bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of a bioinformatics-based prognostic model related to liquid-liquid phase separation in lung adenocarcinoma
Authors: Wang Hanlin , Chen Xiu , Kong Weibo , Dang Yan , Xu Junrui , Zhang Renquan 
Published: January 2024

Abstract
It was reported that liquid-liquid phase separation (LLPS) related genes (LRGs) were involved in the prognosis of a variety of tumors. We aimed to investigate the impact of LRGs on lung adenocarcinoma (LUAD) patients' prognosis, providing further insights for patient treatment and prognosis. TCGA-LUAD, GSE31210 and GSE131907 were applied in this study. Differentially expressed LRGs (DE-LRGs) were identified by intersecting the differentially expressed genes (DEGs) obtained through differential expression analysis with the LRGs acquired from the online database. A total of 17 DE-LRGs were gained by intersecting 5,445 DEGs and LRGs obtained from the online database. Subsequently, TACC3, TPX2, PRC1, FGFR2, ORC1, and PLK4 were identified as prognostic genes for constructing a risk model. The high-risk patients exhibited shorter survival time compared to the low-risk patients in both TCGA-LUAD and GSE31210. The nomogram of pathologic stage and riskScore demonstrated good predictive ability for the 1/3/5-year survival rate of LUAD patients. Next, immune analysis indicated TPX2 exhibited the strongly positive correlation with M0 and M1 macrophages, which displayed the important role of macrophages in the phase separation mechanism. Single cell analysis revealed higher expression levels of prognostic genes in T lymphocytes. We speculated that prognostic genes contributed to tumor development by affecting T-cell activity. Eventually, we verified the differential expression of prognostic genes by testing the expression of clinical samples. In conclusion, TACC3, PRC1, ORC1, and PLK4 were identified to be associated with LLPS on LUAD in this study. It provided further insights into the treatment of LUAD.
Artificial intelligence-powered spatial analysis of tumor-infiltrating lymphocytes as a predictive biomarker for immune checkpoint inhibitors in advanced biliary tract cancer
Authors: Yoo Changhoon , Bang Yeong Hak , Lee Choong-kun , Bang Kyunghye , Kim Hyung-Don , Ryoo Baek-Yeol , Kim Kyu-pyo , Jeong Jae Ho , Park Inkeun , Lee Dong Ki , Choi Hye Jin , Chung Taek , Jeon Seung Hyuck , Shin Eui-Cheol , Oum Chiyoon , Kim Seulki , Lim Yoojoo , Park Gahee , Ahn Changho , Finn Richard , Ock Chan-Young , Shin Jinho 
Published: January 2024

Abstract
The combination of anti-PD-1/L1 with gemcitabine and cisplatin (GemCis) has recently shown significant survival benefits in randomized phase 3 trials for advanced biliary tract cancer (BTC). However, no biomarker predictive of benefit has been established for anti-PD-1/L1 in BTC. Here, we evaluated tumor-infiltrating lymphocytes (TILs) using artificial intelligence-powered immune phenotype (AI-IP) analysis in advanced BTC treated with anti-PD-1. Data and images of BTC cohort from The Cancer Genome Atlas (TCGA) were initially analyzed to evaluate the transcriptomic and mutational characteristics of various AI-IPs in BTC. The inflamed IP showed increased cytolytic activity scores and an interferon-gamma signature compared to the non-inflamed IP. Next, pre-treatment H&E-stained whole-slide images from 339 advanced BTC patients who received anti-PD-1 monotherapy as second-line treatment or beyond, were retrospectively utilized for AI-IP analysis. Overall, AI-IPs were classified as inflamed (high intratumoral TIL [iTIL]) in 40 patients (11.8%), immune-excluded (low iTIL and high stromal TIL) in 167 (49.3%), and immune-deserted (low TIL overall) in 132 (38.9%). The inflamed IP group showed a significantly higher overall response rate compared to the non-inflamed IP groups (27.5% vs. 7.7%, P < 0.001). Median overall survival (OS) and progression-free survival (PFS) were significantly longer in the inflamed IP group than in the non-inflamed IP group (OS: 12.6 vs. 5.1 months, P = 0.002; PFS: 4.5 vs. 1.9 months, P < 0.001). IP classified by AI-powered spatial TIL analysis was effective in predicting the efficacy outcomes of advanced BTC patients treated with anti-PD-1 therapy. Further validation is necessary in the context of anti-PD-1/L1 plus GemCis.
The Correlation between Proximal femur Fracture and Bone Mineral Density in the Elderly
Authors: Chen Beibei , Liang Hairui , Zhang He , Sun Ming , Xu Rongda , Duan Siyu , Cai Zhencun 
Published: January 2024

Abstract

By summarizing the characteristics of bone mineral density (BMD) in older adults with proximal femoral fractures, to explore the relationship between (BMD and type of proximal femoral fractures in older adults. And to compare the BMD of the affected and unaffected sides of the femur, in order to pave ways for the prevention and treatment of proximal femoral fractures. A total of 876 patients with proximal femoral fractures (446 with femoral neck fractures and 430 with trochanteric fractures) were admitted to central hospitals affiliated to Shenyang Medical College over a three-year period. All patients underwent dual-energy x-ray absorptiometry (DXA) to evaluate the BMD of the lumbar spine and both sides of the femur. Differences in BMD were compared between the trochanteric and neck fracture groups, as well as between the affected and unaffected sides of the femur in all patients. The trochanteric fracture group had lower mean lumbar spine BMD (T-score: -2.66 ± 1.63) than the femoral neck fracture group (-1.56 ± 1.42) (P༜0.001). The trochanteric fracture group also had lower mean total BMD of both femurs (T-score: -2.74 ± 1.38) than the femoral neck fracture group (-1.73 ± 1.57) (P༜0.05). In the trochanteric fracture group, the BMD of the affected femur (T-score: -2.22 ± 1.49) was higher than that of the healthy femur (T-score: -3.28 ± 1.58) (P༜0.001). In the femoral neck fracture group, the affected femur had higher BMD (T-score: -1.68 ± 1.26) than the healthy femur (T-score: -2.02 ± 1.09) (P༜0.001). The mean BMD of the affected femur was higher than that of the healthy femur in all patients (T-score: -1.88 ± 1.76 vs. -2.66 ± 1.33) (P༜0.001). Patients with trochanteric fractures have lower BMD than those with femoral neck fractures, and should receive treatment for osteoporosis in addition to fracture management. BMD of the healthy femur was lower than that of the affected femur in Patients with proximal femoral fractures, and it is necessary to prevent the occurrence of secondary fractures on the healthy femur.
A hybrid finite-discrete element method for modelling cracking processes in sandy mudstone containing a single edge-flaw under cyclic dynamic loading
Authors: Zhang Xiaolong , Xu Wenjie , Zhang Xiaoping , Yu Yan , Xu Chong 
Published: January 2024

Abstract

Rock mass deformation and failure are macroscopic manifestations of crack initiation, propagation, and coalescence. However, simulating the transition of rocks from continuous to discontinuous media under dynamic loads remains challenging. This study proposes a hybrid finite-discrete element method (HFDEM) to model crack propagation. Uniaxial compression tests on sandy mudstone with a single edge-flaw are simulated using HFDEM, and the results are compared with laboratory tests. The effects of pre-existing flaw inclination angle and dynamic loading frequency on the crack process are investigated. Results show that under dynamic loading, rock samples exhibit significantly higher compressive strength compared to quasi-static loading, which increases with dynamic frequency. Crack initiation angle also increases with flaw inclination angle and dynamic frequency. Experimental and numerical simulation results demonstrate crack initiation at the defect's tip, formation of wing cracks, and a combination of tensile and shear failure modes. The comparative analysis shows that HFDEM successfully captures crack interaction mechanisms and accurately simulates the overall failure behavior of cracked specimens. This study provides valuable insights into crack development and failure of rocks under seismic loads, offering guidance for engineering practices.
Quality markers based on chromatographic fingerprinting and anti-neuroinflammatory screening: A spectrum–effect correlation for Nardostachys jatamansi DC. with anti-neuroinflammatory potential
Authors: Xue Bian-Xia , Liu Xiao-Jie , Duan Cong-Yan , Zhang Li-Hua , Wang Shao-Xia , Wu Hong-Hua 
Published: January 2024

Abstract
Backgroud
Nardostachys jatamansi DC. (NJ) has long been prescribed to treat neurodegenerative diseases, including Alzheimer’s disease and Parkinson’s disease, in traditional Chinese medicine and other orient ethnomedicinal systems. However, the anti-neuroinflammatory components and the quality markers (Q-markers) underlying NJ remained unclear.
Objective and design
This study aimed to reveal the Q-markers of NJ in treating neuroinflammation-related diseases by developing ‘spectrum–anti-neuroinflammatory effect’ correlation for NJ against neuroinflammation.
Methods
First, a Griess method was applied to evaluate the anti-neuroinflammatory potentials of common NJ extracts and components, discovering the dominant anti-neuroinflammatory component of NJ (NJ_1A). The spectrum–effect correlation of NJ_1A was then accomplished by Pearson’s correlation, GCA, and PLSR modeling between the UPLC–PDA fingerprints and the inhibitory rates of batches of NJ_1A on NO production in BV-2 cells. Finally, the potentially effective constituents were screened and their anti-neuroinflammatory potentials were further verified.
Results
The fingerprint similarity of NJ_1A as well as the content of nardosinone would gradually decrease along with the prolongation of the NJ storage time. Ten promising anti-neuroinflammatory-correlated peaks were screened accordingly by the spectrum–effect correlation of NJ_1A. And seven of them were identified and validated to exert varying degrees of anti-neuroinflammatory effect. Finally, nardosinone, desoxo-narchinol A, and nardosinonediol stood out to be the major active constituents and key Q-markers for NJ_1A in treatment of neuroinflammation.
Conclusion
The current study demonstrated that spectrum–effect correlation was a powerful approach to investigate the active components dedicated for the anti-neuroinflammation underlying NJ, and provided a solid basis for the Q-markers of NJ against neurodegenerative diseases.
Simulation and experimental study on vascular hemodynamics of atherosclerotic plaque
Authors: Zhang Yingying , Sun Xu , Lin Guochang , Wang Jun , Yao Yongtao 
Published: January 2024

Abstract
For atherosclerotic diseases, a large number of associated plaque rather than single plaque are found in diseased vessels during clinic diagnosis. For the study of hemodynamic parameters, this paper uses a simplified model to simulate the fluid-structure interaction during a non-Newtonian blood flowing through arteries with different degrees of stenosis caused by atherosclerosis. The influence of the geometry and location of the anterior plaque on the hemodynamic parameters of the posterior plaque have mainly been discussed. The effects of fluid wall shear stress, gradient, normal stress and shear rate on the posterior plaque were studied by changing of the plaque spacing, the stenosis rate, the spatial angle in diseased artery. The simulation results obtained by the ideal model can reveal more complex blood flow characteristics of arterial stenosis. It shows that with the increase of plaque spacing, V, WSS, WNS and SR increased by an average of about 3.2–6.6%. And when δ1 > 60%, the variables V, WSS, WNS, SR, and WSSG increase by more than 37%.These findings are of great significance to the development and prediction of plaque rupture in the diseased vessels.
Optimal Duration of Medical Expulsive Therapy for Lower Ureteral Stones : a Critical Evaluation
Authors: ERDOĞAN Erhan , ŞİMŞEK¹ Gamze , AŞIK¹ Alper , YAŞAR¹ Hikmet , ŞAHİN¹ Cahit , SARICA¹ Kemal 
Published: January 2024

Abstract
Aim
To evaluate optimal duration of Medical Expulsive Therapy (MET) application for distal ureteric stones on a time period based manner.
Patients and Methods
: 89 patients with 5–10 mm distal ureter stones received tamsulosin (0.4 mg) for MET and diclofenac sodium (75 mg) for analgesia. Patients were evaluated once a week for four weeks. Radiologic evaluation of stone passage was evaluated by kidney ureter bladder (KUB) and ultasonography where non-contrast computed tomography (NCCT) was also performed if needed.
Results
While 23 cases (28.4%) were SF after first week, 23 were SF (28.4%) after two weeks, 9 cases (11.1%) after three and lastly 7 cases (8.6%) became SF after four weeks. 19 (23.5%) cases were not SF after 4 weeks. A positive relationship was found between the time period elapsed for stone passage and ureteral wall thickness (UWT) along with hydronephrosis. Additionally, mean number of renal colics and emergency department (ED) visits were found to be higher in patients passing their stones in the 4th week along with the ones who could not pass their stones.
Conclusions
Following the initiation of MET, SFR were higher in the first three weeks for distal ureteric stones for sizing 5–10 mm. indicating that waiting for a longer period of time will result in an unnecessary analgesic and MET treatment with increased risk of emergency department visits, additional costs and loss of time. Other available treatment options could be considered in such cases who are not SF at the end of the first three weeks.
Characteristic changes of prefrontal and motor areas in patients with type 2 diabetes and major depressive disorder during a motor task of tai chi chuan: A functional near-infrared spectroscopy study
Authors: Zhang Jiaming , Li Yuxi , Liu Xiaobo , Zhong Dongling , Xue Chen , Fan Jin , Xie Cheng , Li Juan , Jin Rongjiang 
Published: January 2024

Abstract
Aim
This cross-sectional study aimed to identify the characteristic changes of prefrontal and motor areas during a tai chi chuan task in patients with type 2 diabetes mellitus (T2DM) and major depressive disorder (MDD) using real-time functional near-infrared spectroscopy (fNIRS).
Methods
Three parallel groups (T2DM with DD group, T2DM group, and healthy group) were included in the study, who were recruited from December 10, 2022, to May 31, 2023. All the groups conducted a motor task of tai chi chuan designed by Eprime 3.0, and fNIRS was used to monitor brain activation, functional connectivity (FC) and lateralization of prefrontal and motor areas in participants.
Results
Ninety older adults (aged ≥ 60) participated in this study, including 30 patients with T2DM and MDD, 30 patients with T2DM, and 30 healthy subjects. The T2DM with MDD group showed altered cerebral function compared to T2DM group and healthy groups, including decreased activation, abnormal lateralization index and left-sided lateralization ratio of prefrontal and motor areas, and decreased FC among supplementary motor area, motor area, and dorsolateral prefrontal cortex.
Conclusions
Patients with T2DM and MDD showed characteristic functional changes in prefrontal and motor areas during a motor task of tai chi chuan which contributed to our understanding of the neuropathology of depression in T2DM patients. This study first confirmed the ability to evaluate real-time brain function of wearable fNIRS which merits further validation in larger sample size.
Finite element modeling and comparative mechanical analysis of several hoeing tools
Authors: Shen Huajie , Zhang Kangkang , Shao Kaiqing , Huang Donghai , Lian Caiping , Zhang Fengwu , Miao Yuan 
Published: January 2024

Abstract
To investigate the material selection basis of hoeing tools, the finite element software ANSYS Workbench was used to compare the material mechanical properties of several typical hoeing tools. Herein, ash wood (Fraxinus chinensis Roxb.), beech wood (Zelkova schneideriana Hand-Mazz), fir wood (Cunninghamia lanceolata (Lamb.) Hook.), oak wood (Cyclobalanopsis glauca (Thunb.) Oerst.), and locust wood (Sophora japonica (L.)) were selected for the hoe handles, and manganese 13 steel, type 45 steel, and spring steel were selected for the cutterhead. The corresponding finite element model was established by Solidworks software, and the force of the hoe tool under general working conditions was presented by ANSYS Workbench simulation, and then the dynamic performance of different materials was analyzed and compared by the comprehensive scoring method. The results of hoeing effect, hoe shank strength and cutter head strength show that the hoeing tool using spring steel as cutter head has higher strength, the hoeing tool using ash wood, beech wood, and Robinia wood as hoe shanks is better than that of zelkova wood and fir wood, and the choice of the material combination of "beech wood shanks + spring steel cutterhead" enables the hoeing tool to realize the best mechanical properties.
Voltage and frequency stability of microgrids considering harmonic distortions
Authors: de Melo Igor Delgado , Teixeira Mariana , Medina Rai N. 
Published: January 2024

Abstract
Traditional power flow algorithms have been widely used for evaluating voltage and frequency stability of microgrids. However, few research papers are found within the context of harmonic analysis and the impact of power quality degradation in the microgrids stability. This paper presents a novel approach for the voltage stability assessment and harmonic analysis in microgrids based on the formulation of an optimal power flow model. In the proposed approach, the objective function determines the maximum loadability factor of the network considering limits for the total harmonic distortion, voltage magnitudes and system frequency. The optimization problem is solved by interior-point method. Simulations are carried out using the IEEE 33-bus test system, modified in order to include distributed generators connected to the grid considering VSI (Voltage Source Inverters) with their frequency droop characteristics. Computational tests are performed considering microgrids in grid-connected and islanded operation modes. Results are validated based on a comparative analysis with the RSCAD (Real-Time Simulation Software Package) software to prove the effectiveness of the proposed formulation.
Physiological and molecular mechanisms of leaf response to high-temperature stress in high-temperature-resistant soybean varieties
Authors: Li Jiajia , Zhi Xianguan , Chen Haoran , Chen Linying , Lu Yun , Liao Wei , Tian Zhuo , Wu Meiyan , Shan Yajing , Wang Heng , Yan Long , Liu Bingqiang , Wang Xiaobo 
Published: January 2024

Abstract

Background
With increasing global temperature, high temperature (HT) has become one of the main factors limiting soybean yield and quality. Exploring HT resistance-related functional genes and their corresponding molecular mechanisms is of great value. Previous physiological mechanism studies have shown that, compared with HD14 (HT sensitive), JD21 is an HT-resistant variety, and further analysis of the transcriptome and proteome has revealed the HT tolerance mechanism of JD21 anthers. Moreover, we found that compared with those of HD14 (28.72%), the leaves of JD21 also exhibited high HT resistance, and the degree of leaf wilting in JD21 plants after HT stress was 11.02%; however, the regulatory mechanism of the response of these plants to HT stress is still unclear.
Results
In this study, comparative transcriptome analysis of JD21 and HD14 soybean leaves after HT stress and field control plants was performed by RNA-seq technology. The results showed that the number of upregulated DEGs in JD21 and HD14 was greater than the number of downregulated DEGs after HT stress, and the number of up- or downregulated DEGs in JD21 was greater than that in HD14. Bioinformatics analysis revealed that many DEGs were involved in various molecular functions and metabolic pathways. QRT‒PCR analysis verified that the gene expression pattern determined via RNA–seq was reliable. In addition, through expression level and conserved domain analyses, 22 key candidate genes related to the response of soybean leaves to HT stress were screened.
Conclusions
The leaf gene expression networks of HT-resistant (JD21) and HT-sensitive (HD14) plants were constructed under HT stress and control conditions. Some DEGs responding to HT stress were screened through transcriptome sequencing. The GO annotations and KEGG pathways of these genes were analyzed to explore the regulatory mechanism of the response of soybean leaves to HT stress. Further through conserved domain analysis, several key candidate DEGs involved in the response to HT stress were identified. This study provides important data for further study of the molecular basis of the effect of HT on soybean leaves at the transcriptional level.
Investigating the relationship between psychological factors (fear of movement and pain catastrophizing) and the functional performance of athletes with patellofemoral pain syndrome
Authors: pirayeh nahid , Talebi Mostafa , Saadat Maryam , Norouzi Sadegh 
Published: January 2024

Abstract
Introduction:
Patellofemoral pain syndrome (PFPS) is one of the most common musculoskeletal complaints accounting for 20–40% of knee problems in adults and active young people. Individuals with PFPS may suffer from anxiety, depression, pain catastrophizing, and fear-related pain. Therefore, a deep understanding of the relationship between psychological factors and functional impairment in these people may improve the choice of treatment strategies and help prevent this disorder from becoming a chronic condition. Therefore, this study aims to investigate the relationship between psychological factors (fear of movement and pain catastrophizing) and the functional performance of athletes with PFPS.
Methods
Sixty-one male athletes with an average age of 18 to 45 years and a history of PFPS for more than 3 months voluntarily participated in this study. At first, the participants completed the Tampa Scale of Kinesiophobia (TSK) and the Pain Catastrophizing Scale (PCS). Then, their function was tested using the Kujala Patellofemoral Scale (KPS) and the tests of step down, bilateral squat, single-leg hop, modified star excursion balance test, and side hop test.
Results
The results of our study showed that all examined functional tests have a weak correlation with the score of TSK and PCS. However, the score of KPS had a strong to moderate correlation with the scores of TSK and PCS.
Discussion
In this study, psychological factors had a significant relationship with functional test results and the self-reported functional measure. Therefore, according to the results of this study, therapists are advised to adopt approaches that consider psychological factors, such as the biopsychosocial approach, in managing the treatment of people with PFPS.