bluuebunny/crossref_metadata_2025_split huggingface dataset:
CD44 promotes angiogenesis in myocardial infarction through regulating plasma exosome uptake and further enhancing FGFR2 signaling transduction
Authors: Zhang Qing , Chen Li , Huang Liyi , Cheng Hongxin , Wang Lu , Xu Lin , Hu Danrong , He Chengqi , Fu Chenying , Wei Quan 
Published: December 2022

Abstract
Background
Since angiogenesis occurs as the pathological process following myocardial infarction to alleviate ischemia, therapeutic angiogenesis has been proposed to be a cardioprotective strategy. CD44 has been implicated in endothelial cell functions and its role has been well established in angiogenesis for years. Although recent studies indicate the close correlation between CD44 and exosome, as well as the two being implicated in myocardial ischemia pathological processes, the effect and the underlying mechanism of CD44 and its regulated plasma exosome in pathological angiogenesis post-myocardial infarction have not been fully elucidated.

Methods
In this study, we used CD44 knockout mice to study the in vivo impacts of CD44 on ischemic angiogenesis in myocardial infarction. Mouse cardiac function was measured by echocardiography, histological changes were observed by Evans Blue and TTC-double staining and Masson’s trichrome staining, and molecular changes were detected by immunofluorescence. In the in vitro study, CD44 knockout HUVECs were generated and CD44 inhibitor was used to study the mechanism of CD44 on angiogenesis. We performed the immunoprecipitation, proximity ligation assay, and super-resolution imaging to study the mechanistic regulation of FGFR2 signaling transduction by CD44. Importantly, we also isolated plasma exosomes from myocardial infarction model mice and studied the effect of plasma exosomes on the activation of the FGFR2 signaling pathway and the related phenotypic alterations, including exosomes uptake and angiogenic function in primary mouse microvascular endothelial cells, and further discovered the regulation mechanism of exosomal miRNAs.

Results
We observed that the expression of CD44 in the border zone of the infarcted heart was tightly related to pathological angiogenesis following myocardial ischemia. The depletion of CD44 impaired angiogenesis and impacts biogenesis and proangiogenic function of plasma exosomes. Subsequently, we found that CD44 mediated the activation of the FGFR2 signaling pathway as well as the caveolin 1-dependent uptake of exosomes in vascular endothelial cells. Most importantly, the proangiogenic therapeutic effect of plasma exosomal miRNAs depended upon the participation of CD44/FGFR2 signaling transduction in vascular endothelial cells.

Conclusion
CD44 and its regulated plasma exosomes have crucial potent angiogenic activity. Our studies elucidate that CD44 plays a key role in plasma exosomal miRNA-enhanced angiogenic FGFR2 singling transduction and ischemic angiogenesis in the early stage of myocardial infarction.
Relative Varying Dynamics Based Whole Cutting Process Optimization for Thin-walled Parts
Authors: Tang Yuyang , Zhang Jun , Yin Jia , Bai Lele , Zhang Huijie , Zhao Wanhua 
Published: December 2022

AbstractThin-walled parts are typically difficult-to-cut components due to the complex dynamics in cutting process. The dynamics is variant for part during machining, but invariant for machine tool. The variation of the relative dynamics results in the difference of cutting stage division and cutting parameter selection. This paper develops a novel method for whole cutting process optimization based on the relative varying dynamic characteristic of machining system. A new strategy to distinguish cutting stages depending on the dominated dynamics during machining process is proposed, and a thickness-dependent model to predict the dynamics of part is developed. Optimal cutting parameters change with stages, which can be divided by the critical thickness of part. Based on the dynamics comparison between machine tool and thickness-varying part, the critical thicknesses are predicted by an iterative algorithm. The proposed method is validated by the machining of three benchmarks. Good agreements have been obtained between prediction and experimental results in terms of stages identification, meanwhile, the optimized parameters perform well during the whole cutting process.
The PPR-Domain Protein SOAR1 Regulates Salt Tolerance in Rice
Authors: Lu Kai , Li Cheng , Guan Ju , Liang Wen-Hua , Chen Tao , Zhao Qing-Yong , Zhu Zhen , Yao Shu , He Lei , Wei Xiao-Dong , Zhao Ling , Zhou Li-Hui , Zhao Chun-Fang , Wang Cai-Lin , Zhang Ya-Dong 
Published: December 2022

AbstractPrevious studies in Arabidopsis reported that the PPR protein SOAR1 plays critical roles in plant response to salt stress. In this study, we reported that expression of the Arabidopsis SOAR1 (AtSOAR1) in rice significantly enhanced salt tolerance at seedling growth stage and promoted grain productivity under salt stress without affecting plant productivity under non-stressful conditions. The transgenic rice lines expressing AtSOAR1 exhibited increased ABA sensitivity in ABA-induced inhibition of seedling growth, and showed altered transcription and splicing of numerous genes associated with salt stress, which may explain salt tolerance of the transgenic plants. Further, we overexpressed the homologous gene of SOAR1 in rice, OsSOAR1, and showed that transgenic plants overexpressing OsSOAR1 enhanced salt tolerance at seedling growth stage. Five salt- and other abiotic stress-induced SOAR1-like PPRs were also identified. These data showed that the SOAR1-like PPR proteins are positively involved in plant response to salt stress and may be used for crop improvement in rice under salinity conditions through transgenic manipulation.
The effect of medical castration on lipid levels in black South African men with prostate cancer
Authors: Minkowitz Shauli , Ayeni Oluwatosin , Haffejee Mohamed , Joffe Maureen 
Published: December 2022

AbstractBackgroundIn South Africa, androgen deprivation therapy (ADT) is commonly given as primary therapy for prostate cancer (PCa) due to many patients presenting with advanced disease. The metabolic adverse effects of ADT on lipid profile and weight gain have been reported mainly in Caucasian populations, but few studies have been performed in African populations. Men of African descent generally have favorable lipid profiles compared to other populations, and our study looked to analyze the effect of medical castration on lipid levels in black South African men with PCa.MethodsThe aim of this study is to describe the changes in blood total cholesterol, triglycerides, LDL and HDL at 6 months and at 1 year in men with prostate cancer newly initiated on ADT. Changes to BMI, waist circumference and HbA1c were also measured after 1 year of ADT.Our study was conducted at Chris Hani Baragwanath Academic Hospital which is a teaching hospital affiliated with the University of the Witwatersrand. It is located in Soweto, South of Johannesburg, and serves the 1.3 million local residents who are predominantly black and of the lower-income bracket. This study enrolled 38 black South African men who were starting to receive ADT for PCa. Subjects were evaluated at baseline and at 6 and 12 months. Lipid profiles and HbA1C levels were measured using blood samples, and body composition was measured using BMI and waist circumference.ResultsIn this prospective single-center study, we found that ADT resulted in a significant rise in triglyceride levels and weight gain in black South African men reaching mean levels of obesity using ethnic-specific definitions. High-density lipoproteins levels decreased significantly particularly in the first 6 months of treatment and thereafter began to rise. ADT also resulted in an increased HbA1C level which is a marker for insulin resistance.ConclusionsAndrogen deprivation therapy unfavorably changed the body habitus and lipid profile of men with PCa. It was demonstrated that even black South Africans who generally have favorable lipid profiles compared to their counterparts are at risk of developing metabolic syndrome while being treated with ADT.
A unique 15-bp InDel in the first intron of BMPR1B regulates its expression in Taihu pigs
Authors: Liu Zhexi , Xu Ran , Zhang Han , Wang Depeng , Wang Ji , Wu Keliang 
Published: December 2022

Abstract
Background
BMPR1B (Bone morphogenetic protein receptor type-1B) is a receptor in the bone morphogenetic protein (BMP) family and has been identified as a candidate gene for reproductive traits in pigs. Our previous study in Taihu pigs found a specific estrogen response element (ERE) in the first intron of the BMPR1B gene that is associated with the number born alive trait. However, little is known about the mechanism by which the ERE regulates the expression of BMPR1B in the endometrium.

Results
Here, a 15-bp InDel (insertion/deletion) (AGCCAGAAAGGAGGA) was identified as a unique variation in Taihu pigs, and was shown to be responsible for the binding of the type I receptor of estrogen (ESR1) to the ERE using dual-luciferase assays. Four BMPR1B transcripts (T1, T2, T3, and T4) were identified by 5′ RACE in endometrial tissue. Expression of T3 and T4 in the endometrium of Meishan pigs was significantly higher than in Duroc pigs during pregnancy. Luciferase assays showed that three distinct BMPR1B promoters may drive expression of T1, T3, and T4. Interestingly, ERE-mediated enhancement of T4 promoter activity significantly increased expression of Transcript T4 in the endometrium of Taihu pigs (P < 0.05). In contrast, the ERE inhibited activity of the T3 promoter and decreased expression of the T3 transcript in the Duroc background (P < 0.05). In summary, we identified a 15-bp InDel in the Taihu ERE that can be used as a molecular marker for the number born alive trait, characterized the 5′ untranslated regions (UTRs) of BMPR1B transcripts in the endometrium, and determined how the transcripts are processed by alternative splicing events.

Conclusions
Our results provide a foundation for understanding the transcriptional regulation of BMPR1B and its contributions to the unique breeding prolificacy characteristics of Taihu pigs.
Comprehensive computational analysis of epigenetic descriptors affecting CRISPR-Cas9 off-target activity
Authors: Mak Jeffrey K. , Störtz Florian , Minary Peter 
Published: December 2022

AbstractBackgroundA common issue in CRISPR-Cas9 genome editing is off-target activity, which prevents the widespread use of CRISPR-Cas9 in medical applications. Among other factors, primary chromatin structure and epigenetics may influence off-target activity.MethodsIn this work, we utilize crisprSQL, an off-target database, to analyze the effect of 19 epigenetic descriptors on CRISPR-Cas9 off-target activity. Termed as 19 epigenetic features/scores, they consist of 6 experimental epigenetic and 13 computed nucleosome organization-related features. In terms of novel features, 15 of the epigenetic scores are newly considered. The 15 newly considered scores consist of 13 freshly computed nucleosome occupancy/positioning scores and 2 experimental features (MNase and DRIP). The other 4 existing scores are experimental features (CTCF, DNase I, H3K4me3, RRBS) commonly used in deep learning models for off-target activity prediction. For data curation, MNase was aggregated from existing experimental nucleosome occupancy data. Based on the sequence context information available in crisprSQL, we also computed nucleosome occupancy/positioning scores for off-target sites.ResultsTo investigate the relationship between the 19 epigenetic features and off-target activity, we first conducted Spearman and Pearson correlation analysis. Such analysis shows that some computed scores derived from training-based models and training-free algorithms outperform all experimental epigenetic features. Next, we evaluated the contribution of all epigenetic features in two successful machine/deep learning models which predict off-target activity. We found that some computed scores, unlike all 6 experimental features, significantly contribute to the predictions of both models. As a practical research contribution, we make the off-target dataset containing all 19 epigenetic features available to the research community.ConclusionsOur comprehensive computational analysis helps the CRISPR-Cas9 community better understand the relationship between epigenetic features and CRISPR-Cas9 off-target activity.
Assessing the relative performance of fast molecular dating methods for phylogenomic data
Authors: Costa Fernanda P. , Schrago Carlos G. , Mello Beatriz 
Published: December 2022

AbstractAdvances in genome sequencing techniques produced a significant growth of phylogenomic datasets. This massive amount of data represents a computational challenge for molecular dating with Bayesian approaches. Rapid molecular dating methods have been proposed over the last few decades to overcome these issues. However, a comparative evaluation of their relative performance on empirical data sets is lacking. We analyzed 23 empirical phylogenomic datasets to investigate the performance of two commonly employed fast dating methodologies: penalized likelihood (PL), implemented in treePL, and the relative rate framework (RRF), implemented in RelTime. They were compared to Bayesian analyses using the closest possible substitution models and calibration settings. We found that RRF was computationally faster and generally provided node age estimates statistically equivalent to Bayesian divergence times. PL time estimates consistently exhibited low levels of uncertainty. Overall, to approximate Bayesian approaches, RelTime is an efficient method with significantly lower computational demand, being more than 100 times faster than treePL. Thus, to alleviate the computational burden of Bayesian divergence time inference in the era of massive genomic data, molecular dating can be facilitated using the RRF, allowing evolutionary hypotheses to be tested more quickly and efficiently.
Carbapenem resistance gene crisis in A. baumannii: a computational analysis
Authors: Zahra Nureen , Zeshan Basit , Ishaq Musarat 
Published: December 2022

AbstractAcinetobacter baumannii (A. baumannii)is one of the members ofESKAPEbacteria which is considered multidrug resistant globally. The objective of this study is to determine the protein docking of different antibiotic resistance gene (ARGs) inA. baumannii. In silico analysis of antibiotic resistance genes against carbapenem are the blaOXA-51, blaOXA-23, blaOXA-58, blaOXA-24, blaOXA-143, NMD-1 and IMP-1 inA. baumannii. The doripenem, imipenem and meropenem were docked to blaOXA-51 and blaOXA-23 using PyRx. The top docking energy was -5.5 kcal/mol by imipenem and doripenem and meropenem showed a binding score of -5. 2 kcal/mol each and blaOXA-23 energy was -4.3 kcal/mol by imipenem and meropenem showed a binding score of -2.3 kcal/mol, while doripenem showed the binding score of -3.4 kcal/mol. Similarly, doripenem imipenem and meropenem were docked to blaOXA-58, IMP-1, Rec A and blaOXA-143, with docking energy was -8.8 kcal/mol by doripenem and meropenem each while imipenem showed a binding score of -4.2 kcal/mol and with IMP-1 demonstrated their binding energies. was -5.7 kcal/mol by meropenem and doripenem showed a binding score of -5.3 kcal/mol, while imipenem showed a binding score of -4.5 kcal/mol. And docking energy was -4.9 kcal/mol by imipenem and meropenem showed binding energy of -3.6 kcal/mol each while doripenem showed a binding score of -3.9 kcal/mol in RecA and with blaOXA-143 docking energy was -3.0 kcal/mol by imipenem and meropenem showed a binding score of -1.9 kcal/mol, while doripenem showed the binding score of -2.5 kcal/mol respectively. Doripenem, imipenem, and meropenem docking findings with blaOXA-24 confirmed their binding energies. Doripenem had the highest docking energy of -5.5 kcal/mol, meropenem had a binding score of -4.0 kcal/mol, and imipenem had a binding score of -3.9 kcal/mol. PyRx was used to dock the doripenem, imipenem, and meropenem to NMD-1. Docking energies for doripenem were all – 4.0 kcal/mol, whereas meropenem had docking energy of -3.3 kcal/mol and imipenem was -1.50 kcal/mol. To the best of our knowledge the underlying mechanism of phenotypic with genotypic resistance molecular docking regarding carbapenem resistanceA. baumanniiis unclear. Our molecular docking finds the possible protein targeting mechanism for carbapenem-resistantA.baumannii.
Suppression of microRNA168 enhances salt tolerance in rice (Oryza sativa L.)
Authors: Wan Jiong , Meng Shujun , Wang Qiyue , Zhao Jiawen , Qiu Xiaoqian , Wang Liangfa , Li Juan , Lin Yuan , Mu Liqin , Dang Kuntai , Xie Qiankun , Tang Jihua , Ding Dong , Zhang Zhanhui 
Published: December 2022

Abstract
Background
Rice is a salt-sensitive crop. Complex gene regulatory cascades are likely involved in salinity stress in rice roots. microRNA168 (miR168) is a conserved miRNA among different plant species. It in-directly regulates the expression of all miRNAs by targeting gene ARGONAUTE1(AGO1). Short Tandem Target Mimic (STTM) technology is an ideal approach to study miRNA functions by in-activating mature miRNA in plants.

Results
In this study, rice miR168 was inactivated by STTM. The T3 generation seedlings of STTM168 exhibited significantly enhanced salt resistance. Direct target genes of rice miR168 were obtained by in silico prediction and further confirmed by degradome-sequencing. PINHEAD (OsAGO1), which was previously suggested to be a plant abiotic stress response regulator. RNA-Seq was performed in root samples of 150mM salt-treated STTM168 and control seedlings. Among these screened 481 differentially expressed genes within STTM168 and the control, 44 abiotic stress response related genes showed significant difference, including four known salt-responsive genes.

Conclusion
Based on sequencing and qRT-PCR, a “miR168-AGO1-downstream” gene regulation model was proposed to be responsible for rice salt stress response. The present study proved miR168-AGO1 cascade to play important role in rice salinity stress responding, as well as to be applied in agronomic improvement in further.
Certified Registered Nurse Anesthetists’ occupational exposure to inhalational anesthetic agents: a survey of anesthetic gas safety
Authors: Masselink Trent , Hardinger Jan , Bowman-Dalley Carrie , O’Guin Crystal , Hendrix Kumudhini , Crowell Nancy , Eshkevari Ladan 
Published: December 2022

Abstract
Background
Anesthetic gases have been known to cause damage when inhaled over long periods of time. Modern safety measures have been put in place to reduce the risk to anesthesia providers, however there is continued lack of information on providers experiencing short term effects (lethargy, fatigue, headache, slowed cognitive ability, nausea, and mucosal irritation) thereby leading to long-term sequalae (sister chromatid exchanges, micronuclei, chromosomal aberrations, and comet assays).

Method
A thirteen item, multiple choice survey was sent to 3,000 anesthesia providers, of which 463 completed the survey. A Chi-square test of independence was used to determine the association between gas exposure and participant self-reported symptoms. A Spearman’s Correlation test was also utilized to interpret this data since both frequency of smelling gas and frequency of symptoms were ordinal variables for which Spearman’s rho correlation was the appropriate measure of association.

Results
The major findings were that as the frequency of smelling anesthetic gas increased, so too did the frequency of self-reported headaches and fatigue. Spearman’s rho = .148 and .092. P value = .002 and .049, respectively.

Conclusion
There have been many efforts to decrease the risk of exposure of anesthesia providers to anesthetic gases. While there is a decrease in reported exposures, indications of possible long-term effects remain a concern in anesthesia providers. Potential implications of exposure could lead to chromosomal aberrations, sister chromatid exchanges, comet assays, spontaneous abortions, and genotoxic effects.
Short- and long-term survival after out-of-hospital cardiac arrest in Kaunas (Lithuania) from 2016 to 2018
Authors: Darginavicius Linas , Kajokaite Ilona , Mikelionis Nerijus , Vencloviene Jone , Dobozinskas Paulius , Vaitkaitiene Egle , Vaitkaitis Dinas , Krikscionaitiene Asta 
Published: December 2022

Abstract
Background
No studies analysing out-of-hospital cardiac arrest (OHCA) epidemiology and outcomes in Lithuania were published in the last decade.

Methods
We conducted a retrospective analysis of prospectively collected data. The incidence of OHCA and the demographics and outcomes of patients who were treated for OHCA between 1 and 2016 and 31 December 2018 at Kaunas Emergency Medical Service (EMS) were collected and are reported in accordance with the Utstein recommendations. Multivariable logistic regression analysis was used to identify predictors of survival to hospital discharge.

Results
In total, 838 OHCA cases of EMS-treated cardiac arrest (CA) were reported (95.8 per 100.000 inhabitants). The median age was 71 (IQR 58–81) years of age, and 66.7% of patients were males. A total of 73.8% of OHCA cases occurred at home, 59.3% were witnessed by a bystander, and 54.5% received bystander cardiopulmonary resuscitation. The median EMS response time was 10 min. Cardiac aetiology was the leading cause of CA (78.8%). The initial rhythm was shockable in 27.6% of all cases. Return of spontaneous circulation at hospital transfer was evident in 24.9% of all cases. The survival to hospital discharge rate was 10.9%, and the 1-year survival rate was 6.9%. The survival to hospital discharge rate in the Utstein comparator group was 36.1%, and the 1-year survival rate was 27.2%. Five factors were associated with improved survival to hospital discharge: shockable rhythm, time from call to arrival at the patient less than 10 min, witnessed OHCA, age < 80 years, and male sex.

Conclusion
This is the first OHCA study from Lithuania examining OHCA epidemiology and outcomes over a three year period. Routine OHCA data collection and analysis will allow us to track the efficacy of service improvements and should become a standard practice in all Lithuanian regions.
Trial registration: This research was registered in the clinicaltrials.gov database: Identifiers: NCT04784117, Unique Protocol ID: LITOHCA. Brief Title: Out-of-hospital Cardiac Arrest Epidemiology and Outcomes in Kaunas 2016–2021.