bluuebunny/crossref_metadata_2025 huggingface dataset:
Combining individual patient data and aggregate data in mixed treatment comparison meta‐analysis: Individual patient data may be beneficial if only for a subset of trials
Authors: Donegan Sarah , Williamson Paula , D'Alessandro Umberto , Garner Paul , Smith Catrin Tudur
Published: September 2012

Background

Individual patient data (IPD) meta‐analysis is the gold standard. Aggregate data (AD) and IPD can be combined using conventional pairwise meta‐analysis when IPD cannot be obtained for all relevant studies. We extend the methodology to combine IPD and AD in a mixed treatment comparison (MTC) meta‐analysis.

Methods

The proposed random‐effects MTC models combine IPD and AD for a dichotomous outcome. We study the benefits of acquiring IPD for a subset of trials when assessing the underlying consistency assumption by including treatment‐by‐covariate interactions in the model. We describe three different model specifications that make increasingly stronger assumptions regarding the interactions. We illustrate the methodology through application to real data sets to compare drugs for treating malaria by using the outcome unadjusted treatment success at day 28. We compare results from AD alone, IPD alone and all data.

Results

When IPD contributed (i.e. either using IPD alone or combining IPD and AD), the chains converged, and we identified statistically significant regression coefficients for the interactions. Using IPD alone, we were able to compare only three of the six treatments of interest. When models were fitted to AD, the treatment effects and regression coefficients for the interactions were far more imprecise, and the chains did not converge.

Conclusions

The models combining IPD and AD encapsulated all available evidence. When exploring interactions, it can be beneficial to obtain IPD for a subset of trials and to combine IPD with additional AD. Copyright © 2012 John Wiley & Sons, Ltd.
Modeling and optimizing energy‐efficient manual driving on high‐speed lines
Authors: Sicre Carlos , Cucala Asunción P. , Fernández Antonio , Lukaszewicz Piotr
Published: September 2012

This paper presents a simulation‐based model for manual driving strategies that will minimize energy consumption for high‐speed trains. Specific characteristics of both high‐speed lines (HSLs) and manual driving strategies are considered in order to obtain achievable designs that can be tested on commercial services. The proposed design model calculates a list of efficient high‐level commands to be systematically executed by the driver on an HSL along the trip. The design is based on a detailed simulation model of the train's motion (taking into account track and train characteristics and operational constraints), combined with a genetic algorithm to select the best driving. Continuous control solution by mathematical optimization is avoided, as it is not an appropriate reference for manual driving in HSL. The validation of the simulation model is focused on running resistance, tractive/braking efficiencies, and consumption of auxiliary equipment, and shows differences between real measurements and simulated results which are lower than 2% both in run time and energy consumption. Finally, a real case is presented in which the proposed model was used to design efficient driving strategies that were subsequently implemented on commercial services along the Spanish HSL Madrid–Barcelona in both directions, measuring average energy savings of 23 and 18%, respectively, when the efficient driving strategies were compared with measured standard manual driving. The future scope will be the application of this model to online recalculation of driving commands. © 2012 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Translanguaging, TexMex, and Bilingual Pedagogy: Emergent Bilinguals Learning Through the Vernacular
Authors: Sayer Peter
Published: September 2012

This article presents an ethnographic study of how bilingual teachers and children use their home language, TexMex, to mediate academic content and standard languages. From the premise thatTESOLeducators can benefit from a fuller understanding of students' linguistic repertoires, the study describes language practices in a second‐grade classroom in a transitional bilingual education program in a well‐established Mexican American community in San Antonio, Texas. The data suggest that the participants move fluidly between not just Spanish and English, but also the standard and vernacular varieties, a movement that is calledtranslanguaging(O. García, 2009). Translanguaging through TexMex enables the teacher and students to create discursive spaces that allow them to engage with the social meanings in school from their position as bilingual Latinos. The teacher's adoption of a flexible bilingual pedagogy (Creese & Blackledge, 2010) allows for translanguaging in the classroom not only as a way of making sense of content and learning language, but also as a legitimized means of performing desired identities.
Complicity or multiplicity? Defining boundaries for graduate teaching assistant success
Authors: Dunn‐Haley Karen , Zanzucchi Anne
Published: September 2012

Providing guidance for graduate teaching assistants on how to establish boundaries is critical to support their teaching and research responsibilities and to advance their professional development.
Synchrotron‐induced EDXRF determination of uranium and thorium in mixed uranium–thorium oxide pellets
Authors: Misra N. L. , Tiwari M. K. , Kumar S. Sanjay , Dhara Sangita , Singh Ajit Kumar , Lodha G. S. , Deb S. K. , Gupta P. D. , Aggarwal S. K.
Published: September 2012

Uranium and thorium in their mixed oxides were determined by synchrotron‐induced energy dispersive X‐ray fluorescence (EDXRF) spectrometry. Mixed oxide calibration mixtures containing uranium and thorium in different relative amounts and approximately fixed amount of yttrium were prepared in the form of pellets. The EDXRF spectra of the pellets were measured at the microfocus XRF (BL‐16) beam line of Indus‐2 synchrotron radiation facility (Raja Ramanna Centre of Advanced Technology, Indore, India). Characteristic X‐ray lines U Lα, Th Lα, and Y Kα were used as analyte lines. Calibration plot for the determination of uranium was prepared by plotting amount ratios of U and Y against the intensity ratios of U Lα and Y Kα. Similarly, a calibration plot for thorium analysis was also made. The amounts of uranium and thorium in the sample mixtures prepared in similar way as the calibration mixtures were determined using the aforementioned calibration plots. The precision values obtained for uranium and thorium determinations were found to be 0.3 and 0.2% (relative standard deviation, 1σ), respectively. The EDXRF results deviated from the expected values by 1% for uranium and 0.9% for thorium determinations. These analytical features are much superior compared with laboratory‐based analysis results. Copyright © 2012 John Wiley & Sons, Ltd.
From Simple Chalcogenidotetrelate Precursors to Complex Structures and Functional Compounds
Authors: Heine Johanna , Dehnen Stefanie
Published: September 2012

Chalcogenidotetrelates show a rich and complex chemistry encompassing intricate structures and useful materials. A step‐wise coordination chemistry approach allows the sequential formation of multinary M/T/E anions (M = transition metal, T = tetrel, E = chalcogen) from simple T/E building blocks in solution. This way, a range of compounds displaying different structure types of molecular as well as extended multinary anions were obtained. To allow for even further variety, the approach can be extended to organo‐functionalized chalcogenidotetrelates. Here, the organic shell of the inorganic cages plays a decisive role in reactivity and resulting structures. The formation structures and properties of these compounds will be discussed in detail in this perspective article.
Referential Communication in Children With ADHD: Challenges in the Role of a Listener
Authors: Nilsen Elizabeth S. , Mangal Leilani , MacDonald Kristi
Published: September 2012

Purpose

Successful communication requires that listeners accurately interpret the meaning of speakers' statements. The present work examined whether children with and without attention-deficit/hyperactivity disorder (ADHD) differ in their ability to interpret referential statements (i.e., phrases that denote objects or events) from speakers.

Method

Children (6 to 9 years old), diagnosed with ADHD (
n
= 27) and typically developing (
n
= 26), took part in an interactive task in which they were asked by an adult speaker to retrieve objects from a display case. Children interpreted the referential statements in contexts that either did or did not require perspective-taking. Children's eye movements and object choices were recorded. Parents completed questionnaires assessing their child's frequency of ADHD symptoms and pragmatic communicative abilities.

Results

Behavioral and eye movement measures revealed that children with ADHD made more interpretive errors and were less likely to consider target referents across the 2 communicative conditions. Furthermore, ADHD symptoms related to children's performance on the communicative task and to parental report of the child's pragmatic skills.

Conclusion

Children with ADHD are less accurate in their interpretations of referential statements. Such difficulties would lead to greater occurrences of miscommunication.
A note on the switching adiabatic theorem
Authors: Elgart Alexander , Hagedorn George A.
Published: September 2012

We derive a nearly optimal upper bound on the running time in the adiabatic theorem for a switching family of Hamiltonians. We assume the switching Hamiltonian is in the Gevrey class Gα as a function of time, and we show that the error in adiabatic approximation remains small for running times of order g−2 |ln g |6α. Here g denotes the minimal spectral gap between the eigenvalue(s) of interest and the rest of the spectrum of the instantaneous Hamiltonian.
Sine gating detector with simple filtering for low-noise infra-red single photon detection at room temperature
Authors: Walenta Nino , Lunghi Tommaso , Guinnard Olivier , Houlmann Raphael , Zbinden Hugo , Gisin Nicolas
Published: September 2012

We present and analyze a gated single photon avalanche detector using a sine gating scheme with a simple but effective low-pass filtering technique for fast low-noise single photon detection at telecom wavelength. The detector is characterized by 130 ps short gates applied with a frequency of 1.25 GHz, yields only 70 ps timing jitter and noise probabilities as low as 7·10−7 per gate at 10% detection efficiency. We show that the detector is suitable for high rate quantum key distribution (QKD) and even at room temperature it could allow for QKD over distances larger than 25 km.
Formation probability of Cr-Nd pair and energy transfer from Cr to Nd in Y3Al5O12 ceramics codoped with Nd and Cr
Authors: Yamaga Mitsuo , Oda Yohei , Uno Hideaki , Hasegawa Kazuo , Ito Hiroshi , Mizuno Shintaro
Published: September 2012

Temperature dependence of decay curves of the Cr3+ and Nd3+ luminescence excited at 432 nm in the Cr3+ absorption bands for YAG ceramics codoped with 1 mol. % Nd3+ and 0.1 mol. % Cr3+ indicates two distinct energy transfer processes from Cr3+ to Nd3+: one is a temperature-independent process via the lowest 2E excited state of Cr3+ through the exchange interaction between Cr3+ and Nd3+ ions; the other is a temperature-dependent process via the higher 4T2 excited states of Cr3+ through the thermal Boltzmann distribution. In order to explain these results, we have proposed a simple model on energy transfer from Cr3+ to Nd3+, taking into account a formation probability of a Cr-Nd pair in YAG as a function of separation distance. This Cr-Nd pair model has estimated that the former and latter energy transfer processes occur from a Cr3+ ion to one of Nd3+ ions substituting for the first nearest neighbor Y3+ ions and near Y3+ ions beyond within a sphere with an approximate radius of less than 0.8 nm, respectively.
Catalyst-free synthesis of reduced graphene oxide–carbon nanotube hybrid materials by acetylene-assisted annealing graphene oxide
Authors: Liu Fuchi , Li Ming , Feng Qian , Tang Nujiang , Zhong Wei , Huang Wei , Du Youwei
Published: September 2012

A facile catalyst-free approach for synthesis of reduced graphene oxide-carbon nanotube (RGO-CNT) hybrid materials was presented by acetylene-assisted annealing graphene oxide. The weight ratio of CNTs to RGO can be adjusted by regulating the annealing temperature, and it can be tuned in a relatively wide range of 0.33 to 7.039. The catalyst-free method opens up the possibility for the synthesis of RGO-CNTs for various applications.
Performance and polarization effects in (112¯2) long wavelength light emitting diodes grown on stress relaxed InGaN buffer layers
Authors: Koslow Ingrid L. , Hardy Matthew T. , Shan Hsu Po , Dang Po-Yuan , Wu Feng , Romanov Alexey , Wu Yuh-Renn , Young Erin C. , Nakamura Shuji , Speck James S. , DenBaars Steven P.
Published: September 2012

Long wavelength (525–575 nm) (112¯2) light emitting diodes were grown pseudomorphically on stress relaxed InGaN buffer layers. Basal plane dislocation glide led to the formation of misfit dislocations confined to the bottom of the InGaN buffer layer. This provided one-dimensional plastic relaxation in the film interior, including the device active region. The change of the stress state of the quantum well due to one-dimensional plastic relaxation altered the valence band structure, which produced a significant shift in polarization of emitted light. Devices grown on relaxed buffers demonstrated equivalent output power compared to those for control samples without relaxation.
Microphase separations of the fluids with spherically symmetric competing interactions
Authors: Kim Soon-Chul , Suh Soong-Hyuck , Seong Baek-Seok
Published: September 2012

A density functional perturbation theory has been developed for studying the phase behaviors of a competing system in the spherical pores. The pore size as well as the intensity of competing interactions exerts a strong influence on the vapor-liquid, vapor-cluster, and cluster-liquid transitions of a competing system. The microdomain spacing (D) of the cluster is commensurate with the periodicity of modulation in the particle density distributions of a competing system in a spherical pore with the pore radius (R). For the cluster phase, we find that the multi-vaporlike void is formed depending on the periodicity of modulation by finite-size artifacts. For R < D, the competing system only shows the vapor-liquid transition at a high amplitude. For R > D, the vapor-cluster and cluster-liquid transitions are found at a high amplitude, whereas at a low amplitude, the cluster-liquid transition only occurs. The competing system exhibits two tricritical points, which are joined to one another by the line of second-order transitions at the low and high densities. A comparison with the result of a slit pore shows that (i) the tricritical points in a spherical pore, which has the highest symmetry, occur at a low amplitude compared with that of a slit pore because of the geometrical properties of the pores, and that (ii) the slit pore relatively shows the wide vapor-cluster and cluster-liquid coexistence regions compared with that of a spherical pore: the geometrical symmetry of a pore results in a weaker tendency for phase separation.
Unforgeable noise-tolerant quantum tokens
Authors: Pastawski Fernando , Yao Norman Y. , Jiang Liang , Lukin Mikhail D. , Cirac J. Ignacio
Published: September 2012

The realization of devices that harness the laws of quantum mechanics represents an exciting challenge at the interface of modern technology and fundamental science. An exemplary paragon of the power of such quantum primitives is the concept of “quantum money” [Wiesner S (1983) ACM SIGACT News 15:78–88]. A dishonest holder of a quantum bank note will invariably fail in any counterfeiting attempts; indeed, under assumptions of ideal measurements and decoherence-free memories such security is guaranteed by the no-cloning theorem. In any practical situation, however, noise, decoherence, and operational imperfections abound. Thus, the development of secure “quantum money”-type primitives capable of tolerating realistic infidelities is of both practical and fundamental importance. Here, we propose a novel class of such protocols and demonstrate their tolerance to noise; moreover, we prove their rigorous security by determining tight fidelity thresholds. Our proposed protocols require only the ability to prepare, store, and measure single quantum bit memories, making their experimental realization accessible with current technologies.
Complexity of chromatin folding is captured by the strings and binders switch model
Authors: Barbieri Mariano , Chotalia Mita , Fraser James , Lavitas Liron-Mark , Dostie Josée , Pombo Ana , Nicodemi Mario
Published: September 2012

Chromatin has a complex spatial organization in the cell nucleus that serves vital functional purposes. A variety of chromatin folding conformations has been detected by single-cell imaging and chromosome conformation capture-based approaches. However, a unified quantitative framework describing spatial chromatin organization is still lacking. Here, we explore the “strings and binders switch” model to explain the origin and variety of chromatin behaviors that coexist and dynamically change within living cells. This simple polymer model recapitulates the scaling properties of chromatin folding reported experimentally in different cellular systems, the fractal state of chromatin, the processes of domain formation, and looping out. Additionally, the strings and binders switch model reproduces the recently proposed “fractal–globule” model, but only as one of many possible transient conformations.
Dynamics of the last glacial maximum Antarctic ice-sheet and its response to ocean forcing
Authors: Golledge Nicholas R. , Fogwill Christopher J. , Mackintosh Andrew N. , Buckley Kevin M.
Published: September 2012

Retreat of the Last Glacial Maximum (LGM) Antarctic ice sheet is thought to have been initiated by changes in ocean heat and eustatic sea level propagated from the Northern Hemisphere (NH) as northern ice sheets melted under rising atmospheric temperatures. The extent to which spatial variability in ice dynamics may have modulated the resultant pattern and timing of decay of the Antarctic ice sheet has so far received little attention, however, despite the growing recognition that dynamic effects account for a sizeable proportion of mass-balance changes observed in modern ice sheets. Here we use a 5-km resolution whole-continent numerical ice-sheet model to assess whether differences in the mechanisms governing ice sheet flow could account for discrepancies between geochronological studies in different parts of the continent. We first simulate the geometry and flow characteristics of an equilibrium LGM ice sheet, using pan-Antarctic terrestrial and marine geological data for constraint, then perturb the system with sea level and ocean heat flux increases to investigate ice-sheet vulnerability. Our results identify that fast-flowing glaciers in the eastern Weddell Sea, the Amundsen Sea, central Ross Sea, and in the Amery Trough respond most rapidly to ocean forcings, in agreement with empirical data. Most significantly, we find that although ocean warming and sea-level rise bring about mainly localized glacier acceleration, concomitant drawdown of ice from neighboring areas leads to widespread thinning of entire glacier catchments—a discovery that has important ramifications for the dynamic changes presently being observed in modern ice sheets.
CD73-generated adenosine facilitatesToxoplasma gondiidifferentiation to long-lived tissue cysts in the central nervous system
Authors: Mahamed Deeqa A. , Mills Jeffrey H. , Egan Charlotte E. , Denkers Eric Y. , Bynoe Margaret S.
Published: September 2012

Toxoplasma gondiiis an obligate intracellular protozoan pathogen that traffics to the central nervous system (CNS) following invasion of its host. In the CNS,T. gondiiundergoes transformation from a rapidly dividing tachyzoite to a long-lived, slow-dividing bradyzoite contained within cysts. The role of extracellular adenosine inT. gondiipathogenesis has not been previously investigated.T. gondiiuses host purines such as adenosine for its energy needs, as it is unable to make its own. Here, we show that CD73−/−mice, which lack the ability to generate extracellular adenosine, are protected fromT. gondiichronic infection, with significantly fewer cysts and reduced susceptibility to reactivation of infection in the CNS independent of host effector function. Parasite dissemination to the brain was unimpaired in CD73−/−hosts, suggesting that the reduced cyst number is due to impaired parasite differentiation in the CNS. Confirming this,T. gondiitachyzoites formed fewer cysts following alkaline pH stress in astrocytes isolated from CD73−/−mice compared with wild type, and in fibroblasts treated with a CD73 inhibitor. Cyst formation was rescued in CD73−/−astrocytes supplemented with adenosine, but not with adenosine receptor agonist 5′-N-ethylcarboxamidoadenosine. Furthermore, mice lacking adenosine receptors had no defect in cyst formation. Based on these findings, we conclude that CD73 expression promotesToxoplasmabradyzoite differentiation and cyst formation by a mechanism dependent on the generation of adenosine, but independent of adenosine receptor signaling. Overall, these findings suggest that modulators of extracellular adenosine may be used to develop therapies aimed at defending against human toxoplasmosis.
Distinct roles of metabotropic glutamate receptor dimerization in agonist activation and G-protein coupling
Authors: El Moustaine Driss , Granier Sébastien , Doumazane Etienne , Scholler Pauline , Rahmeh Rita , Bron Patrick , Mouillac Bernard , Banères Jean-Louis , Rondard Philippe , Pin Jean-Philippe
Published: September 2012

The eight metabotropic glutamate receptors (mGluRs) are key modulators of synaptic transmission and are considered promising targets for the treatment of various brain disorders. Whereas glutamate acts at a large extracellular domain, allosteric modulators have been identified that bind to the seven transmembrane domain (7TM) of these dimeric G-protein-coupled receptors (GPCRs). We show here that the dimeric organization of mGluRs is required for the modulation of active and inactive states of the 7TM by agonists, but is not necessary for G-protein activation. Monomeric mGlu2, either as an isolated 7TM or in full-length, purified and reconstituted into nanodiscs, couples to G proteins upon direct activation by a positive allosteric modulator. However, only a reconstituted full-length dimeric mGlu2 activates G protein upon glutamate binding, suggesting that dimerization is required for glutamate induced activation. These data show that, even for such well characterized GPCR dimers like mGluR2, a single 7TM is sufficient for G-protein coupling. Despite this observation, the necessity of dimeric architecture for signaling induced by the endogenous ligand glutamate confirms that the central core of signaling complex is dimeric.
Altered fear learning across development in both mouse and human
Authors: Pattwell Siobhan S. , Duhoux Stéphanie , Hartley Catherine A. , Johnson David C. , Jing Deqiang , Elliott Mark D. , Ruberry Erika J. , Powers Alisa , Mehta Natasha , Yang Rui R. , Soliman Fatima , Glatt Charles E. , Casey B. J. , Ninan Ipe , Lee Francis S.
Published: September 2012

The only evidence-based behavioral treatment for anxiety and stress-related disorders involves desensitization techniques that rely on principles of extinction learning. However, 40% of patients do not respond to this treatment. Efforts have focused on individual differences in treatment response, but have not examined when, during development, such treatments may be most effective. We examined fear-extinction learning across development in mice and humans. Parallel behavioral studies revealed attenuated extinction learning during adolescence. Probing neural circuitry in mice revealed altered synaptic plasticity of prefrontal cortical regions implicated in suppression of fear responses across development. The results suggest a lack of synaptic plasticity in the prefrontal regions, during adolescence, is associated with blunted regulation of fear extinction. These findings provide insight into optimizing treatment outcomes for when, during development, exposure therapies may be most effective.
Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ
Authors: Mank Nils N. , Berghoff Bork A. , Hermanns Yannick N. , Klug Gabriele
Published: September 2012

The small RNA PcrZ (photosynthesis control RNA Z) of the facultative phototrophic bacterium
Rhodobacter sphaeroides
is induced upon a drop of oxygen tension with similar kinetics to those of genes for components of photosynthetic complexes. High expression of PcrZ depends on PrrA, the response regulator of the PrrB/PrrA two-component system with a central role in redox regulation in
R. sphaeroides
. In addition the FnrL protein, an activator of some photosynthesis genes at low oxygen tension, is involved in redox-dependent expression of this small (s)RNA. Overexpression of full-length PcrZ in
R. sphaeroides
affects expression of a small subset of genes, most of them with a function in photosynthesis. Some mRNAs from the photosynthetic gene cluster were predicted to be putative PcrZ targets and results from an in vivo reporter system support these predictions. Our data reveal a negative effect of PcrZ on expression of its target mRNAs. Thus, PcrZ counteracts the redox-dependent induction of photosynthesis genes, which is mediated by protein regulators. Because PrrA directly activates photosynthesis genes and at the same time PcrZ, which negatively affects photosynthesis gene expression, this is one of the rare cases of an incoherent feed-forward loop including an sRNA. Our data identified PcrZ as a
trans
acting sRNA with a direct regulatory function in formation of photosynthetic complexes and provide a model for the control of photosynthesis gene expression by a regulatory network consisting of proteins and a small noncoding RNA.
Platelet biogenesis and functions require correct protein O-glycosylation
Authors: Wang Yingchun , Jobe Shawn M. , Ding Xiaokun , Choo Hyojung , Archer David R. , Mi Rongjuan , Ju Tongzhong , Cummings Richard D.
Published: September 2012

Platelets express a variety of membrane and secreted glycoproteins, but the importance of glycosylation to platelet functions is poorly understood. To explore the importance of O-glycosylation, we generated mice with a targeted deletion of
Cosmc
in murine endothelial/hematopoietic cells (EHC) (EHC
Cosmc

−/
y

). X-linked
Cosmc
encodes an essential chaperone that regulates protein O-glycosylation. This targeted mutation resulted in lethal perinatal hemorrhage in the majority of mice, and the surviving mice displayed severely prolonged tail-bleeding times and macrothrombocytopenia. EHC
Cosmc

−
/y

platelets exhibited a marked decrease in GPIb-IX-V function and agonist-mediated integrin αIIbβ3 activation, associated with loss of interactions with von Willebrand factor and fibrinogen, respectively. Significantly, three O-glycosylated glycoproteins, GPIbα, αIIb, and GPVI normally on platelet surfaces that play essential roles in platelet functions, were partially proteolyzed in EHC
Cosmc

−
/y

platelets. These results demonstrate that extended O-glycans are required for normal biogenesis of the platelets as well as the expression and functions of their essential glycoproteins, and that variations in O-glycosylation may contribute to altered hemostasis.
Completion of the core β-oxidative pathway of benzoic acid biosynthesis in plants
Authors: Qualley Anthony V. , Widhalm Joshua R. , Adebesin Funmilayo , Kish Christine M. , Dudareva Natalia
Published: September 2012

Despite the importance of benzoic acid (BA) as a precursor for a wide array of primary and secondary metabolites, its biosynthesis in plants has not been fully elucidated. BA formation from phenylalanine requires shortening of the C
3
side chain by two carbon units, which can occur by a non–β-oxidative route and/or a β-oxidative pathway analogous to the catabolism of fatty acids. Enzymes responsible for the first and last reactions of the core BA β-oxidative pathway (cinnamic acid → cinnamoyl-CoA → 3-hydroxy-3-phenylpropanoyl-CoA → 3-oxo-3-phenylpropanoyl-CoA → BA-CoA) have previously been characterized in petunia, a plant with flowers rich in phenylpropanoid/benzenoid volatile compounds. Using a functional genomics approach, we have identified a petunia gene encoding
cinnamoyl-CoA hydratase-dehydrogenase
(
PhCHD
), a bifunctional peroxisomal enzyme responsible for two consecutively occurring unexplored intermediate steps in the core BA β-oxidative pathway.
PhCHD
spatially, developmentally, and temporally coexpresses with known genes in the BA β-oxidative pathway, and correlates with emission of benzenoid volatiles. Kinetic analysis of recombinant PhCHD revealed it most efficiently converts cinnamoyl-CoA to 3-oxo-3-phenylpropanoyl-CoA, thus forming the substrate for the final step in the pathway. Down-regulation of
PhCHD
expression in petunia flowers resulted in reduced CHD enzyme activity, as well as decreased formation of BA-CoA, BA and their derived volatiles. Moreover, transgenic lines accumulated the PhCHD substrate cinnamoyl-CoA and the upstream pathway intermediate cinnamic acid. Discovery of PhCHD completes the elucidation of the core BA β-oxidative route in plants, and together with the previously characterized CoA-ligase and thiolase enzymes, provides evidence that the whole pathway occurs in peroxisomes.
Structural basis for the sheddase function of human meprin β metalloproteinase at the plasma membrane
Authors: Arolas Joan L. , Broder Claudia , Jefferson Tamara , Guevara Tibisay , Sterchi Erwin E. , Bode Wolfram , Stöcker Walter , Becker-Pauly Christoph , Gomis-Rüth F. Xavier
Published: September 2012

Ectodomain shedding at the cell surface is a major mechanism to regulate the extracellular and circulatory concentration or the activities of signaling proteins at the plasma membrane. Human meprin β is a 145-kDa disulfide-linked homodimeric multidomain type-I membrane metallopeptidase that sheds membrane-bound cytokines and growth factors, thereby contributing to inflammatory diseases, angiogenesis, and tumor progression. In addition, it cleaves amyloid precursor protein (APP) at the β-secretase site, giving rise to amyloidogenic peptides. We have solved the X-ray crystal structure of a major fragment of the meprin β ectoprotein, the first of a multidomain oligomeric transmembrane sheddase, and of its zymogen. The meprin β dimer displays a compact shape, whose catalytic domain undergoes major rearrangement upon activation, and reveals an exosite and a sugar-rich channel, both of which possibly engage in substrate binding. A plausible structure-derived working mechanism suggests that substrates such as APP are shed close to the plasma membrane surface following an “N-like” chain trace.
Distinct regions of the
Pseudomonas syringae
coiled-coil effector AvrRps4 are required for activation of immunity
Authors: Sohn Kee Hoon , Hughes Richard K. , Piquerez Sophie J. , Jones Jonathan D. G. , Banfield Mark J.
Published: September 2012

Gram-negative phytopathogenic bacteria translocate effector proteins into plant cells to subvert host defenses. These effectors can be recognized by plant nucleotide-binding–leucine-rich repeat immune receptors, triggering defense responses that restrict pathogen growth. AvrRps4, an effector protein from
Pseudomonas syringae
pv.
pisi
, triggers
RPS4
-dependent immunity in resistant accessions of
Arabidopsis
. To better understand the molecular basis of AvrRps4-triggered immunity, we determined the crystal structure of processed AvrRps4 (AvrRps4
C
, residues 134–221), revealing that it forms an antiparallel α-helical coiled coil. Structure-informed mutagenesis reveals an electronegative surface patch in AvrRps4
C
required for recognition by RPS4; mutations in this region can also uncouple triggering of the hypersensitive response from disease resistance. This uncoupling may result from a lower level of defense activation, sufficient for avirulence but not for triggering a hypersensitive response. Natural variation in AvrRps4 reveals distinct recognition specificities that involve a surface-exposed residue. Recently, a direct interaction between AvrRps4 and
Enhanced Disease Susceptibility 1
has been implicated in activation of immunity. However, we were unable to detect direct interaction between AvrRps4 and
Enhanced Disease Susceptibility 1
after coexpression in
Nicotiana benthamiana
or in yeast cells. How intracellular plant immune receptors activate defense upon effector perception remains an unsolved problem. The structure of AvrRps4
C
, and identification of functionally important residues for its activation of plant immunity, advances our understanding of these processes in a well-defined model pathosystem.
Hemisphere-scale differences in conifer evolutionary dynamics
Authors: Leslie Andrew B. , Beaulieu Jeremy M. , Rai Hardeep S. , Crane Peter R. , Donoghue Michael J. , Mathews Sarah
Published: September 2012

Fundamental differences in the distribution of oceans and landmasses in the Northern and Southern Hemispheres potentially impact patterns of biological diversity in the two areas. The evolutionary history of conifers provides an opportunity to explore these dynamics, because the majority of extant conifer species belong to lineages that have been broadly confined to the Northern or Southern Hemisphere during the Cenozoic. Incorporating genetic information with a critical review of fossil evidence, we developed an age-calibrated phylogeny sampling ∼80% of living conifer species. Most extant conifer species diverged recently during the Neogene within clades that generally were established during the later Mesozoic, but lineages that diversified mainly in the Southern Hemisphere show a significantly older distribution of divergence ages than their counterparts in the Northern Hemisphere. Our tree topology and divergence times also are best fit by diversification models in which Northern Hemisphere conifer lineages have higher rates of species turnover than Southern Hemisphere lineages. The abundance of recent divergences in northern clades may reflect complex patterns of migration and range shifts during climatic cycles over the later Neogene leading to elevated rates of speciation and extinction, whereas the scattered persistence of mild, wetter habitats in the Southern Hemisphere may have favored the survival of older lineages.
Crystal Structures ofPhyscomitrella patensAOC1 and AOC2: Insights into the Enzyme Mechanism and Differences in Substrate Specificity
Authors: Neumann Piotr , Brodhun Florian , Sauer Kristin , Herrfurth Cornelia , Hamberg Mats , Brinkmann Jens , Scholz Julia , Dickmanns Achim , Feussner Ivo , Ficner Ralf
Published: September 2012

In plants, oxylipins regulate developmental processes and defense responses. The first specific step in the biosynthesis of the cyclopentanone class of oxylipins is catalyzed by allene oxide cyclase (AOC) that forms cis(+)-12-oxo-phytodienoic acid. The moss Physcomitrella patens has two AOCs (PpAOC1 and PpAOC2) with different substrate specificities for C18- and C20-derived substrates, respectively. To better understand AOC’s catalytic mechanism and to elucidate the structural properties that explain the differences in substrate specificity, we solved and analyzed the crystal structures of 36 monomers of both apo and ligand complexes of PpAOC1 and PpAOC2. From these data, we propose the following intermediates in AOC catalysis: (1) a resting state of the apo enzyme with a closed conformation, (2) a first shallow binding mode, followed by (3) a tight binding of the substrate accompanied by conformational changes in the binding pocket, and (4) initiation of the catalytic cycle by opening of the epoxide ring. As expected, the substrate dihydro analog cis-12,13S-epoxy-9Z,15Z-octadecadienoic acid did not cyclize in the presence of PpAOC1; however, when bound to the enzyme, it underwent isomerization into the corresponding trans-epoxide. By comparing complex structures of the C18 substrate analog with in silico modeling of the C20 substrate analog bound to the enzyme allowed us to identify three major molecular determinants responsible for the different substrate specificities (i.e. larger active site diameter, an elongated cavity of PpAOC2, and two nonidentical residues at the entrance of the active site).
Evaluation of the convective heat transfer coefficient for minimum quantity lubrication (MQL)
Authors: Kurgin Sheri , Dasch Jean M. , Simon Daniel L. , Barber Gary C. , Zou Qian
Published: September 2012

Purpose

The purpose of this paper is to evaluate the cooling ability of minimum quantity lubrication (MQL) cutting fluid.

Design/methodology/approach

An experimental system is devised to find the heat transfer coefficient of MQL under simulated reaming conditions. Cooling rate of the specimen is measured with an infrared camera. The effect of air pressure and oil volume on cooling rate is tested. Metal cutting tests are performed to evaluate the effect of heat transfer coefficient on workpiece temperature.

Findings

Convective heat transfer coefficient for MQL increases with increasing air pressure. Oil volume has an indeterminate effect on the heat transfer coefficient; however, it is a dominant factor for controlling temperature during reaming.

Practical implications

The results of the study can provide guidance to optimize the temperature controlling ability of MQL for production.

Originality/value

There is limited information available in literature regarding the heat transfer coefficient of metal working fluids, particularly for MQL. In particular, experiments designed to investigate the effect of air pressure and oil volume on the heat transfer coefficient of the mist have not been previously documented. This information may be used to improve the overall cooling ability of MQL mist, thus increasing its effectiveness at controlling tool wear and maintaining part quality. The other major contribution of this work is to separate the role of the cooling and lubrication for controlling temperature while reaming aluminum. Prior to this study, there has been relatively little research performed for the reaming metal cutting operation, and still less for reaming with MQL. The nature of how metal working fluids control temperature is not fully understood, and this work provides insight as to whether cooling or lubrication plays the dominant role for reaming.
Coaching: an effective practice for business competitiveness
Authors: Dolores Vidal‐Salazar María , Ferrón‐Vílchez Vera , Cordón‐Pozo Eulogio
Published: September 2012

Purpose

The purpose of this paper is to analyze the effectiveness of one of the more widespread techniques for personnel development and training: coaching. This technique in the business context entails boosting of a manager's capabilities so as to improve business results through a combination of experience, knowledge, support and the motivation provided by advisers who specialize in business management.

Design/methodology/approach

To analyze the effectiveness of this innovative technique, the authors examined a sample of 40 small companies located in Ceuta (an autonomous Spanish city in North Africa) using a Wilcoxon‐Mann‐Whitney test. Participants were divided into two groups; in one group, an individualized audit process was conducted to obtain an actual picture of managerial practices (focusing on needs and corrective measures). In the other group, an advising process also complemented a coaching phase that was implemented to facilitate employee adoption of the proposed measures. Ultimately, differences between these two groups were found.

Findings

Results indicate that coaching substantially increases the level to which processes of improvement are established within organizations, consequently increasing the competitive capability.

Practical implications

The findings highlight the potential benefits of the use of coaching in the business context. Coaching facilitates the implementation of a set of improvement measures designed to increase business competitiveness, suggesting that this type of advising stands to be very beneficial for companies.

Originality/value

Practices that lead to the development of human capital in organizations are basic tools for managers that are becoming increasingly essential for achieving business efficiency and strategic change. The paper analyzes the implementation of coaching in the business arena, specifically in the case of managers, which is a novelty given the dearth of empirical research on coaching. Thus, the results of the paper provide the wider academic community with empirical evidence on how coaching is a profitable practice for improving human resource management.
Views of HR specialists on formal mentoring: current situation and prospects for the future
Authors: Laiho Maarit , Brandt Tiina
Published: September 2012

Purpose

The article aims to report the findings of quantitative and qualitative analysis of the benefits, drawbacks and future prospects of formal mentoring in medium‐sized and large organisations.

Design/methodology/approach

The empirical data for the study were collected via an online survey, and consist of responses from 152 human resource specialists from companies and public sector organisations in Finland.

Findings

The results reflect the organisations' current situation, and the issues that are important to the HR function. Mentoring is primarily used to transfer tacit knowledge from those near retirement to younger colleagues, foster the personnel development and create well‐being at work. Career advancement and work performance are not as important as might have been thought. The results suggest that mentoring will be more widely used in the future. Among the future potential deliverables of mentoring are strengthening competence management, creating well‐being and enhancing an organisation's image. Young people, in particular, may demand the use of social media alongside mentoring. This could also facilitate mentoring in multicultural organisations.

Practical implications

HR functions intending to make greater use of mentoring in future will require more focus and resources to do so. For example, almost one in five of the respondents saw a lack of information as a barrier to establishing mentoring.

Originality/value

This paper focuses on how organisations view mentoring, which has not been extensively examined previously.
Investigation and prosecution of money laundering cases in Malaysia
Authors: Muhammaddun Mohamed Zakiah , Ahmad Khalijah
Published: September 2012

Purpose

The purpose of this paper is to examine money laundering cases investigated by the Central Bank of Malaysia under the Anti‐Money Laundering and Anti‐Terrorism Financing Act 2001.

Design/methodology/approach

This study analyzes the contents of public releases by the enforcement division of the Central Bank for period 2007 to 2011. Analysis of data is carried out based on three categories: the predicate offence, the perpetrators and current status of the cases.

Findings

Findings reveal that most cases investigated by the Central Bank relate to sec 4(1) of AMLATFA 2001 and the main predicate offence related to the money laundering charges are on illegal deposit taking. Further it is found that directors of companies are the leading group of people charged under the Act for money laundering. In addition, findings also show that only half of the cases investigated have been charged in court.

Research limitations/implications

Data from this research only come from enforcement releases from the Central Bank of Malaysia. Since AMLATFA2001 is administered by multiple agencies, the research may not provide a comprehensive view of all the cases investigated. Future research should look at other agencies and in particular the Royal Police of Malaysia.

Practical implications

Findings from the study suggest that prosecuting money laundering cases by Bank Negara Malaysia are limited to cases with predicate offence of illegal deposit taking. The agency should explore other predicate offences and the concept of “irresistible inference” to increase its effort in prosecuting money laundering activities in the country.

Originality/value

The paper documents and analyzes the actual cases being investigated for money laundering offences. It provides basis for the standard setters to evaluate their effort to curb money laundering activities in Malaysia.
The Portuguese online wine buying consumer
Authors: Freitas Santos José , Cadima Ribeiro José
Published: September 2012

Purpose

This purpose of this paper is to investigate the main characteristics, buying habits, motivations, influences, and overall satisfaction of Portuguese online consumers of wine, as well as to assess whether this market segment can be considered a niche.

Design/methodology/approach

A survey was conducted in a Portuguese online wine shop during the last three months of 2009. The questionnaire included questions about the consumers’ socio‐demographic characteristics, motivations, buying habits and factors influencing online buying behaviour. The questionnaires were delivered by e‐mail to regular and new customers when a transaction was processed online. Of the 82 questionnaires received, 74 were sufficiently complete to be used in the study.

Findings

The online wine market can be considered a niche in Portugal. As the authors’ empirical work shows, this segment is mainly composed of young, male, well‐educated, high‐income consumers who buy wine online from home often less than once a month. They are motivated by convenience, a wider selection of wines, availability, and price. As decision factors, they value the origin/brand of the wine, the price, the recommendation of the online shop, and their own experience. A comparative analysis with international online wine consumers found differences based on profile and consumer buying behaviour (patterns and influences).

Research limitations/implications

The non‐probabilistic sample contained only data from a Portuguese online wine store. Thus, future studies should examine other online wine stores to determine the level of generalisation of the findings to the entire community of online wine consumers.

Originality/value

To the best of the authors’ knowledge, this is the first research conducted in Portugal to identify the main characteristics, buying habits, motivations, influences, and overall satisfaction of the Portuguese online consumers of wine. The paper provides useful insights into the topic, as well as a basis for future studies.