bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive analysis of cuproptosis-related long non-coding RNA signature and personalized therapeutic strategy of breast cancer patients
Authors: Guo Qiaonan , Qiu Pengjun , Pan Kelun , Lin Jianqing 
Published: December 2022

BackgroundBreast cancer (BC) is considered to be one of the primary causes of cancer deaths in women. Cuproptosis was suggested to play an important role in tumor proliferation and tumor immune microenvironment. Therefore, an investigation was conducted to identify the relationship between cuproptosis-related long non-coding RNAs (lncRNAs) and BC prognosis.MethodBased on The Cancer Genome Atlas (TCGA), nine cuproptosis-related lncRNAs were identified by Pearson’s analysis and Cox regression analysis to create a cuproptosis-related lncRNA signature. Subsequently, patients with BC were divided into high-risk and low-risk groups. The Kaplan–Meier curves and a time-dependent receiver operating characteristic (ROC) analysis were employed to elucidate the predictive capability of the signature. After that, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was conducted by Gene Set Enrichment Analysis (GSEA), and the lncRNA–mRNA co-expression network was established by Cytoscape software. Furthermore, the ESTIMATE score was calculated, and the immune cell type component analysis was conducted. Eventually, immunotherapy response analysis was applied to identify the predictive power of cuproptosis-related lncRNAs to tumor immunotherapy response, including immune checkpoint gene expression levels, tumor mutational burden (TMB), and microsatellite instability (MSI).ResultsPatients with BC in the low-risk groups showed better clinical outcomes. The KEGG pathways in the high-risk groups were mainly enriched in immune response and immune cell activation. Furthermore, the ESTIMATE scores were higher in the low-risk groups, and their immune cell infiltrations were dramatically different from those of the high-risk groups. The low-risk groups were shown to have higher infiltration levels of CD8+ T cells and TMB-high status, resulting in better response to immunotherapies.ConclusionThe findings of this study revealed that the nine-cuproptosis-related lncRNA risk score was an independent prognostic factor for BC. This signature was a potential predictor for BC immunotherapy response. What we found will provide novel insight into immunotherapeutic treatment strategies in BC.
Diagnostic and prognostic role of circulating neutrophil extracellular trap markers and prekallikrein in patients with high-grade serous ovarian cancer
Authors: Kim Jisoo G. , Kim Se Ik , Song Sang Hoon , Gu Ja-Yoon , Lee Maria , Kim Hyun Kyung 
Published: December 2022

ObjectiveTumor-promoting inflammation is among the hallmarks of cancer. Prekallikrein is among the acute-phase reactants in the inflammatory response; moreover, neutrophils release nuclear contents into the extracellular space to create neutrophil extracellular traps (NET). We aimed to investigate the diagnostic and prognostic utilities of circulating plasma NET markers and prekallikrein for high-grade serous ovarian cancer (HGSOC).MethodsCirculating levels of three NET markers (histone-DNA complex, cell-free DNA, and neutrophil elastase) and prekallikrein were measured in 75 patients with HGSOC and 23 healthy controls. We used an area under the receiver operating characteristic curve (AUC) analysis to investigate their diagnostic and prognostic utilities for HGSOC.ResultsCompared with healthy controls, patients with HGSOC showed significantly higher levels of the three NET markers and prekallikrein. Patients with advanced-stage HGSOC showed significantly higher levels of the cell-free DNA (87.4 vs. 79.5 ng/ml; P = 0.013), compared with those with early-stage HGSOC. Further, the levels of histone-DNA complex, neutrophil elastase, and prekallikrein did not significantly differ according to the cancer stage. All markers showed significant diagnostic utility. Notably, a logistic regression-based model that comprised all four markers showed the strongest diagnostic power (AUC, 0.966; 95% confidence interval [CI], 0.933−1.000). Specifically, neutrophil elastase was identified as an independent poor prognostic factor for overall survival (adjusted hazard ratio [aHR], 10.17; 95% CI, 1.09−94.97; P = 0.042) and progression-free survival (aHR, 14.47; 95% CI, 1.52−137.35; P = 0.020) in patients with HGSOC.ConclusionsThe levels of the three NET markers and prekallikrein might be novel diagnostic and prognostic markers for HGSOC.
Susceptibility of ECE1 polymorphisms to Hirschsprung's disease in southern Chinese children
Authors: Lan Chaoting , Liu Yanqing , Wu Xiao , Wang Bingtong , Xin Songqing , He Qiuming , Zhong Wei , Liu Zipeng 
Published: December 2022

BackgroundHirschsprung's disease (HSCR) is currently considered to be a congenital gastrointestinal malformation caused mainly by genetic factors. Endothelin Converting Enzyme-1 (ECE1) has been reported to be associated with HSCR. However, the relationship between ECE1 single nucleotide polymorphism (SNP) rs169884 and HSCR in the southern Chinese population remains unknown.Methods1,470 HSCR patients and 1,473 controls from a southern Chinese population were recruited. The intronic SNP rs169884 in ECE1 was genotyped in all samples. We tested the association between rs169884 and HSCR under various genetic models. We also evaluated the effect of rs169884 on HSCR subtypes, including short-segment HSCR (S-HSCR), long-segment HSCR (L-HSCR) and total colonic aganglionosis (TCA). External epigenetic data were integrated to investigate the potential biological function of rs169884.ResultsChromatin states data from derived neuron cells or fetal colon tissue revealed that rs169884 might control ECE1 expression through regulating its enhancer function. We did not find a significant association between rs169884 and HSCR. For HSCR subtypes, although no significant associations were detected between rs169884 and S-HSCR (OR = 1.00, 95% CI: 0.89∼1.12, Padj = 0.77) or TCA (OR = 1.00, 95% CI: 0.72∼1.38, Padj = 0.94), we found that rs169884 could increase the risk of L-HSCR (OR = 1.23, 95% CI 1.02∼1.45, Padj = 0.024).ConclusionThese results suggested that rs169884 might play a regulatory role for ECE1 expression and increase susceptibility of L-HSCR in southern Chinese children.
Flecainide and risk of skin neoplasms: Results of a large nested case–control study in Spain and Denmark
Authors: Reyes Carlen , León-Muñoz Luz M , Pistillo Andrea , Jóhannesdóttir Schmidt Sigrún Alba , Kristensen Kasper Bruun , Puente Diana , LLorente-García Ana , Huerta-Álvarez Consuelo , Pottegård Anton , Duarte-Salles Talita 
Published: December 2022

Background: A previous study in Denmark suggested an increased melanoma risk associated with the use of flecainide.Objective: To study the association between flecainide use and the risk of melanoma and non-melanoma skin cancer in Spain and Denmark.Methods: We conducted a multi-database case–control study in (database/study period) Spain (SIDIAP/2005–2017 and BIFAP/2007–2017) and Denmark (Danish registries/2001–2018). We included incident cases of melanoma or non-melanoma skin cancer (NMSC) aged ≥18 with ≥2 years of previous data (≥10 years for Denmark) before the skin cancer and matched them to controls (10:1 by age and sex). We excluded persons with immunosuppression or previous cancer. We defined ever-use as any prescription fill and high-use as a cumulative dose of at least 200 g (reference: never-use). We categorized a cumulative dose for a dose–response assessment. We used conditional logistic regression to compute ORs (95% CI) adjusted for photosensitizing, anti-neoplastic, disease-specific drugs and comorbidities.Results: The total numbers of melanoma/NMSC cases included were 7,809/64,230 in SIDIAP, 4,661/31,063 in BIFAP, and 27,978/152,821 in Denmark. In Denmark, high-use of flecainide was associated with increased adjusted ORs of skin cancer compared with never-use [melanoma: OR 1.97 (1.38–2.81); NMSC: OR 1.34 (1.15–1.56)]. In Spain, an association between high-use of flecainide and NMSC was also observed [BIFAP: OR 1.42 (1.04–1.93); SIDIAP: OR 1.19 (0.95–1.48)]. There was a non-significant dose–response pattern for melanoma in Denmark and no apparent dose–response pattern for NMSC in any of the three databases. We found similar results for ever-use of flecainide.Conclusion: Flecainide use was associated with an increased risk of melanoma (Denmark only) and NMSC (Denmark and Spain) but without substantial evidence of dose–response patterns. Further studies are needed to assess for possible unmeasured confounders.
Incorporating structural abnormalities in equivalent dipole layer based ECG simulations
Authors: Boonstra Machteld J , Oostendorp Thom F , Roudijk Rob W , Kloosterman Manon , Asselbergs Folkert W , Loh Peter , Van Dam Peter M 
Published: December 2022

Introduction: Electrical activity of the myocardium is recorded with the 12-lead ECG. ECG simulations can improve our understanding of the relation between abnormal ventricular activation in diseased myocardium and body surface potentials (BSP). However, in equivalent dipole layer (EDL)-based ECG simulations, the presence of diseased myocardium breaks the equivalence of the dipole layer. To simulate diseased myocardium, patches with altered electrophysiological characteristics were incorporated within the model. The relation between diseased myocardium and corresponding BSP was investigated in a simulation study.Methods: Activation sequences in normal and diseased myocardium were simulated and corresponding 64-lead BSP were computed in four models with distinct patch locations. QRS-complexes were compared using correlation coefficient (CC). The effect of different types of patch activation was assessed. Of one patient, simulated electrograms were compared to electrograms recorded during invasive electro-anatomical mapping.Results: Hundred-fifty-three abnormal activation sequences were simulated. Median QRS-CC of delayed versus dyssynchronous were significantly different (1.00 vs. 0.97, p &lt; 0.001). Depending on the location of the patch, BSP leads were affected differently. Within diseased regions, fragmentation, low bipolar voltages and late potentials were observed in both recorded and simulated electrograms.Discussion: A novel method to simulate cardiomyopathy in EDL-based ECG simulations was established and evaluated. The new patch-based approach created a realistic relation between ECG waveforms and underlying activation sequences. Findings in the simulated cases were in agreement with clinical observations. With this method, our understanding of disease progression in cardiomyopathies may be further improved and used in advanced inverse ECG procedures.
S-ResNet: An improved ResNet neural model capable of the identification of small insects
Authors: Wang Pei , Luo Fan , Wang Lihong , Li Chengsong , Niu Qi , Li Hui 
Published: December 2022

IntroductionPrecise identification of crop insects is a crucial aspect of intelligent plant protection. Recently, with the development of deep learning methods, the efficiency of insect recognition has been significantly improved. However, the recognition rate of existing models for small insect targets is still insufficient for insect early warning or precise variable pesticide application. Small insects occupy less pixel information on the image, making it more difficult for the model to extract feature information.MethodsTo improve the identification accuracy of small insect targets, in this paper, we proposed S-ResNet, a model improved from the ResNet, by varying its convolution kernel. The branch of the residual structure was added and the Feature Multiplexing Module (FMM) was illustrated. Therefore, the feature expression capacity of the model was improved using feature information of different scales. Meanwhile, the Adjacent Elimination Module (AEM) was furtherly employed to eliminate the useless information in the extracted features of the model.ResultsThe training and validation results showed that the improved residual structure improved the feature extraction ability of small insect targets compared to the original model. With compare of 18, 30, or 50 layers, the S-ResNet enhanced the identification accuracy of small insect targets by 7% than that on the ResNet model with same layer depth.
Transcriptome and targeted hormone metabolome reveal the molecular mechanisms of flower abscission in camellia
Authors: Cai Yanfei , Meng Jing , Cui Yinshan , Tian Min , Shi Ziming , Wang Jihua 
Published: December 2022

IntroductionCamellia is among the most ornamentally valuable flowers and plants worldwide. Flower abscission typically causes significant financial losses by the horticultural landscape. Previous research has revealed that phytohormones, transcription factors, and other genes involved in floral development regulate the maintenance and mortality of flowersMethodsIn this study, for the first time, the transcriptomes and targeted hormone metabolomics of three developmental stages of the receptacles of two distinct camellia strains (CF: abscission strain, CHF: nonabscission strain) were analyzed to determine their roles in regulating blossom abscission in camellia.ResultsABA content was shown to be considerably upregulated throughout all phases of CF development, as were the genes implicated in the ABA production pathway and their downstream counterparts. Highly expressed genes in CF were involved in galactose metabolism, phenylpropanoid biosynthesis, amino and nucleotide sugar metabolism, pentose and glucuronate interconversions, and MAPK. Among others, highly expressed genes in CHF are associated with fructose and mannose metabolism, alpha-linolenic acid metabolism, biosynthesis of secondary metabolites, starch and sucrose metabolism, and cutin, suberin, and wax biosynthesis. A vast variety of stress response-related pathways and redox-related activities were also shown to be active in CHF. In contrast, CF dramatically activated pathways associated with lignin production, keratinogenesis, cell wall biogenesis, and ABA response. A comparative transcriptomic study of the CF and CHF pathways revealed that the downstream response pathways of hormones, including CTK, BR, IAA, ethylene, and GA, were very active in CF, indicating a significant amount of signal transduction and transcriptional regulation by CF. In addition, members of the transcription factor family, such as MYB, bHLH, MADS, and WD40, may regulate flower abscission.DiscussionA comparative transcriptome analysis of two distinct strains of camellia receptacles elucidates the molecular processes and regulatory characteristics of flower abscission and provides direction for the targeted improvement and breeding of camellia.
Genome-wide identification of sucrose non-fermenting-1-related protein kinase genes in maize and their responses to abiotic stresses
Authors: Feng Xue , Meng Quan , Zeng Jianbin , Yu Qian , Xu Dengan , Dai Xuehuan , Ge Lei , Ma Wujun , Liu Wenxing 
Published: December 2022

IntroductionProtein kinases play an important role in plants in response to environmental changes through signal transduction. As a large family of protein kinases, sucrose non-fermenting-1 (SNF1)-related kinases (SnRKs) were found and functionally verified in many plants. Nevertheless, little is known about the SnRK family of Zea mays.MethodsEvolutionary relationships, chromosome locations, gene structures, conserved motifs, and cis-elements in promoter regions were systematically analyzed. Besides, tissue-specific and stress-induced expression patterns of ZmSnRKs were determined. Finally, functional regulatory networks between ZmSnRKs and other proteins or miRNAs were constructed.Results and DiscussionIn total, 60 SnRK genes located on 10 chromosomes were discovered in maize. ZmSnRKs were classified into three subfamilies (ZmSnRK1, ZmSnRK2, and ZmSnRK3), consisting of 4, 14, and 42 genes, respectively. Gene structure analysis showed that 33 of the 42 ZmSnRK3 genes contained only one exon. Most ZmSnRK genes contained at least one ABRE, MBS, and LTR cis-element and a few ZmSnRK genes had AuxRR-core, P-box, MBSI, and SARE ciselements in their promoter regions. The Ka:Ks ratio of 22 paralogous ZmSnRK gene pairs revealed that the ZmSnRK gene family had experienced a purifying selection. Meanwhile, we analyzed the expression profiles of ZmSnRKs, and they exhibited significant differences in various tissues and abiotic stresses. In addition, A total of eight ZmPP2Cs, which can interact with ZmSnRK proteins, and 46 miRNAs, which can target 24 ZmSnRKs, were identified. Generally, these results provide valuable information for further function verification of ZmSnRKs, and improve our understanding of the role of ZmSnRKs in the climate resilience of maize.
TIA-YOLOv5: An improved YOLOv5 network for real-time detection of crop and weed in the field
Authors: Wang Aichen , Peng Tao , Cao Huadong , Xu Yifei , Wei Xinhua , Cui Bingbo 
Published: December 2022

IntroductionDevelopment of weed and crop detection algorithms provides theoretical support for weed control and becomes an effective tool for the site-specific weed management. For weed and crop object detection tasks in the field, there is often a large difference between the number of weed and crop, resulting in an unbalanced distribution of samples and further posing difficulties for the detection task. In addition, most developed models tend to miss the small weed objects, leading to unsatisfied detection results. To overcome these issues, we proposed a pixel-level synthesization data augmentation method and a TIA-YOLOv5 network for weed and crop detection in the complex field environment.MethodsThe pixel-level synthesization data augmentation method generated synthetic images by pasting weed pixels into original images. In the TIA-YOLOv5, a transformer encoder block was added to the backbone to improve the sensitivity of the model to weeds, a channel feature fusion with involution (CFFI) strategy was proposed for channel feature fusion while reducing information loss, and adaptive spatial feature fusion (ASFF) was introduced for feature fusion of different scales in the prediction head.ResultsTest results with a publicly available sugarbeet dataset showed that the proposed TIA-YOLOv5 network yielded an F1-scoreweed, APweed and mAP@0.5 of 70.0%, 80.8% and 90.0%, respectively, which was 11.8%, 11.3% and 5.9% higher than the baseline YOLOv5 model. And the detection speed reached 20.8 FPS.DiscussionIn this paper, a fast and accurate workflow including a pixel-level synthesization data augmentation method and a TIA-YOLOv5 network was proposed for real-time weed and crop detection in the field. The proposed method improved the detection accuracy and speed, providing very promising detection results.
Changes in attitudes towards smoking during smoking cessation courses for Turkish- and Albanian-speaking migrants in Switzerland and its association with smoking behavior: A latent change score approach
Authors: Paz Castro Raquel , Henninger Mirka , Schaub Michael P. , Salis Gross Corina 
Published: December 2022

IntroductionMigrant populations usually report higher smoking rates than locals. At the same time, people with a migration background have little or no access to regular smoking cessation treatment. In the last two decades, regular smoking cessation courses were adapted to reach out to Turkish- and Albanian-speaking migrants living in Switzerland. The main aims of the current study were (1) to analyze the effects of an adapted smoking cessation course for Turkish- and Albanian-speaking migrants in Switzerland on attitudes toward smoking and smoking behavior; and (2) to elucidate whether changes in attitudes toward smoking were associated to changes in smoking behavior in the short- and in the long-term.MethodsA total of 59 smoking cessation courses (Turkish: 37; Albanian: 22) with 436 participants (T: 268; A: 168) held between 2014 and 2019 were evaluated. Attitudes toward smoking and cigarettes smoked per day were assessed at baseline and 3-months follow-up. One-year follow-up calls included assessment of cigarettes smoked per day. Data were analyzed by means of structural equation modeling with latent change scores.ResultsParticipation in an adapted smoking cessation course led to a decrease of positive attitudes toward smoking (T: β = −0.65, p &lt; 0.001; A: β = −0.68, p &lt; 0.001) and a decrease of cigarettes smoked per day in the short-term (T: β = −0.58, p &lt; 0.001; A: β = −0.43, p &lt; 0.001) with only Turkish-speaking migrants further reducing their smoking in the long-term (T: β = −0.59, p &lt; 0.001; A: β = −0.14, p = 0.57). Greater decreases in positive attitudes were associated with greater reductions of smoking in the short-term (T: r = 0.39, p &lt; 0.001; A: r = 0.32, p = 0.03), but not in the long-term (T: r = −0.01, p = 0.88; A: r = −0.001, p = 0.99).ConclusionThe adapted smoking cessation courses fostered changes in positive attitudes toward smoking that were associated with intended behavior change in the short-term. The importance of socio-cognitive characteristics related to behavior change maintenance to further increase treatment effectiveness in the long-term is discussed.
The role of parents in the care for adolescents suffering from emotional and behavioral problems
Authors: Mackova Jaroslava , Veselska Zuzana Dankulincova , Geckova Andrea Madarasova , Jansen Danielle E. M. C. , van Dijk Jitse P. , Reijneveld Sijmen A. 
Published: December 2022

BackgroundParents play an important role in the psychosocial care of their children. Previous research has primarily examined their role in care entry, whereas evidence on their role in other stages of the care process is scarce and lacking particularly in regard to the perspective of care providers. Our aim was therefore to examine how psychosocial care providers perceive the role of parents in the process of psychosocial care for adolescents.MethodsWe used data from 25 semi-structured interviews with psychosocial care providers on the roles of parents in the care process. We analyzed data using consensual qualitative research and thematic analysis.ResultsFour main themes were identified: (1) parents as a source of adolescents’ problems; (2) parents trying to escape from responsibility for adolescents with problems; (3) parents as an active part of the care for adolescents; and (4) parents as a barrier to effective care.ConclusionPsychosocial care providers should specifically address the role of the parents in psychosocial care to improve outcomes. Specific interventions are needed to support the involvement of parents in care, as their role is important. Moreover, professionals can be better trained in working with multi-problem families also to resolve some of the negative perceptions of these parents.