bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electroacupuncture stimulation improves cognitive ability and regulates metabolic disorders in Alzheimer’s disease model mice: new insights from brown adipose tissue thermogenesis
Authors: Li Ting , Tian Junjian , Wu Meng , Tian Yuanshuo , Li Zhigang 
Published: January 2024

BackgroundMetabolic defects play a crucial role in Alzheimer’s disease (AD) development. Brown adipose tissue (BAT) has been identified as a novel potential therapeutic target for AD due to its unique role in energy metabolism. Electroacupuncture (EA) shows promise in improving cognitive ability and brain glucose metabolism in AD, but its effects on peripheral and central metabolism are unclear.MethodsIn this study, SAMP8 mice (AD model) received EA stimulation at specific acupoints. Cognitive abilities were evaluated using the Morris water maze test, while neuronal morphology and tau pathology were assessed through Nissl staining and immunofluorescence staining, respectively. Metabolic variations and BAT thermogenesis were measured using ELISA, HE staining, Western blotting, and infrared thermal imaging.ResultsCompared to SAMR1 mice, SAMP8 mice showed impaired cognitive ability, neuronal damage, disrupted thermoregulation, and metabolic disorders with low BAT activity. Both the EA and DD groups improved cognitive ability and decreased tau phosphorylation (p&lt;0.01 or p&lt;0.05). However, only the EA group had a significant effect on metabolic disorders and BAT thermogenesis (p&lt;0.01 or p&lt;0.05), while the DD group did not.ConclusionThese findings indicate that EA not only improves the cognitive ability of SAMP8 mice, but also effectively regulates peripheral and central metabolic disorders, with this effect being significantly related to the activation of BAT thermogenesis.
Numerical simulation study on evolution law of three-dimensional fracture network in unconventional reservoirs
Authors: Chen Xiyu , Huang Yitao , Li Yongming , Shen Cheng 
Published: January 2024

It has become a consensus that large-scale hydraulic fracturing is adopted to achieve the stimulation of unconventional oil and gas reservoir. The complex fracture network formed by fracturing is closely related to the effect of reservoir stimulation, which has extremely complicated evolution process. Therefore, it is necessary to study the evolution law of fracture network in large-scale hydraulic fracturing of unconventional reservoirs. In this article, the geological engineering parameters of horizontal well H in shale gas reservoir in southern Sichuan are taken as an example, a three-dimensional fracture network expansion model is established based on the boundary element method and finite volume method, and the simulation of the complex fracture network in a whole well section is carried out to analyze the evolution law of reservoir fracture network under different geological and engineering parameters. The results show that the horizontal stress field distribution has a significant effect on fracture geometric form. Hydraulic fractures in reservoirs with larger horizontal stress difference have stronger directivity, while the horizontal wellbore tends to obtain better reservoir stimulation results when it is parallel to the minimum horizontal principal stress setting. The conjugated natural fracture developed in the reservoir inhibits the hydraulic expansion fractures in both directions. Although it increases the complexity of the fractures, it is not necessarily conducive to improving the reservoir stimulation effectiveness. The lower the strength of natural fracture is, the more complex the fracture geometric form becomes, and the smaller the stimulated reservoir volume is. Correspondingly, the higher the strength of natural fracture is, the simpler the fracture geometric form becomes, and the larger the stimulated reservoir volume is. Suitable fracturing construction displacement can not only contribute to form a more complex fracture distribution, but also help to obtain a larger stimulated reservoir volume. The optimal construction displacement ranges from 10 to 14 m3/min. Low viscosity fracturing fluids are suitable for the formation of long-narrow fractures and able to connect with the remote reservoir and form complex fracture networks. Lower viscosity fluids can be used to achieve better reservoir stimulation effectiveness when sand-carrying capacity is met.
Research and application of ‘three zones’ range within overlying strata in goaf of steep coal seam
Authors: Yang Shouguo , Xu Ning , Liu Haoxin , Zhang Xiaofei , Mei Shuxin 
Published: January 2024

The determination of the ‘three zones’ range within the overlying strata in goaf of paramount importance for effective gas extraction in the goaf and the prevention and control of gas levels exceeding limits in both the working face and the upper corner. Due to the influence of their dip angles, the existing formula used to calculate the breaking boundary angle of the overlying strata in the goaf of horizontal coal seams is no longer suitable for steep coal seams. In response to this issue, the movement law of the overlying strata during the mining of steep coal seams was analyzed and a formula for calculating the breaking boundary angle of the overlying strata in the goaf of steep coal seams was derived. The theoretical calculation formula was applied to the 3,103 fully mechanized mining face of a certain mine in southwest China, and compared and analyzed the results with numerical simulation and on-site measurement using microseismic monitoring technology. The research findings demonstrate that the formula effectively quantifies the ‘three zones’ range within the overlying strata in the goaf of steep coal seams. The ‘three zones’ range in steep coal seams is primarily influenced by factors such as the length of the filling area in the lower part of the goaf, changes in roof lithology, coal seam dip angle, length of the working face, and overburden load. The longer the length of the filling area, the larger the upper breaking boundary angle and the smaller the lower breaking boundary angle of the fracture zone. Based on the research results of three methods, the height of the caving zone in the 3,103 fully mechanized mining face is from 6.93 m to 7.7 m, the height of the fracture zone is from 28.91 m to 34.2 m, the lower breaking boundary angle of the fracture zone is from 40° to 44.5°, and the upper breaking boundary angle of the fracture zone is from 57.7° to 62°. The research results offer robust technical support and theoretical guidance for the determination of the ‘three zones’ range within the overlying strata during the future mining of steep coal seams.
ProkBERT family: genomic language models for microbiome applications
Authors: Ligeti Balázs , Szepesi-Nagy István , Bodnár Babett , Ligeti-Nagy Noémi , Juhász János 
Published: January 2024

BackgroundIn the evolving landscape of microbiology and microbiome analysis, the integration of machine learning is crucial for understanding complex microbial interactions, and predicting and recognizing novel functionalities within extensive datasets. However, the effectiveness of these methods in microbiology faces challenges due to the complex and heterogeneous nature of microbial data, further complicated by low signal-to-noise ratios, context-dependency, and a significant shortage of appropriately labeled datasets. This study introduces the ProkBERT model family, a collection of large language models, designed for genomic tasks. It provides a generalizable sequence representation for nucleotide sequences, learned from unlabeled genome data. This approach helps overcome the above-mentioned limitations in the field, thereby improving our understanding of microbial ecosystems and their impact on health and disease.MethodsProkBERT models are based on transfer learning and self-supervised methodologies, enabling them to use the abundant yet complex microbial data effectively. The introduction of the novel Local Context-Aware (LCA) tokenization technique marks a significant advancement, allowing ProkBERT to overcome the contextual limitations of traditional transformer models. This methodology not only retains rich local context but also demonstrates remarkable adaptability across various bioinformatics tasks.ResultsIn practical applications such as promoter prediction and phage identification, the ProkBERT models show superior performance. For promoter prediction tasks, the top-performing model achieved a Matthews Correlation Coefficient (MCC) of 0.74 for E. coli and 0.62 in mixed-species contexts. In phage identification, ProkBERT models consistently outperformed established tools like VirSorter2 and DeepVirFinder, achieving an MCC of 0.85. These results underscore the models' exceptional accuracy and generalizability in both supervised and unsupervised tasks.ConclusionsThe ProkBERT model family is a compact yet powerful tool in the field of microbiology and bioinformatics. Its capacity for rapid, accurate analyses and its adaptability across a spectrum of tasks marks a significant advancement in machine learning applications in microbiology. The models are available on GitHub (https://github.com/nbrg-ppcu/prokbert) and HuggingFace (https://huggingface.co/nerualbioinfo) providing an accessible tool for the community.
Mechanical thrombectomy using the retrograde semi-retrieval technique for patients with underlying intracranial atherosclerotic stenosis
Authors: Wang Wei , Xu Yongbo , Zhang Bohao , Liu Shuling , Ma Zhenjian , Wang Sifei , Zhang Pinyuan , Wei Ming 
Published: January 2024

BackgroundThe retrograde semi-retrieval technique (RESET) has been described as a modified technique for endovascular thrombectomy (EVT) whose safety and efficacy for intracranial atherosclerosis stenosis (ICAS) patients remain uncertain. This article presents our single-center experience, comparing RESET vs. non-RESET in ICAS patients.Materials and methodsWe analyzed 327 consecutive ICAS patients who underwent EVT at Tianjin Huanhu Hospital from January 2018 and December 2022. Patients were categorized into two groups: RESET and non-RESET. The primary outcome was the first-pass effect (FPE). Secondary outcomes included successful reperfusion, functional independence at 90 days, mortality, and symptomatic intracranial hemorrhage (sICH).ResultsRESET was significantly associated with FPE [adjusted odds ratio (aOR) 2.00, 95% confidence interval (CI) 1.03–3.87, p = 0.040]. RESET was not significantly associated with successful reperfusion (aOR 1.5, CI 0.55–4.06, p = 0.425), an mRS of 0–2 at 90 days (aOR 1.36, CI 0.83–2.21, p = 0.223), sICH (aOR 0.39, CI 0.12–1.23, p = 0.108), and mortality (aOR 0.49, CI 0.16–1.44, p = 0.193). After propensity score matching, the results were consistent with the primary analysis.ConclusionCompared to non-RESET, patients treated with RESET showed increased FPE incidence and significantly decreased puncture-to-reperfusion time. RESET was proven to be safe and effective in enhancing reperfusion for LVO patients receiving EVT with underlying ICAS.
High indirect bilirubin levels as an independent predictor of postoperative myasthenic crisis: a single-center, retrospective study
Authors: Sun Chao , Ruan Zhe , Zhang Yu , Guo Rongjing , Li Huanhuan , Wang Tantan , Gao Ting , Tang Yonglan , Song Na , Hao Sijia , Huang Xiaoxi , Li Shuang , Ning Fan , Su Yue , Lu Qiang , Wang Qingqing , Cao Xiangqi , Li Zhuyi , Chang Ting 
Published: January 2024

BackgroundThymectomy is an efficient and standard treatment strategy for patients with myasthenia gravis (MG), postoperative myasthenic crisis (POMC) is the major complication related to thymectomy and has a strongly life-threatening effect. As a biomarker, whether the bilirubin level is a risk factor for MG progression remains unclear. This study aimed to investigate the association between the preoperative bilirubin level and postoperative myasthenic crisis (POMC).MethodsWe analyzed 375 patients with MG who underwent thymectomy at Tangdu Hospital between January 2012 and September 2021. The primary outcome measurement was POMC. The association between POMC and bilirubin level was analyzed by restricted cubic spline (RCS). Indirect bilirubin (IBIL) was divided into two subgroups based on the normal upper limit of IBIL, 14 μmol/L.ResultsCompared with non–POMC group, IBIL levels were significantly higher in patients with POMC. Elevated IBIL levels were closely associated with an increased risk of POMC (p for trend = 0.002). There was a dose-response curve relationship between IBIL levels and POMC incidence (p for non–linearity = 0.93). However, DBIL levels showed a U-shaped association with POMC incidence. High IBIL level (≥14 μmol/L) was an independent predictive factor for POMC [odds ratio = 3.47, 95% confidence interval (CI): 1.56–7.8, p = 0.002]. The addition of high IBIL levels improved the prediction model performance (net reclassification index = 0.186, 95% CI: 0.039–0.334; integrated discrimination improvement = 0.0345, 95% CI: 0.005–0.065).ConclusionHigh preoperative IBIL levels, especially those exceeding the normal upper limit, could independently predict the incidence of POMC.
Effect of non-invasive transcutaneous auricular vagus nerve stimulation on cerebral motor excitability—Study protocol for a randomized, sham controlled trial
Authors: Herr Thorsten , Kleger Paula , Strauss Sebastian , Szeska Christoph , Khalil Nura , Badran Bashar W. , Weymar Mathias , Grothe Matthias 
Published: January 2024

Transcutaneous auricular vagus nerve stimulation (taVNS) is becoming increasingly established in the treatment of various neurological and psychiatric diseases. However, only a few studies have focused on the overall influence of taVNS on cortical excitability in general. The planned study will investigate the effect of taVNS on the excitability of the motor cortex in young healthy subjects. The aim of the study is to gain better understand of the physiological mechanism of taVNS to contribute to new fields of application of taVNS in new areas such as the treatment of stroke or multiple sclerosis. This protocol describes a single-center, prospective, double blind, sham-controlled trial that evaluates the effect of taVNS on motor cortex excitability with a planned sample size of 30 participants. The effect of taVNS is investigated by neuronavigation and electromyography (EMG) coupled transcranial magnetic stimulation (TMS) applied before and after taVNS stimulation. The following parameters are assessed: resting motor threshold (RMT), active motor threshold (AMT), recruitment curve (RC), short intracortical inhibition (SICI), intracortical facilitation (ICF). All parameters will be assessed for taVNS on the basis of perception threshold and tolerance threshold. All investigations performed in the study were reviewed and approved by the local ethics committee of the University Medical Center Greifswald (study reference number: BB048/22).Clinical trial registrationwww.drks.de, number: DRKS00029937.
Association between dietary inflammatory index and mental disorders using multilevel modeling with GLIMMIX
Authors: Beiranvand Reza , Mansournia Mohammad Ali , Vahid Farhad , Nejatisafa Ali-Akbar , Nedjat Saharnaz 
Published: January 2024

IntroductionThe Dietary Inflammatory Index (DII) is a composite nutritional index that has gained significant attention in the past decade due to its association with physical and mental well-being. To accurately assess the precise effects of DII on health outcomes, the effects of nutrients and foods need to be adjusted. This study aimed to investigate the association between DII and mental disorders (depression, anxiety, and stress) using multilevel modeling to minimize the bias of the previous methods.MethodsThis cross-sectional analytical study was conducted using data from the initial phase of the Tehran University of Medical Sciences Employees’ Cohort Study (TEC). Nutritional information was obtained through a dish-based semi-quantitative food frequency questionnaire (DFQ), while psychological data were collected using the depression, anxiety and stress scale (DASS-42). The acquired data were analyzed using multilevel modeling in three levels (foods, nutrients, and DII, respectively) through GLIMMIX in the SAS software.ResultsA total of 3,501 individuals participated in this study. The results of the multilevel model demonstrated a significant statistical association between DII and mental disorders after adjusting for baseline characteristics, nutrients and foods. For each unit increase in DII, the mean scores for stress, anxiety, and depression increased by 3.55, 4.26, and 3.02, respectively (p &lt; 0.001).ConclusionBased on the multilevel model’s findings, it is recommended to minimize the use of pro-inflammatory nutrients and foods to increase the mental health. Multilevel data analysis has also been recommended in nutritional studies involving nested data to obtain more accurate and plausible estimates.
Effect of oral silymarin on liver function in pediatric acute lymphoblastic leukemia in the maintenance phase: a double-blind randomized clinical trial
Authors: Eghbali Aziz , Sadeghian Mahnaz , Ghasemi Ali , Afzal Roghayeh Rahimi , Eghbali Aygin , Ghaffari Kazem 
Published: January 2024

Introduction: Liver dysfunction is one of the most common disorders in patients with acute lymphoblastic leukemia (ALL). In recent studies, silymarin has been observed to have hepatic protective effects. Therefore, in this study, the effect of oral silymarin on the hepatic functions of patients with ALL was investigated.Methods: In the present double-blind clinical trial study, 121 patients with ALL over 5 years of age were divided into two groups after obtaining informed consent. The subjects were randomly divided into a silymarin-treatment group and a placebo group. In the silymarin-treatment group, patients received 70 mg oral capsules of silymarin twice daily or syrup of silymarin three times a day (each 5 ml of syrup contains 50 mg of silymarin). Patients were examined once a month for 9 months to receive capsules and measure the levels of alanine aminotransferase (ALT), aspartate transferase (AST), alkaline phosphatase (ALP), gamma-glutamyl transferase (GGT), bilirubin, albumin, and cholesterol.Results: Comparison of changes before and after treatment in the two groups showed that receiving oral silymarin resulted in a slight significant decrease in the levels of ALT, AST, GGT, and bilirubin (p &lt; 0.05), but had no effect on ALP, albumin, and cholesterol (p &gt; 0.05).Discussion: The results of the present study showed that in pediatric patients with ALL, silymarin intake improves liver function. The very strong antioxidant effect of silymarin may explain its protective effect on the liver.Clinical Trial Registration: IRCT20150119020715N10.
Effect of Astragalus membranaceus on left ventricular remodeling in HFrEF: a systematic review and meta-analysis
Authors: Han Xu , Yu Ting , Chen Xi , Du Zhiyan , Yu Man , Xiong Jiang 
Published: January 2024

Background: Left ventricular remodeling (LVR) is a key factor leading to the onset and progression of heart failure with reduced ejection fraction (HFrEF). Improving LVR can delay the progression of HFrEF and improve quality of life.Objective: To evaluate the improvement effect of Astragalus membranaceus (A. membranaceus) on LVR in patients with HFrEF.Method: We retrieved randomized controlled trials (RCTs) of A. membranaceus in treating HFrEF from eight Chinese and English databases, up until 31 October 2023. To assess the quality of the literature, we utilized the bias risk tool from the Cochrane Handbook. For meta-analysis, we employed Review Manager 5.4.1 software. Additionally, we performed sensitivity analysis and publication bias assessment using Stata 17.0 software.Result: Totally 1,565 patients were included in 19 RCTs. Compared to conventional treatment (CT), the combination therapy of A. membranaceus with CT demonstrated significant improvements in LVR, specifically increasing left ventricular ejection fraction (LVEF, MD = 5.82, 95% CI: 4.61 to 7.03, p &lt; 0.00001), decreasing left ventricular end-diastolic diameter (LVEDD, MD = −4.05, 95% CI: −6.09 to −2.01, p = 0.0001), and left ventricular end-systolic diameter (LVESD, MD = −12.24, 95% CI: −15.24 to −9.24, p &lt; 0.00001). The combination therapy of A. membranaceus with CT also improved clinical efficacy (RR = 4.81, 95% CI: 3.31 to 7.00, p &lt; 0.00001), reduced brain natriuretic peptide (BNP, MD = −113.57, 95% CI: −146.91 to −81.22, p &lt; 0.00001) level, and increased 6-min walking distance (6-MWD, MD = 67.62, 95% CI: 41.63 to 93.60, p &lt; 0.00001). In addition, the combination therapy of A. membranaceus with CT mitigated inflammatory responses by reducing tumor necrosis factor-alpha (TNF-α, MD = −16.83, 95% CI: −22.96 to −10.71, p &lt; 0.00001), interleukin-6 (IL-6, MD = −29.19, 95% CI: −36.08 to −22.30, p &lt; 0.00001), and high-sensitivity C-reactive protein (hs-CRP, MD = −0.98, 95% CI: −1.43 to −0.52, p &lt; 0.0001). Notably, the combination therapy of A. membranaceus with CT did not increase the incidence of adverse reactions (RR = 0.86, 95% CI: 0.25 to 2.96, p = 0.81).Conclusion: This systematic review and meta-analysis revealed that the combination therapy of A. membranaceus with CT has more advantages than CT alone in improving LVR and clinical efficacy in HFrEF patients, without increasing the incidence of adverse reactions. However, due to the limited quality of included studies, more high-quality investigations are required to provide reliable evidence for clinical use.Systematic Review Registration:https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=397571, Identifier: CRD42023397571.
Image-based classification of wheat spikes by glume pubescence using convolutional neural networks
Authors: Artemenko Nikita V. , Genaev Mikhail A. , Epifanov Rostislav UI. , Komyshev Evgeny G. , Kruchinina Yulia V. , Koval Vasiliy S. , Goncharov Nikolay P. , Afonnikov Dmitry A. 
Published: January 2024

IntroductionPubescence is an important phenotypic trait observed in both vegetative and generative plant organs. Pubescent plants demonstrate increased resistance to various environmental stresses such as drought, low temperatures, and pests. It serves as a significant morphological marker and aids in selecting stress-resistant cultivars, particularly in wheat. In wheat, pubescence is visible on leaves, leaf sheath, glumes and nodes. Regarding glumes, the presence of pubescence plays a pivotal role in its classification. It supplements other spike characteristics, aiding in distinguishing between different varieties within the wheat species. The determination of pubescence typically involves visual analysis by an expert. However, methods without the use of binocular loupe tend to be subjective, while employing additional equipment is labor-intensive. This paper proposes an integrated approach to determine glume pubescence presence in spike images captured under laboratory conditions using a digital camera and convolutional neural networks.MethodsInitially, image segmentation is conducted to extract the contour of the spike body, followed by cropping of the spike images to an equal size. These images are then classified based on glume pubescence (pubescent/glabrous) using various convolutional neural network architectures (Resnet-18, EfficientNet-B0, and EfficientNet-B1). The networks were trained and tested on a dataset comprising 9,719 spike images.ResultsFor segmentation, the U-Net model with EfficientNet-B1 encoder was chosen, achieving the segmentation accuracy IoU = 0.947 for the spike body and 0.777 for awns. The classification model for glume pubescence with the highest performance utilized the EfficientNet-B1 architecture. On the test sample, the model exhibited prediction accuracy parameters of F1 = 0.85 and AUC = 0.96, while on the holdout sample it showed F1 = 0.84 and AUC = 0.89. Additionally, the study investigated the relationship between image scale, artificial distortions, and model prediction performance, revealing that higher magnification and smaller distortions yielded a more accurate prediction of glume pubescence.