bluuebunny/crossref_metadata_2025_split huggingface dataset:
The shared circulating diagnostic biomarkers and molecular mechanisms of systemic lupus erythematosus and inflammatory bowel disease
Authors: Sun Hao-Wen , Zhang Xin , Shen Cong-Cong 
Published: May 2024

BackgroundSystemic lupus erythematosus (SLE) is a multi-organ chronic autoimmune disease. Inflammatory bowel disease (IBD) is a common chronic inflammatory disease of the gastrointestinal tract. Previous studies have shown that SLE and IBD share common pathogenic pathways and genetic susceptibility, but the specific pathogenic mechanisms remain unclear.MethodsThe datasets of SLE and IBD were downloaded from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were identified using the Limma package. Weighted gene coexpression network analysis (WGCNA) was used to determine co-expression modules related to SLE and IBD. Pathway enrichment was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis for co-driver genes. Using the Least AbsoluteShrinkage and Selection Operator (Lasso) regressionand Support Vector Machine-Recursive Feature Elimination (SVM-RFE), common diagnostic markers for both diseases were further evaluated. Then, we utilizedthe CIBERSORT method to assess the abundance of immune cell infiltration. Finally,we used the single-cell analysis to obtain the location of common diagnostic markers.Results71 common driver genes were identified in the SLE and IBD cohorts based on the DEGs and module genes. KEGG and GO enrichment results showed that these genes were closely associated with positive regulation of programmed cell death and inflammatory responses. By using LASSO regression and SVM, five hub genes (KLRF1, GZMK, KLRB1, CD40LG, and IL-7R) were ultimately determined as common diagnostic markers for SLE and IBD. ROC curve analysis also showed good diagnostic performance. The outcomes of immune cell infiltration demonstrated that SLE and IBD shared almost identical immune infiltration patterns. Furthermore, the majority of the hub genes were commonly expressed in NK cells by single-cell analysis.ConclusionThis study demonstrates that SLE and IBD share common diagnostic markers and pathogenic pathways. In addition, SLE and IBD show similar immune cellinfiltration microenvironments which provides newperspectives for future treatment.
The effect of infection with the entomopathogenic fungus Conidiobolus coronatus (Entomopthorales) on eighteen cytokine-like proteins in Galleria mellonella (Lepidoptera) larvae
Authors: Wrońska Anna Katarzyna , Kaczmarek Agata , Sobich Justyna , Boguś Mieczysława Irena 
Published: May 2024

BackgroundIn response to the replace mammal research models with insects in preliminary immunological studies, interest has grown in invertebrate defense systems. The immunological response is regulated by cytokines; however, while their role in mammals is well understood, little is known of their function in insects. A suitable target for studies into insect immunology is Galleria mellonella (Lepidoptera), the wax moth: a common host for human fungal and bacterial pathogens. G. mellonella is also a perfect subject for studies into the presence of cytokine-like proteins.Specific objectivesThe main goal of present research was detection in insect immunocompetent cells the 18 mammalian cytokines (IL-1α, IL-1β, IL-2, IL-3, IL-6, IL-7, IL-8, IL-12, IL-13, IL-15, IL-17, IL-19, IFN-γ, TNF-α, TNF-β, GM-CSF, M-CSF, G-CSF), which play important role in immunological response and indication how their level change after fungal infection.MethodologyThe changes of cytokine-like proteins level were detected in hemocytes taken from G. mellonella larvae infected with entomopathogenic fungus, C. coronatus. The presence of cytokine-proteins was confirmed with using fluorescence microscopy (in cultured hemocytes) and flow cytometry (in freshly collected hemolymph). The ELISA test was used to detect changes in concentration of examined cytokine-like proteins.ResultsOur findings indicated the presence of eighteen cytokine-like molecules in G. mellonella hemocytes during infection with C. coronatus. The hemocytes taken from infected larvae demonstrated higher fluorescence intensity for six cytokine-like proteins (GM-CSF, M-CSF, IL-3, IL-15, IL-1β and IL-19) compared to untreated controls. ELISA test indicated significantly higher IL-3 and IL-15. M-CSF, IL-1α and IL-19 concentration in the hemolymph after fungal infection, and significantly lower TNF-β and G-CSF.ConclusionsOur findings confirm that the selected cytokine-like molecules are present in insect hemocytes and that their concentrations change after fungal infection, which might suggest that they play a role in the anti-fungal immunological response.
Distinct T cell responsiveness to different COVID-19 vaccines and cross-reactivity to SARS-CoV-2 variants with age and CMV status
Authors: Brummelman Jolanda , Suárez-Hernández Sara , de Rond Lia , Bogaard-van Maurik Marjan , Molenaar Petra , van Wijlen Emma , Oomen Debbie , Beckers Lisa , Rots Nynke Y. , van Beek Josine , Nicolaie Mioara A. , van Els Cécile A. C. M. , Boer Mardi C. , Kaaijk Patricia , Buisman Anne-Marie , de Wit Jelle 
Published: May 2024

IntroductionAccumulating evidence indicates the importance of T cell immunity in vaccination-induced protection against severe COVID-19 disease, especially against SARS-CoV-2 Variants-of-Concern (VOCs) that more readily escape from recognition by neutralizing antibodies. However, there is limited knowledge on the T cell responses across different age groups and the impact of CMV status after primary and booster vaccination with different vaccine combinations. Moreover, it remains unclear whether age has an effect on the ability of T cells to cross-react against VOCs.MethodsTherefore, we interrogated the Spike-specific T cell responses in healthy adults of the Dutch population across different ages, whom received different vaccine types for the primary series and/or booster vaccination, using IFNɣ ELISpot. Cells were stimulated with overlapping peptide pools of the ancestral Spike protein and different VOCs.ResultsRobust Spike-specific T cell responses were detected in the vast majority of participants upon the primary vaccination series, regardless of the vaccine type (i.e. BNT162b2, mRNA-1273, ChAdOx1 nCoV-19, or Ad26.COV2.S). Clearly, in the 70+ age group, responses were overall lower and showed more variation compared to younger age groups. Only in CMV-seropositive older adults (&gt;70y) there was a significant inverse relation of age with T cell responses. Although T cell responses increased in all age groups after booster vaccination, Spike-specific T cell frequencies remained lower in the 70+ age group. Regardless of age or CMV status, primary mRNA-1273 vaccination followed by BNT162b2 booster vaccination showed limited booster effect compared to the BNT162b2/BNT162b2 or BNT162b2/mRNA-1273 primary-booster regimen. A modest reduction in cross-reactivity to the Alpha, Delta and Omicron BA.1, but not the Beta or Gamma variant, was observed after primary vaccination.DiscussionTogether, this study shows that age, CMV status, but also the primary-booster vaccination regimen influence the height of the vaccination-induced Spike-specific T cell response, but did not impact the VOC cross-reactivity.
The causal relationship between gut microbiota and lymphoma: a two-sample Mendelian randomization study
Authors: Li Biyun , Han Yahui , Fu Zhiyu , Chai Yujie , Guo Xifeng , Du Shurui , Li Chi , Wang Dao 
Published: May 2024

BackgroundPrevious studies have indicated a potential link between the gut microbiota and lymphoma. However, the exact causal interplay between the two remains an area of ambiguity.MethodsWe performed a two-sample Mendelian randomization (MR) analysis to elucidate the causal relationship between gut microbiota and five types of lymphoma. The research drew upon microbiome data from a research project of 14,306 participants and lymphoma data encompassing 324,650 cases. Single-nucleotide polymorphisms were meticulously chosen as instrumental variables according to multiple stringent criteria. Five MR methodologies, including the inverse variance weighted approach, were utilized to assess the direct causal impact between the microbial exposures and lymphoma outcomes. Moreover, sensitivity analyses were carried out to robustly scrutinize and validate the potential presence of heterogeneity and pleiotropy, thereby ensuring the reliability and accuracy.ResultsWe discerned 38 potential causal associations linking genetic predispositions within the gut microbiome to the development of lymphoma. A few of the more significant results are as follows: Genus Coprobacter (OR = 0.619, 95% CI 0.438–0.873, P = 0.006) demonstrated a potentially protective effect against Hodgkin’s lymphoma (HL). Genus Alistipes (OR = 0.473, 95% CI 0.278–0.807, P = 0.006) was a protective factor for diffuse large B-cell lymphoma. Genus Ruminococcaceae (OR = 0.541, 95% CI 0.341–0.857, P = 0.009) exhibited suggestive protective effects against follicular lymphoma. Genus LachnospiraceaeUCG001 (OR = 0.354, 95% CI 0.198–0.631, P = 0.0004) showed protective properties against T/NK cell lymphoma. The Q test indicated an absence of heterogeneity, and the MR-Egger test did not show significant horizontal polytropy. Furthermore, the leave-one-out analysis failed to identify any SNP that exerted a substantial influence on the overall results.ConclusionOur study elucidates a definitive causal link between gut microbiota and lymphoma development, pinpointing specific microbial taxa with potential causative roles in lymphomagenesis, as well as identifying probiotic candidates that may impact disease progression, which provide new ideas for possible therapeutic approaches to lymphoma and clues to the pathogenesis of lymphoma.
Bacterial etiologies, antimicrobial susceptibility pattern and associated factors among patients suspected sterile body site infections at Debre Markos Comprehensive Specialized Hospital, Northwest Ethiopia
Authors: Admas Dires , Demeke Gebreselassie , Adugna Adane , Esmael Ahmed 
Published: May 2024

BackgroundSterile body locations are usually associated with clinical urgency and life-threatening illnesses, and they are typically contaminated with diverse bacterial etiologies. If the bacteria acquire resistance to antimicrobial drugs, the public health crisis will only worsen. In developing countries, drug-resistant bacteria are common because of poor surveillance, diagnostic capacity, and control measures. Early diagnosis, and assessing the drug resistance and factors associated with infection are important to combat the drug resistance and treatment. This study aimed to assess the bacterial etiologies, antimicrobial susceptibility pattern, and possible associated factors among patients suspected of sterile body sites.MethodsA hospital-based cross-sectional study was conducted from June 2022 to August 2022 at Debre Markos Comprehensive Specialized Hospital in Amhara regional state, Ethiopia. One hundred seven study participants were selected using consecutive convenient sampling techniques. A structured questionnaire was used to collect socio-demographic and clinical data. Gram stain was done for a preliminary report and inoculated into blood agar, MacConkey agar, and chocolate agar and incubated aerobically and micro aerobically at 37°C for 24 h. Antimicrobial susceptibility testing was done by the modified Kirby Bauer’s disk diffusion method. Data were analyzed using bivariate and multivariate logistic regression was used. A p-value less than 0.05 is considered as statistically significant.ResultsThe overall magnitude of sterile body site infection among study participants was 7.5% (14/187). The majority of the isolates were Gram-negative bacteria with the predominant species Enterobacter cloacae accounting for 28.57% (4/14). Among isolates 78.57%(11/14) of them were multidrug-resistant isolates. Being inpatient, co-morbidity, and alcohol consumption were significantly associated with sterile body site infection.ConclusionIn our study, Gram-negative bacteria were the predominant bacteria that infects sterile body fluid. The prevalence of multi-drug resistance bacteria isolates was significantly high. Therefore, before prescribing an empirical treatment, a medical professional should identify the bacterial etiology of sterile body fluids and the susceptibility of microbes to the drug.
Online groups show how technology supports healthcare needs for patients and families: an illustrative model for COPD facebook groups
Authors: Boyce LeAnn , Prybutok Gayle , Prybutok Victor 
Published: May 2024

Introduction:This study examines how online technologies can support patients and their families address specific medical needs by creating an integrated theoretical framework based on the Health Belief Model, Social Exchange Theory, and Technology Acceptance Model.Methods:We obtained a total of 264 responses from an online survey posted in several COPD Facebook groups. After data preprocessing, we were left with 155 responses that met our inclusion criteria. Using the Partial Least Squares-Structural Equation Model (PLS-SEM), we evaluate how individuals in Chronic Obstructive Pulmonary Disease (COPD) Facebook groups seek information.Results:This study examines the relationship between demographic variables, psychological attributes (including emotional support and self-worth), perceived disease severity, benefits and barriers, and the perceived utility and ease of internet use in the information-seeking behavior of COPD patients on Facebook.Discussion:The findings underscore the importance of ease of internet use and intuitive platform design as a critical determinant that positively affects user engagement and fosters active participation among online participants. These findings offer critical insights into how online communities help patients and families obtain broad support and enhance the adoption and acceptance of emerging healthcare technologies. This also shows the advantages that online platforms offer individuals managing chronic diseases. Given these insights, we urge healthcare providers to recognize the beneficial effects of online health communities on patient well-being and health outcomes. This understanding is essential for healthcare professionals seeking to enhance patient care, aiming to improve the quality of life for individuals with chronic diseases in an increasingly digital landscape.
Multikinase inhibitors modulate non-constitutive proteasome expression in colorectal cancer cells
Authors: Burov Alexander , Grigorieva Ekaterina , Lebedev Timofey , Vedernikova Valeria , Popenko Vladimir , Astakhova Tatiana , Leonova Olga , Spirin Pavel , Prassolov Vladimir , Karpov Vadim , Morozov Alexey 
Published: May 2024

Introduction: Proteasomes are multi-subunit protein complexes responsible for protein degradation in cells. Immunoproteasomes and intermediate proteasomes (together non-constitutive proteasomes) are specific forms of proteasomes frequently associated with immune response, antigen presentation, inflammation and stress. Expression of non-constitutive proteasome subunits has a prognostic value in several types of cancer. Thus, factors that modulate non-constitutive proteasome expression in tumors are of particular interest. Multikinase inhibitors (MKIs) demonstrate promising results in treatment of cancer. At the same time, their immunomodulatory properties and effects on non-constitutive proteasome expression in colorectal cancer cells are poorly investigated.Methods: Proteasome subunit expression in colorectal cancer was evaluated by bioinformatic analysis of available datasets. Two colorectal cancer cell lines, expressing fluorescent non-constitutive proteasomes were treated with multikinase inhibitors: regorafenib and sorafenib. The proteasome subunit expression was assessed by real-time PCR, Western blotting and flow cytometry. The proteasome activity was studied using proteasome activity-based probe and fluorescent substrates. Intracellular proteasome localization was revealed by confocal microscopy. Reactive oxygen species levels following treatment were determined in cells. Combined effect of proteasome inhibition and treatment with MKIs on viability of cells was estimated.Results: Expression of non-constitutive proteasomes is increased in BRAF-mutant colorectal tumors. Regorafenib and sorafenib stimulated the activity and synthesis of non-constitutive proteasomes in examined cell lines. MKIs induced oxidative stress and redistribution of proteasomes within cells. Sorafenib stimulated formation of cytoplasmic aggregates, containing proteolyticaly active non-constitutive proteasomes, while regorafenib had no such effect. MKIs caused no synergistic action when were combined with the proteasome inhibitor.Discussion: Obtained results indicate that MKIs might affect the crosstalk between cancer cells and immune cells via modulation of intracellular proteasome pool. Observed phenomenon should be considered when MKI-based therapy is applied.
Alzheimer’s disease manifests abnormal sphingolipid metabolism
Authors: Uranbileg Baasanjav , Isago Hideaki , Sakai Eri , Kubota Masayuki , Saito Yuko , Kurano Makoto 
Published: May 2024

IntroductionAlzheimer’s disease (AD) is associated with disturbed metabolism, prompting investigations into specific metabolic pathways that may contribute to its pathogenesis and pathology. Sphingolipids have garnered attention due to their known physiological impact on various diseases.MethodsWe conducted comprehensive profiling of sphingolipids to understand their possible role in AD. Sphingolipid levels were measured in AD brains, Cerad score B brains, and controls, as well as in induced pluripotent stem (iPS) cells (AD, PS, and control), using liquid chromatography mass spectrometry.ResultsAD brains exhibited higher levels of sphingosine (Sph), total ceramide 1-phosphate (Cer1P), and total ceramide (Cer) compared to control and Cerad-B brains. Deoxy-ceramide (Deoxy-Cer) was elevated in Cerad-B and AD brains compared to controls, with increased sphingomyelin (SM) levels exclusively in Cerad-B brains. Analysis of cell lysates revealed elevated dihydroceramide (dhSph), total Cer1P, and total SM in AD and PS cells versus controls. Multivariate analysis highlighted the relevance of Sph, Cer, Cer1P, and SM in AD pathology. Machine learning identified Sph, Cer, and Cer1P as key contributors to AD.DiscussionOur findings suggest the potential importance of Sph, Cer1P, Cer, and SM in the context of AD pathology. This underscores the significance of sphingolipid metabolism in understanding and potentially targeting mechanisms underlying AD.
Learning capabilities to resolve tilt-translation ambiguity in goldfish
Authors: Tadokoro Shin , Shinji Yusuke , Yamanaka Toshimi , Hirata Yutaka 
Published: May 2024

IntroductionSpatial orientation refers to the perception of relative location and self-motion in space. The accurate formation of spatial orientation is essential for animals to survive and interact safely with their environment. The formation of spatial orientation involves the integration of sensory inputs from the vestibular, visual, and proprioceptive systems. Vestibular organs function as specialized head motion sensors, providing information regarding angular velocity and linear acceleration via the semicircular canals and otoliths, respectively. However, because forces arising from the linear acceleration (translation) and inclination relative to the gravitational axis (tilt) are equivalent, they are indistinguishable by accelerometers, including otoliths. This is commonly referred to as the tilt - translation ambiguity, which can occasionally lead to the misinterpretation of translation as a tilt. The major theoretical frameworks addressing this issue have proposed that the interpretation of tilt versus translation may be contingent on an animal’s previous experiences of motion. However, empirical confirmation of this hypothesis is lacking.MethodsIn this study, we conducted a behavioral experiment using goldfish to investigate how an animal’s motion experience influences its interpretation of tilt vs. translation. We examined a reflexive eye movement called the vestibulo-ocular reflex (VOR), which compensatory-rotates the eyes in response to head motion and is known to reflect an animal’s three-dimensional head motion estimate.ResultsWe demonstrated that the VORs of naïve goldfish do not differentiate between translation and tilt at 0.5 Hz. However, following prolonged visual-translation training, which provided appropriate visual stimulation in conjunction with translational head motion, the VORs were capable of distinguishing between the two types of head motion within 3 h. These results were replicated using the Kalman filter model of spatial orientation, which incorporated the variable variance of process noise corresponding to the accumulated motion experience.DiscussionBased on these experimental and computational findings, we discuss the neural mechanism underlying the resolution of tilt-translation ambiguity within a context analogous to, yet distinct from, previous cross-axis VOR adaptations.
Comparative analysis of the image quality and diagnostic performance of the zooming technique with diffusion-weighted imaging using different b-values for thyroid papillary carcinomas and benign nodules
Authors: Jiang Liling , Chen Jiao , Tan Yong , Wu Jian , Zhang Junbin , Liu Daihong , Zhang Jiuquan 
Published: May 2024

ObjectiveTo compare image quality and diagnostic performance using different b-values for the zooming technique with diffusion-weighted imaging (ZOOMit-DWI) in thyroid nodulesMaterials and methodsA total of 51 benign thyroid nodules and 50 thyroid papillary carcinomas were included. ZOOMit-DWI was performed with b-values of 0, 500, 1000, 1500 and 2000 s/mm2. The sharpness was evaluated as subjective index. The signal intensity ratio (SIR), signal-to-noise ratio (SNR) and apparent diffusion coefficient (ADC) were measured as objective indices. Pairwise comparisons were performed among the different b-value groups using the Friedman test. A receiver operating characteristic curve of the ADC value was used to evaluate diagnostic performance. The DeLong test was used to compare diagnostic effectiveness among the different b-value groupsResultsIn both the papillary carcinoma group (P = 0.670) and the benign nodule group (P = 0.185), the sharpness of nodules was similar between b-values of 1000 s/mm2and 1500 s/mm2. In the papillary carcinoma group, the SIRnodule was statistically higher in DWI images with a b-value of 1500 s/mm2than in DWI images with b-values of 500 s/mm2(P = 0.004), 1000 s/mm2(P = 0.002), and 2000 s/mm2(P = 0.003). When the b-values were 1500 s/mm2(P = 0.008) and 2000 s/mm2(P = 0.009), the SIRnodule significantly differed between the papillary carcinoma group and the benign nodule group. When b = 500 s/mm2, the ADC had an AUC of 0.888. When b = 1000 s/mm2, the ADC had an AUC of 0.881. When b = 1500 s/mm2, the ADC had an AUC of 0.896. When b = 2000 s/mm2, the ADC had an AUC of 0.871. The DeLong test showed comparable diagnostic effectiveness among the different b-value groups except for between b-values of 2000 s/mm2and 1500 s/mm2, with a b-value of 2000 s/mm2showing lower effectivenessConclusionThis study suggests that 1500 s/mm2may be a suitable b-value to differentiate benign and malignant thyroid nodules in ZOOMit-DWI images, which yielded better image quality