bluuebunny/crossref_metadata_2025 huggingface dataset:
Interferon lambda inhibits herpes simplex virus type I infection of human astrocytes and neurons
Authors: Li Jieliang , Hu Shuxian , Zhou Lin , Ye Li , Wang Xu , Ho Jie , Ho Wenzhe
Published: September 2010

Herpes simplex virus Type I (HSV‐1) is a neurotropic virus that is capable of infecting not only neurons, but also microglia and astrocytes and can establish latent infection in the central nervous system (CNS). We investigated whether IFN lambda (IFN‐λ), a newly identified member of IFN family, has the ability to inhibit HSV‐1 infection of primary human astrocytes and neurons. Both astrocytes and neurons were found to be highly susceptible to HSV‐1 infection. However, upon IFN‐λ treatment, HSV‐1 replication in both astrocytes and neurons was significantly suppressed, which was evidenced by the reduced expression of HSV‐1 DNA and proteins. This IFN‐λ‐mediated action on HSV‐1 could be partially neutralized by antibody to IFN‐λ receptor. Investigation of the mechanisms showed that IFN‐λ treatment of astrocytes and neurons resulted in the upregulation of endogenous IFN‐α/β and several IFN‐stimulated genes (ISGs). To block IFN‐α/β receptor by a specific antibody could compromise the IFN‐λ actions on HSV‐1 inhibition and ISG induction. In addition, IFN‐λ treatment induced the expression of IFN regulatory factors (IRFs) in astrocytes and neurons. Furthermore, IFN‐λ treatment of astrocytes and neurons resulted in the suppression of suppressor of cytokine signaling 1 (SOCS‐1), a key negative regulator of IFN pathway. These data suggest that IFN‐λ possesses the anti‐HSV‐1 function by promoting Type I IFN‐mediated innate antiviral immune response in the CNS cells. © 2010 Wiley‐Liss, Inc.
Apathy and cortical atrophy in Alzheimer's disease
Authors: Tunnard C. , Whitehead D. , Hurt C. , Wahlund LO. , Mecocci P. , Tsolaki M. , Vellas B. , Spenger C. , Kłoszewska I. , Soininen H. , Lovestone S. , Simmons A. ,   on behalf of the AddNeuroMed Consortium
Published: September 2010

Objectives

Apathy has been reported as the most prevalent behavioural symptom experienced in Alzheimer's disease (AD), associated with greater functional decline and caregiver distress. The aim of the current study was to investigate structural correlates of apathy in AD using magnetic resonance imaging (MRI) regional volume and regional cortical thickness measures.

Methods

Semi‐structured interviews were conducted with 111 AD patients and their caregivers as part of the European multi‐centre study AddNeuroMed. Apathy was measured using the apathy domain of the Neuropsychiatric Inventory (NPI). All AD patients were scanned using a 1.5T MRI scanner and the images analysed using an automated analysis pipeline.

Results

We found apathy to be the most prevalent neuropsychiatric symptom occurring in 57% of patients. Apathetic patients had significantly greater cortical thinning in left caudal anterior cingulate cortex (ACC) and left lateral orbitofrontal cortex (OFC), as well as left superior and ventrolateral frontal regions, than those without apathy symptoms.

Conclusions

Apathy is mediated by frontocortical structures but this is specific to the left hemisphere at least for patients in the mild to moderate stages of AD. Copyright © 2010 John Wiley & Sons, Ltd.
Osteoporosis in COPD outpatients based on bone mineral density and vertebral fractures
Authors: Graat-Verboom Lidwien , van den Borne Ben EEM , Smeenk Frank WJM , Spruit Martijn A , Wouters Emiel FM
Published: September 2010

One of the extrapulmonary effects of chronic obstructive pulmonary disease (COPD) is osteoporosis. Osteoporosis is characterized by a low bone mineral density (BMD) and microarchitectural deterioration. Most studies in COPD patients use dual-energy X-ray absorptiometry (DXA) only to determine osteoporosis; therefore, microarchitectural changes without a low BMD are missed. The aim of this study was to determine the prevalence and correlates of osteoporosis in COPD patients based on DXA, spinal X-rays, and combinations thereof. DXA and spinal X-rays were obtained and pulmonary function tests, body composition, 6-minute walking distance, medical history, and medication use were assessed in 255 clinically stable COPD outpatients of a large teaching hospital in the Netherlands. Half of all patients had radiologic evidence of osteoporosis. Combining the results of DXA with spinal X-rays augmented the proportion of COPD patients with osteoporosis compared with both methods separately. The prevalence of osteoporosis was not significantly different after stratification for Global Strategy for the Diagnosis, Management, and Prevention of COPD (GOLD) stage. Most patients with osteoporosis did not receive pharmacologic treatment. Age, body mass index (BMI), and parathyroid hormone (PTH) level were significant independent correlates for osteoporosis. Chest physicians should be aware of the high prevalence of osteoporosis in patients with COPD, even in the presence of a low GOLD score, as well as especially in elder COPD patients with a low BMI and/or an increased PTH level. © 2011 American Society for Bone and Mineral Research.
Modeling unimolecular reactions in photoelectron photoion coincidence experiments
Authors: Sztáray Bálint , Bodi Andras , Baer Tomas
Published: September 2010

A computer program has been developed to model and analyze the data from photoelectron photoion coincidence (PEPICO) spectroscopy experiments. This code has been used during the past 12 years to extract thermochemical and kinetics information for almost a hundred systems, and the results have been published in over forty papers. It models the dissociative photoionization process in the threshold PEPICO experiment by calculating the thermal energy distribution of the neutral molecule, the energy distribution of the molecular ion as a function of the photon energy, and the resolution of the experiment. Parallel or consecutive dissociation paths of the molecular ion and also of the resulting fragment ions are modeled to reproduce the experimental breakdown curves and time‐of‐flight distributions. The latter are used to extract the experimental dissociation rates. For slow dissociations, either the quasi‐exponential fragment peak shapes or, when the mass resolution is insufficient to model the peak shapes explicitly, the center of mass of the peaks can be used to obtain the rate constants. The internal energy distribution of the fragment ions is calculated from the densities of states using the microcanonical formalism to describe consecutive dissociations. Dissociation rates can be calculated by the RRKM, SSACM or VTST rate theories, and can include tunneling effects, as well. Isomerization of the dissociating ions can also be considered using analytical formulae for the dissociation rates either from the original or the isomer ions. The program can optimize the various input parameters to find a good fit to the experimental data, using the downhill simplex algorithm. Copyright © 2010 John Wiley & Sons, Ltd.
High‐throughput UHPLC–MS/MS method for the detection, quantification and identification of fifty‐five anabolic and androgenic steroids in equine plasma
Authors: Guan Fuyu , Uboh Cornelius E. , Soma Lawrence R. , You Youwen , Liu Ying , Li Xiaoqing
Published: September 2010

Anabolic and androgenic steroids (AASs) are synthetic substances related to the primary male sex hormone, testosterone. AASs can be abused in both human and equine sports and, thus, are banned by the International Olympic Committee and the Association of Racing Commissioners International (ARCI). Enforcement of the ban on the use of AASs in racehorses during competition requires a defensible and robust method of analysis. To address this requirement, a high‐throughput ultra high‐performance liquid chromatography–mass spectrometric (UHPLC–MS) method was developed for the detection, quantification and confirmation of 55 AASs in equine plasma. AASs were recovered from equine plasma samples by liquid–liquid extraction with methyl tert‐butyl ether (MTBE). Analytes were chromatographically separated on a sub‐2 µm particle size C18 column with a mobile phase gradient elution and detected by selected‐reaction monitoring (SRM) on a triple quadrupole mass spectrometer. AASs with isobaric precursor ions were either chromatographically resolved or mass spectrometrically differentiated by unique precursor‐to‐product ion transitions. A few of them that could not be resolved by both approaches were differentiated by intensity ratios of three major product ions. All the epimer pairs, testosterone and epitestosterone, boldenone and epiboldenone, nandrolone and epinandrolone, were chromatographically base‐line separated. The limit of detection and that of quantification was 50 pg/ml for most of the AASs, and the limit of confirmation was 100–500 pg/ml. Full product ion spectra of AASs at concentrations as low as 100–500 pg/ml in equine plasma were obtained using the triple quadrupole instrument, to provide complementary evidentiary data for confirmation. The method is sensitive and selective for the detection, quantification and confirmation of multiple AASs in a single analysis and will be useful in the fight against doping of racehorses with AASs. Copyright © 2010 John Wiley & Sons, Ltd.
Non‐covalent dimers of the lysine containing protonated peptide ions in gaseous state: electrospray ionization mass spectrometric study
Authors: Banerjee Shibdas , Mazumdar Shyamalava
Published: September 2010

Study of the non‐covalent molecular complexes in gas phase by electrospray ionization mass spectrometry (ESI‐MS) represents a promising strategy to probe the intrinsic nature of these complexes. ESI‐MS investigation of a series of synthetic octapeptides containing six alanine and two lysine residues differing only by their positions showed the formation of non‐covalent dimers, which were preserved in the gas phase. Unlike the monomers, the dimers were found to show only singly protonated state. The decrease in the solvent polarity from water to alcohol showed enhanced propensity of formation of the dimer indicating that the electrostatic interaction plays a crucial role to stabilize the dimer. Selective functionalization studies showed that ε‐NH2 of lysine and C‐terminal amide (CONH2) facilitate the dimerization through intermolecular hydrogen bonding network. Copyright © 2010 John Wiley & Sons, Ltd.
Chiral discrimination of β‐3‐homo‐amino acids using the kinetic method
Authors: Berkecz Róbert , Hyyryläinen Anna R. M. , Fülöp Ferenc , Péter Antal , Janáky Tamás , Vainiotalo Pirjo , Pakarinen Jaana M. H.
Published: September 2010

Chiral discrimination of seven enantiomeric pairs of β‐3‐homo‐amino acids was studied by using the kinetic method and trimeric metal‐bound complexes, with natural and unnatural α‐amino acids as chiral reference compounds and divalent metal ions (Cu2+ and Ni2+) as the center ions. The β‐3‐homo‐amino acids were selected for this study because, first of all, chiral discrimination of β‐amino acids has not been extensively studied by mass spectrometry. Moreover, these β‐3‐homo‐amino acids studied have different aromatic side chains. Thus, the emphasis was to study the effect of the side chain (electron density of the phenyl ring, as well as the difference between phenyl and benzyl side chains) for the chiral discrimination. The results showed that by the proper choice of a metal ion and a chiral reference compound, all seven enantiomeric pairs of β‐3‐homo‐amino acids could be differentiated. Moreover, it was noted that the β‐3‐homo‐amino acids with benzyl side chains provided higher enantioselectivity than the corresponding phenyl ones. However, increasing or decreasing the electron density of the aromatic ring by different substituents in both the phenyl and benzyl side chains had practically no role for chiral discrimination of β‐3‐homo‐amino acids studied. When copper was used as the central metal, the phenyl side chain containing reference molecules (S)‐2‐amino‐2‐phenylacetic acid (L‐Phg) and (S)‐2‐amino‐2‐(4‐hydroxyphenyl)‐acetic acid (L‐4′‐OHPhg) gave rise to an additional copper‐reduced dimeric fragment ion, [CuI(ref)(A)]+. The inclusion of this ion improved noticeably the enantioselectivity values obtained. Copyright © 2010 John Wiley & Sons, Ltd.
A Raman spectroscopic study of M2+M3+ sulfate minerals, römerite Fe2+Fe23+ (SO4)4· 14H2O and botryogen Mg2+Fe3+ (SO4)2(OH)·7H2O
Authors: Frost Ray L. , Palmer Sara J. , Čejka Jiří , Sejkora Jiří , Plášil Jakub , Jebavá Ivana , Keeffe Eloise C.
Published: September 2010

The mixed valency (M2+M3+) sulfate minerals, römerite Fe2+Fe23+ (SO4)4· 14H2O and botryogen Mg2+Fe3+ (SO4)2(OH)·7H2O have been studied using Raman spectroscopy. The Raman spectra of the two types of crystals proved very similar but not identical. The observation of two symmetric stretching modes confirmed the presence of the two nonequivalent sulfate units in the römerite structure. The observation of multiple bands in the antisymmetric stretching regions and in the bending regions proves that the symmetry of the sulfate anion is significantly reduced in the römerite structure. The number of Raman bands related to the (SO4)2− symmetric and antisymmetric vibrations supports the X‐ray single crystal structure conclusion that two symmetrically distinct S6+ are present in the structure of botryogen. Römerite is a mineral of environmental significance as it is commonly found in tailings and dumps. Copyright © 2010 John Wiley & Sons, Ltd.
Optical sectioning using single‐plane‐illumination Raman imaging
Authors: Barman Ishan , Tan Khay Ming , Singh Gajendra Pratap
Published: September 2010

Confocal Raman imaging is widely used for optical sectioning of materials. However, for biological applications it often suffers from poor axial resolution, photodamage to the sample of interest, substrate interference, and long acquisition times. We have applied the principles of light sheet microscopy to Raman imaging and show for the first time that optically sectioned Raman images can be obtained in significantly lower acquisition times. Copyright © 2010 John Wiley & Sons, Ltd.
Verdigris pigment: a mixture of compounds. Input from Raman spectroscopy
Authors: San Andrés M. , de la Roja J. M. , Baonza V. G. , Sancho N.
Published: September 2010

The reproduction of an old recipe to obtain the pigment known as verdigris leads to a complex mixture of hydrated copper(II) acetates containing neutral verdigris and two varieties of basic verdigris. Since the characterization of such mixture is complicated by the lack of reference standards, we complemented our Raman measurements with Fourier transform infrared (FTIR) and X‐ray diffraction (XRD) experiments to perform our analysis, which has been compared with available studies. The spectral analysis allowed us to distinguish the different verdigris varieties, with stretching and bending wavenumbers assigned to the following chemical groups: OH groups (OHhydroxyand OHH2O) (3600–3050 cm−1), CuO bonds (CuO and CuOH) (1000–450 cm−1) and those corresponding to the acetate group (CH3COO−), i.e. (CH3: 3000–2850 cm−1) and (COO−: 1600–1400 cm−1and 700–600 cm−1). Both wavenumbers and Raman intensities were used to quantify the relative compositions of the mixture components. Copyright © 2010 John Wiley & Sons, Ltd.
Electro membrane extraction combined with capillary electrophoresis for the determination of amlodipine enantiomers in biological samples
Authors: Nojavan Saeed , Fakhari Ali Reza
Published: September 2010

Electro membrane extraction as a new microextraction method was applied for the extraction of amlodipine (AM) enantiomers from biological samples. During the extraction time of 15 min, AM enantiomers migrated from a 3 mL sample solution, through a supported liquid membrane into a 20 μL acceptor solution presented inside the lumen of the hollow fiber. The driving force of the extraction was 200 V potential, with the negative electrode in the acceptor solution and the positive electrode in the sample solution. 2‐Nitro phenyl octylether was used as the supported liquid membrane. Using 10 mM HCl as background electrolyte in the sample and acceptor solution, enrichment up to 124 times was achieved. Then, the extract was analyzed using CD modified CE method for separation of AM enantiomers. Best results were achieved using a phosphate running buffer (100 mM, pH 2.0) containing 5 mM hydroxypropyl‐α‐CD. The range of quantitation for both enantiomers was 10–500 ng/mL. Intra‐ and interday RSD (n=6) were less than 14%. The limits of quantitation and detection for both enantiomers were 10 and 3 ng/mL respectively. Finally, this procedure was applied to determine the concentration of AM enantiomers in plasma and urine samples.
Intra‐organ biodistribution of gold nanoparticles using intrinsic two‐photon‐induced photoluminescence
Authors: Park Jaesook , Estrada Arnold , Schwartz Jon A. , Diagaradjane Parmeswaran , Krishnan Sunil , Dunn Andrew K. , Tunnell James W.
Published: September 2010

Background and Objectives

Gold nanoparticles (GNPs) such as gold nanoshells (GNSs) and gold nanorods (GNRs) have been explored in a number of in vitro and in vivo studies as imaging contrast and cancer therapy agents due to their highly desirable spectral and molecular properties. While the organ‐level biodistribution of these particles has been reported previously, little is known about the cellular level or intra‐organ biodistribution. The objective of this study was to demonstrate the use of intrinsic two‐photon‐induced photoluminescence (TPIP) to study the cellular level biodistribution of GNPs.

Study Design/Materials and Methods

Tumor xenografts were created in 27 male nude mice (Swiss nu/nu) using HCT 116 cells (CCL‐247; American Type Culture Collection (ATCC), Manassas, VA, human colorectal cancer cell line). GNSs and GNRs were systemically injected 24 hours prior to tumor harvesting. A skin flap with the tumor was excised and sectioned as 8 µm thick tissues for imaging GNPs under a custom‐built multiphoton microscope. For multiplexed imaging, nuclei, cytoplasm, and blood vessels were demonstrated by hematoxylin and eosin (H&E) staining, YOYO‐1 iodide staining, and CD31‐immunofluorescence staining.

Results

Distribution features of GNPs at the tumor site were determined from TPIP images. GNSs and GNRs had a heterogeneous distribution with higher accumulation at the tumor cortex than tumor core. GNPs were also observed in unique patterns surrounding the perivascular region. While most GNSs were confined at the distance of approximately 400 µm inside the tumor edge, GNRs were shown up to 1.5 mm penetration inside the edge.

Conclusions

We have demonstrated the use of TPIP imaging in a multiplexed fashion to image both GNPs and nuclei, cytoplasm, or vasculature simultaneously. We also confirmed that TPIP imaging enabled visualization of GNP distribution patterns within the tumor and other critical organs. These results suggest that direct luminescence‐based imaging of metal nanoparticles holds a valuable and promising position in understanding the accumulation kinetics of GNPs. In addition, these techniques will be increasingly important as the use of these particles progress to human clinical trials where standard histopathology techniques are used to analyze their effects. Lasers Surg. Med. 42:630–639, 2010. © 2010 Wiley‐Liss, Inc.
A constrained least‐squares approach to the automated quantitation of in vivo 1H magnetic resonance spectroscopy data
Authors: Wilson Martin , Reynolds Greg , Kauppinen Risto A. , Arvanitis Theodoros N. , Peet Andrew C.
Published: September 2010

Totally Automatic Robust Quantitation in NMR (TARQUIN), a new method for the fully automatic analysis of short echo time in vivo 1H Magnetic resonance spectroscopy is presented. Analysis is performed in the time domain using non‐negative least squares, and a new method for applying soft constraints to signal amplitudes is used to improve fitting stability. Initial point truncation and Hankel singular value decomposition water removal are used to reduce baseline interference. Three methods were used to test performance. First, metabolite concentrations from six healthy volunteers at 3 T were compared with LCModel™. Second, a Monte‐Carlo simulation was performed and results were compared with LCModel™ to test the accuracy of the new method. Finally, the new algorithm was applied to 1956 spectra, acquired clinically at 1.5 T, to test robustness to noisy, abnormal, artifactual, and poorly shimmed spectra. Discrepancies of less than approximately 20% were found between the main metabolite concentrations determined by TARQUIN and LCModel™ from healthy volunteer data. The Monte‐Carlo simulation revealed that errors in metabolite concentration estimates were comparable with LCModel™. TARQUIN analyses were also found to be robust to clinical data of variable quality. In conclusion, TARQUIN has been shown to be an accurate and robust algorithm for the analysis of magnetic resonance spectroscopy data making it suitable for use in a clinical setting. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
More accurate estimation of diffusion tensor parameters using diffusion kurtosis imaging
Authors: Veraart Jelle , Poot Dirk H. J. , Van Hecke Wim , Blockx Ines , Van der Linden Annemie , Verhoye Marleen , Sijbers Jan
Published: September 2010

With diffusion tensor imaging, the diffusion of water molecules through brain structures is quantified by parameters, which are estimated assuming monoexponential diffusion‐weighted signal attenuation. The estimated diffusion parameters, however, depend on the diffusion weighting strength, the b‐value, which hampers the interpretation and comparison of various diffusion tensor imaging studies. In this study, a likelihood ratio test is used to show that the diffusion kurtosis imaging model provides a more accurate parameterization of both the Gaussian and non‐Gaussian diffusion component compared with diffusion tensor imaging. As a result, the diffusion kurtosis imaging model provides a b‐value‐independent estimation of the widely used diffusion tensor parameters as demonstrated with diffusion‐weighted rat data, which was acquired with eight different b‐values, uniformly distributed in a range of [0,2800 sec/mm2]. In addition, the diffusion parameter values are significantly increased in comparison to the values estimated with the diffusion tensor imaging model in all major rat brain structures. As incorrectly assuming additive Gaussian noise on the diffusion‐weighted data will result in an overestimated degree of non‐Gaussian diffusion and a b‐value‐dependent underestimation of diffusivity measures, a Rician noise model was used in this study. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
In the ring with polycystic kidney disease—avoiding the knockout punch
Authors: Adam Julie , Pollard Patrick J
Published: September 2010

Autosomal dominant polycystic kidney disease (PKD) is an inherited disease that results from mutations in either polycystin (PKD1) or polycystin 2 (PKD2), both of which are large, complex, and multifunctional proteins whose loss results in the development of numerous fluid‐filled cysts and fibrosis that compromise renal function. A number of spontaneous and engineered mouse models of PKD have provided some understanding of many aspects of cyst development, modifier genes, and mechanistic pathways, but fall short of reproducing the human disease accurately. Two recent papers in The Journal of Pathology set out new models using miRNA, or inducible and targeted recombination, that achieve partial or timed suppression of Pkd1. Instead of knocking out Pkd1 immediately, or completely, these more subtle approaches may help deliver more faithful models of this significant human renal disease. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Invited Commentary for Hassane S, Leonhard WN, van der Wal A, et al. Elevated TGFβ–Smad signalling in experimental Pkd1 models and human patients with polycystic kidney disease. J Pathol 2010; 222: 21–31. And for Wang E, Hsieh‐Li HM, Chiou YY, et al. Progressive renal distortion by multiple cysts in transgenic mice expressing artificial microRNAs against Pkd1. J Pathol 2010; 222: 238–248.
Genetically informed lung cancer medicine
Authors: Pao William , Iafrate A John , Su Zengliu
Published: September 2010

Knowledge of tumour mutation status has become increasingly important for the prioritization of targeted therapies for cancer. We review here the major known ‘driver’ mutations with therapeutic relevance in non‐small cell lung cancer. We also discuss a variety of methods now being employed in molecular diagnostic laboratories to detect genetic alterations in lung tumours. A genetically‐informed approach to lung cancer medicine is rapidly becoming the standard of care worldwide and should lead to improved outcomes for patients. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Mutant K‐ras promotes carcinogen‐induced murine colorectal tumourigenesis, but does not alter tumour chromosome stability
Authors: Luo Feijun , Poulogiannis George , Ye Hongtao , Hamoudi Rifat , Zhang Wenyan , Dong Gehong , Arends Mark J
Published: September 2010

K‐ras (KRAS) mutations are observed in around 40% of human colorectal adenomas and carcinomas. Previously, we developed and characterized a strain of transgenic mice with inducible intestinal epithelial expression of K‐ras$^{Val12}$ via a Cre/LoxP system. To evaluate the influence of mutant K‐ras on carcinogen‐induced colorectal tumourigenesis, we induced neoplastic alterations in the large intestines of wild‐type and K‐ras$^{Val12}$ mice using the colon‐selective carcinogen 1,2‐dimethylhydrazine (DMH), which has been widely used to induce colorectal tumours that are histopathologically similar to those observed in humans. K‐ras$^{Val12}$ expression significantly promoted DMH‐induced colorectal tumourigenesis: the average lifespan of the mice decreased from 38.52 ± 1.97 weeks for 40 control mice to 32.42 ± 2.17 weeks for 26 K‐ras$^{Val12}$ mice (mean ± SEM, p < 0.05) and the abundance of large intestinal tumours increased from 2.27 ± 0.15 per control mouse to 3.85 ± 0.20 in K‐ras$^{Val12}$ mice (mean ± SEM, p < 0.01). Adenomas from DMH‐treated K‐ras$^{Val12}$ mice showed significantly higher proportions of Ki‐67‐positive proliferating cells (10.9 ± 0.69%) compared with those from DMH‐treated wild‐type mice (7.77 ± 0.47%) (mean ± SEM, p < 0.01) and a mild increase in apoptotic nuclei staining for cleaved caspase‐3 (1.94 ± 0.21% compared with 1.15 ± 0.14%, mean ± SEM, p < 0.01). In the adenomas from DMH‐treated K‐ras$^{Val12}$ mice, K‐ras$^{Val12}$ transgene recombination and expression were confirmed, with immunohistochemical evidence of strong Erk/MapK and mild PI3K/Akt pathway activation compared with adenomas from DMH‐treated wild‐type mice. Microarray hybridization and clustering analysis demonstrated different expression profiles in adenomas from DMH‐treated wild‐type and DMH‐treated K‐ras$^{Val12}$ mice, indicating involvement of different molecular mechanisms including Erk/MapK and PI3K/Akt signalling in K‐ras$^{Val12}$‐expressing adenomas. Array‐comparative genomic hybridization analysis showed chromosome stability in both cohorts, with only a very few tiny alterations observed in one adenoma from a DMH‐treated K‐ras$^{Val12}$ mouse. Taken together, these data show that mutant K‐ras significantly promotes DMH‐induced colorectal tumourigenesis, resulting in distinct changes in cell signalling and proliferation, but does not alter chromosome stability in the tumours. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Signalling networks associated with urokinase‐type plasminogen activator (uPA) and its inhibitor PAI‐1 in breast cancer tissues: new insights from protein microarray analysis
Authors: Wolff Claudia , Malinowsky Katharina , Berg Daniela , Schragner Kerstin , Schuster Tibor , Walch Axel , Bronger Holger , Höfler Heinz , Becker Karl‐Friedrich
Published: September 2010

The urokinase‐type plasminogen activator (uPA) and the main uPA inhibitor PAI‐1 play important roles in cell migration and invasion in both physiological and pathological contexts. Both factors are clinically applicable predictive markers in node‐negative breast cancer patients that are used to stratify patients for adjuvant chemotherapy. In addition to their classical functions in plasmin regulation, both factors are key components in cancer‐related cell signalling. Such signalling cascades are well described in cell culture systems, but a better understanding of uPA‐ and PAI‐1‐associated signalling networks in clinical tissues is needed. We examined the expression of uPA, PAI‐1, and 21 signalling molecules in 201 primary breast cancer tissues using protein microarrays. Expression of uPA was significantly correlated with the expression of ERK and Stat3, while expression of PAI‐1 was correlated with the uPA receptor and Akt activation, presumably via integrin and HER‐receptor signalling. Analysis of uPA expression did not reveal any significant correlation with staging, grading or age of the patients. The PAI‐1 expression was correlated with nodal stage. Network monitoring for uPA and PAI‐1 in breast cancer reveals interactions with main signalling cascades and extends the findings from cell culture experiments. Our results reveal possible mechanisms underlying cancer development. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Cancer stem cells: problems for therapy?
Authors: Alison Malcolm R , Lim Susan ML , Nicholson Linda J
Published: September 2010

Many, if not all, tumours contain a sub‐population of self‐renewing and expanding stem cells known as cancer stem cells (CSCs). The symmetric division of CSCs is one mechanism enabling expansion in their numbers as tumours grow, while epithelial–mesenchymal transition (EMT) is an increasingly recognized mechanism to generate further CSCs endowed with a more invasive and metastatic phenotype. Putative CSCs are prospectively isolated using methods based on either a surface marker or an intracellular enzyme activity and then assessed by a ‘sphere‐forming’ assay in non‐adherent culture and/or by their ability to initiate new tumour growth when xenotransplanted into immunocompromised mice—hence, these cells are often referred to as tumour‐propagating cells (TPCs). Cell sub‐populations enriched for tumour‐initiating ability have also been found in murine tumours, countering the argument that xenografting human cells merely select human cells with an ability to grow in mice. Cancer progression can be viewed as an evolutionary process that generates new/multiple clones with a fresh identity; this may be a major obstacle to successful cancer stem cell eradication if treatment targets only a single type of stem cell. In this review, we first briefly discuss evidence that cancer can originate from normal stem cells or closely related descendants. We then outline the attributes of CSCs and review studies in which they have been identified in various cancers. Finally, we discuss the implications of these findings for successful cancer therapies, concentrating on the self‐renewal pathways (Wnt, Notch, and Hedgehog), aldehyde dehydrogenase activity, EMT, miRNAs, and other epigenetic modifiers as potential targets for therapeutic manipulation. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
The positive predictive value of a hyperkalemia diagnosis in automated health care data
Authors: Raebel Marsha A. , Smith Michael L. , Saylor Gwyn , Wright Leslie A. , Cheetham Craig , Blanchette Christopher M. , Xu Stanley
Published: September 2010

Purpose

Our objectives were to determine performance of coded hyperkalemia diagnosis at identifying (1) clinically evident hyperkalemia and (2) serum potassium>6 mmol/L.

Methods

This retrospective observational study included 8722 patients with diabetes within an integrated healthcare system who newly initiated an angiotensin converting enzyme inhibitor, angiotensin receptor blocker, or spironolactone. The primary outcome was first hyperkalemia‐associated event (hospitalization, emergency department visit or death within 24 hours of coded diagnosis and/or potassium≥6 mmol/L) during the first year of therapy. Medical records were reviewed.

Results

Among a random sample of 99 patients not coded as having hyperkalemia, none had hyperkalemia upon record review. Among all 64 patients identified as having hyperkalemia, all had hospitalization or emergency department visit associated with coded diagnosis or elevated potassium. Of 55 with coded diagnosis, 42 (PPV 76%) had clinically evident hyperkalemia; 32 (PPV 58%) had potassium≥6. Of 9 identified using only potassium≥6, 7 (PPV 78%) had clinically evident hyperkalemia.

Conclusions

Nearly one‐fourth of patients with coded diagnosis do not have clinically evident hyperkalemia and nearly one‐half do not have potassium≥6. Because both false positives and negatives occur with coded diagnoses, medical record validation of hyperkalemia‐associated outcomes is necessary. Copyright © 2010 John Wiley & Sons, Ltd.
Crystal structure analysis of Bacillus subtilis ferredoxin‐NADP+ oxidoreductase and the structural basis for its substrate selectivity
Authors: Komori Hirofumi , Seo Daisuke , Sakurai Takeshi , Higuchi Yoshiki
Published: September 2010

Bacillus subtilis yumC encodes a novel type of ferredoxin‐NADP+ oxidoreductase (FNR) with a primary sequence and oligomeric conformation distinct from those of previously known FNRs. In this study, the crystal structure of B. subtilis FNR (BsFNR) complexed with NADP+ has been determined. BsFNR features two distinct binding domains for FAD and NADPH in accordance with its structural similarity to Escherichia coli NADPH‐thioredoxin reductase (TdR) and TdR‐like protein from Thermus thermophilus HB8 (PDB code: 2ZBW). The deduced mode of NADP+ binding to the BsFNR molecule is nonproductive in that the nicotinamide and isoalloxazine rings are over 15 Å apart. A unique C‐terminal extension, not found in E. coli TdR but in TdR‐like protein from T. thermophilus HB8, covers the re‐face of the isoalloxazine moiety of FAD. In particular, Tyr50 in the FAD‐binding region and His324 in the C‐terminal extension stack on the si‐ and re‐faces of the isoalloxazine ring of FAD, respectively. Aromatic residues corresponding to Tyr50 and His324 are also found in the plastid‐type FNR superfamily of enzymes, and the residue corresponding to His324 has been reported to be responsible for nucleotide specificity. In contrast to the plastid‐type FNRs, replacement of His324 with Phe or Ser had little effect on the specificity or reactivity of BsFNR with NAD(P)H, whereas replacement of Arg190, which interacts with the 2′‐phosphate of NADP+, drastically decreased its affinity toward NADPH. This implies that BsFNR adopts the same nucleotide binding mode as the TdR enzyme family and that aromatic residue on the re‐face of FAD is hardly relevant to the nucleotide selectivity.
Tetrad selectivity in polarity‐driven switch peptides: the best turn is not always the best nucleation site
Authors: Gehenn Katja , Reed Jennifer
Published: September 2010

In some naturally occurring protein sequences, an abrupt, concerted refolding from β‐sheet to helical conformation occurs when the polarity of the surrounding medium drops below a critical level. This switch‐like behaviour was first observed on the HIV‐1 envelope glycoprotein gp120, where it plays a crucial role in the efficient binding of gp120 to the T‐cell receptor CD4. Previous work had shown that an N‐terminal amino acid tetrad LPCR and a Trp located 5–20 residues downstream to the tetrad are common motifs in polarity‐driven switch peptides. The LPCR tetrad governs the folding of the subsequent residues and acts as a helix initiation site, whereas the Trp is responsible for the cooperative character of the structural change due to multiple, simultaneous interactions of its quadrupole moment with several amino acid residues within the sequences. Here we identify and characterize new families of switch peptides that use different, turn‐probable tetrads (LPST and VPSR) as helix initiation sites at the N‐terminus. We have also been able to demonstrate that some tetrads with extremely high turn probability do not serve as helix initiation sites. Comparison of these with LPCR and the newly discovered tetrads LPST and VPSR has allowed a more comprehensive description of the physico‐chemical properties of helix‐inducing tetrads. The deeper understanding of the intrinsic properties of switch sequences allows the design of artificial polarity‐driven switches, applicable in engineering of, e.g. controllable binding sites in artificial proteins. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.
A case study on modeling and optimizing photolithography stage of semiconductor fabrication process
Authors: Kim Hyun‐Jin , Kim Kwang‐Jae , Kwak Doh‐Soon
Published: September 2010

Photolithography in the semiconductor fabrication process is the core stage that determines the quality of semiconductor chips. The fabrication process is a batch process that causes variation in the quality of chips; thus, uniformity has always been an important goal of the process. This research is a case study on optimizing the photolithography stage to improve uniformity and the target achievement of critical dimension, a quality measure of semiconductor chips. The case study finds the optimal setting of input variables in photolithography by applying multivariate normal linear modeling with operational data obtained by sampling during manufacturing. The predicted performance of the optimal setting is found to be close to the limit of improvement estimated based on the model. For practitioners, several issues that can be considered for better optimization are also provided. Copyright © 2010 John Wiley & Sons, Ltd.
Error propagation in normalization of stable isotope data: a Monte Carlo analysis
Authors: Skrzypek Grzegorz , Sadler Rohan , Paul Debajyoti
Published: September 2010

A higher analytical precision of a stable isotope ratio mass spectrometer does not automatically guarantee accurate determination of the true isotope composition (δ‐value) of samples, since estimates of true δ‐values are obtained from the normalization of raw isotope data. We performed both Monte Carlo simulations and laboratory experiments to investigate aspects of error propagation during the normalization of carbon stable isotope data. We found that increasing both the number of different reference standards and the number of repetitions of each of these standards reduces the normalization error. A 50% reduction in the normalization error can be achieved over the two‐point normalization by either analyzing two standards four times each, or four standards two times each. If the true δ‐value of a sample is approximately known a priori, the normalization error may then be reduced through a targeted choice of locally optimal standards. However, the difference in improvement is minimal and, therefore, a more practical strategy is to use two or more standards covering the whole stable isotope scale. The selection of different sets of standards by different laboratories or for different batches of samples in the same laboratory may lead to significant differences in the normalized δ‐values of the same samples, leading to inconsistent results. Hence, the same set of standards should always be used for a particular element and a particular stable isotope analytical technique. Copyright © 2010 John Wiley & Sons, Ltd.
Marked difference in fragmentation between collision‐induced excitation and chemi‐excitation of keto esters produced from dioxetanes bearing a 4‐(benzothiazol‐2‐yl)‐3‐hydroxyphenyl moiety in negative‐mode matrix‐assisted laser desorption/ionization time‐of‐flight tandem mass spectrometry
Authors: Ijuin Hisako K. , Yamada Masaki , Ohashi Mamoru , Tanimura Masatoshi , Watanabe Nobuko , Matsumoto Masakatsu
Published: September 2010

A dioxetane bearing a hydroxyphenyl group produces an unstable oxidoaryl anion by deprotonation which rapidly decomposes with accompanying emission of light effectively by the intramolecular charge‐transfer‐induced decomposition (CTID) mechanism. Although several mechanisms have been proposed to explain chemi‐excitation in CTID, strong experimental evidence is still lacking. In the course of our investigation to clarify the chemi‐excitation process, negative‐mode matrix‐assisted laser desorption/ionization time‐of‐flight collision‐induced dissociation tandem mass spectrometry (MALDI‐TOF‐CID‐MS/MS) was used to investigate the decomposition of bicyclic dioxetanes bearing a 4‐(benzothiazol‐2‐yl)‐3‐hydroxyphenyl moiety 1 and their related keto esters 2 in a gas phase. Dioxetanes 1 decomposed to give 2 in an electronically excited state, which underwent α‐cleavage of a ketone moiety, while authentic 2 (ground state) hardly showed fragmentation in MS1. On the other hand, 2 displayed fragment ions in CID‐MS/MS, though the fragmentation pattern was significantly different between 2a (R = tert‐butyl) and 2b–2d (R = isopropyl, ethyl and methyl, respectively): 2a exhibited mainly α‐cleavage of a ketone moiety, while 2b–2d showed β‐cleavage of the aromatic ester moiety. The marked difference in fragmentation between 2 (electronically excited state) produced directly from 1 and authentic 2 under CID was most likely due to the difference in the excitation processes: chemi‐excitation of 2 by CTID of 1 versus vibrational excitation of 2 induced by collision in MS/MS. Copyright © 2010 John Wiley & Sons, Ltd.
Role of the UV absorber as a matrix in matrix‐assisted laser desorption/ionization mass spectrometric analysis of a mixture of a UV absorber and a stabilizer
Authors: Im Song‐Hee , Choi Sung‐Seen
Published: September 2010

A mixture of a UV absorber (Tinuvin 234 or Tinuvin 329) and a UV stabilizer (Tinuvin 770) was analyzed using matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) without any matrix. Fragmentation patterns of the UV absorbers and stabilizer were also investigated. The mass spectra showed the [M+H]+ ions and some fragment ions. Tinuvin 234, Tinuvin 329, and Tinuvin 770 generated three (m/z 119, 370, 432), one (m/z 252), and two (m/z 124 and 140) fragment ions, repectively. These fragment ions can be used to identify the chemical structures of the UV absorbers and stabilizer. Since the UV absorber performed a role as the matrix, the ion abundance of the UV stabilizer was enhanced by mixing with the UV absorber. When organic materials extracted from polypropylene (PP) containing the UV absorber and stabilizer were directly analyzed using MALDI‐MS without any matrix, the protonated molecule of the UV stabilizer was detected in abundance but the product ions of the UV absorber were not observed. When 2,5‐dihydroxybenzoic acid was used as a matrix, the protonated molecule of the UV absorber was observed. Copyright © 2010 John Wiley & Sons, Ltd.
Metal displacement and stoichiometry of protein‐metal complexes under native conditions using capillary electrophoresis/mass spectrometry
Authors: Moini Mehdi
Published: September 2010

Increases in the study of protein‐metal complexes, as well as in metal displacement in protein‐metal complexes under native conditions for optimum catalytic properties in drug research and catalyst design, demands a separation/detection technology that can accurately measure metal displacement and stoichiometry in protein‐metal complexes. Both nuclear magnetic resonance (NMR) and X‐ray diffraction techniques have been used for this purpose; however, these techniques lack sensitivity. Electrospray ionization mass spectrometry (ESI‐MS) using direct infusion offers higher sensitivity than the former techniques and provides molecular distribution of various protein‐metal complexes. However, since protein‐metal complexes under native conditions usually are dissolved in salt solutions, their direct ESI‐MS analysis requires off‐line sample clean‐up prior to MS analysis to avoid sample suppression during ESI. Moreover, direct infusion of the salty solution promotes non‐specific salt adduct formation by the protein‐metal complexes under ESI‐MS, which complicates the identification and stoichiometry measurements of the protein‐metal complexes. Because of the high mass of protein‐metal complexes and lack of sufficient resolution by most mass spectrometers to separate non‐specific from specific metal‐protein complexes, accurate protein‐metal stoichiometry measurements require some form of sample clean up prior to ESI‐MS analysis. In this study, we demonstrate that capillary electrophoresis/electrospray ionization in conjunction with a medium‐resolution (∼10 000) mass spectrometer is an efficient and fast method for the measurement of the stoichiometry of the protein‐metal complexes under physiological conditions (pH ∼7). The metal displacement of Co2+ to Cd2+, two metal ions necessary for activation in the monomeric AHL lactonase produced by B. thuringiensis, has been used as a proof of concept. Copyright © 2010 John Wiley & Sons, Ltd.
Gas chromatography/time‐of‐flight mass spectrometry‐based metabonomics of hepatocarcinoma in rats with lung metastasis: elucidation of the metabolic characteristics of hepatocarcinoma at formation and metastasis
Authors: Li Zong‐Fang , Wang Juan , Huang Chen , Zhang Shu , Yang Jun , Jiang An , Zhou Rui , Pan Dun
Published: September 2010

Hepatocarcinoma (HCC) has a very high mortality rate and the high recurrence and metastasis rates contribute to the poor prognosis of HCC patients. To understand HCC formation and metastasis, we assessed the metabonomics of rat HCC and HCC with lung metastasis (HLM). The HLM rat model was established by exposure to diethylnitrosamine (DEN). Levels of serum and urine metabolites were quantified with gas chromatography/time‐of‐flight mass spectrometry (GC/TOFMS), and data were analyzed with partial least‐squares discrimination analysis (PLS‐DA). Serum and urine levels of some metabolites differed significantly between the control, HCC, and HLM groups. The products and intermediates from glycolysis and glutamate metabolism were elevated, while the tricarboxylic acid (TCA) cycle was inhibited, in both HCC and HLM. HLM samples revealed enhanced metabolism of nucleic acids, amino acids and glucuronic acid. PLS‐DA indicated that principal component weighting was greatest for serum serine, phenylalanine, lactic acid, tyrosine and glucuronic acid, and urine glycine, serine, 5‐oxyproline, malate, hippuric acid and uric acid. These data provide novel information that will improve understanding of the pathophysiological processes involved in HCC and HLM, and revealed potential metabolic markers for HCC invasion and metastasis. Copyright © 2010 John Wiley & Sons, Ltd.