bluuebunny/crossref_metadata_2025 huggingface dataset:
Reality check: A comparison of college students and a community sample of mock jurors in a simulated sexual violent predator civil commitment
Authors: McCabe John G. , Krauss Daniel A. , Lieberman Joel D.
Published: October 2009

Despite concerns about generalizability, past mock trial research has concluded that effects of sample (i.e., students versus representative mock jurors) are negligible. The current study was conducted to explore this conclusion within the conceptual framework of cognitive–experiential self‐theory (CEST). Through a mock civil commitment hearing of a sexually violent predator, responses of student (n = 138) and representative (n = 240) mock jurors were compared. Results revealed several important differences between samples: (a) the student sample scored higher on the rational processing measure (i.e., need for cognition); (b) students' verdicts were also significantly correlated to a measure of their cognitive processing style, an enduring personal characteristic related to the extent to which an individual engages in either effortful/effortless cognition; and (c) the representative sample was more punitive, was more persuaded by clinical expert testimony, and evidenced a greater gender effect in its decisions. Implications for jury decision‐making research are discussed. Copyright © 2009 John Wiley & Sons, Ltd.
Blind decomposition of low‐dimensional multi‐spectral image by sparse component analysis
Authors: Kopriva Ivica , Cichocki Andrzej
Published: October 2009

A multilayer hierarchical alternating least square nonnegative matrix factorization approach has been applied to blind decomposition of low‐dimensional multi‐spectral image. The method performs blind decomposition exploiting spectral diversity and spatial sparsity between materials present in the image and, unlike many blind source separation methods, is invariant with respect to statistical (in)dependence among spatial distributions of the materials. As opposed to many existing blind source separation algorithms, the method is capable of estimating the unknown number of materials present in the image. This number can be less than, equal to, or greater than the number of spectral bands. The method is validated on underdetermined blind source separation problems associated with blind decomposition of experimental red‐green‐blue images composed of four materials. Achieved performance has been superior when compared against methods based on minimization of the ℓ1‐norm: linear programming and interior‐point methods. In addition to tumor demarcation, as demonstrated in the paper, other areas that can also benefit from the proposed method include cell, chemical, and tissue imaging. Copyright © 2009 John Wiley & Sons, Ltd.
Bis(4′‐dibutylaminostyryl)benzene: Spectroscopic Behavior upon Protonation or Methylation
Authors: Zucchero Anthony J. , Tolosa Juan , Tolbert Laren M. , Bunz Uwe H. F.
Published: October 2009

We have investigated the UV/Vis absorption and emission of 1,4‐bis(4′‐dibutylaminostyryl)benzene (1) upon protonation with trifluoroacetic acid in dichloromethane and in acetonitrile. We find that 1 does not display significantly dynamic acidity in the excited state, that is, it is not a photoacid. Three protonation states of 1 were investigated, all of which, neutral, singly protonated, and bis‐protonated, are fluorescent. As an isolable model for the mono‐protonated species, a methylated derivative of 1 was prepared by reaction with methyl triflate. This species displays redshifted emission but similar absorption as the non‐quaternized parent, 1. The strong observed emission of all three protonated states of 1 suggests that the kinetic photoacidity of 1* is low or absent. We assume that the lifetime of the excited state is too short to allow solvent reorganization and therefore we cannot make a statement on the thermodynamic photoacidity of the protonated forms of 1.
Synthesis of Iron Oxide Nanoparticles in Listeria innocua Dps (DNA‐Binding Protein from Starved Cells): A Study with the Wild‐Type Protein and a Catalytic Centre Mutant
Authors: Ceci Pierpaolo , Chiancone Emilia , Kasyutich Oksana , Bellapadrona Giuliano , Castelli Lisa , Fittipaldi Maria , Gatteschi Dante , Innocenti Claudia , Sangregorio Claudio
Published: October 2009

A comparative analysis of the magnetic properties of iron oxide nanoparticles grown in the cavity of the DNA‐binding protein from starved cells of the bacterium Listeria innocua, LiDps, and of its triple‐mutant lacking the catalytic ferroxidase centre, LiDps‐tm, is presented. TEM images and static and dynamic magnetic and electron magnetic resonance (EMR) measurements reveal that, under the applied preparation conditions, namely alkaline pH, high temperature (65 °C), exclusion of oxygen, and the presence of hydrogen peroxide, maghemite and/or magnetite nanoparticles with an average diameter of about 3 nm are mineralised inside the cavities of both LiDps and LiDps‐tm. The magnetic nanoparticles (MNPs) thus formed show similar magnetic properties, with superparamagnetic behaviour above 4.5 K and a large magnetic anisotropy. Interestingly, in the EMR spectra an absorption at half‐field is observed, which can be considered as a manifestation of the quantum behaviour of the MNPs. These results indicate that Dps proteins can be advantageously used for the production of nanomagnets at the interface between molecular clusters and traditional MNPs and that the presence of the ferroxidase centre, though increasing the efficiency of nanoparticle formation, does not affect the nature and fine structure of the MNPs. Importantly, the self‐organisation of MNP‐containing Dps on HRTEM grids suggests that Dps‐enclosed MNPs can be deposited on surfaces in an ordered fashion.
Reactivity and Regioselectivity of Noble Gas Endohedral Fullerenes Ng@C60 and Ng2@C60 (Ng=He–Xe)
Authors: Osuna Sílvia , Swart Marcel , Solà Miquel
Published: October 2009

Recently, it was shown that genuine NgNg chemical bonds are present in the endohedral fullerenes Ng2@C60 in the case of Ng=Xe, while it is more debatable whether a chemical bond exist for Ng=Ar and Kr. The lighter homologues with helium and neon are weakly bonded van der Waals complexes. The presence of a noble gas dimer inside the cage is expected to modify the exohedral reactivity of the C60 cage with respect to that of free C60. To investigate the impact of encapsulated diatomic noble gas molecules on the chemical reactivity of C60, we analyzed the thermodynamics and the kinetics of [4+2] Diels–Alder cycloaddition of 1,3‐cis‐butadiene at all nonequivalent bonds in free C60, Ng@C60, and Ng2@C60 (Ng=He, Ne, Ar, Kr, and Xe). Our BP86/TZP calculations reveal that introduction of single noble gas atoms in Ng@C60 and noble gas dimers He2 and Ne2 in Ng2@C60 has almost no effect on the exohedral reactivity compared to free C60, in agreement with experimental results. In all these cases cycloaddition is clearly favored at the [6,6] bonds in the fullerene cage. For the endohedral compounds He2@C60 and Ne2@C60 a slight preference (by less than 2 kcal mol−1) for bonds closer to the C5 symmetry axis is found. This picture changes dramatically for the endohedral compounds with heavier noble gas dimers. Encapsulation of these noble gas dimers clearly enhances the reaction, both under thermodynamic and kinetic control. Moreover, in the case of Xe2@C60, addition to [6,6] and [5,6] bonds becomes equally viable. These reactivity changes in endohedral fullerenes are attributed to stabilization of the LUMO, increased fullerene strain energy, and greater compression of the encapsulated Ng2 unit along the He to Xe series.
Ubiquitous interactive visualization of large‐scale simulations in geosciences over a Java‐based web‐portal
Authors: McLane Jonathan C. , Czech W.Walter , Yuen David A. , Knox Mike R. , Wang Shuo , Greensky Jim B. S. , Sevre Erik O. D.
Published: October 2009

We have designed a web‐based software system for real‐time interactive visualization of results taken from large‐scale simulations of 3‐D mantle convection and other large‐scale modeling efforts. This approach allows for intense visualization sessions for a couple of hours as opposed to storing massive amounts of data in a storage system. Our data sets consist of 3‐D data with over 10 million unknowns at each time‐step to be used for volume rendering. Large‐scale interactive visualization on a display wall holding 15 million pixels has already been accomplished. With the advent of the age of the mobile web, we have now extended this tactic to hand‐held devices, such as the OQO, Nokia N800, netbooks, iPHONE, and Android OS phones. We are developing web‐based software in Java to extend the ubiquitous use of this system across long distances. The software is aimed at creating an interactive and functional application capable of running on multiple browsers by taking advantage of two AJAX‐enabled web frameworks: Echo2 (http://echo.nextapp.com/site/echo2) and Google Web Toolkit (http://code.google.com/webtoolkit/). Modular building of the system allows for components to be swapped out so that other forms of visualization can be accommodated, such as molecular dynamics in mineral physics or 2‐D data sets from the regional convection models. Copyright © 2009 John Wiley & Sons, Ltd.
Analysis of the Self‐Assembly of 4×4 DNA Tiles by Temperature‐Dependent FRET Spectroscopy
Authors: Saccà Barbara , Meyer Rebecca , Niemeyer Christof M.
Published: October 2009

Correct and efficient self‐assembly of oligonucleotides into highly ordered superstructures essentially depends on the structural integrity and thermal stability of DNA motifs such as junctions or tiles that build up the superstructure. To investigate the assembly/disassembly process of DNA tiles, we recently described a microplate‐based method employing Förster resonance energy transfer (FRET) spectroscopy, which enables the analysis of DNA superstructure formation in real time and with high throughput. This method allows thermodynamic parameters of the self‐assembly process to be extracted, and we here apply it for detailed analysis of the self‐assembly of five different 4×4 DNA tile motifs. To specifically investigate whether the FRET probes tethered to the DNA motifs report local thermodynamic stabilities in the immediate proximity of the chromophores, or whether the global stability of the entire motif is monitored, systematic variations of the labeling position within one tile are carried out. Combined with gel electrophoretic, UV spectroscopic, and microcalorimetric analysis, this study reveals that the FRET method mainly reports the thermodynamics of local microenvironment assembly, rather than that of the entire motif. Nonetheless, the thermodynamic data derived from FRET analysis are also influenced by the structural surroundings of the motif, and thus rapid and detailed analysis and identification of potential “weak points” within a superstructure which influence the structural integrity of a given tile design are enabled. Therefore, the microplate FRET method readily provides insights into the assembly process of complex DNA superstructures to verify and complement theoretical design approaches.
Simultaneous Chlamydia trachomatis and HPV infection in pregnant women
Authors: Pereira Sônia Maria Miranda , Etlinger Daniela , Aguiar Luciana Silva , Peres Stela Verzinhasse , Filho Adhemar Longatto
Published: October 2009

Pregnancy is associated with HPV infection and with Chlamydia trachomatis (CT) infection mostly due to the natural immunosuppression. In addition, pregnancy associated to CT infection can lead to adverse conditions to the woman and fetus, and CT is also believed to be a co‐factor in human immunodeficiency virus infection and HPV‐induced cervical cancer. The aim of this study was to establish the odds ratios (OR) of CT infection in to HPV‐infected pregnant women and vice versa of women stratified by age (<25 years) and marital status. This work is part of a national multicentric transversal study carried out in six Brazilian cities supported by the Ministry of Health of Federal Government of Brazil in 2003. Cervical scrapes of 371 pregnant women were sampled. We performed a hybrid capture‐2 technique to diagnose these samples on HPV and CT infection, and the women responded a questionnaire. Significant association was observed between nonstable marital status and hr‐HPV infection [OR = 2.61 (1.38–4.97) P = 0.003)], and age <25 years old [OR = 2.26 (1.09–4.71) P = 0.029]. Nonstable marital status was also associated with lr‐HPV infection [OR = 2.67 (1.59–4.50) P < 0.001), and age <25 years old [OR = 2.55 (1.51–4.32) P < 0.001). Fifty of the 371 pregnant women were infected with hr‐HPV (13.5%) and 111 (30.0%) were infected with lr‐HPV. The coinfections of HPV and CT were found in 31 women, that is, 8.36% of the pregnant women (P < 0.001). The high rate of simultaneous CT and HPV infection in pregnant women favors the recommendation to screen pregnant women for both CT and HPV. Diagn. Cytopathol. 2010. © 2009 Wiley‐Liss, Inc.
Combination of liquid‐chromatography tandem mass spectrometry in different scan modes with human and chimeric mouse urine for the study of steroid metabolism
Authors: Pozo Oscar J. , Lootens Leen , Van Eenoo Peter , Deventer Koen , Meuleman Philip , Leroux‐Roels Geert , Parr Maria K. , Schänzer Wilhelm , Delbeke Frans T.
Published: October 2009

Anabolic steroids are among the most frequently detected compounds in doping analysis. They are extensively metabolized and therefore an in‐depth knowledge about steroid metabolism is needed. In this study, a liquid chromatography tandem mass spectometry (LC‐MS/MS) method based on a precursor ion scan with a uPA‐SCID mouse with humanized liver (a chimeric mouse) was explored for the detection of steroid metabolism. Methandienone was used as a model compound. The application of the precursor ion scan method in positive human samples and chimeric mice samples after methandienone administration allowed the detection of most steroid metabolites without any structural restriction. Three hitherto unreported metabolites were found using this approach. These metabolites were characterized using LC‐MS/MS and feasible structures were proposed. The structure of one of them, 6‐ene‐epimethandienone, was confirmed by the synthesis of the reference compound. A selected reaction monitoring (SRM) method for the specific detection of all these metabolites has been developed. The application of this method to several human and chimeric mouse samples confirmed that more than 80% of the steroid metabolites were found in both samples. Only metabolites that are poorly detectable by LC‐MS/MS were not detected in some urine samples. The metabolic nature of the unreported metabolites was also confirmed. A global strategy for the detection of steroid metabolites combining both human and chimeric mouse urine is proposed. Copyright © 2009 John Wiley & Sons, Ltd.
Design, Synthesis, and Hybridisation of Water‐Soluble, Peptoid Nucleic Acid Oligomers Tagged with Thymine
Authors: Zarra Rosa , Montesarchio Daniela , Coppola Cinzia , Bifulco Giuseppe , Di Micco Simone , Izzo Irene , De Riccardis Francesco
Published: October 2009

The preparation of a new class of backbone‐modified PNA mimetic incorporating thymine is described. Target dipeptoid monomer 21 was synthesised from an N‐[2‐(thymin‐1‐yl)ethyl]glycinate ester and a properly protected iminodiacetic acid. The distinctive structural motif in the backbone is acarboxy group, inserted to impart water solubility to the oligomer. Two achiral oligopeptoid sequences (8‐mer and 12‐mer), characterised by the shift of the amide carbonyl group away from the nucleobase, were efficiently assembled according to solid‐phase synthesis protocols. Thermal denaturation studies showed that the two homopyrimidine oligopeptoids do not effectively hybridise with complementary sequences of DNA and RNA or fully synthetic (2,4‐diamino)triazin‐6‐yl‐tagged peptoid 22. A possible reason could reside in the concurrent unfavourable influence of the anionic N‐(carboxymethyl) moieties and the flexible nucleobase/backbone ethylene linker.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Baylis–Hillman Reaction of 1‐Formyl‐β‐carboline: One‐Step Synthesis of the Canthin‐6‐one Framework by an Unprecedented Cascade Cyclization Reaction
Authors: Singh Virender , Hutait Samiran , Batra Sanjay
Published: October 2009

A one‐step access to the canthin‐6‐one architecture by the Baylis–Hillman reaction of methyl 1‐formyl‐9H‐β‐carboline‐3‐carboxylate or 1‐formyl‐9H‐β‐carboline involving an unprecedented cascade cyclization reaction is reported. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Comparison of Metallothionein Detection by Using Brdicka Reaction and Enzyme‐Linked Immunosorbent Assay Employing Chicken Yolk Antibodies
Authors: Krizkova Sona , Blahova Pavlina , Nakielna Johana , Fabrik Ivo , Adam Vojtech , Eckschlager Tomas , Beklova Miroslava , Svobodova Zdenka , Horak Vratislav , Kizek Rene
Published: October 2009

In this study, two methods for metallothioneins (MT) determination in a biological sample were compared. Particularly, twenty five human and nine pig blood serum samples and liver and kidney samples from thirty five carps (Cyprinus carpio) were analyzed by enzyme‐linked immunosorbent assay and differential pulse voltammetry Brdicka's reaction. The results obtained by these two methods were in good agreement. For commercially available MT standard the correlation coefficient between the single concentrations signal height was 0.99. In biological samples the correlation coefficients were 0.90 for fish liver and kidney samples, 0.91 for pig blood serum and 0.93 for human blood serum.
Simultaneous Determination of Trace Zinc(II) and Cadmium(II) by Differential Pulse Anodic Stripping Voltammetry Using a MWCNTs–NaDBS Modified Stannum Film Electrode
Authors: Tian Yun Qing , Li Nian Bing , Luo Hong Qun
Published: October 2009

A multiwalled carbon nanotubes–sodium dodecyl benzene sulfonate (MWCNTs–NaDBS) modified stannum film electrode was employed for the determination of cadmium(II) and zinc(II). The Sn/MWCNTs‐NaDBS film electrode was prepared by applying MWCNTs–NaDBS suspension to the surface of the GCE, while the Sn film was plated in situ simultaneously with the target metal ions. Under optimal conditions, linear calibration curves were obtained in a range of 5.0 −100.0 μg L−1 with detection limits of 0.9 μg L−1 for zinc(II) and 0.8 μg L−1 for cadmium(II), respectively. This film electrode was successfully applied to the determination of Zn(II) and Cd(II) in tap water sample.
Strategy for Low Background‐Current Levels in the Electrochemical Biosensors Using Horse‐Radish Peroxidase Labels
Authors: Kang Hyun Ju , Aziz Md. Abdul , Jeon Boyoun , Jo Kyungmin , Yang Haesik
Published: October 2009

This article describes an electrochemical strategy to achieve low background‐current levels in horse‐radish peroxidase (HRP)‐based electrochemical immunosensors. The strategy consists of (i) the use of an HRP substrate/product redox couple whose formal potential is high and (ii) the use of an electrode that shows moderate electrocatalytic activity for the redox couple. The strategy is proved by a model biosensor using a catechol/o‐benzoquinone redox couple and an indium tin oxide (ITO) electrode. The combined effect of high formal potential and moderate electrocatalytic activity allows o‐benzoquinone electroreduction with minimal catechol electrooxidation and H2O2 electroreduction. The detection limit for mouse‐IgG is 100 pg/mL.
Disposable Bismuth Oxide Screen Printed Electrodes for the High Throughput Screening of Heavy Metals
Authors: Kadara Rashid O. , Jenkinson Norman , Banks Craig E.
Published: October 2009

We present a simplified approach for the trace screening of toxic heavy metals utilizing bismuth oxide screen printed electrodes. The use of bismuth oxide instead of toxic mercury films facilitates the reliable sensing of lead(II), cadmium(II) and zinc(II). A linear range over 5 to 150 μg L−1 with detection limits of 2.5 and 5 μg L−1 are readily observed for cadmium and lead in 0.1 M HCl, respectively. Conducting a simultaneous multi‐elemental voltammetric detection of zinc, cadmium and lead in a higher pH medium (0.1 M sodium acetate solution) exhibited a linear range between 10 and 150 μg L−1 with detection limits of 5, 10 and 30 μg L−1 for cadmium, lead and zinc respectively. The sensor is greatly simplified over those recently reported such as bismuth nanoparticle modified electrodes and bismuth film coated screen printed electrodes. The scope of applications of this sensor with the inherent advances in electroanalysis coupled with the negliable toxicity of bismuth is extensive allowing high throughput electroanalysis.
Simultaneous Determination of Thallium and Lead on a Chemically Modified Electrode with Langmuir– Blodgett Film of a p‐tert‐Butylcalix[4]arene Derivative
Authors: Zou Lina , Zhang Yufeng , Qin Haili , Ye Baoxian
Published: October 2009

A new voltammetric sensor, Langmuir–Blodgett (LB) film of a p‐tert‐butylcalix[4]arene derivative modified glassy carbon electrode, was designed and successfully used in simultaneous determination of Tl+ and Pb2+ by square‐wave anodic stripping voltammetry. Under the optimum experimental conditions, this newly developed sensor reveal good linear response for Tl+ and Pb2+ in the concentration range of 3×10−8–4×10−6 mol L−1 and 2×10−7–2×10−5 mol L−1 respectively. The detect limits are 2×10−8 mol L−1 for Tl+ and 8×10−8 mol L−1 for Pb2+. Using proposed method, Tl+ and Pb2+ in environment samples were determined with satisfactory results.
Cooperative breeding and human cognitive evolution
Authors: Burkart J. M. , Hrdy S. B. , Van Schaik C. P.
Published: October 2009

Despite sharing a recent common ancestor, humans are surprisingly different from other great apes. The most obvious discontinuities are related to our cognitive abilities, including language, but we also have a markedly different, cooperative breeding system. Among many nonhuman primates and mammals in general, cooperative breeding is accompanied by psychological changes leading to greater prosociality, which directly enhances performance in social cognition. Here we propose that these cognitive consequences of cooperative breeding could have become more pervasive in the human lineage because the psychological changes were added to an ape‐level cognitive system capable of understanding simple mental states, albeit mainly in competitive contexts. Once more prosocial motivations were added, these cognitive abilities could also be used for cooperative purposes, including a willingness to share mental states, thereby enabling the emergence of shared intentionality. Shared intentionality has been identified as the original source of many uniquely human cognitive abilities, including cumulative culture and language. Shared intentionality rests on a fundamentally prosocial disposition that is strikingly absent in chimpanzees, but present in cooperatively breeding primates. Thus, our hypothesis is that while chimpanzees and perhaps all great apes exhibit many of the importantcognitivepreconditions for uniquely human mental capacities to evolve, they lack thepsychologicalpreconditions. In humans, we argue, the two components merged, the cognitive component due to common descent from ape ancestors and the motivational component due to convergent evolution of traits typical of many cooperative breeders.
The emergence of human uniqueness: Characters underlying behavioral modernity
Authors: Hill Kim , Barton Michael , Hurtado A. Magdalena
Published: October 2009

Although scientists are aware that humans share the same biological heritage as do all other organisms on the planet, the reliance ofHomo sapienson culture and cooperation has resulted in what can best be described as “a spectacular evolutionary anomaly.”1:11The extra‐somatic adaptations, technological dominance, and success of our species in colonizing every terrestrial habitat have no parallel.2Moreover,Homo sapiensaccounts for about eight times as much biomass as do all other terrestrial wild vertebrates combined,3an amount equivalent to the biomass of all 14,000+ species of ants,4the most successful terrestrial invertebrates. Human societies are complex, with more specialized economic niches in the United States than the total number of mammalian species on the planet.5While some might suggest that only post‐industrial humans achieved stunning biological success, data suggest that humans living as hunter‐gatherers would have attained a world population of more than 70 million individuals6and a total biomass greater than that of any other large vertebrate on the planet if agriculture had not been repeatedly invented as they spread.
The lost dream of ecological determinism: Time to say goodbye? … Or a White Queen's proposal?
Authors: Koenig Andreas , Borries Carola
Published: October 2009

“‘What is the matter?’ she [Alice] said, as soon as there was a chance of making herself heard. ‘Have you pricked your finger?’ ‘I haven't pricked it yet,’ the [White] Queen said, ‘but I soon shall – oh, oh, oh!’” (emphasis as in1:82)
Cooperation and competition in chimpanzees: Current understanding and future challenges
Authors: Mitani John C.
Published: October 2009

Two goals in the study of evolutionary anthropology are to determine the factors that make humans unique and to reconstruct the evolution of our behavior. As humans' closest living relatives, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) have always been of special interest in this regard. Because of their close evolutionary relationship to us, these animals provide the requisite comparative data to evaluate claims made about human uniqueness. In addition, knowledge of the differences among chimpanzees, bonobos, and us furnishes important insights into the changes that occurred during human evolution. Given these circumstances, studies of chimpanzees and bonobos remain high priorities for research. The volatile political situation in the Democratic Republic of the Congo, home to bonobos, has made long‐term study of their behavior difficult, if not impossible. In contrast, field research on chimpanzees, initiated by Jane Goodall1and Toshisada Nishida2nearly 50 years ago, continues to grow and thrive. While past and ongoing field work has added enormously to our understanding of the behavior of chimpanzees,3–8gaps in knowledge persist. In this paper, I summarize some of these gaps, giving special emphasis to male cooperation and female competition.
Metal ionophores – An emerging class of anticancer drugs
Authors: Ding Wei‐Qun , Lind Stuart E.
Published: October 2009

Compounds that bind metals such as copper and zinc have many biological activities, including the ability to induce apoptosis in cancer cells. Although some of these compounds have been considered to act as chelators of metals, decreasing their bioavailability, others increase intracellular metal concentrations. We review recent work regarding the recognition of the biological effects of metal ionophores with different structures, particularly with regard to their actions upon cancer cells focusing on dithiocarbamates, pyrithione, and the 8‐hydroxyquinoline derivative, clioquinol. We provide a biologically based classification of metal‐binding compounds that allows an experimental distinction between chelators and ionophores that can be readily used by biologists, which may lead to further study and classification of metal‐binding drugs. Metal ionophores may kill cancer cells by a number of mechanisms, including lysosomal disruption and proteasome inhibition, and likely others. Because some of these compounds have been safely administered to animals and humans, they have the potential to become clinically useful anticancer agents. © 2009 IUBMB IUBMB Life, 61(11): 1013–1018, 2009
Methionine gamma‐lyase: The unique reaction mechanism, physiological roles, and therapeutic applications against infectious diseases and cancers
Authors: Sato Dan , Nozaki Tomoyoshi
Published: October 2009

Sulfur‐containing amino acids (SAAs) are essential components in many biological processes and ubiquitously distributed to all organisms. Both biosynthetic and catabolic pathways of SAAs are heterogeneous among organisms and between developmental stages, and regulated by the environmental changes. Limited lineage of organisms ranging from archaea to plants, but not human, possess a unique enzyme methionine gamma‐lyase (MGL, EC 4.4.1.11) to directly degrade SAA to α‐keto acids, ammonia, and volatile thiols. The reaction mechanisms and the physiological roles of this enzyme are partially demonstrated by the enzymological analyzes, structure determination, isotopic labeling of the intermediate metabolites, and functional analyzes of deficient mutants. MGL has been exploited as a drug target for the infectious diseases caused by parasitic protozoa and anaerobic periodontal bacteria. In addition, MGL has been utilized to develop therapeutic interventions of various cancers, by introducing recombinant proteins to deplete methionine essential for the growth of cancer cells. In this review, we discuss the current understanding of enzymological properties, putative physiological roles, and therapeutic applications of MGL. © 2009 IUBMB IUBMB Life, 61(11): 1019–1028, 2009
Fluorescent proteins for live cell imaging: Opportunities, limitations, and challenges
Authors: Wiedenmann Jörg , Oswald Franz , Nienhaus Gerd Ulrich
Published: October 2009

The green fluorescent protein (GFP) from the jellyfish Aequorea victoria can be used as a genetically encoded fluorescence marker due to its autocatalytic formation of the chromophore. In recent years, numerous GFP‐like proteins with emission colors ranging from cyan to red were discovered in marine organisms. Their diverse molecular properties enabled novel approaches in live cell imaging but also impose certain limitations on their applicability as markers. In this review, we give an overview of key structural and functional properties of fluorescent proteins that should be considered when selecting a marker protein for a particular application and also discuss challenges that lie ahead in the further optimization of the glowing probes. © 2009 IUBMB IUBMB Life, 61(11): 1029–1042, 2009
Fabry Disease: Treatment and diagnosis
Authors: Rozenfeld Paula A.
Published: October 2009

Fabry disease is an X‐linked lysosomal disorder that results from a deficiency of the lysosomal enzyme α‐galactosidase A leading to accumulation of glycolipids, mainly globotriaosylceramide in the cells from different tissues. Classical Fabry disease affects various organs. Clinical manifestations start at early age and include angiokeratoma, acroparesthesia, hypohydrosis, heat/exercise intolerance, gastrointestinal pain, diarrhea, and fever. The main complications of Fabry disease are more prominent after the age of 30 when kidney, heart, and/or cerebrovascular disorders appear. Most of the heterozygous females are symptomatic. Enzyme replacement therapy (ERT) is the only specific treatment for Fabry disease. The beneficial effect of ERT on different organs/systems has been extensively evaluated. Quality of life of patients receiving ERT is improved. Enzyme replacement stabilizes or slows the decline in renal function and reduces left ventricular hypertrophy. Fabry disease may be underdiagnosed because of nonspecific and multiorgan symptoms. Different screening strategies have been carried out in different at‐risk populations in order to detect undiagnosed Fabry patients. An increasing knowledge about Fabry disease within the medical community increases the chances of patients to receive a timely diagnosis and, consequently, to access the appropriate therapy. © 2009 IUBMB IUBMB Life, 61(11): 1043–1050, 2009
Design, development, synthesis, and docking analysis of 2′‐substituted triclosan analogs as inhibitors for Plasmodium falciparum Enoyl‐ACP reductase
Authors: Kapoor Neha , Banerjee Tanushree , Babu Ponnusamy , Maity Koustav , Surolia Namita , Surolia Avadhesha
Published: October 2009

A structure‐based approach has been adopted to develop 2′‐substituted analogs of triclosan. The Cl at position 2′ in ring B of triclosan was chemically substituted with other functional groups like NH2, NO2 and their inhibitory potencies against PfENR were determined. The binding energies of the 2′ substituted analogs of triclosan for enoyl‐acyl carrier protein reductase (ENR) of Plasmodium falciparum were determined using Autodock. Based on the autodock results, we synthesized the potential compounds. The IC50 and inhibition constant (Ki) of 2′ substituted analogs of triclosan were determined against purified PfENR. Among them, two compounds, 2‐(2′‐Amino‐4′‐chloro‐phenoxy)‐5‐chloro‐phenol (compound 4) and 5‐chloro‐2‐(4′‐chloro‐2′‐nitro‐phenoxy)‐phenol) (compound 5) exhibited good potencies. Compound 4 followed uncompetitive inhibition kinetics with crotonoyl CoA and competitive with NADH. It was shown to have an IC50 of 110 nM; inhibition constant was 104 nM with the substrate and 61 nM with the cofactor. IC50 of compound 5 was determined to be 229 nM. Compounds 4 and 5 showed significant inhibition of the parasite growth in P. falciparum culture. © 2009 IUBMB IUBMB Life, 61(11): 1083–1091, 2009
PGC‐1α activation as a therapeutic approach in mitochondrial disease
Authors: Wenz Tina
Published: October 2009

Mitochondria play a central role in cellular homeostasis. Hence, mitochondrial dysfunction resulting in impaired ATP supply is detrimental to cell viability and causes severe and often fatal disorders. Current treatment of these mitochondrial disorders is limited and mostly addresses the symptoms, but not the deficiency itself. Recent work in cell and animal models of mitochondrial disease shows that increased mitochondrial biogenesis can boost residual OXPHOS capacity and thereby prevent the bioenergetic crisis. In animal models, this strategy results in increased health and lifespan. Here, I review which mitochondrial processes are affected in known mitochondrial disorders and discuss why PGC‐1α mediated mitochondrial biogenesis offers a promising venue for treatment of mitochondrial disorders. © 2009 IUBMB IUBMB Life, 61(11): 1051–1062, 2009
Galactose toxicity in animals
Authors: Lai Kent , Elsas Louis J. , Wierenga Klaas J.
Published: October 2009

In most organisms, productive utilization of galactose requires the highly conserved Leloir pathway of galactose metabolism. Yet, if this metabolic pathway is perturbed due to congenital deficiencies of the three associated enzymes, or an overwhelming presence of galactose, this monosaccharide which is abundantly present in milk and many non‐dairy foodstuffs, will become highly toxic to humans and animals. Despite more than four decades of intense research, little is known about the molecular mechanisms of galactose toxicity in human patients and animal models. In this contemporary review, we take a unique approach to present an overview of galactose toxicity resulting from the three known congenital disorders of galactose metabolism and from experimental hypergalactosemia. Additionally, we update the reader about research progress on animal models, as well as advances in clinical management and therapies of these disorders. © 2009 IUBMB IUBMB Life, 61(11): 1063–1074, 2009
The rate of learning‐by‐doing: estimates from a search‐matching model
Authors: Prat Julien
Published: October 2009

We construct and estimate by maximum likelihood a job search model where wages are set by Nash bargaining and idiosyncratic productivity follows a geometric Brownian motion. The proposed framework enables us to endogenize job destruction and to estimate the rate of learning‐by‐doing. Although the range of the observations is not independent of the parameters, we establish that the estimators satisfy asymptotic normality. The structural model is estimated using Current Population Survey data on accepted wages and employment durations. We show that it accurately captures the joint distribution of wages and job spells. We find that the rate of learning‐by‐doing has an important positive effect on aggregate output and a small impact on employment. Copyright © 2009 John Wiley & Sons, Ltd.
Accurate free energy calculation along optimized paths
Authors: Chen Changjun , Xiao Yi
Published: October 2009

The path‐based methods of free energy calculation, such as thermodynamic integration and free energy perturbation, are simple in theory, but difficult in practice because in most cases smooth paths do not exist, especially for large molecules. In this article, we present a novel method to build the transition path of a peptide. We use harmonic potentials to restrain its nonhydrogen atom dihedrals in the initial state and set the equilibrium angles of the potentials as those in the final state. Through a series of steps of geometrical optimization, we can construct a smooth and short path from the initial state to the final state. This path can be used to calculate free energy difference. To validate this method, we apply it to a small 10‐ALA peptide and find that the calculated free energy changes in helix‐helix and helix‐hairpin transitions are both self‐convergent and cross‐convergent. We also calculate the free energy differences between different stable states of β‐hairpin trpzip2, and the results show that this method is more efficient than the conventional molecular dynamics method in accurate free energy calculation. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Quantum mechanics and quasiclassical study of the H/D+FO → OH/OD+F, HF/DF+O reactions: Chemical stereodynamics
Authors: Chu Tianshu
Published: October 2009

The time‐dependent quantum wave packet and the quasi‐classical trajectory (QCT) calculations for the title reactions are carried out using three recent‐developed accurate potential energy surfaces of the 11A′, 13A′, and 13A″ states. The two commonly used polarization‐dependent differential cross sections, dσ00/dωt, dσ20/dωt, with ωt being the polar coordinates of the product velocity ω′, and the three angular distributions, P(θr), P(Φr), and P(θr,Φr), with θr, Φr being the polar angles of the product angular momentum, are generated in the center‐of‐mass frame using the QCT method to gain insight into the alignment and the orientation of the product molecules. Influences of the potential energy surface, the collision energy, and the isotope mass on the stereodynamics are shown and discussed. Validity of the QCT calculation has been examined and proved in the comparison with the quantum wave packet calculation. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
TNF‐α‐mediated reduction in PGC‐1α may impair skeletal muscle function after cigarette smoke exposure
Authors: Tang Kechun , Wagner Peter D. , Breen Ellen C.
Published: October 2009

Skeletal muscle dysfunction contributes to exercise limitation in COPD. In this study cigarette smoke exposure was hypothesized to increase expression of the inflammatory cytokine, TNF‐α, thereby suppressing PGC‐1α, and hence affecting down stream molecules that regulate oxygen transport and muscle function. Furthermore, we hypothesized that highly vascularized oxidative skeletal muscle would be more susceptible to cigarette smoke than less well‐vascularized glycolytic muscle. To test these hypotheses, mice were exposed to cigarette smoke daily for 8 or 16 weeks, resulting in 157% (8 weeks) and 174% (16 weeks) increases in serum TNF‐α. Separately, TNF‐α administered to C2C12 myoblasts was found to dose‐dependently reduce PGC‐1α mRNA. In the smoke‐exposed mice, PGC‐1α mRNA was decreased, by 48% in soleus and 23% in EDL. The vascular PGC‐1α target molecule, VEGF, was also down‐regulated, but only in the soleus, which exhibited capillary regression and an oxidative to glycolytic fiber type transition. The apoptosis PGC‐1α target genes, atrogin‐1 and MuRF1, were up‐regulated, and to a greater extent in the soleus than EDL. Citrate synthase (soleus—19%, EDL—17%) and β‐hydroxyacyl CoA dehydrogenase (β‐HAD) (soleus—22%, EDL—19%) decreased similarly in both muscle types. There was loss of body and gastrocnemius complex mass, with rapid soleus but not EDL fatigue and diminished exercise endurance. These data suggest that in response to smoke exposure, TNF‐α‐mediated down‐regulation of PGC‐1α may be a key step leading to vascular and myocyte dysfunction, effects that are more evident in oxidative than glycolytic skeletal muscles. J. Cell. Physiol. 222: 320–327, 2010. © 2009 Wiley‐Liss, Inc.
Cholera toxin‐sensitive GTP‐binding protein‐coupled activation of augmenter of liver regeneration (ALR) receptor and its function in rat kupffer cells
Authors: Gandhi Chandrashekhar R. , Murase Noriko , Starzl Thomas E.
Published: October 2009

Mitogenic effect of augmenter of liver regeneration (ALR), a protein produced and released by hepatocytes, on hepatocytes in vivo but not in vitro suggests that the effect is mediated by nonparenchymal cells. Since mediators produced by Kupffer cells are implicated in hepatic regeneration, we investigated receptor for ALR and its functions in rat Kupffer cells. Kupffer cells were isolated from rat liver by enzymatic digestion and centrifugal elutriation. Radioligand ([125I] ALR) receptor binding, ALR‐induced GTP/G‐protein association, and nitric oxide (NO), tumor necrosis factor (TNF)‐α, and interleukin‐6 (IL‐6) synthesis were determined. High‐affinity receptor for ALR, belonging to the G‐protein family, with Kd of 1.25 ± 0.18 nM and Bmax of 0.26 ± 0.02 fmol/µg DNA was identified. ALR stimulated NO, TNF‐α, and IL‐6 synthesis via cholera toxin‐sensitive G‐protein, as well as p38‐MAPK activity and nuclear translocation of NFκB. While inhibitor of NFκB (MG132) inhibited ALR‐induced NO synthesis, MG132 and p38‐MAPK inhibitor (SB203580) abrogated ALR‐induced TNF‐α and IL‐6 synthesis. ALR also prevented the release of mediator(s) from Kupffer cells that cause inhibition of DNA synthesis in hepatocytes. Administration of ALR to 40% partially hepatectomized rats increased expression of TNF‐α, IL‐6, and inducible nitric oxide synthase (iNOS) and caused augmentation of hepatic regeneration. These results demonstrate specific G‐protein coupled binding of ALR and its function in Kupffer cells and suggest that mediators produced by ALR‐stimulated Kupffer cells may elicit physiologically important effects on hepatocytes. J. Cell. Physiol. 222: 365–373, 2010. © 2009 Wiley‐Liss, Inc.
Absorbable polymer stent technologies for vascular regeneration
Authors: Grabow Niels , Martin David P. , Schmitz Klaus‐Peter , Sternberg Katrin
Published: October 2009

Stents are structural implants with widespread clinical use in vascular intervention to re‐open stenotic vessels for the treatment of coronary artery disease and peripheral arterial occlusive disease. Apart from their mechanical function, current drug‐eluting stents (DES) utilize local drug delivery from a drug‐incorporated permanent polymer coating to prevent in‐stent restenosis. This delayed closure of the stented vessel is considered one of the major limitations of conventional bare metal stents (BMS). The long‐term safety of DES, however, is still under debate, with reported cases of delayed healing, late thrombosis and hypersensitivity demanding further evolution in this field. A promising approach to circumvent the limitations of first generation DES is the application of degradable polymer coatings in second generation DES, and fully absorbable polymer stents. From a materials and engineering perspective, this paper provides a mini‐review of current clinically relevant DES technology and recent advancements in the development of stents from degradable polymeric materials as an alternative to permanent BMS and DES. This review, includes work on degradable stents and coatings based on blends of polylactic acid and the microbially‐produced poly(4‐hydroxybutyrate). Copyright © 2009 Society of Chemical Industry
Kinetic modeling of lipase‐mediated one‐pot chemo‐bio cascade synthesis of R‐1‐phenyl ethyl acetate starting from acetophenone
Authors: Sahin Serap , Wärnå Johan , Mäki‐Arvela Päivi , Salmi Tapio , Murzin Dmitry Yu.
Published: October 2009

BACKGROUND: A systematic investigation of mutual interference between a hydrogenation catalyst, Pd/Al2O3, and an immobilized lipase in a one‐pot synthesis of R‐1‐phenyl ethyl acetate at 70 °C has been undertaken. This paper reports the kinetic modeling of lipase‐mediated chemo‐bio cascade synthesis of R‐1‐phenyl ethyl acetate starting from acetophenone.

RESULTS: The kinetic results revealed that these catalysts were not acting independently but in concert. A mechanism which predicts the experimental observations for this reaction is proposed.

CONCLUSION: The parameters of the kinetic model, which are in good agreement with the experimental data, were estimated through numerical data fitting. The reliability of the estimated parameters was analyzed using the Markov Chain Monte Carlo (MCMC) method. Copyright © 2009 Society of Chemical Industry
Hadwiger number and chromatic number for near regular degree sequences
Authors: Robertson Neil , Song Zi‐Xia
Published: October 2009

We consider a problem related to Hadwiger's Conjecture. Let D=(d1, d2, …, dn) be a graphic sequence with 0⩽d1⩽d2⩽···⩽dn⩽n−1. Any simple graph G with D its degree sequence is called a realization of D. Let R[D] denote the set of all realizations of D. Define h(D)=max{h(G): G∈R[D]} and χ(D)=max{χ(G): G∈R[D]}, where h(G) and χ(G) are Hadwiger number and chromatic number of a graph G, respectively. Hadwiger's Conjecture implies that h(D)⩾χ(D). In this paper, we establish the above inequality for near regular degree sequences. © 2009 Wiley Periodicals, Inc. J Graph Theory 64: 175–183, 2010
Acyclic dominating partitions
Authors: Addario‐Berry Louigi , Kang Ross J. , Müller Tobias
Published: October 2009

Given a graph G=(V, E), let \documentclass{article}\footskip=0pc\pagestyle{empty}\begin{document}${\mathcal{P}}$\end{document} be a partition of V. We say that \documentclass{article}\footskip=0pc\pagestyle{empty}\begin{document}${\mathcal{P}}$\end{document} is dominating if, for each part P of \documentclass{article}\footskip=0pc\pagestyle{empty}\begin{document}${\mathcal{P}}$\end{document}, the set V\P is a dominating set in G (equivalently, if every vertex has a neighbor of a different part from its own). We say that \documentclass{article}\footskip=0pc\pagestyle{empty}\begin{document}${\mathcal{P}}$\end{document} is acyclic if for any parts P, P′ of \documentclass{article}\footskip=0pc\pagestyle{empty}\begin{document}${\mathcal{P}}$\end{document}, the bipartite subgraph G[P, P′] consisting of the edges between P and P′ in \documentclass{article}\footskip=0pc\pagestyle{empty}\begin{document}${\mathcal{P}}$\end{document} contains no cycles. The acyclic dominating number ad(G) of G is the least number of parts in any partition of V that is both acyclic and dominating; and we shall denote by ad(d) the maximum over all graphs G of maximum degree at most d of ad(G). In this article, we prove that ad(3)=2, which establishes a conjecture of P. Boiron, É. Sopena, and L. Vignal, DIMACS/DIMATIA Conference “Contemporary Trends in Discrete Mathematics”, 1997, pp. 1–10. For general d, we prove the upper bound ad(d)=O(dlnd) and a lower bound of ad(d)=Ω(d). © 2009 Wiley Periodicals, Inc. J Graph Theory 64: 292–311, 2010