bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative physiological and transcriptome analysis in cultivated and wild sugarcane species in response to hydrogen peroxide-induced oxidative stress
Authors: Manimekalai R. , Selvi A , Narayanan Jini , Vannish Ram , Shalini R. , Gayathri S , Rabisha V.P 
Published: March 2023

AbstractBackgroundSugarcane is an important energy crop grown worldwide,supplementing various renewable energy sources. Cultivated and wild sugarcane species respond differently to biotic and abiotic stresses. Generally, wild species are tolerant to various abiotic stresses. In the present study, the physiological and molecular responses of cultivated and wild sugarcane species to oxidative stress at the transcriptional levels were compared. Transcriptional responses were determined using RNAseq. The representative RNA-seq transcript values were validated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and confirmed through physiological responses.ResultsOxidative stress causes leaf-rolling and -tip drying in cultivated sugarcane, but the wild species are tolerant. Higher chlorophyll fluorescence was observed in the wild species than that in the cultivated varieties under stress. Wild species can maintain a higher chlorophyll stability index than the cultivated species, which was confirmed by the lower transcripts of the chlorophyllase gene in the wild species than that in the cultivated variety. Transcription factor genes (NAC,MYB, andWRKY) were markedly expressed in response to oxidative stress, revealing their involvement in stress tolerance. The analysis revealed synchronized expression of acetyl-transferase, histone2A, cellulose synthase, and secondary cell wall biosynthetic genes in the wild species. The validation of selected genes and 15 NAC transcription factors using RT-qPCR revealed that their expression profiles were strongly correlated with RNA-seq. To the best of our knowledge, this is the first report on the oxidative stress response in cultivated and wild sugarcane species.ConclusionPhysiological and biochemical changes in response to oxidative stress markedly differ between cultivated and wild sugarcane species. The differentially expressed stress-responsive genes are grouped intothe response to oxidative stress, heme-binding, peroxidase activity, and metal ion binding categories. Chlorophyll maintenance is a stress tolerance response enhanced by the differential regulation of the chlorophyllase gene.There is a considerable difference in the chlorophyll stability index between wild and cultivated varieties. We observed a substantial regulation of secondary wall biosynthesis genes in the wild species compared with that in the cultivated variety, suggesting differences in stress tolerance mechanisms.
Genome-wide identification of RNA modification-related single nucleotide polymorphisms associated with rheumatoid arthritis
Authors: Wang Mimi , Wu Jingyun , Lei Shufeng , Mo Xingbo 
Published: March 2023

Abstract
Background
RNA modification plays important roles in many biological processes, such as gene expression control. The aim of this study was to identify single nucleotide polymorphisms related to RNA modification (RNAm-SNPs) for rheumatoid arthritis (RA) as putative functional variants.

Methods
We examined the association of RNAm-SNPs with RA in summary data from a genome-wide association study of 19,234 RA cases and 61,565 controls. We performed eQTL and pQTL analyses for the RNAm-SNPs to find associated gene expression and protein levels. Furthermore, we examined the associations of gene expression and circulating protein levels with RA using two-sample Mendelian randomization analysis methods.

Results
A total of 160 RNAm-SNPs related to m6A, m1A, A-to-I, m7G, m5C, m5U and m6Am modifications were identified to be significantly associated with RA. These RNAm-SNPs were located in 62 protein-coding genes, which were significantly enriched in immune-related pathways. RNAm-SNPs in important RA susceptibility genes, such as PADI2, SPRED2, PLCL2, HLA-A, HLA-B, HLA-DRB1, HLA-DPB1, TRAF1 and TXNDC11, were identified. Most of these RNAm-SNPs showed eQTL effects, and the expression levels of 26 of the modifiable genes (e.g., PADI2, TRAF1, HLA-A, HLA-DRB1, HLA-DPB1 and HLA-B) in blood cells were associated with RA. Circulating protein levels, such as CFB, GZMA, HLA-DQA2, IL21, LRPAP1 and TFF3, were affected by RNAm-SNPs and were associated with RA.

Conclusion
The present study identified RNAm-SNPs in the reported RA susceptibility genes and suggested that RNAm-SNPs may affect RA risk by affecting the expression levels of corresponding genes and proteins.
Single-cell transcriptome analysis and in vitro differentiation of testicular cells reveal novel insights into male sterility of the interspecific hybrid cattle-yak
Authors: Mipam TserangDonko , Chen Xuemei , Zhao Wangsheng , Zhang Peng , Chai Zhixin , Yue Binglin , Luo Hui , Wang Jikun , Wang Haibo , Wu Zhijuan , Wang Jiabo , Wang Mingxiu , Wang Hui , Zhang Ming , Wang Hongying , Jing Kemin , Zhong Jincheng , Cai Xin 
Published: March 2023

Abstract
Background
Interspecific hybridization plays vital roles in enriching animal diversity, while male hybrid sterility (MHS) of the offspring commonly suffered from spermatogenic arrest constitutes the postzygotic reproductive isolation. Cattle-yak, the hybrid offspring of cattle (Bos taurus) and yak (Bos grunniens) can serve as an ideal MHS animal model. Although meiotic arrest was found to contribute to MHS of cattle-yak, yet the cellular characteristics and developmental potentials of male germline cell in pubertal cattle-yak remain to be systematically investigated.

Results
Single-cell RNA-seq analysis of germline and niche cell types in pubertal testis of cattle-yak and yak indicated that dynamic gene expression of developmental germ cells was terminated at late primary spermatocyte (meiotic arrest) and abnormal components of niche cell in pubertal cattle-yak. Further in vitro proliferation and differentially expressed gene (DEG) analysis of specific type of cells revealed that undifferentiated spermatogonia of cattle-yak exhibited defects in viability and proliferation/differentiation potentials.

Conclusion
Comparative scRNA-seq and in vitro proliferation analysis of testicular cells indicated that not only meiotic arrest contributed to MHS of cattle-yak. Spermatogenic arrest of cattle-yak may originate from the differentiation stage of undifferentiated spermatogonia and niche cells of cattle-yak may provide an adverse microenvironment for spermatogenesis.
The characteristics of elevated blood pressure in abdominal obesity correspond to primary hypertension: a cross-sectional study
Authors: Taurio Jyrki , Hautaniemi Elina J. , Koskela Jenni K. , Eräranta Arttu , Hämäläinen Mari , Tikkakoski Antti , Kettunen Jarkko A. , Kähönen Mika , Niemelä Onni , Moilanen Eeva , Mustonen Jukka , Pörsti Ilkka 
Published: March 2023

Abstract
Background
Obesity-related hypertension and the associated metabolic abnormalities are considered as a distinct hypertensive phenotype. Here we examined how abdominal fat content, as judged by waist:height ratio, influenced blood pressure and hemodynamic profile in normotensive subjects and never-treated hypertensive patients.

Methods
The 541 participants (20–72 years) underwent physical examination and laboratory analyses and were divided into age and sex-adjusted quartiles of waist:height ratio. Supine hemodynamics were recorded using whole-body impedance cardiography, combined with analyses of radial tonometric pulse wave form and heart rate variability.

Results
Mean waist:height ratios in the quartiles were 0.46, 0.51, 0.55 and 0.62. Radial and aortic blood pressure, systemic vascular resistance, pulse wave velocity, markers of glucose and lipid metabolism, leptin levels and C-reactive protein were higher in quartile 4 when compared with quartiles 1 and 2 (p < 0.05 for all). Cardiac index was lower in quartile 4 versus quartile 1, while no differences were seen in heart rate variability, augmentation index, plasma renin activity, and aldosterone concentration between the quartiles. Linear regression analyses showed independent associations of abdominal obesity with higher aortic systolic and diastolic blood pressure, systemic vascular resistance, and pulse wave velocity (p < 0.05 for waist:height ratio in all regression models).

Conclusion
Higher waist:height ratio was associated with elevated blood pressure, systemic vascular resistance, and arterial stiffness, but not with alterations in cardiac sympathovagal modulation or activation of the circulating renin-angiotensin-aldosterone system. Although obesity-related elevation of blood pressure has distinct phenotypic features, these results suggest that its main characteristics correspond those of primary hypertension.

Trial registration
ClinicalTrails.gov NCT01742702 (date of registration 5th December 2012).
Lower attenuation and higher kurtosis of coronary artery calcification associated with vulnerable plaque – an agatston score propensity-matched CT radiomics study
Authors: Huang Eric Po-Yu , Lin Huey-Shyan , Chen Yi-Chun , Li Yi-He , Huang Yi-Luan , Ju Yu-Jeng , Yu Hsien-Chung , Kicska Gregory A. , Wu Ming-Ting 
Published: March 2023

Abstract
Background
Coronary artery calcification (CAC) burden assessed by Agatston score (AS) is currently recommended to stratify patients at risk for future acute coronary syndrome (ACS). Besides the CAC burden, the biostructure of CAC may also play a vital role in the vulnerability of CAC, which CT radiomics could reveal. Propensity-score matching of the traditional risk factors and CAC burden between the ACS and asymptomatic groups could radically remove biases and allow the exploration of characteristic features of CAC in ACS.

Methods
We retrospectively identified 77 patients with ACS who had a CAC scan before percutaneous coronary intervention between 2016 and 2019. These 77 patients were one-to-two propensity-score matched for traditional risk factors of ACS and AS ranks to select 154 subjects from 2890 asymptomatic subjects. A validation cohort of 30 subjects was also enrolled. Radiomics features of each plaque were extracted and averaged in each person. Conditional logistic regression and area-under-curve analysis were used for statistical analysis.

Results
A higher number of coronary segments involved, lower mean, median, first quartile, and standard deviation of attenuation, and increased kurtosis of attenuation of CAC were associated with the ACS group compared to the control group (p < 0.05 for all). Multivariable analysis showed that the lower median attenuation (OR = 0.969, p < 0.001) and higher Kurtosis (OR = 18.7, p < 0.001) were associated with the ACS group. The median attenuation and kurtosis significantly increase across AS ranks 1 to 4 (p = 0.001). The AUC of kurtosis (0.727) and median attenuation (0.66) were both significantly higher than that of the standard AS (AUC = 0.502) and the number of TRF (AUC = 0.537). The best cut-off of kurtosis at 2.74 yielded an accuracy of 74%, and the cut-off of median attenuation at 196 yielded an accuracy of 68%. The accuracy of kurtosis was 64%, and the accuracy of median attenuation was 55% in the validation cohort.

Conclusion
After propensity-matching traditional risk factors and CAC burden, CT radiomics highlighted that lower median attenuation and higher kurtosis were the CAC characteristics of vulnerable plaques. These features improve the understanding of the biomechanics of CAC evolution and enhance the value of CAC scan in ACS risk assessment.
Time-resolved simulation of blood flow through left anterior descending coronary artery: effect of varying extent of stenosis on hemodynamics
Authors: Zhao Yinghong , Wang Huihui , Chen Wenbing , Sun Wenyue , Yu Xianchao , Sun Cunjie , Hua Gang 
Published: March 2023

Abstract
Background and objectives
Real-time blood flow variation is crucial for understanding the dynamic development of coronary atherosclerosis. The main objective of this study is to investigate the effect of varying extent of stenosis on the hemodynamic features in left anterior descending coronary artery.

Methods
Various Computational fluid dynamics (CFD) models were constructed with patient-specific CT image data, using actual fractional flow reserve (FFR) as boundary conditions to provide a real-time quantitative description of hemodynamic properties. The hemodynamic parameters, such as the local and instantaneous wall shear stress (WSS), oscillating shear index (OSI) and relative residence time (RRT), blood flow velocity and pressure drop during various phases of cardiac cycle were provided in detail.

Results
There was no evident variation in hemodynamic parameters in the cases of less than 50% stenosis while there were abrupt and dramatic changes in hemodynamics when the stenosis aggravated from 60 to 70%. Furthermore, when the stenosis was beyond 70%, there existed substantial pressure difference, WSS, and blood flow velocity in the center of the stenosis. Although OSI and RRT increased along with the aggravation of stenosis, they appeared with obvious abnormalities across all cases, even in mild stenosis.

Conclusion
The simulation could present a dynamic and comprehensive profile of how hemodynamic parameters vary in accordance with divergent severities of stenosis, which could serve as an effective reference for the clinicians to have a deeper insight into the pathological mechanism of coronary atherosclerosis and stenosis.
Statistical methods for exploring spontaneous adverse event reporting databases for drug-host factor interactions
Authors: Lu Zhiyuan , Suzuki Ayako , Wang Dong 
Published: March 2023

AbstractBackgroundDrug toxicity does not affect patients equally; the toxicity may only exert in patients who possess certain attributes of susceptibility to specific drug properties (i.e., drug-host interaction). This concept is crucial for personalized drug safety but remains under-studied, primarily due to methodological challenges and limited data availability. By monitoring a large volume of adverse event reports in the postmarket stage, spontaneous adverse event reporting systems provide an unparalleled resource of information for adverse events and could be utilized to explore risk disparities of specific adverse events by age, sex, and other host factors. However, well-formulated statistical methods to formally address such risk disparities are currently lacking.MethodsIn this paper, we present a statistical framework to explore spontaneous adverse event reporting databases for drug-host interactions and detect risk disparities in adverse drug events by various host factors, adapting methods for safety signal detection. We proposed four different methods, including likelihood ratio test, normal approximation test, and two tests using subgroup ratios. We applied our proposed methods to simulated data and Food and Drug Administration (FDA) Adverse Event Reporting Systems (FAERS) and explored sex-/age-disparities in reported liver events associated with specific drug classes.ResultsThe simulation result demonstrates that two tests (likelihood ratio, normal approximation) can detect disparities in adverse drug events associated with host factors while controlling the family wise error rate. Application to real data on drug liver toxicity shows that the proposed method can be used to detect drugs with unusually high level of disparity regarding a host factor (sex or age) for liver toxicity or to determine whether an adverse event demonstrates a significant unbalance regarding the host factor relative to other events for the drug.ConclusionThough spontaneous adverse event reporting databases require careful data processing and inference, the sheer size of the databases with diverse data from different countries provides unique resources for exploring various questions for drug safety that are otherwise impossible to address. Our proposed methods can be used to facilitate future investigation on drug-host interactions in drug toxicity using a large number of reported adverse events.
A novel predictive model of microvascular invasion in hepatocellular carcinoma based on differential protein expression
Authors: Wang Zhenglu , Cao Lei , Wang Jianxi , Wang Hanlin , Ma Tingting , Yin Zhiqi , Cai Wenjuan , Liu Lei , Liu Tao , Ma Hengde , Zhang Yamin , Shen Zhongyang , Zheng Hong 
Published: March 2023

Abstract
Background
This study aims to construct and verify a nomogram model for microvascular invasion (MVI) based on hepatocellular carcinoma (HCC) tumor characteristics and differential protein expressions, and explore the clinical application value of the prediction model.

Methods
The clinicopathological data of 200 HCC patients were collected and randomly divided into training set and validation set according to the ratio of 7:3. The correlation between MVI occurrence and primary disease, age, gender, tumor size, tumor stage, and immunohistochemical characteristics of 13 proteins, including GPC3, CK19 and vimentin, were statistically analyzed. Univariate and multivariate analyzes identified risk factors and independent risk factors, respectively. A nomogram model that can be used to predict the presence of MVI was subsequently constructed. Then, receiver operating characteristic (ROC) curve, calibration curve, and decision curve analysis (DCA) were conducted to assess the performance of the model.

Results
Multivariate logistic regression analysis indicated that tumor size, GPC3, P53, RRM1, BRCA1, and ARG were independent risk factors for MVI. A nomogram was constructed based on the above six predictors. ROC curve, calibration, and DCA analysis demonstrated the good performance and the clinical application potential of the nomogram model.

Conclusions
The predictive model constructed based on the clinical characteristics of HCC tumors and differential protein expression patterns could be helpful to improve the accuracy of MVI diagnosis in HCC patients.
Older adult communication types and emotional well-being outcomes during COVID-19 pandemic
Authors: Cone Nicholas , Lee Jeong Eun 
Published: March 2023

Abstract
Background:
The rationale for the present study is a result of the COVID-19 pandemic, as there are fewer opportunities available for older adults to engage in face-to-face interaction and social activities, which may result in changes in the communication methods with their social contacts. The purpose of this study was to explore the relationship between methods of social connectedness and emotional well-being outcomes among older adults at the start of the pandemic.

Methods:
Two thousand five hundred and fifty-eight older adults Medicare beneficiaries (65 + years of age) in the National Health and Aging Trends Study at wave 10 (June 2020 to January 2021) were selected for cross-sectional analysis. Participants were measured on brief questionnaires regarding forms of communication with family and friends before and during the pandemic. Emotional well-being outcomes were measured on single items of sadness/depressed and loneliness; as well as a 6-item Likert scale of anxiety during the pandemic. Paired sample t-tests were utilized to examine the forms of communication between before and during pandemic. Hierarchical regressions were conducted to assess the relationship between forms of communication and emotional well-being outcomes.

Results:
We found that there were overall decreases in communication frequency during pandemic. Findings from regression analyses indicated information communication technology (ICT) are associated with negative emotional well-being outcomes, whereas in-person social contact are associated with lower levels of negative affect.

Conclusion:
These findings suggest utilizing higher levels of ICT has negative implications for older adults’ emotional well-being, contrasting with the positive implication of in-person contacts. These findings highlight the role of ICT in emotional well-being among older adults during pandemic.
Effectiveness of auricular acupressure on constipation and related quality of life among the older people in the residential care home: a randomized clinical trial
Authors: Aminizadeh Mahdi , Tirgari Batool , Rashtabadi Omsalimeh Roudi , Jahani Yunes , Tajadini Haleh 
Published: March 2023

Abstract
Introduction
Constipation can be one of the biggest health problems for the older people that has negative effects on their quality of life. Some studies have reported that new non-pharmacological interventions such auricular acupressure have promising results in the management of constipation. This study was performed to investigate the effect of auricular acupressure on constipation and health-related quality of life in the older people living in the residential care home.

Methods
Sample of this randomized clinical trial consisted of 53 older people with chronic constipation living in a residential care home in the southeast of Iran (Kerman city). The participants were randomly assigned to intervention (n = 27) and control (n = 26) groups. Auricular acupressure was applied to seven auricular acupoints (large intestine, rectum, San Jiao, spleen, lung, sympathetic, and subcortex) using Vaccaria seeds for the intervention group and for the control group, seedless auricular plasters were used at the seven auricular acupoints for 10 days. Data were collected before the intervention, end of the intervention, and 10-day follow-up using demographic and clinical, Patient Assessment of Constipation-Symptom, and Patient Assessment of Constipation-Quality of Life questionnaires. The SPSS-22 software was used for data analysis.

Results
The difference between groups and times was significant in constipation and related quality of life and scores. The mean score of constipation at the end of intervention was 0.41 less in the intervention group than the control group (P < 0.0001). This mean score, in the intervention group also on the 10-day follow-up was 0.09 less than the control group (P = 0.004), which indicates a decrease in the severity of constipation symptoms. In the intervention group, mean score of quality of life related to constipation at the end of intervention and the 10-day follow-up was 0.56 and 0.19 less than the control group (Decrease in the mean score of quality of life related to constipation indicates an improvement in the quality of life) (P < 0.0001).

Conclusion
The results showed the positive effect of auricular acupressure on reducing the severity of constipation symptoms and improving the quality of life in old patients living in the residential care home. This non-pharmaceutical practice can be used by nurses as an inexpensive, safe, acceptable, and non-invasive nursing care for older people with constipation in homes, medical centers, or nursing homes.