bluuebunny/crossref_metadata_2025 huggingface dataset:
Accuracy assessment of an integrated profiling technique for operationally deriving profiles of temperature, humidity, and cloud liquid water
Authors: Löhnert Ulrich , van Meijgaard Erik , Baltink Henk Klein , Groß Silke , Boers Reinout
Published: February 2007

An integrated profiling technique (IPT) for the simultaneous retrieval of the atmospheric state parameters temperature, humidity, and liquid water content profiles is assessed. The method combines measurements of a modern, ground‐based profiling station equipped with a microwave profiler, cloud radar, and ceilometer, with the closest operational radiosonde measurement and standard surface‐based meteorological measurements. All are combined within an optimal estimation procedure. The accuracy assessment is carried out in a virtual environment of a regional climate model. The model thermodynamic state is converted into the measurement space via so‐called forward modeling. The IPT is then applied to the simulated measurements to retrieve the desired atmospheric state parameters which can be evaluated with the original model state. It is found that IPT‐derived temperature and humidity profiles can add significant information for the time period between two operational radiosonde ascents, both if the measurements take place at the radiosonde site or if they are spatially apart. The benefits of a profiling station that applies an IPT can be valuable both for the reprocessing of dedicated field campaign data to obtain the best representation of the atmospheric state and for nowcasting and data assimilation applications. Depending on the density of the given operational radiosonde network, a ground‐based profiling station has the potential of either significantly improving the quality of such a network or even substituting a small number of radiosonde stations. A further benefit of a ground‐based profiling station is the retrieval of cloud microphysical properties, where IPT liquid water path retrieval accuracies show values better than 10 g m−2, and liquid water content profiles can be derived with relative accuracies of ∼30%.
[11C]NNC 112 Selectivity for Dopamine D1 and Serotonin 5-HT2A Receptors: A PET Study in Healthy Human Subjects
Authors: Slifstein Mark , Kegeles Lawrence S , Gonzales Robyn , Frankle William G , Xu Xiaoyan , Laruelle Marc , Abi-Dargham Anissa
Published: February 2007

The dopamine D1 receptor antagonist radioligand [11C]NNC 112 has previously been reported to have 100-fold selectivity for the D1 receptor compared with the serotonin 5-HT2A receptor. In this study, we tested the selectivity by scanning seven healthy human research volunteers with [11C]NNC 112 before and after 2mg of the antipsychotic drug risperidone, a dose that putatively blocks all 5-HT2A receptors with negligible effect on D1 receptors. We found that specific binding in cortical regions was reduced by 20% to 30%, whereas the striatum showed no change. Based on the known relative densities of these receptors in humans, our results suggest 5- to 10-fold selectivity of [11C]NNC 112 for D1 versus 5-HT2A as opposed to 100-fold selectivity. These results suggest caution in interpreting data from studies using this tracer to measure cortical D1 receptors as well as the need for more selective radioligands to assess cortical D1 receptors.
Global analytical potential energy surfaces for HO2(X̃A″2) based on high-level ab initio calculations
Authors: Xie Daiqian , Xu Chuanxiu , Ho Tak-San , Rabitz Herschel , Lendvay György , Lin Shi Ying , Guo Hua
Published: February 2007

Two global analytical potential energy surfaces for the HO2(X̃A″2) system have been developed by fitting ∼15000 ab initio points at the icMRCI+Q∕aug-cc-pVQZ level of theory, using the reproducing kernel Hilbert space method. One analytical potential is designed to give a very accurate representation of the low energy range that determines the vibrational spectrum, while the other attempts to provide a fast and uniformly accurate potential function for reaction dynamics. The quality of the fitted potential functions is confirmed by good agreement of the (J=0) HO2 vibrational spectrum and (J=0) quantum reaction probability for the H+O2(ji=0,νi=0) reaction with those obtained using the spline fitted potential. Quasiclassical trajectory calculations carried out on the new potential energy surface provided the reaction probability with a zero impact parameter (b=0), which is in reasonably good agreement with the J=0 quantum results.
Stochastic Moyal product on the Wiener space
Authors: Dito Giuseppe , Léandre Rémi
Published: February 2007

We propose a stochastic extension of deformation quantization on a Hilbert space. The Moyal product is defined in this context on the space of functionals belonging to all of the Sobolev spaces of the Malliavin calculus.
Reactions of CF3CH2I+O(P3): Competing mechanisms of HF elimination
Authors: Stevens Jonathan E. , Davis Lauren W. , Mertes Cynthia D.
Published: February 2007

Ab initio density functional and molecular orbital calculations provide singlet and triplet electronic potential energy surfaces for the reactions of CF3CH2I+O(P3) leading to OI and HF eliminations, reactions which have been the subject of recent experimental studies. A barrier to OI formation occurs on the triplet potential energy surface; there is no reverse barrier to OI formation on the singlet pathway. Findings suggest that two competing pathways may form HF. One is an addition-insertion-elimination process involving insertion of O into the C–I bond. The alternate path involves OI elimination, addition of an O atom to CF3CH2, and subsequent HF elimination. The computed reactant pathways and energetics are discussed in relation to recent experiments.
Role of order and disorder on the electronic performances of oxide semiconductor thin film transistors
Authors: Martins R. , Barquinha P. , Ferreira I. , Pereira L. , Gonçalves G. , Fortunato E.
Published: February 2007

The role of order and disorder on the electronic performances of n-type ionic oxides such as zinc oxide, gallium zinc oxide, and indium zinc oxide used as active (channel) or passive (drain/source) layers in thin film transistors (TFTs) processed at room temperature are discussed, taking as reference the known behavior observed in conventional covalent semiconductors such as silicon. The work performed shows that while in the oxide semiconductors the Fermi level can be pinned up within the conduction band, independent of the state of order, the same does not happen with silicon. Besides, in the oxide semiconductors the carrier mobility is not bandtail limited and so disorder does not affect so strongly the mobility as it happens in covalent semiconductors. The electrical properties of the oxide films (resistivity, carrier concentration, and mobility) are highly dependent on the oxygen vacancies (source of free carriers), which can be controlled by changing the oxygen partial pressure during the deposition process and/or by adding other metal ions to the matrix. In this case, we make the oxide matrix less sensitive to the presence of oxygen, widening the range of oxygen partial pressures that can be used and thus improving the process control of the film resistivity. The results obtained in fully transparent TFT using polycrystalline ZnO or amorphous indium zinc oxide (IZO) as channel layers and highly conductive poly/nanocrystalline ZGO films or amorphous IZO as drain/source layers show that both devices work in the enhancement mode, but the TFT with the highest electronic saturation mobility and on/off ratio 49.9cm2∕Vs and 4.3×108, respectively, are the ones in which the active and passive layers are amorphous. The ZnO TFT whose channel is based on polycrystalline ZnO, the mobility and on/off ratio are, respectively, 26cm2∕Vs and 3×106. This behavior is attributed to the fact that the electronic transport is governed by the s-like metal cation conduction bands, not significantly affected by any type of angular disorder promoted by the 2p O states related to the valence band, or small amounts of incorporated metal impurities that lead to a better control of vacancies and of the TFT off current.
Enhanced hydrogen bonding strength observed in hydrogenated SiC and SiO2∕SiC structures
Authors: Soares G. V. , Baumvol I. J. R. , Radtke C. , Stedile F. C.
Published: February 2007

Thermally induced H incorporation, depth distribution, and loss in SiC and in thermally grown SiO2 films on SiC were investigated using isotopic substitution and nuclear reaction analyses. Hydrogen (deuterium) is found near the SiO2 film surface or close to the SiO2∕SiC interface depending on the oxidation/D2-annealing sequence, being much more strongly bound to SiC-based structures than to their Si counterparts. C compounds near the interface seem to play a significant role on the physicochemical and consequently on the electrical characteristics of the D passivated SiO2∕SiC interface.
Critical analysis of short-term negative bias temperature instability measurements: Explaining the effect of time-zero delay for on-the-fly measurements
Authors: Islam Ahmad Ehteshamul , Kufluoglu Haldun , Varghese Dhanoop , Alam Muhammad Ashraful
Published: February 2007

Recently several groups have used the reaction-diffusion (R-D) model with H2 diffusion in interpreting negative bias temperature Instability (NBTI) degradation. While the classical “H2 R-D” model can interpret long-term NBTI behavior, it is inconsistent with short-term stress data obtained by recently developed ultrafast measurements and widely used on-the-fly measurements. Moreover, experimental data from various techniques are not consistent with each other. Here, the authors show that the H2 R-D model must be generalized to consistently interpret NBTI at all time scales. The generalized model highlights the previously unappreciated role of time-zero delay in reconciling differences among the so-called delay-free on-the-fly measurements.
Energy dependent decay rates of Lennard-Jones clusters for use in nucleation theory
Authors: Barrett Jonathan C.
Published: February 2007

Decay rates of small clusters (containing between 10 and 40 Lennard-Jones atoms) are determined by molecular dynamics simulations. The cluster is defined by the condition that the atoms must lie within a specified distance of their center of mass, and initial isothermal states are generated using a Metropolis Monte Carlo method. Plots of the logarithm of the survival fraction against time are found to be nonlinear, indicating that the decay of constant temperature clusters is non-Markovian and depends on the collision rate with a thermalizing gas. However, when the clusters are banded according to their energies, exponential decay is seen. The energy dependent decay rates from simulations agree to within a factor of 2 with those estimated from equilibrium considerations (using free energies from thermodynamic integration and assuming a Gaussian energy distribution), indicating that clusters defined in this way can be used in Markovian rate equations. During nucleation, the cluster energy distribution is shifted from its equilibrium value, leading to a reduction in the nucleation rate by a temperature dependent factor of 100 or more, in the absence of a thermalizing carrier gas.
Interfacial compound suppression and dielectric properties enhancement of F–N codoped ZrO2 thin films
Authors: Huang A. P. , Chu Paul K.
Published: February 2007

Fluorine and nitrogen codoped ZrO2 is produced on p-type Si (100) wafers by cathodic arc deposition and the interfacial and dielectric characteristics of the thin films are investigated. F–N codoping is found to effectively suppress the interfacial compounds between ZrO2 and silicon and the dielectric properties are also improved. Negligible flatband shift and hysteresis are achieved, implying that the fixed charge centers in the thin films and the interfacial states are obviously reduced. The improvement can be attributed in part to the large electronegativity of F radicals that are chemically more active.
A eukaryotic-type Ser/Thr kinase in
Enterococcus faecalis
mediates antimicrobial resistance and intestinal persistence
Authors: Kristich Christopher J. , Wells Carol L. , Dunny Gary M.
Published: February 2007

Antibiotic-resistant enterococci are major causes of hospital-acquired infections. The emergence of
Enterococcus faecalis
as a significant nosocomial pathogen is a consequence of its inherent resistance to certain antibiotics and of its ability to survive and proliferate in the intestinal tract. Genetic determinants of
E. faecalis
conferring these properties are largely unknown. Here we show that PrkC, a one-component signaling protein containing a eukaryotic-type Ser/Thr kinase domain, modulates inherent antimicrobial resistance and intestinal persistence of
E. faecalis
. An
E. faecalis
mutant lacking PrkC grows at a wild-type rate in the absence of antimicrobial stress but exhibits enhanced sensitivity to cell-envelope-active compounds, including antibiotics that target cell-wall biogenesis and bile detergents. Consistent with its bile sensitivity, the mutant was also impaired at persistence in the intestine of mice. Thus, PrkC regulates key physiological processes in
E. faecalis
associated with its success as a nosocomial pathogen. The predicted domain architecture of PrkC comprises a cytoplasmic kinase domain separated by a transmembrane segment from extracellular domains thought to bind uncross-linked peptidoglycan, suggesting that PrkC is a transmembrane receptor that monitors the integrity of the
E. faecalis
cell wall and mediates adaptive responses to maintain cell-wall integrity. Given its role in modulating traits of
E. faecalis
important for its ability to cause nosocomial infections, we suggest that the one-component signaling protein PrkC represents an attractive target for the development of novel therapies to prevent infections by antibiotic-resistant enterococci.
Apoptotic surge of potassium currents is mediated by p38 phosphorylation of Kv2.1
Authors: Redman Patrick T. , He Kai , Hartnett Karen A. , Jefferson Bahiyya S. , Hu Linda , Rosenberg Paul A. , Levitan Edwin S. , Aizenman Elias
Published: February 2007

Kv2.1, the primary delayed rectifying potassium channel in neurons, is extensively regulated by phosphorylation. Previous reports have described Kv2.1 phosphorylation events affecting channel gating and the impact of this process on cellular excitability. Kv2.1, however, also provides the critical exit route for potassium ions during neuronal apoptosis via p38 MAPK-dependent membrane insertion, resulting in a pronounced enhancement of K+currents. Here, electrophysiological and viability studies using Kv2.1 channel mutants identify a p38 phosphorylation site at Ser-800 (S800) that is required for Kv2.1 membrane insertion, K+current surge, and cell death. In addition, a phospho-specific antibody for S800 detects a p38-dependent increase in Kv2.1 phosphorylation in apoptotic neurons and reveals phosphorylation of S800 in immunopurified channels incubated with active p38. Consequently, phosphorylation of Kv2.1 residue S800 by p38 leads to trafficking and membrane insertion during apoptosis, and remarkably, the absence of S800 phosphorylation is sufficient to prevent completion of the cell death program.
Quantifying DNA–protein binding specificities by using oligonucleotide mass tags and mass spectroscopy
Authors: Zhang Lingang , Kasif Simon , Cantor and Charles R.
Published: February 2007

The ability to determine the relative binding affinity of different transcription-factors (TF) to their DNA binding sites is fundamentally important for a comprehensive understanding of gene regulation. Here we present a general approach for multiplex quantification of DNA-TF binding specificities
in vitro
using oligonucleotide mass tag (OMT) labeling and mass spectroscopic quantification. An OMT is a short nucleic acid sequence with a distinct mass that can be resolved by a mass spectrometer. Each putative binding sequence is labeled with a unique OMT, and PCR amplification of OMTs is performed after removing nonbound DNA. Subsequently, a primer extension reaction is carried out, and the extension products are quantified by MALDI-TOF mass spectroscopy. Using the TF NF-κB P50, we have quantified the binding specificities of up to 15 binding sequences in a single assay. The results from the multiplex assay are consistent with data from the traditional gel shift assay. The approach allows the competitive binding of multiple DNA sequences to the given protein in a homogeneous reaction. By using the commercially available homogeneous MassEXTEND platform (SEQUENOM), it is scalable for high-throughput DNA-TF binding applications, including genome-wide TF binding site mapping and analyses of SNPs in promoter regions.
TGFβ promotes conversion of CD16+peripheral blood NK cells into CD16−NK cells with similarities to decidual NK cells
Authors: Keskin Derin B. , Allan David S. J. , Rybalov Basya , Andzelm Milena M. , Stern Joel N. H. , Kopcow Hernan D. , Koopman Louise A. , Strominger Jack L.
Published: February 2007

During pregnancy the uterine decidua is populated by large numbers of natural killer (NK) cells with a phenotype CD56superbrightCD16−CD9+KIR+distinct from both subsets of peripheral blood NK cells. Culture of highly purified CD16+CD9−peripheral blood NK cells in medium containing TGFβ1 resulted in a transition to CD16−CD9+NK cells resembling decidual NK cells. Decidual stromal cells, when isolated and culturedin vitro, were found to produce TGFβ1. Incubation of peripheral blood NK cells with conditioned medium from decidual stromal cells mirrored the effects of TGFβ1. Similar changes may occur upon NK cell entry into the decidua or other tissues expressing substantial TGFβ. In addition, Lin−CD34+CD45+hematopoietic stem/progenitor cells could be isolated from decidual tissue. These progenitors also produced NK cells when cultured in conditioned medium from decidual stromal cells supplemented with IL-15 and stem cell factor.
Brain protection using autologous bone marrow cell, metalloproteinase inhibitors, and metabolic treatment in cerebral ischemia
Authors: Baker Andrew H. , Sica Vincenzo , Work Lorraine M. , Williams-Ignarro Sharon , de Nigris Filomena , Lerman Lilach O. , Casamassimi Amelia , Lanza Alessandro , Schiano Concetta , Rienzo Monica , Ignarro Louis J. , Napoli Claudio
Published: February 2007

Despite advances in imaging, understanding the underlying pathways, and clinical translation of animal models of disease there remains an urgent need for therapies that reduce brain damage after stroke and promote functional recovery in patients. Blocking oxidant radicals, reducing matrix metalloproteinase-induced neuronal damage, and use of stem cell therapy have been proposed and tested individually in prior studies. Here we provide a comprehensive integrative management approach to reducing damage and promoting recovery by combining biological therapies targeting these areas. In a rat model of transient cerebral ischemia (middle cerebral artery occlusion) gene delivery vectors were used to overexpress tissue inhibitor of matrix metalloproteinase 1 and 2 (TIMP1 and TIMP2) 3 days before ischemia. After occlusion, autologous bone marrow cells alone or in combination with agents to improve NO bioavailability were administered intraarterially. When infarct size, BrdU incorporation, and motor function recovery were determined in the treatment groups the largest beneficial effect was seen in rats receiving the triple combined therapy, surpassing effects of single or double therapies. Our study highlights the utility of combined drug, gene, and cell therapy in the treatment of stroke.
Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in
Arabidopsis
Authors: Chen Ho-Ming , Li Yi-Hang , Wu Shu-Hsing
Published: February 2007

Small RNAs play pivotal roles in regulating gene expression in higher eukaryotes. Among them, trans-acting siRNAs (ta-siRNAs) are a class of small RNAs that regulate plant development. The biogenesis of ta-siRNA depends on microRNA-targeted cleavage followed by the DCL4-mediated production of small RNAs phased in 21-nt increments relative to the cleavage site on both strands. To find
TAS
genes, we have used these characteristics to develop the first computational algorithm that allows for a comprehensive search and statistical evaluation of putative
TAS
genes from any given small RNA database. A search in
Arabidopsis
small RNA massively parallel signature sequencing (MPSS) databases with this algorithm revealed both known and previously unknown ta-siRNA-producing loci. We experimentally validated the biogenesis of ta-siRNAs from two
PPR
genes and the trans-acting activity of one of the ta-siRNAs. The production of ta-siRNAs from the identified
PPR
genes was directed by the cleavage of a
TAS2
-derived ta-siRNA instead of by microRNAs as was reported previously for
TAS1a
, -
b
, -
c
,
TAS2
, and
TAS3
genes. Our results indicate the existence of a small RNA regulatory cascade initiated by miR173-directed cleavage and followed by the consecutive production of ta-siRNAs from two
TAS
genes.
Cortical pooling algorithms for judging global motion direction
Authors: Webb Ben S. , Ledgeway Timothy , McGraw Paul V.
Published: February 2007

Physiological studies suggest that decision networks read from the neural representation in the middle temporal area to determine the perceived direction of visual motion, whereas psychophysical studies tend to characterize motion perception in terms of the statistical properties of stimuli. To reconcile these different approaches, we examined whether estimating the central tendency of the physical direction of global motion was a better indicator of perceived direction than algorithms (e.g., maximum likelihood) that read from directionally tuned mechanisms near the end of the motion pathway. The task of human observers was to discriminate the global direction of random dot kinematograms composed of asymmetrical distributions of local directions with distinct measures of central tendency. None of the statistical measures of image direction central tendency provided consistently accurate predictions of perceived global motion direction. However, regardless of the local composition of motion directions, a maximum-likelihood decoder produced global motion estimates commensurate with the psychophysical data. Our results suggest that mechanism-based, read-out algorithms offer a more accurate and robust guide to human motion perception than any stimulus-based, statistical estimate of central tendency.
RNA-binding proteins that inhibit RNA virus infection
Authors: Zhu Jian , Gopinath Kodetham , Murali Ayaluru , Yi Guanghui , Hayward S. Diane , Zhu Heng , Kao Cheng
Published: February 2007

Arrays of >5,000
Saccharomyces cerevisiae
proteins were screened to identify proteins that can preferentially bind a small RNA hairpin that contains a clamped adenine motif (CAM). A CAM is required for the replication of Brome Mosaic Virus (BMV), a plant-infecting RNA virus that can replicate in
S. cerevisiae
. Several hits were selected for further characterization in
Nicotiana benthamiana
. Pseudouridine Synthase 4 (Pus4) and the Actin Patch Protein 1 (App1) modestly reduced BMV genomic plus-strand RNA accumulation, but dramatically inhibited BMV systemic spread in plants. Pus4 also prevented the encapsidation of a BMV RNA in plants and the reassembly of BMV virions
in vitro
. These results demonstrate the feasibility of using proteome arrays to identify specific RNA-binding proteins for antiviral activities. Furthermore, the effects of Pus4 suggest that the CAM-containing RNA motif provides a regulatory link between RNA replication and encapsidation.
The molecular basis of CO
2
reception in
Drosophila
Authors: Kwon Jae Young , Dahanukar Anupama , Weiss Linnea A. , Carlson John R.
Published: February 2007

CO
2
elicits a response from many insects, including mosquito vectors of diseases such as malaria and yellow fever, but the molecular basis of CO
2
detection is unknown in insects or other higher eukaryotes. Here we show that
Gr21a
and
Gr63a
, members of a large family of
Drosophila
seven-transmembrane-domain chemoreceptor genes, are coexpressed in chemosensory neurons of both the larva and the adult. The two genes confer CO
2
response when coexpressed in an
in vivo
expression system, the “empty neuron system.” The response is highly specific for CO
2
and dependent on CO
2
concentration. The response shows an equivalent dependence on the dose of
Gr21a
and
Gr63a
. None of 39 other chemosensory receptors confers a comparable response to CO
2
. The identification of these receptors may now allow the identification of agents that block or activate them. Such agents could affect the responses of insect pests to the humans they seek.
Matrix-specific p21-activated kinase activation regulates vascular permeability in atherogenesis
Authors: Orr A. Wayne , Stockton Rebecca , Simmers Michael B. , Sanders John M. , Sarembock Ian J. , Blackman Brett R. , Schwartz Martin Alexander
Published: February 2007

Elevated permeability of the endothelium is thought to be crucial in atherogenesis because it allows circulating lipoproteins to access subendothelial monocytes. Both local hemodynamics and cytokines may govern endothelial permeability in atherosclerotic plaque. We recently found that p21-activated kinase (PAK) regulates endothelial permeability. We now report that onset of fluid flow, atherogenic flow profiles, oxidized LDL, and proatherosclerotic cytokines all stimulate PAK phosphorylation and recruitment to cell–cell junctions. Activation of PAK is higher in cells plated on fibronectin (FN) compared to basement membrane proteins in all cases. In vivo, PAK is activated in atherosclerosis-prone regions of arteries and correlates with FN in the subendothelium. Inhibiting PAK in vivo reduces permeability in atherosclerosis-prone regions. Matrix-specific PAK activation therefore mediates elevated vascular permeability in atherogenesis.
DNMT1 but not its interaction with the replication machinery is required for maintenance of DNA methylation in human cells
Authors: Spada Fabio , Haemmer Andrea , Kuch David , Rothbauer Ulrich , Schermelleh Lothar , Kremmer Elisabeth , Carell Thomas , Längst Gernot , Leonhardt Heinrich
Published: February 2007

DNA methylation plays a central role in the epigenetic regulation of gene expression in vertebrates. Genetic and biochemical data indicated that DNA methyltransferase 1 (Dnmt1) is indispensable for the maintenance of DNA methylation patterns in mice, but targeting of the DNMT1 locus in human HCT116 tumor cells had only minor effects on genomic methylation and cell viability. In this study, we identified an alternative splicing in these cells that bypasses the disrupting selective marker and results in a catalytically active DNMT1 protein lacking the proliferating cell nuclear antigen–binding domain required for association with the replication machinery. Using a mechanism-based trapping assay, we show that this truncated DNMT1 protein displays only twofold reduced postreplicative DNA methylation maintenance activity in vivo. RNA interference–mediated knockdown of this truncated DNMT1 results in global genomic hypomethylation and cell death. These results indicate that DNMT1 is essential in mouse and human cells, but direct coupling of the replication of genetic and epigenetic information is not strictly required.
Regulation of protrusion, adhesion dynamics, and polarity by myosins IIA and IIB in migrating cells
Authors: Vicente-Manzanares Miguel , Zareno Jessica , Whitmore Leanna , Choi Colin K. , Horwitz Alan F.
Published: February 2007

We have used isoform-specific RNA interference knockdowns to investigate the roles of myosin IIA (MIIA) and MIIB in the component processes that drive cell migration. Both isoforms reside outside of protrusions and act at a distance to regulate cell protrusion, signaling, and maturation of nascent adhesions. MIIA also controls the dynamics and size of adhesions in central regions of the cell and contributes to retraction and adhesion disassembly at the rear. In contrast, MIIB establishes front–back polarity and centrosome, Golgi, and nuclear orientation. Using ATPase- and contraction-deficient mutants of both MIIA and MIIB, we show a role for MIIB-dependent actin cross-linking in establishing front–back polarity. From these studies, MII emerges as a master regulator and integrator of cell migration. It mediates each of the major component processes that drive migration, e.g., polarization, protrusion, adhesion assembly and turnover, polarity, signaling, and tail retraction, and it integrates spatially separated processes.
MTP regulated by an alternate promoter is essential for NKT cell development
Authors: Dougan Stephanie K. , Rava Paul , Hussain M. Mahmood , Blumberg Richard S.
Published: February 2007

Microsomal triglyceride transfer protein (MTP), an endoplasmic reticulum lipid transfer protein critical for apolipoprotein B (apoB) secretion, regulates CD1d antigen presentation. We identified MTP variant 1 (MTPv1), a novel splice variant of mouse MTP, by polymerase chain reaction and Northern analysis in non–apoB-secreting tissues, including thymocytes and antigen-presenting cells (APCs). Edman degradation of MTPv1 isolated from transfected cells revealed three unique residues; however, recombinant MTP and MTPv1 had an equivalent protein disulfide isomerase association, subcellular localization, triglyceride transfer, phospholipid transfer, response to inhibitors, and ability to support apoB secretion. MTP and MTPv1 efficiently transferred phosphatidylethanolamine to CD1d in vitro. NKT cells fail to develop in fetal thymic organ culture (FTOC) treated with MTP antagonists. MTP-inhibited FTOCs produced negligible numbers of CD1d tetramer–positive cells and exhibited marked defects in IL-4 production upon stimulation with anti-CD3 or α-galactosylceramide–pulsed APCs. CD1d expression on CD4+CD8+ FTOC cells was unaffected by MTP inhibition. Thus, our results demonstrate that MTPv1 in thymocytes is critical to NKT cell development. We hypothesize that, when MTP is inactive, CD1d traffics to the cell surface and presents no lipid or a lipid that is incapable of mediating NKT cell selection and/or is refractory to lysosomal editing.
Influence of translation efficiency of homologous viral proteins on the endogenous presentation of CD8+ T cell epitopes
Authors: Tellam Judy , Fogg Mark H. , Rist Michael , Connolly Geoff , Tscharke David , Webb Natasha , Heslop Lea , Wang Fred , Khanna Rajiv
Published: February 2007

A significant proportion of endogenously processed CD8+ T cell epitopes are derived from newly synthesized proteins and rapidly degrading polypeptides (RDPs). It has been hypothesized that the generation of rapidly degrading polypeptides and CD8+ T cell epitopes from these RDP precursors may be influenced by the efficiency of protein translation. Here we address this hypothesis by using the Epstein-Barr virus–encoded nuclear antigen 1 protein (EBNA1), with or without its internal glycine-alanine repeat sequence (EBNA1 and EBNA1ΔGA, respectively), which display distinct differences in translation efficiency. We demonstrate that RDPs constitute a significant proportion of newly synthesized EBNA1 and EBNA1ΔGA and that the levels of RDPs produced by each of these proteins directly correlate with the translation efficiency of either EBNA1 or EBNA1ΔGA. As a consequence, a higher number of major histocompatibility complex–peptide complexes can be detected on the surface of cells expressing EBNA1ΔGA, and these cells are more efficiently recognized by virus-specific cytotoxic T lymphocytes compared to the full-length EBNA1. More importantly, we also demonstrate that the endogenous processing of these CD8+ T cell epitopes is predominantly determined by the rate at which the RDPs are generated rather than the intracellular turnover of these proteins.
A general conformal geometric reflection principle
Authors: Roth Oliver
Published: February 2007

We prove a generalization of the Schwarz–Carathéodory reflec- tion principle for analytic maps

f
f

from the unit disk into arbitrary Riemann surfaces equipped with a complete real analytic conformal Riemannian metric

λ
(
w
)

|

d
w

|

\lambda (w) \, |dw|

. This yields a necessary and sufficient condition for

f
f

to have an analytic continuation in terms of the pullback of the metric

λ
(
w
)

|

d
w

|

\lambda (w) \, |dw|

under the map

f
f

.
Sharp Sobolev inequalities in the presence of a twist
Authors: Collion Stephane , Hebey Emmanuel , Vaugon Michel
Published: February 2007

Let

(
M
,
g
)

(M,g)

be a smooth compact Riemannian manifold of dimension

n
≥
3

n \ge 3

. Let also

A
A

be a smooth symmetrical positive

(
0
,
2
)

(0,2)

-tensor field in

M
M

. By the Sobolev embedding theorem, we can write that there exist

K
,
B
>
0

K,B>0

such that for any

u
∈

H
1
2

(
M
)

u \in H_1^2(M)

,
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="left-parenthesis integral Underscript upper M Endscripts StartAbsoluteValue u EndAbsoluteValue Superscript 2 Super Superscript star Superscript Baseline d v Subscript g Baseline right-parenthesis Superscript 2 slash 2 Super Superscript star Baseline less-than-or-equal-to upper K integral Underscript upper M Endscripts upper A Subscript x Baseline left-parenthesis nabla u comma nabla u right-parenthesis d v Subscript g Baseline plus upper B integral Underscript upper M Endscripts u squared d v Subscript g Baseline">

(

∫
M

|
u

|

2
⋆

d

v
g

)

2

/

2
⋆

≤
K

∫
M

A
x

(
∇
u
,
∇
u
)
d

v
g

+
B

∫
M

u
2

d

v
g

\left (\int _M\vert u\vert ^{2^\star }dv_g\right )^{2/2^\star }\le K \int _MA_x(\nabla u, \nabla u)dv_g + B\int _Mu^2dv_g

\]
where

H
1
2

(
M
)

H_1^2(M)

is the standard Sobolev space of functions in

L
2

L^2

with one derivative in

L
2

L^2

. We investigate in this paper the value of the sharp

K
K

in the equation above, the validity of the corresponding sharp inequality, and the existence of extremal functions for the saturated version of the sharp inequality.
Coarse classification of constant mean curvature cylinders
Authors: Dorfmeister J. , Kobayashi S.-P.
Published: February 2007

We give a coarse classification of constant mean curvature (CMC) immersions of cylinders into

R

3

\mathbb {R}^3

via the loop group method. Particularly for this purpose, we consider double loop groups and a new type of “potentials” which are meromorphic 1-forms on Riemann surfaces.
The combinatorics of twisted involutions in Coxeter groups
Authors: Hultman Axel
Published: February 2007

The open intervals in the Bruhat order on twisted involutions in a Coxeter group are shown to be PL spheres. This implies results conjectured by F. Incitti and sharpens the known fact that these posets are Gorenstein

∗

^*

over

Z

2

\mathbb {Z}_2

. We also introduce a Boolean cell complex which is an analogue for twisted involutions of the Coxeter complex. Several classical Coxeter complex properties are shared by our complex. When the group is finite, it is a shellable sphere, shelling orders being given by the linear extensions of the weak order on twisted involutions. Furthermore, the

h
h

-polynomial of the complex coincides with the polynomial counting twisted involutions by descents. In particular, this gives a type-independent proof that the latter is symmetric.
Invariant curves for birational surface maps
Authors: Diller Jeffrey , Jackson Daniel , Sommese Andrew
Published: February 2007

We classify invariant curves for birational surface maps that are expanding on cohomology. When the expansion is exponential, the arithmetic genus of an invariant curve is at most one. This implies severe constraints on both the type and number of irreducible components of the curve. In the case of an invariant curve with genus equal to one, we show that there is an associated invariant meromorphic two-form.
Linear relations in the Calkin algebra for composition operators
Authors: Kriete Thomas , Moorhouse Jennifer
Published: February 2007

We consider this and related questions: When is a finite linear combination of composition operators, acting on the Hardy space or the standard weighted Bergman spaces on the unit disk, a compact operator?
Homologous non-isotopic symplectic surfaces of higher genus
Authors: Park B. , Poddar Mainak , Vidussi Stefano
Published: February 2007

We construct an infinite family of homologous, non-isotopic, symplectic surfaces of any genus greater than one in a certain class of closed, simply connected, symplectic four-manifolds. Our construction is the first example of this phenomenon for surfaces of genus greater than one.
Harnack inequality for non-divergence form operators on stratified groups
Authors: Bonfiglioli Andrea , Uguzzoni Francesco
Published: February 2007

We prove lower bounds for the fundamental solutions of the non-divergence form operators\[<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="sigma-summation Underscript i comma j Endscripts a Subscript i comma j Baseline left-parenthesis x comma t right-parenthesis upper X Subscript i Baseline upper X Subscript j Baseline minus partial-differential Subscript t Baseline and sigma-summation Underscript i comma j Endscripts a Subscript i comma j Baseline left-parenthesis x right-parenthesis upper X Subscript i Baseline upper X Subscript j Baseline comma">∑i,jai,j(x,t)XiXj−∂tand∑i,jai,j(x)XiXj,{\textstyle \sum _{i,j}} a_{i,j}(x,t)\,X_iX_j-\partial _t \quad \text {and}\quad {\textstyle \sum _{i,j}}a_{i,j}(x)\,X_iX_j,\]where theXiX_i’s are Hörmander vector fields generating a stratified groupG\mathbb {G}and(ai,j)i,j(a_{i,j})_{i,j}is a positive-definite matrix with Hölder continuous entries. We then prove an invariant Harnack inequality for such operators. As a byproduct we also study some relevant properties of the Green functions on bounded domains.
The real cohomology of virtually nilpotent groups
Authors: Dekimpe Karel , Pouseele Hannes
Published: February 2007

In this paper we present a method to compute the real cohomology of any finitely generated virtually nilpotent group. The main ingredient in our setup consists of a polynomial crystallographic action of this group. As any finitely generated virtually nilpotent group admits such an action (which can be constructed quite easily), the approach we present applies to all these groups. Our main result is an algorithmic way of computing these cohomology spaces. As a first application, we prove a kind of Poincaré duality (also in the nontorsion free case) and we derive explicit formulas in the virtually abelian case.
Literature review: decision‐making regarding slow resuscitation
Authors: Kelly Jacinta
Published: February 2007

Aims and objectives.  Applying ethical principles as a framework, a review of the literature will be presented regarding the decision‐making process of slow codes.

Background.  Slow codes are cardiopulmonary resuscitative efforts intentionally conducted too slowly for resuscitation to occur. While some authors argue that a slow code is a non‐maleficent and beneficent act towards the hopelessly ill patient, others believe that this practice is harmful and deceptive, that it disregards patient and surrogate autonomy and deprives the patient of a peaceful death.

Method.  Literature review.

Results.  Decision‐making surrounding cardiopulmonary resuscitation receives considerable attention in the literature. However, data relating to the decision‐making process in slow codes is sparse. One ethnographic study described the practice of slow codes as doing good and preventing harm to the patient.

Conclusions.  It was evident from the literature review that slow codes, even in the most limited form, are invasive and undignified and that they prolong death and suffering. Further research is needed to examine why slow codes happen despite the availability of a do‐not‐resuscitate order.

Relevance to clinical practice.  Decision‐making regarding cardiopulmonary resuscitation is increasingly problematic in Ireland. The literature review suggests that clinical guidelines regarding decision‐making and cardiopulmonary resuscitation should be introduced to reduce the likelihood of slow codes occurring, but also that nurses and doctors endeavour to communicate more effectively with patients and family.
Cryptococcosis in liver and kidney transplant recipients receiving anti‐thymocyte globulin or alemtuzumab
Authors: Silveira F.P. , Husain S. , Kwak E.J. , Linden P.K. , Marcos A. , Shapiro R. , Fontes P. , Marsh J.W. , De Vera M. , Tom K. , Thai N. , Tan H.P. , Basu A. , Soltys K. , Paterson D.L.
Published: February 2007

Abstract:Rabbit anti‐thymocyte globulin (ATG) and alemtuzumab have been used for induction or preconditioning and for the treatment of acute rejection in organ transplant recipients in many centers. Such regimens may lead to a substantial decline in the CD4 lymphocyte count to levels seen in other population groups at high risk of cryptococcosis. In view of this, we examined the impact of such therapy on the cumulative incidence of cryptococcosis among liver and kidney recipients. A total of 834 liver and 727 kidney transplants were performed during the study period. Seven hundred and eighty‐one patients did not receive ATG or alemtuzumab; 646 received 1 dose of either drug, and 134 patients received 2 doses of either drug. The cumulative incidence of cryptococcosis was 0.26% (2/781) among those who did not receive ATG or alemtuzumab; 0.3% (2/646) among those who received only 1 dose, and 2.24% (3/134) among those who received 2 doses (P=0.03). There were 5 cases of cryptococcosis in liver recipients and 2 in kidney recipients. There were 3 cases of cryptococcal meningitis, 3 of pneumonia, and 1 of disseminated disease. The 2 kidney recipients had meningitis. Diagnosis occurred at a median of 255 days (range 7–517) after transplantation. The mortality rate was 14.2%. We conclude that the use of 1 dose of ATG or alemtuzumab is not associated with an increased cumulative incidence of cryptococcosis, but that those patients receiving 2 doses are at increased risk.
Mapping major genes and quantitative trait loci controlling agronomic traits in almond
Authors: Sánchez‐Pérez R. , Howad W. , Dicenta F. , Arús P. , Martínez‐Gómez P.
Published: February 2007

Six tree traits (self‐compatibility, blooming date, blooming density, productivity, leafing date and ripening time) and five pomological traits (kernel taste, in‐shell weight, shell hardness, kernel weight and double kernel) were studied in an F1 almond progeny of 167 seedlings from the cross between the French cultivar ‘R1000’ and the Spanish cultivar ‘Desmayo Largueta’. In addition, a set of 135 codominant microsatellites or simple‐sequence repeat (SSR) markers developed from peach, cherry and almond were used for the molecular characterization of the progeny. A genetic linkage map was constructed with 56 of these SSRs. Cosegregation analysis allowed the identification of the map positions of two major genes to be confirmed for kernel taste (Sk) in linkage group five (G5) and for self‐incompatibility (S) in G6. QTLs mapped include two for leafing date (Lf‐Q1 and Lf‐Q2) in G1 and G4, one for shell hardness (D‐Q) in G2, one each for double kernel (Dk‐Q) and productivity (P‐Q) in G4, one for blooming date (Lb‐Q) in G4, two for kernel weight (Kw‐Q1 and Kw‐Q2) in G1 and G4, and two for in‐shell weight (Shw‐Q1 and Shw‐Q2) in G1 and G2. Four SSR loci (BPPCT011, UDP96‐013, UDP96‐003 and PceGA025) were linked to the important agronomic traits of leafing date, shell hardness, blooming date and kernel taste. Finally, the development of efficient marker‐assisted selection strategies applied to almond and other Prunus breeding programmes was also discussed.
Genetic variation for sinapate ester content in winter rapeseed (Brassica napus L.) and development of NIRS calibration equations
Authors: Zum Felde T. , Baumert A. , Strack D. , Becker H. C. , Möllers C.
Published: February 2007

Increasing the meal and protein quality of winter rapeseed (Brassica napus L.) for food and feed purposes is gaining importance in rapeseed breeding programmes. Rapeseed meal has a high content of phenolic acid esters, mainly sinapate esters, which have been shown to cause a dark colour and a bitter taste in rapeseed meal and derived protein products. The aim of the present study was to analyse the genetic variation for individual and total sinapate ester content, to develop Near Infrared Reflectance Spectroscopic (NIRS) calibrations, and to identify genotypes with a low sinapate ester content after testing in the field. The following sinapate esters were analysed by HPLC: sinapoylcholine (sinapine), sinapoylglucose, and a minor group of ‘other sinapate esters’ which includes free sinapate. A genotypically diverse set of seed samples of winter oilseed rape (old and new cultivars, breeding lines, resynthesized rapeseed) from different years and locations was collected, their NIRS spectra recorded and the samples were further analysed by HPLC. The complete NIRS calibration seed sample set (n = 575) showed a large variation in total sinapate ester content, ranging from 3.2 to 12.7 mg sinapate equivalents per g seeds. The NIRS calibration equations showed high fractions of explained variances in cross validation () ranging from 0.75 (other sinapate esters) to 0.85 (sinapoylglucose). The standard errors of cross validation (SECV) ranged from 0.38 (other sinapate esters) to 0.70 mg/g seed (total sinapate esters). In validation and in independent validations the predicted results were not always acceptable, indicating that the NIRS calibrations need to be extended by analysing samples from new populations. Following replicated field experiments, a doubled haploid line obtained from the old Dutch cultivar Mansholts’ Hamburger Raps, and related DH lines from the cross DH Mansholts’ × Express were confirmed to have a 30–40% lower sinapate ester content compared to check cultivars.
Development of early‐flowering Kabuli chickpea with compound and simple leaves
Authors: Bonfil D. J. , Goren O. , Mufradi I. , Lichtenzveig J. , Abbo S.
Published: February 2007

Terminal drought is a major constraint to chickpea (Cicer arietinum L.) production. Autumn sowing and early flowering have been suggested as ways to benefit from the winter rains in short rainy seasons under dryland cropping. High‐yielding, late‐flowering, simple‐leafed (slv/slv) chickpea cultivars with good field resistance to Ascochyta blight have been bred recently. Changing plant architecture, by altering leaf shape, may affect agronomic performance. As no information is available on the effect of leaf shape on phenology and seed yield, this study was aimed at: (i) introducing the simple leaf trait into an early‐flowering chickpea background; (ii) comparing the grain yield of the two leaf types in early vs. late flowering backgrounds and (iii) producing breeding lines combining early flowering, large seeds and Ascochyta tolerance with both leaf types. Hybrid progeny were studied from the cross of ‘Sanford’ (slv/slv) and ICC7344, (compound, SLV/SLV). Four early‐podding, F8 breeding lines were selected with either simple or compound leaves. In three different field experiments under dryland conditions (334–379 mm), they yielded ca. 1.4 t/ha as compared with 1.0 t/ha in the standard Israeli ‘Yarden’ on one site, but no significant differences in yield were obtained in the other two experiments.