bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishment of a new prognostic risk model of MAPK pathway-related molecules in kidney renal clear cell carcinoma based on genomes and transcriptomes analysis
Authors: Zhang Peizhi , Li Jiayi , Wang Zicheng , Zhao Leizuo , Qiu Jiechuan , Xu Yingkun , Wu Guangzhen , Xia Qinghua 
Published: March 2023

PurposeThe mitogen-activated protein kinase (MAPK) signaling pathway is often studied in oncology as the most easily mentioned signaling pathway. This study aims to establish a new prognostic risk model of MAPK pathway related molecules in kidney renal clear cell carcinoma (KIRC) based on genome and transcriptome analysis.MethodsIn our study, RNA-seq data were acquired from the KIRC dataset of The Cancer Genome Atlas (TCGA) database. MAPK signaling pathway-related genes were obtained from the gene enrichment analysis (GSEA) database. We used “glmnet” and the “survival” extension package for LASSO (Least absolute shrinkage and selection operator) regression curve analysis and constructed a prognosis-related risk model. The survival curve and the COX regression analysis were used the “survival” expansion packages. The ROC curve was plotted using the “survival ROC” extension package. We then used the “rms” expansion package to construct a nomogram plot. We performed a pan-cancer analysis of CNV (copy number variation), SNV (single nucleotide variant), drug sensitivity, immune infiltration, and overall survival (OS) of 14 MAPK signaling pathway-related genes using several analysis websites, such as GEPIA website and TIMER database. Besides, the immunohistochemistry and pathway enrichment analysis used The Human Protein Atlas (THPA) database and the GSEA method. Finally, the mRNA expression of risk model genes in clinical renal cancer tissues versus adjacent normal tissues was further verified by real-time quantitative reverse transcription (qRT-PCR).ResultsWe performed Lasso regression analysis using 14 genes and created a new KIRC prognosis-related risk model. High-risk scores suggested that KIRC patients with lower-risk scores had a significantly worse prognosis. Based on the multivariate Cox analysis, we found that the risk score of this model could serve as an independent risk factor for KIRC patients. In addition, we used the THPA database to verify the differential expression of proteins between normal kidney tissues and KIRC tumor tissues. Finally, the results of qRT-PCR experiments suggested large differences in the mRNA expression of risk model genes.ConclusionsThis study constructs a KIRC prognosis prediction model involving 14 MAPK signaling pathway-related genes, which is essential for exploring potential biomarkers for KIRC diagnosis.
Perioperative and long-term survival outcomes of laparoscopic versus open hepatectomy for BCLC stage A large hepatocellular carcinoma patients in difficult segments: A two-centre, propensity score matching analysis
Authors: Ding Dong-yang , Liu Lei , Lin Kong-ying , Gan Xiao-jie , Guo Xing-gang , Ding Wen-bin , Sun Da-peng , Li Wen , Tao Qi-fei , Gu Fang-ming , Guo Wei-xing , Zeng Yong-yi , Zhou Wei-ping , Yuan Sheng-xian 
Published: March 2023

BackgroundThe differences in short- and long-term outcome between laparoscopic liver resection (LLR) and open liver resection (OLR) for BCLC stage A large hepatocellular carcinoma (HCC) in difficult segments (I, IVa, VII, VIII) remain unclear. This PSM two-centre study aimed to compare perioperative and long-term survival outcomes of LLR with OLR for this HCC.MethodsHCC patients with BCLC stage A who underwent OLR or LLR in two medical centres were enrolled in the study. PSM analysis was performed to match patients between the LLR cohort and OLR cohort. Survival was analysed based on the Kaplan–Meier method. Independent risk factors were identified by Cox regression.ResultsAfter PSM, 35 patients remained in the LLR cohort, and 84 remained in the OLR cohort. Patients in the LLR cohort had more intraoperative blood loss (p=0.036) and shorter hospital stays after surgery (p&lt;0.001). The LLR cohort and OLR cohort had no difference in intraoperative blood transfusion, surgical margin or postoperative short-term outcomes. The OS and RFS were not significantly different between the two cohorts. The OS and RFS of these two cohorts were not different in the subgroup analysis. Surgical margin was identified as an independent risk factor for tumour recurrence.ConclusionFor BCLC stage A large HCC patients with lesions in difficult segments, LLR was feasible and had shorter hospital stay than OLR. In addition, a surgical margin ≥1 cm could significantly decrease the recurrence probability for large HCC located in different segments without compromising short-term outcomes.
Non-canonical Wnt/Ca2+ signaling is essential to promote self-renewal and proliferation in colon cancer stem cells
Authors: Sarabia-Sánchez Miguel Angel , Moreno-Londoño Angela Patricia , Castañeda-Patlán María Cristina , Alvarado-Ortiz Eduardo , Martínez-Morales Juan Carlos , Robles-Flores Martha 
Published: March 2023

IntroductionCancer Stem Cells (CSC) are responsible for maintaining tumor growth, chemoresistance, and metastasis. Therefore, understanding their characteristics is critical to progress in cancer therapy. While the contribution of the canonical Wnt/b-catenin signaling in both normal and CSCs had been well established, the function of non-canonical Wnt signaling cascades in stem cells is unclear. Recently, we reported that Wnt ligands trigger complex signaling in which the canonical and non-canonical responses can be simultaneously activated by one ligand in colon cancer cells, suggesting, therefore, that noncanonical Wnt pathways may also be important in CSCs.MethodsThe present work aimed to know the role of the Wnt/Ca2+ pathway in colon CSCs. We used tumorspheres as a model of CSCs enrichment of CRC cell lines with different Wnt/b-catenin contexts.ResultsUsing Wnt3a and Wnt5a as prototype ligands to activate the canonical or the non-canonical pathways, respectively, we found that both Wnt3a and Wnt5a promote sphere-formation capacity and proliferation without stimulating b-catenin-dependent transcription. Upregulation of sphere formation by Wnt5a or Wnt3a requires the downstream activation of Phospholipase C and transcriptional factor NFAT. Moreover, the single specific inhibition of PLC or NFAT, using U73122 and 11R-VIVIT, respectively, leads to impaired sphere formation.DiscussionOur results indicate that both types of ligands activate the Wnt/Ca2+ signaling axis to induce/maintain the self-renewal efficiency of CSCs, demonstrating to be essential for the functions of CSC in colon cancer.
Risk factors for length of NICU stay of newborns: A systematic review
Authors: Fu Maoling , Song Wenshuai , Yu Genzhen , Yu Yaqi , Yang Qiaoyue 
Published: March 2023

BackgroundThe improvement in survival of preterm infants is accompanied by an increase in neonatal intensive care unit (NICU) admissions. Prolonged length of stay in the NICU (LOS-NICU) increases the incidence of neonatal complications and even mortality and places a significant economic burden on families and strain on healthcare systems. This review aims to identify risk factors influencing LOS-NICU of newborns and to provide a basis for interventions to shorten LOS-NICU and avoid prolonged LOS-NICU.MethodsA systematic literature search was conducted in PubMed, Web of Science, Embase, and Cochrane library for studies that were published in English from January 1994 to October 2022. The PRISMA guidelines were followed in all phases of this systematic review. The Quality in Prognostic Studies (QUIPS) tool was used to assess methodological quality.ResultsTwenty-three studies were included, 5 of which were of high quality and 18 of moderate quality, with no low-quality literature. The studies reported 58 possible risk factors in six broad categories (inherent factors; antenatal treatment and maternal factors; diseases and adverse conditions of the newborn; treatment of the newborn; clinical scores and laboratory indicators; organizational factors).ConclusionsWe identified several of the most critical risk factors affecting LOS-NICU, including birth weight, gestational age, sepsis, necrotizing enterocolitis, bronchopulmonary dysplasia, and retinopathy of prematurity. As only a few high-quality studies are available at present, well-designed and more extensive prospective studies investigating the risk factors affecting LOS-NICU are still needed in the future.
Voluntary exercise modulates pathways associated with amelioration of retinal degenerative diseases
Authors: Chu-Tan Joshua A. , Cioanca Adrian V. , Wooff Yvette , Kirkby Max , Ellis Marissa , Gulati Pranay , Karl Tim , Boatright Jeffrey H. , Bales Katie , Nickerson John , Natoli Riccardo 
Published: March 2023

Background: Exercise has been shown to promote a healthier and longer life and linked to a reduced risk of developing neurodegenerative diseases including retinal degenerations. However, the molecular pathways underpinning exercise-induced cellular protection are not well understood. In this work we aim to profile the molecular changes underlying exercise-induced retinal protection and investigate how exercise-induced inflammatory pathway modulation may slow the progression of retinal degenerations.Methods: Female C57Bl/6J mice at 6 weeks old were given free access to open voluntary running wheels for a period of 28 days and then subjected to 5 days of photo-oxidative damage (PD)-induced retinal degeneration. Following, retinal function (electroretinography; ERG), morphology (optical coherence tomography; OCT) and measures of cell death (TUNEL) and inflammation (IBA1) were analysed and compared to sedentary controls. To decipher global gene expression changes as a result of voluntary exercise, RNA sequencing and pathway and modular gene co-expression analyses were performed on retinal lysates of exercised and sedentary mice that were subjected to PD, as well as healthy dim-reared controls.Results: Following 5 days of PD, exercised mice had significantly preserved retinal function, integrity and reduced levels of retinal cell death and inflammation, compared to sedentary controls. In response to voluntary exercise, inflammatory and extracellular matrix integrity pathways were significantly modulated, with the gene expression profile of exercised mice more closely trending towards that of a healthy dim-reared retina.Conclusion: We suggest that voluntary exercise may mediate retinal protection by influencing key pathways involved in regulating retinal health and shifting the transcriptomic profile to a healthy phenotype.
In silico analysis of the contribution of cardiomyocyte-fibroblast electromechanical interaction to the arrhythmia
Authors: Kursanov Alexander , Balakina-Vikulova Nathalie A. , Solovyova Olga , Panfilov Alexander , Katsnelson Leonid B. 
Published: March 2023

Although fibroblasts are about 5–10 times smaller than cardiomyocytes, their number in the ventricle is about twice that of cardiomyocytes. The high density of fibroblasts in myocardial tissue leads to a noticeable effect of their electromechanical interaction with cardiomyocytes on the electrical and mechanical functions of the latter. Our work focuses on the analysis of the mechanisms of spontaneous electrical and mechanical activity of the fibroblast-coupled cardiomyocyte during its calcium overload, which occurs in a variety of pathologies, including acute ischemia. For this study, we developed a mathematical model of the electromechanical interaction between cardiomyocyte and fibroblasts and used it to simulate the impact of overloading cardiomyocytes. In contrast to modeling only the electrical interaction between cardiomyocyte and fibroblasts, the following new features emerge in simulations with the model that accounts for both electrical and mechanical coupling and mechano-electrical feedback loops in the interacting cells. First, the activity of mechanosensitive ion channels in the coupled fibroblasts depolarizes their resting potential. Second, this additional depolarization increases the resting potential of the coupled myocyte, thus augmenting its susceptibility to triggered activity. The triggered activity associated with the cardiomyocyte calcium overload manifests itself in the model either as early afterdepolarizations or as extrasystoles, i.e., extra action potentials and extra contractions. Analysis of the model simulations showed that mechanics contribute significantly to the proarrhythmic effects in the cardiomyocyte overloaded with calcium and coupled with fibroblasts, and that mechano-electrical feedback loops in both the cardiomyocyte and fibroblasts play a key role in this phenomenon.
Phenotyping grapevine red blotch virus and grapevine leafroll-associated viruses before and after symptom expression through machine-learning analysis of hyperspectral images
Authors: Sawyer Erica , Laroche-Pinel Eve , Flasco Madison , Cooper Monica L. , Corrales Benjamin , Fuchs Marc , Brillante Luca 
Published: March 2023

IntroductionGrapevine leafroll-associated viruses (GLRaVs) and grapevine red blotch virus (GRBV) cause substantial economic losses and concern to North America’s grape and wine industries. Fast and accurate identification of these two groups of viruses is key to informing disease management strategies and limiting their spread by insect vectors in the vineyard. Hyperspectral imaging offers new opportunities for virus disease scouting.MethodsHere we used two machine learning methods, i.e., Random Forest (RF) and 3D-Convolutional Neural Network (CNN), to identify and distinguish leaves from red blotch-infected vines, leafroll-infected vines, and vines co-infected with both viruses using spatiospectral information in the visible domain (510-710nm). We captured hyperspectral images of about 500 leaves from 250 vines at two sampling times during the growing season (a pre-symptomatic stage at veraison and a symptomatic stage at mid-ripening). Concurrently, viral infections were determined in leaf petioles by polymerase chain reaction (PCR) based assays using virus-specific primers and by visual assessment of disease symptoms.ResultsWhen binarily classifying infected vs. non-infected leaves, the CNN model reaches an overall maximum accuracy of 87% versus 82.8% for the RF model. Using the symptomatic dataset lowers the rate of false negatives. Based on a multiclass categorization of leaves, the CNN and RF models had a maximum accuracy of 77.7% and 76.9% (averaged across both healthy and infected leaf categories). Both CNN and RF outperformed visual assessment of symptoms by experts when using RGB segmented images. Interpretation of the RF data showed that the most important wavelengths were in the green, orange, and red subregions.DiscussionWhile differentiation between plants co-infected with GLRaVs and GRBV proved to be relatively challenging, both models showed promising accuracies across infection categories.
Significant increases in Donghong kiwifruit yield by a novel umbrella-shaped trellis system and identification of associated molecular mechanisms
Authors: Deng Honghong , Li Yao , Pang Changqing , Zhang Kun , Tian Xinbo , Wang Tong , Liang Yan , He Zunzhen , Lang Yuxuan , Fang Jinbao , Lin Lijin , Wang Jin , Lv Xiulan , Xia Hui , Liang Dong 
Published: March 2023

China is the largest kiwifruit producer in the world, accounting for more than half of the total. However, in terms of yield per unit area, China is much lower than the global average and lags behind that of other countries. Yield improvement is of critical importance for the current kiwifruit industry in China. In this study, an improved overhead pergolas trellis (OPT) system, namely, the umbrella-shaped trellis (UST) system, was developed for Donghong kiwifruit, which is now the second most popular and widely cultivated red-fleshed kiwifruit in China. Surprisingly, the estimated yield on the UST system was more than two times higher than that with a traditional OPT, while the external fruit quality was maintained and the internal fruit quality was improved. One of the mechanisms contributing to the yield improvement was the significant promotion of the vegetative growth of canes at 6 ~ 10 mm in diameter by the UST system. The upper canopy of the UST treatment served as a natural shading condition for the lower fruiting canopy and thus had positive effects on the accumulation of chlorophylls and total carotenoids in the fruiting canopy. The most productive zones on the fruiting canes (6 ~ 10 mm in diameter) contained significantly higher (P&lt; 0.05) levels of zeatin riboside (ZR) and auxin (IAA) and ratios of ZR/gibberellin (GA), ZR/abscisic acid (ABA), and ABA/GA. A relatively high carbon/nitrogen ratio may promote the flower bud differentiation process of Donghong kiwifruit. The outcomes of this study provide a scientific basis for manifold increase in production of kiwifruit and contribute to the sustainability of the kiwifruit industry.
Effects of various seed priming on morphological, physiological, and biochemical traits of rice under chilling stress
Authors: Zhang Hua , Zhang Xiaoli , Gao Guoqing , Ali Izhar , Wu Xiaoyan , Tang Maoyan , Chen Lei , Jiang Ligeng , Liang Tianfeng 
Published: March 2023

Introduction/BackgroundDirect-seeded rice is exceptionally vulnerable to chilling stress, especially at the seed germination and seedling growth stages in the early season of the double cropping system.MethodsTherefore, we conducted two experiments to evaluate the role of various seed primings and their different concentrations of plant growth regulators [experiment 1—abscisic acid (ABA), gibberellin (GA3), salicylic acid (SA), brassinolide (BR), paclobutrazol, uniconazole (UN), melatonin (MT), and jasmonic acid (JA)] and osmopriming substances (chitosan, polyethylene glycol 6000 (PEG6000), and CaCl2) and experiment 2—GA, BR (two best), CaCl2 (worst), and control (CK)] on rice seedlings under low temperature condition.ResultsResults showed that the maximum germination rate of 98% was recorded in GA3 (10 mgL−1) and BR (0.3 mgL−1) among treatments. Compared to CK, root and shoot length were improved in ABA (0.5 mgL−1) and GA3 (100 mgL−1) by 64% and 68%, respectively. At the same time, root and shoot weights (fresh and dry) were enhanced in Paclobutrazol (300 mgL−1) and GA3 among treatments. Furthermore, the average root volume, average root diameter, and total root surface area were increased by 27%, 38%, and 33% in Paclobutrazol (300 mgL−1), Paclobutrazol (200 mgL−1) and JA (1 mgL−1) treatments, respectively compared to CK. In the second experiment, a respective increase of 26%, 19%, 38%, and 59% was noted in SOD, POD, CAT, and APX enzyme activities in GA treatment compared to CK. Similarly, proline, soluble sugar, soluble protein, and GA content were also improved by 42%, 25.74%, 27%, and 19%, respectively, in GA treatment compared to CK. However, a respective reduction of 21% and 18% was noted in MDA and ABA content in GA treatment compared to CK. Our finding highlighted that better germination of primed-rice seedlings was associated with fresh and dry weights of the roots and shoots and the average root volume of the seedlings.DiscussionOur results suggested that GA3 (10 mg L−1) and BR (0.3 mg L−1) seed priming prevent rice seedlings from chilling-induced oxidative stress by regulating antioxidant enzyme activities and maintaining ABA, GA, MDA, soluble sugar, and protein content. However, further studies (transcriptome and proteome) are needed to explore the molecular mechanisms involved in seed priming-induced chilling tolerance under field conditions.
Characteristics and associated factors of violence in male patients with schizophrenia in China
Authors: Guo Weilong , Gu Yu , Zhou Jiansong , Wang Xiaoping , Sun Qiaoling 
Published: March 2023

ObjectiveTo investigate the characteristics and associated factors of violence in male patients with schizophrenia in China.MethodsA total of 507 male patients with schizophrenia were recruited, including 386 non-violent and 121 violent patients. The socio-demographic information and medical history of the patients were collected. Psychopathological characteristics, personality traits psychopathology, and factors related to risk management were assessed using the Brief Psychiatric Rating Scale (BPRS), the History of Violence, Clinical, Risk Assessment Scale (HCR-20), and the Psychopathy Checklist-Revised (PCL-R), as appropriate. Differences in these factors were compared between the violent and non-violent patients, and logistic regression analysis was performed to explore the risk factors for violence in male patients with schizophrenia.ResultsThe results showed that the violent group had a lower level of education, longer duration of illness, as well as a higher rate of hospitalization, history of suicidal attempts, and history of alcohol compared with the non-violent group. The violent group scored higher in items of symptoms in BPRS, personality traits and psychopathy in PCL-R, and risk management in HCR-20. The regression analysis showed that previous suicidal behavior (OR = 2.07,95% CI [1.06-4.05], P = 0.033), antisocial tendency in PCL-R (OR = 1.21, 95% CI [1.01-1.45], P = 0.038), H2: young age at violent incident (OR = 6.39, 95% CI [4.16-9.84], P &lt; 0.001), C4: impulsivity (OR = 1.76, 95% CI [1.20-2.59], P = 0.004), and H3: relationship instability (OR = 1.60, 95% CI [1.08-2.37], P = 0.019) in HCR-20 were risk factors of violence among male patients with schizophrenia.ConclusionThe present study found significant differences in socio-demographic information, history of treatment, and psychopathy characteristics between male patients with schizophrenia who had engaged in violent behaviors and their non-violent counterparts in China. Our findings suggested the necessity of individualized treatment for male patients with schizophrenia who had engaged in violent behaviors as well as the use of both HCR-20 and PCL-R for their assessment.
Occupational stress and burnout among intensive care unit nurses during the pandemic: A prospective longitudinal study of nurses in COVID and non-COVID units
Authors: Saravanan Pratima , Nisar Tariq , Zhang Qian , Masud Faisal , Sasangohar Farzan 
Published: March 2023

BackgroundIntensive care unit (ICU) nurses are highly prone to occupational stress and burnout, affecting their physical and mental health. The occurrence of the pandemic and related events increased nurses’ workload and further exacerbated their stress and burnout. This work investigates occupational stress and burnout experienced by ICU nurses working with COVID and non-COVID patients.MethodA prospective longitudinal mixed-methods study was conducted with a cohort of ICU nurses working in medical ICU (COVID unit; n = 14) and cardiovascular ICU (non-COVID unit; n = 5). Each participant was followed for six 12-h shifts. Data on occupational stress and burnout prevalence were collected using validated questionnaires. Physiological indices of stress were collected using wrist-worn wearable technologies. Participants elaborated on the causes of stress experienced each shift by completing open-ended questions. Data were analyzed using statistical and qualitative methods.ResultsParticipants caring for COVID patients at the COVID unit were 3.71 times more likely to experience stress (p &lt; 0.001) in comparison to non-COVID unit participants. No differences in stress levels were found when the same participants worked with COVID and non-COVID patients at different shifts (p = 0.58) at the COVID unit. The cohorts expressed similar contributors to stress, based in communication tasks, patient acuity, clinical procedures, admission processes, proning, labs, and assisting coworkers.ConclusionNurses in COVID units, irrespective of whether they care for a COVID patient, experience occupational stress and burnout.