bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of potential hub genes linked to immune and metabolic alterations in postoperative systemic inflammatory dysregulation
Authors: Cao Silu , Tang Jinxuan , Fei Miaomiao , Jing Qi , Meng Fanbing , Zhang Meixian , Liu Qidong , Zhang Hui , Li Cheng 
Published: September 2023

BackgroundPostoperative systemic inflammatory dysregulation (PSID) is characterised by strongly interlinked immune and metabolic abnormalities. However, the hub genes responsible for the interconnections between these two systemic alterations remain to be identified.MethodsWe analysed differentially expressed genes (DEGs) of individual peripheral blood nucleated cells in patients with PSID (n = 21, CRP &gt; 250 mg/L) and control patients (n = 25, CRP &lt; 75 mg/L) following major abdominal surgery, along with their biological functions. Correlation analyses were conducted to explore the interconnections of immune-related DEGs (irDEGs) and metabolism-related DEGs (mrDEGs). Two methods were used to screen hub genes for irDEGs and mrDEGs: we screened for hub genes among DEGs via 12 algorithms using CytoHubba in Cytoscape, and also screened for hub immune-related and metabolic-related genes using weighted gene co-expression network analysis. The hub genes selected were involved in the interaction between changes in immunity and metabolism in PSID. Finally, we validated our results in mice with PSID to confirm the findings.ResultsWe identified 512 upregulated and 254 downregulated DEGs in patients with PSID compared with controls. Gene enrichment analysis revealed that DEGs were significantly associated with immune- and metabolism-related biological processes and pathways. Correlation analyses revealed a close association between irDEGs and mrDEGs. Fourteen unique hub genes were identified via 12 screening algorithms using CytoHubba in Cytoscape and via weighted gene co-expression network analysis. Among these, CD28, CD40LG, MAPK14, and S100A12 were identified as hub genes among both immune- and metabolism-related genes; these genes play a critical role in the interaction between alterations in immunity and metabolism in PSID. The experimental results also showed that the expression of these genes was significantly altered in PSID mice.ConclusionThis study identified hub genes associated with immune and metabolic alterations in patients with PSID and hub genes that link these alterations. These findings provide novel insights into the mechanisms underlying immune and metabolic interactions and new targets for clinical treatment can be proposed on this basis.
Molecular characterization and differential effects of levofloxacin and ciprofloxacin on the potential for developing quinolone resistance among clinical Pseudomonas aeruginosa isolates
Authors: Kanafani Zeina A. , Sleiman Ahmad , Frem Jim Abi , Doumat George , Gharamti Amal , El Hafi Bassam , Doumith Michel , AlGhoribi Majed F. , Kanj Souha S. , Araj George F. , Matar Ghassan M. , Abou Fayad Antoine G. 
Published: September 2023

BackgroundFluoroquinolones are some of the most used antimicrobial agents for the treatment of Pseudomonas aeruginosa. This study aimed at exploring the differential activity of ciprofloxacin and levofloxacin on the selection of resistance among P. aeruginosa isolates at our medical center.Methods233 P. aeruginosa clinical isolates were included in this study. Antimicrobial susceptibility testing (AST) was done using disk diffusion and broth microdilution assays. Random Amplification of Polymorphic DNA (RAPD) was done to determine the genetic relatedness between the isolates. Induction of resistance against ciprofloxacin and levofloxacin was done on 19 isolates. Fitness cost assay was done on the 38 induced mutants and their parental isolates. Finally, whole genome sequencing was done on 16 induced mutants and their 8 parental isolates.ResultsAST results showed that aztreonam had the highest non-susceptibility. RAPD results identified 18 clusters. The 19 P. aeruginosa isolates that were induced against ciprofloxacin and levofloxacin yielded MICs ranging between 16 and 256 μg/mL. Levofloxacin required fewer passages in 10 isolates and the same number of passages in 9 isolates as compared to ciprofloxacin to reach their breakpoints. Fitness cost results showed that 12 and 10 induced mutants against ciprofloxacin and levofloxacin, respectively, had higher fitness cost when compared to their parental isolates. Whole genome sequencing results showed that resistance to ciprofloxacin and levofloxacin in sequenced mutants were mainly associated with alterations in gyrA, gyrB and parC genes.ConclusionUnderstanding resistance patterns and risk factors associated with infections is crucial to decrease the emerging threat of antimicrobial resistance.
A study on feature selection using multi-domain feature extraction for automated k-complex detection
Authors: Li Yabing , Dong Xinglong , Song Kun , Bai Xiangyun , Li Hongye , Karray Fakhreddine 
Published: September 2023

BackgroundK-complex detection plays a significant role in the field of sleep research. However, manual annotation for electroencephalography (EEG) recordings by visual inspection from experts is time-consuming and subjective. Therefore, there is a necessity to implement automatic detection methods based on classical machine learning algorithms. However, due to the complexity of EEG signal, current feature extraction methods always produce low relevance to k-complex detection, which leads to a great performance loss for the detection. Hence, finding compact yet effective integrated feature vectors becomes a crucially core task in k-complex detection.MethodIn this paper, we first extract multi-domain features based on time, spectral analysis, and chaotic theory. Those features are extracted from a 0.5-s EEG segment, which is obtained using the sliding window technique. As a result, a vector containing twenty-two features is obtained to represent each segment. Next, we explore several feature selection methods and compare their performance in detecting k-complex. Based on the analysis of the selected features, we identify compact features which are fewer than twenty-two features and deemed as relevant and proceeded to the next step. Additionally, three classical classifiers are employed to evaluate the performance of the feature selection models.ResultsThe results demonstrate that combining different features significantly improved the k-complex detection performance. The best performance is achieved by applying the feature selection method, which results in an accuracy of 93.03%±7.34, sensitivity of 93.81%±5.62%, and specificity 94.13±5.81, respectively, using a smaller number of the combined feature sets.ConclusionThe proposed method in this study can serve as an efficient tool for the automatic detection of k-complex, which is useful for neurologists or doctors in the diagnosis of sleep research.
Expression of the schizophrenia associated gene FEZ1 in the early developing fetal human forebrain
Authors: Alhesain Maznah , Ronan Hannah , LeBeau Fiona E. N. , Clowry Gavin J. 
Published: September 2023

IntroductionThe protein fasciculation and elongation zeta-1 (FEZ1) is involved in axon outgrowth but potentially interacts with various proteins with roles ranging from intracellular transport to transcription regulation. Gene association and other studies have identified FEZ1 as being directly, or indirectly, implicated in schizophrenia susceptibility. To explore potential roles in normal early human forebrain neurodevelopment, we mapped FEZ1 expression by region and cell type.MethodsAll tissues were provided with maternal consent and ethical approval by the Human Developmental Biology Resource. RNAseq data were obtained from previously published sources. Thin paraffin sections from 8 to 21 post-conceptional weeks (PCW) samples were used for RNAScope in situ hybridization and immunohistochemistry against FEZ1 mRNA and protein, and other marker proteins.ResultsTissue RNAseq revealed that FEZ1 is highly expressed in the human cerebral cortex between 7.5–17 PCW and single cell RNAseq at 17–18 PCW confirmed its expression in all neuroectoderm derived cells. The highest levels were found in more mature glutamatergic neurons, the lowest in GABAergic neurons and dividing progenitors. In the thalamus, single cell RNAseq similarly confirmed expression in multiple cell types. In cerebral cortex sections at 8–10 PCW, strong expression of mRNA and protein appeared confined to post-mitotic neurons, with low expression seen in progenitor zones. Protein expression was observed in some axon tracts by 16–19 PCW. However, in sub-cortical regions, FEZ1 was highly expressed in progenitor zones at early developmental stages, showing lower expression in post-mitotic cells.DiscussionFEZ1 has different expression patterns and potentially diverse functions in discrete forebrain regions during prenatal human development.
Organoids and metastatic orthotopic mouse model for mismatch repair-deficient colorectal cancer
Authors: Song Yurong , Kerr Travis D. , Sanders Chelsea , Dai Lisheng , Baxter Shaneen S. , Somerville Brandon , Baugher Ryan N. , Mellott Stephanie D. , Young Todd B. , Lawhorn Heidi E. , Plona Teri M. , Xu Bingfang , Wei Lei , Hu Qiang , Liu Song , Hutson Alan , Karim Baktiar , Burkett Sandra , Difilippantonio Simone , Pinto Ligia , Gebert Johannes , Kloor Matthias , Lipkin Steven M. , Sei Shizuko , Shoemaker Robert H. 
Published: September 2023

BackgroundGenome integrity is essential for the survival of an organism. DNA mismatch repair (MMR) genes (e.g., MLH1, MSH2, MSH6, and PMS2) play a critical role in the DNA damage response pathway for genome integrity maintenance. Germline mutations of MMR genes can lead to Lynch syndrome or constitutional mismatch repair deficiency syndrome, resulting in an increased lifetime risk of developing cancer characterized by high microsatellite instability (MSI-H) and high mutation burden. Although immunotherapy has been approved for MMR-deficient (MMRd) cancer patients, the overall response rate needs to be improved and other management options are needed.MethodsTo better understand the biology of MMRd cancers, elucidate the resistance mechanisms to immune modulation, and develop vaccines and therapeutic testing platforms for this high-risk population, we generated organoids and an orthotopic mouse model from intestine tumors developed in a Msh2-deficient mouse model, and followed with a detailed characterization.ResultsThe organoids were shown to be of epithelial origin with stem cell features, to have a high frameshift mutation frequency with MSI-H and chromosome instability, and intra- and inter-tumor heterogeneity. An orthotopic model using intra-cecal implantation of tumor fragments derived from organoids showed progressive tumor growth, resulting in the development of adenocarcinomas mixed with mucinous features and distant metastasis in liver and lymph node.ConclusionsThe established organoids with characteristics of MSI-H cancers can be used to study MMRd cancer biology. The orthotopic model, with its distant metastasis and expressing frameshift peptides, is suitable for evaluating the efficacy of neoantigen-based vaccines or anticancer drugs in combination with other therapies.
Implementation of pharmacogenetic testing in oncology: DPYD-guided dosing to prevent fluoropyrimidine toxicity in British Columbia
Authors: Wu Angela , Anderson Helen , Hughesman Curtis , Young Sean , Lohrisch Caroline , Ross Colin J. D. , Carleton Bruce C. 
Published: September 2023

Background: Fluoropyrimidine toxicity is often due to variations in the gene (DPYD) encoding dihydropyrimidine dehydrogenase (DPD). DPYD genotyping can be used to adjust doses to reduce the likelihood of fluoropyrimidine toxicity while maintaining therapeutically effective drug levels.Methods: A multiplex QPCR assay was locally developed to allow genotyping for six DPYD variants. The test was offered prospectively for all patients starting on fluoropyrimidines at the BC Cancer Centre in Vancouver and then across B.C., Canada as well as retrospectively for patients suspected to have had an adverse reaction to therapy. Dose adjustments were made for variant carriers. The incidence of toxicity in the first three cycles was compared between DPYD variant allele carriers and non-variant carriers. Subsequent to an initial implementation phase, this test was made available province-wide.Results: In 9 months, 186 patients were tested and 14 were found to be heterozygous variant carriers. Fluoropyrimidine-related toxicity was higher in DPYD variant carriers. Of 127 non-variant carriers who have completed chemotherapy, 18 (14%) experienced severe (grade ≥3, Common Terminology Criteria for Adverse Events version 5.0). Of note, 22% (3 patients) of the variant carriers experienced severe toxicity even after DPYD-guided dose reductions. For one of these carriers who experienced severe thrombocytopenia within the first week, DPYD testing likely prevented lethal toxicity. In DPYD variant carriers who tolerate reduced doses, a later 25% increase led to chemotherapy discontinuation. As a result, a recommendation was made to clinicians based on available literature and expert opinion specifying that variant carriers who tolerated two cycles without toxicity can have a dose escalation of only 10%.Conclusion:DPYD-guided dose reductions were a feasible and acceptable method of preventing severe toxicity in DPYD variant carriers. Even with dose reductions, there were variant carriers who still experienced severe fluoropyrimidine toxicity, highlighting the importance of adhering to guideline-recommended dose reductions. Following the completion of the pilot phase of this study, DPYD genotyping was made available province-wide in British Columbia.
The accordion technique enhances bone regeneration via angiogenesis factor in a rat distraction osteogenesis model
Authors: Liu Kai , Wang Sulong , Yalikun Ainizier , Ren Peng , Yusufu Aihemaitijiang 
Published: September 2023

Objective: The purpose of this study was to observe the effect of the accordion technique (AT) during the distraction phase on chondrogenesis and bone regeneration in a rat femoral distraction osteogenesis (DO) model, and investigate its potential mechanism for reducing the total treatment time of DO.Methods: Fifty-four male Sprague-Dawley (SD) rats that were specific-pathogen-free (SPF) were subjected to DO surgery on the right femur. The distraction rate was 0.5 mm/day for 10 days, following a latency period of 5 days. Rats were randomly divided into Control (no AT, n = 18), Group LA (low amplitude with AT, n = 18), and Group HA (high amplitude with AT, n = 18) according to different AT protocols in the distraction phase. Rats were respectively euthanized by anesthesia overdose at 2, 4 and 6 weeks of the consolidation phase, and the femurs were harvested. Digital radiography, micro-computed tomography (micro-CT), biomechanical tests, and histomorphological analysis were used to assess the quality of regenerated bone in the distraction area.Results: Digital radiographic, micro-CT, biomechanical tests, and histological analysis revealed an increase in early-stage callus formation (p &lt; 0.05) and improved blood supply to the callus tissue in Group LA, as compared to both the Control and Group HA. The enhanced differentiation of fibrous and cartilaginous tissue into bone tissue was also observed in Group LA, leading to improved strength and stiffness (p &lt; 0.05) of the regenerated bone at 6 weeks of the consolidation phase. The angiogenic (hypoxia-inducible factor—1α (HIF—1α) and vascular endothelial growth factor (VEGF), p &lt; 0.05) and osteogenic (runt-related transcription factor 2 (RUNX2), osteocalcin (OCN) and osteopontin (OPN), p &lt; 0.05) biomarkers were higher expressed in Group LA at 2 and 4 weeks of consolidation phase, whereas decreased at 6 weeks of consolidation phase.Conclusion: The application of AT with low amplitude during the distraction phase can enhance chondrogenesis and bone regeneration by activating the angiogenesis factor pathway and upregulating the expression of osteogenic-related biomarkers such as HIF-1α, VEGF, RUNX2, OCN, and OPN.
Secondary succession of shrub-herb communities in the hilly area of Taihang Mountain
Authors: Liu Xiuping , Zhou Wangming , Li Xiaoxin , Zhang Yuming , Dong Wenxu 
Published: September 2023

IntroductionTo document the successional processes of shrub-herb communities after large-scale human disturbance, and understand how changing environmental conditions affect species replacement in semi-humid hilly areas.MethodsUtilizing the established permanent plots in the hilly area of Taihang Mountain, we evaluated temporal patterns of vegetation and soil following grass-to-shrub succession.Results and DiscussionAlong secondary succession, Vitex negundo var. heterophylla gradually dominated in dry sunny slope and shared the dominance with Leptodermis oblonga in shaded slope. Herbaceous dominant species in shrub-herb communities switched from Themeda japonica, Bothriochloa ischaemum, Artemisia sacrorum, and Cleistogenes chinensis in 1986 census to B. ischaemum and A. sacrorum in 2008 census, but herb was no longer dominant in 2020 census. As succession progresses, species dominance increased while richness decreased generally, and herb cover and aboveground biomass decreased, whereas shrub height, cover, and aboveground biomass increased significantly. Soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), and total potassium (TK) in topsoil increased significantly while pH declined by 1.04 units over the past three decades. Plant communities transitioned from perennial herbs to shrub-herb and then shrub communities, and V. negundo var. heterophylla dominated in the succession of shrub-herb communities. Climate and soil properties, combined with plant attributes, together drive post-disturbance secondary succession. From a management perspective, the tight coupling between vegetation and soil under local climatic conditions should be considered to improve the fragile ecosystem in the hilly area of Taihang Mountain.
Hyperspectral imaging combined with CNN for maize variety identification
Authors: Zhang Fu , Zhang Fangyuan , Wang Shunqing , Li Lantao , Lv Qiang , Fu Sanling , Wang Xinyue , Lv Qingfeng , Zhang Yakun 
Published: September 2023

IntroductionAs the third largest food crop in the world, maize has wide varieties with similar appearances, which makes identification difficult. To solve the problem of identification of hybrid maize varieties, a method based on hyperspectral image technology combined with a convolutional neural network (CNN) is proposed to identify maize varieties.MethodsIn this study, 735 maize seeds from seven half-parent hybrid maize varieties were regarded as the research object. The maize seed images in the range of 900 ~ 1700nm were obtained by hyperspectral image acquisition system. The region of interest (ROI) of the embryo surface was selected, and the spectral reflectance of maize seeds was extracted. After Savitzky-Golay (SG) Smoothing pretreatment, Maximum Normalization (MN) pretreatment was performed. The 56 feature wavelengths were selected by Competitive Adaptive Reweighting Algorithm (CARS) and Successive Projection Algorithm (SPA). And the 56 wavelengths were mapped to high-dimensional space by high-dimensional feature mapping and then reconstructed into three-dimensional image features. A five-layer convolution neural network was used to identify three-dimensional image features, and nine (SG+MN)-(CARS+SPA)-CNN maize variety identification models were established by changing the input feature dimension and the depth factor size of the model layer.Results and DiscussionThe results show that the maize variety classification model works best, when the input feature dimension is 768 and the layer depth factor d is 1.0. At this point, the model accuracy of the test set is 96.65% and the detection frame rate is1000 Fps/s in GPU environment, which can realize the rapid and effective non-destructive detection of maize varieties. This study provides a new idea for the rapid and accurate identification of maize seeds and seeds of other crops.
Gender representations and portrayal of adults in children’s television advertising: content analysis of prime cartoon channels in India
Authors: Chitra Kamalakannan Ravishankaran , Senthilkumar Nakkeeran 
Published: September 2023

IntroductionGender stereotyping in television advertising is a universal phenomenon and has the potential to influence children’s perceptions of gender roles. Despite India’s enormous child population, gender representation in television advertising is hardly researched.MethodsThis study was conducted using a content analysis methodology to examine gender stereotypes in children’s television advertising in India. A total of 189 unique advertisements were selected from six prime cartoon channels, namely Nickelodeon, Disney Channel, Hungama, Cartoon Network, Discovery Kids, and Pogo TV. A stratified constructed sample of 319 central figures from 102 hours of TV viewing was collected over two consecutive weeks in November 2018 during children’s prime-time viewings.ResultsThis study examines gender role cues in children’s television advertising using McArthur and Resko’s coding method. The sample was subsequently analyzed using chi-square statistics, and the findings were contextualized and compared with those from other Asian nations. The results indicated that men significantly dominate (voice-over, product authority, autonomous roles, fact-based arguments, other products, end comments, pleasure, and practical rewards), whereas females are stereotyped (dependent roles, product users, portrayal of domestic products in domestic settings, opinion-based arguments, and self-enhancement rewards).DiscussionHowever, the results reveal a reduction in certain stereotypical aspects, such as a significant increase in women performing voice-overs and portraying characters with product authority and autonomy, while men exhibit increased involvement with domestic products and rewards such as self-enhancement, practical, and pleasure rewards. The theoretical (social learning and role congruity theory) and practical implications for advertisers and marketers are discussed based on these findings.