bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding the Acid–Base Properties of Adenosine: The Intrinsic Basicities of N1, N3 and N7
Authors: Kapinos Larisa E. , Operschall Bert P. , Larsen Erik , Sigel Helmut
Published: May 2011

Adenosine (Ado) can accept three protons, at N1, N3, and N7, to give H3(Ado)3+, and thus has three macro acidity constants. Unfortunately, these constants do not reflect the real basicity of the N sites due to internal repulsions, for example, between (N1)H+ and (N7)H+. However, these macroconstants are still needed for the evaluations and the first two are taken from our own earlier work, that is, ${{\rm{p}}K_{{\rm{H}}_{\rm{3}} {\rm{(Ado)}}}^{\rm{H}} }$=−4.02 and ${{\rm{p}}K_{{\rm{H}}_{\rm{2}} {\rm{(Ado)}}}^{\rm{H}} }$=−1.53; the third one was re‐measured as ${{\rm{p}}K_{{\rm{H(Ado)}}}^{\rm{H}} }$=3.64±0.02 (25 °C; I=0.5 M, NaNO3), because it is the main basis for evaluating the intrinsic basicities of N7 and N3. Previously, contradicting results had been published for the micro acidity constant of the (N7)H+ site; this constant has now been determined in an unequivocal manner, and that of the (N3)H+ site was obtained for the first time. The micro acidity constants, which describe the release of a proton from an (N)H+ site under conditions for which the other nitrogen atoms are free and do not carry a proton, decrease in the order ${{\rm{p}}k_{{\rm{N7(Ado)N1}} \cdot {\rm{H}}}^{{\rm{N7}} - {\rm{N1}}} }$=3.63±0.02 > ${{\rm{p}}k_{{\rm{H}} \cdot {\rm{N7(Ado)N1}}}^{{\rm{N7}} - {\rm{N1}}} }$=2.15±0.15 > ${{\rm{p}}k_{{\rm{H}} \cdot {\rm{N3(Ado)N1}}{\rm{,N7}}}^{{\rm{N3}} - {\rm{N1}}{\rm{,N7}}} }$=1.5±0.3, reflecting the decreasing basicity of the various nitrogen atoms, that is, N1>N7>N3. Application of the above‐mentioned microconstants allows one to calculate the percentages (formation degrees) of the tautomers formed for monoprotonated adenosine, H(Ado)+, in aqueous solution; the results are 96.1, 3.2, and 0.7 % for N7(Ado)N1⋅H+, +H⋅N7(Ado)N1, and +H⋅N3(Ado)N1,N7, respectively. These results are in excellent agreement with theoretical DFT calculations. Evidently, H(Ado)+ exists to the largest part as N7(Ado)N1⋅H+ having the proton located at N1; the two other tautomers are minority species, but they still form. These results are not only meaningful for adenosine itself, but are also of relevance for nucleic acids and adenine nucleotides, as they help to understand their metal ion‐binding properties; these aspects are briefly discussed.
Unidirectional Redox‐Stimulated Movement around a CC Single Bond
Authors: Tepper Christina , Haberhauer Gebhard
Published: May 2011

A remarkable challenge for the design of molecular machines is the realization of a synchronized and unidirectional movement caused by an external stimulus. Such a movement can be achieved by a unidirectionally controlled change of the conformation or the configuration. Biphenol derivatives are one possibility to realize a redox‐driven unidirectional molecular switch. For this reason, a 4,4′‐biphenol derivative was fixed to a chiral cyclopeptidic scaffold and stimulated by chemical oxidants and reduction agents. The conformation of the switch was determined by DFT calculations by using B3LYP and the 6‐31G* basis set. The switching process was observed by UV and circular dichroism (CD) spectroscopic measurements. Several oxidation agents and various conditions were tested, among which (diacetoxy)iodobenzene (DAIB) in methanol proved to be the best. In this way it was possible to synthesize a redox‐stimulated molecular switch with a movement that is part of a rotation around a biaryl binding axis.
Investigation of Aromaticity and Photophysical Properties in [18]/[20]π Porphycene Derivatives
Authors: Kim Kil Suk , Sung Young Mo , Matsuo Takashi , Hayashi Takashi , Kim Dongho
Published: May 2011

In this study, we have investigated the relationship between aromaticity and photophysical properties of trifluoromethyl‐substituted [18]/[20]π porphycenes by using theoretical calculations and various spectroscopic methodologies. Interestingly, we have found that the HOMO–LUMO gap of [20]π porphycene is larger than that of [18]π porphycene, which is in a sharp contrast with those of typical [4n]/[4n+2]π porphyrinoids. Based on our observations, we demonstrate that the origin of this contrasting feature of [20]π porphycene arises from the uniquely large energy splitting between LUMO and LUMO+1 of [18]π porphycene compared with other aromatic [4n+2]π porphyrinoids with nearly degenerate LUMO/LUMO+1. Consequently, we can propose that the energy difference between LUMO and LUMO+1 levels of aromatic [4n+2]π porphyrinoids is an important factor in determining the electronic nature of their corresponding antiaromatic [4n]π porphyrinoids. Moreover, to the best of our knowledge, this is the first study to illustrate the photophysical properties of porphycenes with [4n]π electronic circuits.
Chiral Metallo–Supramolecular Complexes Selectively Induce Human Telomeric G‐Quadruplex Formation under Salt‐Deficient Conditions
Authors: Zhao Chuanqi , Geng Jie , Feng Lingyan , Ren Jinsong , Qu Xiaogang
Published: May 2011

Chiral molecular recognition of human telomeric DNA is important for rational drug design and developing structural probes of G‐quadruplexes. Here we report that a chiral supramolecular complex can selectively induce human telomeric G‐quadruplex formation and discriminate different G‐quadruplex sequences under salt‐deficient conditions studied by circular dichroism (CD), UV meltings, stopped‐flow spectroscopy, fluorescence resonance energy transfer, enzyme cleavage, and gel electrophoresis. P‐enantiomer induced G‐quadruplex formation is fast and does not require a large excess of P enantiomer. More importantly, this chiral compound induces loop sequence‐dependent G‐quadruplex formation.
Homogeneous Nucleophilic Radiofluorination and Fluorination with Phosphazene Hydrofluorides
Authors: Mathiessen Bente , Jensen Andreas T. I. , Zhuravlev Fedor
Published: May 2011

A series of phosphazenium hydrofluorides, P1tBu⋅[18/19F]HF, P1tOct⋅[18/19F]HF, P2Et⋅[18/19F]HF, and P4tBu⋅[18/19F]HF, was synthesized. The radioactive phosphazenium [18F]hydrofluorides were obtained by the one‐step formation and trapping of gaseous [18F]HF with the respective phosphazene bases. The [19F] isotopomers were prepared from the corresponding phosphazene bases and Et3N⋅3HF. Under the design of experiment (DoE)‐optimized conditions, P2Et⋅HF and P4tBu⋅HF fluorinated alkyl chlorides, bromides, and pseudohalides in 76–98 % yield, but gave lower yields with iodides and electron‐deficient arenes. DoE models showed that fluorination can be performed in glass vessels, and that the reactivity of P2Et⋅HF and P4tBu⋅HF is dominated by solvent polarity but is insensitive to water to at least 2 equiv. In contrast, P1tBu⋅HF and P1tOct⋅HF were unstable towards autofluorolysis. DFT calculations were performed to rationalize this finding in terms of diminished steric bulk, higher Parr’s electrophilicity, and chemical hardness of P1RH+. The corresponding radiofluorination reaction gave no valid DoE model but displayed similar substrate scope. High specific activity and excellent radiochemical yields with various pseudohalides (81–91 %) suggest that the proposed radiofluorination methodology can complement the current [18F]KF/Kryptofix methods, particularly in the areas for which nonpolar reaction conditions are required.
Controlled Self‐Assembly of Re‐engineered Insulin by FeII
Authors: Munch Henrik K. , Heide Søren Thiis , Christensen Niels Johan , Hoeg‐Jensen Thomas , Thulstrup Peter W. , Jensen Knud J.
Published: May 2011

Self‐assembly of proteins mediated by metal ions is crucial in biological systems and a better understanding and novel strategies for its control are important. An abiotic metal ion ligand in a protein offers the prospect of control of the oligomeric state, if a selectivity over binding to the native side chains can be achieved. Insulin binds ZnII to form a hexamer, which is important for its storage in vivo and in drug formulations. We have re‐engineered an insulin variant to control its self‐assembly by covalent attachment of 2,2′‐bipyridine. The use of FeII provided chemoselective binding over the native site, forming a homotrimer in a reversible manner, which was easily followed by the characteristic color of the FeII complex. This provided the first well‐defined insulin trimer and the first insulin variant for which self‐assembly can be followed visually.
Fast, Ligand‐ and Solvent‐Free Synthesis of 1,4‐Substituted Buta‐1,3‐diynes by Cu‐Catalyzed Homocoupling of Terminal Alkynes in a Ball Mill
Authors: Schmidt Robert , Thorwirth Rico , Szuppa Tony , Stolle Achim , Ondruschka Bernd , Hopf Henning
Published: May 2011

A method for the Glaser coupling reaction of alkynes by using a vibration ball mill has been developed. The procedure avoids the use of ligands and solvents during the reaction. Aryl‐ and alkyl‐substituted terminal alkynes undergo homocoupling if coground with KF–Al2O3 and CuI as a milling auxiliary and catalyst. Furthermore, an alternative protocol has been developed incorporating 1,4‐diazabicyclo[2.2.2]octane (DABCO) as an additional base allowing the use of KF–Al2O3 with a lower KF loading. Besides Cu salts, the homocoupling of phenylacetylene is also catalyzed by Ni or Co salts, as well as by PdCl2. TMS‐protected phenylacetylene could be directly converted into the homocoupling product after in situ deprotection of the alkyne by fluoride‐initiated removal of the trimethylsilyl group.
Four Iodine‐Mediated Electrophilic Cyclizations of Rigid Parallel Triple Bonds Mapped from 1,8‐Dialkynylnaphthalenes
Authors: Chen Xiaopeng , Lu Ping , Wang Yanguang
Published: May 2011

Four different types of fused arenes, including fluoranthene, indeno[2,1‐a]phenalene, (8H)cyclopenta[a]acenaphthylene, and pyridine[a]acenaphthylene, were efficiently constructed through iodine‐mediated electrophilic cyclizations of 1,8‐dialkynyl naphthalenes in a single step. Theoretical calculations supported our hypothesis that these reactions had high regioselectivity. Oxidative coupling of the fluoranthene skeleton, followed by aromatization, effectively synthesized perylene derivative 14, which emitted light at 597 nm in dichloromethane with an emission efficiency of 0.81 referred to 5,6,11,12‐tetraphenylnaphthacene as a standard.
Synthesis of a Large Functional Cage Compound Based on Four GaGa Single Bonds and Its Application as an Oligoacceptor: On the Way to Bio‐Organogallium Hybrid Molecules
Authors: Uhl Werner , Voß Matthias , Müller Jens , Seubert Kristof
Published: May 2011

The digallium compound R2GaGaR2 (1; R=CH(SiMe3)2) reacts with citracinic acid by the release of two equivalents of bis(trimethylsilyl)methane and the formation of a unique oligofunctional cage compound (2). Four GaGa bonds in a tetrahedral arrangement are bridged by four spacer ligands that are located on the faces of the tetrahedron and bridge the gallium atoms of three different GaGa bonds. Four pyridinium groups result from the shift of one of the three acidic protons of four citracinic acid molecules to the nitrogen atoms of the aromatic rings. The NH groups are arranged in pairs and are capable of acting as chelating acceptors for the coordination of THF molecules (2(THF)2) or the nitrogen atoms of 1‐deazapurine (3(OEt2)4). In particular, the last reaction verifies the potential applicability of this relatively water‐ and air‐resistant acceptor compound for the generation of bioorganometallic hybrid molecules.
Investigation of Chemical Compositions of Urban, Industrial, Agricultural, and Rural Top‐soils in Izmir, Turkey
Authors: Yatkin Sinan , Bayram Abdurrahman
Published: May 2011

The top‐soil samples were collected from urban, industrial, agricultural, and rural sites to investigate the modification in the elemental composition due to anthropogenic influence in one of the biggest city of Turkey, namely Izmir. The elemental profiles were dominated by lithophilic elements such as Al, Ca, Fe, Mg, K, and sea salt element, Na, which is typical for Mediterranean region. The trace elemental concentrations showed significant variation with higher concentrations in the industrial sites, particularly in the vicinity of iron‐steel producers from scrap materials (EAF‐Steels). Lead, Zn, and Cd around EAF‐Steels were found to be higher than other sites. Comparison to universal upper crusts and local reference soil has shown that Izmir top‐soils were contaminated in terms of many trace elements, most probably due to anthropogenic activities. Correlation matrix, crustal enrichment factors, and factor analysis were applied to investigate the extent of soil modification and possible sources. The results indicated that the elemental profiles of top‐soils were mainly determined by parent materials; however, anthropogenic activities were found to be factor effective on the profile.
Concurrent FFT computing on multicore processors
Authors: Barhen J. , Humble T. , Mitra P. , Imam N. , Schleck B. , Kotas C. , Traweek M.
Published: May 2011

The emergence of streaming multicore processors with multi‐SIMD (single‐instruction multiple‐data) architectures and ultra‐low power operation combined with real‐time compute and I/O reconfigurability opens unprecedented opportunities for executing sophisticated signal processing algorithms faster and within a much lower energy budget. Here, we present an unconventional Fast Fourier Transform (FFT) implementation scheme for the IBM Cell, named transverse vectorization. It is shown to outperform (both in terms of timing and GFLOP throughput) the fastest FFT results reported to date for the Cell in the open literature. We also provide the first results for multi‐FFT implementation and application on the novel, ultra‐low power Coherent Logix HyperX processor. Copyright © 2011 John Wiley & Sons, Ltd.
Worst‐case execution time analysis‐driven object cache design
Authors: Huber Benedikt , Puffitsch Wolfgang , Schoeberl Martin
Published: May 2011

Hard real‐time systems need a time‐predictable computing platform to enable static worst‐case execution time (WCET) analysis. All performance‐enhancing features need to be WCET analyzable. However, standard data caches containing heap‐allocated data are very hard to analyze statically. In this paper we explore a new object cache design, which is driven by the capabilities of static WCET analysis. Simulations of standard benchmarks estimating the expected average case performance usually drive computer architecture design. The design decisions derived from this methodology do not necessarily result in a WCET analysis‐friendly design. Aiming for a time‐predictable design, we therefore propose to employ WCET analysis techniques for the design space exploration of processor architectures. We evaluated different object cache configurations using static analysis techniques. The number of field accesses that can be statically classified as hits is considerable. The analyzed number of cache miss cycles is 3–46% of the access cycles needed without a cache, which agrees with trends obtained using simulations. Standard data caches perform comparably well in the average case, but accesses to heap data result in overly pessimistic WCET estimations. We therefore believe that an early architecture exploration by means of static timing analysis techniques helps to identify configurations suitable for hard real‐time systems. Copyright © 2011 John Wiley & Sons, Ltd.
Surfactin Self‐Assembles into Direct and Reverse Aggregates in Equilibrium and Performs Selective Metal Cation Extraction
Authors: Déjugnat Christophe , Diat Olivier , Zemb Thomas
Published: May 2011

On tie‐lines between water‐rich and alkane‐rich solutions, it is shown via scattering experiments that natural lipopeptide surfactin self‐assembles into direct and reverse micelles in equilibrium. Elongated direct micelles in the aqueous phase are present together with small reverse globular aggregates in the organic phase. These latter are made from hydrated surfactant without any “water pool” in the organic phase. The resulting biphasic system is used for liquid–liquid extraction of model metal cations. It is efficient with iron but not with copper or neodymium. Competitive extractions show high selectivity towards iron.
Psychodynamic Group Psychotherapy: Impact of Group Length and Therapist Professional Characteristics on Development of Therapeutic Alliance
Authors: Lorentzen Steinar , Bakali Jan Vegard , Hersoug Anne Grete , Hagtvet Knut A. , Ruud Torleif , Høglend Per
Published: May 2011

Objectives

Little research has been done on therapeutic alliance in group psychotherapy, especially the impact of treatment duration and therapist professional characteristics.

Methods

Therapeutic alliance was rated by patients on the Working Alliance Inventory—Short Form at three time points (sessions 3, 10 and 17) in a randomized controlled trial of short‐term and long‐term psychodynamic group psychotherapy. As predictors we selected therapist clinical experience and length of didactic training, which have demonstrated ambiguous results in previous research. Linear latent variable growth curve models (structural equation modeling) were developed for the three Working Alliance Inventory—Short Form subscales bond, task and goal.

Results

We found a significant variance in individual growth curves (intercepts and slopes) but no differential development due to group length. Longer therapist formal training had a negative impact on early values of subscale task in both treatments. There was an interaction between length of the therapists' clinical experience and group length on early bond, task and goal: therapists with longer clinical experience were rated lower on initial bond in the long‐term group but less so in the short‐term group. Longer clinical experience influenced initial task and goal positively in the short‐term group but was unimportant for task or significantly negative for goal in the long‐term group.

Conclusion

There was no mean development of alliance, and group length did not differentially impact the alliance during 6 months. Early ratings of the three Working Alliance Inventory—Short Form subscales partly reflected different preparations of patients in the two group formats, partly therapist characteristics, but more research is needed to see how these aspects impact alliance development and outcome. Therapists should pay attention to all three aspects of the alliance, when they prepare patients for group therapy. Copyright © 2011 John Wiley & Sons, Ltd.

Key Practitioner Message

In psychodynamic groups, length of therapy does not differentiate the overall level or the development of member‐leader alliance.

Within psychodynamic groups, each individual appear to have their unique perception of the member‐leader alliance.

Therapists with longer formal psychotherapy training may be less successful in establishing early agreement with patients on the tasks of psychodynamic group psychotherapy.

Patients perceive a somewhat lower degree of early emotional bonding with the more clinically experienced therapists in long‐term psychodynamics groups.

Therapists with more clinical experience may contribute to a stronger degree of initial agreement with patients on the tasks and goals of short‐term group psychotherapy.
Nucleation and Chemical Transformation of RuO2 Films Grown on (100) Si Substrates by Atomic Layer Deposition
Authors: Salaün Amelie , Newcomb Simon B. , Povey Ian M. , Salaün Mathieu , Keeney Lynette , O'Mahony Aileen , Pemble Martyn E.
Published: May 2011

We describe the formation of RuO2 thin films grown using atomic layer deposition (ALD) on (100) Si substrates from Ru(EtCp)2 and O2, and the subsequent influence of annealing temperature and atmosphere on the surface morphology and structure of the deposited layers. The films are characterized using scanning electron microscopy (SEM), atomic force microscopy (AFM), X‐ray diffraction (XRD), transmission electron microscopy (TEM), and electron diffraction (ED). The as‐deposited films consist of RuO2 islands. No significant changes in composition or morphology are observed following annealing in N2 for 4 h at either 500 or 700°C. Higher temperature annealing in N2 (820°C, 4 h) results in some modifications to the morphology and structure where ED data indicate the formation of some Ru metal. However, complete transformation from as‐deposited RuO2 to Ru metal is, obtained after annealing in forming gas (95% N2/5% H2) at 420°C for 5 min.
Distributed multichannel assignment with congestion control in wireless mesh networks
Authors: Valarmathi K. , Malmurugan N.
Published: May 2011

In Multichannel Wireless Mesh Network architecture, topology discovery, traffic profiling, channel assignment and routing are essential. From the existing work done so far, we can observe that no work has been carried out on the combined solution of multichannel assignment with routing protocol and congestion control. In this paper, we propose to design a Distributed Multichannel Assignment with Congestion control (DMAC) routing protocol. In this protocol, a traffic‐aware metric provides the solution for multichannel assignment and congestion control. Hence, the proposed protocol can improve the throughput and channel utilization to a very high extent. The proposed algorithm avoids self‐interference by not assigning a channel to any link whose incident links have already been assigned channels. By our simulation results, we show that our proposed protocol attains high throughput and delivery ratio along with reduced delay. Copyright © 2011 John Wiley & Sons, Ltd.
In‐line coupling SPE and CE for DNA preconcentration and separation
Authors: Feng Airong , Tran Nguyet Thuy , Chen Chen , Hu Jiming , Taverna Myriam , Zhou Ping
Published: May 2011

An in‐line SPE method coupled to CE was developed for the analysis of DNA. The amino silica monolith was prepared in situ by polymerization of tetraethoxysilane and N‐(β‐aminoethyl)‐γ‐aminopropyltriethoxysilane in ethanol aqueous solution at the inlet end of a 100 μm id fused‐silica capillary, and the remaining part of the capillary was used as separation channel. The procedure for this in‐line SPE‐CE method was constructed on the basis of investigation on operational conditions such as the introduction mode of sieving matrix, the composition of elution solvent and the elution time. Twenty millimolar ammonium hydroxide was demonstrated to be effective for DNA desorption from the monolith, and linear poly(N‐isopropylacrylamide) was used as the separation matrix. The proposed method could achieve limits of detection of 0.065–0.123 ng/mL for six DNA fragments ranging 100–2000 bp. Compared with conventional CE, preconcentration factors of over 100 times were obtained. The applicability of the in‐line SPE‐CE method was further demonstrated by analyzing plasmid DNA from Escherichia coli crude lysate.
Micropreparative isoelectric focusing protein separation in a suspended drop
Authors: Egatz‐Gomez Ana , Thormann Wolfgang
Published: May 2011

IEF protein binary separations were performed in a 12‐μL drop suspended between two palladium electrodes, using pH gradients created by electrolysis of simple buffers at low voltages (1.5–5 V). The dynamics of pH gradient formation and protein separation were investigated by computer simulation and experimentally via digital video microscope imaging in the presence and absence of pH indicator solution. Albumin, ferritin, myoglobin, and cytochrome c were used as model proteins. A drop containing 2.4 μg of each protein was applied, electrophoresed, and allowed to evaporate until it splits to produce two fractions that were recovered by rinsing the electrodes with a few microliters of buffer. Analysis by gel electrophoresis revealed that anode and cathode fractions were depleted from high pI and low pI proteins, respectively, whereas proteins with intermediate pI values were recovered in both fractions. Comparable data were obtained with diluted bovine serum that was fortified with myoglobin and cytochrome c.
Is metabolomics reachable? Different purification strategies of human colon cancer cells provide different CE‐MS metabolite profiles
Authors: Simó Carolina , Ibáñez Clara , Gómez‐Martínez Ángeles , Ferragut José A. , Cifuentes Alejandro
Published: May 2011

In this work, four different metabolite purification approaches are investigated prior to metabolomics of human HT29 colon cancer cells. Namely, methanol deproteinization, ultrafiltration and two SPE methods using C18 and polymer‐based cartridges were studied. The extracts were characterized via a metabolomic approach based on the application of CE TOF MS (CE‐MS). CE‐MS analysis time was less than 20 min per sample and allowed the simultaneous and reproducible analysis of more than 80 metabolites in a single run with a minimum consumption of sample and reagents. Metabolome analysis revealed in some cases important differences among the studied metabolite purification procedures. No significant differences were observed in the metabolite profile using C18 and polymer‐based cartridges, or between ultrafiltration and methanol deproteinization. However, important differences were observed in the metabolomic profiles obtained from SPE and methanol deproteinization samples. These results demonstrate the crucial role of the metabolite purification strategy in metabolomics since it can bias (and in some cases mislead) the conclusions achieved by the metabolomic study.
2‐DE and MALDI‐TOF‐MS analysis of therapeutic fusion protein abatacept
Authors: Nebija Dashnor , Urban Ernst , Stessl Martina , Noe Christian R. , Lachmann Bodo
Published: May 2011

2‐DE and MALDI‐TOF MS are useful techniques for the quality evaluation of medicinal products derived from recombinant DNA technology. The principal objective of this study has been to evaluate the suitability of 2‐DE in combination with MALDI‐TOF MS for the quality study of the therapeutic recombinant protein, abatacept. 1‐DE SDS‐PAGE, under reducing and nonreducing conditions, and 2‐DE analysis were used for the assessment of Mr, pI, and enzymatic deglycosylation efficiency of abatacept. 2‐DE allowed the assessment of product identity, purity, charge heterogeneity, isoform pattern, and post‐translational modifications. Furthermore, optimization of the deglycosylation procedure, charge heterogeneity, and sample preparation for the subsequent MALDI‐TOF MS analysis has been addressed. PMF analysis allowed rapid identity confirmation of abatacept.
IRAP: An efficient retrotransposon‐based electrophoretic technique for studying genetic variability among geographical isolates of Schistosoma japonicum
Authors: Li Juan , Zhao Guang‐Hui , Li Xiao‐Yan , Chen Fen , Chen Jing‐Bin , Zou Feng‐Cai , Yang Jian‐Fa , Lin Rui‐Qing , Weng Ya‐Biao , Zhu Xing‐Quan
Published: May 2011

In the present study, a inter‐retrotransposon‐amplified polymorphism (IRAP) technique, based on retrotransposons, was used to examine genetic variability among Schistosoma japonicum isolates from different provinces in mainland China. Of the 15 primers screened, 5 produced highly reproducible IRAP patterns. Using these primers, 54 discernible DNA fragments were generated with 40 (74.07%) being polymorphic, indicating considerable genetic variation among the examined S. japonicum isolates. The primer LTR‐11 was found to be able to differentiate male and female parasites, producing one constant specific band for female S. japonicum isolates. The percentages of polymorphic bands (PPB) among all parasites, among isolates from mountainous provinces and among those from the lake/marshland areas were 74.07, 48.15, and 66.67%, respectively. UPGMA analysis revealed that the IRAP profiles could group S. japonicum isolates in mainland China into two clades (mountainous and lake/marshland types), and samples from the same geographical origins clustered together. These results demonstrated that the IRAP technique is suitable for studying genetic diversity and population structures, and also provides an effective technique for studying sex differentiation of S. japonicum.
PCR‐free digital minisatellite tandem repeat genotyping
Authors: Chen Yuchao , Seo Tae Seok
Published: May 2011

We demonstrated a proof‐of‐concept for novel minisatellite tandem repeat typing, called PCR‐free digital VNTR (variable number tandem repeat) typing, which is composed of three steps: a ligation reaction instead of PCR thermal cycling, magnetic bead‐based solid‐phase capture for purification, and an elongated sample stacking microcapillary electrophoresis (μCE) for sensitive digital coding of repeat number. We designed a 16‐bp fluorescently labeled ligation probe which is complementary to a repeat unit of a biotinylated synthetic template mimicking the human D1S80 VNTR locus and is randomly hybridized with the minisatellite tandem repeats. A quick isothermal ligation reaction was followed to link the adjacent ligation probes on the DNA templates, and then the ligated products were purified by streptavidin‐coated magnetic beads. After a denaturing step, a large amount of ligated products whose size difference was equivalent to the repeat unit were released and recovered. Through the elongated sample stacking μCE separation on a microdevice, the fluorescence signal of the ligated products was generated in the electropherogram and the peak number was directly counted which was exactly matched with the repeat number of VNTR locus. We could successfully identify the minisatellite tandem repeat number with only 5 fmol of DNA template in 30 min.
Cultivation of Chlorella vulgaris in microfluid segments and microtoxicological determination of their sensitivity against CuCl2 in the nanoliter range
Authors: Kürsten Dana , Cao Jialan , Funfak Anette , Müller Philipp , Köhler J. Michael
Published: May 2011

The cultivation of the monocellular green alga Chlorella vulgaris was implemented into microfluid segments to demonstrate the possibility of an automated screening of toxic effects of the common algaecide CuCl2. Therefore, the nutritional as well as light and carbon dioxide requirements of the algae had to be adapted to the microfluidic device. Generally, sequences of about 350 fluid segments with single volumes of about 500 nL were applied for the dose–response experiments. The growth of algae cultures inside microfluidic segments was non‐invasively measured by microflow through techniques using two different optical channels. A multi‐endpoint detection was realized by the photometric characterization of cell density by transmission measurements and the measurement of density of autofluorescent cells. The different methods revealed comparable half maximal effective concentrations (EC50) in the range between 34.6 and 39.9 μg/mL for the toxicity of CuCl2 to the green algae C. vulgaris. By reference experiments in microtiter plates lower EC50 were achieved presumably caused by increased alkalinity of the growth medium due to higher photosynthesis. The results show that the microsegmented flow technique is well suited for the automated determination of dose/response functions for microorganisms like C. vulgaris and for the application of multi‐endpoint procedures at the nanoliter scale.
Antibacterial effect of essential oil vapours against different strains of Staphylococcus aureus, including MRSA
Authors: Nedorostova Lenka , Kloucek Pavel , Urbanova Klara , Kokoska Ladislav , Smid Jakub , Urban Jan , Valterova Irena , Stolcova Miluse
Published: May 2011

The aim of this study was to identify antimicrobial properties of selected essential oils in the vapour phase against different strains of Staphylococcus aureus, including MRSA and resistant clinical isolates. The resistance pattern of used S. aureus strains was checked by disc diffusion method against three antibiotics. Essential oils tested were obtained by hydro‐distillation and characterized by GC‐MS and SPME‐GC. Their antimicrobial properties in the vapour phase were determined by the micro‐atmosphere method. Among the essential oils tested, the most active was Armoracia rusticana with MICs ranging from 8.3 to 17 µl/l, followed by Origanum syriacum (8.3–130 µl/l), Allium sativum (8.3–530 µl/l), Satureja hortensis (17–130 µl/l), Satureja montana (33–260 µl/l), Thymus vulgaris (33–260 µl/l), and Thymus serpyllum (33–530 µl/l). To the best of our knowledge, this is the first report of their antimicrobial properties in vapour phase against a collection of strains and clinical isolates of S. aureus, including MRSA. Based on the results, the essential oils tested can be considered as effective anti‐staphylococcal natural products with specific application possibilities due to the activity in the vapour phase. Copyright © 2011 John Wiley & Sons, Ltd.
Flow and heat transfer with prescribed skin friction in a rotating fluid
Authors: Iqbal Z. , Sajid M. , Hayat T. , Obaidat S.
Published: May 2011

This paper investigates the rotating flow and heat transfer of a viscous fluid induced by a stretching surface. The nonlinear problem subject to a given skin friction at the boundary is solved. Analytic solution is obtained using homotopy analysis method. The velocity, temperature, and stretching velocity is calculated for different values of the rotation parameter (λ). The obtained results are compared with the well known results of rotating flow induced by a stretching surface by using four sets of boundary conditions. Copyright © 2011 John Wiley & Sons, Ltd.
Simulation of three‐dimensional flows over moving objects by an improved immersed boundary–lattice Boltzmann method
Authors: Wu J. , Shu C.
Published: May 2011

An improved immersed boundary–lattice Boltzmann method (IB–LBM) developed recently [28] was applied in this work to simulate three‐dimensional (3D) flows over moving objects. By enforcing the non‐slip boundary condition, the method could avoid any flow penetration to the wall. In the developed IB–LBM solver, the flow field is obtained on the non‐uniform mesh by the efficient LBM that is based on the second‐order one‐dimensional interpolation. As a consequence, its coefficients could be computed simply. By simulating flows over a stationary sphere and torus [28] accurately and efficiently, the proposed IB–LBM showed its ability to handle 3D flow problems with curved boundaries. In this paper, we further applied this method to simulate 3D flows around moving boundaries. As a first example, the flow over a rotating sphere was simulated. The obtained results agreed very well with the previous data in the literature. Then, simulation of flow over a rotating torus was conducted. The capability of the improved IB–LBM for solving 3D flows over moving objects with complex geometries was demonstrated via the simulations of fish swimming and dragonfly flight. The numerical results displayed quantitative and qualitative agreement with the date in the literature. Copyright © 2011 John Wiley & Sons, Ltd.
A dissipative particle dynamics study of flow in periodically grooved nanochannels
Authors: Kasiteropoulou D. , Karakasidis T. E. , Liakopoulos A.
Published: May 2011

The effect of periodic rectangular wall roughness on planar nanochannel flow is investigated by dissipative particle dynamics simulation. The wall protrusion length is varied, and its effect on the flow is examined. Analysis of particle trajectories and average residence time reveals temporary trapping of fluid particles inside the rectangular cavities for a considerable amount of time. This trapping affects the density, velocity, pressure, and temperature distribution inside and close to the cavities. Inside the cavities, low‐velocity regions and regions of high density related to high pressure and high temperature are observed. When compared with that of the channel with flat walls case, lower flow velocities, temperatures, and pressures are observed for grooved channels. The reduction of the above quantities is more pronounced as the protrusion length, that is, the roughness characteristic length, decreases. Finally, the relation of friction factor, f, with the flow Reynolds number is discussed. The model predicts  = constant in the range . The results of this work are of direct relevance to the design of nanofluidic devices. Copyright © 2011 John Wiley & Sons, Ltd.
The accuracy of family physicians' dementia diagnoses at different stages of dementia: a systematic review
Authors: van den Dungen Pim , van Marwijk Harm W. M. , van der Horst Henriëtte E. , Moll van Charante Eric P. , MacNeil Vroomen Janet , van de Ven Peter M. , van Hout Hein P. J.
Published: May 2011

Objective

Optimising care for dementia patients and their informal carers is imperative in light of the impending dementia epidemic. An important aspect of care is accurate recognition and diagnosis of dementia. The aim of this review was to estimate family physicians' diagnostic accuracy at the different stages of dementia.

Methods

Pubmed, Embase, CINAHL, PsycINFO and the Cochrane Library were searched for articles comparing family physicians' ‘dementia’ and ‘cognitive impairment’ diagnoses in the primary care setting to reference standard dementia diagnoses.

Results

Data from six cross‐sectional studies of moderate to reasonable methodological quality were extracted for the analysis. One study considered the accuracy of family physicians' recollected diagnoses, and three studies focussed on documented diagnoses. In these four studies, the sensitivity of family physicians' combined diagnostic categories of ‘cognitive impairment’ together with ‘dementia’ was 0.48–0.67 for mild dementia and 0.76–0.85 for moderate to severe dementia. The sensitivity of their diagnostic category ‘dementia’ alone was 0.14–0.33 for mild and 0.28–0.61 for moderate to severe dementia. Specificity was excellent for all severity stages in both comparisons.

Three studies examined the accuracy of family physicians' judgement of cognition during consultation. Compared with the studies on recollection and documentation, these studies reported higher sensitivity and lower specificity.

Conclusion

Many individuals with dementia are not recognised or not diagnosed as such; particularly mild dementia is under‐diagnosed. Collaboration within primary care and education focussing both on knowledge and attitude are recommended to improve the accuracy of family physicians' dementia diagnosis. Copyright © 2011 John Wiley & Sons, Ltd.
CXC chemokine signaling in the liver: Impact on repair and regeneration
Authors: Van Sweringen Heather L. , Sakai Nozomu , Tevar Amit D. , Burns Justin M. , Edwards Michael J. , Lentsch Alex B.
Published: May 2011

The process of liver repair and regeneration following hepatic injury is complex and relies on a temporally coordinated integration of several key signaling pathways. Pathways activated by members of the CXC family of chemokines play important roles in the mechanisms of liver repair and regeneration through their effects on hepatocytes. However, little is known about the signaling pathways used by CXC chemokine receptors in hepatocytes. Here we review our current understanding of the pathways involved in both CXC chemokine receptor signaling in other cell types, most notably neutrophils, and similar pathways operant during hepatocyte proliferation/liver regeneration to formulate a basis for the function of CXC chemokine receptor signaling in hepatocytes. (Hepatology 2011;)
Limited use of interleukin 28B in the setting of response-guided treatment with detailed on-treatment virological monitoring
Authors: Mangia Alessandra , Thompson Alexander J. , Santoro Rosanna , Piazzolla Valeria , Copetti Massimiliano , Minerva Nicola , Petruzzellis Daniela , Mottola Leonardo , Bacca Donato , McHutchison John G.
Published: May 2011

A single-nucleotide polymorphism upstream of the interleukin-28B

(IL28B)

gene is associated with pegylated interferon-alfa–induced viral clearance in hepatitis C virus (HCV) genotype 1 patients. Using a well-characterized cohort of patients randomized to standard versus response-guided therapy, we studied whether the favorable CC type allows shortening of treatment duration. Association with viral kinetics, sustained viral response (SVR), and predictors of response were also analyzed. In the original study, 696 patients were randomized to either standard or variable therapy of 24, 48, or 72 weeks according to first undetectable HCV RNA. Association between

IL28B

determined by genotyping rs12979860 and end of treatment response and SVR by treatment arm was tested; baseline predictors of response were analyzed using multiple logistic regression. A total of 454 patients were evaluated. The frequency of

IL28B

type was CC = 29%, CT = 53%, TT = 18%. CC type was strongly associated with rapid virological response (RVR) as well as higher rates of week 8 and week 12 response. CC type was associated with SVR in both arms. In patients with RVR, SVR was high and

IL28B

type was not associated with SVR. In RVR patients, there was no significant difference in SVR or relapse rates after 24 or 48 weeks by

IL28B

type. Among non-RVR patients, CC type was associated with SVR at a higher rate than CT/TT, both in standard and variable analysis. However, when week 8 and week 12 responders were considered separately,

IL28B

type was no longer predictive of SVR. Few CC patients remained viremic beyond week 8 to allow the analysis of relationships between

IL28B

type and extended treatment. In HCV-1 patients, the favorable CC type strongly predicted higher rates of on-treatment virological milestones and SVR. However, achievement of on-treatment virological milestones was the critical factor in determining outcome.

IL28B

type appeared to have limited potential for response-guided treatment strategies. (HEPATOLOGY 2011;)
Compromising mitochondrial function with the antiretroviral drug efavirenz induces cell survival-promoting autophagy
Authors: Apostolova Nadezda , Gomez-Sucerquia Leysa J. , Gortat Anna , Blas-Garcia Ana , Esplugues Juan V.
Published: May 2011

Hepatotoxicity is a very common side effect associated with the pharmacological treatment of human immunodeficiency virus (HIV) infection and its pathogenesis is poorly understood. Efavirenz (EFV) is the most widely used nonnucleoside reverse transcriptase inhibitor administered for the control of HIV and some of its toxic effects in hepatic cells have been recently shown to display features of mitochondrial dysfunction. Here we studied the activation of autophagy and, in particular, mitophagy, the main mitochondrial turnover mechanism, in human hepatic cells treated with clinically relevant concentrations of this drug. EFV-treated cells had altered mitochondria, characterized by a relative increase in mitochondrial mass and defective morphology. This was followed by induction of autophagy as shown by the presence of autophagic vacuoles and the presence of the specific autophagic marker proteins microtubule-associated protein 1A/1B light chain 3 and Beclin-1. Importantly, whereas moderate levels of EFV activated autophagy, higher concentrations led to blockage in the autophagic flux, a condition that promotes “autophagic stress” and produces severe cellular damage. Finally, pharmacological inhibition of autophagy exacerbated the deleterious effect of EFV on cell survival/proliferation promoting apoptosis, which suggests that autophagy acts as an adaptive mechanism of cell survival.

Conclusion:

Clinical concentrations of EFV induce autophagy and, in particular, mitophagy in hepatic cells. Activation of this process promotes cell survival, but exceeding a certain threshold of mitochondrial dysfunction is associated with an autophagic overload or stress. This effect could be involved in the EFV-associated hepatotoxicity and may constitute a new mechanism implicated in the genesis of drug-induced liver damage. (HEPATOLOGY 2011;)
Rapid emergence of telaprevir resistant hepatitis C virus strain from wildtype clone in vivo
Authors: Hiraga Nobuhiko , Imamura Michio , Abe Hiromi , Hayes Nelson C. , Kono Tomohiko , Onishi Mayu , Tsuge Masataka , Takahashi Shoichi , Ochi Hidenori , Iwao Eiji , Kamiya Naohiro , Yamada Ichimaro , Tateno Chise , Yoshizato Katsutoshi , Matsui Hirotaka , Kanai Akinori , Inaba Toshiya , Tanaka Shinji , Chayama Kazuaki
Published: May 2011

Telaprevir is a potent inhibitor of hepatitis C virus (HCV) NS3-4A protease. However, the emergence of drug-resistant strains during therapy is a serious problem, and the susceptibility of resistant strains to interferon (IFN), as well as the details of the emergence of mutant strains

in vivo,

is not known. We previously established an infectious model of HCV using human hepatocyte chimeric mice. Using this system we investigated the biological properties and mode of emergence of mutants by ultra-deep sequencing technology. Chimeric mice were injected with serum samples obtained from a patient who had developed viral breakthrough during telaprevir monotherapy with strong selection for resistance mutations (A156F [92.6%]). Mice infected with the resistant strain (A156F [99.9%]) developed only low-level viremia and the virus was successfully eliminated with interferon therapy. As observed in patients, telaprevir monotherapy in viremic mice resulted in breakthrough, with selection for mutations that confer resistance to telaprevir (e.g., a high frequency of V36A [52.2%]). Mice were injected intrahepatically with HCV genotype 1b clone KT-9 with or without an introduced resistance mutation, A156S, in the NS3 region, and treated with telaprevir. Mice infected with the A156S strain developed lower-level viremia compared to the wildtype strain but showed strong resistance to telaprevir treatment. Although mice injected with wildtype HCV showed a rapid decline in viremia at the beginning of therapy, a high frequency (11%) of telaprevir-resistant NS3 V36A variants emerged 2 weeks after the start of treatment.

Conclusion:

Using deep sequencing technology and a genetically engineered HCV infection system, we showed that the rapid emergence of telaprevir-resistant HCV was induced by mutation from the wildtype strain of HCV

in vivo.

(HEPATOLOGY 2011;).
Acetaminophen overdose-induced liver injury in mice is mediated by peroxynitrite independently of the cyclophilin d-regulated permeability transition
Authors: LoGuidice Amanda , Boelsterli Urs A.
Published: May 2011

Acetaminophen (APAP) is safe at therapeutic dosage but can cause severe hepatotoxicity if used at overdose. The mechanisms of injury are not yet fully understood, but previous reports had suggested that the mitochondrial permeability transition (mPT) may be involved in triggering hepatocellular necrosis. We aimed at inhibiting mitochondrial cyclophilin D (CypD), a key regulator of the mPT, as a potential therapeutic target in APAP hepatotoxicity. Wildtype mice treated with a high dose of APAP (600 mg/kg, intraperitoneal) developed typical centrilobular necrosis, which could not, however, be prevented by cotreatment with the selective CypD inhibitor, Debio 025 (alisporivir, DEB025, a nonimmunosuppressive cyclosporin A analog). Similarly, genetic ablation of mitochondrial CypD in

Ppif

-null mice did not afford protection from APAP hepatotoxicity. To determine whether APAP-induced peroxynitrite stress might directly activate mitochondrial permeabilization, independently of the CypD-regulated mPT, we coadministered the peroxynitrite decomposition catalyst Fe-TMPyP (10 mg/kg, intraperitoneal, 90 minutes prior to APAP) to CypD-deficient mice. Liver injury was greatly attenuated by Fe-TMPyP pretreatment, and mitochondrial 3-nitrotyrosine adduct levels (peroxynitrite marker) were decreased. Acetaminophen treatment increased both the cytosolic and mitochondria-associated P-JNK levels, but the c-jun-
N

-terminal kinase (JNK) signaling inhibitor SP600125 was hepatoprotective in wildtype mice only, indicating that the JNK pathway may not be critically involved in the absence of CypD. These data support the concept that an overdose of APAP results in liver injury that is refractory to pharmacological inhibition or genetic depletion of CypD and that peroxynitrite-mediated cell injury predominates in the absence of CypD. (HEPATOLOGY 2011;)