bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats
Authors: TerAvest Michaela A. , He Zhen , Rosenbaum Miriam A. , Martens Eric C. , Cotta Michael A. , Gordon Jeffrey I. , Angenent Largus T. 
Published: July 2013

ABSTRACTBacteroides thetaiotaomicron is a prominent member of the human distal gut microbiota that specializes in breaking down diet and host‐derived polysaccharides. While polysaccharide utilization has been well studied in B. thetaiotaomicron, other aspects of its behavior are less well characterized, including the factors that allow it to maintain itself in the gut. Biofilm formation may be a mechanism for bacterial retention in the gut. Therefore, we used custom GeneChips to compare the transcriptomes of biofilm and planktonic B. thetaiotaomicron during growth in mono‐colonized chemostats. We identified 1,154 genes with a fold‐change greater than 2, with confidence greater than or equal to 95%. Among the prominent changes observed in biofilm populations were: (i) greater expression of genes in polysaccharide utilization loci that are involved in foraging of O‐glycans normally found in the gut mucosa; and (ii) regulated expression of capsular polysaccharide biosynthesis loci. Hierarchical clustering of the data with different datasets, which were obtained during growth under a range of conditions in minimal media and in intestinal tracts of gnotobiotic mice, revealed that within this group of differentially expressed genes, biofilm communities were more similar to the in vivo samples than to planktonic cells and exhibited features of substrate limitation. The current study also validates the use of chemostats as an in vitro “gnotobiotic” model to study gene expression of attached populations of this bacterium. This is important to gut microbiota research, because bacterial attachment and the consequences of disruptions in attachment are difficult to study in vivo. Biotechnol. Bioeng. 2014;111: 165–173. © 2013 Wiley Periodicals, Inc.
Direct resolution and quantitative analysis of flurbiprofen enantiomers using microcrystalline cellulose triacetate plates: applications to the enantiomeric purity control and optical isomer determination in widely consumed drugs
Authors: Del Bubba M. , Checchini L. , Ciofi L. , Furlanetto S. , Lepri L. 
Published: July 2013

ABSTRACTFlurbiprofen enantiomers have very different pharmacological properties, since the (S)‐(+) form has a much higher anti‐inflammatory activity than the (R)‐(−) isomer, the latter being responsible for very undesirable side effects, such as gastrointestinal irritation. Based on the different biological properties of flurbiprofen enantiomers, the development of chiral chromatographic methods for the control of the enantiomeric purity is a very important topic. In this study the separation of flurbiprofen enantiomers was achieved using for the first time noncommercial MCTA layers with polyvinyl alcohol as binder, which gives to these plates a mechanical stability equivalent to that of marketed ones. Baseline resolution (α = 1.31; RS = 2.0) was obtained with ethanol–acetic acid solution (pH 3.0 ± 0.1; 60:40, v/v) as eluent and a migration distance of about 14.5 cm. Under these experimental conditions, the thin‐layer chromatography determination of the enantiomeric purity of the pharmacologically active (S)‐(+)‐flurbiprofen in the presence of 1% of the undesired (R)‐(−) form was demonstrated. Moreover, the quantitative analysis of flurbiprofen enantiomers was achieved, obtaining quantification limits and detection limits of 50 and 25 ng of each enantiomer applied to the plate, respectively. The method was succesfully applied to the enantiomer determination in widely consumed drugs, obtaining results consistent with the flurbiprofen content declared in the drug facts. Copyright © 2013 John Wiley & Sons, Ltd.
Kinetic Study on Polyethylenimine‐Assisted Reactive Crystallization of Monodisperse Strontium Sulfate Microcrystals
Authors: Mikami T. , Hirasawa I. 
Published: July 2013

AbstractDouble‐jet reactive crystallization of SrSO4 was carried out in the presence of polyethylenimine (PEI). A simple kinetic model of primary nucleation as well as crystal growth was investigated under the condition of producing monodisperse microcrystals. Furthermore, surface free energy in the solution of PEI was estimated. PEI addition causes growth inhibition leading to smaller sizes and modifies the Gibbs free energy gap required for occurring nucleation.
A Covalent Reporter of β‐Lactamase Activity for Fluorescent Imaging and Rapid Screening of Antibiotic‐Resistant Bacteria
Authors: Shao Qing , Zheng Yan , Dong Xueming , Tang Kai , Yan Xiaomei , Xing Bengang 
Published: July 2013

AbstractBacterial resistance to antibiotics poses a great clinical challenge in fighting serious infectious diseases due to complicated resistant mechanisms and time‐consuming testing methods. Chemical reaction‐directed covalent labeling of resistance‐associated bacterial proteins in the context of a complicated environment offers great opportunity for the in‐depth understanding of the biological basis conferring drug resistance, and for the development of effective diagnostic approaches. In the present study, three fluorogenic reagents LRBL1–3 for resistant bacteria labeling have been designed and prepared on the basis of fluorescence resonance energy transfer (FRET). The hydrolyzed probes could act as reactive electrophiles to attach the enzyme, β‐lactamase, and thus facilitated the covalent labeling of drug resistant bacterial strains. SDS electrophoresis and MALDI‐TOF mass spectrometry characterization confirmed that these probes were sensitive and specific to β‐lactamase and could therefore serve for covalent and localized fluorescence labeling of the enzyme structure. Moreover, this β‐lactamase‐induced covalent labeling provides quantitative analysis of the resistant bacterial population (down to 5 %) by high resolution flow cytometry, and allows single‐cell detection and direct observation of bacterial enzyme activity in resistant pathogenic species. This approach offers great promise for clinical investigations and microbiological research.
Synthesis, Chiroptical Properties and Density Functional Theory Calculations of 3,3’‐Biphenyl‐2,2’‐BiTropone
Authors: Cavazza Marino , Cifelli Mario , Domenici Valentina , Funaioli Tiziana , Mennucci Benedetta , Alberto Veracini Carlo , Zandomeneghi Maurizio 
Published: July 2013

ABSTRACTThe synthesis of new bitropone derivatives, namely, 3,3'‐biphenyl‐2,2'‐bitropone and 7,7’‐biphenyl‐2,2'‐bitropone, are reported. Isolation of enantiomers arising from restricted rotation around the C‐C bond connecting the tropone moieties was attempted by means of chiral high performance liquid chromatography (HPLC). No separation was obtained for 7,7’‐biphenyl‐2,2'‐bitropone. For 3,3'‐biphenyl‐2,2'‐bitropone, difficulties were encountered because of the low separation factor of the peaks and the presence of a rapid racemization process. However, quantitative chiroptical data on the antipodes were obtained by linking a circular dichroism (CD) spectrometer and a UV–vis spectrophotometric detector in series to the HPLC instrument. The analysis of the CD and UV–vis spectra in terms of absolute conformations was done with the help of theoretical calculations performed at the Density Functional Theory (DFT) level. The most stable conformations of the 3,3'‐biphenyl‐2,2'‐bitropone in its ground state were obtained. Starting from these minimum energy conformations, it was possible to compute theoretical CD and UV absorption spectra that fit well with the experimental ones. From this comparison the absolute configuration to the antipodes was assigned. Finally, the effect of the presence of the two lateral phenyl substituents on the structure of the bitropone and hence on the CD spectrum is discussed. Chirality 25:648–655, 2013. © 2013 Wiley Periodicals, Inc.
Two‐Dimensional Nanostructures by the Assembly of n‐Type Tetraazaanthracene‐Based Conjugated Molecules
Authors: He Chunyang , Wu Dongqing , Zhang Fan , Xue Minzhao , Zhuang Xiaodong , Qiu Feng , Feng Xinliang 
Published: July 2013

AbstractOn the basis of our previous communication concerning a new family of thiophene‐armed tetraazaanthracene molecules, we present a further intensive investigation on this class of compounds substituted with different alkyl chains and their self‐assembled two‐dimensional (2D) nanostructures. These tetraazaanthracene molecules with different alkyl chains were prepared in good yields using the synthetic strategy we developed. In addition to the expected typical n‐type character, one compound exhibited aggregation behavior upon electrochemical reduction. Moreover, all molecules in the neutral state showed a strong tendency to aggregate in a binary solvent, as confirmed by optical spectral measurements. To investigate such self‐assembly behavior, a phase‐transfer method with a dichloromethane/methanol (2:3) binary solvent system was used to prepare the nanostructures. By means of atomic force microscopy, transmission electron microscopy, and X‐ray diffraction, we found that the morphology of assembled 2D sheet‐like structures could be adjusted by varying the alkyl chain. The weak interactions arising from the heteroatoms (N and S) in the conjugated backbones play a key role in the formation and stabilization of layered structures.
Homotropic Allosterism: In‐Depth Structural Analysis of the Gas‐Phase Noncovalent Complexes Associating a Double‐Cavity Cucurbit[n]uril‐Type Host and Size‐Selected Protonated Amino Compounds
Authors: Lemaur Vincent , Carroy Glenn , Poussigue Frédéric , Chirot Fabien , De Winter Julien , Isaacs Lyle , Dugourd Philippe , Cornil Jérôme , Gerbaux Pascal 
Published: July 2013

AbstractNoncovalent interactions between several protonated amines and an original ditopic receptor, nor‐seco‐cucurbit[10]uril, are investigated by combining mass spectrometry‐based methods and computational chemistry. Electrospray ionization is used to transfer the intact supramolecular assemblies from their acidic solution to the gas phase, provided fine‐tuning of the source parameters is achieved. Ternary complexes, associating two guest molecules and one host cavity, are observed systematically in the mass spectrometry analyses and the quasi‐exclusive occurrence of these 2:1 associations reveals the allosteric nature of the complexation reaction. It is demonstrated that the binary 1:1 complex ions that are detected arise from collision‐induced dissociation processes undergone by the ternary complex ions inside the ion source. Based on ion mobility experiments supported by theoretical calculations, the inclusion nature of the gas‐phase ternary complexes is clearly evidenced independent of the size of the probed guest molecule and the charge state of the complex ions. The allosteric nature of the complexation reactions is dictated by size criteria. This is demonstrated on the basis of mass spectrometry experiments by analyzing solutions containing ligands of different sizes in competition for inclusion within the guest cavity. Computational chemistry is also used to characterize the three‐dimensional structures of the complexes.
ZnO Nanorod Arrays and Hollow Spheres through a Facile Room‐Temperature Solution Route and Their Enhanced Ethanol Gas‐Sensing Properties
Authors: Bao Di , Gao Peng , Wang Longqiang , Wang Ying , Chen Yujin , Chen Guorui , Li Guobao , Chang Cheng , Qin Wei 
Published: July 2013

AbstractA new two‐phase solution strategy has been developed for the synthesis of multifarious zinc oxide one‐dimensional (1D) nanostructures, in which nanorod arrays (NAs), nanorod hollow spheres (NHSs), nanoribbons, nanowires, nanotubes, and nanonetworks were easily obtained at room temperature without using any catalysts, templates, or precursors. More importantly, an interesting formation mechanism of the 1D nanostructures in the benzene/water system and its distinctive size‐ and morphology‐controlling ability were also discovered. Through a series of directed comparison experiments, it was found that the zinc source, reactant concentration, substrate, and reaction time played significant roles in this dipolar binary liquid technique. In addition, and considering their importance to semiconductor ZnO gas‐sensing properties, the energy state and surface status of the as‐obtained NA and NHS products were investigated through photoluminescence and surface wetting measurements. It was found that a large concentration of oxygen vacancies and high surface energy were present on the surface of the NAs and NHSs, which resulted in their enhanced ethanol gas‐sensing properties at a relatively low temperature.
Formation, Molecular Structure, and Morphology of Humins in Biomass Conversion: Influence of Feedstock and Processing Conditions
Authors: van Zandvoort Ilona , Wang Yuehu , Rasrendra Carolus B. , van Eck Ernst R. H. , Bruijnincx Pieter C. A. , Heeres Hero J. , Weckhuysen Bert M. 
Published: July 2013

AbstractNeither the routes through which humin byproducts are formed, nor their molecular structure have yet been unequivocally established. A better understanding of the formation and physicochemical properties of humins, however, would aid in making biomass conversion processes more efficient. Here, an extensive multiple‐technique‐based study of the formation, molecular structure, and morphology of humins is presented as a function of sugar feed, the presence of additives (e.g., 1,2,4‐trihydroxybenzene), and the applied processing conditions. Elemental analyses indicate that humins are formed through a dehydration pathway, with humin formation and levulinic acid yields strongly depending on the processing parameters. The addition of implied intermediates to the feedstocks showed that furan and phenol compounds formed during the acid‐catalyzed dehydration of sugars are indeed included in the humin structure. IR spectra, sheared sum projections of solid‐state 2DPASS 13C NMR spectra, and pyrolysis GC–MS data indicate that humins consist of a furan‐rich polymer network containing different oxygen functional groups. The structure is furthermore found to strongly depend on the type of feedstock. A model for the molecular structure of humins is proposed based on the data presented.
Small‐block interleaving for low‐delay cross‐packet forward error correction over burst‐loss channels
Authors: Shih Chi‐Huang , Kuo Chun‐I , Shieh Ce‐Kuen , Chou Yeh‐Kai 
Published: July 2013

SUMMARYBy adding the redundant packets into source packet block, cross‐packet forward error correction (FEC) scheme performs error correction across packets and can recover both congestion packet loss and wireless bit errors accordingly. Because cross‐packet FEC typically trades the additional latency to combat burst losses in the wireless channel, this paper presents a FEC enhancement scheme using the small‐block interleaving technique to enhance cross‐packet FEC with the decreased delay and improved good‐put. Specifically, adopting short block size is effective in reducing FEC processing delay, whereas the corresponding effect of lower burst‐error correction capacity can be compensated by deliberately controlling the interleaving degree. The main features include (i) the proposed scheme that operates in the post‐processing manner to be compatible with the existing FEC control schemes and (ii) to maximize the data good‐put in lossy networks; an analytical FEC model is built on the interleaved Gilbert‐Elliott channel to determine the optimal FEC parameters. The simulation results show that the small‐block interleaved FEC scheme significantly improves the video streaming quality in lossy channels for delay‐sensitive video. Copyright © 2013 John Wiley & Sons, Ltd.
Direct Synthesis of 2,5‐Bis(dodecanoxy)phenyleneethynylene‐Butadiynes by Sonogashira Coupling Reaction
Authors: Arias Eduardo , Moggio Ivana , Torres Román , Ziolo Ronald F. , Maldonado José‐Luis , Green Kirk , Cooper Thomas M. , Wicks Geoffrey , Rebane Aleksander , Drobizhev Mikhail , Makarov Nikolay S. , Ottonelli Massimo , Dellepiane Giovanna 
Published: July 2013

AbstractThe synthesis of a 2,5‐bis(dodecanoxy)phenyleneethynylene‐butadiyne series with 2, 4, 6 and 8 phenyl rings is reported. Sonogashira coupling reaction, rather than the Glaser/Eglinton/Hay reactions classically used for butadiyne formation was applied. The molecular structures of all compounds were confirmed by 1H, DEPT‐135, APT 13C, MALDI‐TOF, FTIR and FT‐Raman analyses. The linear and nonlinear optical properties were studied in solution by UV/Vis, static and time‐resolved fluorescence, and by two‐photon absorption (2PA) spectroscopy. With the exception of the dimer, for which intersystem crossing is very favoured due to the low energy gap between the singlet and triplet states as theoretically predicted, the other oligomers present high fluorescence quantum yields (0.77–0.82) and large cross‐sections (up to 5000 GM for the octamer) that could be applied in multiphoton microscopy or nonlinear optics.
The Impact of Changing the Compression Ratio on the Performance of an Engine fueled by Biodiesel Blends
Authors: Ibrahim Amr , El‐Adawy M. , El‐Kassaby M. M. 
Published: July 2013

AbstractUsing waste‐cooking‐oil biodiesel as a renewable fuel for diesel engines can have several environmental benefits. However, the engine design parameters such as the compression ratio need to be optimized to achieve the best engine performance. The aim of this paper was to experimentally study the effect of changing the compression ratio on the engine performance and combustion characteristics of a compression–ignition engine fueled by different biodiesel/diesel fuel blends. It was found that the engine performance deteriorated when a high percentage of biodiesel was used in the fuel blend. However, the engine performance was significantly improved when the engine compression ratio was increased. The engine torque increased by 11.1 % when the engine was fueled by a biodiesel blend of 50 % at a compression ratio of 18 in comparison to the torque produced when the engine was fueled by the diesel fuel at a compression ratio of 14. Also, the engine brake thermal efficiency increased by 6 %. Both the ignition delay period and combustion duration decreased with the increase of engine compression ratio.
TerEx Toolbox for semi‐automated selection of fluvial terrace and floodplain features from lidar
Authors: Stout Justin C. , Belmont Patrick 
Published: July 2013

ABSTRACTTerraces and floodplains are important indicators of near‐channel sediment dynamics, serving as potential sediment sources and sinks. Increasing availability of high resolution topography data over large areas calls for development of semi‐automated techniques for identification and measurement of these features. In this study we introduce a novel tool that accommodates user‐defined parameters including, a local‐relief threshold selected by a variable‐size moving window, minimum area threshold, and maximum distance from the channel to identify and map discrete terrace and floodplain surfaces. Each of the parameters can easily be calibrated for a given watershed or reach. Subsequently, the tool automatically measures planform area, absolute elevation, and height relative to the local river channel for each terrace polygon. We validate the tool in two locations where terrace maps were previously developed via manual digitization from lidar and extensive field mapping campaigns. The tool is also tested on six different types of rivers to provide examples of starting selection parameters, and to test effectiveness of the tool across a wide range of landscapes. Generally, the tool provides a high quality draft map of terrace and floodplain surfaces across the wide range of environmental conditions for which it has been tested. We find that the tool functions best in catchments where the terraces are spatially extensive, with distinct differences between the terrace and floodplain. The most challenging environments for semi‐automated terrace and floodplain mapping include steep catchments with dense riparian vegetation, and very small terraces (~10 m2 in areal extent). We then apply the tool to map terraces and floodplains in the Root River watershed, southeastern Minnesota and generate exceedance plots for terrace heights. These plots provide a first pass analysis to indicate the tributaries and reaches of the river where terraces constitute a significant source of sediment. Copyright © 2013 John Wiley & Sons, Ltd.
Morphological records of storm floods exemplified by the impact of the 1872 Baltic storm on a sandy spit system in south‐eastern Denmark
Authors: Clemmensen Lars B. , Bendixen Mette , Hede Mikkel U. , Kroon Aart , Nielsen Lars , Murray Andrew S. 
Published: July 2013

ABSTRACTBeach‐ridge systems are important geo‐archives providing evidence for past wave climate including catastrophic storm flood events. This study investigates the morphological impacts of the 1872 Baltic storm flood on a beach‐ridge system (sandy spit) in south‐eastern Denmark and evaluates the frequency of extreme storm flood events in the area over a longer time perspective. This paper combines field studies of morphology and sedimentary deposits, studies of historical maps, digital terrain model, ground‐penetrating radar profiles, and luminescence dating. Sea water reached 2.8 m above mean sea level (amsl) during peak inundation and, based on studies of the morphological impacts of the 1872 storm flood, the event can be divided into four phases. Phase 1: increasing mean water levels and wave activity at the beach brought sediments from the beach (intertidal bars and normal berm) higher up in the profile and led to the formation of a storm‐berm. Phase 2: water levels further increased and sediment in the upper part of the profile continued to build up the storm‐berm. Phase 3: water levels now reached the top of the dune ridge and were well above the storm‐berm level. Sea water was breaching the dune ridge at several sites and wash‐over fans were generated until a level where the mean water level had dropped too much. Phase 4: the non‐vegetated wash‐over fans functioned as pathways for aeolian sand transport and relatively high dunes were formed in particular along the margins of the fan where aeolian sand was trapped by existing vegetation. The studied beach‐ridge system records about 4500 years of accumulation; the storm flood sediments described are unique suggesting that the 1872 Baltic storm flood event was an extreme event. Thus studies of beach‐ridge systems form a new source for understanding storm surge risk. Copyright © 2013 John Wiley & Sons, Ltd.
Optimizing fluorescent protein choice for transgenic embryonic medaka models
Authors: Loire Nicolas , Barbeau Emilie , Lemkine Gregory F. , Léonard Marc A. , Tindall Andrew J. 
Published: July 2013

Abstract

Early-life-stage transgenic medaka are recognized as a pertinent model by the Organisation for Economic Co-operation and Development and are noncompliant with the European definition of a laboratory animal. However, autofluorescence confounds readout of fluorescent biomarkers. The authors determined the fluorescence emission spectrum of different embryonic stages of medaka submitted to a range of excitation wavelengths. This allows selection of high signal-to-noise ratio fluorescent proteins and combining multiple biomarkers within a single embryo. Environ Toxicol Chem 2013;32:2396–2401. © 2013 SETAC