bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radiological and Clinical Features associated with Epidermal Growth Factor Receptor Mutation Status of Exon 19 and 21 in Lung Adenocarcinoma
Authors: Shi Zhang , Zheng Xuan , Shi Ruifeng , Song Changen , Yang Runhong , Zhang Qianwen , Wang Xinrui , Lu Jianping , Yu Yongwei , Liu Qi , Jiang Tao 
Published: March 2017

AbstractThe exon 19 and 21 in Epidermal Growth Factor Receptor (EGFR) mutation are the most common subtype of lung adenocarcinoma, and the strongest predictive biomarker for progression-free survival and tumor response. Although some studies have shown differences in radiological features between cases with and without EFGR mutations, they lacked necessary stratification. This article is to evaluate the association of CT features between the wild type and the subtype (exon 19 and 21) of EGFR mutations in patients with lung adenocarcinoma. Of the 721 finally included patients, 132 were positive for EGFR mutation in exon 19, 140 were positive for EGFR mutation in exon 21, and 449 were EGFR wild type. EGFR mutation in exon 19 was associated with a small-maximum diameter (28.51 ± 14.07) (p < 0.0001); sex (p < 0.0001); pleural retraction (p = 0.0034); and the absence of fibrosis (p < 0.0001), while spiculated margins (p = 0.0095), subsolid density (p < 0.0001) and no smoking (p < 0.0001) were associated with EGFR mutation in exon 21. Receiver Operating Characteristic (ROC) curves suggested that the maximum Area Under the Curve (AUC) was related to the female gender (AUC = 0.636) and the absence of smoking (AUC = 0.681). This study demonstrated the radiological and clinical features could be used to prognosticate EGFR mutation subtypes in exon 19 and 21.
Rheumatoid Arthritis Fibroblast-like Synoviocyte Suppression Mediated by PTEN Involves Survivin Gene Silencing
Authors: Chen Danna , Liu Dongdong , Liu Dan , He Min , Peng Anping , Xu Jiarui , Lin Li , Luo Fudong , Chen Lin , Huang Xianzhang , Zhuang Junhua , Xu Jianhua 
Published: March 2017

AbstractSurvivin is a proto-oncogene biomarker known for its anti-apoptotic and cell cycle regulating properties induced by the activation of the phosphoinositide 3-kinase (PI3K)/Akt pathway. In the context of non-cancer pathology, such as rheumatoid arthritis (RA), survivin has emerged as a feature associated with severe joint damage and poor treatment response. Phosphatase and tensin homolog (PTEN) is a phosphatase antagonizing all classes of PI3K. The interplay between survivin oncogenic mechanisms and proliferation suppression networks in RA has remained largely elusive. This study investigated the effect of PTEN on survivin gene expression in rheumatiod arthritis fibroblast-like synoviocyte (RA-FLS). We showed for the first time that the suppression of RA-FLS was mediated by PTEN involving survivin silencing. Considering that survivin suppressants are currently available in clinical trials and clinical use, their effects in RA-FLS support a probably RA therapy to clinical practice.
Voltage-induced Interface Reconstruction and Electrical Instability of the Ferromagnet-Semiconductor Device
Authors: Chang Shu-Jui , Chang Po-Chun , Lin Wen-Chin , Lo Shao-Hua , Chang Liang-Chun , Lee Shang-Fan , Tseng Yuan-Chieh 
Published: March 2017

AbstractUsing x-ray magnetic spectroscopy with in-situ electrical characterizations, we investigated the effects of external voltage on the spin-electronic and transport properties at the interface of a Fe/ZnO device. Layer-, element-, and spin-resolved information of the device was obtained by cross-tuning of the x-ray mode and photon energy, when voltage was applied. At the early stage of the operation, the device exhibited a low-resistance state featuring robust Fe-O bonds. However, the Fe-O bonds were broken with increasing voltage. Breaking of the Fe-O bonds caused the formation of oxygen vacancies and resulted in a high-resistance state. Such interface reconstruction was coupled to a charge-transfer effect via Fe-O hybridization, which suppressed/enhanced the magnetization/coercivity of Fe electronically. Nevertheless, the interface became stabilized with the metallic phase if the device was continuously polarized. During this stage, the spin-polarization of Fe was enhanced whereas the coercivity was lowered by voltage, but changes of both characteristics were reversible. This stage is desirable for spintronic device applications, owing to a different voltage-induced electronic transition compared to the first stage. The study enabled a straightforward detection of the spin-electronic state at the ferromagnet-semiconductor interface in relation to the transport and reversal properties during operation process of the device.
Analyses of publicly available genomics resources define FGF-2-expressing bladder carcinomas as EMT-prone, proliferative tumors with low mutation rates and high expression of CTLA-4, PD-1 and PD-L1
Authors: McNiel Elizabeth A , Tsichlis Philip N 
Published: March 2017

AbstractFibroblast growth factor 2 (FGF-2) is overexpressed in a subset of invasive bladder carcinomas and its overexpression correlates with poor prognosis. Analyses of publicly available databases addressing the molecular mechanisms that may be responsible for the poor prognosis of these tumors, revealed that FGF-2 expression correlates positively with the expression of epithelial to mesenchymal transition (EMT)-promoting transcription factors and with changes in gene expression that are characteristic of EMT. The same analyses also revealed that FGF-2 correlates negatively with the expression, mutation and copy number variations of FGFR-3, all of which are associated with noninvasive bladder carcinomas. Finally, they showed that FGF-2 expression correlates with the expression of FGFR-1, the expression of the IIIc variant of FGFR-2 and with the expression of Akt3. The latter observation is significant because our earlier studies had shown that Akt3 regulates FGFR-2 alternative splicing, shifting the balance toward the IIIc relative to the IIIb FGFR-2 splice variant. As the IIIc variant is recognized by FGF-2, while the IIIb variant is not, we conclude that Akt3 may facilitate the FGF-2 response. FGF-2 is known to promote the expression of KDM2B, which functions in concert with EZH2 to repress the EZH2-targeting microRNA miR-101, activating a switch, which stably upregulates EZH2. The cancer genome atlas (TCGA) data showing a correlation between KDM2B and EZH2 expression and Oncomine data, showing a correlation between KDM2B and tumor progression, strongly support the role of the FGF-2/KDM2B/miR-101/EZH2 pathway in bladder cancer. These observations combined, suggest a model according to which FGF-2 induces EMT, cell proliferation and cancer stem cell self-renewal by coupling the Akt3 and KDM2B-controlled pathways outlined above, in bladder carcinomas. Further analyses of publicly available databases, revealed that FGF-2-expressing bladder carcinomas carry fewer genetic alterations and they tend to express high levels of CTLA-4, PD-1 and PD-L1, which suggests immune blockade by checkpoint activation. EMT, enhanced proliferation and immune checkpoint activation combined, may be responsible for the poor prognosis of FGF-2-expressing bladder carcinomas.
Locus-specific Retention Predictor (LsRP): A Peptide Retention Time Predictor Developed for Precision Proteomics
Authors: Lu Wenyuan , Liu Xiaohui , Liu Shanshan , Cao Weiqian , Zhang Yang , Yang Pengyuan 
Published: March 2017

AbstractThe precision prediction of peptide retention time (RT) plays an increasingly important role in liquid chromatography–tandem mass spectrometry (LC–MS/MS) based proteomics. Owing to the high reproducibility of liquid chromatography, RT prediction provides promising information for both identification and quantification experiment design. In this work, we present a Locus-specific Retention Predictor (LsRP) for precise prediction of peptide RT, which is based on amino acid locus information and Support Vector Regression (SVR) algorithm. Corresponding to amino acid locus, each peptide sequence was converted to a featured locus vector consisting of zeros and ones. With locus vector information from LC-MS/MS data sets, an SVR computational process was trained and evaluated. LsRP finally provided a prediction correlation coefficient of 0.95~0.99. We compared our method with two common predictors. Results showed that LsRP outperforms these methods and tracked up to 30% extra peptides in an extraction RT window of 2 min. A new strategy by combining LsRP and calibration peptide approach was then proposed, which open up new opportunities for precision proteomics.
Changes in miRNA in the lung and whole blood after whole thorax irradiation in rats
Authors: Gao Feng , Liu Pengyuan , Narayanan Jayashree , Yang Meiying , Fish Brian L. , Liu Yong , Liang Mingyu , Jacobs Elizabeth R. , Medhora Meetha 
Published: March 2017

AbstractWe used a rat model of whole thorax x-ray irradiation to profile the microRNA (miRNA) in lung and blood up to 4 weeks after radiation. MiRNA from normal and irradiated Wistar rat lungs and whole blood were analyzed by next-generation sequencing and the changes by radiation were identified by differential deRNA-seq 1, 2, 3 and 4 weeks after irradiation. The average total reads/library was 2,703,137 with a mean of 88% mapping to the rat genome. Detailed profiles of 100 of the most abundant miRNA in rat blood and lung are described. We identified upregulation of 4 miRNA, miR-144-5p, miR-144-3p, miR-142-5p and miR-19a-3p in rat blood 2 weeks after radiation that have not previously been shown to be altered after radiation to the lung. Ingenuity Pathway Analysis identified signaling of inflammatory response pathways. These findings will support development of early detection methods, as well as mechanism(s) of injury and mitigation in patients after radiotherapy or radiological accidents.
Exploring the under-investigated “microbial dark matter” of drinking water treatment plants
Authors: Bruno Antonia , Sandionigi Anna , Rizzi Ermanno , Bernasconi Marzia , Vicario Saverio , Galimberti Andrea , Cocuzza Clementina , Labra Massimo , Casiraghi Maurizio 
Published: March 2017

AbstractScientists recently reported the unexpected detection of unknown or poorly studied bacterial diversity in groundwater. The ability to uncover this neglected biodiversity mainly derives from technical improvements, and the term “microbial dark matter” was used to group taxa poorly investigated and not necessarily monophyletic. We focused on such under-investigated microbial dark matter of drinking water treatment plant from groundwater, across carbon filters, to post-chlorination. We tackled this topic using an integrated approach where the efficacy of stringent water filtration (10000 MWCO) in recovering even the smallest environmental microorganisms was coupled with high-throughput DNA sequencing to depict an informative spectrum of the neglected microbial diversity. Our results revealed that the composition of bacterial communities varies across the plant system: Parcubacteria (OD1) superphylum is found mainly in treated water, while groundwater has the highest heterogeneity, encompassing non-OD1 candidate phyla (Microgenomates, Saccharibacteria, Dependentiae, OP3, OP1, BRC1, WS3). Carbon filters probably act as substrate for microorganism growth and contribute to seeding water downstream, since chlorination does not modify the incoming bacterial community. New questions arise about the role of microbial dark matter in drinking water. Indeed, our results suggest that these bacteria might play a central role in the microbial dynamics of drinking water.
Vitamin D inhibits lymphangiogenesis through VDR-dependent mechanisms
Authors: Yazdani Saleh , Poosti Fariba , Toro Luis , Wedel Johannes , Mencke Rik , Mirković Katarina , de Borst Martin H. , Alexander J. Steven , Navis Gerjan , van Goor Harry , van den Born Jacob , Hillebrands Jan-Luuk 
Published: March 2017

AbstractExcessive lymphangiogenesis is associated with cancer progression and renal disease. Attenuation of lymphangiogenesis might represent a novel strategy to target disease progression although clinically approved anti-lymphangiogenic drugs are not available yet. VitaminD(VitD)-deficiency is associated with increased cancer risk and chronic kidney disease. Presently, effects of VitD on lymphangiogenesis are unknown. Given the apparently protective effects of VitD and the deleterious associations of lymphangiogenesis with renal disease, we here tested the hypothesis that VitD has direct anti-lymphangiogenic effects in vitro and is able to attenuate lymphangiogenesis in vivo. In vitro cultured mouse lymphatic endothelial cells (LECs) expressed VitD Receptor (VDR), both on mRNA and protein levels. Active VitD (calcitriol) blocked LEC tube formation, reduced LEC proliferation, and induced LEC apoptosis. siRNA-mediated VDR knock-down reversed the inhibitory effect of calcitriol on LEC tube formation, demonstrating how such inhibition is VDR-dependent. In vivo, proteinuric rats were treated with vehicle or paricalcitol for 6 consecutive weeks. Compared with vehicle-treated proteinuric rats, paricalcitol showed markedly reduced renal lymphangiogenesis. In conclusion, our data show that VitD is anti-lymphangiogenic through VDR-dependent anti-proliferative and pro-apoptotic mechanisms. Our findings highlight an important novel function of VitD demonstrating how it may have therapeutic value in diseases accompanied by pathological lymphangiogenesis.
Synergistic efficacy of Bisbenzimidazole and Carbonyl Cyanide 3-Chlorophenylhydrazone combination against MDR bacterial strains
Authors: Sinha Devapriya , Pandey Stuti , Singh Raja , Tiwari Vinod , Sad Kirti , Tandon Vibha 
Published: March 2017

AbstractActivation of efflux systems and the formation of biofilm are majorly adapted by microbes to resist antimicrobial agents. PPEF (bisbenzimidazole) targeting topoisomerase IA is observed to be an effective bactericidal agent against both Gram-positive and Gram-negative bacterial strains and thus can be developed as potent broad-spectrum antibiotic against MDR strains. PPEF treatment did not cause target specific mutation instead it leads to up-regulation of efflux gene in E. coli K12 as a mechanism of resistance. Microscopy, fluorescence spectroscopy and flow cytometry result demonstrate higher accumulation of PPEF in efflux gene deleted E. coli K12 mutants, and also suggest that Carbonyl Cyanide 3-Chlorophenylhydrazone (CCCP), resist the efflux of PPEF, and thus increases efficacy of PPEF. Herein, we report, PPEF and CCCP synergistically killed the persistent bacterial cells, which are not killed by PPEF alone. The above two compounds together inhibited biofilm formation, eradicate preformed biofilms and kills the biofilm cells of P. aeruginosa. PPEF and CCCP together reduced bacterial load of E. coli ATCC25922 by 6 log10 in neutropenic thigh infection model of balb/c mice. Present study suggests that combination therapy could be a promising antimicrobial strategy to handle MDR pathogenic strains.
Strain differences in arsenic-induced oxidative lesion via arsenic biomethylation between C57BL/6J and 129X1/SvJ mice
Authors: Wu Ruirui , Wu Xiafang , Wang Huihui , Fang Xin , Li Yongfang , Gao Lanyue , Sun Guifan , Pi Jingbo , Xu Yuanyuan 
Published: March 2017

AbstractArsenic is a common environmental and occupational toxicant with dramatic species differences in its susceptibility and metabolism. Mouse strain variability may provide a better understanding of the arsenic pathological profile but is largely unknown. Here we investigated oxidative lesion induced by acute arsenic exposure in the two frequently used mouse strains C57BL/6J and 129X1/SvJ in classical gene targeting technique. A dose of 5 mg/kg body weight arsenic led to a significant alteration of blood glutathione towards oxidized redox potential and increased hepatic malondialdehyde content in C57BL/6J mice, but not in 129X1/SvJ mice. Hepatic antioxidant enzymes were induced by arsenic in transcription in both strains and many were higher in C57BL/6J than 129X1/SvJ mice. Arsenic profiles in the liver, blood and urine and transcription of genes encoding enzymes involved in arsenic biomethylation all indicate a higher arsenic methylation capacity, which contributes to a faster hepatic arsenic excretion, in 129X1/SvJ mice than C57BL/6J mice. Taken together, C57BL/6J mice are more susceptible to oxidative hepatic injury compared with 129X1/SvJ mice after acute arsenic exposure, which is closely associated with arsenic methylation pattern of the two strains.
Reduced Regional Grey Matter Volumes in Pediatric Obstructive Sleep Apnea
Authors: Philby Mona F. , Macey Paul M. , Ma Richard A. , Kumar Rajesh , Gozal David , Kheirandish-Gozal Leila 
Published: March 2017

AbstractPediatric OSA is associated with cognitive risk. Since adult OSA manifests MRI evidence of brain injury, and animal models lead to regional neuronal losses, pediatric OSA patients may also be affected. We assessed the presence of neuronal injury, measured as regional grey matter volume, in 16 OSA children (8 male, 8.1 ± 2.2 years, AHI:11.1 ± 5.9 events/hr), and 200 control subjects (84 male, 8.2 ± 2.0 years), 191 of whom were from the NIH-Pediatric MRI database. High resolution T1-weighted whole-brain images were assessed between groups with voxel-based morphometry, using ANCOVA (covariates, age and gender; family-wise error correction, P < 0.01). Significant grey matter volume reductions appeared in OSA throughout areas of the superior frontal and prefrontal, and superior and lateral parietal cortices. Other affected sites included the brainstem, ventral medial prefrontal cortex, and superior temporal lobe, mostly on the left side. Thus, pediatric OSA subjects show extensive regionally-demarcated grey matter volume reductions in areas that control cognition and mood functions, even if such losses are apparently independent of cognitive deficits. Since OSA disease duration in our subjects is unknown, these findings may result from either delayed neuronal development, neuronal damaging processes, or a combination thereof, and could either reflect neuronal atrophy or reductions in cellular volume (neurons and glia).
The Golgi protein ACBD3 facilitates Enterovirus 71 replication by interacting with 3A
Authors: Lei Xiaobo , Xiao Xia , Zhang Zhenzhen , Ma Yijie , Qi Jianli , Wu Chao , Xiao Yan , Zhou Zhuo , He Bin , Wang Jianwei 
Published: March 2017

AbstractEnterovirus 71 (EV71) is a human pathogen that causes hand, foot, mouth disease and neurological complications. Although EV71, as well as other enteroviruses, initiates a remodeling of intracellular membrane for genomic replication, the regulatory mechanism remains elusive. By screening human cDNA library, we uncover that the Golgi resident protein acyl-coenzyme A binding domain-containing 3 (ACBD3) serves as a target of the 3A protein of EV71. This interaction occurs in cells expressing 3A or infected with EV71. Genetic inhibition or deletion of ACBD3 drastically impairs viral RNA replication and plaque formation. Such defects are corrected upon restoration of ACBD3. In infected cells, EV71 3A redirects ACBD3, to the replication sites. I44A or H54Y substitution in 3A interrupts the binding to ACBD3. As such, viral replication is impeded. These results reveal a mechanism of EV71 replication that involves host ACBD3 for viral replication.
The metabolic waste ammonium regulates mTORC2 and mTORC1 signaling
Authors: Merhi Ahmad , Delrée Paul , Marini Anna Maria 
Published: March 2017

AbstractTwo structurally and functionally distinct mammalian TOR complexes control cell growth and metabolism in physiological and pathological contexts including cancer. Upregulated glutaminolysis is part of the metabolic reprogramming occurring in cancer, providing fuels for growth but also liberating ammonium, a potent neurotoxic waste product. Here, we identify ammonium as a novel dose-dependent signal mediating rapid mTORC2 activation and further regulating mTORC1. We show that ammonium induces rapid RICTOR-dependent phosphorylation of AKT-S473, a process requiring the PI3K pathway and further involving the Src-family kinase YES1, the FAK kinase and the ITGβ1 integrin. Release of calcium from the endoplasmic reticulum store triggers rapid mTORC2 activation, similar to ammonium-induced activation, the latter being conversely prevented by calcium chelation.Moreover, in analogy to growth factors, ammonium triggers the AKT-dependent phosphoinhibition of the TSC complex and of PRAS40, two negative regulators of mTORC1. Consistent with mTORC1 stimulation, ammonium induces the inhibitory phosphorylation of 4EBP1, a negative regulator of protein biogenesis. Ammonium however dually impacts on the phosphorylation of p70S6K1 triggering a transient AKT-independent decrease in the phosphorylation of this second mTORC1 readout. Finally, we reveal ammonium as a dose-dependent stimulator of proliferation. This study underscores an mTORC2 and mTORC1 response to the so-called ammonium waste.
Anticipatory action planning in blind and sighted individuals
Authors: Cavallo Andrea , Ansuini Caterina , Gori Monica , Tinti Carla , Tonelli Alessia , Becchio Cristina 
Published: March 2017

AbstractSeveral studies on visually guided reach-to-grasp movements have documented that how objects are grasped differs depending on the actions one intends to perform subsequently. However, no previous study has examined whether this differential grasping may also occur without visual input. In this study, we used motion capture technology to investigate the influence of visual feedback and prior visual experience on the modulation of kinematics by intention in sighted (in both full-vision and no-vision conditions), early-blind and late-blind participants. Results provide evidence of modulation of kinematics by intention to a similar degree under both full-vision and no-vision conditions. Moreover, they demonstrate that prior visual experience has little impact on the tailoring of grasping movements to intention. This suggests that sequential action planning does not depend on visual input, and may instead be ascribed to the function of multisensory-motor cortical network that operates and develops not only in light, but also in darkness.
Generating highly accurate prediction hypotheses through collaborative ensemble learning
Authors: Arsov Nino , Pavlovski Martin , Basnarkov Lasko , Kocarev Ljupco 
Published: March 2017

AbstractEnsemble generation is a natural and convenient way of achieving better generalization performance of learning algorithms by gathering their predictive capabilities. Here, we nurture the idea of ensemble-based learning by combining bagging and boosting for the purpose of binary classification. Since the former improves stability through variance reduction, while the latter ameliorates overfitting, the outcome of a multi-model that combines both strives toward a comprehensive net-balancing of the bias-variance trade-off. To further improve this, we alter the bagged-boosting scheme by introducing collaboration between the multi-model’s constituent learners at various levels. This novel stability-guided classification scheme is delivered in two flavours: during or after the boosting process. Applied among a crowd of Gentle Boost ensembles, the ability of the two suggested algorithms to generalize is inspected by comparing them against Subbagging and Gentle Boost on various real-world datasets. In both cases, our models obtained a 40% generalization error decrease. But their true ability to capture details in data was revealed through their application for protein detection in texture analysis of gel electrophoresis images. They achieve improved performance of approximately 0.9773 AUROC when compared to the AUROC of 0.9574 obtained by an SVM based on recursive feature elimination.