bluuebunny/crossref_metadata_2025_split huggingface dataset:
GRAS gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses
Authors: Fan Yu , Wan Xianqi , Zhang Xin , Zhang Jieyu , Zheng Chunyu , Yang Qiaohui , Yang Li , Li Xiaolong , Feng Liang , Zou Liang , Xiang Dabing 
Published: January 2024

Abstract
Background
The GRAS transcription factor family plays a crucial role in various biological processes in different plants, such as tissue development, fruit maturation, and environmental stress. However, the GRAS family in rye has not been systematically analyzed yet.

Results
In this study, 67 GRAS genes in S. cereale were identified and named based on the chromosomal location. The gene structures, conserved motifs, cis-acting elements, gene replications, and expression patterns were further analyzed. These 67 ScGRAS members are divided into 13 subfamilies. All members include the LHR I, VHIID, LHR II, PFYRE, and SAW domains, and some nonpolar hydrophobic amino acid residues may undergo cross-substitution in the VHIID region. Interested, tandem duplications may have a more important contribution, which distinguishes them from other monocotyledonous plants. To further investigate the evolutionary relationship of the GRAS family, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. The response characteristics of 19 ScGRAS members from different subfamilies to different tissues, grains at filling stages, and different abiotic stresses of rye were systematically analyzed. Paclobutrazol, a triazole-based plant growth regulator, controls plant tissue and grain development by inhibiting gibberellic acid (GA) biosynthesis through the regulation of DELLA proteins. Exogenous spraying of paclobutrazol significantly reduced the plant height but was beneficial for increasing the weight of 1000 grains of rye. Treatment with paclobutrazol, significantly reduced gibberellin levels in grain in the filling period, caused significant alteration in the expression of the DELLA subfamily gene members. Furthermore, our findings with respect to genes, ScGRAS46 and ScGRAS60, suggest that these two family members could be further used for functional characterization studies in basic research and in breeding programmes for crop improvement.

Conclusions
We identified 67 ScGRAS genes in rye and further analysed the evolution and expression patterns of the encoded proteins. This study will be helpful for further analysing the functional characteristics of ScGRAS genes.
Nitrogen application in pod zone improves yield and quality of two peanut cultivars by modulating nitrogen accumulation and metabolism
Authors: Li Guanghui , Guo Xin , Sun Wei , Hou Lei , Wang Guanghao , Tian Ruizheng , Wang Xingjun , Qu Chunjuan , Zhao Chuanzhi 
Published: January 2024

AbstractCultivated peanut (Arachis hypogaea L.) represents one of the most important oil and cash crops world-widely. Unlike many other legumes, peanuts absorb nitrogen through their underground pods. Despite this unique feature, the relationship between yield and nitrogen uptake within the pod zone remains poorly understood. In our pot experiment, we divided the underground peanut part into two zones—pod and root—and investigated the physiological and agronomic traits of two peanut cultivars, SH11 (large seeds, LS) and HY23 (small seeds, SS), at 10 (S1), 20 (S2), and 30 (S3) days after gynophores penetrated the soil, with nitrogen application in the pod zone. Results indicated that nitrogen application increased pod yield, kernel protein content, and nitrogen accumulation in plants. For both LS and SS peanut cultivars, optimal nitrogen content was 60 kg·hm− 2, leading to maximum yield. LS cultivar exhibited higher yield and nitrogen accumulation increases than SS cultivar. Nitrogen application up-regulated the expression of nitrogen metabolism-related genes in the pod, including nitrate reductase (NR), nitrite reductase (NIR), glutamine synthetase (GS), glutamate synthase (NADH-GOGAT), ATP binding cassette (ABC), and nitrate transporter (NRT2). Additionally, nitrogen application increased enzyme activity in the pod, including NR, GS, and GOGAT, consistent with gene expression levels. These nitrogen metabolism traits exhibited higher up-regulations in the large-seeded cultivar than in the small-seeded one and showed a significant correlation with yield in the large-seeded cultivar at S2 and S3. Our findings offer a scientific basis for the judicious application and efficient utilization of nitrogen fertilization in peanuts, laying the groundwork for further elucidating the molecular mechanisms of peanut nitrogen utilization.
Genome-wide identification and integrated analysis of TCP genes controlling ginsenoside biosynthesis in Panax ginseng
Authors: Liu Chang , Lv Tingting , Shen Yanhua , Liu Tao , Liu Mingming , Hu Jian , Liu Sizhang , Jiang Yang , Zhang Meiping , Zhao Mingzhu , Wang Kangyu , Wang Yi 
Published: January 2024

AbstractPanax ginseng is an important medicinal plant, and ginsenosides are the main bioactive molecules of ginseng. The TCP (TBI, CYC, PCF) family is a group of transcription factors (TFs) that play an important role in plant growth and development, hormone signalling and synthesis of secondary metabolites. In our study, 78 PgTCP transcripts were identified from the established ginseng transcriptome database. A phylogenetic tree analysis showed that the 67 PgTCP transcripts with complete open reading frames were classified into three subfamilies, including CIN, PCF, and CYC/TB1. Protein structure analysis showed that PgTCP genes had bHLH structures. Chromosomal localization analysis showed that 63 PgTCP genes were localized on 17 of the 24 chromosomes of the Chinese ginseng genome. Expression pattern analysis showed that PgTCP genes differed among different lineages and were spatiotemporally specific. Coexpression network analysis indicated that PgTCP genes were coexpressed and involved in plant activities or metabolic regulation in ginseng. The expression levels of PgTCP genes from class I (PCF) were significantly downregulated, while the expression levels of PgTCP genes from class II (CIN and CYC/TB1) were upregulated, suggesting that TCP genes may be involved in the regulation of secondary metabolism in ginseng. As the PgTCP26-02 gene was found to be related to ginsenoside synthesis, its predicted protein structure and expression pattern were further analysed. Our results provide new insights into the origin, differentiation, evolution and function of the PgTCP gene family in ginseng, as well as the regulation of plant secondary metabolism.
Sex differences in the association between epicardial adipose tissue volume and left atrial volume index
Authors: Yamaguchi Satoshi , Maeda Minetaka , Oba Kageyuki , Maimaituxun Gulinu , Arasaki Osamu , Yagi Shusuke , Kusunose Kenya , Soeki Takeshi , Yamada Hirotsugu , Fukuda Daiju , Masuzaki Hiroaki , Sata Masataka , Shimabukuro Michio 
Published: January 2024

Abstract
Background
Sex disparities in the association between epicardial adipose tissue volume (EATV) and cardiovascular disease have been reported. The sex-dependent effects of EATV on left atrial (LA) size have not been elucidated.

Methods
Consecutive 247 subjects (median 65 [interquartile range 57, 75] years; 67% of men) who underwent multi-detector computed tomography without significant coronary artery disease or moderate to severe valvular disease were divided into two groups: patients with sinus rhythm (SR) or atrial fibrillation (AF). Sex differences in the association between the EATV index (EATVI) (mL/m2) and LA volume index (LAVI) in 63 SR (28 men and 35 women) and 184 AF (137 men and 47 women) patients were evaluated using univariate and multivariate regression analyses.

Results
In overall that includes both men and women, the relationship between EATVI and LAVI was not significantly correlated for patients with SR and AF. The relationship between EATVI and LAVI differed between men and women in both SR and AF groups. In SR patients, there was a positive relationship between EATVI and LAVI in men, but not in women. In contrast, in patients with AF, a negative relationship was found between EATVI and LAVI in women, whereas no association was found in men.

Conclusions
We evaluated sex differences in the association between EATVI and LAVI in patients with either SR or AF, and found a positive relationship in men with SR and a negative relationship in women with AF. This is the first report to evaluate sex differences in the relationship between EATVI and LAVI, suggesting that EAT may play a role, at least in part, in sex differences in the etiology of AF.
The usefulness of contrast echocardiography in the evaluation of cardiac masses: a multicenter study
Authors: Wang Qingtao , Wang Bing , Zhang Xiaofeng , Zhong Xin , Chang Shuai , Yang Jinbo , Liang Jian , You Qiangqiang , Zhou Heng , Zhang Jiaqi 
Published: January 2024

Abstract
Background
Cardiac masses can encompass a variety of conditions, such as tumors, thrombi, vegetations, calcific lesions, and other rare diseases. Treatment and management of these types of cardiac masses differ considerably. Thus, accurately distinguishing among thrombi, benign tumors, and malignant tumors in the heart is of great importance. Contrast echocardiography (CE) has emerged as a promising technology. Although published guidelines suggest that CE can enhance image quality and assist in differentiating between benign and malignant lesions, most studies on CE diagnosis of cardiac masses are limited to case reports or retrospective/small-sample-sized prospective cohorts. This study aims to evaluate the diagnostic accuracy of CE in patients with suspected cardiac masses and address the insufficient evidence for differential diagnosis using CE.

Methods
Between April 2018 and July 2022, a prospective multicenter study was conducted, which included 145 consecutive patients suspected to have cardiac masses based on transthoracic echocardiography. All patients underwent CE examinations. The echocardiographic diagnosis relied on qualitative factors such as echogenicity, boundary, morphology of the base, mass perfusion, pericardial effusion, and motility as well as quantitative factors such as the area of the masses and the peak intensity ratio of the masses to adjacent myocardium (A1/A2).

Results
The final confirmed diagnoses were as follows: 2 patients had no cardiac mass, 4 patients had pseudomass, 43 patients had thrombus, 66 patients had benign tumors, and 30 patients had malignant tumors. The receiver operating characteristic (ROC) analysis indicated that an optimal A1/A2 cutoff value of 0.499 distinguished a cardiac tumor from a thrombus, with AUC, sensitivity, specificity, PPV, and NPV of 0.977, 97.9%, 90.7%, 95.9%, and 95.1%, respectively. The optimal A1/A2 cutoff value of 1.583 distinguished a cardiac tumor from a thrombus, with AUC, sensitivity, specificity, PPV, and NPV of 0.950, 93.3%, 93.9%, 87.5%, and 96.9%, respectively.

Conclusions
Combined with qualitative and quantitative analyses, CE has the potential to accurately differentiate among different types of cardiac masses.
Late presentation of traumatic tricuspid valve chordal rupture and pericardial rupture with cardiac herniation: a case report
Authors: Radovanovic Nebojsa , Prodanovic Maja , Radosavljevic-Radovanovic Mina , Bilbija Ilija , Petrovic Olga , Lojovic Nina , Kecman Emilija , Djekic Aleksandar , Radovanovic Milos , Matic Dragan 
Published: January 2024

Abstract
Background
Although chest trauma happens very often, accompanying tricuspid valve injuries occur rarely and may be manifested by scarce symptoms and signs. Pericardial rupture with cardiac herniation is even a bigger rarity. Transthoracic echocardiography plays a key role in the diagnosis of valve injuries but is of limited value in cardiac herniation.

Case presentation
We present the case of 58-year-old man who experienced severe chest trauma in a car accident. Symptoms of right heart failure occurred 10 years after the injury, due to the loss of tricuspid leaflet support caused by the rupture of tendinous chords with significant tricuspid regurgitation. Intraoperatively, old posttraumatic pericardial rupture into left pleura was also found, with partial cardiac herniation and pressure of the edge of pericardium on all left-sided coronary arteries simultaneously. The patient was successfully operated and is free of symptoms 4 years later.

Conclusions
This case emphasizes the importance of timely diagnosis and underlines a mechanism that leads to delayed rupture of the tricuspid valve apparatus. Repeated echocardiography in all patients who experienced chest trauma could be of great importance. Also, given the limited value of echocardiography in posttraumatic pericardial rupture and cardiac herniation, cardiac computed tomography should be performed.
Continuous cardiac monitoring in epilepsy: an implantable loop manual activation algorithm for improving ECG signal acquisition accuracy
Authors: Davtyan Karapet , Serdyuk Svetlana , Topchyan Arpi , Simonyan Georgiy , Kharlap Maria , Burd Sergey 
Published: January 2024

Abstract
Background
The muscle artifacts, caused by prominent muscle contractions, mimicking cardiac arrhythmias, might compromise the ECG signal quality and the implantable loop recorder memory capacity in patients with epilepsy. We developed an epileptic seizures clinical pattern-based implantable loop recorder manual activation algorithm, presenting its real-world efficacy here.

Methods
One hundred ninety-three patients (18–60 years) with drug-resistant focal epilepsy were consecutively enrolled and underwent a subcutaneous loop recorder implantation. Patients with focal onset-aware seizures and patients with focal impaired awareness seizures /bilateral tonic-clonic seizures without aura were recommended to use the activator once - just after the episode. Patients with focal impaired awareness seizures/bilateral tonic-clonic seizures with aura, the caregivers of patients experiencing status epilepticus, were advised to use the activator twice - during the aura and after the episode/ regaining consciousness.

Results
Six thousand four hundred ninety-four ECG traces (4826 - auto-triggered events, 1668 - person-activated events) were recorded and analyzed. The rate of true positive events in the person-activated group was statistically higher than in the autoactivation group (72.5% vs.19.4%, p < 0.0001). Person-activated false-positive events were observed in 30.5% of patients with focal impaired awareness seizures and 27.7% in patients with bilateral tonic-clonic seizures. The highest rate of false-positive events (61.5%) was detected in patients undergoing epileptic status, and the lowest rate (3.8%) - was in patients with focal onset aware seizures. The rate of false-positive events was significantly higher in patients with impaired awareness seizures without aura both in focal impaired awareness (45.5% vs. 19.3%, p < 0.0001) and bilateral tonic-clonic seizure groups (38.8% vs. 5.9%, p < 0.0001).

Conclusions
Arrhythmias with varying clinical outcomes are expected in epilepsy patients and have been monitored continuously. The specified loop recorder external activation algorithm can improve the clinically relevant cardiac arrhythmia detection accuracy in epilepsy patients and the value of future studies.
Two-step spatiotemporal anomaly detection corrected for lag reporting time with application to real-time dengue surveillance in Thailand
Authors: Rotejanaprasert Chawarat , Areechokchai Darin , Maude Richard J. 
Published: January 2024

AbstractBackgroundDengue infection ranges from asymptomatic to severe and life-threatening, with no specific treatment available. Vector control is crucial for interrupting its transmission cycle. Accurate estimation of outbreak timing and location is essential for efficient resource allocation. Timely and reliable notification systems are necessary to monitor dengue incidence, including spatial and temporal distributions, to detect outbreaks promptly and implement effective control measures.MethodsWe proposed an integrated two-step methodology for real-time spatiotemporal cluster detection, accounting for reporting delays. In the first step, we employed space-time nowcasting modeling to compensate for lags in the reporting system. Subsequently, anomaly detection methods were applied to assess adverse risks. To illustrate the effectiveness of these detection methods, we conducted a case study using weekly dengue surveillance data from Thailand.ResultsThe developed methodology demonstrated robust surveillance effectiveness. By combining space-time nowcasting modeling and anomaly detection, we achieved enhanced detection capabilities, accounting for reporting delays and identifying clusters of elevated risk in real-time. The case study in Thailand showcased the practical application of our methodology, enabling timely initiation of disease control activities.ConclusionOur integrated two-step methodology provides a valuable approach for real-time spatiotemporal cluster detection in dengue surveillance. By addressing reporting delays and incorporating anomaly detection, it complements existing surveillance systems and forecasting efforts. Implementing this methodology can facilitate the timely initiation of disease control activities, contributing to more effective prevention and control strategies for dengue in Thailand and potentially other regions facing similar challenges.
Implementing the time-to-event continual reassessment method in the presence of partial orders in a phase I head and neck cancer trial
Authors: Patel Amit , Brock Kristian , Slade Daniel , Gaunt Claire , Kong Anthony , Mehanna Hisham , Billingham Lucinda , Gaunt Piers 
Published: January 2024

Abstract
Background
In this article we describe the methodology of the time-to-event continual reassessment method in the presence of partial orders (PO-TITE-CRM) and the process of implementing this trial design into a phase I trial in head and neck cancer called ADePT-DDR. The ADePT-DDR trial aims to find the maximum tolerated dose of an ATR inhibitor given in conjunction with radiotherapy in patients with head and neck squamous cell carcinoma.

Methods
The PO-TITE-CRM is a phase I trial design that builds upon the time-to-event continual reassessment method (TITE-CRM) to allow for the presence of partial ordering of doses. Partial orders occur in the case where the monotonicity assumption does not hold and the ordering of doses in terms of toxicity is not fully known.

Results
We arrived at a parameterisation of the design which performed well over a range of scenarios. Results from simulations were used iteratively to determine the best parameterisation of the design and we present the final set of simulations. We provide details on the methodology as well as insight into how it is applied to the trial.

Conclusions
Whilst being a very efficient design we highlight some of the difficulties and challenges that come with implementing such a design. As the issue of partial ordering may become more frequent due to the increasing investigations of combination therapies we believe this account will be beneficial to those wishing to implement a design with partial orders.

Trial registration
ADePT-DDR was added to the European Clinical Trials Database (EudraCT number: 2020-001034-35) on 2020-08-07.
Predictive value of adipokines for the severity of acute pancreatitis: a meta-analysis
Authors: Yu Xuehua , Zhang Ning , Wu Jing , Zhao Yunhong , Liu Chengjiang , Liu Gaifang 
Published: January 2024

Abstract
Background
Severe acute pancreatitis (SAP) is a dangerous condition with a high mortality rate. Many studies have found an association between adipokines and the development of SAP, but the results are controversial. Therefore, we performed a meta-analysis of the association of inflammatory adipokines with SAP.

Methods
We screened PubMed, EMBASE, Web of Science and Cochrane Library for articles on adipokines and SAP published before July 20, 2023. The quality of the literature was assessed using QUADAS criteria. Standardized mean differences (SMD) with 95% confidence intervals (CI) were calculated to assess the combined effect. Subgroup analysis, sensitivity analysis and publication bias tests were also performed on the information obtained.

Result
Fifteen eligible studies included 1332 patients with acute pancreatitis (AP). Pooled analysis showed that patients with SAP had significantly higher serum levels of resistin (SMD = 0.78, 95% CI:0.37 to 1.19, z = 3.75, P = 0.000). The difference in leptin and adiponectin levels between SAP and mild acute pancreatitis (MAP) patients were not significant (SMD = 0.30, 95% CI: -0.08 to 0.68, z = 1.53, P = 0.127 and SMD = 0.11, 95% CI: -0.17 to 0.40, z = 0.80, P = 0.425, respectively). In patients with SAP, visfatin levels were not significantly different from that in patients with MAP (SMD = 1.20, 95% CI: -0.48 to 2.88, z = 1.40, P = 0.162).

Conclusion
Elevated levels of resistin are associated with the development of SAP. Resistin may serve as biomarker for SAP and has promise as therapeutic target.
Anti-metabolic glutamate receptor 5 encephalitis with gangliocytoma: a case and review of the literature
Authors: Shi Kaili , Zhao Huimin , Li Ying , Li Xiaojing , Chen Wenxiong 
Published: January 2024

Abstract
Background
There are very limited reports on anti-metabolic glutamate receptor5 (mGluR5) encephalitis, especially lacking of pediatric research. The disease was mostly accompanied by tumors, mainly Hodgkin's lymphoma. No reports of other tumors, such as gangliocytoma have been reported to associate with anti-mGluR5 encephalitis so far.

Case presentation and literature reviews
We reported a case of a 12-year-old boy with anti-mGluR5 encephalitis complicated with gangliocytoma. The patient suffered from mental disorders including auditory hallucination, and sleep disorders. His cranial magnetic resonance imaging (MRI) showed an abnormality in the right insular lobe. Autoimmune encephalitis antibodies testing was positive for mGluR5 IgG antibody both in cerebrospinal fluid and serum (1:3.2, 1:100 respectively). Abdominal CT indicated a mass in left retroperitoneal confirmed with gangliocytoma via pathology. The patient underwent resection of gangliocytoma. After first-line immunotherapy (glucocorticoid, gamma globulin), his condition was improved. Furthermore, we provide a summary of 6 pediatric cases of Anti-mGluR5 encephalitis. Most of them complicated with Hodgkin's lymphoma, except the case currently reported comorbid with gangliocytoma. The curative effect is satisfactory.

Conclusions
We report the first patient with anti-mGlur5 encephalitis complicated with gangliocytoma. It suggests that in addition to paying attention to the common lymphoma associated with anti-mGlur5 encephalitis, we should also screen the possibility of other tumors for early detection of the cause, active treatment and prevention of recurrence.