bluuebunny/crossref_metadata_2025_split huggingface dataset:
tRNA-Cys gene clusters exhibit high variability in Arabidopsis thaliana
Authors: Szymanski Maciej , Maurya Anand , Kopec Piotr , Karlowski Wojciech M. 
Published: December 2023

AbstractAlthough most of the genes encoding tRNAs in plants are dispersed throughout the genome, a fraction of them form tRNA gene clusters. In Arabidopsis thaliana, the smallest of tRNA clusters on chromosome 5 consists of four tRNA-Cys-GCA genes placed within repeating units of 0.4 kbp. A systematic analysis of the genomic sequences of syntenic regions from various ecotypes of A. thaliana showed that the general structure of the cluster, consisting of a tRNA-Cys pseudogene followed by repeating units containing tRNA-Cys genes, is well conserved. However, there is significant heterogeneity in the number of repeating units between different ecotypes. A unique feature of this cluster is the presence of putative transposable elements (Helitron). In addition, two further tRNA-Cys gene mini-clusters (gene pairs) in A. thaliana were identified. RNA-seq-based evaluation of expression of tRNA-Cys-GCA genes showed a positive signal for 11 out of 13 unique transcripts. An analysis of the conservation of the tRNA-Cys clusters from A. thaliana with the corresponding regions from four other Arabidopsis species suggests a sequence of events that led to the divergence of these regions.
Genome-wide characterization of the wall-associated kinase-like (WAKL) family in sesame (Sesamum indicum) identifies a SiWAKL6 gene involved in resistance to Macrophomina Phaseolina
Authors: Yan Wenqing , Hu Peilin , Ni Yunxia , Zhao Hui , Liu Xintao , Cao Hengchun , Jia Min , Tian Baoming , Miao Hongmei , Liu Hongyan 
Published: December 2023

Abstract
Background
Sesame charcoal rot caused by Macrophomina phaseolina is one of the most serious fungal diseases in sesame production, and threatens the yield and quality of sesame. WAKL genes are important in the plant response to biotic stresses by sensing and transmitting external signals to the intracellular receptor. However, there is still a lack about the WAKL gene family and its function in sesame resistance to M. phaseolina. The aim of this study was to interpret the roles of WAKL genes in sesame resistance to M. phaseolina.

Results
In this study, a comprehensive study of the WAKL gene family was conducted and 31 WAKL genes were identified in the sesame genome. Tandem duplication events were the main factor in expansion of the SiWAKL gene family. Phylogenetic analysis showed that the sesame SiWAKL gene family was divided into 4 groups. SiWAKL genes exhibited different expression patterns in diverse tissues. Under M. phaseolina stress, most SiWAKL genes were significantly induced. Notably, SiWAKL6 was strongly induced in the resistant variety “Zhengzhi 13”. Functional analysis showed that SiWAKL6 was induced by salicylic acid but not methyl jasmonate in sesame. Overexpression of SiWAKL6 in transgenic Arabidopsis thaliana plants enhanced their resistance to M. phaseolina by inducing the expression of genes involved in the salicylic acid signaling pathway and reconstructing reactive oxygen species homeostasis.

Conclusions
Taken together, the results provide a better understanding of functions about SiWAKL gene family and suggest that manipulation of these SiWAKL genes can improve plant resistance to M. phaseolina. The findings contributed to further understanding of functions of SiWAKL genes in plant immunity.
Effect of thermal softening of double-lumen endobronchial tubes on postoperative sore throat in patients with prior SARS-CoV-2 infection: a randomized controlled trial
Authors: Yan Wenlong , Cai Jianyue , Zhu Chenchen , Chen Yu , Fang Jun , Xu Hui , Zheng Xiaojing , Zhou Yingting , Xie Yanhu , Zhang Min , Shu Shuhua 
Published: December 2023

Abstract
Background
The incidence of postoperative sore throat (POST) after tracheal intubation using double-lumen endobronchial tubes (DLTs) is higher in patients with prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection than in the general population. This prospective trial was conducted to determine whether thermal softening of DLTs could decrease the incidence of POST or other airway injuries in patients with prior SARS-CoV-2 infection.

Methods
A total of 120 patients with prior SARS-CoV-2 infection undergoing thoracoscopic surgery were randomly assigned to two groups (n = 60 each). In the thermal softening group, the distal portion of the DLT was placed in thermostatic saline (50 °C) for 10 min before endotracheal intubation. In the control group, the distal portion of the DLT was placed in room temperature saline for 10 min before endotracheal intubation. The incidence and severity of POST and hoarseness were assessed at 1, 6 and 24 h postoperatively. The primary outcomes were the incidence and severity of POST at 6 h postoperatively. The secondary outcomes were the incidence and severity of hoarseness, vocal cord and tracheal injuries, and hemodynamic changes in patients at intubation.

Results
The incidence of POST at 6 h postoperatively was greater in the control group than in the thermal softening group [41 (68%) vs. 22 (37%), P = 0.001]. The overall incidence of POST at 24 h postoperatively was greater in the control group than in the thermal softening group [46 (76%) vs. 24 (40%), P < 0.001]. The overall incidence of tracheal injuries was also greater in the control group than in the thermal softening group (P = 0.016). Vocal cord injuries occurred more frequently in the control group than in the thermal softening group (P = 0.006).

Conclusion
Thermal softening of DLTs before intubation can reduce the incidence of POST and airway injuries in patients with prior SARS-CoV-2 infection undergoing DLT insertion.

Trial registration
This trial has been registered at www.chictr.org.cn (registration number: ChiCTR2200066821; registration date: December 19, 2022).
A novel nomogram for predicting the prolonged length of stay in post-anesthesia care unit after elective operation
Authors: Fang Fuquan , Liu Tiantian , Li Jun , Yang Yanchang , Hang Wenxin , Yan Dandan , Ye Sujuan , Wu Pin , Hu Yuhan , Hu Zhiyong 
Published: December 2023

AbstractBackgroundProlonged length of stay in post-anesthesia care unit (PLOS in PACU) is a combination of risk factors and complications that can compromise quality of care and operating room efficiency. Our study aimed to develop a nomogram to predict PLOS in PACU of patients undergoing elective surgery.MethodsData from 24017 patients were collected. Least absolute shrinkage and selection operator (LASSO) was used to screen variables. A logistic regression model was built on variables determined by a combined method of forward selection and backward elimination. Nomogram was designed with the model. The nomogram performance was evaluated with the area under the receiver operating characteristic curve (AUC) for discrimination, calibration plot for consistency between predictions and actuality, and decision curve analysis (DCA) for clinical application value.ResultsA nomogram was established based on the selected ten variables, including age, BMI < 21 kg/m2, American society of Anesthesiologists Physical Status (ASA), surgery type, chill, delirium, pain, naloxone, operation duration and blood transfusion. The C-index value was 0.773 [95% confidence interval (CI) = 0.765 - 0.781] in the development set and 0.757 (95% CI = 0.744-0.770) in the validation set. The AUC was > 0.75 for the prediction of PLOS in PACU. The calibration curves revealed high consistencies between the predicted and actual probability. The DCA showed that if the threshold probability is over 10% , using the models to predict PLOS in PACU and implement intervention adds more benefit.ConclusionsThis study presented a nomogram to facilitate individualized prediction of PLOS in PACU for patients undergoing elective surgery.
Hemoglobin levels and clinical outcomes after extracorporeal circulation auxiliary to open heart surgery: a retrospective cohort study
Authors: Fan Zhao-kun , Zhang Zhi-rong , Yi Ru-qin , Feng Wen , Li Cheng-en , Chen Wei , Shen Ying-ying 
Published: December 2023

Abstract
Background
Extracorporeal circulation auxiliary to open heart surgery is a common procedure used to treat heart diseases. However, the optimal transfusion strategy for patients undergoing this surgery remains a subject of debate. This study aims to investigate the association between hemoglobin levels and clinical outcomes in patients undergoing extracorporeal circulation auxiliary to open heart surgery, with the ultimate goal of improving surgical success rates and enhancing patients' quality of life.

Methods
A retrospective analysis was conducted on data from the Medical Information Mart for Intensive Care IV 2.2 (MIMIC-IV 2.2) database, including 4144 patients. The patients were categorized into five groups based on their minimum hemoglobin levels during hospitalization. Baseline characteristics, clinical scores, laboratory results, and clinical outcome data were collected. Statistical analyses utilized descriptive statistics, ANOVA or Kruskal-Wallis tests, Kaplan-Meier method, and Log-rank test.

Results
The results revealed a significant correlation between hemoglobin levels and in-hospital mortality, as well as mortality rates at 30 days, 60 days, and 180 days (p < 0.001). Patients with lower hemoglobin levels exhibited higher mortality rates. However, once hemoglobin levels exceeded 7g/dL, no significant difference in mortality rates was observed (p = 0.557). Additionally, lower hemoglobin levels were associated with prolonged hospital stay, ICU admission time, and mechanical ventilation time (p < 0.001). Furthermore, hemoglobin levels were significantly correlated with complication risk, norepinephrine dosage, and red blood cell transfusion volume (p < 0.001). However, there was no significant difference among the groups in terms of major complications, specifically sepsis (p > 0.05).

Conclusion
The study highlights the importance of managing hemoglobin levels in patients undergoing heart surgery with extracorporeal circulation. Hemoglobin levels can serve as valuable indicators for predicting clinical outcomes and guiding treatment decisions. Physicians should carefully consider hemoglobin levels to optimize transfusion strategies and improve postoperative patient outcomes. Further research and intervention studies are warranted to validate and implement these findings in clinical practice.
Healthcare and community stakeholders’ perceptions of barriers and facilitators to implementing a behavioral activation intervention for people with dementia and depression: a qualitative study using Normalization Process Theory
Authors: Svedin Frida , Blomberg Oscar , Brantnell Anders , Farrand Paul , Åberg Anna Cristina , Woodford Joanne 
Published: December 2023

Abstract
Background
Depression is commonly experienced by people with dementia, and associated with lower quality of life and functional decline. However, access to evidence-based psychological interventions for people with dementia and depression is limited. One potential solution is guided low-intensity behavioral activation. Following the new Medical Research Council Framework, considering factors such as potential barriers and facilitators to implementation is recommended during the development of new interventions. Aims of this study were to: (1) develop an understanding of existing healthcare and community support in the Swedish context for people with dementia and their informal caregivers; and (2) identify barriers and facilitators to intervention uptake informed by Normalization Process Theory.

Methods
Semi-structured interviews and focus groups were held with healthcare (n = 18) and community (n = 7) stakeholders working with people with dementia and/or informal caregivers. Interview questions were informed by Normalization Process Theory. Data was analysed utilizing a two-step deductive analysis approach using the Normalization Process Theory coding manual, with inductive categories applied to data related to the main mechanisms of the theory, but not captured by its sub-constructs.

Results
Ten deductive and three inductive categories related to three Normalization Process Theory primary mechanisms (Coherence, Cognitive Participation, and Collective Action) were identified. Identified barriers to intervention uptake included: (1) additional burden for informal caregivers; (2) lack of appropriate workforce to provide guidance; (3) lack of time and financial resources; (4) people with dementia not recognising their diagnosis of dementia and/or a need for support; and (5) stigma. Identified facilitators to intervention uptake included: (1) intervention has potential to fill a large psychological treatment gap in Sweden; (2) objectives and potential benefits understood and agreed by most stakeholders; and (3) some healthcare professionals recognized their potential role in providing intervention guidance.

Conclusions
Several barriers and facilitators for future implementation, specific to the intervention, individuals and families, as well as professionals, were identified during intervention development. Barriers were mapped into evidence-based implementation strategies, which will be adopted to overcome identified barriers. A feasibility study further examining implementation potential, acceptability and feasibility, alongside clinical, methodological, and procedural uncertainties associated with the intervention will be conducted.

Trial registration
Not applicable.
MedFusionGAN: multimodal medical image fusion using an unsupervised deep generative adversarial network
Authors: Safari Mojtaba , Fatemi Ali , Archambault Louis 
Published: December 2023

Abstract
Purpose
This study proposed an end-to-end unsupervised medical fusion generative adversarial network, MedFusionGAN, to fuse computed tomography (CT) and high-resolution isotropic 3D T1-Gd Magnetic resonance imaging (MRI) image sequences to generate an image with CT bone structure and MRI soft tissue contrast to improve target delineation and to reduce the radiotherapy planning time.

Methods
We used a publicly available multicenter medical dataset (GLIS-RT, 230 patients) from the Cancer Imaging Archive. To improve the models generalization, we consider different imaging protocols and patients with various brain tumor types, including metastases. The proposed MedFusionGAN consisted of one generator network and one discriminator network trained in an adversarial scenario. Content, style, and L1 losses were used for training the generator to preserve the texture and structure information of the MRI and CT images.

Results
The MedFusionGAN successfully generates fused images with MRI soft-tissue and CT bone contrast. The results of the MedFusionGAN were quantitatively and qualitatively compared with seven traditional and eight deep learning (DL) state-of-the-art methods. Qualitatively, our method fused the source images with the highest spatial resolution without adding the image artifacts. We reported nine quantitative metrics to quantify the preservation of structural similarity, contrast, distortion level, and image edges in fused images. Our method outperformed both traditional and DL methods on six out of nine metrics. And it got the second performance rank for three and two quantitative metrics when compared with traditional and DL methods, respectively. To compare soft-tissue contrast, intensity profile along tumor and tumor contours of the fusion methods were evaluated. MedFusionGAN provides a more consistent, better intensity profile, and a better segmentation performance.

Conclusions
The proposed end-to-end unsupervised method successfully fused MRI and CT images. The fused image could improve targets and OARs delineation, which is an important aspect of radiotherapy treatment planning.
Value of the stroke 1-2-0 prehospital stroke education system: the experience of a general practitioner team
Authors: Liu Yang , Wang Daosheng , Chu Min , Yang Zhenzhen , Luo Yunhe , Wang Delong , Zhao Jing 
Published: December 2023

Abstract
Background
Stroke is one of the leading causes of death worldwide, especially in developing countries. In China, there is an urgent need to educate people about stroke awareness and the importance of using emergency medical services (EMS) quickly after a stroke has occurred.

Objective
We sought to explore the effects of the Stroke 1-2-0 Prehospital Stroke Education System based on the experience of a general practitioner team.

Method
We prospectively enrolled 119 community general practitioners to be trained in the procedures advocated by the Stroke 1-2-0 Prehospital Stroke Education System. The training content included early detection of ischemic stroke, first aid for stroke, and intravenous thrombolysis; The effects of the training were later evaluated via a before-and-after comparison. The 119 enrolled physicians formed a Stroke 1-2-0 lecturer group and taught stroke knowledge to community residents. The group remained active for 6 months, during which the medical treatment data of stroke patients (i.e., stroke onset time, prehospital delay, whether an ambulance was called, and whether thrombolytic therapy was performed) in each of 5 jurisdictions were recorded for the month before (January 2021) and that after (August 2021) the 6-month community education program. Finally, the effects of the community education program were evaluated.

Results
The participants’ understanding of intravenous thrombolysis in the treatment of acute ischemic stroke improved significantly after the training as compared with their earlier understanding (96% vs. 78.99%; P < .001), and their understanding of the time window for intravenous thrombolysis increased from 26.05% before to 72% (P < .001) after the training. Most of the participants (90% vs. 67.23%; P < .001) said that they would immediately call the 120 emergency number of China’s emergency phone system if they encountered individuals who appeared to be victims of acute stroke. A total of 82 stroke patients were seen before and 67 after the community education program. As for the use of the emergency call system, more patients with stroke activated that system after the program versus before (21.95% vs. 37.31%; P = .04). The 3-hour arrival rate after the program was nearly three times higher than that before the program (62.69% vs. 19.51%; P < .001). Also, regarding receiving thrombolysis after the occurrence of a stroke, the program triggered a substantial increase compared with the total earlier (19.4% vs. 6.1%; P = .013).

Conclusion
We found that the Stroke 1-2-0 Prehospital Stroke Education System significantly improved community residents’ knowledge regarding stroke.
Promising preclinical patient-derived organoid (PDO) and xenograft (PDX) models in upper gastrointestinal cancers: progress and challenges
Authors: Gao Jing , Lan Jianqiang , Liao Haiyan , Yang Fang , Qiu Pei , Jin Feng , Wang Shubin , Shen Lin , Chao Tengfei , Zhang Cheng , Zhu Yu 
Published: December 2023

AbstractGastrointestinal (GI) cancers (gastric cancer, oesophageal cancer, liver cancer, colorectal cancer, etc.) are the most common cancers with the highest morbidity and mortality in the world. The therapy for most GI cancers is difficult and is associated with a poor prognosis. In China, upper GI cancers, mainly gastric cancer (GC) and oesophageal cancer (EC), are very common due to Chinese people’s characteristics, and more than half of patients are diagnosed with distant metastatic or locally advanced disease. Compared to other solid cancers, such as lung cancer and breast cancer, personalized therapies, especially targeted therapy and immunotherapy, in GC and EC are relatively lacking, leading to poor prognosis. For a long time, most studies were carried out by using in vitro cancer cell lines or in vivo cell line-derived xenograft models, which are unable to reproduce the characteristics of tumours derived from patients, leading to the possible misguidance of subsequent clinical validation. The patient-derived models represented by patient-derived organoid (PDO) and xenograft (PDX) models, known for their high preservation of patient tumour features, have emerged as a very popular platform that has been widely used in numerous studies, especially in the research and development of antitumour drugs and personalized medicine. Herein, based on some of the available published literature, we review the research and application status of PDO and PDX models in GC and EC, as well as detail their future challenges and prospects, to promote their use in basic and translational studies or personalized therapy.
The aetiology and burden of myeloproliferative neoplasms in the United Kingdom: the MyelOproliferative neoplasmS: an In-depth case-control (MOSAICC) study protocol
Authors: Abutheraa Nouf , Tarburn Emma-Louise , McShane Charlene M. , Duncombe Andrew , McMullin Mary Frances , Anderson Lesley Ann 
Published: December 2023

Abstract
Background
Myeloproliferative neoplasms (MPNs) are a group of haematological malignancies that affect approximately 8 people in every 100,000 individuals in the UK. Little is known about the aetiology of MPNs, as previous studies have been hampered by small sample sizes, thus it is important to understand the cause of MPNs in a larger study to identify prevention strategies and improve treatment strategies. This study aims to determine environmental, lifestyle, genetic and medical causes of MPNs and to assess the relevance of occupational carcinogen exposures and quality of life impacts.

Methods
A UK-wide case-control study of 610 recently diagnosed MPN patients (within 24 months) receiving clinical care at 21 NHS study sites in Scotland, England, Wales and Northern Ireland and 610 non-blood relative/friend controls is underway. Data on occupational and residential history, medical and environmental factors, and quality of life are being collected from the participants via a structured interview and self-complete questionnaires. Clinical data is being provided by the clinical team. Blood, saliva and toenail samples are also being collected for genetic and elemental analysis. Adjusted odds ratios (ORs) and 95% confidence intervals (95%CI) will be calculated using a p < 0.05 to investigate potential risk factors for the MPN clinical and genetic subtypes, and further analyses will be conducted based on the type of data and outcome of interest at a later stage.

Discussion
The study design is most effective for investigating the aetiology of rare diseases. The study will enable identification of potential causes of MPNs through in-depth assessment of potential risk factors with potential for longer follow-up of a number of outcomes.