, there has been no prior research on discovering comprehensive innovation indices at the farm level, marking a novel aspect of this study.Method and resultsThe current research is applied in terms of its purpose and falls into the category of mixed research (quantitative and qualitative), as well as exploratory and descriptive research. This study has been conducted in three stages: The first phase involved reviewing existing literature and extracting indices for measuring innovation. In the second phase, a tool was designed specifically to gauge innovation at the farm level. The third phase entailed face and content validation of the identified indices. This validation process was conducted quantitatively and qualitatively through surveys of subject-matter experts in Iran, and by calculating the content validity ratio (CVR) and content validity index (CVI).To measure innovation at the farm level, 90 items across 7 dimensions (education, infrastructure, market sophistication, business sophistication, knowledge and technology outputs, creative outputs, and innovative outputs) were extracted, localized, and developed. According to the results, dimensions such as innovative outputs (product innovation, process innovation, and marketing innovation), education (farmers’ education status in technology and innovation), and infrastructure (familiarity, access, and application of Information and Communication Technology [ICT]) demonstrated high credibility based on CVR and CVI scores.ConclusionThe utilization of innovation assessment indices can help mitigate the challenges associated with evaluating innovation status on farms, thereby enhancing their condition and increasing farmers’ profitability. Accurate and reliable data on innovation status empower farmers in market competition and improve economic performance. Attention to innovation and the use of assessment tools can facilitate the attraction of new investors to the agricultural industry. Furthermore, improving agricultural processes through innovative technologies can contribute to the preservation of natural resources and the reduction of environmental pollution.