bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of NIA and GSNOR family genes and nitric oxide homeostasis in response to wheat-leaf rust interaction
Authors: Hurali Deepak T. , Bhurta Ramesh , Tyagi Sandhya , Sathee Lekshmy , Sandeep Adavi B. , Singh Dalveer , Mallick Niharika , Vinod  , Jha Shailendra K. 
Published: January 2022

AbstractNitric oxide (NO) modulates plant response to biotic and abiotic stresses by S-nitrosylation-mediated protein post-translational modification. Nitrate reductase (NR) and S-nitrosoglutathione reductase (GSNOR) enzymes are essential for NO synthesis and the maintenance of Nitric oxide/S-nitroso glutathione (NO/GSNO) homeostasis, respectively. S-nitrosoglutathione, formed by the S-nitrosylation reaction of NO with glutathione, plays a significant physiological role as the mobile reservoir of NO. The genome-wide analysis identified nine NR(NIA) and three GSNOR genes in the wheat genome. Phylogenic analysis revealed that the nine NIA genes +were clustered into four groups and the 3 GSNORs into two groups. qRT-PCR expression profiling of NIAs and GSNORs was done in Chinese spring (CS), a leaf rust susceptible wheat line showing compatible interaction, and Transfer (TR), leaf rust-resistant wheat line showing incompatible interaction, post-inoculation with leaf rust pathotype 77–5 (121-R-63). All the NIA genes showed upregulation during incompatible interaction in comparison with the compatible reaction. The GSNOR genes showed a variable pattern of expression: the TaGSNOR1 showed little change, whereas TaGSNOR2 showed higher expression during the incompatible response. TaGSNOR3 showed a rise of expression both in compatible and incompatible reactions. Before inoculation and after 72 h of pathogen inoculation, NO localization was studied in both compatible and incompatible reactions. The S-nitrosothiol accumulation, NR, and glutathione reductase activity showed a consistent increase in the incompatible interactions. The results demonstrate that both NR and GSNOR plays significant role in defence against the leaf rust pathogen in wheat by modulating NO homeostasis or signalling.
Quadriceps physiological response during the 1-min sit-to-stand test in people with severe COPD and healthy controls
Authors: Gephine Sarah , Mucci Patrick , Bielmann Mathieu , Martin Mickael , Bouyer Laurent , Saey Didier , Maltais François 
Published: January 2022

AbstractWe compared quadriceps oxygenation and surface electromyography (sEMG) responses during the 1-min sit-to-stand (1STS) in 14 people with severe COPD and 12 controls, in whom cardiorespiratory response, near-infrared spectroscopy signals (oxy [Hb-Mb], deoxy [Hb-Mb], total [Hb-Mb], and SmO2) and sEMG signals of the quadriceps were recorded. Time duration of each sit-to-stand cycle and the total work performed during the 1STS were measured. The quadriceps oxygenation parameters were normalized by reporting their values according to the total work during 1STS. The rate of sit-to-stand maneuvers decelerated in people with COPD leading to smaller total work compared with controls. The pattern of quadriceps oxygenation response during 1STS was similar between groups. However, in COPD, the recovery after 1STS was characterized by larger overshoots in oxy [Hb-Mb], total [Hb-Mb], and SmO2. When corrected for the cumulative total work, the increase in muscle O2 extraction (deoxy [Hb-Mb]) during the first 30 s of recovery was greater in people with COPD compared to controls. Quadriceps sEMG changes suggestive of a fatiguing contraction pattern was observed only in people with COPD. All together, these results highlighted physiological misadaptation of people with severe COPD to the 1STS.
Essential oil from Lavandula angustifolia elicits expression of three SbWRKY transcription factors and defense-related genes against sorghum damping-off
Authors: Rashad Younes M. , Abdel Razik Elsayed S. , Darwish Doaa B. 
Published: January 2022

AbstractSorghum damping-off, caused byFusarium solani(Mart.) Sacc., is a serious disease which causes economic loss in sorghum production. In this study, antagonistic activity of lavender essential oil (EO) at 0.5, 0.75, 1.0, 1.25, 1.5, and 1.6% againstF. solaniwas studied in vitro. Their effects on regulation of threeSbWRKYtranscription factors, the response factorJERF3and eight defense-related genes, which mediate different signaling pathways, in sorghum were investigated. Effects of application under greenhouse conditions were also evaluated. The results showed that lavender EO possesses potent antifungal activity againstF. solani. A complete inhibition in the fungal growth was recorded for lavender EO at 1.6%. Gas chromatography–mass spectrometric analysis revealed that EO antifungal activity is most likely attributed to linalyl anthranilate, α-terpineol, eucalyptol, α-Pinene, and limonene. Observations using transmission electron microscopy revealed many abnormalities in the ultrastructures of the fungal mycelium as a response to treating with lavender EO, indicating that multi-mechanisms contributed to their antagonistic behavior. Results obtained from Real-time PCR investigations demonstrated that the genes studied were overexpressed, to varying extents in response to lavender EO. However,SbWRKY1was the highest differentially expressed gene followed byJERF3, which suggest they play primary role(s) in synchronously organizing the transcription-regulatory-networks enhancing the plant resistance. Under greenhouse conditions, treating of sorghum grains with lavender EO at 1.5% prior to infection significantly reduced disease severity. Moreover, the growth parameters evaluated, the activities of antioxidant enzymes, and total phenolic and flavonoid contents were all enhanced. In contrast, lipid peroxidation was highly reduced. Results obtained from this study support the possibility of using lavender EO for control of sorghum damping-off. However, field evaluation is highly needed prior to any usage recommendation.
A data-driven ultrasound approach discriminates pathological high grade prostate cancer
Authors: Akatsuka Jun , Numata Yasushi , Morikawa Hiromu , Sekine Tetsuro , Kayama Shigenori , Mikami Hikaru , Yanagi Masato , Endo Yuki , Takeda Hayato , Toyama Yuka , Yamaguchi Ruri , Kimura Go , Kondo Yukihiro , Yamamoto Yoichiro 
Published: January 2022

AbstractAccurate prostate cancer screening is imperative for reducing the risk of cancer death. Ultrasound imaging, although easy, tends to have low resolution and high inter-observer variability. Here, we show that our integrated machine learning approach enabled the detection of pathological high-grade cancer by the ultrasound procedure. Our study included 772 consecutive patients and 2899 prostate ultrasound images obtained at the Nippon Medical School Hospital. We applied machine learning analyses using ultrasound imaging data and clinical data to detect high-grade prostate cancer. The area under the curve (AUC) using clinical data was 0.691. On the other hand, the AUC when using clinical data and ultrasound imaging data was 0.835 (p = 0.007). Our data-driven ultrasound approach offers an efficient tool to triage patients with high-grade prostate cancers and expands the possibility of ultrasound imaging for the prostate cancer detection pathway.
RBL2/DREAM-mediated repression of the Aurora kinase A/B pathway determines therapy responsiveness and outcome in p53 WT NSCLC
Authors: Duan Lei , Perez Ricardo E. , Calhoun Sarah , Maki Carl G. 
Published: January 2022

AbstractWild-type p53 is a stress-responsive transcription factor and potent tumor suppressor. P53 activates or represses genes involved in cell cycle progression or apoptosis in order to arrest the cell cycle or induce cell death. Transcription repression by p53 is indirect and requires repressive members of the RB-family (RB1, RBL1, RBL2) and formation of repressor complexes of RB1-E2F and RBL1/RBL2-DREAM. Many aurora kinase A/B (AURKA/B) pathway genes are repressed in a p53-DREAM-dependent manner. We found heightened expression of RBL2 and reduced expression of AURKA/B pathway genes is associated with improved outcomes in p53 wild-type but not p53 mutant non-small cell lung cancer (NSCLC) patients. Knockdown of p53, RBL2, or the DREAM component LIN37 increased AURKA/B pathway gene expression and reduced paclitaxel and radiation toxicity in NSCLC cells. In contrast, pharmacologic inhibition of AURKA/B or knockdown of AURKA/B pathway components increased paclitaxel and IR sensitivity. The results support a model in which p53-RBL2-DREAM-mediated repression of the AURKA/B pathway contributes to tumor suppression, improved tumor therapy responses, and better outcomes in p53 wild-type NSCLCs.
Statistical estimation of deltoid subcutaneous fat pad thickness: implications for needle length for vaccination
Authors: Sebro Ronnie 
Published: January 2022

AbstractCurrent US Centers for Disease Control and Prevention intramuscular injection needle length guidelines for injection fo the deltoid muscle are based on weight and gender. The aims of this study are (1) to evaluate whether other biometric data (age, gender, height, weight and body mass index (BMI)) are better predictors of the thickness of the deltoid subcutaneous fat pad (DSFP) than weight and gender and (2) to evaluate the performance of the CDC weight-based needle length guidelines. This was a retrospective single center cohort study of 386 patients who underwent surveillance PET/CT between 01/01/2020 and 04/01/2021. Patient age, gender, height, weight, BMI and CT measurements of the DSFP were evaluated. DSFP was positively correlated with weight and BMI in men (r = 0.67, P < 0.001; r = 0.74, P < 0.001) and women (r = 0.69, P < 0.001; r = 0.75, P < 0.001) respectively. DSFP was negatively correlated with age in women (r =  − 0.19, P = 0.013). Age and BMI were better predictors of DSFP than weight. The best model to predict the DSFP is: $$DSFP in mm= 6.267199 -2.711159*Male + 0.228407*BMI + 0.012295*{BMI}^{2} -0.294211*BMI*Male -0.110063*Age + 0.085589*Age*Male$$

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A 1-inch needle is expected to reach the deltoid in 85.3% of women less than 200 pounds, and 98.6% of men less than 260 pounds. This rate differed between genders (P < 0.001, odds ratio (OR) 0.08, 95% CI (0.02, 0.29)). A 1.5-inch needle is expected to reach the deltoid in 76.7% of women greater than 200 pounds, and 75.0% of men greater than 260 pounds. Current CDC deltoid intramuscular injection needle length guidelines result in women and obese individuals being more likely to receive subcutaneous injections. Age and BMI based guidelines for needle length selection are more accurate.
Feeder-supported in vitro exercise model using human satellite cells from patients with sporadic inclusion body myositis
Authors: Li Yuqing , Chen Weijian , Ogawa Kazumi , Koide Masashi , Takahashi Tadahisa , Hagiwara Yoshihiro , Itoi Eiji , Aizawa Toshimi , Tsuchiya Masahiro , Izumi Rumiko , Suzuki Naoki , Aoki Masashi , Kanzaki Makoto 
Published: January 2022

AbstractContractile activity is a fundamental property of skeletal muscles. We describe the establishment of a “feeder-supported in vitro exercise model” using human-origin primary satellite cells, allowing highly-developed contractile myotubes to readily be generated by applying electrical pulse stimulation (EPS). The use of murine fibroblasts as the feeder cells allows biological responses to EPS in contractile human myotubes to be selectively evaluated with species-specific analyses such as RT-PCR. We successfully applied this feeder-supported co-culture system to myotubes derived from primary satellite cells obtained from sporadic inclusion body myositis (sIBM) patients who are incapable of strenuous exercise testing. Our results demonstrated that sIBM myotubes possess essentially normal muscle functions, including contractility development, de novo sarcomere formation, and contraction-dependent myokine upregulation, upon EPS treatment. However, we found that some of sIBM myotubes, but not healthy control myotubes, often exhibit abnormal cytoplasmic TDP-43 accumulation upon EPS-evoked contraction, suggesting potential pathogenic involvement of the contraction-inducible TDP-43 distribution peculiar to sIBM. Thus, our “feeder-supported in vitro exercise model” enables us to obtain contractile human-origin myotubes, potentially utilizable for evaluating exercise-dependent intrinsic and pathogenic properties of patient muscle cells. Our approach, using feeder layers, further expands the usefulness of the “in vitro exercise model”.
Low heart rate variability from 10-s electrocardiograms is associated with development of non-alcoholic fatty liver disease
Authors: Choi In Young , Chang Yoosoo , Kang Geonggyu , Jung Hyun-Suk , Shin Hocheol , Wild Sarah H. , Byrne Christopher D. , Ryu Seungho 
Published: January 2022

AbstractReduced heart rate variability (HRV) is reflective of autonomic imbalance. However, its impact on non-alcoholic fatty liver disease (NAFLD) is unknown. We investigated the association between 10-s HRV and incident NAFLD. A cohort of 154,286 Korean adults with no NAFLD at baseline were followed up. 10-s electrocardiograms were used to estimate two time-domain HRV, the standard deviation of normal-to-normal intervals (SDNN) and the root mean square of successive differences in RR intervals (RMSSD). Hepatic steatosis (HS) and liver fibrosis were assessed using ultrasonography and the fibrosis-4 index (FIB-4). A total of 27,279 incident HS (median follow up of 4.2 years) and 1250 incident HS plus high FIB-4 (median follow up of 4.2 years) cases were identified at follow-up. The multivariable adjusted hazard ratios (aHRs) (95% confidence intervals [CIs]) in a model with time-dependent variables for incident HS, comparing the lowest quintile to the highest and reference quintile of the RMSSD, was 1.43 (1.37–1.49), and the corresponding HR for incident HS plus intermediate/high FIB-4 was 1.70 (1.35–2.15). Similarly, SDNN was inversely associated with incident HS and HS plus intermediate/high FIB-4. The results were similar using the NAFLD fibrosis score. Autonomic imbalance assessed by HRV may help to identify individuals at a high risk of HS and its progression and warrant further studies.
Objective evaluation of deep uncertainty predictions for COVID-19 detection
Authors: Asgharnezhad Hamzeh , Shamsi Afshar , Alizadehsani Roohallah , Khosravi Abbas , Nahavandi Saeid , Sani Zahra Alizadeh , Srinivasan Dipti , Islam Sheikh Mohammed Shariful 
Published: January 2022

AbstractDeep neural networks (DNNs) have been widely applied for detecting COVID-19 in medical images. Existing studies mainly apply transfer learning and other data representation strategies to generate accurate point estimates. The generalization power of these networks is always questionable due to being developed using small datasets and failing to report their predictive confidence. Quantifying uncertainties associated with DNN predictions is a prerequisite for their trusted deployment in medical settings. Here we apply and evaluate three uncertainty quantification techniques for COVID-19 detection using chest X-Ray (CXR) images. The novel concept of uncertainty confusion matrix is proposed and new performance metrics for the objective evaluation of uncertainty estimates are introduced. Through comprehensive experiments, it is shown that networks pertained on CXR images outperform networks pretrained on natural image datasets such as ImageNet. Qualitatively and quantitatively evaluations also reveal that the predictive uncertainty estimates are statistically higher for erroneous predictions than correct predictions. Accordingly, uncertainty quantification methods are capable of flagging risky predictions with high uncertainty estimates. We also observe that ensemble methods more reliably capture uncertainties during the inference. DNN-based solutions for COVID-19 detection have been mainly proposed without any principled mechanism for risk mitigation. Previous studies have mainly focused on on generating single-valued predictions using pretrained DNNs. In this paper, we comprehensively apply and comparatively evaluate three uncertainty quantification techniques for COVID-19 detection using chest X-Ray images. The novel concept of uncertainty confusion matrix is proposed and new performance metrics for the objective evaluation of uncertainty estimates are introduced for the first time. Using these new uncertainty performance metrics, we quantitatively demonstrate when we could trust DNN predictions for COVID-19 detection from chest X-rays. It is important to note the proposed novel uncertainty evaluation metrics are generic and could be applied for evaluation of probabilistic forecasts in all classification problems.
Visualization of tumor heterogeneity and prediction of isocitrate dehydrogenase mutation status for human gliomas using multiparametric physiologic and metabolic MRI
Authors: Hagiwara Akifumi , Tatekawa Hiroyuki , Yao Jingwen , Raymond Catalina , Everson Richard , Patel Kunal , Mareninov Sergey , Yong William H. , Salamon Noriko , Pope Whitney B. , Nghiemphu Phioanh L. , Liau Linda M. , Cloughesy Timothy F. , Ellingson Benjamin M. 
Published: January 2022

AbstractThis study aimed to differentiate isocitrate dehydrogenase (IDH) mutation status with the voxel-wise clustering method of multiparametric magnetic resonance imaging (MRI) and to discover biological underpinnings of the clusters. A total of 69 patients with treatment-naïve diffuse glioma were scanned with pH-sensitive amine chemical exchange saturation transfer MRI, diffusion-weighted imaging, fluid-attenuated inversion recovery, and contrast-enhanced T1-weighted imaging at 3 T. An unsupervised two-level clustering approach was used for feature extraction from acquired images. The logarithmic ratio of the labels in each class within tumor regions was applied to a support vector machine to differentiate IDH status. The highest performance to predict IDH mutation status was found for 10-class clustering, with a mean area under the curve, accuracy, sensitivity, and specificity of 0.94, 0.91, 0.90, and 0.91, respectively. Targeted biopsies revealed that the tissues with labels 7–10 showed high expression levels of hypoxia-inducible factor 1-alpha, glucose transporter 3, and hexokinase 2, which are typical of IDH wild-type glioma, whereas those with labels 1 showed low expression of these proteins. In conclusion, A machine learning model successfully predicted the IDH mutation status of gliomas, and the resulting clusters properly reflected the metabolic status of the tumors.
Essential function of adaptor protein Nck1 in platelet-derived growth factor receptor signaling in human lens epithelial cells
Authors: Paensuwan Pussadee , Ngoenkam Jatuporn , Wangteeraprasert Apirath , Pongcharoen Sutatip 
Published: January 2022

AbstractBinding of platelet-derived growth factor-BB (PDGF-BB) to its cognate receptor (PDGFR) promotes lens epithelial cell (LEC) proliferation and migration. After cataract surgery, these LEC behaviors have been proposed as an influential cause of posterior capsule opacification (PCO). Stimulated PDFGR undergoes dimerization and tyrosine phosphorylation providing docking sites for a SH2-domain-containing noncatalytic region of tyrosine kinase (Nck). Nck is an adaptor protein acting as a linker of the proximal and downstream signaling events. However, the functions of Nck1 protein in LEC have not been investigated so far. We reported here a crucial role of Nck1 protein in regulating PDGFR-mediated LEC activation using LEC with a silenced expression of Nck1 protein. The knockdown of Nck1 suppressed PDGF-BB-stimulated LEC proliferation and migration and disrupted the cell cycle progression especially G1/S transition. LEC lacking Nck1 protein failed to exhibit actin polymerization and membrane protrusions. The downregulation of Nck1 protein in LEC impaired PDGFR‐induced phosphorylation of intracellular signaling proteins, including Erk1/2, Akt, CREB and ATF1, which resulted in inhibition of LEC responses. Therefore, these data suggest that the loss of Nck1 expression may disturb LEC activation and Nck1 may potentially be a drug target to prevent PCO and lens-related disease.
A digital clock and data strobe aligner for write calibration of dynamic random access memory
Authors: Jung Chae‐Young , Lee Won‐Young 
Published: January 2022

AbstractThis paper proposes a digital clock and data strobe aligner for write calibration of dynamic random access memory (DRAM). The edge recognizer determines the input phase skew between a falling edge of clock and a rising edge of data strobe (DQS) signal to maximize setup and hold margins of DQS and clock synchronization. According to experimental results, the proposed circuit achieves the minimum and maximum output skews are −6.9 ps and 7.5 ps when DQS skews of ±227 ps are applied. The chip has been fabricated in 180 nm CMOS technology and the active chip area is 0.091 mm2.
Pinellic Acid Isolated from Quercetin-rich Onions has a Peroxisome Proliferator-Activated Receptor-Alpha/Gamma (PPAR-α/γ) Transactivation Activity
Authors: Doi Mikio , Morita Naoki , Okuzawa Tsugumi , Ohgiya Satoru , Okamoto Daisaku , Sato Kenichi , Ito Yukiya , Matsuura Hideyuki , Hashidoko Yasuyuki 
Published: January 2022

AbstractQuercetin, a flavonol, is a functional compound that is abundant in onions and is known to have antioxidant and anti-inflammatory effects. Quercetin and its glucoside are known to function as peroxisome proliferator-activated receptor (PPAR) ligands and showed high PPAR-α transactivation activity but little PPAR-γ transactivation activity in some reports. In this study, we demonstrated that an aqueous extract of a quercetin-rich onion cultivar increased transactivation activities not only of PPAR-α but also of PPAR-γ. We isolated (9S,12S,13S)-(10E)-9,12,13-trihydroxyoctadec-10-enoic acid (pinellic acid) obtained from the aqueous extract using PPAR-γ transactivation as an index. Furthermore, it was revealed that pinellic acid could transactivate PPAR-α. Our findings are the first report mentioned showing that trihydroxyoctadec-10-enoic acids showed PPAR-α/γ transactivation activities.
Microwave-Assisted Aminoalkylation of Phenols via Mustard Carbonate Analogues
Authors: Aricò Fabio , Viviano Monica , Trapasso Giacomo , Annatelli Mattia , Milite Ciro , Castellano Sabrina 
Published: January 2022

AbstractA microwave-assisted chlorine-free direct phenol substitution is presented, which is indicated as a key green chemistry research area for pharmaceuticals manufacturers. The reaction of β-aminocarbonates (mustard carbonates) with several substituted phenols in the presence of a polar solvent (acetonitrile or butanol) led to the related aminoalkylated products via the anchimeric assistance of the nitrogen incorporated in the organic carbonate backbone. The aminoalkylation required short reaction time (7 min) and the related products were isolated in high yields (>90%) via quick liquid-liquid extraction or column chromatography depending on the solvent employed. Furthermore, microwave irradiation also promoted the one-pot aminoalkylation of phenol in excellent yield. In this approach a β-aminoalcohol was reacted with phenol in the presence of diethyl carbonate, used for the in situ formation β-aminocarbonate, key intermediate in the consequent anchimerically driven alkylation. The resulting product, namely N,N-dimethyl-2-phenoxyethanamine, was isolated as pure in almost quantitative yield.