bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vigorous rootstocks improve yields and increase fruit sizes in grafted fresh market tomatoes
Authors: Ingram Thomas W. , Sharpe Suzette , Trandel Marlee , Perkins-Veazie Penelope , Louws Frank J. , Meadows Inga 
Published: December 2022

Grafting high yielding tomato cultivars (Solanum lycopersicum L.) onto vigorous rootstocks can increase marketable yields, but questions remain regarding optimal cultural and growing conditions such as pinching and plant spacing. This study addressed some of the dynamics between grafted plants and cultural practices. Two scions, ‘Tasti-Lee’ (TL) and ‘Mountain Fresh Plus’ (MFP) were grafted onto each of three rootstocks, ‘Beaufort’, ‘Arnold’, and ‘Shield’. Plants were pinched (removal of main shoot to induce both axillary shoots to grow) or non-pinched, and spaced at 56 or 61 cm. All 32 grafted treatments were compared to the grower standard: non-grafted TL and MFP spaced at 46 cm, which were non-pinched. Fruit quality traits including soluble solids content, pH, lycopene concentration, and titratable acidity were recorded for fruit harvested from tomatoes grafted onto ‘Arnold’, ‘Beaufort’, ‘Shield’ and non-grafted TL. The overall effect of grafting TL and MFP onto vigorous rootstocks ‘Arnold’, ‘Beaufort’, and ‘Fortamino’ increased marketable yields per hectare by 24-35% compared to non-grafted grower standards. The rootstock ‘Shield’ did not significantly increase yields with either scion. TL had a more positive response to grafting than MFP. ‘Arnold’, ‘Beaufort’, and ‘Fortamino’ significantly increased TL fruit size, but the fruit size results were not as significantly impacted by graft treatments for MFP. Plants spaced at 56 compared to 61 cm generated similar yields. Pinched plants significantly increased yields over non-pinched plants by 15% in 2018 but did not impact yield in 2017. No consistent difference was observed between pinched and non-pinched plants with regard to fruit size, only plants grafted with ‘Shield’ benefited significantly from being pinched. Soluble solids content, pH, total lycopene concentration, and titratable acidity differed slightly between grafted and non-grafted plants but was unlikely to positively or negatively affect overall perception of fruit quality in tomatoes. A partial budget analysis revealed that grafting with ‘Arnold’ or ‘Beaufort’ consistently increased profits in this low-disease field.
NR4A2 may be a potential diagnostic biomarker for myocardial infarction: A comprehensive bioinformatics analysis and experimental validation
Authors: Wei Dongsheng , Qi Jiajie , Wang Yuxuan , Li Luzhen , Yang Guanlin , He Xinyong , Zhang Zhe 
Published: December 2022

BackgroundMyocardial infarction is a well-established severe consequence of coronary artery disease. However, the lack of effective early biomarkers accounts for the lag time before clinical diagnosis of myocardial infarction. The present study aimed to predict critical genes for the diagnosis of MI by immune infiltration analysis and establish a nomogram.MethodsGene microarray data were downloaded from Gene Expression Omnibus (GEO). Differential expression analysis, single-cell sequencing, and disease ontology (DO) enrichment analysis were performed to determine the distribution of Differentially Expressed Genes (DEGs) in cell subpopulations and their correlation with MI. Next, the level of infiltration of 16 immune cells and immune functions and their hub genes were analyzed using a Single-sample Gene Set Enrichment Analysis (ssGSEA). In addition, the accuracy of critical markers for the diagnosis of MI was subsequently assessed using receiver operating characteristic curves (ROC). One datasets were used to test the accuracy of the model. Finally, the genes with the most diagnostic value for MI were screened and experimentally validated.Results335 DEGs were identified in GSE66360, including 280 upregulated and 55 downregulated genes. Single-cell sequencing results demonstrated that DEGs were mainly distributed in endothelial cells. DO enrichment analysis suggested that DEGs were highly correlated with MI. In the MI population, macrophages, neutrophils, CCR, and Parainflammation were significantly upregulated compared to the average population. NR4A2 was identified as the gene with the most significant diagnostic value in the immune scoring and diagnostic model. 191 possible drugs for the treatment of myocardial infarction were identified by drug prediction analysis. Finally, our results were validated by Real-time Quantitativepolymerase chain reaction and Western Blot of animal samples.ConclusionOur comprehensive in silico analysis revealed that NR4A2 has huge prospects for application in diagnosing patients with MI.
Platelet abnormalities in autoimmune thyroid diseases: A systematic review and meta-analysis
Authors: Cao Yu-tian , Zhang Kai-yu , Sun Jing , Lou Yan , Lv Tian-su , Yang Xinyi , Zhang Wen-hui , Yu Jiang-yi , Wu Qi-biao , Zhou Xi-qiao 
Published: December 2022

BackgroundSome degree of platelet index abnormality has been found clinically in the autoimmune thyroid disease (AITD), but the findings are not uniform.MethodsThe PubMed, Web of Science, Cochrane Library, and Embase databases were searched for relevant articles published up to August 16th, 2022, with no restrictions on the language of the articles. Reference lists of eligible articles were also searched. A random effect model was used to pool the standardized mean difference (SMD) and 95% confidence interval (95% CI) of platelet count (PLT), mean platelet volume (MPV), and platelet distribution width (PDW) between AITD patients and healthy controls, and subgroup analyses were performed.ResultsA total of 19 articles with 6173 people (3824 AITD patients and 2349 healthy people) were included in the meta-analysis. The results showed that PLT and MPV values were significantly increased in AITD patients when compared with healthy people (SMD: 0.164, 95% CI: 0.044 to 0.285; SMD: 0.256, 95% CI: 0.013 to 0.500), while no significant difference was found in PDW between the AITD group and the control group (SMD: 0.060, 95% CI: -0.164 to 0.284). Subgroup analysis according to disease type and thyroid function revealed that for PLT, this difference was only found in the Hashimoto’s thyroiditis (HT) and hypothyroid groups, but not in the Graves’ disease (GD) and hyperthyroid groups. For MPV, the results were the opposite of those for PLT: MPV was significantly higher in the GD, hyperthyroid, and euthyroid groups than in the control group, but not in the HT and hypothyroid groups. Sensitivity analysis showed that the stability of the pooled MPV was not good. No publication bias was found.ConclusionsPLT and MPV are significantly elevated in patients with AITD, with PLT being more significantly elevated in HT and hypothyroidism, and MPV being more significantly increased in GD and hyperthyroidism. Appropriate clinical attention can be paid to the thyroid function of patients when abnormal platelet indices are found, and conversely, the consequences of abnormal platelet parameters such as elevated MPV lead to an increased occurrence of cardiovascular events, which should also be addressed in the AITD population.Systematic review registrationhttps://www.crd.york.ac.uk/PROSPERO/, identifier CRD42022341823.
Microbiota of preterm infant develops over time along with the first teeth eruption
Authors: Zhang Yu , Wu Yi-Pei , Feng Vivien , Cao Gui-Zhi , Feng Xi-Ping , Chen Xi 
Published: December 2022

ObjectiveThe temporal growth of the infant microbiome in the early years of life influences short- and long-term infant health. The aim of this longitudinal study was to investigate bacterial dynamics in the microbiome of preterm infants during tooth eruption.MethodsSaliva samples from normally delivered (n = 24) and preterm infants (n = 31) were collected 30 days after birth and after the eruption of two primary mandibular incisors. Based on Illumina MiSeq Sequencing of the 16S rRNA gene, the dynamic microbial changes of newborns at two-time points were investigated. Meanwhile, the Human Oral Microbiome Database was adopted for assigning taxonomy.ResultsUsing alpha and beta diversity analyses, different shift patterns of microbiome structures in preterm and healthy participants and bacterial diversity over time were observed. The relative abundance and shifts trend, along with the two lower primary central incisors eruption, of core oral flora varies in full-term and preterm groups, including Gemella spp., Rothia mucilaginosa, Veillonella atypica, etc. Several microorganisms colonize later in the oral microbiome development of premature babies, such as Gemella spp. In addition to teeth eruption, the growth of the saliva microbiome in preterm infants could be influenced by breastfeeding durations and birth weight.ConclusionThis study provided insights into how the oral microbiota changes during tooth eruption in preterm infants and how the colonization of the oral cavity with bacteria in preterm infants differs significantly from that in full-term infants.
A diagnostic accuracy study comparing RNA LAMP, direct LAMP, and rapid antigen testing from nasopharyngeal swabs
Authors: Cao Guojun , Lin Ke , Ai Jingwen , Cai Jianpeng , Zhang Haocheng , Yu Yiqi , Liu Qihui , Zhang Xinyun , Zhang Yi , Fu Zhangfan , Song Jieyu , Wang Hongyu , Yuan Guanmin , Wang Sen , Guan Ming , Zhang Wenhong 
Published: December 2022

IntroductionDuring the coronavirus disease 2019 (COVID-19) pandemic, the early detection and isolation of individuals infected with severe acute respiratory syndrome coronavirus disease 2 (SARS-CoV-2) through mass testing can effectively prevent disease transmission. SARS-CoV-2 nucleic acid rapid detection based on loop-mediated isothermal amplification (LAMP) may be appropriate to include in testing procedures.MethodsWe used 860 nasopharyngeal specimens from healthcare workers of Huashan Hospital and COVID-19 patients collected from April 7th to 21st, 2022, to assess the clinical diagnostic performance of the LAMP assay marketed by Shanghai GeneSc Biotech and compared it to the result of a rapid antigen test (RAT) head-to-head.ResultsOverall, the diagnostic performance of LAMP assay and RAT were as follows. The LAMP assay represented higher sensitivity and specificity than RAT, especially in the extracted RNA samples. The sensitivity was 70.92% and 92.91% for direct LAMP and RNA-LAMP assay, respectively, while the specificity was 99.86% and 98.33%. The LAMP assay had overall better diagnostic performance on the specimens with relatively lower Ct values or collected in the early phase (≤7 days) of COVID-19. The combination of LAMP assay and RAT improved diagnostic efficiency, providing new strategies for rapidly detecting SARS-CoV-2.ConclusionThe LAMP assay are suitable for mass screenings of SARS-CoV-2 infections in the general population.
Application of convolutional neural network in fusion and classification of multi-source remote sensing data
Authors: Ye Fanghong , Zhou Zheng , Wu Yue , Enkhtur Bayarmaa 
Published: December 2022

IntroductionThrough remote sensing images, we can understand and observe the terrain, and its application scope is relatively large, such as agriculture, military, etc.MethodsIn order to achieve more accurate and efficient multi-source remote sensing data fusion and classification, this study proposes DB-CNN algorithm, introduces SVM algorithm and ELM algorithm, and compares and verifies their performance through relevant experiments.ResultsFrom the results, we can find that for the dual branch CNN network structure, hyperspectral data and laser mines joint classification of data can achieve higher classification accuracy. On different data sets, the global classification accuracy of the joint classification method is 98.46%. DB-CNN model has the highest training accuracy and fastest speed in training and testing. In addition, the DB-CNN model has the lowest test error, about 0.026, 0.037 lower than the ELM model and 0.056 lower than the SVM model. The AUC value corresponding to the ROC curve of its model is about 0.922, higher than that of the other two models.DiscussionIt can be seen that the method used in this paper can significantly improve the effect of multi-source remote sensing data fusion and classification, and has certain practical value.
Postoperative red blood cell distribution width predicts functional outcome in aneurysmal subarachnoid hemorrhage after surgical clipping: A single-center retrospective study
Authors: Zhao Long , Zhang Yi , Lin Ping , Li Weida , Huang Xingyuan , Li Hangyang , Xia Mingkai , Chen Xinlong , Zhu Xi , Tang Xiaoping 
Published: December 2022

ObjectiveRed blood cell (RBC) parameters are associated with outcomes following aneurysmal subarachnoid hemorrhage (aSAH), but their predictive value remains uncertain. This study aimed to detect the association between RBC parameters and functional outcome in aSAH patients undergoing surgical clipping.MethodsThis retrospective observational study included aSAH patients who underwent surgical clipping at Affiliated Hospital of North Sichuan Medical College between August 2016 and September 2019. The functional outcome following aSAH was assessed by modified Rankin Scale (mRS), and mRS 3–6 was defined as poor functional outcome.ResultsOut of 187 aSAH patients included (62% female, 51–66 years old), 73 patients had poor functional outcome. Multivariate logistic regression of admission parameters showed that World Federation of Neurosurgical Societies (WFNS) grade (odds ratio [95% CI]: 1.322 [1.023–1.707], p = 0.033) and white blood cell (WBC) (odds ratio [95% CI]: 1.136 [1.044–1.236], p = 0.003) were independently associated with poor functional outcome. In postoperative parameters, RBC distribution width (RDW) (odds ratio [95% CI]: 1.411 [1.095–1.818], p = 0.008), mean platelet volume (MPV, odds ratio [95% CI]: 1.253 [1.012–1.552], p = 0.039) and admission WFNS grade (odds ratio [95% CI]: 1.439 [1.119–1.850], p = 0.005) were independently associated with poor functional outcome. The predictive model including WFNS grade, admission WBC, and postoperative RDW and MPV had significantly higher predictive power compared to WFNS grade alone (0.787 [0.722–0.852] vs. 0.707 [0.630–0.784], p = 0.024). The combination of WFNS grade and WBC on admission showed the highest positive predictive value (75.5%) and postoperative RDW and MPV combined with admission WFNS grade and WBC showed the highest negative predictive value (83.7%).ConclusionPostoperative RDW is independently associated with poor functional outcome in aSAH patients undergoing surgical clipping. A combined model containing postoperative RDW may help predict good outcome in patients with aSAH after timely aneurysm clipping.
Too risky, too large, too late, or too mild—Reasons for not treating ischemic stroke patients and the related outcomes
Authors: Behrndtz Anne Brink , Damsbo Andreas Gammelgaard , Blauenfeldt Rolf Ankerlund , Andersen Grethe , Speiser Lasse Ole , Simonsen Claus Ziegler 
Published: December 2022

BackgroundDespite effective treatments, many patients are still not offered reperfusion therapy for acute ischemic stroke.MethodsWe present a single-center observational study on acute ischemic stroke patients, who presented as candidates for reperfusion therapy but were deemed ineligible after work-up. Reasons for non-treatment were obtained by studying patient files and subsequently grouped into “too risky” (e.g., anticoagulant use, comorbidities), “too large” (large infarct), “too late” (late presentation of stroke and wake-up strokes), or “too mild” (clinically mild/remitting symptoms). Modified Rankin scale (mRS) score was prospectively collected in all patients by a structured telephone interview. All non-treated patients with a National Institute of Health Stroke Scale (NIHSS) score of 0–5 were compared with a similar cohort that was treated.ResultsOf 529 patients with acute ischemic stroke arriving as reperfusion therapy candidates, 198 (37.4%) were not treated. The majority (42%) were not treated due to admission outside the treatment window (too late) and 24% had absolute contraindications (too risky). Only 8% was excluded because their infarct was too large [median Alberta Stroke Program Early CT score 3 (2–4)]. In the “too mild” group (14%) the percentage of patients not being independent at 90 days was 30%. The adjusted odds ratio for a better outcome (lower mRS) among treated patients with NIHSS 0–5 compared with non-treated was 1.93 (95% confidence interval 1.15–3.23).ConclusionPresenting outside the treatment window is still the most common reason for not receiving therapy. Our study suggests a benefit of thrombolysis for patients with mild symptoms.
The inhibition of PGAM5 suppresses seizures in a kainate-induced epilepsy model via mitophagy reduction
Authors: Zhong Fuxin , Gan Yunhao , Song Jiaqi , Zhang Wenbo , Yuan Shiyun , Qin Zhangjin , Wu Jiani , Lü Yang , Yu Weihua 
Published: December 2022

BackgroundEpilepsy is a common neurological disease, and excessive mitophagy is considered as one of the major triggers of epilepsy. Mitophagy is a crucial pathway affecting reactive oxygen species. Phosphoglycerate mutase 5 (PGAM5) is a protein phosphatase present in mitochondria that regulates many biological processes including mitophagy and cell death. However, the mechanism of PGAM5 in epilepsy remains unclear. The purpose of the present study was to examine whether PGAM5 affects epilepsy through PTEN-induced putative kinase 1 (PINK1)-mediated mitophagy.MethodsAfter the knockdown of PGAM5 expression by the adeno-associated virus, an epilepsy model was created by kainic acid. Next, the seizure activity was recorded by local field potentials before evaluating the level of mitochondrial autophagy marker proteins. Lastly, the ultrastructure of mitochondria, neuronal damage and oxidative stress levels were further observed.ResultsA higher PGAM5 level was found in epilepsy, and its cellular localization was in neurons. The interactions between PGAM5 and PINK1 in epilepsy were further found. After the knockdown of PGAM5, the level of PINK1 and light chain 3B was decreased and the expression of the translocase of the inner mitochondrial membrane 23 and translocase of the outer mitochondrial membrane 20 were both increased. Knockdown of PGAM5 also resulted in reduced neuronal damage, decreased malondialdehyde levels, decreased reactive oxygen species production and increased superoxide dismutase activity. In addition, the duration of spontaneous seizure-like events (SLEs), the number of SLEs and the time spent in SLEs were all reduced in the epilepsy model after inhibition of PGAM5 expression.ConclusionInhibition of PGAM5 expression reduces seizures via inhibiting PINK1-mediated mitophagy.
Prediction of prognosis and immunotherapy response of amino acid metabolism genes in acute myeloid leukemia
Authors: Zhou Hui , Wang Fengjuan , Niu Ting 
Published: December 2022

BackgroundAmino acid (AA) metabolism plays a crucial role in cancer. However, its role in acute myeloid leukemia (AML) is still unavailable. We screened out AA metabolic genes, which related to prognosis, and analyzed their correlation with tumor immune microenvironment in AML.MethodsWe evaluated 472 amino acid metabolism-related genes in 132 AML patients. The predictive risk model was developed according to differentially expressed genes, univariate Cox and LASSO analyses. We validated the risk signature by survival analysis and independence tests. Single-sample gene set enrichment analysis (ssGSEA), tumor immune microenvironment (TME), tumor mutation burden (TMB), functional enrichment, and the IC50 of drugs were assessed to explore the correlations among the risk model, immunity, and drug sensitivity of AML.ResultsSix amino acid metabolism-related genes were confirmed to develop the risk model, including TRH, HNMT, TFEB, SDSL, SLC43A2, and SFXN3. The high-risk subgroup had an immune “hot” phenotype and was related to a poor prognosis. The high-risk group was also associated with more activity of immune cells, such as Tregs, had higher expression of some immune checkpoints, including PD1 and CTLA4, and might be more susceptible to immunotherapy. Xenobiotic metabolism, the reactive oxygen species (ROS) pathway, fatty acid metabolism, JAK/STAT3, and the inflammatory response were active in the high-risk subgroup. Furthermore, the high-risk subgroup was sensitive to sorafenib, selumetinib, and entospletinib. ssGSEA discovered that the processes of glutamine, arginine, tryptophan, cysteine, histidine, L-serine, isoleucine, threonine, tyrosine, and L-phenylalanine metabolism were more active in the high-risk subgroup.ConclusionThis study revealed that AA metabolism-related genes were correlated with the immune microenvironment of AML patients and could predict the prognosis and immunotherapy response of AML patients.
Is there any association between dietary inflammatory index and quality of life? A systematic review
Authors: Golmohammadi Mona , Kheirouri Sorayya , Ebrahimzadeh Attari Vahideh , Moludi Jalal , Sulistyowati Reny , Nachvak Seyed Mostafa , Mostafaei Roghayeh , Mansordehghan Maryam 
Published: December 2022

BackgroundThe inflammatory potential of unhealthy diets can lead to the development of chronic diseases and also exacerbating their complications. Therefore, the present systematic review aimed to evaluate the association of dietary inflammatory index (DII) and quality of life (QOL) in human subjects.MethodsA systematic search was conducted in PubMed, Web of Science, and Scopus databases, using the combination of all search terms related to DII and QOL until May 2022. All eligible human studies published in English were included.ResultsThree hundred twenty-seven studies were obtained from the first systematic search of the databases although, only eight studies were eligible for the evaluation. Seven studies reported that there was a significant reverse association between DII scores and overall QOL and/or its subscales in different populations including patients with asthma, osteoarthritis, hemodialysis patients, multiple sclerosis, obese women, and also in healthy subjects. While, one study on postmenopausal women found no evidence of this association.ConclusionThis systematic review demonstrated that an anti-inflammatory diet might be associated with better QOL. However, future well-designed clinical trials can provide better conclusions especially regarding the quantifying of this relationship.