bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate Determination of Human CPR Conformational Equilibrium by smFRET Using Dual Orthogonal Noncanonical Amino Acid Labeling
Authors: Quast Robert B. , Fatemi Fataneh , Kranendonk Michel , Margeat Emmanuel , Truan Gilles 
Published: November 2018

AbstractConjugation of fluorescent dyes to proteins—a prerequisite for the study of conformational dynamics by single‐molecule (sm) FRET—can lead to substantial changes in a dye's photophysical properties, ultimately biasing the determination of inter‐dye distances. In particular, cyanine dyes and their derivatives, the most commonly used dyes in smFRET experiments, exhibit such behavior. To overcome this, we developed a general strategy to equip proteins site‐specifically with FRET pairs through chemoselective reactions with two distinct noncanonical amino acids simultaneously incorporated through genetic code expansion in Escherichia coli. Application of this technique to human NADPH‐cytochrome P450 reductase (CPR) demonstrated the importance of homogenously labeled samples for accurate determination of FRET efficiencies and unveiled the effect of NADP+ on the ionic‐strength‐dependent modulation of the conformational equilibrium of CPR. Thanks to its generality and accuracy, the presented methodology establishes a new benchmark for deciphering of complex molecular dynamics in single molecules.
Genotypic diversity of bran weight of whole grain rice and its relationship with grain physical traits
Authors: Chen Ming‐Hsuan , McClung Anna M. 
Published: November 2018

AbstractBackground and objectivesRice bran, the outer most layer of the whole grain, is where nutrients, minerals, and bioactive compounds, except starch, are primarily deposited. Rice bran accounts for a small portion of the whole grain weight. Increasing the weight proportion of bran will enhance the health beneficial value of whole grain rice.FindingsWe determined the physical and bran traits of 135 rice genotypes grown in two years. More than a 2.3‐ and 2.5‐fold variation was found for bran weight per gram of whole grain and bran weight per surface area of the whole grain (BWS, representing bran thickness), respectively. Principle component analysis of the seven physical traits and two bran traits grouped the bran traits into PC3 and accounted for an average of 15.5% of the total variance, whereas kernel weight, width, thickness, and grain surface area were in PC1, and kernel length and length/width ratio were in PC2. Mean comparison among bran color classes showed that purple bran genotypes had the highest BWS, followed by red, white, light brown, and brown. BWS moderately correlated with kernel weight, width, and thickness.ConclusionsThis report demonstrates high bran weight genotypes can be selected to improve the nutritional value of whole grain rice.Significance and noveltyExpressing bran weight based on grain surface area removed the confounding factor of differences in grain size and allowed identification of genotypes having high bran weight consistently across two years, suggesting this trait is genetically regulated and can be used in traditional breeding to improve bran weight proportion of whole grain rice leading to higher nutritional value of the rice.
Effect of Carbon Nanotubes and Carbon Nanotubes/Gold Nanoparticles Composite on the Photocatalytic Activity of TiO2 and TiO2‐SiO2
Authors: Chinh Vu Duc , Hung Le Xuan , Di Palma Luca , Hanh Vu Thi Hong , Vilardi Giorgio 
Published: November 2018

AbstractA carbon nanotube (CNT)/gold nanoparticle (NP) nanocomposite was synthesized by simultaneously reducing the Au ions and depositing Au NPs on the surface of a CNT. The functional groups were investigated with Fourier transform infrared spectra. From the Raman spectra, the D‐band and G‐band of the CNT were identified. The deposition of nanometer‐sized Au NPs on the CNT sites was observed by transmission electron microscopy. The photodegradation of methylene blue (MB) in aqueous solutions was studied using various photocatalysts, including TiO2, TiO2‐SiO2, CNT/TiO2, CNT/TiO2‐SiO2, Au/TiO2, CNT‐Au/TiO2, and CNT‐Au/TiO2‐SiO2 composites. CNT addition leads to a synergic effect, improving the photoactivity of the catalysts. A possible physically based mechanism was proposed involving the reduction of electron‐hole recombination and fast electron‐transfer possibility.
Regional differences in gallbladder cancer pathogenesis: Insights from a multi‐institutional comparison of tumor mutations
Authors: Narayan Raja R. , Creasy John M. , Goldman Debra A. , Gönen Mithat , Kandoth Cyriac , Kundra Ritika , Solit David B. , Askan Gokce , Klimstra David S. , Basturk Olca , Allen Peter J. , Balachandran Vinod P. , D’Angelica Michael I. , DeMatteo Ronald P. , Drebin Jeffrey A. , Kingham T. Peter , Simpson Amber L. , Abou‐Alfa Ghassan K. , Harding James J. , O’Reilly Eileen M. , Butte Jean M. , Matsuyama Ryusei , Endo Itaru , Jarnagin William R. 
Published: November 2018

AbstractBackgroundAlthough rare in the United States, gallbladder cancer (GBCA) is a common cause of cancer death in some parts of the world. To investigate regional differences in pathogenesis and outcomes for GBCA, tumor mutations were analyzed from a sampling of specimens.MethodsPrimary tumors from patients with GBCA who were treated in Chile, Japan, and the United States between 1999 and 2016 underwent targeted sequencing of known cancer‐associated genes. Fisher exact and Kruskal‐Wallis tests assessed differences in clinicopathologic and genetic factors. Kaplan‐Meier methods evaluated differences in overall survival from the time of surgery between mutations.ResultsA total of 81 patients were included. Japanese patients (11 patients) were older (median age, 72 years [range, 54‐81 years]) compared with patients from Chile (21 patients; median age, 59 years [range, 32‐73 years]) and the United States (49 patients; median age, 66 years [range, 46‐87 years]) (P = .002) and had more well‐differentiated tumors (46% vs 0% for Chile/United States; P < .001) and fewer gallstone‐associated cancers (36% vs 67% for Chile and 69% for the United States; P = .13). Japanese patients had a median mutation burden of 6 (range, 1‐23) compared with Chile (median mutation burden, 7 [range, 3‐20]) and the United States (median mutation burden, 4 [range, 0‐27]) (P = .006). Tumors from Japanese patients lacked AT‐rich interaction domain 1A (ARID1A) and phosphatidylinositol‐4,5‐bisphosphate 3‐kinase catalytic subunit alpha (PIK3CA) mutations, whereas Chilean tumors lacked Erb‐B2 receptor tyrosine kinase 3 (ERBB3) and AT‐rich interaction domain 2 (ARID2) mutations. SMAD family member 4 (SMAD4) was found to be mutated similarly across centers (38% in Chile, 36% in Japan, and 27% in the United States; P = .68) and was univariately associated with worse overall survival (median, 10 months vs 25 months; P = .039). At least one potentially actionable gene was found to be altered in 80% of tumors.ConclusionsDifferences in clinicopathologic variables suggest the possibility of distinct GBCA pathogenesis in Japanese patients, which may be supported by differences in mutation pattern. Among all centers, SMAD4 mutations were detected in approximately one‐third of patients and may represent a converging factor associated with worse survival. The majority of patients carried mutations in actionable gene targets, which may inform the design of future trials.
A monolithic fluid‐structure interaction framework applied to red blood cells
Authors: Cetin Ayse , Sahin Mehmet 
Published: November 2018

AbstractA parallel fully coupled (monolithic) fluid‐structure interaction (FSI) algorithm has been applied to the deformation of red blood cells (RBCs) in capillaries, where cell deformability has significant effects on blood rheology. In the present FSI algorithm, fluid domain is discretized using the side‐centered unstructured finite volume method based on the Arbitrary Lagrangian‐Eulerian (ALE) formulation; meanwhile, solid domain is discretized with the classical Galerkin finite element formulation for the Saint Venant‐Kirchhoff material in a Lagrangian frame. In addition, the compatible kinematic boundary condition is enforced at the fluid‐solid interface in order to conserve the mass of cytoplasmic fluid within the red cell at machine precision. In order to solve the resulting large‐scale algebraic linear systems in a fully coupled manner, a new matrix factorization is introduced similar to that of the projection method, and the parallel algebraic multigrid solver BoomerAMG is used for the scaled discrete Laplacian provided by the HYPRE library, which we access through the PETSc library. Three important physical parameters for the blood flow are simulated and analyzed: (1) the effect of capillary diameter, (2) the effect of red cell membrane thickness, and (3) the effect of red cell spacing (hematocrit). The numerical calculations initially indicate a shape deformation in which biconcave discoid shape changes to a parachute‐like shape. Furthermore, the parachute‐like cell shape in small capillaries undergoes a cupcake‐shaped buckling instability, which has not been observed in the literature. The instability forms thin riblike features, and the red cell deformation is not axisymmetric but three‐dimensional.
Retracted: Complex image denoising framework with CNN‐wavelet under concurrency scenarios for informatics systems
Authors: Wang Liping , Huang Wenzhun , Zhang Shanwen , Liu Zhe 
Published: November 2018

SummaryImage denoising based on convolutional neural networks and wavelet transform is a novel approach for the applications. In the image acquisition process, images are often contaminated by noise, which affects the image quality; therefore, it is necessary to eliminate noise before analyzing and using images. Wavelet analysis is a local analysis method with multi‐resolution characteristics, which is developed on the basis of short‐time Fourier transform. It can be used for the multi‐scale analysis of signals by means of expansion, translation and other operations, and extracting effective information from signals, which is a powerful tool for analyzing non‐stationary signals. Wavelet has good time‐frequency local characteristics, low entropy, and decorrelation. In this paper, we propose MRI image denoising framework based on convolutional neural networks and wavelet transform, and the experiment results show that the proposed method can keep the edge and curvature structure better while denoising. Compared with the other novel methodologies, the proposed algorithm can provide the higher robustness. In the future research, we will try the implementations of the methodologies.
Algorithms for in‐place matrix transposition
Authors: Gustavson Fred G. , Walker David W. 
Published: November 2018

SummaryThis paper presents implementations of in‐place algorithms for transposing rectangular matrices. One implementation is a swap‐based algorithm described by Tretyakov and Tyrtyshnikov,1 to which we have introduced a number of variations. In particular, we show how the original algorithm can be modified to require constant additional memory. A proof of correctness is also sketched. This algorithm is compared with cycle‐following approaches and with the swap‐based GCD Transpose algorithm that partitions the matrix into a hierarchy of square submatrices. The performance of parallel implementations on a multicore system is also investigated.
Multiferroic Nature of Microwave‐Processed and Sol‐Gel Synthesized NanoPb1‐xCoxTiO3 (x = 0.2–0.8) Ceramics
Authors: Kumar Nagasamudram Suresh , Suvarna Reniguntla Padma , Naidu Kadiyala Chandra Babu 
Published: November 2018

AbstractThe lead cobalt titanate (PCT) nanoparticles are prepared through sol‐gel technique by changing the Co content from 0.2 to 0.8. Later, the prepared materials are microwave‐heated at 1023 K for ¾ h. The X‐ray diffraction analysis reveals the change of structure of PCT nanoparticles from tetragonal (T) to rhombohedral (R) phases at higher cobalt contents. In addition, the Williamson–Hall (W–H) plots are drawn to determine microstrain (ε′) and crystallite size (D′) values. The surface morphology is carried out using field emission scanning and transmission electron microscopes. Moreover, the room temperature multiferroic nature is described using polarization versus electric field (P–E) and magnetization versus applied magnetic field (M–H) curves. The magnetic hysteresis loop results indicate a transition from ferromagnetic to paramagnetic state.
Distribution of Yb3+ and Yb2+ Ions along YbF3‐Doped BaF2 Crystals
Authors: Stef Marius , Nicoara Irina , Vizman Daniel 
Published: November 2018

AbstractBaF2 crystals doped with 0.05, 0.1, and 0.2 mol% YbF3 are grown using vertical Bridgman method. Transparent crystals, ≈5–6 cm in length, ≈10 mm in diameter, are obtained in vacuum using a shaped graphite furnace. The absorption spectra reveal the characteristic absorption bands of the Yb3+and Yb2+ ions in the as‐grown crystals. The distribution of ytterbium ions along the crystals and the effective segregation coefficient of the Yb3+ and Yb2+ ions in the BaF2 host are determined by using the optical absorption method. The crystals are cleaved from the bottom to the top into 10–17 slices of ≈2 mm thickness. The optical absorption spectrum of every slice is recorded. The dopant distribution along the crystal is estimated studying the absorption spectrum of every slice. Two well‐shaped and strong characteristic bands, 968 nm and 352 nm, respectively, are chosen. The Yb3+ and Yb2+ ions are not uniformly distributed along the BaF2 crystals. The calculated effective segregation coefficients of the Yb3+ range from 0.7 to 0.84 and from 0.66 to 0.82 for Yb2+ ions.
VyCAP's puncher technology for single cell identification, isolation, and analysis
Authors: Stevens Michiel , Oomens Lisa , Broekmaat Joska , Weersink Joris , Abali Fikri , Swennenhuis Joost , Tibbe Arjan 
Published: November 2018

AbstractHere we present the Puncher technology for the isolation of single cells. This technology combines a silicon chip with microwells, fluorescence imaging, and a punching method to isolate and transfer the single cells to standard reaction tubes. The technology is compatible with commercially available downstream workflows and instrumentation. Here we focus on the isolation of CTC but the Puncher technology can be applied to isolate single cells from liquid biopsies and more general from cell suspensions. It is especially suited for cell suspensions that contain:
Cells of interest at a frequency of 1 per 10,000 or less
A low total number of cells ranging from 1 to 100,000, that are present in a volume of 0.01 to 50 mL.
The frequency of appearance of CTC in blood is in the order of the 1 per 106 leukocytes. To be able to isolate the single CTC with the Puncher technology, enrichment of the CTC by a 3 logs reduction of the leukocytes is required. Here we describe the use of Rosettesep and Parsortix as examples of pre‐enrichment methods that are compatible with the Puncher technology and further downstream applications. © 2018 International Society for Advancement of Cytometry
Identification of functionally primitive and immunophenotypically distinct subpopulations in secondary acute myeloid leukemia by mass cytometry
Authors: Bandyopadhyay Shovik , Fowles Jared S. , Yu Liyang , Fisher Daniel A.C. , Oh Stephen T. 
Published: November 2018

BackgroundBackground: Mass cytometry (CyTOF) is a powerful tool for analyzing cellular networks at the single cell level. Due to the high‐dimensional nature of this approach, analysis algorithms have been developed to visualize and interpret mass cytometry data. In this study, we applied these approaches to a cohort of patients with secondary acute myeloid leukemia (sAML).MethodsWe utilized mass cytometry to interrogate localization and intensity of thrombopoietin‐mediated intracellular signaling in sAML. Extracellular and intracellular phenotypes were dissected using SPADE, viSNE, and PhenoGraph.ResultsHealthy controls exhibited highly localized signaling responses largely restricted to the hematopoietic stem/progenitor cell (HSPC) compartment. In contrast, sAML samples contained subpopulations outside the HSPC compartment exhibiting thrombopoietin (TPO) sensitivity comparable to or greater than immunophenotypically defined HSPCs. We employed unsupervised clustering by PhenoGraph to elucidate distinct subpopulations within these heterogeneous samples. One metacluster composed almost exclusively of Lin− CD61+ CD34− CD38− CD45low cells was identified. This subpopulation was not readily identified by established manual gating approaches, and generally exhibited greater STAT phosphorylation in response to TPO stimulation than did Lin− CD61− CD34+ CD38− cells. Lin− CD61+ CD34− CD38− CD45low cells were identified in three additional sAML patients analyzed independently using a manual gating approach based upon PhenoGraph results. Each patient exhibited a similar TPO hypersensitivity to the PhenoGraph metacluster.ConclusionsThe identification of this cellular subpopulation highlights the limitations of manual gating in sAML. Our study demonstrates the potential for mass cytometry to elucidate rare subpopulations in highly heterogeneous tumors by utilizing unsupervised high dimensional analysis. © 2018 International Clinical Cytometry Society
An efficient resource allocation scheme in a dense RFID network based on cellular learning automata
Authors: Assarian Ali , Khademzadeh Ahmad , Hosseinzadeh Mehdi , Setayeshi Saeed 
Published: November 2018

SummaryRadio‐frequency identification (RFID) is a wireless communication technology. Radio frequencies can cause interference in a dense RFID system, thus decreasing efficiency. In recent years, many protocols have been proposed to reduce reader collisions based on multiple‐access techniques. The main weakness of Time Division Multiple Access (TDMA)‐based schemes is the random selection of resources. Additionally, they do not consider the distance between the interfering readers. Therefore, the likelihood of interference in an RFID system will be increased. To address this problem, we propose a new scheme for allocating resources to readers using a learning technique. The proposed scheme takes into account the distance between interfering readers, and these readers acquire the necessary knowledge to select new resources based on the results of the previous selection of neighboring readers using cellular learning automata. This approach leads to reduced interference in an RFID system. The proposed scheme is fully distributed and operates without hardware redundancy. In this scheme, the readers select new resources without exchanging information with each other. The simulation results show that the percentage of kicked readers decreased by more than 20%, and the proposed scheme also provides higher throughput than do state‐of‐the‐art schemes for dense reader environments and leads to further recognition of tags.
End‐to‐end security‐reliability analysis of multi‐hop cognitive relaying protocol with TAS/SC‐based primary communication, total interference constraint and asymmetric fading channels
Authors: Nam Pham Minh , Duy Tran Trung , Ca Phan Van 
Published: November 2018

SummaryIn this paper, we analyze the tradeoff between outage probability (OP) and intercept probability (IP) for a multi‐hop relaying scheme in cognitive radio (CR) networks. In the proposed protocol, a multi‐antenna primary transmitter (PT) communicates with a multi‐antenna primary receiver (PR), using transmit antenna selection (TAS) / selection combining (SC) technique, while a secondary source attempts to transmit its data to a secondary destination via a multi‐hop approach in presence of a secondary eavesdropper. The secondary transmitters such as source and relays have to adjust their transmit power to satisfy total interference constraint given by PR. We consider an asymmetric fading channel model, where the secondary channels are Rician fading, while the remaining ones experience the Rayleigh fading. Moreover, an optimal interference allocation method is proposed to minimize OP of the primary network. For the secondary network, we derive exact expressions of end‐to‐end OP and IP which are verified by Monte Carlo simulations.
Development of an ultra‐high performance liquid chromatography–tandem mass spectrometry method for the determination of anabolic steroids currently available on the black market in the Czech Republic and Slovakia
Authors: Tircova Barbora , Bosakova Zuzana , Kozlik Petr 
Published: November 2018

AbstractOver the past decade, the use of anabolic androgenic steroids (AAS) by recreational bodybuilders and regular gym members has been increasing exponentially. However, there is a lack of knowledge on AAS products sold in the Czech Republic and Slovakia. The aim of this study was to assess the quantity of active substances in AAS products obtained from AAS users in the Czech Republic and Slovakia. In addition, the study also examines the current trends in counterfeit AAS products used by recreational bodybuilders and regular gym members. For this purpose, the authors developed and validated a universal ultra‐high performance liquid chromatography with tandem mass spectrometry method to determine the most popular doping substances in different pharmaceutical formulations (oil‐based injectables, tablets, and capsules). This method was successfully utilized for the analysis of 358 AAS products. Our results showed that 58.9% AAS products analyzed contained the declared active substances at the declared concentrations, 15.9% contained no active substance, 16.8% were under‐concentrated, 4.5% contained active substances different from those declared on the label, and 3.6% products were over‐concentrated. Alarmingly, the results demonstrated that over 40% of the AAS analyzed failed to meet label claims and therefore may pose serious health risks to consumers. This study also highlighted that the availability of AAS should be more rigorously restricted and their quality closely monitored in order to protect AAS users. In conclusion, the authors have developed a precise, accurate, sensitive, selective, and robust method for the routine screening of products containing anabolic androgenic steroids.
Conventional versus real‐time quantitative PCR for rare species detection
Authors: Xia Zhiqiang , Johansson Mattias L. , Gao Yangchun , Zhang Lei , Haffner Gordon Douglas , MacIsaac Hugh J. , Zhan Aibin 
Published: November 2018

AbstractDetection of species in nature at very low abundance requires innovative methods. Conventional PCR (cPCR) and real‐time quantitative PCR (qPCR) are two widely used approaches employed in environmental DNA (eDNA) detection, though lack of a comprehensive comparison of them impedes method selection. Here we test detection capacity and false negative rate of both approaches using samples with different expected complexities. We compared cPCR and qPCR to detect invasive, biofouling golden mussels (Limnoperna fortunei), in samples from laboratory aquaria and irrigation channels where this mussel was known to occur in central China. Where applicable, the limit of detection (LoD), limit of quantification (LoQ), detection rate, and false negative rate of each PCR method were tested. Quantitative PCR achieved a lower LoD than cPCR (1 × 10−7 vs. 10−6 ng/μl) and had a higher detection rate for both laboratory (100% vs. 87.9%) and field (68.6% vs. 47.1%) samples. Field water samples could only be quantified at a higher concentration than laboratory aquaria and total genomic DNA, indicating inhibition with environmental samples. The false negative rate was inversely related to the number of sample replicates. Target eDNA concentration was negatively related to distance from sampling sites to the water (and animal) source. Detection capacity difference between cPCR and qPCR for genomic DNA and laboratory aquaria can be translated to field water samples, and the latter should be prioritized in rare species detection. Field environmental samples may involve more complexities—such as inhibitors—than laboratory aquaria samples, requiring more target DNA. Extensive sampling is critical in field applications using either approach to reduce false negatives.