bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dogs can detect an odor profile associated with Staphylococcus aureus biofilms in cultures and biological samples
Authors: Ramos Meghan T. , Chang Gerard , Wilson Clara , Gilbertie Jessica , Krieg James , Parvizi Javad , Chen Antonia F. , Otto Cynthia M. , Schaer Thomas P. 
Published: February 2024

IntroductionThe study investigated the utilization of odor detection dogs to identify the odor profile of Staphylococcus aureus (S. aureus) biofilms in pure in vitro samples and in in vivo biosamples from animals and humans with S. aureus periprosthetic joint infection (PJI). Biofilms form when bacterial communities aggregate on orthopedic implants leading to recalcitrant infections that are difficult to treat. Identifying PJI biofilm infections is challenging, and traditional microbiological cultures may yield negative results even in the presence of clinical signs.MethodsDogs were trained on pure in vitro S. aureus biofilms and tested on lacrimal fluid samples from an in vivo animal model (rabbits) and human patients with confirmed S. aureus PJI.ResultsThe results demonstrated that dogs achieved a high degree of sensitivity and specificity in detecting the odor profile associated with S. aureus biofilms in rabbit samples. Preliminary results suggest that dogs can recognize S. aureus volatile organic compounds (VOCs) in human lacrimal fluid samples.DiscussionTraining odor detection dogs on in vitro S. aureus, may provide an alternative to obtaining clinical samples for training and mitigates biosecurity hazards. The findings hold promise for culture-independent diagnostics, enabling early disease detection, and improved antimicrobial stewardship. In conclusion, this research demonstrates that dogs trained on in vitro S. aureus samples can identify the consistent VOC profile of PJI S. aureus biofilm infections. The study opens avenues for further investigations into a retained VOC profile of S. aureus biofilm infection. These advancements could revolutionize infectious disease diagnosis and treatment, leading to better patient outcomes and addressing the global challenge of antimicrobial resistance.
Cytokine expression in subjects with Mycobacterium avium ssp. paratuberculosis positive blood cultures and a meta-analysis of cytokine expression in Crohn’s disease
Authors: Kuenstner J. Todd , Xu Qiang , Bull Tim J. , Foddai Antonio C. G. , Grant Irene R. , Naser Saleh A. , Potula Raghava , Zhang Peilin , Shafran Ira , Akhanli Serhat Emre , Khaiboullina Svetlana , Kruzelock Russell 
Published: February 2024

Objectives1) Culture Mycobacterium avium ssp. paratuberculosis (MAP)from blood, 2) assess infection persistence, 3) determine Crohn’s disease (CD) cytokine expression, 4) compare CD cytokine expression to tuberculosis, and 5) perform a meta-analysis of cytokine expression in CD.MethodsThe Temple University/Abilene Christian University (TU/ACU) study had a prospective case control design with 201 subjects including 61 CD patients and 140 non-CD controls. The culture methods included MGIT, TiKa and Pozzato broths, and were deemed MAP positive, if IS900 PCR positive. A phage amplification assay was also performed to detect MAP. Cytokine analysis of the TU/ACU samples was performed using Simple Plex cytokine reagents on the Ella ELISA system. Statistical analyses were done after log transformation using the R software package. The meta-analysis combined three studies.ResultsMost subjects had MAP positive blood cultures by one or more methods in 3 laboratories. In our cytokine study comparing CD to non-CD controls, IL-17, IFNγ and TNFα were significantly increased in CD, but IL-2, IL-5, IL-10 and GM-CSF were not increased. In the meta-analysis, IL-6, IL-8 and IL-12 were significantly increased in the CD patients.ConclusionMost subjects in our sample had MAP infection and 8 of 9 subjects remained MAP positive one year later indicating persistent infection. While not identical, cytokine expression patterns in MAP culture positive CD patients in the TU/ACU study showed similarities (increased IL-17, IFNγ and TNFα) to patterns of patients with Tuberculosis in other studies, indicating the possibilities of similar mechanisms of pathogen infection and potential strategies for treatment.
Risk of hepatitis B virus reactivation and its effect on survival in advanced hepatocellular carcinoma patients treated with hepatic arterial infusion chemotherapy and lenvatinib plus programmed death receptor-1 inhibitors
Authors: Yang Zhenyun , Guan Renguo , Fu Yizhen , Hu Dandan , Zhou Zhongguo , Chen Minshan , Zhang Yaojun 
Published: February 2024

BackgroundHepatitis B virus (HBV) reactivation is a common complication in hepatocellular carcinoma (HCC) patients treated with chemotherapy or immunotherapy. This study aimed to evaluate the risk of HBV reactivation and its effect on survival in HCC patients treated with HAIC and lenvatinib plus PD1s.MethodsWe retrospectively collected the data of 213 HBV-related HCC patients who underwent HAIC and lenvatinib plus PD1s treatment between June 2019 to June 2022 at Sun Yat-sen University, China. The primary outcome was the risk of HBV reactivation. The secondary outcomes were overall survival (OS), progression−free survival (PFS), and treatment−related adverse events.ResultsSixteen patients (7.5%) occurred HBV reactivation in our study. The incidence of HBV reactivation was 5% in patients with antiviral prophylaxis and 21.9% in patients without antiviral prophylaxis, respectively. The logistic regression model indicated that for HBV reactivation, lack of antiviral prophylaxis (P=0.003) and tumor diameter (P=0.036) were independent risk factors. The OS and PFS were significantly shorter in the HBV reactivation group than the non-reactivation group (P=0.0023 and P=0.00073, respectively). The number of AEs was more in HBV reactivation group than the non-reactivation group, especially hepatic AEs.ConclusionHBV reactivation may occur in HCC patients treated with HAIC and lenvatinib plus PD1s. Patients with HBV reactivation had shorter survival time compared with non-reactivation. Therefore, HBV-related HCC patients should undergo antiviral therapy and HBV-DNA monitoring before and during the combination treatment.
Transcriptome and proteomic analysis of mpox virus F3L-expressing cells
Authors: Wang Yihao , Zhang Junzhe , Li Mingzhi , Jia Mengle , Yang Lingdi , Wang Ting , Wang Yu , Kang Lumei , Li Meifeng , Kong Lingbao 
Published: February 2024

BackgroundMonkeypox or mpox virus (mpox) is a double-stranded DNA virus that poses a significant threat to global public health security. The F3 protein, encoded by mpox, is an apoenzyme believed to possess a double-stranded RNA-binding domain (dsRBD). However, limited research has been conducted on its function. In this study, we present data on the transcriptomics and proteomics of F3L-transfected HEK293T cells, aiming to enhance our comprehension of F3L.MethodsThe gene expression profiles of pCAGGS-HA-F3L transfected HEK293T cells were analyzed using RNA-seq. Proteomics was used to identify and study proteins that interact with F3L. Real-time PCR was used to detect mRNA levels of several differentially expressed genes (DEGs) in HEK293T cells (or Vero cells) after the expression of F3 protein.ResultsA total of 14,822 genes were obtained in cells by RNA-Seq and 1,672 DEGs were identified, including 1,156 up-regulated genes and 516 down-regulated genes. A total of 27 cellular proteins interacting with F3 proteins were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and 19 cellular proteins with large differences in abundance ratios were considered to be candidate cellular proteins. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that the DEGs were significantly enriched in immune-related pathways, including type I interferon signaling pathway, response to virus, RIG-I-like receptor signaling pathway, NOD-like receptor signaling pathway, etc. Moreover, some selected DEGs were further confirmed by real-time PCR and the results were consistent with the transcriptome data. Proteomics data show that cellular proteins interacting with F3 proteins are mainly related to RNA splicing and protein translation.ConclusionsOur analysis of transcriptomic and proteomic data showed that (1) F3L up-regulates the transcript levels of key genes in the innate immune signaling pathway, such as RIGI, MDA5, IRF5, IRF7, IRF9, ISG15, IFNA14, and elicits a broad spectrum of antiviral immune responses in the host. F3L also increases the expression of the FOS and JNK genes while decreasing the expression of TNFR2, these factors may ultimately induce apoptosis. (2) F3 protein interacts with host proteins involved in RNA splicing and protein translation, such as SNRNP70, POLR2H, HNRNPA1, DDX17, etc. The findings of this study shed light on the function of the F3 protein.
Treatment of coronary lesions with a novel crystalline sirolimus-coated balloon
Authors: Madanchi Mehdi , Attinger-Toller Adrian , Gjergjizi Varis , Majcen Irena , Cioffi Giacomo M. , Epper Angelika , Gnan Eleonora , Koch Tanja , Zhi Yuan , Cuculi Florim , Bossard Matthias 
Published: February 2024

BackgroundThere is mounting data supporting the use of drug-coated balloons (DCB) not only for treatment of in-stent restenosis (ISR), but also in native coronary artery disease. So far, paclitaxel-coated balloons represented the mainstay DCBs. The SeQuent® crystalline sirolimus-coated balloon (SCB) (B.Braun Medical Inc, Germany) represents a novel DCB, which allows a sustained release of the limus-drug. We evaluated its performance in an all-comer cohort, including complex coronary lesions.MethodsConsecutive patients treated with the SeQuent® SCB were analyzed from the prospective SIROOP registry (NCT04988685). We assessed clinical outcomes, including major adverse cardiovascular events (MACE), target lesion revascularization (TLR), target vessel myocardial infarction (TV-MI) and cardiovascular death. Angiograms and outcomes were independently adjudicated.ResultsFrom March 2021 to March 2023, we enrolled 126 patients and lesions, of which 100 (79%) treated using a “DCB-only” strategy and 26 (21%) with a hybrid approach (DES + DCB). The mean age was 68 ± 10 years, 48 (38%) patients had an acute coronary syndrome. Regarding lesion characteristics, ISR was treated in 27 (21%), 11 (9%) underwent CTO-PCI and 59 (47%) of the vessels were moderate to severe calcified. Procedural success rate was 100%. At a median follow-up time of 12.7 (IQR 12; 14.2) months, MACE occurred in 5 patients (4.3%). No acute vessel closure was observed.ConclusionsOur data indicates promising outcomes following treatment with this novel crystalline SCB in an all-comer cohort with complex coronary lesions. These results require further investigation with randomized trials.
Construction of a co-expression network affecting intramuscular fat content and meat color redness based on transcriptome analysis
Authors: Wang Binbin , Hou Liming , Yang Wen , Men Xiaoming , Qi Keke , Xu Ziwei , Wu Wangjun 
Published: February 2024

Introduction: Intramuscular fat content (IFC) and meat color are vital indicators of pork quality.Methods: A significant positive correlation between IFC and redness of meat color (CIE a* value) indicates that these two traits are likely to be regulated by shared molecular pathways.To identify candidate genes, hub genes, and signaling pathways that regulate these two traits, we measured the IFC and CIE a* value in 147 hybrid pigs, and selected individuls with extreme phenotypes for transcriptome analysis.Results: The results revealed 485 and 394 overlapping differentially expressed genes (DEGs), using the DESeq2, limma, and edgeR packages, affecting the IFC and CIE a* value, respectively. Weighted gene co-expression network analysis (WGCNA) identified four modules significantly correlated with the IFC and CIE a* value. Moreover, we integrated functional enrichment analysis results based on DEGs, GSEA, and WGCNA conditions to identify candidate genes, and identified 47 and 53 candidate genes affecting the IFC and CIE a* value, respectively. The protein protein interaction (PPI) network analysis of candidate genes showed that 5 and 13 hub genes affect the IFC and CIE a* value, respectively. These genes mainly participate in various pathways related to lipid metabolism and redox reactions. Notably, four crucial hub genes (MYC, SOX9, CEBPB, and PPAGRC1A) were shared for these two traits.Discussion and conclusion: After functional annotation of these four hub genes, we hypothesized that the SOX9/CEBPB/PPARGC1A axis could co-regulate lipid metabolism and the myoglobin redox response. Further research on these hub genes, especially the SOX9/CEBPB/PPARGC1A axis, will help to understand the molecular mechanism of the co-regulation of the IFC and CIE a* value, which will provide a theoretical basis for improving pork quality.
Barriers and enablers to exclusive breastfeeding by mothers in Polokwane, South Africa
Authors: Makwela Maishataba Solomon , Mashaba Reneilwe Given , Ntimana Cairo Bruce , Seakamela Kagiso Peace , Maimela Eric 
Published: February 2024

BackgroundExclusive breastfeeding (EBF) for six months, with the introduction of appropriate complementary feeding thereafter, and breastfeeding continuing for up to 2 years and beyond, is highly recommended. This could save the lives of up to 1.4 million children each year worldwide. Despite this, breastfeeding rates in South Africa remain sub-optimal, with the recommended target of 50% by the World Health Assembly (WHA) not being achieved. The study aimed to investigate the reasons influencing mothers' practice of exclusive breastfeeding in the Polokwane municipality of Limpopo province in South Africa.MethodologyA cross-sectional health facility-based quantitative and descriptive survey was conducted using a validated-structured questionnaire administered to 146 mothers. The data was analyzed using STATA. Chi-square tests were used to determine the relationship between selected demographic variables and their reasons not to breastfeed exclusively.ResultsAlthough 94% of the mothers had initiated breastfeeding, at the time of data collection 8% had stopped. Of those who had stopped breastfeeding, 5% did so within one month of starting. Thirty- nine percent of mothers' breastfed exclusively, while 61% practiced mixed feeding. A positive association between exclusive breastfeeding practices and the age of the mother were observed, with older mothers more likely to breastfeed. The reasons mothers stopped breastfeeding were: the mother was ill (45%) or they returned to school or work (27%). Reasons for not breastfeeding were cited as: medical conditions, not enough milk, and infant refusal to breastfeed (33%). Mothers believe that HIV-positive women should breastfeed their infants (57%), and health workers were found to be the main source of HIV information to mothers (77%).DiscussionExclusive breastfeeding during the first six months was less practiced. Infant formula and solid foods were introduced at an early age, usually within the first month of breastfeeding. This study sheds light on factors influencing the early initiation of breastfeeding and the practice of EBF as practiced in Polokwane.
Innate immune cell activation after HIV-1 vaccine administration is associated with increased antibody production
Authors: N’guessan Kombo F. , Machmach Kawthar , Swafford Isabella , Costanzo Margaret C. , Wieczorek Lindsay , Kim Dohoon , Akapirat Siriwat , Polonis Victoria R. , Pitisuttithum Punnee , Nitayaphan Sorachai , Gurunathan Sanjay , Sinangil Faruk , Chariyalertsak Suwat , Ake Julie A. , O’connell Robert J. , Vasan Sandhya , Paquin-Proulx Dominic 
Published: February 2024

The RV144 Thai phase III clinical trial’s canarypox–protein HIV vaccine regimen showed modest efficacy in reducing infection. We therefore sought to determine the effects of vaccine administration on innate cell activation and subsequent associations with vaccine-induced immune responses. RV306 was a randomized, double-blind clinical trial in HIV-uninfected Thai adults that tested delayed boosting following the RV144 regimen. PBMC collected from RV306 participants prior to and 3 days after the last boost were used to investigate innate immune cell activation. Our analysis showed an increase in CD38+ mucosal associated invariant T (MAIT) cells, CD38+ invariant natural killer T (iNKT) cells, CD38+ γδ T cells, CD38+, CD69+ and HLA-DR+ NK cells 3 days after vaccine administration. An increase in CD14-CD16+ non-classical monocytes and CD14+CD16+ intermediate monocytes accompanied by a decrease in CD14+CD16- classical monocytes was also associated with vaccine administration. Inclusion of ALVAC-HIV in the boost did not further increase MAIT, iNKT, γδ T, and NK cell activation or increase the proportion of non-classical monocytes. Additionally, NK cell activation 3 days after vaccination was positively associated with antibody titers of HIV Env-specific total IgG and IgG1. Vδ1 T cell activation 3 days after vaccine administration was associated with HIV Env-specific IgG3 titers. Finally, we observed trending associations between MAIT cell activation and Env-specific IgG3 titers and between NK cell activation and TH023 pseudovirus neutralization titers. Our study identifies a potential role for innate cells, specifically NK, MAIT, and γδ T cells, in promoting antibody responses following HIV-1 vaccine administration.
Songorine modulates macrophage polarization and metabolic reprogramming to alleviate inflammation in osteoarthritis
Authors: He Xi-Xi , Huang Yuan-Jun , Hu Chun-Long , Xu Qiong-Qian , Wei Qing-Jun 
Published: February 2024

IntroductionOsteoarthritis (OA) is a prevalent joint disorder characterized by multifaceted pathogenesis, with macrophage dysregulation playing a critical role in perpetuating inflammation and joint degeneration. MethodsThis study focuses on Songorine, derived from Aconitum soongaricum Stapf, aiming to unravel its therapeutic mechanisms in OA. Comprehensive analyses, including PCR, Western blot, and immunofluorescence, were employed to evaluate Songorine's impact on the joint microenvironment and macrophage polarization. RNA-seq analysis was conducted to unravel its anti-inflammatory mechanisms in macrophages. Metabolic alterations were explored through extracellular acidification rate monitoring, molecular docking simulations, and PCR assays. Oxygen consumption rate measurements were used to assess mitochondrial oxidative phosphorylation, and Songorine's influence on macrophage oxidative stress was evaluated through gene expression and ROS assays.ResultsSongorine effectively shifted macrophage polarization from a pro-inflammatory M1 phenotype to an anti-inflammatory M2 phenotype. Notably, Songorine induced metabolic reprogramming, inhibiting glycolysis and promoting mitochondrial oxidative phosphorylation. This metabolic shift correlated with a reduction in macrophage oxidative stress, highlighting Songorine's potential as an oxidative stress inhibitor.DiscussionIn an in vivo rat model of OA, Songorine exhibited protective effects against cartilage damage and synovial inflammation, emphasizing its therapeutic potential. This comprehensive study elucidates Songorine's multifaceted impact on macrophage modulation, metabolic reprogramming, and the inflammatory microenvironment, providing a theoretical foundation for its therapeutic potential in OA.
Enhancing efficiency in photo chemical machining: a multivariate decision-making approach
Authors: Sapkota Gaurav , Ghadai Ranjan Kumar , Čep Robert , Shanmugasundar G. , Chohan Jasgurpreet Singh , Kalita Kanak 
Published: February 2024

Non-Traditional Machining (NTM) outperforms traditional processes by offering superior geometric and dimensional accuracy, along with a better surface finish. Photo Chemical Machining (PCM) represents one such NTM process, using chemical etching for material removal. PCM finds substantial application in the creation of microchannels in pharmaceutical, chemical and energy industries. Several input parameters—such as etchant concentration, etching time and etchant temperature—profoundly influence the machining’s quality and efficiency. Therefore, the optimization of these parameters is crucial. This study presents a comparative analysis of five Multiple Criteria Decision Making (MCDM) techniques—Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS), Multi-Objective Optimization on the basis of Ratio Analysis (MOORA), Additive Ratio Assessment (ARAS), Weighted aggregated sum product assessment method (WASPAS) and Multi-Attributive Border Approximation Area Comparison Method (MABAC)—for the optimization of the PCM process. Key performance metrics considered are Material Removal Rate (MRR), Surface Roughness (SR), Undercut (Uc) and etch factor (EF). The weights of these criteria were calculated using the Criterion-Induced Aggregation Technique (CRITIC) and was compared with other popular methods like MEREC, Entropy and equal weights. MRR and EF are seen as beneficial criteria, while SR and Uc are perceived as cost criteria. Optimum process parameters were identified as 850 g/L etchant concentration, 40 min etching time and 70°C etchant temperature. Two of the three employed MCDM techniques agreed on these optimal parameters, reinforcing the findings. Furthermore, a strong correlation was observed amongst the employed MCDM techniques, further validating the results.
Balanced-force shim system for correcting magnetic-field inhomogeneities in the heart due to implanted cardioverter defibrillators
Authors: Hrovat Mirko , Kolandaivelu Aravindan , Wang Yifan , Gunderman Anthony , Halperin Henry R. , Chen Yue , Schmidt Ehud J. 
Published: February 2024

BackgroundIn the US, 1.4 million people have implanted ICDs for reducing the risk of sudden death due to ventricular arrhythmias. Cardiac MRI (cMR) is of particular interest in the ICD patient population as cMR is the optimal imaging modality for distinguishing cardiac conditions that predispose to sudden death, and it is the best method to plan and guide therapy. However, all ICDs contain a ferromagnetic transformer which imposes a large inhomogeneous magnetic field in sections of the heart, creating large image voids that can mask important pathology. A shim system was devised to resolve these ICD issues. A shim coil system (CSS) that corrects ICD artifacts over a user-selected Region-of-Interest (ROI), was constructed and validated.MethodsA shim coil was constructed that can project a large magnetic field for distances of ~15 cm. The shim-coil can be positioned safely anywhere within the scanner bore. The CSS includes a cantilevered beam to hold the shim coil. Remotely controlled MR-conditional motors allow 2 mm-accuracy three-dimensional shim-coil position. The shim coil is located above the subjects and the imaging surface-coils. Interaction of the shim coil with the scanner’s gradients was eliminated with an amplifier that is in a constant current mode. Coupling with the scanners’ radio-frequency (rf) coils, was reduced with shielding, low-pass filters, and cable shield traps. Software, which utilizes magnetic field (B0) mapping of the ICD inhomogeneity, computes the optimal location for the shim coil and its corrective current. ECG gated single- and multiple-cardiac-phase 2D GRE and SSFP sequences, as well as 3D ECG-gated respiratory-navigated IR-GRE (LGE) sequences were tested in phantoms and N = 3 swine with overlaid ICDs.ResultsWith all cMR sequences, the system reduced artifacts from &gt;100 ppm to &lt;25 ppm inhomogeneity, which permitted imaging of the entire left ventricle in swine with ICD-related voids. Continuously acquired Gradient recalled echo or Steady State Free Precession images were used to interactively adjust the shim current and coil location.ConclusionThe shim system reduced large field inhomogeneities due to implanted ICDs and corrected most ICD-related image distortions. Externally-controlled motorized translation of the shim coil simplified its utilization, supporting an efficient cardiac MRI workflow.