bluuebunny/crossref_metadata_2025 huggingface dataset:
The K
v
channel blocker 4-aminopyridine enhances Ag
+
uptake: A scanning electrochemical microscopy study of single living cells
Authors: Zhan Dongping , Fan Fu-Ren F. , Bard Allen. J.
Published: August 2008

We report that silver ion (Ag
+
) uptake is enhanced by 4-aminopyridine (4-AP), a well known voltage-sensitive potassium ion channel (K
v
) blocker. Both bacterial (
Escherichia coli
) and mammalian (3T3 fibroblast) cells were used as model systems. Ag
+
uptake was monitored with a scanning electrochemical microscope with an amperometric Ag
+
ion-selective electrode (Ag
+
-ISE) and the respiration rates of
E. coli
cells were measured by oxygen reduction at an ultramicroelectrode. The results showed that not only the amount but also the rate of silver uptake by the cells increased significantly when 4-AP was added to the solution. For fibroblasts, the Ag
+
uptake rate was 4.8 × 10
7
ions per cell per sec without 4-AP compared with 1.0 × 10
8
ions per cell per sec with 0.2 mM 4-AP. For
E. coli
cells, the uptake rate was 1.5 × 10
4
ions per cell per sec without 4-AP vs. 3.5 × 10
4
ions per cell per sec with 0.5 mM 4-AP and 5.9 × 10
4
ions per cell per sec with 1 mM 4-AP. Thus, 4-AP might be useful where silver is used as antimicrobial agent to speed its uptake.
Transcriptional profiling of endogenous germ layer precursor cells identifies
dusp4
as an essential gene in zebrafish endoderm specification
Authors: Brown Jamie L. , Snir Mirit , Noushmehr Houtan , Kirby Martha , Hong Sung-Kook , Elkahloun Abdel G. , Feldman Benjamin
Published: August 2008

A major goal for developmental biologists is to define the behaviors and molecular contents of differentiating cells. We have devised a strategy for isolating cells from diverse embryonic regions and stages in the zebrafish, using computer-guided laser photoconversion of injected Kaede protein and flow cytometry. This strategy enabled us to perform a genome-wide transcriptome comparison of germ layer precursor cells. Mesendoderm and ectoderm precursors cells isolated by this method differentiated appropriately in transplantation assays. Microarray analysis of these cells reidentified known genes at least as efficiently as previously reported strategies that relied on artificial mesendoderm activation or inhibition. We also identified a large set of uncharacterized mesendoderm-enriched genes as well as ectoderm-enriched genes. Loss-of-function studies revealed that one of these genes, the MAP kinase inhibitor
dusp4
, is essential for early development. Embryos injected with antisense morpholino oligonucleotides that targeted Dusp4 displayed necrosis of head tissues. Marker analysis during late gastrulation revealed a specific loss of
sox17
, but not of other endoderm markers, and analysis at later stages revealed a loss of foregut and pancreatic endoderm. This specific loss of
sox17
establishes a new class of endoderm specification defect.
Transmembrane domain length of viral K
+
channels is a signal for mitochondria targeting
Authors: Balss Jörg , Papatheodorou Panagiotis , Mehmel Mario , Baumeister Dirk , Hertel Brigitte , Delaroque Nicolas , Chatelain Franck C. , Minor Daniel L. , Van Etten James L. , Rassow Joachim , Moroni Anna , Thiel Gerhard
Published: August 2008

K
+
channels operate in the plasma membrane and in membranes of organelles including mitochondria. The mechanisms and topogenic information for their differential synthesis and targeting is unknown. This article describes 2 similar viral K
+
channels that are differentially sorted; one protein (Kesv) is imported by the Tom complex into the mitochondria, the other (Kcv) to the plasma membrane. By creating chimeras we discovered that mitochondrial sorting of Kesv depends on a hierarchical combination of N- and C-terminal signals. Crucial is the length of the second transmembrane domain; extending its C terminus by ≥2 hydrophobic amino acids redirects Kesv from the mitochondrial to the plasma membrane. Activity of Kesv in the plasma membrane is detected electrically or by yeast rescue assays only after this shift in sorting. Hence only minor structural alterations in a transmembrane domain are sufficient to switch sorting of a K
+
channel between the plasma membrane and mitochondria.
Stress resistance and signal fidelity independent of nuclear MAPK function
Authors: Westfall Patrick J. , Patterson Jesse C. , Chen Raymond E. , Thorner Jeremy
Published: August 2008

Elevated external solute stimulates a conserved MAPK cascade that elicits responses that maintain osmotic balance. The yeast high-osmolarity glycerol (HOG) pathway activates Hog1 MAPK (mammalian ortholog p38α/SAPKα), which enters the nucleus and induces expression of >50 genes, implying that transcriptional up-regulation is necessary to cope with hyperosmotic stress. Contrary to this expectation, we show here that cells lacking the karyopherin required for Hog1 nuclear import or in which Hog1 is anchored at the plasma membrane (or both) can withstand long-term hyperosmotic challenge by ionic and nonionic solutes without exhibiting the normal change in transcriptional program (comparable with
hog1
Δ cells), as judged by mRNA hybridization and microarray analysis. For such cells to survive hyperosmotic stress, systematic genetic analysis ruled out the need for any Hog1-dependent transcription factor, the Hog1-activated MAPKAP kinases, or ion, glycerol, and water channels. By contrast, enzymes needed for glycerol production were essential for viability. Thus, control of intracellular glycerol formation by Hog1 is critical for maintenance of osmotic balance but not transcriptional induction of any gene.
Molecular basis for the autoregulation of the protein acetyl transferase Rtt109
Authors: Stavropoulos Pete , Nagy Vivien , Blobel Günter , Hoelz André
Published: August 2008

Rtt109 is a protein acetyltransferase (PAT) that is responsible for the acetylation of lysine-56 of histone 3 (H3K56) in yeast. H3K56 acetylation has been implicated in the weakening of the interaction between the histone core and the surrounding DNA in the nucleosomal particle. Rtt109, in cooperation with various histone chaperones, promotes genomic stability and is required for resistance to DNA damaging agents. Here, we present the crystal structure of Rtt109 in complex with acetyl-CoA at a 2.0-Å resolution. Rtt109 consists of a core PAT domain, which binds the acetyl-CoA cofactor. A second domain, the activation domain, is tightly associated with the PAT domain. Autoacetylation of lysine-290 within the activation domain is required for stabilizing the interaction between the two domains and is essential for catalysis. Biochemical analysis demonstrates the requirement of a loop within the PAT domain for the binding of the histone chaperone Vps75, and mutational analysis identifies key residues for catalysis. We propose a model in which the autoacetylation of Rtt109 is crucial for the regulation of its catalytic activity.
Information flow and optimization in transcriptional regulation
Authors: Tkačik Gašper , Callan Curtis G. , Bialek William
Published: August 2008

In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be possible to transmit much more than just one regulatory bit. Realizing this optimal information capacity would require that the dynamic range of TF concentrations used by the cell, the input/output relation of the regulatory module, and the noise in gene expression satisfy certain matching relations, which we derive. These results provide parameter-free, quantitative predictions connecting independently measurable quantities. Although we have considered only the simplified problem of a single gene responding to a single TF, we find that these predictions are in surprisingly good agreement with recent experiments on the Bicoid/Hunchback system in the early
Drosophila
embryo and that this system achieves ∼90% of its theoretical maximum information transmission.
In vivostudies fail to reveal a role for IL-4 or STAT6 signaling in Th2 lymphocyte differentiation
Authors: van Panhuys Nicholas , Tang Shiau-Choot , Prout Melanie , Camberis Mali , Scarlett Debbie , Roberts Joanna , Hu-Li Jane , Paul William E. , Le Gros Graham
Published: August 2008

The expression of interleukin-4 (IL-4) is viewed as the hallmark of a Th2 lymphocyte, whereas the subsequent action of IL-4 and IL-13, mediated through the STAT6 signaling pathway, is seen as a prerequisite for the full development of Th2 immune responses to parasites and allergens. G4 mice, whose IL-4 gene locus contains the fluorescent reporter eGFP, were used to quantify the number of Th2 cells that develop duringNippostrongylus brasiliensis- or allergen-induced immune responses under conditions where IL-4 or STAT6 was absent. Here, we show that deletion of IL-4 or STAT6 had little impact on the number or timing of appearance of IL-4-producing Th2 cells. These data indicate thatin vivodifferentiation of naïve CD4 T cells to Th2 status often occurs independently of IL-4 and STAT6 and that recently described pathways of Th2 cell differentiation may explain how allergens and parasites selectively induce Th2-mediated immunity.
Beyond tumor necrosis factor receptor: TRADD signaling in toll-like receptors
Authors: Chen Nien-Jung , Chio Iok In Christine , Lin Wen-Jye , Duncan Gordon , Chau Hien , Katz David , Huang Huey-Lan , Pike Kelly A. , Hao Zhenyue , Su Yu-Wen , Yamamoto Kazuo , de Pooter Renée F. , Zúñiga-Pflücker Juan Carlos , Wakeham Andrew , Yeh Wen-Chen , Mak Tak W.
Published: August 2008

Tumor necrosis factor receptor 1-associated death domain protein (TRADD) is the core adaptor recruited to TNF receptor 1 (TNFR1) upon TNFα stimulation. In cells from TRADD-deficient mice, TNFα-mediated apoptosis and TNFα-stimulated NF-κB, JNK, and ERK activation are defective. TRADD is also important for germinal center formation, DR3-mediated costimulation of T cells, and TNFα-mediated inflammatory responses
in vivo
. TRADD deficiency does not enhance IFNγ-induced signaling. Importantly, TRADD has a novel role in TLR3 and TLR4 signaling. TRADD participates in the TLR4 complex formed upon LPS stimulation, and TRADD-deficient macrophages show impaired cytokine production in response to TLR ligands
in vitro
. Thus, TRADD is a multifunctional protein crucial both for TNFR1 signaling and other signaling pathways relevant to immune responses.
Phantom-calibrated versus automatic coronary artery mass quantification with multidetector-row computed tomography: in vitro and in vivo study
Authors: Serafin Z. , Lasek W. , Laskowska K.
Published: August 2008

Background: Coronary artery calcium scoring is used as a method for cardiovascular risk stratification and monitoring of coronary heart disease. Automatic software-based calcium mass calculation has been proposed to improve the performance of the procedure.

Purpose: To compare two algorithms of calcium mass measurement, automatic and phantom calibrated, with respect to correlation, measurement error, and accuracy in vitro and in vivo.

Material and Methods: A cardiac phantom with calcium cylinder inserts was scanned with sequential non-overlapping collimation 4×2.5 mm, at 120 kV and 165 mAs. Fifty adults (37 men; mean age 46.2 years) were examined with the same settings using prospective electrocardiographic triggering to detect and quantify coronary artery calcifications. Calculations were performed with two methods: software-based automatic calcium mass measurement (ACM) and phantom-calibrated calcium mass measurement (CCM).

Results: The total phantom calcium masses measured with ACM and CCM were 175.0±13.8 mg and 163.0±4.4 mg, respectively ( P<0.0001), and ACM produced a higher mean error (4.5 vs. 3.2; P<0.05). Results of ACM and CCM were strongly correlated to each other ( R=0.73–0.96; P<0.0001). Mean image noise in the patient study was 8.72±1.68 HU. Results of patient calcium scoring with ACM and CCM were significantly different (median 70.3 mg and 59.7 mg, respectively; P<0.0001), with a mean systematic error of 17.5% (limit of agreement between 14.6% and 20.4%). The use of ACM resulted in an altered quartile classification for 14% of patients, as compared to CCM; all of these patients were classified into a higher category.

Conclusion: Our data indicate that multidetector-row computed tomography coronary calcium mass determination based on dedicated phantom calibration shows lower measurement error than an automatic software-based calculation method. The tested automatic software does not yet seem to be a reliable option for calcium mass measurement.
Recurrence after percutaneous ethanol ablation of simple hepatic, renal, and splenic cysts: is it true recurrence requiring an additional treatment?
Authors: Hahn S. T. , Han S. Y. , Yun E. H. , Park S. H. , Lee S. H. , Lee H. J. , Hahn H. J. , Hahn H. M.
Published: August 2008

Background: Recurrence after percutaneous ethanol ablation (PEA) of benign hepatic and renal cysts has been common, resulting in re-treatment or additional surgery. However, in recent years, a few cases of spontaneous regression of recurrent cysts following PEA have been experienced, which led to the design of this study to evaluate cyst recurrence after PEA and the necessity of additional treatment.

Purpose: To evaluate whether the initial recurrence after PEA of benign hepatic, renal, and splenic cysts is true recurrence, and to decide whether additional treatment is needed.

Material and Methods: Thirty-nine benign cysts (21 hepatic, 17 renal, and one splenic) were treated with PEA. PEA was performed with injection of 13–900 ml (40–50% of the volume of aspirated fluid) of absolute ethanol into the cysts. For cysts larger than 100 ml, two or more PEAs were given in one session. Ultrasonography was then performed during a period of 12 months with 1–2-month intervals.

Results: Two months after PEA, eight cysts (20.5%) regressed completely; another 31 cysts recurred with decreased size. After 6 months, 10 of the recurrent cysts had regressed spontaneously. Another four recurrent cysts regressed after 8 months, and three regressed after 12 months. Hence, 25 out of 39 (64.1%) cysts regressed within 12 months after PEA. The mean regression time of the 25 recurrent cysts was 6.3 months. All recurrent cysts, including the 14 that were lost to complete follow-up, showed gradual decrease overtime. There were no major complications associated with PEA.

Conclusion: Initial relapse of a cyst following PEA does not signify true recurrence, but transient, reactive, or inflammatory fluid collections which eventually disappear within several months, and thus does not necessitate additional treatment.
A piglet model for detection of hypoxic-ischemic brain injury with magnetic resonance imaging
Authors: Munkeby B. H. , De Lange C. , Emblem K. E. , Bjørnerud A. , Kro G. A. B. , Andresen J. , Winther-Larssen E. H. , Løberg E. M. , Hald J. K.
Published: August 2008

Background: Early detection of hypoxic-ischemic (HI) injury in the asphyxic newborn is important because present prognostic factors are inadequate. Furthermore, therapeutic interventions may have additional benefit if initiated in time.

Purpose: To assess whether the use of a combined protocol including conventional magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), diffusion tensor imaging (DTI), and proton MR spectroscopy (MRS) could detect pathological findings in a piglet model 7 hours after HI.

Material and Methods: Ten piglets were submitted to HI for 30 min followed by reoxygenation with 21% O2 for 7 hours. MRI at 1.5T was done prior to and 7 hours after the HI. Single-voxel proton MRS was performed, and apparent diffusion coefficient (ADC) and fractional anisotropy (FA) were measured in the basal ganglia. MRS identified N-acetylaspartate (NAA), choline (Cho), creatine (Cr), and lactate (Lac). Histology and microtubule-associated protein 2 (MAP-2) staining was performed in the basal ganglia at the end of the experiment.

Results: Compared to baseline, ADC, NAA/Cho, and NAA/Cr were significantly reduced after 7 hours ( P<0.001, P=0.01, and P=0.05, respectively) and FA values were increased ( P<0.025). The ratios of Lac/Cho and Lac/NAA were significantly higher after 7 hours compared to baseline ( P<0.001). Presence of necrosis correlated well with reduced ADC ( RS=0.91) and presence of Lac ( RS=0.80). Histology and MAP-2 staining showed more than 90% necrosis in eight piglets, 60% in one piglet, and no necrosis in one piglet.

Conclusion: Diffusion MRI and proton MRS can detect HI injury in the piglet brain 7 hours after hypoxia. DWI and MRS can be used to give useful prognostic information. This piglet model may potentially be used to mimic clinical situations and is suitable for further research investigating HI injury.
An unsupervised conditional random fields approach for clustering gene expression time series
Authors: Li Chang-Tsun , Yuan Yinyin , Wilson Roland
Published: August 2008

Motivation: There is a growing interest in extracting statistical patterns from gene expression time-series data, in which a key challenge is the development of stable and accurate probabilistic models. Currently popular models, however, would be computationally prohibitive unless some independence assumptions are made to describe large-scale data. We propose an unsupervised conditional random fields (CRF) model to overcome this problem by progressively infusing information into the labelling process through a small variable voting pool.

Results: An unsupervised CRF model is proposed for efficient analysis of gene expression time series and is successfully applied to gene class discovery and class prediction. The proposed model treats each time series as a random field and assigns an optimal cluster label to each time series, so as to partition the time series into clusters without a priori knowledge about the number of clusters and the initial centroids. Another advantage of the proposed method is the relaxation of independence assumptions.

Contact:  ctli@dcs.warwick.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users
Authors: Shatkay Hagit , Pan Fengxia , Rzhetsky Andrey , Wilbur W. John
Published: August 2008

Motivation: Much current research in biomedical text mining is concerned with serving biologists by extracting certain information from scientific text. We note that there is no ‘average biologist’ client; different users have distinct needs. For instance, as noted in past evaluation efforts (BioCreative, TREC, KDD) database curators are often interested in sentences showing experimental evidence and methods. Conversely, lab scientists searching for known information about a protein may seek facts, typically stated with high confidence. Text-mining systems can target specific end-users and become more effective, if the system can first identify text regions rich in the type of scientific content that is of interest to the user, retrieve documents that have many such regions, and focus on fact extraction from these regions. Here, we study the ability to characterize and classify such text automatically. We have recently introduced a multi-dimensional categorization and annotation scheme, developed to be applicable to a wide variety of biomedical documents and scientific statements, while intended to support specific biomedical retrieval and extraction tasks.

Results: The annotation scheme was applied to a large corpus in a controlled effort by eight independent annotators, where three individual annotators independently tagged each sentence. We then trained and tested machine learning classifiers to automatically categorize sentence fragments based on the annotation. We discuss here the issues involved in this task, and present an overview of the results. The latter strongly suggest that automatic annotation along most of the dimensions is highly feasible, and that this new framework for scientific sentence categorization is applicable in practice.

Contact:  shatkay@cs.queensu.ca
Local coherence in genetic interaction patterns reveals prevalent functional versatility
Authors: Pu Shuye , Ronen Karen , Vlasblom James , Greenblatt Jack , Wodak Shoshana J.
Published: August 2008

Motivation: Epistatic or genetic interactions, representing the effects of mutating one gene on the phenotypes caused by mutations in one or moredistinct genes, can be very helpful for uncovering functional relationships between genes. Recently, the epistatic miniarray profiles (E-MAP) method has emerged as a powerful approach for identifying such interactions systematically. For E-MAP data analysis, hierarchical clustering is used to partition genes into groups on the basis of the similarity between their global interaction profiles, and the resulting descriptions assign each gene to only one group, thereby ignoring the multifunctional roles played by most genes.

Results: Here, we present the original local coherence detection (LCD) algorithm for identifying groups of functionally related genes from E-MAP data in a manner that allows individual genes to be assigned to more than one functional group. This enables investigation of the pleiotropic nature of gene function. The performance of our algorithm is illustrated by applying it to two E-MAP datasets and an E-MAP-like in silico dataset for the yeast Saccharomyces cerevisiae. In addition to recapitulating the majority of the functional modules and many protein complexes reported previously, our algorithm uncovers many recently documented and novel multifunctional relationships between genes and gene groups. Our algorithm hence represents a valuable tool for uncovering new roles for genes with annotated functions and for mapping groups of genes and proteins into pathways.

Availability: A Java implementation of the LCD algorithm is available at URL http://genepro.ccb.sickkids.ca/biclustering.html

Contact:  shuyepu@sickkids.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
siDRM: an effective and generally applicable online siRNA design tool
Authors: Gong Wuming , Ren Yongliang , Zhou Haiyan , Wang Yejun , Kang Shuli , Li Tongbin
Published: August 2008

Summary: Small interfering RNAs (siRNAs) have become an indispensable tool for the investigation of gene functions. Most existing siRNA design tools were trained on datasets assembled from confined origins, incompatible with the diverse siRNA laboratory practice to which these tools will ultimately be applied. We have performed an updated analysis using the disjunctive rule merging (DRM) approach on a large and diverse dataset compiled from siRecords, and implemented the resulting rule sets in siDRM, a new online siRNA design tool. siDRM also implements a few high-sensitivity rule sets and fast rule sets, links to siRecords, and uses several filters to check unwanted detrimental effects, including innate immune responses, cell toxic effects and off-target activities in selecting siRNAs. A performance comparison using an independent dataset indicated that siDRM outperforms 19 existing siRNA design tools in identifying effective siRNAs.

Availability:  siDRM can be accessed at http://siRecords.umn.edu/siDRM/.

Contact:  toli@biocompute.umn.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Seeder: discriminative seeding DNA motif discovery
Authors: Fauteux François , Blanchette Mathieu , Strömvik Martina V.
Published: August 2008

Motivation: The computational identification of transcription factor binding sites is a major challenge in bioinformatics and an important complement to experimental approaches.

Results: We describe a novel, exact discriminative seeding DNA motif discovery algorithm designed for fast and reliable prediction of cis-regulatory elements in eukaryotic promoters. The algorithm is tested on biological benchmark data and shown to perform equally or better than other motif discovery tools. The algorithm is applied to the analysis of plant tissue-specific promoter sequences and successfully identifies key regulatory elements.

Availability: The Seeder Perl distribution includes four modules. It is available for download on the Comprehensive Perl Archive Network (CPAN) at http://www.cpan.org.

Contact:  martina.stromvik@mcgill.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Analyzing gene perturbation screens with nested effects models in R and bioconductor
Authors: Fröhlich Holger , Beißbarth Tim , Tresch Achim , Kostka Dennis , Jacob Juby , Spang Rainer , Markowetz F.
Published: August 2008

Summary: Nested effects models (NEMs) are a class of probabilistic models introduced to analyze the effects of gene perturbation screens visible in high-dimensional phenotypes like microarrays or cell morphology. NEMs reverse engineer upstream/downstream relations of cellular signaling cascades. NEMs take as input a set of candidate pathway genes and phenotypic profiles of perturbing these genes. NEMs return a pathway structure explaining the observed perturbation effects. Here, we describe the package nem, an open-source software to efficiently infer NEMs from data. Our software implements several search algorithms for model fitting and is applicable to a wide range of different data types and representations. The methods we present summarize the current state-of-the-art in NEMs.

Availability: Our software is written in the R language and freely avail-able via the Bioconductor project at http://www.bioconductor.org.

Contact:  rainer.spang@klinik.uni-regensburg.de
Ethical Considerations for Acupuncture and Chinese Herbal Medicine Clinical Trials: A Cross‐Cultural Perspective
Authors: Zaslawski Christopher
Published: August 2008

Many ethical concerns revolve around the four basic principles of research: merit and integrity, respect for human beings, weighting of risk–benefit and justice. These principles form the basis for any discussion concerning human research ethics and are applicable to all areas of research including acupuncture and Chinese herbal medicine. World Health Organisation document, Guidelines for Clinical Research on Acupuncture, states that ‘consideration should be given to the different value systems that are involved in human rights such as social, cultural and historical issues’ and that ‘further studies should be conducted in relation to ethical issues involved in clinical research on acupuncture’. In addition to outlining the four basic principles, this paper will also examine the effect of Asian culture on Western human research ethics and how this may impact upon issues such as informed consent and weighting of risk–benefit.
The entropy dissipation method for spatially inhomogeneous reaction–diffusion-type systems
Authors: Di Francesco Marco , Fellner Klemens , Markowich Peter A
Published: August 2008

We study the long-time asymptotics of reaction–diffusion-type systems that feature a monotone decaying entropy (Lyapunov, free energy) functional. We consider both bounded domains and confining potentials on the whole space for arbitrary space dimensions. Our aim is to derive quantitative expressions for (or estimates of) the rates of convergence towards an (entropy minimizing) equilibrium state in terms of the constants of diffusion and reaction and with respect to conserved quantities. Our method, the so-called entropy approach, seeks to quantify convergence to equilibrium by using functional inequalities, which relate quantitatively the entropy and its dissipation in time. The entropy approach is well suited to nonlinear problems and known to be quite robust with respect to model variations. It has already been widely applied to scalar diffusion–convection equations, and the main goal of this paper is to study its generalization to systems of partial differential equations that contain diffusion and reaction terms and admit fewer conservation laws than the size of the system. In particular, we successfully apply the entropy approach to general linear systems and to a nonlinear example of a reaction–diffusion–convection system arising in solid-state physics as a paradigm for general nonlinear systems.
POWTEX – the high-intensity time-of-flight diffractometer at FRM II for structure analysis of polycrystalline materials
Authors: Conrad Harald , Brückel Thomas , Schäfer Wolfgang , Voigt Jörg
Published: August 2008

In order to provide the large chemistry and materials science as well as the geosciences communities with a powerful tool for rapid data acquisition, a time-of-flight powder diffractometer to be installed at the new Munich reactor has been designed. The time-of-flight technique is expected to outperform a monochromator instrument by at least an order of magnitude in data acquisition time, particularly on small samples of less than a cubic centimetre. The construction of this innovative type of diffractometer utilizes modern components such as focusing super-mirror neutron guides, a four-unit high-speed disk chopper system and linear position-sensitive detectors covering a solid angle of about 2π steradian. The diffractometer design enables an easy enlargement of the focal spot size and is therefore equally well suited for the texture analysis of large geological and archaeological samples.
An electron diffraction and Monte Carlo simulation study of diffuse scattering in Pb(Zr,Ti)O3
Authors: Baba-Kishi K. Z. , Welberry T. R. , Withers R. L.
Published: August 2008

Transverse polarized diffuse streaks have been recordedviatransmission electron microscopy for a range of Pb(Zr1−xTix)O3ceramics spanning the entire phase diagram from the rhombohedral phase (x= 0.3), through the monoclinic morphotropic phase boundary region (MPB;x= 0.48) to the tetragonal phase (x = 0.7). Although the same type of streaks are observed over the whole composition range, they are strongest and most distinct in the rhombohedral phase and diminish in clarity as the MPB is approached. The streaks have been shown to correspond to diffuse planes of scattering in three dimensions and are oriented normal to the (cubic) 〈111〉cdirections. A Monte Carlo computer simulation model has been developed that convincingly reproduces the observed diffraction patterns in the rhombohedral phase. In this model the displacements of Pb ions in chains running along each of the 〈111〉cdirections are directed along the chain and are strongly correlated from cell to cell. There is no evidence of lateral correlation, indicating that neighbouring chains are essentially independent.
catena-Poly[[(2-{1-[2-(2-aminoethylamino)ethylimino]ethyl}-5-methoxyphenolato-κ4
N,N′,N′′,O)copper(II)]-μ-nitrato-κ2
O:O′]
Authors: Wang Suwen , Li Zhongfang , Wang Xutao , Yu Xianjin
Published: August 2008

In the title compound, [Cu(C13H20N3O2)(NO3)]
n
, the CuII atom is chelated by the Schiff base ligand via three N atoms and one O atom lying in an approximate square plane (r.m.s. deviation = 0.04 Å). The complex molecules are linked into a polymeric chain by bridging nitrate anions, forming axial Cu—O bonds of 2.535 (6) and 2.676 (7) Å, completing a distorted octahedral coordination geometry. The NH groups of the ligand form hydrogen bonds to the nitrate anions.
2-Acetylhydrazono-2-phenylacetohydrazide
Authors: Feng Bai-Cheng , Yang Zhi , Yi Xu
Published: August 2008

The title compound, C10H12N4O2, was prepared as an intermediate for the synthesis of metamitron. The benzene ring plane forms dihedral angles of 66.0 (1) and 3.5 (5)° with the hydrazine plane and the acetylimino plane, respectively. The crystal structure involves intermolecular N—H...O hydrogen bonds.
Bis[2-(2-pyridylmethyleneamino)benzenesulfonato-κ3
N,N′,O]zinc(II) dihydrate
Authors: Cai Cheng-Xiang , Ou-Yang Miao , Zhao Zhi-Yuan , Jiang Yi-Min
Published: August 2008

In the title complex, [Zn(C12H9N2O3S)2]·2H2O, the ZnII ion lies on a crystallographic inversion center and is coordinated by four N atoms and two O atoms from two tridentate 2-(2-pyridylmethyleneamino)benzenesulfonate ligands in a slightly distorted octahedral environment. In the crystal structure, the complex forms a two-dimensional network through intermolecular O—H...O and C—H...O hydrogen bonds.
Poly[aqua[μ-N′-(carboxymethyl)ethylenediamine-N,N,N′-triacetato]neodymium(III)]
Authors: Huang Xiao-Hui , Xu Xiao-Hong , Pan Wei-Bo , Zeng Rong-Hua
Published: August 2008

In the title complex, [Nd(C10H13N2O8)(H2O)]
n
, each NdIII ion is coordinated by six O atoms and two N atoms from one N′-(carboxymethyl)ethylenediamine-N,N,N′-triacetate (edta) ligand and one water molecule, displaying a bicapped trigonal-prismatic geometry. The edta ligands link the neodymium metal centres, forming polymeric chains running along the a axis of the unit cell. These chains are further assembled via intermolecular O—H...O hydrogen-bonding interactions into a three-dimensional supramolecular network.
catena-Poly[[[(1-ethyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylato-κ2
O
3,O
4)copper(II)]-μ-1-ethyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylato-κ3
N
7′:O
3,O
4] tetrahydrate]
Authors: Wang Shu-Ye , Song Xue-Ming , Duan Li-Xiang , An Zhe
Published: August 2008

In the title compound, {[Cu(C16H17FN3O3)2]·4H2O}
n
, the CuII atom is bonded to two O,O′-bidentate 1-ethyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylate (norf) monoanions and a symmetry-generated N-bonded norf anion, resulting in a distorted square-pyramidal coordination environment with the N atom occupying the apical site. The bridging norf anion results in one-dimensional chains propogating along [010]. A network of O—H...O and N—H...O hydrogen bonds helps to establish the crystal structure.
catena-Poly[[[diaquacobalt(II)]bis(μ-1,3-di-4-pyridylpropane-κ2
N:N′)] bis(perchlorate) bis(1,3-di-4-pyridylpropane) bis(2-methyl-4-nitroaniline)]
Authors: Fu Zhiyong , Chen Yuan , Yi Jianglong
Published: August 2008

In the title compound, {[Co(C13H14N2)2(H2O)2](ClO4)2·2C13H14N2·2C7H8N2O2}
n
, the CoII ion lies on a crystallographic inversion center and is coordinated by four N atoms from four symmetry-related 1,3-di-4-pyridylpropane ligands and two O atoms from two water ligands in a slightly distorted octahedral coordination environment. The 1,3-di-4-pyridylpropane ligands are doubly bridging and connect the CoII ions into one-dimensional chains. The asymmetric unit also contains one uncoordinated 1,3-di-4-pyridylpropane molecule, one 2-methyl-4-nitroaniline molecule and one perchlorate anion. In the crystal structure, intermolecular O—H...N hydrogen bonds connect the one-dimensional chains into a two-dimensional network.
6,7-Dimethoxy-1,4-anthraquinone
Authors: Kitamura Chitoshi , Akamatsu Naoki , Yoneda Akio , Kawase Takeshi
Published: August 2008

The molecule of the title compound, C16H12O4, is almost planar; the two methoxy groups are slightly out of the plane of the anthraquinone ring system, with C—C—O—C torsion angles of −6.25 (19) and −10.22 (19)°. In the crystal structure, the molecules adopt a herringbone arrangement and form face-to-face slipped antiparallel π–π stacking interactions along the b axis, with an interplanar distance of 3.278 (2) Å.
2-Nitro-p-phenylene bis(toluenesulfonate)
Authors: Ji Xiujie , Cheng Bowen , Song Jun , Liu Chao
Published: August 2008

In the molecule of the title compound, C20H17NO8S2, the two toluene rings are oriented at a dihedral angle of 3.65 (4)°, while the nitrophenyl ring is oriented at dihedral angles of 44.39 (3) and 47.44 (3)° with respect to the toluene rings. An intramolecular C—H...O hydrogen bond results in the formation of a five-membered ring, which adopts an envelope conformation. In the crystal structure, intermolecular C—H...O hydrogen bonds link the molecules. There is a π–π contact between the toluene rings [centroid–centroid distance = 4.035 (1) Å].
4,4′-Dimethyl-2,2′-bipyridinium dichloride
Authors: Eckensberger Urs David , Lerner Hans-Wolfram , Bolte Michael
Published: August 2008

In the title compound, C12H14N2
2+·2Cl−, the 4,4′-dimethyl-2,2′-bipyridinium cation is essentially planar (r.m.s. deviation for all non-H atoms = 0.004 Å) and is located on a crystallographic inversion centre. The cations and chloride anions lie in planes parallel to (111) and are connected by N—H...Cl and C—H...Cl hydrogen bonds.
Tetrakis(1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidin-9-ido-κ2
N
1,N
9)niobium(V) hexafluoridophosphate
Authors: Cotton F. Albert , Murillo Carlos A. , Poplaukhin Pavel V. , Bhuvanesh Nattamai , Tiekink Edward R. T.
Published: August 2008

The title complex, [Nb(C7H12N3)4]PF6, features chelating hpp anions (hpp is 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine) that define a distorted dodecahedral coordination geometry based on an N8 donor set. The Nb atom is situated on a site of symmetry \overline{4}, and the PF6
− anion has crystallographic fourfold symmetry.
5-Bromo-2,4,6-trimethyl-3-phenylsulfinyl-1-benzofuran
Authors: Choi Hong Dae , Seo Pil Ja , Son Byeng Wha , Lee Uk
Published: August 2008

The title compound, C17H15BrO2S, which was synthesized by the oxidation of 5-bromo-2,4,6-trimethyl-3-phenylsulfanyl-1-benzofuran with 3-chloroperoxybenzoic acid, features a trigonally-coordinated S atom. The phenyl ring is approximately perpendicular to the plane of the benzofuran fragment [dihedral angle 75.11 (7)°]. The crystal structure is stabilized by non-classical C—H...O and Br...Br interactions [3.7169 (6) Å].
6,6′-Dihydroxy-2,2′-[(propane-1,3-diyldioxy)bis(nitrilomethylidyne)]diphenol
Authors: Dong Wen-Kui , He Xue-Ni , Guan Yong-Hong , Xu Li , Ren Zong-Li
Published: August 2008

The molecule of the title compound, C17H18N2O6, adopts a V-shaped conformation, the dihedral angle between the two halves of the molecule being 81.31 (4) °. There is one half-molecule in the asymmetric unit, with a crystallographic twofold rotation axis passing through the central C atom. There are strong intramolecular O—H...N and O—H...O hydrogen bonds involving the hydroxy group and adjacent O and N atoms. In the crystal structure, intermolecular O—H...O hydrogen bonds link the molecules, forming an infinite three-dimensional supramolecular structure.
Phenyl quinoxalin-2-yl ether
Authors: Hassan Nor Duha , Tajuddin Hairul Anuar , Abdullah Zanariah , Ng Seik Weng
Published: August 2008

The aromatic ring systems in the title compound, C14H10N2O, form a dihedral angle of 63.8 (1)°, resulting in an opening up of the ether-O atom angle to 118.2 (1)°.
Quinoxalin-2-yl m-tolyl ether
Authors: Hassan Nor Duha , Tajuddin Hairul Anuar , Abdullah Zanariah , Ng Seik Weng
Published: August 2008

The dihedral angle between the two aromatic ring systems in the title compound, C15H12N2O, is 79.4 (1)°. The angle at the O atom is widened to 116.93 (9)°.
Quinoxalin-2-yl p-tolyl ether
Authors: Hassan Nor Duha , Tajuddin Hairul Anuar , Abdullah Zanariah , Ng Seik Weng
Published: August 2008

The dihedral angle between the two aromatic ring systems in the title compound, C15H12N2O, is 42.6 (1)°. The angle at the O atom is widened to 117.7 (1)°.
N-Acetyl-2-hydroxy-N′-[methoxy(1-methylindol-2-yl)methyl]benzohydrazide
Authors: Yehye Wagee A. , Rahman Noorsaadah Abdul , Ariffin Azhar , Ng Seik Weng
Published: August 2008

In the crystal structure of the title Schiff-base, C20H21N3O4, the amino group forms an N—H...O hydrogen bond to the acetyl group of an adjacent molecule, forming a zigzag chain. The 2-hydroxy group is internally hydrogen bonded to the amido group though an O—H...O hydrogen bond.
Rietveld refinement of Ba5(AsO4)3Cl from high-resolution synchrotron data
Authors: Bell Anthony M. T. , Henderson C. Michael B. , Wendlandt Richard F. , Harrison Wendy J.
Published: August 2008

The apatite-type compound Ba5(AsO4)3Cl, pentabarium tris[arsenate(V)] chloride, has been synthesized by ion exchange at high temperature from a synthetic sample of mimetite (Pb5(AsO4)3Cl) with BaCO3 as a by-product. The results of the Rietveld refinement, based on high resolution synchrotron X-ray powder diffraction data, show that the title compound crystallizes in the same structure as other halogenoapatites with general formula A
5(YO4)3
X (A = divalent cation, Y = pentavalent cation, X = Cl, Br) in space group P63/m. The structure consists of isolated tetrahedral AsO4
3− anions (m symmetry), separated by two crystallographically independent Ba2+ cations that are located on mirror planes and threefold rotation axes, respectively. The Cl− anions are at the 2b sites (\overline{3} symmetry) and are located in the channels of the structure.
2-Hydroxy-N′-(2-methoxynaphthylidene)benzohydrazide
Authors: Qiu Xiao-Yang
Published: August 2008

The title Schiff base compound, C19H16N2O3, prepared by the reaction of 2-methoxy-1-naphthylaldehyde and 2-hydroxybenzohydrazide, crystallizes with two independent molecules in the asymmetric unit. Each molecule exists in a trans configuration with respect to the methylidene group. The naphthyl ring system make dihedral angles of 65.0 (2)° and 55.8 (2)° with the planes of the benzene rings. Intramolecular N—H...O and O—H...O hydrogen bonds help to stabilize the molecular conformations. In the crystal structure, molecules are linked into one-dimensional chains parallel to the c axis by intermolecular O—H...N and O—H...O hydrogen bonds.
4-Methoxy-N′-(2-methoxynaphthylidene)benzohydrazide
Authors: Qiu Xiao-Yang
Published: August 2008

The molecule of the title Schiff base compound, C20H18N2O3, prepared by the reaction of 2-methoxy-1-naphthylaldehyde and 4-methoxybenzohydrazide, exists in a trans configuration with respect to the imine group. The naphthyl ring system makes a dihedral angle of 71.4 (2)° with the mean plane of the benzene ring. In the crystal structure, molecules are linked into one-dimensional chains parallel to the c axis by intermolecular N—H...O hydrogen bonds.
The subcellular Sox11 distribution pattern identifies subsets of mantle cell lymphoma: correlation to overall survival
Authors: Wang Xiao , Asplund A. Charlotta , Porwit Anna , Flygare Jenny , Smith C. I. Edvard , Christensson Birger , Sander Birgitta
Published: August 2008

Gene expression analysis demonstrated high expression of the neuronal transcription factor SOX11 in mantle cell lymphoma (MCL). In contrast to follicular lymphoma, small lymphocytic lymphoma and reactive lymphoid tissue, most MCLs tested (48/53 patients) expressed sox11 protein in the nucleus. Therefore nuclear sox11 expression represents a new tumour marker for a subset of MCL. However, 5/53 MCL cases expressed sox11 only in the cytoplasm; these MCL patients had a shorter survival compared to MCL with nuclear sox11 expression. These results suggest sox11 expression as a new diagnostic marker in MCL that could be related to the clinical and biological behaviour of MCL.
Practical blood dendritic cell vaccination for immunotherapy of multiple myeloma
Authors: Vari F. , Munster D. J. , Hsu J. L. , Rossetti T. R. , Mahler S. M. , Gray P. P. , Turtle C. J. , Prue R. L. , Hart D. N. J.
Published: August 2008

Therapeutic vaccination combined with new drugs may cure multiple myeloma (MM). We have developed a bio‐process to purify CMRF‐56 monoclonal antibody (mAb) and a standard operating procedure to immunoselect blood dendritic cells (BDC). Leucopheresed mononuclear cells were cultured overnight, labelled with CMRF‐56 mAb and BDC prepared using a clinical scale immunoselection system. The mean BDC yield from healthy donors was 48% (n = 6, purity 28%). Preparations from MM patients (n = 6, yield 47%, purity 35%) primed cytotoxic T lymphocytes (CTL) to clinically relevant MM antigens. This procedure can be performed readily by clinical cell manufacturing units to facilitate BDC vaccination studies.
MOZ/TIF2‐induced acute myeloid leukaemia in transgenic fish
Authors: Zhuravleva Julia , Paggetti Jérôme , Martin Laurent , Hammann Arlette , Solary Eric , Bastie Jean‐Noël , Delva Laurent
Published: August 2008

The inv(8)(p11q13) chromosomal abnormality, described in acute myeloid leukaemias (AML), fuses the histone acetyl‐transferase (HAT) MYST3 (MOZ) gene with another HAT gene, NCOA2 (TIF2). We generated a transgenic zebrafish in which the MYST3/NCOA2 fusion gene was expressed under control of the spi1 promoter. An AML developed in 2 of 180 MYST3/NCOA2‐EGFP‐expressing embryos, 14 and 26 months after injection of the fusion gene in a one‐cell embryo, respectively. This leukaemia was characterised by an extensive invasion of kidneys by myeloid blast cells. This model, which is the first zebrafish model of AML, demonstrates the oncogenic potency of MYST3/NCOA2 fusion gene.
Influence of ethnicity on IGF‐I and procollagen III peptide (P‐III‐P) in elite athletes and its effect on the ability to detect GH abuse
Authors: Erotokritou‐Mulligan Ioulietta , Bassett E. Eryl , Cowan David A. , Bartlett Christiaan , McHugh Cathy , Sönksen Peter H. , Holt Richard I. G. ,   The GH‐2004 group
Published: August 2008

Context  A method based on the two GH dependent markers, IGF‐I and procollagen III peptide (P‐III‐P) has been proposed to detect exogenously administered GH. As previous studies involved predominantly white European elite athletes, it is necessary to validate the method in other ethnic groups.

Objective  To examine serum IGF‐I and P‐III‐P in elite athletes of different ethnicities within 2 h of competing at national or international events.

Design  Cross‐sectional observational study.

Setting  National and International sporting events.

Subjects  1085 elite athletes of different ethnicities.

Intervention  Serum IGF‐I and P‐III‐P were measured and GH‐2000 discriminant function score was calculated. Effect of ethnicity was assessed.

Results  In men, IGF‐I was 21·7 ± 2·6% lower in Afro‐Caribbeans than white Europeans (P < 0·0001) but there were no differences between other ethnic groups. In women, IGF‐I was 14·2 ± 5·1% lower in Afro‐Caribbeans (P = 0·005) and 15·6 ± 7·0% higher in Orientals (P = 0·02) compared with white Europeans. P‐III‐P was 15·2 ± 3·5%, 26·6 ± 6·6% and 19·3 ± 5·8% lower in Afro‐Caribbean (P < 0·0001), Indo‐Asian (P < 0·0001) and Oriental men (P = 0·001), respectively, compared with white European men. In women, P‐III‐P was 15·7 ± 4·7% lower in Afro‐Caribbeans compared to white Europeans (P =0·0009) but there were no differences between other ethnicities. Despite these differences, most observations were below the upper 99% prediction limits derived from white European athletes. All GH‐2000 scores lay below the cut‐off limit proposed for doping.

Conclusions  The GH‐2000 detection method based on IGF‐I and P‐III‐P would be valid in all ethnic groups.