bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel, smaller scaffold for Affitins: Showcase with binders specific for EpCAM
Authors: Kalichuk Valentina , Renodon‐Cornière Axelle , Béhar Ghislaine , Carrión Federico , Obal Gonzalo , Maillasson Mike , Mouratou Barbara , Préat Véronique , Pecorari Frédéric 
Published: October 2017

AbstractAffitins are highly stable engineered affinity proteins, originally derived from Sac7d and Sso7d, two 7 kDa DNA‐binding polypeptides from Sulfolobus genera. Their efficiency as reagents for intracellular targeting, enzyme inhibition, affinity purification, immunolocalization, and various other applications has been demonstrated. Recently, we have characterized the 7 kDa DNA‐binding family, and Aho7c originating from Acidianus hospitalis was shown to be its smallest member with thermostability comparable to those of Sac7d and Sso7d. Here, after four rounds of selection by ribosome display against the human recombinant Epithelial Cell Adhesion Molecule (hrEpCAM), we obtained novel Aho7c‐based Affitins. The binders were expressed in soluble form in Escherichia coli, displayed high stability (up to 74°C; pH 0–12) and were shown to be specific for the hrEpCAM extracellular domain with picomolar affinities (KD = 110 pM). Thus, we propose Aho7c as a good candidate for the creation of Affitins with a 10% smaller size than the Sac7d‐based ones (60 vs. 66 amino acids).
Effect of NADPH availability on free fatty acid production in Escherichia coli
Authors: Li Wei , Wu Hui , Li Mai , San Ka‐Yiu 
Published: October 2017

AbstractMicrobial conversion of renewable carbon sources to free fatty acids has attracted significant attention in recent years. Accumulation of free fatty acids in Escherichia coli by overexpression of an acyl‐ACP thioesterase which can break the fatty acid elongation has been well established. Various efforts have been made to increase fatty acid production in E. coli by enhancing the enzymes involved in the fatty acid synthesis cycle or host strain manipulations. The current study focused on the effect of NADPH availability on free fatty acids (FFAs) productivity. There are two reduction steps in the fatty acid elongation cycle which are catalyzed by beta keto‐ACP reductase (FabG) and enoyl‐ACP reductase (FabI), respectively. It is reported that FabI can use either NADH or NADPH as cofactor, while FabG only uses NADPH in E. coli. Fatty acid production dropped dramatically in the glucose‐6‐phosphate dehydrogenase (encoded by the zwf gene) deficient strain. Similarly, the pntB (which encodes one of the subunit of proton‐translocating membrane bounded transhydrogenase PntAB) and udhA (which encodes the energy dependent cytoplasmic transhydrogenase UdhA) double mutant strain also showed an 88.8% decrease in free fatty acid production. Overexpression of PntAB and NadK restored the fatty acid production capability of these two mutant strains. These results indicated that the availability of NADPH played a very important role in fatty acid production.
Ketamine and norketamine stability in whole blood at ambient and 4°C conditions
Authors: Tran Benjamin Duy , Moorthy Ganesh S. , Zuppa Athena F. 
Published: October 2017

AbstractA study was implemented to describe the pharmacokinetics (PK) of ketamine (K) and its metabolite norketamine (NK) in critically ill adults. Conducting studies in these subjects is hindered by the immediate need to process and freeze samples obtained in a busy intensive care setting. The ability to store unprocessed samples at room temperature for an extended time period would overcome this barrier. Stability and blood to plasma partitioning of K and NK were investigated in whole blood for up to 120 h at room temperature and 4°C. Whole blood was spiked with K and NK (1000 ng/mL each). Blood samples were aliquoted at different time points (0–120 h), extracted and analyzed using a validated high‐performance liquid chromatography tandem mass spectrometry assay. The study demonstrated the stability of both K and NK in whole blood up to 120 h. These in vitro studies suggest that the concentrations of K and NK measured in the PK samples are reliable. The established stability results were successfully employed to investigate K and NK pharmacology studies in critically ill adults.
A Fusion of Biomimetic Fuel and Solar Cells Based on Hydrogenase, Photosystem II, and Cytochrome c Oxidase
Authors: Kikkawa Mitsuhiro , Yatabe Takeshi , Matsumoto Takahiro , Yoon Ki‐Seok , Suzuki Kazuharu , Enomoto Takao , Kaneko Kenji , Ogo Seiji 
Published: October 2017

AbstractWe report an Ir complex as an anode catalyst capable of switching between a hydrogenase‐type fuel‐cell mode and a photosystem II‐type solar‐cell mode. This catalyst is connected to carbon‐black‐supported platinum as a cathode catalyst, which reduces dioxygen in a manner analogous to cytochrome c oxidase. Together, they make a system capable of switching between the two modes.
Chemical Absorption of Carbon Dioxide Using Aqueous Piperidine Derivatives
Authors: Park Dong Jun , Choi Jeong Ho , Kim Young Eun , Nam Sung Chan , Lee Ki Bong , Yoon Yeo Il 
Published: October 2017

AbstractThe heat of CO2 absorption is one of the important factors determining the operating cost of the CO2 absorption process when using aqueous amine solutions. Aqueous monoethanolamine (MEA) solution is a commercial absorbent, but has several drawbacks. Although piperidine (PIPD) has a high heat of absorption, it shows good CO2 absorption performance, including a high rate of CO2 absorption and a high CO2 loading capacity in comparison to MEA. PIPD derivatives were selected to identify the effect of functional groups of PIPD on the CO2 loading and heat of absorption. Introduction of a methyl group to the PIPD molecule increased the heat of absorption, whereas a hydroxyl group reduced it. The results indicate that the introduction of functional groups in particular positions could provide advantages in CO2 absorption and stripping performance.
The Intermetalloid Cluster Cation (CuBi8)3+
Authors: Knies Maximilian , Kaiser Martin , Isaeva Anna , Müller Ulrike , Doert Thomas , Ruck Michael 
Published: October 2017

AbstractThe reaction of Bi, BiCl3, and CuCl in the ionic liquid [BMIm]Cl⋅4 AlCl3(BMIm=1‐n‐butyl‐3‐methylimidazolium) at 180 °C yielded air‐sensitive shiny black crystals of (CuBi8)[AlCl4]2[Al2Cl7] and (CuBi8)[AlCl4]3. For both compounds X‐ray diffraction on single crystals revealed monoclinic structures that contain the intermetalloid cluster (CuBi8)3+. It is the first pure bismuth cluster with a 3d metal and the first with a metal that does not form binary intermetallics with bismuth under ambient pressure. The cluster can be interpreted either as a copper(I) cation,η4‐coordinated by a square‐antiprismatic Bi82+polycation (Bi−Cu 267 pm), or as a nine‐atomic intermetalloid nido‐cluster with 22 skeletal electrons and theC4vsymmetry. One of the chloride ions of a tetrahedral [AlCl4]−group coordinates the copper atom (Cu−Cl 228 pm) and thereby completes its 18 electron count. DFT‐based calculations, followed by real‐space bonding analysis, revealed a multicenter bonding situation between copper and bismuth atoms with about seven shared electrons.
Controlled release of an optically active compound by hydrogels of acrylic acid and its online detection
Authors: Aguiar Leandro G. , Iwakura Daniel C. , Semeano Ana T. S. , Li Rosamaria W. C. , Souza Esmar F. , Gruber Jonas , Giudici Reinaldo 
Published: October 2017

AbstractHydrogels of acrylic acid were produced through solution free radical polymerization at 70 °C. The materials obtained were put in contact with D‐fructose solution and the swelling behaviour was registered. The swollen hydrogels were immersed in distilled water and the D‐fructose released was quantified in real time by a low‐cost polarized light optoelectronic detection system. A simplified mathematical model was developed in order to represent the system under study. This model was tested against experimental data, showing good agreement. Additionally, the effect of the model parameters on the prediction profiles was evaluated.
Computational Macrocyclization: From de novo Macrocycle Generation to Binding Affinity Estimation
Authors: Wagner Vincent , Jantz Linda , Briem Hans , Sommer Kai , Rarey Matthias , Christ Clara D. 
Published: October 2017

AbstractMacrocycles play an increasing role in drug discovery, but their synthesis is often demanding. Computational tools that suggest macrocyclization based on a known binding mode and that estimate the binding affinity of these macrocycles could have a substantial impact on the medicinal chemistry design process. For both tasks, we established a workflow with high practical value. For five diverse pharmaceutical targets we show that the effect of macrocyclization on binding can be calculated robustly and accurately. Applying this method to macrocycles designed by LigMac, a search tool for de novo macrocyclization, our results suggest that we have a robust protocol in hand to design macrocycles and prioritize them prior to synthesis.
Structure–Activity Studies of N‐Butyl‐1‐deoxynojirimycin (NB‐DNJ) Analogues: Discovery of Potent and Selective Aminocyclopentitol Inhibitors of GBA1 and GBA2
Authors: Gu Xingxian , Gupta Vijayalaxmi , Yang Yan , Zhu Jin‐Yi , Carlson Erick J. , Kingsley Carolyn , Tash Joseph S. , Schönbrunn Ernst , Hawkinson Jon , Georg Gunda I. 
Published: October 2017

AbstractAnalogues of N‐butyl‐1‐deoxynojirimycin (NB‐DNJ) were prepared and assayed for inhibition of ceramide‐specific glucosyltransferase (CGT), non‐lysosomal β‐glucosidase 2 (GBA2) and the lysosomal β‐glucosidase 1 (GBA1). Compounds 5 a–6 f, which carry sterically demanding nitrogen substituents, and compound 13, devoid of the C3 and C5 hydroxy groups present in DNJ/NB‐DGJ (N‐butyldeoxygalactojirimycin) showed no inhibitory activity for CGT or GBA2. Inversion of stereochemistry at C4 of N‐(n‐butyl)‐ and N‐(n‐nonyl)‐DGJ (compounds 24) also led to a loss of activity in these assays. The aminocyclopentitols N‐(n‐butyl)‐ (35 a), N‐(n‐nonyl)‐4‐amino‐5‐(hydroxymethyl)cyclopentane‐ (35 b), and N‐(1‐(pentyloxy)methyl)adamantan‐1‐yl)‐1,2,3‐triol (35 f), were found to be selective inhibitors of GBA1 and GBA2 that did not inhibit CGT (>1 mm), with the exception of 35 f, which inhibited CGT with an IC50 value of 1 mm. The N‐butyl analogue 35 a was 100‐fold selective for inhibiting GBA1 over GBA2 (Ki values of 32 nm and 3.3 μm for GBA1 and GBA2, respectively). The N‐nonyl analogue 35 b displayed a Ki value of ≪14 nm for GBA1 inhibition and a Ki of 43 nm for GBA2. The N‐(1‐(pentyloxy)methyl)adamantan‐1‐yl) derivative 35 f had Ki values of ≈16 and 14 nm for GBA1 and GBA2, respectively. The related N‐bis‐substituted aminocyclopentitols were found to be significantly less potent inhibitors than their mono‐substituted analogues. The aminocyclopentitol scaffold should hold promise for further inhibitor development.
Improving I/O bandwidth with Cray DVS Client‐side Caching
Authors: Hicks Bryce 
Published: October 2017

SummaryCray's Data Virtualization Service, DVS, is an I/O forwarder providing access to native parallel filesystems and to Cray DataWarp application I/O accelerator at the largest system scales while still maximizing data throughput. This paper introduces DVS Client‐side Caching, a new option for DVS to improve I/O bandwidth, reduce network latency costs, and decrease the load on both DVS servers and backing parallel filesystems. Client‐side caching allows application writes to target local in‐memory cache on compute nodes. This provides low latency and high throughput for write operations. It also allows aggregation of data to be written back to the filesystem so fewer network and parallel filesystem operations are required. Caching also enables applications to reuse data previously read or written without further network overhead. This paper will discuss motivations for this work, detailed design and architecture, acceptable use cases, benchmark testing results, and possibilities for future improvement.
Bivariate flow cytometric analysis and sorting of different types of maize starch grains
Authors: Zhang Xudong , Feng Jiaojiao , Wang Heng , Zhu Jianchu , Zhong Yuyue , Liu Linsan , Xu Shutu , Zhang Renhe , Zhang Xinghua , Xue Jiquan , Guo Dongwei 
Published: October 2017

AbstractParticle‐size distribution, granular structure, and composition significantly affect the physicochemical properties, rheological properties, and nutritional function of starch. Flow cytometry and flow sorting are widely considered convenient and efficient ways of classifying and separating natural biological particles or other substances into subpopulations, respectively, based on the differential response of each component to stimulation by a light beam; the results allow for the correlation analysis of parameters. In this study, different types of starches isolated from waxy maize, sweet maize, high‐amylose maize, pop maize, and normal maize were initially classified into various subgroups by flow cytometer and then collected through flow sorting to observe their morphology and particle‐size distribution. The results showed that a 0.25% Gelzan solution served as an optimal reagent for keeping individual starch particles homogeneously dispersed in suspension for a relatively long time. The bivariate flow cytometric population distributions indicated that the starches of normal maize, sweet maize, and pop maize were divided into two subgroups, whereas high‐amylose maize starch had only one subgroup. Waxy maize starch, conversely, showed three subpopulations. The subgroups sorted by flow cytometer were determined and verified in terms of morphology and granule size by scanning electron microscopy and laser particle distribution analyzer. Results showed that flow cytometry can be regarded as a novel method for classifying and sorting starch granules. © 2017 International Society for Advancement of Cytometry
Gut feelings: Studying enteric nervous system development, function, and disease in the zebrafish model system
Authors: Ganz Julia 
Published: October 2017

AbstractThe enteric nervous system (ENS) is the largest part of the peripheral nervous system and is entirely neural crest–derived. It provides the intrinsic innervation of the gut, controlling different aspects of gut function, such as motility. In this review, we will discuss key points of Zebrafish ENS development, genes, and signaling pathways regulating ENS development, as well as contributions of the Zebrafish model system to better understand ENS disorders. During their migration, enteric progenitor cells (EPCs) display a gradient of developmental states based on their proliferative and migratory characteristics, and show spatiotemporal heterogeneity based on gene expression patterns. Many genes and signaling pathways that regulate the migration and proliferation of EPCs have been identified, but later stages of ENS development, especially steps of neuronal and glial differentiation, remain poorly understood. In recent years, Zebrafish have become increasingly important to test candidate genes for ENS disorders (e.g., from genome‐wide association studies), to identify environmental influences on ENS development (e.g., through large‐scale drug screens), and to investigate the role the gut microbiota play in ENS development and disease. With its unique advantages as a model organism, Zebrafish will continue to contribute to a better understanding of ENS development, function, and disease. Developmental Dynamics 247:268–278, 2018. © 2017 Wiley Periodicals, Inc.
Why are nitrogen‐fixing trees rare at higher compared to lower latitudes?
Authors: Menge Duncan N. L. , Batterman Sarah A. , Hedin Lars O. , Liao Wenying , Pacala Stephen W. , Taylor Benton N. 
Published: October 2017

AbstractSymbiotic nitrogen (N) fixation provides a dominant source of new N to the terrestrial biosphere, yet in many cases the abundance of N‐fixing trees appears paradoxical. N‐fixing trees, which should be favored when N is limiting, are rare in higher latitude forests where N limitation is common, but are abundant in many lower latitude forests where N limitation is rare. Here, we develop a graphical and mathematical model to resolve the paradox. We use the model to demonstrate that N fixation is not necessarily cost effective under all degrees of N limitation, as intuition suggests. Rather, N fixation is only cost effective when N limitation is sufficiently severe. This general finding, specific versions of which have also emerged from other models, would explain sustained moderate N limitation because N‐fixing trees would either turn N fixation off or be outcompeted under moderate N limitation. From this finding, four general hypothesis classes emerge to resolve the apparent paradox of N limitation and N‐fixing tree abundance across latitude. The first hypothesis is that N limitation is less common at higher latitudes. This hypothesis contradicts prevailing evidence, so is unlikely, but the following three hypotheses all seem likely. The second hypothesis, which is new, is that even if N limitation is more common at higher latitudes, more severe N limitation might be more common at lower latitudes because of the capacity for higher N demand. Third, N fixation might be cost effective under milder N limitation at lower latitudes but only under more severe N limitation at higher latitudes. This third hypothesis class generalizes previous hypotheses and suggests new specific hypotheses. For example, greater trade‐offs between N fixation and N use efficiency, soil N uptake, or plant turnover at higher compared to lower latitudes would make N fixation cost effective only under more severe N limitation at higher latitudes. Fourth, N‐fixing trees might adjust N fixation more at lower than at higher latitudes. This framework provides new hypotheses to explain the latitudinal abundance distribution of N‐fixing trees, and also provides a new way to visualize them. Therefore, it can help explain the seemingly paradoxical persistence of N limitation in many higher latitude forests.
GC‐MS Characterization of Hydroxy Fatty Acids Generated From Lipid Oxidation in Vegetable Oils
Authors: Xia Wei , Budge Suzanne M. 
Published: October 2017

Lipid oxidation has long been described as following a radical chain reaction mechanism, where hydrogen abstraction is considered the preferred pathway. Hydroxy compounds are, in theory, major products formed from hydrogen abstraction but their presence is rarely monitored. In this study, a GC‐MS technique to characterize hydroxy fatty acids (FA) formed during the oxidation of sunflower and canola oils is described. First, hydroxy FA in oxidized oils are methylated and isolated from non‐oxygenated structures using solid phase extraction (SPE). Then they are converted into their trimethylsilyl (TMS) derivatives using a N,O‐bis (trimethylsilyl) trifluoroacetamide (BSTFA)‐pyridine method and identified by their electron ionization (EI) and positive chemical ionization (PCI) spectra. Separation of most isomeric hydroxy FA with very similar structures is accomplished using a DB‐23 capillary column with (50%‐cyanopropyl)‐methylpolysiloxane phase. The fragmentation patterns of the TMS derivatives are discussed in detail and several easily applicable rules for spectral interpretations are presented. The major hydroxy FA arising from oxidation of sunflower and canola oils are allylic and conjugated structures, specifically 8‐, 9‐, 10‐, and 11‐hydroxyoctadecenoic acid (OH‐C18:1) and 9‐ and 13‐hydroxyoctadecadienoic acid (OH‐C18:2).Practical Applications: Unsaturated hydroxy FA are potential indicators of hydrogen abstraction reactions by FA alkoxyl radicals during lipid oxidation. A prerequisite for the quantification of these hydroxy FA is knowledge of their structures. In this work a GC‐MS method, coupled with SPE and TMS derivatization, to characterize the hydroxy FA derived from oxidation of vegetable oils, which will enable future quantifications of these compounds is employed. In addition, the use of EI and PCI spectra provided clear strategies to interpret mass spectra for both saturated and unsaturated hydroxy FA. The fragmentation patterns in EI and PCI presented in this paper will benefit future studies on identification or quantification of both saturated and unsaturated hydroxy FA in other lipid samples.Hydroxy fatty acids in oils are methylated and isolated using solid phase extraction. They are converted into their trimethylsilyl (TMS) derivatives, which enabled identification by the electron ionization and positive chemical ionization spectra. Here, the fragmentation patterns of the TMS derivatives are discussed in detail and several easily applicable rules for spectral interpretations are presented.
Effects of electrothermal vortices on insulator‐based dielectrophoresis for circulating tumor cell separation
Authors: Aghilinejad Arian , Aghaamoo Mohammad , Chen Xiaolin , Xu Jie 
Published: October 2017

AbstractInsulator‐based dielectrophoresis (iDEP) is a powerful technique for separation and manipulation of bioparticles. In recent years, iDEP designs using arrays of insulating posts have shown promising results toward reaching high‐efficiency bioparticle manipulation. Joule heating (JH) and electrothermal (ET) flows have been observed in iDEP microdevices and significantly affecting their performances. In this research, we utilize mathematical modeling to study, iDEP technique and the effects of JH and ET flow on device performance and propose a separation scenario for selective trapping of circulating tumor cells (CTCs). A robust numerical model is developed to calculate the distribution of electric and fluid flow fields in the presence of JH and ET flow, and predict the cells’ trajectory inside the system. Our results indicate that JH not only induces temperature rise in the system, but also may alter the design iDEP separation scenario by inducing ET vortices that affect the cell's trajectory. To investigate the impact of JH‐induced ET flow characteristics and vortex generation on separation efficiency, we introduce a dimensionless force ratio encompassing the effects of electrical field, drag forces, JH, and ET flow. Interestingly, it was found that ET flows can be used to significantly enhance the separation efficiency, even in higher inlet flow rates. Lastly, the effect of post geometry has been discussed.