bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV-1 Infection in Cyprus, the Eastern Mediterranean European Frontier: A Densely Sampled Transmission Dynamics Analysis from 1986 to 2012
Authors: Pineda-Peña Andrea-Clemencia , Theys Kristof , Stylianou Dora C. , Demetriades Ioannis ,   SPREAD/ESAR Program, Puchhammer Elisabeth , Vandamme Anne-Mieke , Aleksiev Ivailo , Lepej Snjezana Zidovec , Linka Marek , Fonager Jannik , Liitsola Kirsi , Kaiser Rolf , Hamouda Osamah , Paraskevis Dimitrios , Coughlan Suzie , Grossman Zehava , Mor Orna , Zazzi Maurizio , Griskevicius Algirdas , Lipnickiene Vilnele , Devaux Carole , Boucher Charles , Hofstra Marije , Wensing Annemarie , Bakken-Kran Anne-Marte , Horban Andrzej , Camacho Ricardo , Paraschiv Simona , Otelea Dan , Stanojevic Maja , Stanekova Danika , Poljak Mario , Garcia Federico , Paredes Roger , Albert Jan , Abecasis Ana B. , Kostrikis Leondios G. 
Published: January 2018

AbstractSince HIV-1 treatment is increasingly considered an effective preventionstrategy, it is important to study local HIV-1 epidemics to formulate tailored preventionpolicies. The prevalence of HIV-1 in Cyprus was historically low until 2005. To investigatethe shift in epidemiological trends, we studied the transmission dynamics of HIV-1 in Cyprususing a densely sampled Cypriot HIV-1 transmission cohort that included 85 percent ofHIV-1-infected individuals linked to clinical care between 1986 and 2012 based on detailedclinical, epidemiological, behavioral and HIV-1 genetic information. Subtyping andtransmission cluster reconstruction were performed using maximum likelihood and Bayesianmethods, and the transmission chain network was linked to the clinical, epidemiological andbehavioral data. The results reveal that for the main HIV-1 subtype A1 and B sub-epidemics,young and drug-naïve HIV-1-infected individuals in Cyprus are driving the dynamics of thelocal HIV-1 epidemic. The results of this study provide a better understanding of thedynamics of the HIV-1 infection in Cyprus, which may impact the development of preventionstrategies. Furthermore, this methodology for analyzing densely sampled transmissiondynamics is applicable to other geographic regions to implement effective HIV-1 preventionstrategies in local settings.
A new bound on polymer quantization via an opto-mechanical setup
Authors: Khodadi Mohsen , Nozari Kourosh , Dey Sanjib , Bhat Anha , Faizal Mir 
Published: January 2018

AbstractThe existence of a minimal measurable length as a characteristic length in the Planck scale is one of the main features of quantum gravity and has been widely explored in the context. Various different deformations of spacetime have been employed successfully for the purpose. However, polymer quantization approach is a relatively new and dynamic field towards the quantum gravity phenomenology, which emerges from the symmetric sector of the loop quantum gravity. In this article, we extend the standard ideas of polymer quantization to find a new and tighter bound on the polymer deformation parameter. Our protocol relies on an opto-mechanical experimental setup that was originally proposed to explore some interesting phenomena by embedding the minimal length into the standard canonical commutation relation. We extend this scheme to probe the polymer length deformed canonical commutation relation of the center of mass mode of a mechanical oscillator with a mass around the Planck scale. The method utilizes the novelty of exchanging the relevant mechanical information with a high intensity optical pulse inside an optical cavity. We also demonstrate that our proposal is within the reach of the current technologies and, thus, it could uncover a decent realization of quantum gravitational phenomena thorough a simple table-top experiment.
Impact of left atrial appendage morphology on thrombus formation after successful left atrial appendage occlusion: Assessment with cardiac-computed-tomography
Authors: Dieker Wulf , Behnes Michael , Fastner Christian , Sartorius Benjamin , Wenke Annika , Sing-Gill Ishar , El-Battrawy Ibrahim , Kuschyk Jürgen , Papavassiliu Theano , Hoffmann Ursula , Mashayekhi Kambis , Schoenberg Stefan O. , Borggrefe Martin , Henzler Thomas , Akin Ibrahim 
Published: January 2018

AbstractA standardized imaging algorithm by cardiac computed tomography angiography (cCTA) (LOVE-view) was used in 30 patients to evaluate the influence of different left atrial appendage (LAA) morphologies on development of thrombosis in the LAA 6 months after implantation of an occlusion device (Watchman or Amplatzer-Cardiac-Plug) in patients with non-valvular atrial fibrillation, CHA2DS2-VASc-Score >1 and a contraindication for oral anticoagulation. The distribution of different LAA morphologies was 40% windsock, 17% broccoli and 43% chicken wing type. There was no significant difference in the level of thrombosis regarding LAA morphology or the type of chosen occlusion device. The rates of complete LAA thrombosis was 40% in broccoli type, 33% in windsock and 15% in chicken wing type. Independently of LAA type, 13% had none and 60% incomplete thrombosis. The ratio of density (LA/LAA) was 0.14 in patients with complete thrombosis and 0.67 in those with none or incomplete thrombosis. cCTA and the LOVE-view-imaging-algorithm were shown to be a valuable method for standardized imaging in clinical routine in a greater set of patients. Surprisingly thrombosis of the occluded LAA was still in progress in most cases at 6 months, whereas further studies are needed defining its clinical consequences, especially for the selection of the optimal post-procedural antithrombotic treatment strategy.
Three-dimensional reconstruction and NURBS-based structured meshing of coronary arteries from the conventional X-ray angiography projection images
Authors: Vukicevic Arso M. , Çimen Serkan , Jagic Nikola , Jovicic Gordana , Frangi Alejandro F. , Filipovic Nenad 
Published: January 2018

AbstractDespite its two-dimensional nature, X-ray angiography (XRA) has served as the gold standard imaging technique in the interventional cardiology for over five decades. Accordingly, demands for tools that could increase efficiency of the XRA procedure for the quantitative analysis of coronary arteries (CA) are constantly increasing. The aim of this study was to propose a novel procedure for three-dimensional modeling of CA from uncalibrated XRA projections. A comprehensive mathematical model of the image formation was developed and used with a robust genetic algorithm optimizer to determine the calibration parameters across XRA views. The frames correspondences between XRA acquisitions were found using a partial-matching approach. Using the same matching method, an efficient procedure for vessel centerline reconstruction was developed. Finally, the problem of meshing complex CA trees was simplified to independent reconstruction and meshing of connected branches using the proposed nonuniform rational B-spline (NURBS)-based method. Because it enables structured quadrilateral and hexahedral meshing, our method is suitable for the subsequent computational modelling of CA physiology (i.e. coronary blood flow, fractional flow reverse, virtual stenting and plaque progression). Extensive validations using digital, physical, and clinical datasets showed competitive performances and potential for further application on a wider scale.
HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir
Authors: Yasutake Yoshiaki , Hattori Shin-ichiro , Hayashi Hironori , Matsuda Kouki , Tamura Noriko , Kohgo Satoru , Maeda Kenji , Mitsuya Hiroaki 
Published: January 2018

AbstractHepatitis B virus (HBV) reverse transcriptase (RT) is essential for viral replication and is an important drug target. Nonetheless, the notorious insolubility of HBV RT has hindered experimental structural studies and structure-based drug design. Here, we demonstrate that a Q151M substitution alone at the nucleotide-binding site (N-site) of human immunodeficiency virus type-1 (HIV-1) RT renders HIV-1 highly sensitive to entecavir (ETV), a potent nucleoside analogue RT inhibitor (NRTI) against HBV. The results suggest that Met151 forms a transient hydrophobic interaction with the cyclopentyl methylene of ETV, a characteristic hydrophobic moiety of ETV. We thus solved the crystal structures of HIV-1 RTQ151M:DNA complex with bound dGTP or ETV-triphosphate (ETV-TP). The structures revealed that ETV-TP is accommodated at the N-site slightly apart from the ribose ring of the 3′-end nucleotide, compared to the position of bound dGTP and previously reported NRTI/dNTP. In addition, the protruding methylene group of bound ETV-TP directly pushes the side-chain of Met184 backward. Met184 is a key residue that confers ETV resistance upon substitution with smaller Ile/Val. These results provide novel insights into NRTI binding to the N-site and further provide important clues for the development of novel anti-HBV/HIV-1 RT inhibitors to overcome critical drug resistance.
Nanopillars with E-field accessible multi-state (N ≥ 4) magnetization having giant magnetization changes in self-assembled BiFeO3-CoFe2O4/Pb(Mg1/3Nb2/3)-38at%PbTiO3 heterostructures
Authors: Tang Xiao , Viswan Ravindranath , Gao Min , Leung Chung Ming , Folger Carlos , Luo Haosu , Howe Brandon , Li Jiefang , Viehland Dwight 
Published: January 2018

AbstractWe have deposited self-assembled BiFeO3-CoFe2O4 (BFO-CFO) thin films on (100)-oriented SrRuO3-buffered Pb(Mg1/3Nb2/3)0.62Ti0.38O3 (PMN-38PT) single crystal substrates. These heterostructures were used for the study of real-time changes in the magnetization with applied DC electric field (E
DC
). With increasing E
DC
, a giant magnetization change was observed along the out-of-plane (easy) axis. The induced magnetization changes of the CFO nanopillars in the BFO/CFO layer were about ΔM/M
rDC
= 93% at E
DC
= −3 kv/cm. A giant converse magnetoelectric (CME) coefficient of 1.3 × 10−7 s/m was estimated from the data. By changing E
DC
, we found multiple(N ≥ 4) unique possible values of a stable magnetization with memory on the removal of the field.
Three-dimensional histochemistry and imaging of human gingiva
Authors: Azaripour Adriano , Lagerweij Tonny , Scharfbillig Christina , Jadczak Anna Elisabeth , Swaan Britt van der , Molenaar Manon , Waal Rens van der , Kielbassa Karoline , Tigchelaar Wikky , Picavet Daisy I. , Jonker Ard , Hendrikx Esther M. L. , Hira Vashendriya V. V. , Khurshed Mohammed , Noorden Cornelis J. F. Van 
Published: January 2018

AbstractIn the present study, 3D histochemistry and imaging methodology is described for human gingiva to analyze its vascular network. Fifteen human gingiva samples without signs of inflammation were cleared using a mixture of 2-parts benzyl benzoate and 1-part benzyl alcohol (BABB), after being immunofluorescently stained for CD31, marker of endothelial cells to visualize blood vessels in combination with fluorescent DNA dyes. Samples were imaged in 3D with the use of confocal microscopy and light-sheet microscopy and image processing. BABB clearing caused limited tissue shrinkage 13 ± 7% as surface area and 24 ± 1% as volume. Fluorescence remained intact in BABB-cleared gingiva samples and light-sheet microscopy was an excellent tool to image gingivae whereas confocal microscopy was not. Histochemistry on cryostat sections of gingiva samples after 3D imaging validated structures visualized in 3D. Three-dimensional images showed the vascular network in the stroma of gingiva with one capillary loop in each stromal papilla invading into the epithelium. The capillary loops were tortuous with structural irregularities that were not apparent in 2D images. It is concluded that 3D histochemistry and imaging methodology described here is a promising novel approach to study structural aspects of human gingiva in health and disease.
Development and characterisation of a panel of phosphatidylinositide 3-kinase – mammalian target of rapamycin inhibitor resistant lung cancer cell lines
Authors: Heavey Susan , Dowling Paul , Moore Gillian , Barr Martin P. , Kelly Niamh , Maher Stephen G. , Cuffe Sinead , Finn Stephen P. , O’Byrne Kenneth J. , Gately Kathy 
Published: January 2018

AbstractThe PI3K-mTOR pathway is involved in regulating all hallmarks of cancer, and is often dysregulated in NSCLC, making it an attractive therapeutic target in this setting. Acquired resistance to PI3K-mTOR inhibition is a major hurdle to overcome in the success of PI3K-mTOR targeted agents. H460, A549, and H1975 resistant cells were generated by prolonged treatment in culture with Apitolisib (GDC-0980), a dual PI3K-mTOR inhibitor over a period of several months, from age-matched parent cells. Resistance was deemed to have developed when a log fold difference in IC50 had been achieved. Resistant cell lines also exhibited resistance to another widely investigated PI3K-mTOR dual inhibitor; Dactolisib (BEZ235). Cell lines were characterised at the level of mRNA (expression array profiling expression of >150 genes), miRNA (expression array profiling of 2100 miRNAs), protein (bottoms-up label-free mass spectrometry) and phosphoprotein (expression array profiling of 84 phospho/total proteins). Key alterations were validated by qPCR and Western blot. H1975 cells were initially most sensitive to Apitolisib (GDC-0980), but developed resistance more quickly than the other cell lines, perhaps due to increased selective pressure from the impressive initial effect. In-depth molecular profiling suggested epithelial-mesenchymal transition (EMT) may play a role in resistance to PI3K-mTOR dual inhibition in NSCLC.
High-resolution seismic event detection using local similarity for Large-N arrays
Authors: Li Zefeng , Peng Zhigang , Hollis Dan , Zhu Lijun , McClellan James 
Published: January 2018

AbstractWe develop a novel method for seismic event detection that can be applied to large-N arrays. The method is based on a new detection function named local similarity, which quantifies the signal consistency between the examined station and its nearest neighbors. Using the 5200-station Long Beach nodal array, we demonstrate that stacked local similarity functions can be used to detect seismic events with amplitudes near or below noise levels. We apply the method to one-week continuous data around the 03/11/2011 Mw 9.1 Tohoku-Oki earthquake, to detect local and distant events. In the 5–10 Hz range, we detect various events of natural and anthropogenic origins, but without a clear increase in local seismicity during and following the surface waves of the Tohoku-Oki mainshock. In the 1-Hz low-pass-filtered range, we detect numerous events, likely representing aftershocks from the Tohoku-Oki mainshock region. This high-resolution detection technique can be applied to both ultra-dense and regular array recordings for monitoring ultra-weak micro-seismicity and detecting unusual seismic events in noisy environments.
Oxidative stress induced by Cu nutritional disorders in Citrus depends on nitrogen and calcium availability
Authors: Hippler Franz Walter Rieger , Boaretto Rodrigo Marcelli , Dovis Veronica Lorena , Quaggio José Antônio , Azevedo Ricardo Antunes , Mattos-Jr Dirceu 
Published: January 2018

AbstractNutritional stress caused by copper (Cu) deficiency or toxicity affects fruit production of citrus orchards worldwide, but this could be minimised by fine-tuned fertilisation in the orchards. Two experiments were performed aiming to evaluate the photosynthetic capacity and the antioxidant enzyme activities of Swingle citrumelo seedlings, grown in nutrient solution (NS) with two levels of nitrogen (N) in the first experiment (adequate-N and high-N) and two levels of calcium (Ca) in the second (low-Ca and adequate-Ca). Plants were then exposed to various Cu levels (low, medium and high) for 15 days. Plants under Cu-toxicity exhibited specific effects on reactive oxygen species formation and root-to-shoot plant signalling. Copper absorption was greater with increased Cu concentration in the NS, which reduced plant biomass accumulation, gas exchange measurements, the activity of nitrate reductase and affected Cu partitioning between roots and shoots. Despite these effects, oxidative stress induced by excess-Cu was reduced at the highest N dose when compared to control and, on the contrary, increased with low-Ca supply. Therefore, a rational supply of N or Ca minimises Cu-induced stress damages to roots and leaves of plants, by directly enhancing the antioxidant system and protecting the associated antioxidative enzyme activities, whilst maintaining photosynthesis.
Interplay between TETs and microRNAs in the adult brain for memory formation
Authors: Kremer Eloïse A. , Gaur Niharika , Lee Melissa A. , Engmann Olivia , Bohacek Johannes , Mansuy Isabelle M. 
Published: January 2018

Abstract5-hydroxymethylation (5-hmC) is an epigenetic modification on DNA that results from the conversion of 5-methylcytosine by Ten-Eleven Translocation (TET) proteins. 5-hmC is widely present in the brain and is subjected to dynamic regulation during development and upon neuronal activity. It was recently shown to be involved in memory processes but currently, little is known about how it is controlled in the brain during memory formation. Here, we show that Tet3 is selectively up-regulated by activity in hippocampal neurons in vitro, and after formation of fear memory in the hippocampus. This is accompanied by a decrease in miR-29b expression that, through complementary sequences, regulates the level of Tet3 by preferential binding to its 3′UTR. We newly reveal that SAM68, a nuclear RNA-binding protein known to regulate splicing, acts upstream of miR-29 by modulating its biogenesis. Together, these findings identify novel players in the adult brain necessary for the regulation of 5-hmC during memory formation.
Transcriptomic characterization and potential marker development of contrasting sugarcane cultivars
Authors: Xu Shiqiang , Wang Jihua , Shang Heyang , Huang Youzong , Yao Wei , Chen Baoshan , Zhang Muqing 
Published: January 2018

AbstractSugarcane (Saccharum officinarumL.) is an important crop for sugar production and bioenergy worldwide. In this study, we performed transcriptome sequencing for six contrasting sugarcane genotypes involved in leaf abscission, tolerance to pokkah boeng disease and drought stress. More than 465 million high-quality reads were generated, which werede novoassembled into 93,115 unigenes. Based on a similarity search, 43,526 (46.74%) unigenes were annotated against at least one of the public databases. Functional classification analyses showed that these unigenes are involved in a wide range of metabolic pathways. Comparative transcriptome analysis revealed that many unigenes involved in response to abscisic acid and ethylene were up-regulated in the easy leaf abscission genotype, and unigenes associated with response to jasmonic acid and salicylic acid were up-regulated in response to the pokkah boeng disease in the tolerance genotype. Moreover, unigenes related to peroxidase, antioxidant activity and signal transduction were up-regulated in response to drought stress in the tolerant genotype. Finally, we identified a number of putative markers, including 8,630 simple sequence repeats (SSRs) and 442,152 single-nucleotide polymorphisms (SNPs). Our data will be important resources for future gene discovery, molecular marker development, and genome studies in sugarcane.
A retrospective cohort study on the outcomes of ischemic stroke patients with adjuvant Korean Medicine treatment
Authors: Lee Ye-Seul , Kwon Seungwon , Chae Younbyoung , Jang Bo-Hyoung , Ko Seong-Gyu 
Published: January 2018

AbstractThis study aims to examine the long-term effect of adjuvant treatment in Korean Medicine (KM) clinics in ischemic stroke patients, using a national sample cohort from the National Health Insurance Service in Korea between 2010 and 2013. The National Health Insurance Service – National Sample Cohort database from 2002 to 2013 was used in this study. Ischemic stroke patients were defined and covariates were included to account for socioeconomic variables, comorbidities and disease severity. Propensity score matching was applied. Cox proportional hazards modeling and Kaplan-Meier analysis were applied to determine the differences between KM and non-KM treated groups. The results shows that KM-treated group had a higher probability of survival than non-KM group patients. No significant difference was observed between the risk of readmission between the treated and non-treated patients. Kaplan-Meier analysis showed a weak effect of KM treatments in the patients with 8 to 28 days of hospital stay for a lower risk of recurrence than in non-treated patients. In conclusion, KM treatment of mild to moderate ischemic stroke patients has a mild effect on the survival probability of stroke. Its effect for improving long-term recurrence need to be explored in the future studies.
2-Phenylquinazolinones as dual-activity tankyrase-kinase inhibitors
Authors: Nkizinkiko Yves , Desantis Jenny , Koivunen Jarkko , Haikarainen Teemu , Murthy Sudarshan , Sancineto Luca , Massari Serena , Ianni Federica , Obaji Ezeogo , Loza Maria I. , Pihlajaniemi Taina , Brea Jose , Tabarrini Oriana , Lehtiö Lari 
Published: January 2018

AbstractTankyrases (TNKSs) are enzymes specialized in catalyzing poly-ADP-ribosylation of target proteins. Several studies have validated TNKSs as anti-cancer drug targets due to their regulatory role in Wnt/β-catenin pathway. Recently a lot of effort has been put into developing more potent and selective TNKS inhibitors and optimizing them towards anti-cancer agents. We noticed that some 2-phenylquinazolinones (2-PQs) reported as CDK9 inhibitors were similar to previously published TNKS inhibitors. In this study, we profiled this series of 2-PQs against TNKS and selected kinases that are involved in the Wnt/β-catenin pathway. We found that they were much more potent TNKS inhibitors than they were CDK9/kinase inhibitors. We evaluated the compound selectivity to tankyrases over the ARTD enzyme family and solved co-crystal structures of the compounds with TNKS2. Comparative structure-based studies of the catalytic domain of TNKS2 with selected CDK9 inhibitors and docking studies of the inhibitors with two kinases (CDK9 and Akt) revealed important structural features, which could explain the selectivity of the compounds towards either tankyrases or kinases. We also discovered a compound, which was able to inhibit tankyrases, CDK9 and Akt kinases with equal µM potency.
Chirality recognition of winding vine-shaped heterobiaryls with molecular asymmetry. Kinetic and dynamic kinetic resolution by Shi’s asymmetric epoxidation
Authors: Maruhashi Kazuki , Okayama Yoichi , Inoue Ryo , Ashida Shiomi , Toyomori Yuka , Okano Kentaro , Mori Atsunori 
Published: January 2018

AbstractThe chirality of winding vine-shaped heterobiaryls with molecular asymmetry is recognized by a sugar-based chiral oxidant. Kinetic resolution of (±)-bisbenzoimidazole bearing an olefin moiety takes place with Shi’s asymmetric epoxidation to observe krel value up to ca. 35 affording the corresponding epoxide. The reaction of a (±)-bithiophene derivative also recognized the chirality to give the corresponding epoxide with er of 96:4 at 39% conversion. Dynamic kinetic resolution is found to take place when unsymmetrical biaryl composed of benzoimidazole/thiophene is subjected to Shi’s epoxidation, whose conversion of the racemic substrate exceeds to 50%.