bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered expression patterns of circular RNAs between implantation sites and interimplantation sites in early pregnant mice
Authors: Zhang Shuang , Ding Yubin , He Junlin , Zhang Juanjuan , Liu Xueqing , Chen Xuemei , Su Yan , Wang Yingxiong , Gao Rufei 
Published: October 2018

AbstractCircular RNAs (circRNAs), a class of newly discovered endogenous noncoding RNAs, have been found to play important roles in regulating gene expression and participate in several biological processes. However, their specific roles in embryo implantation remain unclear. This study aims to investigate the roles of circRNAs in embryo implantation. In the current study, we screened the expression profiles of circRNAs between implantation sites and interimplantation sites in the endometrial tissue of early pregnant mice on Day 5 using microarray assay. Quantitative reverse transcription polymerase chain reaction (qRT‐PCR) of four dysregulated circRNAs was performed to validate the microarray results. Bioinformatics analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and circRNA–microRNA (miRNA)–messenger RNA (mRNA) negative correlation network analyses were performed. The microarray results showed 101 upregulated and 75 downregulated circRNAs (fold change [FC] ≥ 1.5 and p value < 0.05) at implantation sites compared with interimplantation sites. Four randomly selected circRNAs were successfully verified by qRT‐PCR. The GO and KEGG analyses revealed some meaningful terms. Moreover, based on circRNAs microarray data and the miRNA and mRNA high‐throughput data previously published by our groups, differently expressed circRNAs, miRNAs, and mRNAs were performed to conjoint analysis. Then circRNA–miRNA–mRNA negative correlation networks were constructed and 21 downregulated circRNAs, 14 upregulated miRNAs, and 79 downregulated mRNAs were involved in the networks. The findings of this study may provide a novel perspective on circRNAs and lay a foundation for future research into the potential roles of circRNAs in embryo implantation.
Modeling of gas pipeline in order to implement a leakage detection system using artificial neural networks based on instrumentation
Authors: Rahmati Mohsen 
Published: October 2018

AbstractIn this paper, by using of gas flow pattern, a novel neural network‐based fault detection method is presented to detect the leakage in the gas pipeline. The pipe is divided into four segments, and each segment is modeled by using input/output pressure of the gas flow. For this purpose, the acquired practical data from the real life gas pipeline are gathered and utilized for training a neural network to model the process. Some of the data are used for training set to adjust the neural network weights, and others are used to evaluate the performance of the neural network‐based fault detection system. Gathered practical data from a real life pipeline made sure that the proposed method is prominent and applicable for practical implementations. The model was verified with the data obtained from the test in the actual pipeline and compared with leakage mode.
On contributions by wind‐induced mixing and eddy pumping to interannual chlorophyll variability during different ENSO phases in the northern South China Sea
Authors: Xiu Peng , Dai Minhan , Chai Fei , Zhou Kuanbo , Zeng Lili , Du Chuanjun 
Published: October 2018

AbstractThe chlorophyll in the northern South China Sea (NSCS) shows strong interannual variability between different phases of the El Niño‐Southern Oscillation (ENSO), primarily due to the influence from Kuroshio intrusion. Chlorophyll observations also reveal that significant year‐to‐year variation remains in the same ENSO phase, but its controlling mechanism is unknown. In this study, we examined driving mechanisms for such regional ecosystem variability on a year‐to‐year timescale. Using observational data and modeling results, we found that both cyclonic eddies (CEs) and wind‐induced mixing affect phytoplankton variability, but the former is the dominant factor regulating the interannual variability of chlorophyll during La Niña years, while the latter becomes the dominant one during El Niño years. The underlying mechanisms leading to the contrast in biological responses are attributable to changes in background nutricline depth and mixed‐layer depth (MLD) during different ENSO phases. During La Niña, both thermocline and nutricline are deepened in the NSCS. Thus, wind mixing is less effective in non‐eddy areas due to the deepened nutricline, while the CE‐induced subsurface nutrient anomaly associated with increased MLD is able to control the interannual variability of chlorophyll. During El Niño, wind‐induced mixing is more effective than CEs because the surface wind can influence a larger area.
Comparative genomics of the Komagataeibacter strains—Efficient bionanocellulose producers
Authors: Ryngajłło Małgorzata , Kubiak Katarzyna , Jędrzejczak‐Krzepkowska Marzena , Jacek Paulina , Bielecki Stanisław 
Published: October 2018

AbstractKomagataeibacter species are well‐recognized bionanocellulose (BNC) producers. This bacterial genus, formerly assigned to Gluconacetobacter, is known for its phenotypic diversity manifested by strain‐dependent carbon source preference, BNC production rate, pellicle structure, and strain stability. Here, we performed a comparative study of nineteen Komagataeibacter genomes, three of which were newly contributed in this work. We defined the core genome of the genus, clarified phylogenetic relationships among strains, and provided genetic evidence for the distinction between the two major clades, the K. xylinus and the K. hansenii. We found genomic traits, which likely contribute to the phenotypic diversity between the Komagataeibacter strains. These features include genome flexibility, carbohydrate uptake and regulation of its metabolism, exopolysaccharides synthesis, and the c‐di‐GMP signaling network. In addition, this work provides a comprehensive functional annotation of carbohydrate metabolism pathways, such as those related to glucose, glycerol, acetan, levan, and cellulose. Findings of this multi‐genomic study expand understanding of the genetic variation within the Komagataeibacter genus and facilitate exploiting of its full potential for bionanocellulose production at the industrial scale.
Site‐specific alert criteria to detect patient‐related errors with 3D EPID transit dosimetry
Authors: Olaciregui‐Ruiz Igor , Rozendaal Roel , Mijnheer Ben , Mans Anton 
Published: October 2018

PurposeTo assess the sensitivity of various EPID dosimetry alert indicators to patient‐related variations and to determine alert threshold values that ensure excellent error detectability.MethodsOur virtual dose reconstruction method uses in air EPID measurements to calculate virtual 3D dose distributions within a CT data set. Patient errors are introduced by transforming the plan‐CT into an error‐CT data set. Virtual patient dose distributions reconstructed using the plan‐CT and the error‐CT data set are compared to the planned dose distributions by γ(3%/3 mm) and DVH analysis using seven indicators: ΔDISOC, γ‐mean, near γ‐max, γ‐pass rate, ΔPTVD2, ΔPTVD50, and ΔPTVD98. Translation and rotation patient setup errors and uniform contour changes are studied for 104 VMAT plans of 4 treatment sites. Lung expansions and contractions to simulate changes in lung density are considered for 26 IMRT lung plans. A ROC curve is generated for each combination of error and indicator. For each ROC curve, the AUC value and the optimal alert threshold value of the indicator are determined.ResultsAUC values for γ‐indicators and ΔPTVD2 are consistently higher than for ΔDISOC and ΔPTVD98. For VMAT plans, error detectability to patient position shifts is worse for pelvic treatments and best for head‐and‐neck and brain plans. Excellent detectability is observed for 5 mm translations in head‐and‐neck plans (AUC = 0.94) and for 4° rotations in brain plans (AUC = 0.89). All sites but prostate show good‐to‐excellent detectability (AUC > 0.8) for 10 mm translations and 8° rotations and excellent detectability (AUC > 0.9) for ±6 mm patient contour changes. For head‐and‐neck, excellent detectability is obtained with γ‐mean and γ‐pass rate threshold values of around 0.63 and 83%, respectively. For brain and rectum, these threshold values are 0.53 and 90%, respectively. In IMRT lung plans, expansions of 3 mm and contractions of 6 mm are detected (AUC > 0.8).ConclusionsBy combining virtual dose reconstructions with synthetic patient data, we developed a framework to assess the sensitivity of our 3D EPID transit dosimetry method to patient‐related variations. The detectability of each introduced error is specific to the treatment site and indicator used. Optimal alert criteria can be determined to ensure excellent detectability for each combination of error type and indicator. The alert threshold values and the magnitude of the error that can be detected are site‐specific. In situations where the minimum error that can be detected is larger than the clinically desirable action level, EPID transit dosimetry must be used in combination with IGRT procedures to ensure correct patient positioning and early detection of anatomy variations.
Whole‐heart coronary MR angiography using a 3D cones phyllotaxis trajectory
Authors: Malavé Mario O. , Baron Corey A. , Addy Nii Okai , Cheng Joseph Y. , Yang Phillip C. , Hu Bob S. , Nishimura Dwight G. 
Published: October 2018

PurposeTo develop a 3D cones steady‐state free precession sequence with improved robustness to respiratory motion while mitigating eddy current artifacts for free‐breathing whole‐heart coronary magnetic resonance angiography.MethodThe proposed sequence collects cone interleaves using a phyllotaxis pattern, which allows for more distributed k‐space sampling for each heartbeat compared to a typical sequential collection pattern. A Fibonacci number of segments is chosen to minimize eddy current effects with the trade‐off of an increased number of acquisition heartbeats. For verification, phyllotaxis‐cones is compared to sequential‐cones through simulations, phantom studies, and in vivo coronary scans with 8 subjects using 2D image‐based navigators for retrospective motion correction.ResultsSimulated point spread functions and moving phantom results show less coherent motion artifacts for phyllotaxis‐cones compared to sequential‐cones. Assessment of the right and left coronary arteries using reader scores and the image edge profile acutance vessel sharpness metric indicate superior image quality and sharpness for phyllotaxis‐cones.ConclusionPhyllotaxis 3D cones results in improved qualitative image scores and coronary vessel sharpness for free‐breathing whole‐heart coronary magnetic resonance angiography compared to standard sequential ordering when using a steady‐state free precession sequence.
Segmented radial cardiac MRI during arrhythmia using retrospective electrocardiogram and respiratory gating
Authors: Chava Raghuram , Assis Fabrizio , Herzka Daniel , Kolandaivelu Aravindan 
Published: October 2018

PurposeTo improve segmented cardiac MRI image quality during arrhythmia.Methods Electrocardiogram (ECG) and respiratory waveforms were recorded during imaging. Imaging readouts were retrospectively classified into heartbeat‐types based on the RR interval of the current and preceding beats, QRS morphology, and respiratory phase. Image data were sorted by these classifiers to generate separate cine images of different heartbeat‐types during sinus rhythm and arrhythmia. A simulation study evaluated the efficiency of K‐space sampling over a range of heart rhythms, heart rates, and respiratory rates. In vivo imaging was performed in volunteers with sinus rhythm, swine with arrhythmia simulated by pacing, and a human subject with spontaneous premature beats.Results K‐space sampling uniformity and image quality incrementally improve with additional occurrences of the desired normal sinus or arrhythmia heartbeat‐type. To approach the image quality of breath‐hold imaging, sufficiently restrictive gating parameters are required. Compared with real‐time imaging, retrospective gated images had reduced noise and improved sharpness while maintaining desired cine temporal resolution. Variations of cardiac function between arrhythmia heartbeats could be observed in arrhythmia imaging cases that are not captured by conventional segmented imaging.ConclusionRetrospective ECG and respiratory gating permits imaging of various heartbeats during arrhythmia with fewer resolution restrictions compared to real‐time imaging. For a fixed imaging time, imaging quality depends on frequency of the imaged heartbeat‐type. Imaging additional heartbeats permits incremental improvement in image quality.
A parallel time integrator for solving the linearized shallow water equations on the rotating sphere
Authors: Schreiber Martin , Loft Richard 
Published: October 2018

SummaryWith the stagnation of processor core performance, further reductions in the time to solution for geophysical fluid problems are becoming increasingly difficult with standard time integrators. Parallel‐in‐time exposes and exploits additional parallelism in the time dimension, which is inherently sequential in traditional methods. The rational approximation of exponential integrators (REXI) method allows taking arbitrarily long time steps based on a sum over a number of decoupled complex PDEs that can be solved independently massively parallel. Hence, REXI is assumed to be well suited for modern massively parallel super computers, which are currently trending. To date, the study and development of the REXI approach have been limited to linearized problems on the periodic two‐dimensional plane. This work extends the REXI time stepping method to the linear shallow‐water equations on the rotating sphere, thus moving the method one step closer to solving fully nonlinear fluid problems of geophysical interest on the sphere. The rotating sphere poses particular challenges for finding an efficient solver due to the zonal dependence of the Coriolis term. Here, we present an efficient REXI solver based on spherical harmonics, showing the results of a geostrophic balance test, a comparison with alternative time stepping methods, an analysis of dispersion relations indicating superior properties of REXI, and finally, a performance comparison on the Cheyenne supercomputer. Our results indicate that REXI not only can take larger time steps but also can be used to gain higher accuracy and significantly reduced time to solution compared with currently existing time stepping methods.
Inverse optimal control for unmanned aerial helicopters with disturbances
Authors: Ma Haoxiang , Chen Mou , Wu Qingxian 
Published: October 2018

SummaryThis paper proposes an optimal control method of an unmanned aerial helicopter (UAH) with unknown disturbances. Solving the Hamilton‐Jacobi‐Bellman (HJB) equation is considered as the common approach to design an optimal controller under a meaningful cost function when facing the nonlinear optimal control problem. However, the HJB equation is hard to solve even for a simple problem. The inverse optimal control method that avoids the difficulties of solving the HJB equation has been adopted. In this inverse optimal control approach, a stabilizing optimal control law and a particular cost function that are obtained by a control Lyapunov function are required. An integrator backstepping method is used in designing the optimal control law of the UAH. Furthermore, a disturbance‐observer–based control (DOBC) approach has been adopted in the optimal control law for dealing with the unknown disturbances of the UAH system. Simulation results have been given to certify the stability of the nonlinear UAH system and the validity of this developed control method.
Sex steroids in serum and prostatic tissue of human cancerous prostate (STERKPROSER trial)
Authors: Meunier Matthias E. , Neuzillet Yann , Raynaud Jean‐Pierre , Radulescu Camelia , Ghoneim Tarek , Fiet Jean , Giton Franck , Rouanne Mathieu , Dreyfus Jean‐François , Lebret Thierry , Botto Henry 
Published: October 2018

BackgroundCurrently, there is no consensus regarding the expected concentration levels of intra‐prostatic sex steroids in patients with Prostate Cancer (PCa). Our objective was to assess the concentration levels of sex steroids in prostatic tissue and serum, in two cohorts of patients with localized PCa or benign prostatic hyperplasia (BPH).MethodsBetween September 2014 and January 2017, men selected for radical cystectomy (for bladder cancer) or open prostatectomy (for BPH), and men selected for radical prostatectomy for localized PCa were included. Blood samples were collected at baseline before surgery, and steroid concentrations were assessed following the recommendations of the Endocrine Society. Intra‐prostatic samples were collected from fresh surgical samples, and assessed by gas chromatography and mass spectrometry (GC/MS). Permanova analysis was performed. Analyses were adjusted for age, prostate weight, and prostate‐specific antigen (PSA) level.ResultsA total of 73 patients (41 patients with PCa and 32 patients with BPH) were included in this study. Patients with PCa were younger, and had smaller prostate volumes with higher levels of PSA. The levels of Total Testosterone (TT), Di‐Hydro‐Testosterone (DHT), and Estradiol (E2) in the serum were not significantly different between PCa and BPH. In PCa tissue, TT concentrations were significantly lower (0.11 ng/g vs 0.47 ng/g, P = 0.0002), however its derivative E2 had significantly higher concentrations (31.0 ng/g vs 22.3 ng/g, P = 0.01). DHT tissue concentrations were not significantly different between the two groups (5.55 ng/g vs 5.42 ng/g, P = 0.70). Intra‐prostatic TT concentrations were significantly lower in the peripheral zone than in the central zone for the CaP group (0.07 ng/g vs 0.15 ng/g, P = 0.004).ConclusionsPatients with PCa had lower intra‐prostatic TT and higher E2 concentrations levels compared to the patients with BPH. PCa seem to consume more TT and produce more E2, especially in the peripheral zone.
Refinement of protein‐protein complexes in contact map space with metadynamics simulations
Authors: Pfeiffenberger Erik , Bates Paul A. 
Published: October 2018

AbstractAccurate protein‐protein complex prediction, to atomic detail, is a challenging problem. For flexible docking cases, current state‐of‐the‐art docking methods are limited in their ability to exhaustively search the high dimensionality of the problem space. In this study, to obtain more accurate models, an investigation into the local optimization of initial docked solutions is presented with respect to a reference crystal structure. We show how physics‐based refinement of protein‐protein complexes in contact map space (CMS), within a metadynamics protocol, can be performed. The method uses 5 times replicated 10 ns simulations for sampling and ranks the generated conformational snapshots with ZRANK to identify an ensemble of n snapshots for final model building. Furthermore, we investigated whether the reconstructed free energy surface (FES), or a combination of both FES and ZRANK, referred to as CSα, can help to reduce snapshot ranking error.
Effect of garlic supplementation on serum C‐reactive protein level: A systematic review and meta‐analysis of randomized controlled trials
Authors: Taghizadeh Mohsen , Hamedifard Zahra , Jafarnejad Sadegh 
Published: October 2018

The present study was designed to systematically review randomized controlled trials (RCTs) that report on the effects of garlic supplementation on serum C‐reactive protein (CRP) levels. We conducted a literature search of Scopus, PubMed, Cochrane Library, and Google Scholar up to January 2018. Weighted mean differences (WMD) were estimated for net change in serum CRP. Subgroup analyses were also performed by duration of study, dose of supplementation, baseline CRP level, and the quality of studies. From 438 articles found and screened in our initial search, nine RCTs with the sum of total sample size of 363 were included in the meta‐analysis. Compared with the controls, garlic intake significantly reduced the concentrations of serum CRP by 0.8 mg/L (95% CI [−1.5, −0.1], p = 0.02) with the evidence of heterogeneity among studies. Subgroup analyses showed that garlic significantly lowered CRP by 0.82 mg/L (95% CI [−1.02, −0.62], p < 0.001) among studies with a daily garlic dose ≥1,200 mg/day and by 2.44 mg/L (95% CI [−4.02, −0.87], p = 0.002) among studies with baseline CRP ≥2 mg/L. Current data confirmed that garlic supplementation would reduce serum CRP levels. However, the changes were related to the supplemental doses and baseline levels of serum CRP.
Orf virus: A promising new therapeutic agent
Authors: Wang Ruixue , Wang Yong , Liu Fang , Luo Shuhong 
Published: October 2018

SummaryThe orf virus (ORFV) is a zoonotic, epitheliotropic, DNA parapoxvirus that infects principally sheep and goats. Exposure of animals to the virus or immunization by an ORFV preparation can accentuate the severity of disease, which has provoked an interest in the underlying cellular, virological, and molecular mechanisms. The identified ORFV virulence genes and the fact that the virus can repeatedly infect a host, owing to its evasive mechanisms, contribute to the development of potent immune modulators in various animal species. ORFV has been developed as a vaccine in veterinary medicine. The unique host immune‐evasion ability of ORFV has made it an important candidate for vaccine vectors and biological agents (as an oncolytic virus). Genetic modifications using ORFV to obtain safe and efficient preparations and mechanistic studies are improvements to the currently available methods for disease treatment.
Charge Density Waves Driven by Peierls Instability at the Interface of Two‐Dimensional Lateral Heterostructures
Authors: Choi Jin‐Ho , Liu Shuyuan , Zhang Wan , Liu Zhongfan , Rummeli Mark Hermann 
Published: October 2018

AbstractThe origin of charge density wave (CDW) observed in low‐dimensional systems is, for long, a subject of intensive debate in contemporary condensed matter physics. Specifically, a simple and well established model, namely, the Peierls instability is often (but not always) used to clearly explain CDW states in real systems. Here, first‐principles density functional theory calculations are used to show CDW formation at a one‐dimensional interface embedded in a lateral heterostructure comprising blue and black phosphorene, even at room temperature. The CDW formation is fully explained by the Peierls mechanism, including a double‐periodicity lattice distortion energy lowering and a bandgap opening. The lattice distortion also substantially modifies the band alignment of the heterostructure. Comparison with a freestanding P chain shows that the structural distortion is confined to one dimension within the heterostructures, ruling out competing non‐Peierls‐type distortions in two dimensions. In addition, similar Peierls‐type distortions for other lateral heterostructures are shown by using the example of a graphene–hexagonal boron nitride heterostructure, which may stimulate related studies in different 2D systems. These findings not only shed more light on the Peierls mechanism, but also have important implications for devices based on 2D lateral heterostructures.