bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strong cytoskeleton activity on millisecond timescales upon particle binding revealed by ROCS microscopy
Authors: Jünger Felix , Rohrbach Alexander 
Published: July 2018

AbstractCells change their shape within seconds, cellular protrusions even on subsecond timescales enabling various responses to stimuli of approaching bacteria, viruses or pharmaceutical drugs. Typical response patterns are governed by a complex reorganization of the actin cortex, where single filaments and molecules act on even faster timescales. These dynamics have remained mostly invisible due to a superposition of slow and fast motions, but also due to a lack of adequate imaging technology. Whereas fluorescence techniques require too long integration times, novel coherent techniques such as ROCS microscopy can achieve sufficiently high spatiotemporal resolution. ROCS uses rotating back‐scattered laser light from cellular structures and generates a consistently high image contrast at 150 nm resolution and frame rates of 100 Hz—without fluorescence or bleaching. Here, we present an extension of ROCS microscopy that exploits the principles of dynamic light scattering for precise localization, visualization and quantification of the cytoskeleton activity of mouse macrophages. The locally observed structural reorganization processes, encoded by dynamic speckle patterns, occur upon distinct mechanical stimuli, such as soft contacts with optically trapped beads. We find that a substantial amount of the near‐membrane cytoskeleton activity takes place on millisecond timescales, which is much faster than reported ever before.
GLP‐1 neurons form a local synaptic circuit within the rodent nucleus of the solitary tract
Authors: Card J. Patrick , Johnson Aaron L. , Llewellyn‐Smith Ida J. , Zheng Huiyuan , Anand Rishi , Brierley Daniel I. , Trapp Stefan , Rinaman Linda 
Published: July 2018

AbstractGlutamatergic neurons that express pre‐proglucagon (PPG) and are immunopositive (+) for glucagon‐like peptide‐1 (i.e., GLP‐1+ neurons) are located within the caudal nucleus of the solitary tract (cNTS) and medullary reticular formation in rats and mice. GLP‐1 neurons give rise to an extensive central network in which GLP‐1 receptor (GLP‐1R) signaling suppresses food intake, attenuates rewarding, increases avoidance, and stimulates stress responses, partly via GLP‐1R signaling within the cNTS. In mice, noradrenergic (A2) cNTS neurons express GLP‐1R, whereas PPG neurons do not. In this study, confocal microscopy in rats confirmed that prolactin‐releasing peptide (PrRP)+ A2 neurons are closely apposed by GLP‐1+ axonal varicosities. Surprisingly, GLP‐1+ appositions were also observed on dendrites of PPG/GLP‐1+ neurons in both species, and electron microscopy in rats revealed that GLP‐1+ boutons form asymmetric synaptic contacts with GLP‐1+ dendrites. However, RNAscope confirmed that rat GLP‐1 neurons do not express GLP‐1R mRNA. Similarly, Ca2+ imaging of somatic and dendritic responses in mouse ex vivo slices confirmed that PPG neurons do not respond directly to GLP‐1, and a mouse crossbreeding strategy revealed that <1% of PPG neurons co‐express GLP‐1R. Collectively, these data suggest that GLP‐1R signaling pathways modulate the activity of PrRP+ A2 neurons, and also reveal a local “feed‐forward” synaptic network among GLP‐1 neurons that apparently does not use GLP‐1R signaling. This local GLP‐1 network may instead use glutamatergic signaling to facilitate dynamic and potentially selective recruitment of GLP‐1 neural populations that shape behavioral and physiological responses to internal and external challenges.
Stimuli‐Responsive Lanthanide‐Based Smart Luminescent Materials for Optical Encoding and Bio‐applications
Authors: Yang Yiwei , Su Pingru , Tang Yu 
Published: July 2018

AbstractLanthanide based luminescent materials have attracted extensive attention in a wide range of fields including chemistry, biology and logic due to the narrow emission band, long decay time of the excited state, low auto‐fluorescence background and excellent photostability. More interestingly, stimuli‐responsive lanthanide‐based luminescent materials have exhibited enormous application prospects in optical encoding and bio‐applications. In this review, we summarize these aspects of the development of stimuli‐responsive smart lanthanide luminescent materials by sorting the stimuli into several categories, including photo‐, pH‐, thermo‐ and molecule‐responsive. These unique stimuli‐responsive properties endow these materials with great potential in enriching code library and expanding data storage. Additionally, these properties have also been studied widely for bio‐applications, including drug release, imaging biosensing, cell adhesion, and cancer therapy. Based on these two aspects, we highlight the recent progress of lanthanide‐based smart luminescent materials.
T7 Expression Systems for Inducible Production of Proteins from Cloned Genes in E. coli
Authors: Studier F. William 
Published: July 2018

AbstractInducible T7 expression systems are capable of producing a wide range of proteins in E. coli. Improvements over common practice include: (1) preventing unintended induction by establishing and maintaining expression strains in non‐inducing growth media composed entirely of purified components instead of complex growth media that may variably induce target proteins on approach to saturation; and (2) expressing many target proteins in parallel by convenient and productive auto‐induction in BL21(DE3) and other suitable hosts, instead of IPTG induction. From the earliest days, basal expression prevented establishment of inducible strains for producing proteins that are stressful to the host. Newly developed pAL vectors now reduce basal expression to levels where coding sequences for even the most stressful proteins can be maintained and induced. Asymmetric ligation allows simple and efficient cloning of individual coding sequences or simultaneous cloning of two or three coding sequences for co‐expression from a single pAL vector. © 2018 by John Wiley & Sons, Inc.
Genetic Manipulation of Cryptococcus neoformans
Authors: Jung Kwang‐Woo , Lee Kyung‐Tae , So Yee‐Seul , Bahn Yong‐Sun 
Published: July 2018

AbstractCryptococcus neoformans is an opportunistic fungal pathogen, which causes life‐threatening meningoencephalitis in immunocompromised individuals and is responsible for more than 1,000,000 infections and 600,000 deaths annually worldwide. Nevertheless, anti‐cryptococcal therapeutic options are limited, mainly because of the similarity between fungal and human cellular structures. Owing to advances in genetic and molecular techniques and bioinformatics in the past decade, C. neoformans, belonging to the phylum basidiomycota, is now a major pathogenic fungal model system. In particular, genetic manipulation is the first step in the identification and characterization of the function of genes for understanding the mechanisms underlying the pathogenicity of C. neoformans. This unit describes protocols for constructing target gene deletion mutants using double‐joint (DJ) PCR, constitutive overexpression strains using the histone H3 gene promoter, and epitope/fluorescence protein‐tagged strains in C. neoformans. © 2018 by John Wiley & Sons, Inc.
Continuous Flow for the Photochemical C‐H Amination of Arenes
Authors: Cosgrove Sebastian C. , Douglas Gayle E. , Raw Steven A. , Marsden Stephen P. 
Published: July 2018

AbstractThe direct C−H amination of arenes by aminium radicals generated by photolysis of N‐chloroamines is demonstrated under continuous flow conditions. The reactions proceed with comparable efficiency to small scale batch processes but are superior to larger scale batch operations. The continuous generation of the N‐chloroamine from the amine precursor can be integrated into the process, facilitating the continuous direct conversion of secondary amines to their arylated derivatives.
FPGA implementation of adaptive time delay estimation for real‐time near‐field electromagnetic ranging
Authors: Wang Peng , Zhang Xiaotong , Liu Zhiyang , Xu Liyuan , He Jie , Xu Jinwu 
Published: July 2018

SummaryThe near‐field electromagnetic ranging systems exploit the near‐field phase behavior of low frequency signals for indoor real‐time ranging. Conventionally, phase detector is used to determine the phase of electric and magnetic fields. Subsequently, the phase difference is used to estimate a distance value. In adaptive time delay estimation approach, the time delay between electric and magnetic signals is used instead of phase difference for an estimation. This method does not require a priori knowledge of the transmitting signals and can obtain better performance in low signal‐to‐noise ratio environment. In this paper, we propose a digital near‐field electromagnetic ranging system design and implement it on field‐programmable gate array. This system is composed of time delay estimator, frequency estimator, and received signal strength indicator. A maximum correntropy criterion–based explicit time delay estimation algorithm with a delay in the coefficient update is implemented to estimate the time delay in real time. The fast Fourier transform and received signal strength indicator modules determine the signal frequency and the signal strength received, respectively. Our experimental results indicate that the delayed maximum correntropy criterion–based explicit time delay estimation algorithm has fast convergence rate and good steady‐state performance in an impulsive noise environment.
Phytoestrogens in soy‐based meat substitutes: Comparison of different extraction methods for the subsequent analysis by liquid chromatography‐tandem mass spectrometry
Authors: Benedetti Barbara , Di Carro Marina , Magi Emanuele 
Published: July 2018

AbstractThis paper presents the development of an efficient extraction procedure followed by a high performance liquid chromatography‐tandem mass spectrometry (HPLC‐MS/MS) method for the determination of five phytoestrogens (genistein, daidzein, formononetin, biochanin A, and coumestrol) in soy‐based meat substitutes. Phytoestrogens are considered endocrine disrupting compounds, and their quantification is important in soy‐based products, whose diffusion is increasing nowadays.The HPLC‐MS/MS method, with electrospray ionization (ESI) source, was optimized to obtain high specificity and sensitivity, as well as rapidity of the analysis. Three extraction techniques were applied to soy burgers and compared: ultrasound assisted extraction, ultrasound assisted extraction followed by solid phase extraction and the Quick Easy Cheap Effective Rugged and Safe (QuEChERS) methodology. Both ultrasound assisted extraction and QuEChERS proved to be suitable for the determination of phytoestrogens, showing high recoveries, in the range of 86% to 99% and 75% to 105%, respectively. Matrix effect was evaluated, and ion suppression was observed for coumestrol and formononetin, demonstrating the importance of matrix effect assessment when complex samples are analyzed by HPLC‐ESI‐MS.The complete analytical protocols provided limits of detection and quantitation in soy‐burgers at the ng g−1 level for all the considered phytoestrogens. Some soy burger samples were analyzed by both ultrasound assisted extraction and QuEChERS followed by HPLC‐MS/MS. High concentration levels of daidzein and genistein (2‐59 μg g−1 and 2‐72 μg g−1, respectively) were found; formononetin was in the range of 5 to 26 ng g−1, while biochanin A and coumestrol were under the limit of quantitation in all samples. The results obtained with the two different sample treatment were in good agreement, proving the precision and accuracy of the described techniques.
A systematic approach toward comparing electrospray ionization efficiencies of derivatized and non‐derivatized amino acids and biogenic amines
Authors: Gornischeff Artur , Liigand Jaanus , Rebane Riin 
Published: July 2018

AbstractIonization efficiency (IE) in mass spectrometry (MS) has been studied for many different compounds, and different IE scales have been constructed in order to quantitatively characterize IE. In the case of MS, derivatization has been used to increase the sensitivity of the method and to lower the limits of detection. However, the influence of derivatization on IE across different compounds and different derivatization reagents has not been thoroughly researched, so that practitioners do not have information on the IE‐enhancing abilities of different derivatization reagents.Moreover, measuring IE via direct infusion of compounds cannot be considered fully adequate. Since derivatized compounds are in complex mixtures, a chromatographic method is needed to separate these compounds to minimize potential matrix effects.In this work, an IE measurement system with a chromatographic column was developed for mainly amino acids and some biogenic amines. IE measurements with liquid chromatography electrospray ionization mass spectrometry (LC/ESI/MS) were carried out, and IE scales were constructed with a calibration curve for compounds with and without derivatization reagent diethyl ethoxymethylenemalonate. Additionally, eluent composition effects on ionization were investigated.Results showed that derivatization increases IE for most of the compounds (by average 0.9 and up to 2‐2.5 logIE units) and derivatized compounds have more similar logIE values than without derivatization. Mobile phase composition effects on ionization efficiencies were negligible. It was also noted that the use of chromatographic separation instead of flow injection mode slightly increases IE.In this work, for the first time, IE enhancement of derivatization reagents was quantified under real LC/ESI/MS conditions and obtained logIE values of derivatized compounds were linked with the existing scale.
Synthesis and characterization of a poly(p‐phenylenediamine)‐based electrospun nanofiber for the micro‐solid‐phase extraction of organophosphorus pesticides from drinking water and lemon and orange juice samples
Authors: Mehrani Zahra , Ebrahimzadeh Homeira , Asgharinezhad Ali Akbar 
Published: July 2018

AbstractA new micro‐solid‐phase extraction sorbent was synthesized by electrospinning poly(p‐phenylenediamine)/poly(vinyl alcohol) in the presence of cetyltrimethylammonium bromide. The modified nanofiber was prepared by removing the majority of the poly(vinyl alcohol) from the nanofiber blend by exposing it to the hot water. Scanning electron microscopy and surface analysis were performed to study the homogeneity and porosity of the electrospun nanofiber. In addition, Fourier transform infrared spectroscopy was applied for more characterization. The capability of the new nanofiber was explored by applying it in the extraction and preconcentration of organophosphorus pesticides from aqueous medium. After solvent desorption, the extracted analytes were analyzed by high‐performance liquid chromatography with diode array detection. Under the optimum conditions, the relative standard deviation values at the concentration level of 50 ng/mL were in the range of 4.8–8.3%. The calibration curve showed linearity in the range of 0.5–500 ng/mL, and the limits of detection (S/N = 3) for the studied compounds were 0.15 ng/mL. By analyzing Tehran drinking water, lemon juice, sour lemon juice, orange juice and sour orange juice, the applicability of the presented method was investigated and the relative recoveries were in the range of 76–102%.
Development of Bioink from Decellularized Tendon Extracellular Matrix for 3D Bioprinting
Authors: Toprakhisar Burak , Nadernezhad Ali , Bakirci Ezgi , Khani Navid , Skvortsov Gozde Akdeniz , Koc Bahattin 
Published: July 2018

AbstractUsing decellularized extracellular matrix (dECM) hydrogels as bioinks has been an important step forward for bioprinting of functional tissue constructs, considering their rich microenvironment and their high degree of biomimicry. However, directly using dECM hydrogels as bioinks may not be suitable for bioprinting processes because of the loss of shape fidelity and geometrical precision of bioprinted structure due to their slow gelation kinetics. In this article, the development and direct bioprinting of dECM hydrogel bioink from bovine Achilles tendon were presented. The developed bioink is used for a microcapillary‐based bioprinting process without any support structure and/or any additional cross‐linker components. The reported decellularization and solubilization methods yield dECM pre‐gels which turn into stable hydrogels in a short time at physiological conditions. The gelation kinetics and mechanical strength of bioinks with different concentrations and digestion times are characterized. A support structure‐free 3D bioprinting of the developed bioink is shown by aspirating dECM bioinks and then in situ gelation and extrusion through a fine microcapillary nozzle. The viability assays indicate that the developed dECM bioink has no cytotoxic effect on encapsulated NIH 3T3 cells and the cells show lineage‐specific morphology in the early days of culture as well.
Preparation and Gas Separation Properties of Spirobichroman‐Based Polyimides
Authors: Zhang Caili , Li Pei 
Published: July 2018

AbstractPolymers with rigid and contorted structures are always preferred for use as gas separation membranes. Owing to the contorted nature of the spiro‐center, the spirobichroman structure is an effective scaffold for impeding polymer chain packing. Two spirobichroman‐based diamines, 6,6′‐bis(4‐amino‐2‐trifluoromethylphenoxy)‐4,4,4′,4′,7,7′‐hexamethyl‐2,2′‐spirobichroman (FSBC) and 6,6′‐bis(4‐aminophenoxy)‐4,4,4′,4′,7,7′‐hexamethyl‐2,2′‐spirobichroman (SBC), with or without CF3 side groups are prepared. The two diamines are separately reacted with 3,3′,4,4′‐benzophenonetetracarboxylic dianhydride (BTDA) and 3,3′,4,4′‐diphenylsulfonetetracarboxylic dianhydride (DSDA) to obtain four spirobichroman‐based polyimides, denoted as BTDA‐FSBC, BTDA‐SBC, DSDA‐FSBC, and DSDA‐SBC. The different molecular structures among the four monomers are expected to alter the fractional free volume of the corresponding polyimides by impacting chain‐packing conditions, and then controlling the gas transport properties. Chemical structures, thermal and physical properties of the polyimides are fully characterized. Two different methods, molecular dynamics simulation and Bondi's group contribution method are employed to characterize the fractional free volumes (FFVs) of these polyimides. In the end, it is found that FSBC‐based polyimides exhibit relatively higher gas permeability than SBC‐based polyimides.
Convenient Graphical Visualization of Messages Encoded in Sequence‐Defined Synthetic Polymers Using Kendrick Mass Defect Analysis of their MS/MS Data
Authors: Poyer Salomé , Fouquet Thierry , Sato Hiroaki , Lutz Jean‐François , Charles Laurence 
Published: July 2018

AbstractKendrick mass defect (KMD) analysis is shown here to be a convenient method to read binary messages encoded in the structure of two types of sequence‐defined synthetic polymers, namely, polyurethanes and poly(alkoxyamine phosphodiester)s. KMD analysis allows graphical ranking of mass data obtained for species containing repeating units. This is performed on MS/MS data in which distribution of fragments reveals the comonomer sequence of digital macromolecules. Choosing one coding monomer as the base unit, KMD computation of MS/MS data leads to stair‐like plots where flat steps correspond to that monomer selected as the base unit while oblique steps reveal the other monomer. To correct for any point misalignments resulting from slight inaccuracy of fragment mass measurement, fractional base units are used to perform resolution‐enhanced KMD (RE‐KMD) analysis. As the length of the chain increased, a procedure aiming at correct aliased points is also implemented to achieve continuous, more convenient, stair‐like plots.
A Tunable Nanoimprint System to Create New Features
Authors: Zhang Xiang , Hu Xin , Shen Lei , Chen Xinrui , Ge Haixiong 
Published: July 2018

AbstractFabrication of different patterns based on the same nanoimprint mould is very attractive due to the time and cost consumption of fabricating hard mould. This paper demonstrates a tunable photo‐curing nanoimprint system to create new features based on the same polydimethylsiloxane (PDMS) mould and a Ti‐containing resist synthesized by titanium (IV) ethoxide and 2‐(methacryloyloxy)ethyl acetoacetate. The resist exhibits very high oxygen RIE resistance and is able to take the place of traditional polysiloxance based resists to fabricate high‐aspect‐ratio patterns. The resist also has a low shrinkage (about 2.45%) and a high Young’s modulus of 10.85 GPa after photo‐curing. High polarity contrast of PDMS and Ti‐resist makes the release process freely and PDMS mould can be directly used without further anti‐stick treatment. A number of new features are imprinted into Ti‐resist based on the same PDMS mould by controlling the deformation and the stretched PDMS mould can be repeatedly used after relaxation.
A robust intensity modulated proton therapy optimizer based on Monte Carlo dose calculation
Authors: Ma Jiasen , Wan Chan Tseung Hok Seum , Herman Michael G. , Beltran Chris 
Published: July 2018

PurposeAccuracy of dose calculation models and robustness under various uncertainties are key factors influencing the quality of intensity modulated proton therapy (IMPT) plans. To mitigate the effects of uncertainties and to improve the dose calculation accuracy, an all‐scenario robust IMPT optimization based on accurate Monte Carlo (MC) dose calculation was developed.MethodsIn the all‐scenario robust IMPT optimization, dose volume histograms (DVHs) were computed for the nominal case and for each uncertainty scenario. All scenarios were weighted by DVH values dynamically throughout optimization iterations. In contrast, probabilistic approach weighted scenarios with fixed scenario weights and worst case optimizations picked one single scenario — the worst scenario for each iteration. Uncertainties in patient setup and proton range were considered in all clinical cases studied. Graphics processing unit (GPU) computation was employed to reduce the computational time in both the MC dose calculation and optimization stages. A previously published adaptive quasi‐Newton method for proton optimization was extended to include robustness. To validate the all‐scenario algorithm extension, it was compared with the single scenario optimization target volume (OTV) based approach in clinical cases of three different disease sites. Additional comparisons with worst case optimization methods were conducted to evaluate the performance of the all‐scenario robust optimization against other robust optimizations.ResultsThe all‐scenario robust IMPT optimization spared organs at risk (OARs) better than the OTV‐based method while maintaining target coverage and improving the robustness of targets and OARs. Compared with composite and voxel‐wise worst case optimization, the all‐scenario robust optimization converged faster, and arrived at solutions of tighter DVH robustness spread, better target coverage and lower OAR dose.ConclusionAn all‐scenario robust IMPT treatment planning system was developed using an adaptive quasi‐Newton optimization method. The optimization system was GPU‐accelerated and based on MC dose calculation. Improved performance was observed in clinical cases when compared with worst case optimization methods.