bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediagnostic concentrations of circulating bile acids and hepatocellular carcinoma risk: REVEAL‐HBV and HCV studies
Authors: Petrick Jessica L. , Florio Andrea A. , Koshiol Jill , Pfeiffer Ruth M. , Yang Baiyu , Yu Kelly , Chen Chien‐Jen , Yang Hwai‐I , Lee Mei‐Hsuan , McGlynn Katherine A. 
Published: May 2020

AbstractHepatocellular carcinoma (HCC) is the dominant histologic type of liver cancer, accounting for 75% of cases. Growing evidence suggests that the cross‐talk between the gut microbiome and metabolome (ie, gut‐liver axis) are related to the development of hepatic inflammation, and ultimately, HCC. Bile acids are metabolites, derived from cholesterol and synthesized in the liver, which may have a critical role in regulation of the gut‐liver axis. We investigated whether prediagnostic circulating bile acids were associated with HCC risk, using the Risk Evaluation of Viral Load Elevation and Associated Liver Disease/Cancer (REVEAL)‐Hepatitis B Virus (HBV) and REVEAL‐Hepatitis C Virus (HCV) cohorts from Taiwan. Fifteen bile acids were quantitated using liquid chromatography, from 185 cases and 161 matched controls in REVEAL‐HBV and 96 cases and 96 matched controls in REVEAL‐HCV. Odds ratios (ORs) and 95% confidence intervals (CIs) for associations between bile acid levels and HCC were calculated using multivariable‐adjusted logistic regression. Higher levels of glycine and taurine conjugated primary bile acids were associated with a 2‐ to 8‐fold increased risk of HBV‐ (eg, glycocholic acid ORQ4vsQ1 = 3.38, 95% CI: 1.48‐7.71, Ptrend < .003) and HCV‐related HCC (eg, OR = 8.16, 95% CI: 2.21‐30.18, Ptrend < .001). However, higher levels of the secondary bile acid deoxycholic acid were inversely associated with HBV‐related HCC risk (OR = 0.41, 95% CI: 0.19‐0.88, Ptrend = .02). Our study provides evidence that higher concentrations of bile acids—specifically, conjugated primary bile acids—are associated with increased HCC risk. However, our study does not support the hypothesis that higher levels of secondary bile acids increase liver cancer risk; indeed, deoxycholic acid may be associated with a decreased HCC risk.
An EGFR signature predicts cell line and patient sensitivity to multiple tyrosine kinase inhibitors
Authors: Cheng Chao , Zhao Yanding , Schaafsma Evelien , Weng Yi‐Lan , Amos Christopher 
Published: May 2020

AbstractEGFR is an oncogene with a high frequency of activating mutations in nonsmall cell lung cancer (NSCLC). EGFR inhibitors have been FDA‐approved for NSCLC and have shown efficacy in patients with certain EGFR mutations. However, only 9% to 26% of these patients achieve objective responses. In our study, we developed an EGFR gene signature based on The Cancer Genome Atlas (TCGA) RNA‐seq data of lung adenocarcinoma (LUAD) to direct the preselection of patients for more effective EGFR‐targeted therapy. This signature infers baseline EGFR signaling pathway activity (denoted as EGFR score) in tumor samples, which is associated with tumor sensitivity to EGFR inhibitors and other tyrosine kinase inhibitors (TKIs). EGFR score predicted sensitivity of lung cancer cell lines to Erlotinib, Gefitinib and Sorafenib. Importantly, EGFR score calculated from pretreated samples was associated with patient response to Gefitinib and Sorafenib in lung cancer. Additionally, integration of the EGFR signature with TCGA LUAD data showed that it accurately predicted functional effects of different somatic EGFR mutations, and identified other mutations affecting EGFR pathway activity. Finally, using cancer cell line and clinical trial data, the EGFR score was associated with patient response to TKIs in liver cancer and other cancer types. The EGFR signature provides a useful biomarker that can expand the application of EGFR inhibitors or other TKIs and improve their treatment efficacy through patient stratification.
Efficacy of Nasal Airflow‐Inducing Maneuver in Laryngectomy Patients: A Retrospective Cohort Study
Authors: Ishikawa Yukinobu , Suzuki Michi , Yanagi Yukiko , Kurihara Miyuki , Kawamura Nagomi , Konomi Ujimoto 
Published: May 2020

ObjectiveTo evaluate the effectiveness of the nasal airflow‐inducing maneuver (NAIM) using the Sniffin' Sticks (Burghart, Wedel, Germany) olfactory threshold test, Open Essence (OE, FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) olfactory identification test, and self‐administered odor questionnaire (SAOQ) for olfactory perception in NAIM experienced and NAIM first‐time groups. For NAIM first‐time group, the relationships between time from laryngectomy to first NAIM, olfactory threshold, and identification ability were also evaluated.Study DesignRetrospective cohort study.MethodsSixty‐six patients who had undergone laryngectomy (NAIM experienced group: 23; NAIM first‐time group: 43) underwent the threshold test, OE, and SAOQ.ResultsMean results of the threshold test were 2.7 (±2.3) and 2.5 (±3.0) for the NAIM experienced and NAIM first‐time groups, respectively, indicating no significant differences (P = .35). The mean number of correct responses in OE was 4.5 (±2.7) and 3.2 (±3.0) in the NAIM experienced and nonrehabilitation groups, respectively, indicating a higher number in the NAIM experienced group (P = .06). Mean result of SAOQ was 47.9% (±30.9%) and 25.5% (±27.0%) in the NAIM experienced and NAIM first‐time groups, respectively, indicating a significantly higher result in the NAME experienced group (P = .003). There were no correlations of threshold test and identification test scores with time from laryngectomy to the first NAIM (threshold test: r = 0.03, P = .87; OE: r = −0.03, P = .87).ConclusionNAIM enabled odor perception in patients who underwent laryngectomy, and SAOQ was an effective method for evaluating this. Further, olfactory tests in both groups showed that NAIM might restore olfaction irrespective of time elapsed since laryngectomy.Level of Evidence4. Laryngoscope, 130: 2013–2018, 2020
Rapid Diagnosis of Spinocerebellar Ataxia 36 in a Three‐Generation Family Using Short‐Read Whole‐Genome Sequencing Data
Authors: Rafehi Haloom , Szmulewicz David J. , Pope Kate , Wallis Mathew , Christodoulou John , White Susan M. , Delatycki Martin B. , Lockhart Paul J. , Bahlo Melanie 
Published: May 2020

AbstractBackgroundSpinocerebellar ataxias are often caused by expansions of short tandem repeats. Recent methodological advances have made repeat expansion (RE) detection with whole‐genome sequencing (WGS) feasible.ObjectivesThe objective of this study was to determine the genetic basis of ataxia in a multigenerational Australian pedigree with autosomal‐dominant inheritance.Methods and ResultsWGS was performed on 3 affected relatives. The sequence data were screened for known pathogenic REs using 2 RE detection tools: exSTRa and ExpansionHunter. This screen provided a clear and rapid diagnosis (<5 days from receiving the sequencing data) of spinocerebellar ataxia 36, a rare form of ataxia caused by an intronic GGCCTG RE in NOP56.ConclusionsThe diagnosis of rare ataxias caused by REs is highly feasible and cost‐effective with WGS. We propose that WGS could potentially be implemented as the frontline, cost‐effective methodology for the molecular testing of individuals with a clinical diagnosis of ataxia. © 2020 International Parkinson and Movement Disorder Society
Improved transmission length in the presences of ambient noise and scintillation effect using duobinary modulation in 40 Gbps free space optical channel
Authors: Manzoor Habib Ullah , Manzoor Sanaullah , Manzoor Tareq , Khan Talha , Hussain Ashiq 
Published: May 2020

AbstractFree space optical (FSO) communication has gained significant popularity in recent years due to large bandwidth, license‐free spectrum, high data rates, less power consumption, and low mass requirements. However, system performance strongly depends on atmospheric conditions and ambient noise. In this letter, the duobinary modulation technique is applied and the system performance is investigated in the presence of ambient noise. The system is evaluated on the basis of Q‐factor, eye diagram, input power, transmission distance, and bit error rate. A significant improvement is observed in the presence of noise while using duobinary modulation. This study exploits extensive simulations to investigate the performance of the system. All simulations are performed for a single link of FSO communication network having a data rate of 40 Gbps in the Optisystem simulator and ambient noise is created using LEDs. After the exhaustive set of simulations, a significant improvement in transmission length is observed. It is also observed that at low input power, doubinary modulation provides better results when compared with on‐off keying (OOK) format. Scintillation effect has also be observed for doubinary modulation and compared with OOK modulation format. It is concluded that doubinary modulation provides better results in the presence of low and moderate scintillation.
Technical Note: New similarity index for radiotherapy and medical imaging
Authors: Kuperman Vadim Y. , Figueiredo Gustavo 
Published: May 2020

PurposeTo describe a new similarity index and consider its biomedical applications.MethodsSimilarity index for a pair of objects is defined by the number of shared features and total number of features in these objects. Similarity measure for more than two objects is commonly defined by using pairwise similarity indices. In the current study we suggest a novel similarity index which depends on the number of features shared between multiple objects and does not have the limitations of the recently described similarity measures. In order to introduce the new index, we consider a concept of “commonality.” For a collection of sets

, commonality of a given element equals the number of sets this element belongs to. The similarity index for the compared sets is then defined by a weighted sum of normalized commonalities.ResultsThe considered biomedical applications of the proposed index include comparison of independent delineations of critical cranial structures in MR images and comparison of isodose distributions from different radiotherapy plans.ConclusionsThis study describes a novel similarity index which can be used to assess the similarity of multiple independent delineations of the anatomical structure or similarity of multiple dose distributions. Unlike the commonly used pairwise similarity indices, the new index is defined by the number of elements shared between multiple sets. Potential applications of the suggested similarity index for radiotherapy and medical imaging have been described.
Deep learning for identification of critical regions associated with toxicities after liver stereotactic body radiation therapy
Authors: Ibragimov Bulat , Toesca Diego A. S. , Chang Daniel T. , Yuan Yixuan , Koong Albert C. , Xing Lei , Vogelius Ivan R. 
Published: May 2020

PurposeRadiation therapy (RT) is prescribed for curative and palliative treatment for around 50% of patients with solid tumors. Radiation‐induced toxicities of healthy organs accompany many RTs and represent one of the main limiting factors during dose delivery. The existing RT planning solutions generally discard spatial dose distribution information and lose the ability to recognize radiosensitive regions of healthy organs potentially linked to toxicity manifestation. This study proposes a universal deep learning‐based algorithm for recognitions of consistent dose patterns and generation of toxicity risk maps for the abdominal area.MethodsWe investigated whether convolutional neural networks (CNNs) can automatically associate abdominal computed tomography (CT) images and RT dose plans with post‐RT toxicities without being provided segmentation of abdominal organs. The CNNs were also applied to study RT plans, where doses at specific anatomical regions were reduced/increased, with the aim to pinpoint critical regions sparing of which significantly reduces toxicity risks. The obtained risk maps were computed for individual anatomical regions inside the liver and statistically compared to the existing clinical studies.ResultsA database of 122 liver stereotactic body RT (SBRT) executed at Stanford Hospital from July 2004 and November 2015 was assembled. All patients treated for primary liver cancer, mainly hepatocellular carcinoma and cholangiocarcinoma, with complete follow‐ups were extracted from the database. The SBRT treatment doses ranged from 26 to 50 Gy delivered in 1–5 fractions for primary liver cancer. The patients were followed up for 1–68 months depending on the survival time. The CNNs were trained to recognize acute and late grade 3+ biliary stricture/obstruction, hepatic failure or decompensation, hepatobiliary infection, liver function test (LFT) elevation or/and portal vein thrombosis, named for convenience hepatobiliary (HB) toxicities. The toxicity prediction accuracy was of 0.73 measured in terms of the area under the receiving operator characteristic curve. Significantly higher risk scores (P < 0.05) of HB toxicity manifestation were associated with irradiation for the hepatobiliary tract in comparison to the risk scores for liver segments I–VIII and portal vein. This observation is in strong agreement with anatomical and clinical expectations.ConclusionIn this work, we proposed and validated a universal deep learning‐based solution for the identification of radiosensitive anatomical regions. Without any prior anatomical knowledge, CNNs automatically recognized the importance of hepatobiliary tract sparing during liver SBRT.
Multi‐parametric liver tissue characterization using MR fingerprinting: Simultaneous T1, T2, T2*, and fat fraction mapping
Authors: Jaubert Olivier , Arrieta Cristobal , Cruz Gastão , Bustin Aurélien , Schneider Torben , Georgiopoulos Georgios , Masci Pier‐Giorgio , Sing‐Long Carlos , Botnar Rene M. , Prieto Claudia 
Published: May 2020

PurposeQuantitative T1, T2, T2*, and fat fraction (FF) maps are promising imaging biomarkers for the assessment of liver disease, however these are usually acquired in sequential scans. Here we propose an extended MR fingerprinting (MRF) framework enabling simultaneous liver T1, T2, T2*, and FF mapping from a single ~14 s breath‐hold scan.MethodsA gradient echo (GRE) liver MRF sequence with nine readouts per TR, low flip angles (5‐15°), varying magnetisation preparation and golden angle radial trajectory is acquired at 1.5T to encode T1, T2, T2*, and FF simultaneously. The nine‐echo time‐series are reconstructed using a low‐rank tensor constrained reconstruction and used to fit T2*, B0 and to separate the water and fat signals. Water‐ and fat‐specific T1, T2, and M0 are obtained through dictionary matching, whereas FF estimation is extracted from the M0 maps. The framework was evaluated in a standardized T1/T2 phantom, a water‐fat phantom, and 12 subjects in comparison to reference methods. Preliminary clinical feasibility is shown in four patients.ResultsThe proposed water T1, water T2, T2*, and FF maps in phantoms showed high coefficients of determination (r2 > 0.97) relative to reference methods. Measured liver MRF values in vivo (mean ± SD) for T1, T2, T2*, and FF were 671 ± 60 ms, 43.2 ± 6.8 ms, 29 ± 6.6 ms, and 3.2 ± 2.6% with biases of 92 ms, −7.1 ms, −1.4 ms, and 0.63% when compared to conventional methods.ConclusionA nine‐echo liver MRF sequence allows for quantitative multi‐parametric liver tissue characterization in a single breath‐hold scan of ~14 s. Future work will aim to validate the proposed approach in patients with liver disease.
Impact of multimedia learning tools in agricultural science classes
Authors: Ulery April , Smith Muise Amy , Carroll Kenneth C. , Chamberlin Barbara , White Laura , Martinez Pamela , Spears LaJoy , Gleason Jeanne 
Published: May 2020

AbstractAgricultural and environmental scientists collaborated with educational technology researchers to create multimedia learning tools to fill gaps in student understanding of key concepts that undergraduates often struggle with, including sorption, cation exchange capacity, inner and outer sphere bonding, and soil system complexity. These resources are freely available online at ScienceOfAgriculture.org. The modules were evaluated in several soil, environmental science, and agriculture classes using pre‐ and post‐tests via survey tool Qualtrics. After watching the videos, nearly all students (95%) stated the videos would be “extremely valuable” or “valuable” to their studies, and 90% said, “other students in an introductory class on agricultural topics” would benefit from the tools. Key chemistry concepts also gained traction, especially concepts related to soils and charged particles. Before watching “Cation Exchange,” 49% of the students identified divalent cations (vs. monovalent) as the ions that would be held tightest in soils typical of temperate regions. After watching, 83% answered correctly. Before watching Cation Exchange, only 56% of students correctly identified clay and organic matter in soil as usually being negatively charged, but after watching, 97% of students correctly identified the particle charge. The study was hampered by the fact that as many as 53% of the survey attempts were not successful, either because the student did not complete both pre‐ and post‐tests or they did not sign the permission page.
Micromechanical modeling and characterization of elastic behavior of carbon nanotube‐reinforced polymer nanocomposites: A combined numerical approach and experimental verification
Authors: Kassa Mesfin Kebede , Arumugam Ananda Babu 
Published: May 2020

AbstractIn this study, a combined analytical and finite element‐based micromechanical modeling is performed to characterize the elastic properties of carbon nanotube (CNT) reinforced polymer nanocomposites and validated with experimental work. First, coordinates of armchair and zigzag type CNTs are generated using MATLAB based on the geometric structure of the CNTs and imported to the computational software ANSYS to model and characterize the elastic properties of the individual single‐walled CNT (SWCNT) and multi‐walled CNT by applying various loading and boundary conditions. The present developed finite element method (FEM) model of CNTs is validated with the available literature in terms of elastic properties. Subsequently, the equivalent elastic properties of CNT reinforced epoxy nanocomposites are determined through representative volume element (RVE) model by finite element simulations and Mori‐Tanaka homogenization techniques by replacing CNTs with equivalent fibers as microinclusions. The equivalent elastic properties of nanocomposite obtained by the FEM and analytical model are compared and validated with the experimental results. Further, the detailed parametric study is performed to investigate the influence of tube chirality, volume fraction, and orientation of CNT in terms of the elastic properties of the nanocomposite. It was observed that the armchair type CNT reinforced nanocomposites are stiffer than the zigzag type SWCNT reinforced nanocomposites in terms of elastic moduli. Further, it was noticed that the tube chirality and the number of walls of CNTs have significantly influenced the elastic behavior of nanocomposites. It can be concluded that the presented combined model provides an efficient methodology and comprehensive understanding to analyze the elastic behavior of CNTs and CNT reinforced nanocomposites. So, the presented combined numerical and experimental study could serve as a guideline in micromechanical modeling and characterization of elastic behavior of CNT‐reinforced polymer nanocomposites.
Nano‐silica modification of UV‐curable EVA resin for additive manufacturing
Authors: Xue Hanyu , Ye Yuansong , Li Xinzhong , Xia Jianrong , Lin Qi 
Published: May 2020

AbstractDue to layer by layer printing, the interlayer adhesion of resin used in extrusion‐based additive manufacturing (AM) is poor, while thermal curing affects the accuracy of the resin. Therefore, methods of photo‐curing and nanomodification were used in this work to improve the adhesion between layers and the overall performance of AM resins. Specifically, ethylene‐vinyl acetate (EVA) copolymer with dual curing agent of benzophenone/triallyl isocyanurate (BP/TAIC) and nano‐silica (NS) were introduced. The results of light transmittance, scanning electron microscopy and gel content test showed that BP/TAIC with NS were proved to be able to improve the curing process of EVA. The filling of a small amount of NS did not act as ultraviolet light barrier, but instead improved the photo‐curing of the resin and reduced the amount of agents. UV curing also improved the adhesion between layers of EVA resin. The tensile strength was 7.1% higher than that of EVA/NS/BT without curing. At the same time, due to good interface bonding and dispersion, the thermal conductivity of resin improved from 0.212 W/m·k to 0.252 W/m·k. A 16.1% raise in tensile strength and a 10.0% increase in the volume resistivity were demonstrated for the 3.0 wt% NS. Furthermore, this resin is potential to be used in AM.
Ignition and Combustion Developments of Granular Explosive (RDX/HMX) in Response to Mild‐Impact Loading
Authors: Wu Yanqing , Duan Hongzheng , Yang Kun , Guo Hongfu , Huang Fenglei 
Published: May 2020

AbstractThe experimental analyses of ignition and burning responses of mild‐impacted granular explosive, namely, cyclotrimethylene trinitramine (RDX) and cyclotetramethylene tetranitramine (HMX), were performed based on an optimized drop‐weight system equipped with a High‐Speed Camera (HSC). It has been found that jetting phenomena observed by HSC is the result of the energy released by gaseous products, which push the pulverized or melted explosives to splash radially. Jetting is the only and the most obvious difference between reactive and inert particles prior to combustion so that it can be regarded as the sign of ignition more accurately than other ways. For RDX sample, the molten phase plays an important role in the hot‐spots formation. After a piece of waxed paper is put on the glass anvil, the jetting of molten‐phase RDX will be limited due to the high‐roughness of waxed paper. Moreover, ignition growth to burning probability of RDX particles is increased compared with the non‐waxed paper case. Radial deformation velocity, jetting velocity, and flame propagation velocity have been estimated via image processing, making it possible to quantify the violence of mechanical deformation and chemical reaction.
Identification and transcriptional response of ATP‐binding cassette transporters to chlorantraniliprole in the rice striped stem borer, Chilo suppressalis
Authors: Meng Xiangkun , Yang Xuemei , Wu Zhaolu , Shen Qinwen , Miao Lijun , Zheng Yang , Qian Kun , Wang Jianjun 
Published: May 2020

AbstractBACKGROUNDAs the largest transporter gene family in metazoans, ATP‐binding cassette (ABC) transporters regulate the efflux of a broad spectrum of substrates from the cytoplasm to the outside of the cell. In arthropods, ABC transporters are involved in phase III of the detoxification process, and play important roles in the metabolism and transport of insecticides.RESULTSWe identified 54 ABC transporters from the genome and transcriptome of Chilo suppressalis, one of the most damaging pests of rice in China. The identified ABC transporters were classified into eight subfamilies (ABCA to ABCH) based on NCBI BLAST and phylogenetic analysis. Synergism studies showed that treatment with verapamil, a potent inhibitor of ABC transporters, resulted in significantly increased toxicity of chlorantraniliprole against C. suppressalis larvae. Among the 21 tested ABC genes, three ABC transporter genes including CsABCC8, CsABCG1C and CsABCH1 were significantly upregulated after chlorantraniliprole treatment.CONCLUSIONABC transporters play important roles in the detoxification and transport of chlorantraniliprole in C. suppressalis. The results from our study provide valuable information on C. suppressalis ABC transporters, and are helpful in understanding the roles of ABC transporters in chlorantraniliprole resistance mechanisms in C. suppressalis and other insect pests. © 2020 Society of Chemical Industry