bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction and validation of an angiogenesis-related lncRNA prognostic model in lung adenocarcinoma
Authors: Gong Quan , Huang Xianda , Chen Xiaobo , Zhang Lijuan , Zhou Chunyan , Li Shijuan , Song Tingting , Zhuang Li 
Published: March 2023

Background: There is increasing evidence that long non-coding RNAs (lncRNAs) can be used as potential prognostic factors for cancer. This study aimed to develop a prognostic model for lung adenocarcinoma (LUAD) using angiogenesis-related long non-coding RNAs (lncRNAs) as potential prognostic factors.Methods: Transcriptome data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed to identify aberrantly expressed angiogenesis-related lncRNAs in LUAD. A prognostic signature was constructed using differential expression analysis, overlap analysis, Pearson correlation analysis, and Cox regression analysis. The model’s validity was assessed using K-M and ROC curves, and independent external validation was performed in the GSE30219 dataset. Prognostic lncRNA-microRNA (miRNA)-messenger RNA (mRNA) competing endogenous RNA (ceRNA) networks were identified. Immune cell infiltration and mutational characteristics were also analyzed. The expression of four human angiogenesis-associated lncRNAs was quantified using quantitative real-time PCR (qRT-PCR) gene arrays.Results: A total of 26 aberrantly expressed angiogenesis-related lncRNAs in LUAD were identified, and a Cox risk model based on LINC00857, RBPMS-AS1, SYNPR-AS1, and LINC00460 was constructed, which may be an independent prognostic predictor for LUAD. The low-risk group had a significant better prognosis and was associated with a higher abundance of resting immune cells and a lower expression of immune checkpoint molecules. Moreover, 105 ceRNA mechanisms were predicted based on the four prognostic lncRNAs. qRT-PCR results showed that LINC00857, SYNPR-AS1, and LINC00460 were significantly highly expressed in tumor tissues, while RBPMS-AS1 was highly expressed in paracancerous tissues.Conclusion: The four angiogenesis-related lncRNAs identified in this study could serve as a promising prognostic biomarker for LUAD patients.
Model for predicting immunotherapy based on M2 macrophage infiltration in TNBC
Authors: Wu Haoming , Feng Jikun , Zhong Wenjing , Zouxu Xiazi , Xiong Zhengchong , Huang Weiling , Zhang Chao , Wang Xi , Yi Jiarong 
Published: March 2023

IntroductionCompared to other types of breast cancer, triple-negative breast cancer (TNBC) does not effectively respond to hormone therapy and HER2 targeted therapy, showing a poor prognosis. There are currently a limited number of immunotherapeutic drugs available for TNBC, a field that requires additional development.MethodsCo-expressing genes with M2 macrophages were analyzed based on the infiltration of M2 macrophages in TNBC and the sequencing data in The Cancer Genome Atlas (TCGA) database. Consequently, the influence of these genes on the prognoses of TNBC patients was analyzed. GO analysis and KEGG analysis were performed for exploring potential signal pathways. Lasso regression analysis was conducted for model construction. The TNBC patients were scored by the model, and patients were divided into high- and low-risk groups. Subsequently, the accuracy of model was further verified using GEO database and patients information from the Cancer Center of Sun Yat-sen University. On this basis, we analyzed the accuracy of prognosis prediction, correlation with immune checkpoint, and immunotherapy drug sensitivity in different groups.ResultsOur findings revealed that OLFML2B, MS4A7, SPARC, POSTN, THY1, and CD300C genes significantly influenced the prognosis of TNBC. Moreover, MS4A7, SPARC, and CD300C were finally determined for model construction, and the model showed good accuracy in prognosis prediction. And 50 immunotherapy drugs with therapeutic significance in different groups were screened, which were assessed possible immunotherapeutics that have potential application and demonstrated the high precision of our prognostic model for predictive analysis.ConclusionMS4A7, SPARC, and CD300C, the three main genes used in our prognostic model, offer good precision and clinical application potential. Fifty immune medications were assessed for their ability to predict immunotherapy drugs, providing a novel approach to immunotherapy for TNBC patients and a more reliable foundation for applying drugs in subsequent treatments.
Seismic airgun sound propagation in shallow water of the East Siberian shelf and its prediction with the measured source signature
Authors: Han Dong-Gyun , Kim Sookwan , Landrø Martin , Son Wuju , Lee Dae Hyeok , Yoon Young Geul , Choi Jee Woong , Yang Eun Jin , Choi Yeonjin , Jin Young Keun , Hong Jong Kuk , Kang Sung-Ho , Rhee Tae Siek , Shin Hyoung Chul , La Hyoung Sul 
Published: March 2023

Seismic airgun sound was measured with an autonomous passive acoustic recorder as a function of distance from 18.6 to 164.2 km in shallow water (&lt;70 m) at the continental shelf of the East Siberian Sea in September 2019. The least-square regression curves were derived in the zero-to-peak sound pressure level, sound exposure level, and band level in a frequency range between 10 and 300 Hz using the initial amplitude scaled from the near-field hydrophone data. In addition, propagation modeling based on the parabolic equation with the measured source spectrum was performed for range-dependent bathymetry, and the results were compared with the band level of the measurements. The sediment structure of the measurement area was a thin layer of iceberg-scoured postglacial mud overlying a fast bottom with high density based on grounding events of past ice masses. The observed precursor arrivals, modal dispersion, and rapid decrease in spectrum level at low frequencies can be explained by the condition of the high-velocity sediment. Our results can be applied to studies on the inversion of ocean boundary conditions and measurement geometry and basic data for noise impact assessment.
Rhizosphere microbial community assembly and association networks strongly differ based on vegetation type at a local environment scale
Authors: Liu Luxian , Ma Liya , Zhu Mengmeng , Liu Bo , Liu Xu , Shi Yu 
Published: March 2023

IntroductionRhizosphere microbes perform critical functions for their hosts, and their structure is strongly influenced by vegetation type. Although studies on the effects of vegetation on rhizosphere microbial community structure have been conducted at large and global environment scales, studies at local environment scales would eliminate numerous external factors such as climate and soil type, while highlighting the potential influence of local vegetation type.MethodsHere, we compared rhizosphere microbial communities using 54 samples under three vegetation types (herb, shrubs, and arbors, with bulk soil as the control) at the campus of Henan University. 16S rRNA and ITS amplicons were sequenced using Illumina high throughput sequencing.Results and DiscussionRhizosphere bacterial and fungal community structures were influenced considerably by vegetation type. Bacterial alpha diversity under herbs was significantly different from that under arbors and shrubs. The abundance of phyla such as Actinobacteria was extremely higher in bulk soil than in the rhizosphere soils. Herb rhizosphere harbored more unique species than other vegetation type soils. Furthermore, bacterial community assembly in bulk soil was more dominated by deterministic process, whereas the rhizosphere bacterial community assembly was dominated by stochasticity and the construction of fungal communities was all dominated by deterministic processes. In addition, rhizosphere microbial networks were less complex than bulk soil networks, and their keystone species differed based on vegetation type. Notably, bacterial community dissimilarities were strongly correlated with plant phylogenetic distance. Exploring rhizosphere microbial community patterns under different vegetation types could enhance our understanding of the role of rhizosphere microbes in ecosystem function and service provision, as well as basic information that could facilitate plant and microbial diversity conservation at the local environment scale.
Accuracy-speed-stability trade-offs in a targeted stepping task are similar in young and older adults
Authors: Muijres Wouter , Arnalsteen Sylvie , Daenens Cas , Afschrift Maarten , De Groote Friedl 
Published: March 2023

IntroductionStepping accuracy, speed, and stability are lower in older compared to young adults. Lower stepping performance in older adults may be due to larger accuracy-speed-stability trade-offs because of reduced ability to simultaneously fulfill these task-level goals. Our goal was to evaluate whether trade-offs are larger in older compared to young adults in a targeted stepping task. Since sensorimotor function declines with age, our secondary goal was to evaluate whether poorer sensorimotor function was associated with larger trade-offs.MethodsTwenty-five young (median 22 years old) and 25 older (median 70 years old) adults stepped into projected targets in conditions with various levels of accuracy, speed, and stability requirements. We determined trade-offs as the change in performance, i.e., foot placement error, step duration, and mediolateral center of pressure path length, between each of these conditions and a control condition. To assess age-related differences in the magnitude of trade-offs, we compared the change in performance between age groups. Associations between trade-offs and measures of sensorimotor function were tested using correlations.ResultsWe found an accuracy-speed and an accuracy-stability trade-off in both young and older adults, but trade-offs were not different between young and older adults. Inter-subject differences in sensorimotor function could not explain inter-subject differences in trade-offs.ConclusionAge-related differences in the ability to combine task-level goals do not explain why older adults stepped less accurate and less stable than young adults. However, lower stability combined with an age-independent accuracy-stability trade-off could explain lower accuracy in older adults.
Differences in clinical and biological factors between patients with PFO-related stroke and patients with PFO and no cerebral vascular events
Authors: Badea Raluca Ştefania , Ribigan Athena Cristina , Grecu Nicolae , Terecoasǎ Elena , Antochi Florina Anca , Bâldea Mihǎilǎ Sorina , Tiu Cristina , Popescu Bogdan Ovidiu 
Published: March 2023

BackgroundWhile stroke is one of the most dissected topics in neurology, the primary prevention of PFO-related stroke in young patients is still an unaddressed subject. We present a study concerning clinical, demographic, and laboratory factors associated with stroke and transient ischemic attack in patients with patent foramen ovale (PFO), as well as comparing PFO-patients with and without cerebrovascular ischemic events (CVEs).Patients and methodsConsecutive patients with PFO-associated CVEs were included in the study; control group was selected from patients with a PFO and no history of stroke. All participants underwent peripheral routine blood analyses, as well as, on treating physician's recommendations, screening for thrombophilia.ResultsNinety-five patients with CVEs and 41 controls were included. Females had a significantly lower risk of CVEs than males (p = 0.04). PFO size was similar between patients and controls. Patients with CVEs had more often hypertension (n = 33, 34.7%), p = 0.007. No significant differences were found between the two groups with regard to routine laboratory tests and thrombophilia status. Hypertension and gender were identified in a binomial logistic regression model as independent predictors for CVEs, but with an area under the ROC curve of 0.531, suggesting a very poor level of discrimination between the two groups.Discussion and conclusionsThere is little difference between patients with PFO with and without CVEs in terms of PFO size and routine laboratory analyses. While still a controversial topic in the specialty literature, classic first-level thrombophilic mutations are not a risk factor for stroke in patients with PFO. Hypertension and male gender were identified as factors associated with a higher risk of stroke in the setting of PFO.
The immediate effects of iTBS on the muscle activation pattern under challenging balance conditions in the patients with chronic low back pain: A preliminary study
Authors: Yang Jiajia , Fu Ruochen , Hao Zengming , Lin Nanhe , Cheng Xue , Ma Jinjin , Zhang Yushu , Li Yan , Lo Wai Leung Ambrose , Yu Qiuhua , Wang Chuhuai 
Published: March 2023

BackgroundThe patients with chronic low back pain (CLBP) showed impaired postural control, especially in challenging postural task. The dorsolateral prefrontal cortex (DLPFC) is reported to involve in the complex balance task, which required considerable attentional control. The effect of intermittent theta burst stimulation (iTBS) over the DLPFC to the capacity of postural control of CLBP patients is still unknown.MethodsParticipants diagnosed with CLBP received a single-session iTBS over the left DLPFC. All the participants completed the postural control tasks of single-leg (left/right) standing before and after iTBS. The activation changes of the DLPFC and M1 before and after iTBS were recorded by functional near-infrared spectroscopy (fNIRS). The activation pattern of the trunk [transversus abdominis (TrA), superficial lumbar multifidus (SLM)] and leg [tibialis anterior (TA), gastrocnemius medialis (GM)] muscles including root mean square (RMS) and co-contraction index (CCI) during single-leg standing were measured by surface electromyography (sEMG) before and after the intervention. The paired t-test was used to test the difference before and after iTBS. Pearson correlation analyses were performed to test the relationship between the oxyhemoglobin concentration and sEMG outcome variables (RMS and CCI).ResultsOverall, 20 participants were recruited. In the right-leg standing condition, compared with before iTBS, the CCI of the right TrA/SLM was significantly decreased (t = −2.172, p = 0.043), and the RMS of the right GM was significantly increased (t = 4.024, p = 0.001) after iTBS. The activation of the left DLPFC (t = 2.783, p = 0.012) and left M1 (t = 2.752, p = 0.013) were significantly decreased and the relationship between the left DLPFC and M1 was significant after iTBS (r = 0.575, p = 0.014). Correlation analysis showed the hemoglobin concentration of M1 was negatively correlated with the RMS of the right GM (r = −0.659, p = 0.03) and positively correlated between CCI of the right TrA/SLM (r = 0.503, p = 0.047) after iTBS. There was no significant difference in the brain or muscle activation change in the left leg-standing condition between before and after iTBS.ConclusionIntermittent theta burst stimulation over the left DLPFC seems to be able to improve the muscle activation pattern during postural control ability in challenging postural task, which would provide a new approach to the treatment of CLBP.
Acute effects of fresh versus dried Hayward green kiwifruit on sleep quality, mood, and sleep-related urinary metabolites in healthy young men with good and poor sleep quality
Authors: Kanon Alexander P. , Giezenaar Caroline , Roy Nicole C. , McNabb Warren C. , Henare Sharon J. 
Published: March 2023

Background and aimsDaily kiwifruit (KF) consumption has been associated with improved sleep quality, but underlying physiological mechanisms are unknown. This study examined acute effects of fresh and dried green KF, compared with a water control, on sleep quality, mood, and urinary serotonin and melatonin metabolite concentrations.Methods24 men (age: 29 ± 1 years, body mass index: 24 ± 1 kg/m2) with poor (n = 12) or good (n = 12) sleep quality participated in a randomized, single-blind crossover study. One of three treatments was consumed with a standardized evening meal; (1) the flesh of two fresh green KF, (2) dried green KF powder (including skin; equivalent to dry matter of two fresh KF) mixed with water, or (3) a water control, in their own home. Subjective and objective sleep quality, mood, waking urinary 5-hydroxyindoleacetic acid (5-HIAA), 6-sulfatoxymelatonin (aMT6s), vitamin C and B-vitamin concentrations were determined.ResultsRegardless of sleep quality group, compared to control, morning sleepiness, alertness upon awakening, and vigor were improved (p &lt; 0.05) after dried KF consumption. Compared to control, both fresh and dried KF treatments tended (p &lt; 0.1) toward improved esteem and total mood disturbance. Both KF treatments increased (fresh +1.56 ± 0.4 ng/g, p = 0.001; dried: +1.30 ± 0.4 ng/g, p = 0.004) urinary concentration of the serotonin metabolite 5-HIAA compared to the control (4.32 ± 0.4 ng/g). In poor sleepers, ease of awakening improved by 24% after dried KF consumption (p = 0.005) and tended to improve by 13% after fresh KF intake (p = 0.052) compared to the control. Good sleepers tended toward 9% improved ratings of getting to sleep with fresh KF (p = 0.053) compared to the control. Poor sleepers had lower amounts of some B-vitamins compared to good sleepers (p &lt; 0.05).ConclusionConsumption of dried or fresh KF with a standard evening meal, was associated with improved aspects of sleep quality and mood, possibly mediated through changes in serotonin metabolism.Clinical trial registration[www.anzctr.org.au], identifier [ACTRN12621000046808].Graphical Abstract
Compositional analysis of natural pomegranate peel powder dried by different methods and nutritional and sensory evaluation of cookies fortified with pomegranate peel powder
Authors: Muhammad Ali , Dayisoylu Kenan Sinan , Pei Jinjin , Khan Muhammad Rafiullah , Salman Muhammad , Ahmad Rafiq , Ullah Hakim , Noor Gul Rah 
Published: March 2023

IntroductionFortification of cereal products with natural plant extract is an interesting approach to fulfill the dietary requirement of the people.Materials and methodsPeels of pomegranate (rich source of natural compounds) were cut into small pieces and dried in three different methods such as solar drying (SOD), oven drying (OD), and sun drying (SUD). The fine powder was prepared and proximate compositions (protein, ash, moisture, fats, fiber, and carbohydrates), minerals (zinc, iron, calcium, and potassium), total phenolic content (TPC), total flavonoid content (TFC), and antioxidant activity (DPPH) of the pomegranate peel powder (PP) were evaluated. Fine wheat flour (FWF) was fortified with different concentrations (3, 6, 8, 10, and 12 g) of PP powder, cookies were prepared and all the above analysis along with physical parameters (weight, width, thickness, spread ration) and sensory analysis were conducted. Cookies without PP powder were served as control.Results and discussionResults showed that a SOD was the best for drying PP powder in terms of compositional analysis. Addition of PP powder significantly (P &lt; 0.05) enhanced the nutritional value, minerals profile and physical attributes of the fortified cookies. Sensory analysis of fortified cookies indicated that the cookies were acceptable to the sensory panel. Therefore, in conclusion, PP powder dried by SOD method could be used commercially in baking industries to provide nutritional enriched cookies to fulfill the dietary requirements of the people.
Multifactor dimensionality reduction method identifies novel SNP interactions in the WNT protein interaction networks that are associated with recurrence risk in colorectal cancer
Authors: Curtis Aaron A. , Yu Yajun , Carey Megan , Parfrey Patrick , Yilmaz Yildiz E. , Savas Sevtap 
Published: March 2023

BackgroundInteractions among genetic variants are rarely studied but may explain a part of the variability in patient outcomes.ObjectivesIn this study, we aimed to identify 1 to 3 way interactions among SNPs from five Wnt protein interaction networks that predict the 5-year recurrence risk in a cohort of stage I-III colorectal cancer patients.Methods423 patients recruited to the Newfoundland Familial Colorectal Cancer Registry were included. Five Wnt family member proteins (Wnt1, Wnt2, Wnt5a, Wnt5b, and Wnt11) were selected. The BioGRID database was used to identify the proteins interacting with each of these proteins. Genotypes of the SNPs located in the interaction network genes were retrieved from a genome-wide SNP genotype data previously obtained in the patient cohort. The GMDR 0.9 program was utilized to examine 1-, 2-, and 3-SNP interactions using a 5-fold cross validation step. Top GMDR 0.9 models were assessed by permutation testing and, if significant, prognostic associations were verified by multivariable logistic regression models.ResultsGMDR 0.9 has identified novel 1, 2, and 3-way SNP interactions associated with 5-year recurrence risk in colorectal cancer. Nine of these interactions were multi loci interactions (2-way or 3-way). Identified interaction models were able to distinguish patients based on their 5-year recurrence-free status in multivariable regression models. The significance of interactions was the highest in the 3-SNP models. Several of the identified SNPs were eQTLs, indicating potential biological roles of the genes they were associated with in colorectal cancer recurrence.ConclusionsWe identified novel interacting genetic variants that associate with 5-year recurrence risk in colorectal cancer. A significant portion of the genes identified were previously linked to colorectal cancer pathogenesis or progression. These variants and genes are of interest for future functional and prognostic studies. Our results provide further evidence for the utility of GMDR models in identifying novel prognostic biomarkers and the biological importance of the Wnt pathways in colorectal cancer.
Anomaly detection in radiotherapy plans using deep autoencoder networks
Authors: Huang Peng , Shang Jiawen , Xu Yingjie , Hu Zhihui , Zhang Ke , Dai Jianrong , Yan Hui 
Published: March 2023

PurposeTreatment plans are used for patients under radiotherapy in clinics. Before execution, these plans are checked for safety and quality by human experts. A few of them were identified with flaws and needed further improvement. To automate this checking process, an unsupervised learning method based on an autoencoder was proposed.MethodsFirst, features were extracted from the treatment plan by human experts. Then, these features were assembled and used for model learning. After network optimization, a reconstruction error between the predicted and target signals was obtained. Finally, the questionable plans were identified based on the value of the reconstruction error. A large value of the reconstruction error indicates a longer distance from the standard distribution of normal plans. A total of 576 treatment plans for breast cancer patients were used for the test. Among them, 19 were questionable plans identified by human experts. To evaluate the performance of the autoencoder, it was compared with four baseline detection algorithms, namely, local outlier factor (LOF), hierarchical density-based spatial clustering of applications with noise (HDBSCAN), one-class support vector machine (OC-SVM), and principal component analysis (PCA).ResultsThe results showed that the autoencoder achieved the best performance than the other four baseline algorithms. The AUC value of the autoencoder was 0.9985, while the second one was 0.9535 (LOF). While maintaining 100% recall, the average accuracy and precision of the results by the autoencoder were 0.9658 and 0.5143, respectively. While maintaining 100% recall, the average accuracy and precision of the results by LOF were 0.8090 and 0.1472, respectively.ConclusionThe autoencoder can effectively identify questionable plans from a large group of normal plans. There is no need to label the data and prepare the training data for model learning. The autoencoder provides an effective way to carry out an automatic plan checking in radiotherapy.