bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide DNA methylation profiles and small non-coding RNAs signatures study of sperm with high DNA fragmentation index
Authors: Liu Minghua , Liu Peiru , Chang Yunjian , Xu Beiying , Wang Nengzhuang , Qin Lina , Zheng Jufen , Liu Yun , Wu Ligang , Yan Hongli 
Published: February 2022

Abstract
Background
Sperm DNA fragmentation index (DFI) is a more accurate measure of sperm quality than traditional semen analysis (sperm motility, concentration, and morphology) because DFI can better predict male fertility potential and assisted reproductive technology (ART) outcomes. However, no studies have compared the genome-wide DNA methylation profiles and small noncoding RNAs (sncRNAs) signatures of high DFI and low DFI sperm samples.
Methods
Whole-genome bisulfite sequencing (WGBS) and sncRNAs deep sequencing were performed to compare the genome-wide DNA methylation profiles and sncRNAs signatures of sperm samples of weak group(DFI > 30%) and normal group(DFI < 15%). In addition, we used the WGBS data to construct DNA methylation correlation matrices of the weak and normal group sperm.
Results
A total of 4939 diferentially methylated regions (DMRs) (3083 hypermethylated and 1856 hypomethylated) were identifed in the two group sperm samples. The hypermethylated DMRs were found to be mainly signifcantly enriched in the area of neurons and microtubule. Compared with the normal group, the global DNA methylation level of the weak group sperm showed a downward trend and the methylation correlation within the chromosomes of weak group sperm was weakened. 27 miRNAs, 151 tsRNAs and 70 rsRNAs were differently expressed between the two group sperm samples. Finally, we identified nine sncRNAs as candidate sperm quality biomarkers. In addition, the target genes of both the downregulated and upregulated miRNAs were involved in the nervous system and cell development
Conclusions
Our findings suggest that the genome-wide DNA methylation levels and sncRNAs expression of sperm were significantly correlated with sperm DFI levels. Therefore, our study provides useful biomarkers for improving the success rate of natural pregnancy and ART. The chromosomes of high DFI sperm became loose and more vulnerable to ROS attack. The increase of sperm DFI level may affect embryonic nervous system development.
Methionine regulates self-renewal, pluripotency, and cell death of GIC through cholesterol - rRNA axis
Authors: Yokogami Kiyotaka , Kikuchi Taisei , Watanabe Takashi , Nakatake Yasutaka , Yamashita Shinji , Mizuguchi Asako , Takeshima Hideo 
Published: February 2022

Abstract
Background. Glioma-initiating cells (GICs) are the source of glioma cells that can self-renew, have pluripotency, and are treatment-resistant, so are the starting point for relapse and eventual death despite multimodality therapy. L-[methyl-11C]methionine PET has observed high accumulation at the time of recurrence, it is important to understand the mechanism of tumor cell activation caused by the reorganization of methionine metabolism.Methods. We cultured cells in methionine-deprived culture medium for comprehensive analysis. Based on the obtained results, the possible target molecules were chemically inhibited and the respective markers were analyzed.Results. Methionine depletion markedly decreased proliferation and increased cell death of GICs. Decreased S-adenosyl-methionine, which is synthesized intracellularly by catalyzed by methionine adenosyltransferase using methionine, triggered the following: (i) global DNA demethylation, (ii) hyper-methylation of signaling pathways regulating pluripotency of stem cells, (iii) decreased expression of the core-genes and pluripotent markers of stem cells including FOXM1, SOX2, SOX4, PROM1, and OLIG2, (iv) decreased cholesterol synthesis and increased excretion mainly through decreased SREBF2, and (v) down-regulation of the large subunit of ribosomal protein configured 28S and ACA43, small nucleolar RNA guiding the pseudouridylation of 28S rRNA, which is essential for translation. In addition, inhibition of cholesterol synthesis with statin resulted in a phenotype similar to that of methionine depletion and decreases in stem cell markers and small nucleolar RNA ACA43. Moreover, suppression of FOXM1 decreased stem cell markers such as SOX4 and PROM1. The gene expression profile for cholesterol production was obtained from the Ivy Glioblastoma Atlas Project database and compared between tumor cells with relatively low methionine levels in areas of pseudopalisading arrangement around necrosis and tumor cells in the infiltrating region, showing that cells in the infiltrating region have higher capacity to produce cholesterol.Conclusions. Methionine metabolism is closely related with self-renewal, pluripotency, and cell death in GICs through modification of cholesterol biosynthesis, especially in the SREBF2-FOXM1 and ACA43 axis with modification of rRNA.
Neutralizing GM-CSF autoantibodies in pulmonary alveolar proteinosis, cryptococcal meningitis and severe nocardiosis
Authors: Salvator Hélène , Cheng Aristine , Rosen Lindsey Belle , Williamson Peter R , Bennett John E , Kashyap Anuj , Ding Li , Kwon-Chung Kyung June , Namkoong Ho , Zerbe Christa S , Holland Steven M 
Published: February 2022

Abstract
Background Anti GM-CSF autoantibodies (aAb) have been related to acquired pulmonary alveolar proteinosis (PAP) and described in cases of severe infections such as cryptococcosis and nocardiosis in previously healthy subjects. Whether there are different anti-GM-CSF autoantibodies corresponding to these phenotypes is unclear.MethodsPlasma samples gathered in the National Institute of Health from patients with anti GM-CSF aAb and either PAP (n=15), cryptococcal meningitis (n=15), severe nocardiosis (n=5) or overlapping phenotypes (n=6) were compared in terms of titer and neutralizing activity as assessed by inhibition of GM-CSF-induced intracellular phospho-STAT5 (pSTAT5) in monocytes.ResultsAnti GM-CSF aAb titers were higher in PAP patients compared to those with cryptococcosis (mean 495±464 ug/ml vs 197±159 ug/ml, p = 0.02); there was no difference with patients with nocardiosis (430±493 ug/ml) nor between the two type of infections. The concentration of anti-GM-CSF autoantibody resulting in 50% inhibition of GM-CSF-induced pSTAT5 (IC50) was not significantly different between groups of patients (2.46 ± 2.3, 3.7 ± 3.3 and 1.94 ± 1.1 ug/ml in PAP patients, cryptococcosis and nocardiosis patients, respectively). Nor was the concentration of GM-CSF necessary to induce 50% of maximal GM-CSF-induced pSTAT5 in presence of 10 ug/ml of anti-GM-CSF aAb (EC50). When studying longitudinal samples from patients with PAP or disseminated nocardiosis, the neutralizing effect of anti GM-CSF aAb was relatively constant over time despite targeted treatments and variations in aAb levels. ConclusionsDespite different clinical manifestations, anti-GM-CSF antibodies were similar across PAP, cryptococcosis and nocardiosis. Underlying host genetics and functional analyses may help further differentiate the biology of these conditions.
Value of Transbronchial Needle Aspiration Combined with Rapid on-Site Evaluation of Cytology in Diagnosis of Peripheral Pulmonary Lesions
Authors: liang long , Duan Hongxia , Zhu Huiyuan , Yang Huiqiong , Wang Changhui , Xie Shuanshuan , Li Xuan 
Published: February 2022

Abstract
Background: The diagnostic value of rapid on-site evaluation (ROSE) of cytology during endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) remains controversial. The purpose of this study was to validate the value of EUBS-TBNA combined with ROSE in the diagnosis of peripheral pulmonary lesions (PPLs).Methods: Enrolled in this study were 260 patients with nodules, masses, cavities or inflammatory lesions on pulmonary CT images, and age ranged from 23 to 83 years old. They were assigned to undergo EBUS-TBNA with ROSE (n=134) or without ROSE (n=126). The diagnostic results of ROSE during EBUS-TBNA and the final pathologic reports were analyzed and compared by utilizing SPSS21.0 software to see whether the ROSE method during EBUS-TBNA would increase the risk of procedure-related complications, improve the diagnostic yield, and evaluate the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV). Results: The number of punctures in ROSE group was significantly lower than that in non-ROSE group (P<0.001). There was no significant difference in hemoptysis between the two groups (P=0.402). The overall diagnostic yield of EBUS-TBNA for malignant diseases in the ROSE-group and the non-ROSE group was 29.9% and 11.1%, respectively. The sensitivity, specificity, PPV and NPV of ROSE during EBUS-TBNA were 97.4%, 96.9%, 92.5% and 98.90% respectively, showing a high agreement with the pathological results. Youden index reached 94.3%. Conclusions: ROSE examination during EBUS-TBNA could effectively improve the diagnostic yield and reduce the number of intraoperative punctures with the diagnostic results in cytology well consistent with those of traditional pathology, and therefore is worth promoting and applying in clinical practice.
Superior capsule reconstruction versus Reverse shoulder arthroplasty in massive rotator cuff tears: A comparative study
Authors: Ohta Satoru , Ueda Yoshiyuki , Komai Osamu 
Published: February 2022

Abstract
Introduction: Superior capsule reconstruction (SCR) was developed in Japan in 2010 as a surgical treatment strategy for massive rotator cuff tears, This study was aimed at performing a comparative analysis of the postoperative results for SCR versus reverse shoulder arthroplasty (RSA), two surgical approaches currently used to treat massive rotator cuff tears.Materials and Methods: Patients who underwent surgeries from 2014 to 2018 and were followed up for at least 2 years were included in the study. Subsequently, the cases of Hamada classifications 1–3 were retrospectively targeted. SCR comprised 38 patients (mean age 71.4 years) and RSA comprised 24 patients (mean age 78.9 years). The Japanese Orthopaedic Association (JOA) score, University of California at Los Angeles (UCLA) score, active elevation angle, and downward external rotation and internal rotation angles before and after the surgery were evaluated and compared between the groups.Results: In postoperative group comparison (observed value), SCR significantly improved from RSA in terms of JOA score (p = 0.0060), UCLA score (p = 0.0042), elevation angle (p = 0.0070), downward external rotation (p < 0.001), and internal rotation (p < 0.001). In terms of postoperative comparison between groups (amount of change), RSA was superior in terms of JOA score (p = 0.0128) and UCLA score (p = 0.0055) and SCR showed improvement in terms of downward external rotation (p < 0.001) and internal rotation (p = 0.0016).　Conclusions: The results of treatment of massive rotator cuff tears in patients with Hamada's classification 1–3 were good for both techniques. In the postoperative comparison between the groups, downward external rotation and internal rotation showed a significant improvement in SCR in both the observed values and the amount of change.
Subfascial infiltration of 0.5% ropivacaine, but not 0.25% ropivacaine, exacerbates damage and inflammation in surgically incised abdominal muscles of rats
Authors: Shen Dandan , Sugiyama Yuki , Ishida Kumiko , Fuseya Satoshi , Ishida Takashi , Kawamata Mikito , Tanaka Satoshi 
Published: February 2022

Abstract
Ropivacaine-induced myotoxicity in surgically incised muscles has not been fully investigated. We evaluated the effects of infiltration anesthesia with ropivacaine on damage, inflammation and regeneration in the incised muscles of rats undergoing laparotomy. Ropivacaine or saline was infiltrated below the muscle fascia over the incised muscles. Pain-related behaviors and histological muscle damage were assessed. Macrophage infiltration at days 2 and 5 and proliferation of satellite cells at day 5 were detected by CD68 and MyoD immunostaining, respectively. Pain-related behaviors were inhibited by 0.25% and 0.5% of ropivacaine for 2 hours after surgery. Single infiltration of 0.5% ropivacaine did not induce injury in intact muscles without incision, but single and repeated infiltration of 0.5% ropivacaine significantly augmented laparotomy-induced muscle injury and increased the numbers of CD68-positve macrophages and MyoD-positive cells compared to those in rats with infiltration of saline or 0.25% ropivacaine. In contrast, there were no significant differences in them between rats with saline infusion and rats with 0.25% ropivacaine infiltration. In conclusion, single or repeated subfascial infiltration of 0.25% ropivacaine can be used without exacerbating the damage and inflammation in surgically incised muscles, but the use of 0.5% ropivacaine may be a concern because of potentially increased muscle damage.
Fractional Boundary Element Solution of Three-Temperature Thermoelectric Problems
Authors: Fahmy Mohamed , Almehmadi Mohammed , Sohail Ayesha , Subhi Fahad Al 
Published: February 2022

Abstract
The primary goal of this article is to propose a new fractional boundary element technique for solving nonlinear three-temperature (3T) thermoelectric problems. Analytical solution of the current problem is extremely difficult to obtain. To overcome this difficulty, a new numerical technique must be developed to solve such problem. As a result, we propose a novel fractional boundary element method (BEM) to solve the governing equations of our considered problem. Because of the advantages of the BEM solution, such as the ability to treat problems with complicated geometries that were difficult to solve using previous numerical methods, and the fact that the internal domain does not need to be discretized. As a result, the BEM can be used in a wide variety of thermoelectric applications. The numerical results show the effects of the magnetic field and the graded parameter on thermal stresses. The numerical results also validate the validity and accuracy of the proposed technique.
Tissue damage, mutagenic effect and alteration in antioxidant defense in Danio rerio (Cypriniformes: Cyprinidae) after chronic exposure to Metformin hydrochloride.
Authors: Demarco Natani Ribeiro , Zanardini Bárbara , Zazula Matheus Felipe , Sobjak Thaís , D’Arce Luciana Gregório , Guimarães Ana Tereza Bittencourt 
Published: February 2022

Abstract

Metformin hydrochloride (MET) is an oral medication very prescribed for patients with diabetes, with a large part of its metabolites being eliminated in the urine. Basic sanitation systems are not fully effective in removing all the contaminants, promoting contamination to rivers and supply reservoirs. The objective of this study was to test the potential acute and chronic effects of MET on the antioxidant system, mutagenicity effects and tissue damages in the bioindicator D. rerio. The animals were acclimatized and separated into six groups and exposed to different concentrations of MET (0.00, 0.25, 0.50, 0.75, 1.25 g.L− 1) over a 96 hour period to determine the LC50. In another experiment, five groups of ten animals were separated as follows: four groups for evaluation of the chronic effect of 0.45 g.L− 1 of metformin hydrochloride (15, 30, 45 and 60 days) and, a negative control group (NC). The antioxidant system and the tissue damages of the muscle samples and, the mutagenicity in the blood samples were evaluated. The presence of oxidative stress and mutagenicity, together with the activation of the antioxidant system, can be visualized up to 30 days of treatment, with intense tissue damages in 60 days and the emergence of apoptotic cells, which is evidence of the toxic potential of this drug to non-target aquatic populations.
Serum Anti-Müllerian Hormone as a Predictor of Polycystic Ovarian Syndrome among Women of Reproductive Age
Authors: Butt Muhammad Salman , Saleem Javeria , Aiman Sobia , Zakar Rubeena , Sadique Iftikhar , Fischer Florian 
Published: February 2022

Abstract
Background: The Polycystic Ovarian Syndrome (PCOS) affects up to a fifth of women of reproductive age and causes anovulatory subfertility. Some studies have recommended that an Anti-Müllerian Hormone (AMH) level greater than 3.8-5 ng/mL can be used for diagnosing PCOS. Therefore, this study aims to analyze the serum AMH level as a predictor of PCOS among women of reproductive age.Methods: A total of 51 women of reproductive age, recently diagnosed with PCOS (meeting the Rotterdam criteria), were selected. A cross-sectional study design was used to estimate the AMH levels among PCOS women. Baseline variables, menstrual cycle length, ovarian morphology on the ultrasound, hirsutism, sex hormones, gonadotropin, and serum AMH levels were analyzed during the follicular phase (1–5 days) of the menstrual cycle. Results: A high serum AMH level (7.23 ± 4.67 ng/ml) was recorded with normal sex hormone levels. Women with oligo-/amenorrhea had a significant mean difference for luteinizing hormone (p=0.02) and AMH levels (p=0.03) when compared with women of normal menstrual cycle length. PCOS women with high AMH levels (≥3.9 ng/ml) showed a significant difference in ovarian morphology (p<0.05) when compared with the normal AMH group. Conclusions: Serum AMH level can be used as a strong predictor for disturbance in reproductive characteristics such as menstrual cycle disturbance, polycystic ovarian morphology, and clinical signs of hyperandrogenism. An elevated serum AMH level could reflect the certainty of PCOS diagnosis among women of reproductive age with a greater number of PCOS features.
Investigation on Layered Elliptical Vibration-Assisted Cutting of Micro Groove
Authors: Zhang Chen 
Published: February 2022

Abstract
Elliptical vibration-assisted cutting (EVC) is a method for rapidly creating ultra-precision free-form surfaces with micro groove features, which have a wide array of industrial applications such as drag reduction, self-cleaning action, optical tuning behavior, etc. The complicated fabrication process and limited shape and deep control of micro-groove features by using EVC limit the applications of current EVC process in the fabrication of micro-groove. To overcome these limitations and improve overall performance, a layered elliptical vibration-assisted cutting(LEVC) process is presented to fabricate deep micro groove with different shape. First, a detailed layered elliptical vibration-assisted cutting method is described and a key step, the layered elliptical vibration-assisted tool path planning, is analyzed and established. Then the machining stress under the proposed LEVC method and layered conventional cutting (LCC) process were simulated and compared through finite element analysis. The simulation results show that the LEVC process can generate the lower residual stress compared to the LCC process. To validate the machining performance of the proposed LEVC process, the machining experiments for two groups of micro grooves under the proposed LEVC process and LCC process are performed. The performance tests and comparison results between the generated micro grooves under the proposed LEVC method and LCC process indicate that the proposed LEVC method is effective for generating micro groove with the controllable shape and depth. The actual experiments show that the machining capability of the developed LEVC method for micro groove is satisfactory.
Evaluation of screening parameters and machine learning models for the prediction of neonatal sepsis: A systematic review
Authors: Ezeobi Dennis Peace , Wasswa William , Musimenta Angella , Kyoyagala Stella 
Published: February 2022

Abstract
About 2.9 million neonates die every year worldwide, and most of these deaths occur in low-resource settings. Neonatal sepsis occurs when there is a bacterial invasion in the bloodstream; the immune system begins a systemic inflammatory response syndrome (SIRS) damaging to the body and can quickly advance to severe sepsis, multi-organ failure, and finally, death. Sepsis in neonates can progress more rapidly than in adults; therefore, a timely diagnosis is critical. The standard gold test for diagnosing neonatal sepsis is blood culture, which takes at least 72 hours. Hence, identifying key predictor variables and models that work best can help reduce neonatal morbidity and mortality. The matching articles were identified by searching the PubMed, IEEE, and Cochrane bibliography databases. For the inclusion of articles, the abstract and titles were first screened based on some predetermined criteria and then, the full-text articles were screened. Thirty-one studies met the full inclusion criteria. The duration of ROM was found to be more significant than other maternal risk factors. Heart rate and heart rate variability were found to be more significant than other neonatal clinical signs. C reactive protein and I/T ratio were found to be more significant than other laboratory tests. The main limitation is the variation in the performance measures used in the studies, which made it difficult to perform a quantitative assessment. A combination of predictor variables has been shown to strengthen neonatal sepsis prediction, as shown by some of the reviewed studies. Predictive algorithms that combine multiple variables are urgently needed to improve models for early detection, prognosis, and treatment of neonatal sepsis.
Dihydroartemisinin Extract from Artemisia hedinii inhibits spore germination of Alternaria alternata involving membrane peroxidation
Authors: You Cong , Ma YiMing , Hu Guoyuan , Yang Chunlei 
Published: February 2022

Abstract
Dihydroartemisinin (DHA) extract is expected to be useful as a biological pesticide for fungal disease control. This study preliminarily explored the mechanism for inhibiting spore germination of Alternaria alternate by DHA extract. The results showed that the EC50, EC90, MIC and MFC of DHA extract on the spores of A. alternata were 1.63 mg/mL, 3.14 mg/mL, 4 mg/mL and 8mg/mL, respectively. The cell membrane permeability of spores treated with DHA extract was enhanced and the integrity was decreased. Meanwhile, the contents of reactive oxygen species (ROS) and malondialdehyde (MDA) increased significantly, indicating that membrane peroxidation occurred in the spores. Significant changes in catalase (CAT) activity were observed, which also demonstrated that an oxidation reaction took place within the spores. These results indicated that the DHA extract produced ROS in the spores, which caused membrane peroxidation and destroyed the membrane, thus, inhibited spores germination of A. alternata. The antifungal activity against A. alternata mechanism of DHA could pave the way for the development of control of tobacco brown spot and other fungal diseases.
Random-Forest Model for Drug Target-Interaction Prediction via Kullbeck–Leibler Divergence
Authors: Ahn Sangjin , Lee Sieun , Kim Mi-hyun 
Published: February 2022

Abstract
Virtual screening has significantly improved the rate of success of early drug discovery. Recent virtual screening methods have improved along with advances in machine learning (ML) and chemical information. Among these advances, the creative extraction of drug features is important for predicting drug-target interaction (DTI), a large-scale virtual screening of known drugs. Herein, we report on Kullbeck–Leibler divergence (KLD) as a DTI feature and the feature driven classification model applicable to DTI prediction. Thus, E3FP 3D molecular fingerprints of drugs as molecular representation allowed the computation of 3D-similarities between ligands within each target (Q-Q matrix) for uniqueness of pharmacological targets and between query–ligand (Q-L vector) for DTI. The 3D similarity matrices were transformed into probability density functions using kernel density estimation (KDE) as a nonparametric estimation. Each density model could exploit the characteristics of each pharmacological target and measure the quasi-distance between ligands. Furthermore, we developed a random-forest (RF) model from the KLD feature vectors to successfully predict DTI, irrespective of whether each query belongs to a target.