bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of plasma membrane autoantigens in autoimmune hepatitis type 1 using a proteomics tool
Authors: Tahiri Fatima , Le Naour François , Huguet Stéphanie , Lai-Kuen René , Samuel Didier , Johanet Catherine , Saubamea Bruno , Tricottet Viviane , Duclos-Vallee Jean-Charles , Ballot Eric
Published: February 2008

Autoimmune hepatitis (AIH) is a liver disease with circulating autoantibodies predominantly directed against widely held cellular components. Because AIH is a liver-specific disease, autoantibodies against plasma membrane antigens may be involved in its pathogenesis and have been reported; however, no definite identification has been described. We thus investigated the fine specificity of anti-hepatocyte plasma membrane autoantibodies in type 1 AIH (AIH-1) using a proteomic tool. A plasma membrane–enriched fraction was validated using enzymatic activity and western blot analysis experiments. Sera from AIH-1 patients (n = 65) and from 90 controls, that is, healthy blood donors (n = 40) and patients with systemic diseases (n = 20) or other liver diseases (n = 30), were studied by immunoblot performed with plasma membrane proteins resolved by either sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) or 2-dimensional (2D) electrophoresis. Proteins contained in the immunoreactive spots were identified by sequences provided by ion-trap mass spectrometry. Hepatocytes probed with sera were also studied using confocal immunofluorescence and immunoelectron microscopy. The more prominent bands stained by patient sera were located at 38 kDa, 48, 50, 52 kDa, 62 kDa, 70 kDa, and a 95-kDa double band. Six proteins with known potential plasma membrane expression were identified: liver arginase (38 kDa), cytokeratins (CK) 8 and 18 (48-52 kDa), heat shock proteins (HSP) of 60, 70, 90 kDa, and valosin-containing protein (VCP) of 92 kDa. The presence of anti-membrane antibodies was confirmed by immunofluorescence and immunoelectron microscopy.

Conclusion:

Overall, our data demonstrate that liver arginase, CK 8/18, HSP 60, HSP 70, HSP 90, and VCP represent potential candidate targets on liver membrane for autoantibodies in AIH-1.
Synaptic protein expression in the medial temporal lobe and frontal cortex following chronic bilateral vestibular loss
Authors: Goddard Matthew , Zheng Yiwen , Darlington Cynthia L. , Smith Paul F.
Published: February 2008

Several studies have reported that bilateral vestibular deafferentation (BVD) results in the disruption of place cell function and theta activity in the hippocampus. Recent magnetic resonance imaging (MRI) studies in humans demonstrated that bilateral but not unilateral vestibular loss is associated with a bilateral atrophy of the hippocampus. In this study we investigated whether BVD in rats resulted in changes in the expression of four proteins related to neuronal plasticity, synaptophysin, SNAP‐25, drebrin and neurofilament‐L, in the hippocampal subregions (CA1, CA2/3, the DG) and the entorhinal (EC), perirhinal (PRC) and frontal cortices (FC), using western blotting. At 6 months following BVD, there were no significant differences in the expression of synaptophysin in any region. There were also no significant differences in SNAP‐25 expression in CA1, CA2/3, EC, PRC, or the FC; however, there was a significant increase in SNAP‐25 expression in the DG compared to sham controls. Drebrin A and E expression was significantly reduced in the EC and drebrin A was significantly reduced in the FC of BVD animals. NF‐L expression was not significantly different in CA1, CA2/3, DG, EC, or the PRC. However, its expression was significantly reduced in the FC of BVD animals. These data suggest that circumscribed neurochemical changes in SNAP‐25, drebrin and NF‐L expression occur in the DG, EC, and the FC over 6 months following BVD. © 2008 Wiley‐Liss, Inc.
New semantic learning in patients with large medial temporal lobe lesions
Authors: Bayley P.J. , O'Reilly R.C. , Curran T. , Squire L.R.
Published: February 2008

Two patients with large lesions of the medial temporal lobe were given four tests of semantic knowledge that could only have been acquired after the onset of their amnesia. In contrast to previous studies of postmorbid semantic learning, correct answers could be based on a simple, nonspecific sense of familiarity about single words, faces, or objects. According to recent computational models (for example, Norman and O'Reilly (2003) Psychol Rev 110:611–646), this characteristic should be optimal for detecting the kind of semantic learning that might be supported directly by the neocortex. Both patients exhibited some capacity for new learning, albeit at a level substantially below control performances. Notably, the correct answers appeared to reflect declarative memory. It was not the case that the correct answers simply popped out in some automatic way in the absence of any additional knowledge about the items. Rather, the few correct choices made by the patients tended to be accompanied by additional information about the chosen items, and the available knowledge appeared to be similar qualitatively to the kind of factual knowledge that healthy individuals gradually acquire over the years. The results are consistent with the idea that neocortical structures outside the medial temporal lobe are able to support some semantic learning, albeit to a very limited extent. Alternatively, the small amount of learning detected in the present study could depend on tissue within the posterior medial temporal lobe that remains intact in both patients. © 2008 Wiley‐Liss, Inc.
Preferential exchange rate effect of isotopic fractionation in a melting snowpack
Authors: Zhou Shiqiao , Nakawo Masayoshi , Hashimoto Shigemasa , Sakai Akiko
Published: February 2008

Stable isotope exchange processes between solid and liquid phases of a natural melting snowpack are investigated in detail by separating the liquid water from snow grains at different depths of the snowpack and collecting the bottom discharge using a lysimeter. In the melting–freezing mass exchange process between the two phases, the theoretical slope of the δDδ18O line for newly refrozen ice is calculated to be nearly that of pore water. However, based on observations of the isotopic evolution and snow grain coarsening of the snowpack, it is demonstrated that the slope of the δDδ18O line for newly refrozen ice is equal to that of the original ice. This is proved to be due to preferential water flow in the snowpack, which leads to relatively more deuterium and less oxygen‐18 in the mobile water than the immobile water because of the kinetic effect. Higher mass exchange rate in the mobile water region results in excess deuterium in the bulk refrozen ice, compared with the fractionation of uniform fractionation factors and exchange rate. This effect, which is termed the ‘preferential exchange rate effect of isotopic fractionation’, is shown to be larger in the lower part than the upper part of the snowpack. Copyright © 2008 John Wiley & Sons, Ltd.
Controlled preparation of thin fibrin films immobilized at solid surfaces
Authors: Riedel Tomáš , Brynda Eduard , Dyr Jan E. , Houska Milan
Published: February 2008

A technique for coating surfaces with attached fibrin structures without the formation of fibrin gel in bulk solution was developed. It is based on the catalytic effect of the surface‐bound thrombin on fibrinogen stabilized with inhibitor which inhibits thrombin in solution but not the thrombin on the surface. Such an inhibitor is antithrombin, the effect of which may be enhanced with heparin. Fibrinogen is first adsorbed on the substrate surface and then incubated with thrombin. The unbound thrombin is washed out and the surface is incubated with fibrinogen solution containing antithrombin III and heparin. A fibrin gel forms at the surface by the action of surface‐bound thrombin on ambient fibrinogen solution; however, the gel formation in bulk solution catalyzed by thrombin partially released from the surface is suppressed. By utilizing antithrombin‐independent inhibitors or repeating thrombin binding and incubation with fibrinogen solution, the amount of surface‐attached fibrin gel can be controlled. The formation of immobilized fibrin networks was observed using surface plasmon resonance and turbidity measurements and morphology was observed by TEM, SEM, and AFM. Using this technique, a porous scaffold made of polylactide fibers was coated with fibrin without filling the space between fibers with a bulk fibrin gel. The technique makes it possible to coat the inner surface of porous scaffolds with surface‐attached fibrin gel while preserving free volume for cell migration into the pores. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res 2009
Accuracy of brief and full forms of the child mania rating scale
Authors: Henry David B. , Pavuluri Mani N. , Youngstrom Eric , Birmaher Boris
Published: February 2008

This study assesses the sensitivity of full and brief forms of a parent‐rated mania scale to variations in diagnoses. Parents of a sample of 150 subjects either diagnosed with bipolar disorder (BD) or attention deficit hyperactivity disorder (ADHD), or healthy controls (HC), completed the full Child Mania Rating Scale and other measures. We used single‐parameter item‐response theory models to produce a brief parent mania rating scale from the full version. The 10‐item, brief Child Mania Rating Scale—Parent (CMRS‐P) version correlated .93 with 11 items from the full CMRS‐P that were not used in constructing the brief version, and showed accuracy comparable to the full scale in differentiating BD from ADHD, and in discriminating among bipolar subtypes. © 2008 Wiley Periodicals, Inc. J Clin Psychol 64:1–14, 2008.
Plasmid growth hormone releasing hormone therapy in healthy and laminitis‐afflicted horses—evaluation and pilot study
Authors: Brown Patricia A. , Bodles‐Brakhop Angela , Draghia‐Akli Ruxandra
Published: February 2008

Background

In vivoelectroporation dramatically improves the potency of plasmid‐mediated therapies, including in large animal models. Laminitis and arthritis are common and debilitating diseases in the horse, as well as humans.

Methods

The effects of growth hormone releasing hormone (GHRH) on healthy horses and on horses with laminitis that were followed for 6 months after a single intramuscular injection and electroporation of 2.5 mg of an optimized myogenic GHRH‐expressing plasmid were examined.

Results

In the first study on six healthy horses, we observed a significant increase in body mass by day 180 compared to baseline (P< 0.003), and an increase in erythrocyte production (hematocrit, red blood cells, hemoglobin,P= 0.03). IGF‐I levels were increased by 7% by day 120 (P= 0.02). A pilot study was performed on two horses with chronic laminitis, a vascular condition often associated with arthritis, with two horses with similar clinical disease serving as non‐treated controls. Treated horses experienced an increase in weight compared to control horses that received standard care (P= 0.007). By 6 months post‐treatment, treated subjects were rated pasture sound. Physical and radiographic evaluation demonstrated significant improvement with reduced inflammation and decreased lameness.

Conclusions

These results demonstrate that a plasmid therapy delivered by electroporation can potentially be used to treat chronic conditions in horses, and possibly other very large mammals. While further studies are needed, overall this proof‐of‐concept work presents encouraging data for studying gene therapeutic treatments for Raynaud's syndrome and arthritis in humans. Copyright © 2008 John Wiley & Sons, Ltd.
Accelerated hypertrophic chondrocyte kinetics in GDF‐7 deficient murine tibial growth plates
Authors: Mikic Borjana , Ferreira Maria P. , Battaglia Todd C. , Hunziker Ernst B.
Published: February 2008

The Growth/Differentiation Factors (GDFs) are a subgroup of the Bone Morphogenetic Proteins (BMPs) well known for their role in joint formation and chondrogenesis. Mice deficient in one of these signaling molecules, GDF‐5, have recently been shown to exhibit a decreased rate of endochondral bone growth in the proximal tibia due to a significantly longer hypertrophic phase duration. GDF‐7 is a related family member, which exhibits a high degree of sequence identity with GDF‐5. The purpose of the present study was to determine whether GDF‐7 deficiency also alters the endochondral bone growth rate in mice and, if so, how this is achieved. Stereologic and cell kinetic parameters in proximal tibial growth plates from 5‐week‐old female GDF‐7 −/− mice and wild type control littermates were examined. GDF‐7 deficiency resulted in a statistically significant increase in growth rate (+26%; p = 0.0084) and rate of cell loss at the chondrosseous junction (+25%; p = 0.0217). Cells from GDF‐7 deficient mice also exhibited a significantly shorter hypertrophic phase duration compared to wild type controls (−27%; p = 0.0326). These data demonstrate that, in the absence of GDF‐7, the rate of endochondral bone growth is affected through the modulation of hypertrophic phase duration in growth plate chondrocytes. These findings further support a growing body of evidence implicating the GDFs in the formation, maturation, and maintenance of healthy cartilage. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:986–990, 2008
Solid‐state P‐31 NMR study of the formation of hydroxyapatite in the presence of glutaric acid
Authors: Tseng Yao‐Hung , Mou Yun , Chen Peng‐Huan , Tsai Tim W. T. , Hsieh Cheng‐I. , Mou Chung‐Yuan , Chan Jerry C. C.
Published: February 2008

We demonstrate that glutaric acid can be used to prepare nanorods of hydroxyapatite under hydrothermal condition at 100 °C with a Ca2+:glutaric acid molar ratio of 1:4. Frequency‐switched Lee–Goldburg irradiation is employed to obtain high‐resolution31P{1H} correlation spectra of the reaction mixture at two different reaction periods, from which it is shown that octacalcium phosphate is the precursor phase of the final hydroxyapatite product. In addition, the spectra show that a substantial amount of water molecules is trapped between the glutaric acid and the hydroxyapatite surface, indicating that water molecules may play a prominent role in the noncovalent interaction of the glutaric acid and the HAp surface. Copyright © 2008 John Wiley & Sons, Ltd.
Revisiting silicate substituted hydroxyapatite by solid‐state NMR
Authors: Gasquères G. , Bonhomme C. , Maquet J. , Babonneau F. , Hayakawa S. , Kanaya T. , Osaka A.
Published: February 2008

Silicon‐substituted hydroxyapatite (Si‐HAp) has shown promising properties such as high‐bone remodeling around implants. So far, the techniques used for the structural characterization of the Si‐HAp have given indirect evidence of the presence of silicon inside the structure (by X‐ray and neutron diffraction). In this paper, we focus on Si‐HAp derivatives obtained by a precipitation method (widely described in the literature). We demonstrate here by solid‐state NMR spectroscopy that only a fraction of the silicon atoms are incorporated into the HAp lattice in the form of Q0 (SiO44−) species, for 4.6 wt% Si‐HAp. A large amount of silicate units are located outside the HAp structure and correspond to silica‐gel units. All results were established through 29Si MAS, 1H →29Si CP MAS and T1ρ(1H) edited 1H →29Si CP MAS experiments. This last pulse scheme acted as a powerful editing sequence, leading to unambiguous spectroscopic conclusions, concerning the location of the SiO44− moieties. Copyright © 2008 John Wiley & Sons, Ltd.
Towards a model of the mineral–organic interface in bone: NMR of the structure of synthetic glycosaminoglycan‐ and polyaspartate‐calcium phosphate composites
Authors: Best Serena M. , Duer Melinda J. , Reid David G. , Wise Erica R. , Zou Shuo
Published: February 2008

We have synthesised three materials–chondroitin sulphate (ChS, a commercial product derived from shark cartilage and predominantly chondroitin‐6‐sulphate (Ch‐6‐S)) bound to pre‐formed hydroxyapatite (HA, Ca10(PO4)6(OH)2), HA formed in the presence of ChS and poly‐Asp bound to pre‐formed HA–to generate models for the mineral–organic interface in bone. The three materials have been investigated by 13C cross polarisation magic‐angle spinning (CPMAS) NMR, 13C{31P} rotational echo double resonance (REDOR) and powder x‐ray diffraction (XRD) in order to verify their composition and to determine the nature of their binding to HA. Our results show that for HA formed in the presence of Ch‐6‐S, all carbon atoms in the Ch‐6‐S having contact with mineral phosphate. We propose that HA in this case forms all around the Ch‐6‐S polymer rather than along one face of it as is more commonly supposed in cases of templating by organic molecules. However, Ch‐6‐S binding to pre‐formed HA probably occurs via a surface layer of water on the mineral rather than to the mineral directly. In contrast, poly‐Asp binds closely to the pre‐formed HA surface and so is clearly able to displace at least some of the surface‐bound water. Copyright © 2008 John Wiley & Sons, Ltd.
Variable angle spinning (VAS) experiments for strongly oriented systems: methods development and preliminary results
Authors: Qian Chunqi , Thureau Pierre , Martin Rachel W.
Published: February 2008

Variable angle spinning (VAS) experiments provide a useful method for measuring long‐range dipolar couplings and obtaining isotropic–anisotropic correlation spectra. These experiments make it possible to obtain correlations between isotropic and anisotropic spectra without altering the chemical composition of the sample. They also allow working with very strongly oriented systems that are not accessible to solution‐state techniques. In this communication, we discuss recent hardware developments in our laboratory and show representative data from small molecules in strongly oriented liquid‐crystalline samples. Copyright © 2008 John Wiley & Sons, Ltd.
Quantitative FLASH MRI at 3T using a rational approximation of the Ernst equation
Authors: Helms Gunther , Dathe Henning , Dechent Peter
Published: February 2008

From the half‐angle substitution of trigonometric terms in the Ernst equation, rational approximations of the flip angle dependence of the FLASH signal can be derived. Even the rational function of the lowest order was in good agreement with the experiment for flip angles up to 20°. Three‐dimensional maps of the signal amplitude and longitudinal relaxation rates in human brain were obtained from eight subjects by dual‐angle measurements at 3T (nonselective 3D‐FLASH, 7° and 20° flip angle, TR = 30 ms, isotropic resolution of 0.95 mm, each 7:09 min). The corresponding estimates of T1 and signal amplitude are simple algebraic expressions and deviated about 1% from the exact solution. They are ill‐conditioned to estimate the local flip angle deviation but can be corrected post hoc by division of squared RF maps obtained by independent measurements. Local deviations from the nominal flip angles strongly affected the relaxation estimates and caused considerable blurring of the T1 histograms. Magn Reson Med 59:667–672, 2008. © 2008 Wiley‐Liss, Inc.
A case from the department of neurology
Authors: Krieger Stephen , Finkel Jennifer , Gligorov Nada
Published: February 2008

Uncompleted suicide attempts are a significant cause of morbidity, which in catastrophic cases can be both medically and ethically challenging to manage. We discuss the case of a 63‐year‐old man who survived a suicide attempt by venlafaxine (Effexor) overdose, causing an intracranial hemorrhage and leaving him in an apparently awake but noncommunicative state. Ethical concerns arose when considering if he should be indefinitely maintained on life support. These include the difficulties of characterizing his level of consciousness and prognosis; establishing his decisional capacity regarding end‐of‐life decisions in a setting of depression and suicidality; and assessing the suitability of a surrogate decision‐maker. In conclusion, we discuss whether the fact that his grave neurological condition was caused by a suicide attempt was relevant to the decision to continue or withdraw life support. Mt Sinai J Med 75:53–56, 2008. © 2008 Mount Sinai School of Medicine
A model for using community‐based participatory research to address the diabetes epidemic in east harlem
Authors: Horowitz Carol R. , Goldfinger Judith Z. , Muller Sara E. , Pulichino Romina S. , Vance Thomas L. , Arniella Guedy , Lancaster Kristie J.
Published: February 2008

Objective: Diabetes prevalence and mortality are increasing, with minority populations disproportionately affected. Despite evidence that weight loss due to improved nutrition and increased physical activity can prevent or control diabetes, there is often a disconnect between this evidence and individuals' lifestyles.

Methods: East Harlem is a predominantly African‐American and Latino neighborhood that has the highest rates of diabetes prevalence and mortality in New York City. The East Harlem Diabetes Center of Excellence is a community‐centered coalition. To help direct their work, the coalition used their experiences, research, outreach, and literature review to build a conceptual model describing how local factors affect health behaviors and health outcomes such as obesity and diabetes.

Results: This model describes the relationship between the physical environment, the social/medical environment and individual factors including demographic data, food and exercise beliefs and behaviors, and health outcomes. The coalition inserted local data from surveys and focus groups into the model to identify targets for future interventions, research, and activism.

Conclusions: This type of collaboration and the model may be useful tools to help communities identify and address the deficits that prevent their residents from enjoying the health benefits of improved nutrition and increased physical activity, and that also lead to racial and ethnic disparities in health. Mt Sinai J Med 75:13–21, 2008. © 2008 Mount Sinai School of Medicine
Criteria for static equilibrium in particulate mechanics computations
Authors: Tu Xuxin , Andrade José E.
Published: February 2008

The underlying physics of granular matter can be clearly solved using particulate mechanics methods, e.g. the discrete element method (DEM) that is inherently discontinuous and heterogeneous. To solve static problems, explicit schemes using dynamic relaxation procedures have been widely employed, in which naturally dynamic material parameters are typically adapted into pure numerical artifacts with the sole purpose of attaining meaningful results. In discrete computations using these explicit schemes, algorithmic calibration is demanded under general conditions in order to achieve quasi‐static states. Until now, procedures for algorithmic calibration have remained rather heuristic. This paper presents two criteria, using the concept of homogenized stresses, for evaluating equilibrium in quasi‐static applications of particulate mechanics methods. It is shown, by way of numerical examples, that the criteria for static equilibrium can be applied successfully to obtain quasi‐static solutions in explicit DEM codes through algorithmic calibrations. A general procedure is proposed herein for carrying out the algorithmic calibration effectively and efficiently. Copyright © 2008 John Wiley & Sons, Ltd.
Accidental release of pressurized liquid gases
Authors: Kunsch Jean‐Paul
Published: February 2008

Storage tanks with pressurized liquid gases such as propane or chlorine represent a substantial hazardous potential. The dynamics of the release, for example through an accidentally generated opening, are studied. The most important quantities are the time required to empty the reservoir and the cooling of the fluid. The temperature of the liquid phase influences the vapour pressure which represents a driving force of the outflow dynamics. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Overview: Data Assimilation and Model Reduction
Authors: Nichols N.K.
Published: February 2008

For the very large systems that arise in the environmental sciences, the available data are not sufficient to initiate a complex computational forecasting model. The technique of data assimilation enables measured observations (over time) to be combined with model predictions to generate accurate estimates of the system states – both current and future. An overview of data assimilation is presented here and the major types of assimilation method for treating very large nonlinear systems are described. Novel numerical assimilation techniques based on model reduction methods from control theory are then presented. The benefits of these techniques are demonstrated in a practical application from atmosphere and ocean modelling. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A Review of artificial boundary conditions for the Schrödinger equation
Authors: Antoine Xavier , Arnold Anton , Besse Christophe , Ehrhardt Matthias , Schädle Achim
Published: February 2008

In this review we discuss techniques to solve numerically the time–dependent linear Schrödinger equation on unbounded domains. We present some recent approaches and describe alternative ideas pointing out the relations between these works. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Systems theoretic questions in coding theory
Authors: Kelley Christine , Rosenthal Joachim , Sridhara Deepak
Published: February 2008

A central theme of current research in coding theory are low density parity‐check (LDPC) codes and more generally codes defined via graphs. There exist various decoding algorithms which work in a decentralized manner and which can be viewed as discrete dynamical systems. In this talk, we explain these algorithms from a systems theoretic point of view. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Asymptotic expansions of multiply scattered surface currents
Authors: Ecevit Fatih
Published: February 2008

We have recently uncovered the convergence characteristics of multiple scattering iterations for “two‐dimensional” as well as “three‐dimensional scalar (acoustics)” scattering models in the high‐frequency regime. As we have demonstrated, a most distinctive property of these latermodels, compared to their two‐dimensional counterparts, is the dependence of corresponding asymptotic expansions on the relative angle of rotation between the principal axes of the successive reflection points of the optical rays. Concerning the case of fully “three‐dimensional vector (electromagnetic)” scattering problems, here we show that the vectorial nature of the problem, in turn, gives rise to new additional complex structure. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Equation‐free methods for molecular dynamics: a lifting procedure
Authors: Frederix Yves , Samaey Giovanni , Vandekerckhove Christophe , Roose Dirk
Published: February 2008

We present a lifting procedure for the initialization of molecular dynamics simulations of dense fluids in the context of equation‐free computing. As the macroscopic system description we use a smooth representation of the density and velocity profile using a kernel density estimation, of which the dimensionality is reduced via a spline fit. The proposed initialization procedure generates initial atom positions on a grid, as well as initial velocities, such that the desired macroscopic density and velocity profiles are well approximated. We illustrate the approach on a model problem, and point out some inherent caveats in the design of good lifting operators for molecular dynamics. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Identification of the Alzheimer's disease amyloid precursor protein (APP) and its homologue APLP2 as essential modulators of glucose and insulin homeostasis and growth
Authors: Needham BE , Wlodek ME , Ciccotosto GD , Fam BC , Masters CL , Proietto J , Andrikopoulos S , Cappai R
Published: February 2008

The amyloid precursor protein (APP), the source of the neurotoxic amyloid β (Aβ) peptide involved in Alzheimer's disease (AD), belongs to a conserved family of related proteins. In mammals, the APP family contains amyloid precursor‐like protein 1 (APLP1) and amyloid precursor‐like protein 2 (APLP2). Whilst a number of activities have been attributed to the APP family, an overall function has not been definitively established. While ablating either the APP or APLP2 gene in mice produces minimal phenotypic change, the combined knockout of these genes in mice causes postnatal mortality. Postnatal survival therefore requires a shared but unknown function of APP and APLP2. To investigate the biochemical basis for the postnatal lethality, plasma was analysed from double knockout mice (APP−/− APLP2−/−) 2 days before birth, at gestational day E17, and from mice at 12–16 h after birth. The postnatal double knockouts had 66% lower plasma glucose levels than their wild‐type controls and 50% lower than their single knockout counterparts. Interestingly, the postnatal double knockouts displayed hyperinsulinaemia, as shown by inappropriate plasma insulin levels, given their degree of hypoglycaemia. The single knockout mice also showed hyperinsulinaemia and had 31% lower plasma glucose than the wild‐types. While the double knockouts did not survive more than 24 h after birth, the single knockouts reached adulthood and their hypoglycaemia continued. Therefore, APP and APLP2 expression modulates plasma insulin and glucose concentrations. Plasma calcium, magnesium and phosphate were also significantly reduced in the double knockouts compared to the wild‐types, and they showed distinctive growth restriction, suggesting the involvement of a metabolic impairment. These results link the expression of the APP and APLP2 genes with glucose homeostasis and growth and therefore identify a novel function for the APP family. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
SsrA genes of streptomycetes and association of proteins to the tmRNA during development and cellular differentiation
Authors: Mikulík Karel , Palečková Petra , Felsberg Jürgen , Bobek Jan , Zídková Jarmila , Halada Petr
Published: February 2008

Transfer‐messenger RNA (tmRNA, 10Sa RNA, ssrA) is bacterial RNA having both tRNA and mRNA properties and playing an essential role in recycling of 70S ribosomes that are stalled on defective mRNA. The trans‐translational system is thought to play a crucial role in bacterial survival under adverse conditions. Streptomycetes are Gram‐positive soil bacteria exposed to various physical and chemical stresses that activate specialized responses such as synthesis of antibiotics and morphological differentiation. Comparative sequence analysis of ssrA genes of streptomycetes revealed the most significant differences in the central parts of tag‐reading frames, in the stop codons and in the 15–34 nucleotide sequences following stop codons. A major challenge in understanding the interactions that control the function of tmRNA is the definition of protein interactions. Proteins from various phases of development of Streptomyces aureofaciens associated with tmRNA were analyzed. Using affinity chromatography on tmRNA‐Sepharose and photo cross‐linking experiments with [32P]labeled tmRNA seven proteins, the β and β′‐subunits of DNA dependent RNA polymerase, polyribonucleotide nucleotidyltransferase (PNPase), ribosomal protein SS1, ATP‐binding cassette transporters, elongation factor Tu, and SmpB were identified among the proteins associated with tmRNA of S. aureofaciens. We examined the functional role of ribosomal protein SS1 in a defined in vitro trans‐translation system. Our data show that the protein SS1 that structurally differs from S1 of Escherichia coli is required for translation of the tmRNA tag‐reading frame.
The origin and control of ex vivo oxidative peptide modifications prior to mass spectrometry analysis
Authors: Froelich Jennifer M. , Reid Gavin E.
Published: February 2008

The origin and control of ex vivo sample handling related oxidative modifications of methionine‐, S‐alkyl cysteine‐, and tryptophan‐containing peptides obtained from typical “in‐solution” or “in‐gel” proteolytic digestion strategies, have been examined by capillary HPLC and MS/MS. The origin of increased oxidation levels were found to be predominantly associated with the extensive ex vivo sample handling steps required for gel electrophoresis and/or in‐gel proteolytic digestion of proteins prior to analysis by MS. Conditions for deliberately controlling the oxidation state (both oxidation and reduction) of these peptides, as well as for those containing cysteine, have been evaluated using a series of model synthetic peptides and standard tryptic protein digests. Essentially complete oxidation of methionine‐ and S‐alkyl cysteine‐containing peptides was achieved by reaction with 30% hydrogen peroxide/5% acetic acid at room temperature for 30 min. Under these conditions, cysteine was also converted to cysteic acid, while only limited oxidation of tryptophan to oxindolylalanine, and methionine and S‐alkyl cysteine sulfoxides to their respective sulfones, were observed. Efficient reduction of methionine‐ and S‐alkyl cysteine sulfoxide‐containing peptides was achieved by reaction in 1 M dimethylsulfide/10 M hydrochloric acid at room temperature for 10 and 45 min, respectively. None of the reduction conditions evaluated were found to result in the reduction of oxindolylalanine, cysteic acid, or methionine sulfone.
Reduced airway function in early adulthood among subjects with wheezing disorder before two years of age
Authors: Goksör Emma , Gustafsson Per M , Alm Bernt , Åmark Mainor , Wennergren Göran
Published: February 2008

Aim

To compare airway function in early adulthood in subjects with wheezing in infancy with age‐matched controls and to analyze what accounts for a possible difference.

Methods

Asthma development has been prospectively studied in 101 children hospitalized due to wheezing before the age of two. The cohort was re‐investigated at age 17–20 years and tested with spirometry and for bronchial hyper‐responsiveness and allergic sensitization. An age‐matched population (n = 294) was used for comparison.

Results

The cohort had a significantly lower FEV1/FVC ratio and MEF50, both pre‐ and post‐bronchodilation, compared with the controls, P < 0.01. The reduction in airway function was most evident in current asthmatic female subjects, but a reduced pre‐bronchodilation FEV1/FVC ratio was also seen in symptom‐free cohort subjects, P = 0.03. In the multivariate analysis, female gender was the most prominent independent risk factor for reduced airway function in early adulthood, pre‐bronchodilation OR 4.0 (1.4–11.3) and post‐bronchodilation OR 8.8 (1.8–42.0). In addition, a history of early wheezing, that is, belonging to the cohort, was an independent risk factor for reduced airway function pre‐bronchodilation, OR 3.3 (1.3–8.7). Furthermore, there was an association between current bronchial hyper‐responsiveness and an increased risk of reduced airway function post‐bronchodilation, OR 7.3 (2.0–26.6).

Conclusion

Reduced airway function in early adulthood was found in subjects with wheezing early in life, compared with age‐matched controls. The reduction was most prominent in females with current asthma. Pediatr Pulmonol. 2008; 43:396–403. © 2008 Wiley‐Liss, Inc.
Isotopic evidence for condensed aromatics from non‐pyrogenic sources in soils – implications for current methods for quantifying soil black carbon
Authors: Glaser Bruno , Knorr Klaus‐Holger
Published: February 2008

Black carbon (BC) is a complex continuum of partly charred organic matter predominantly consisting of condensed aromatic and graphitic moieties and it has high potential for long‐term carbon sequestration in soils and sediments. There has been common agreement that BC is exclusively formed by incomplete combustion of organic matter, while non‐pyrogenic sources are negligible. In this study, we investigated the stable carbon isotope signature of benzenepolycarboxylic acids (BPCAs) as molecular markers for BC to test if there is also a significant contribution of non‐pyrogenic carbon to this fraction in soils. BPCAs were formed by hot nitric acid oxidation of different soils and analyzed by three different procedures: (i) elemental analysis – isotope ratio mass spectrometry (EA‐IRMS) of bulk BPCAs and gas chromatography – combustion – isotope ratio mass spectrometry (GC‐C‐IRMS) of (ii) BPCA trimethylsilyl (TMS) derivatives, and (iii) BPCA methyl derivatives. Best accuracy and precision of isotope measurements were obtained by EA‐IRMS of bulk BPCAs although this method has a risk of contamination by non‐BC‐derived compounds. The accuracy and precision of GC‐C‐IRMS measurements were superior for methyl derivatives (±0.1‰ and 0.5‰, respectively) to those for TMS derivatives (+3.5‰ and 2.2‰, respectively).

Comparison of BPCA δ13C values of soil samples prior to and after laboratory and field incubations with both positive and negative 13C labels at natural and artificial abundances revealed that up to 25% of the isolated BC fraction in soils had been produced in situ, without fire or charring. Commonly applied methods to quantify BC exclusively formed by pyrogenic processes may thus be biased by a significant non‐pyrogenic fraction. Further research is encouraged to better define isolated BC fractions and/or understand mechanisms for non‐pyrogenic BC production in soils. Copyright © 2008 John Wiley & Sons, Ltd.
A model to predict outbreak periods of the pest blackfly Simulium chutteri Lewis (simuliidae, Diptera) in the Great Fish River, Eastern Cape province, South Africa
Authors: Rivers‐Moore N. A. , Hughes D. A. , de Moor F. C.
Published: February 2008

Elevated, more constant flows characterize the current flow regime of the Great Fish River (Eastern Cape province, South Africa) following the completion of an interbasin transfer scheme (IBT) in 1977, where prior to this the winter months were often characterized by zero flows. Changes in aquatic macroinvertebrate communities, and in particular outbreaks of the pest blackfly Simulium chutteri Lewis (Diptera: Simuliidae) have been documented in response to these altered flows. Integrated control measures of pest blackfly have been advocated based on flow reductions during the winter months. In this study, a site‐specific discharge threshold of 2 m3 s−1 was identified as a flow reduction target based on the amount of hydraulic habitat available to S. chutteri larvae within a particular rapid. Hydrological analyses showed that flow conditions have created ideal blackfly larval habitat in this rapid, with prolonged uninterupted periods (>3 months) exceeding this threshold. A model was developed to predict probabilities and severities of blackfly outbreaks, based on flow periods and water temperatures, both of which determine the success and duration respectively of the aquatic phase of S. chutteri. July was identified as the critical month for flow restriction to 2 m3 s−1 for a period of 38 days, in order to reduce the winter populations of S. chutteri in the Great Fish River at the study site and avoid the typical spring outbreaks of blackfly. Copyright © 2008 John Wiley & Sons, Ltd.
Optimum fish passage and guidance designs are based in the hydrogeomorphology of natural rivers
Authors: Nestler J. M. , Goodwin R. A. , Smith D. L. , Anderson J. J. , Li S.
Published: February 2008

Understanding hydrodynamic cues used by outmigrating juvenile salmon (emigrants) to guide fine‐scale swim path selection is critical to successful fish guidance and passage at man‐made structures. We show how these cues can be inferred from channel features and complex flow fields of natural rivers through which emigrants pass. We then describe a new cue, ‘total hydraulic strain’, integrating properties of flow acceleration and turbulence through the spatial gradients in velocity to create a single flow field distortion metric amenable to the analysis of fish movement at the scale of large man‐made structures. We explain how total hydraulic strain, together with the magnitude of velocity, provide sufficient information for any fish to distinguish between the two categories of channel features with their mechanosensory system. We demonstrate that total hydraulic strain, velocity magnitude and hydrostatic pressure can be integrated into rule‐sets (the Strain–Velocity–Pressure (SVP) Hypothesis) to explain emigrant swim path selection near dams. To confirm the reasonableness of the SVP Hypothesis, we describe how its separate elements can be detected by different components of the fish mechanosensory system. We evaluate the SVP Hypothesis by (1) using it to explain the traces made by acoustically tagged emigrants overlaid on coincident total hydraulic strain and velocity magnitude fields, (2) using it to explain different passage efficiencies of competing bypass designs and (3) testing it via stepwise discriminant analysis to infer the relationship between hydrodynamic pattern and emigrant orientation. We conclude the SVP Hypothesis is a reasonable and useful approximation of the strategy used by emigrants to select their swim path through complex flow fields sufficient to serve as the basis of guidance and bypass system design. Published in 2008 by John Wiley & Sons, Ltd.
The security and improvement of an ultra‐lightweight RFID authentication protocol
Authors: Li Tieyan , Deng Robert H. , Wang Guilin
Published: February 2008

It is very challenging on designing cryptographically strong security functions that can be incorporated into low‐cost radio frequency identification (RFID) tags. Some RFID authentication protocols were proposed using only ultra‐lightweight primitives, while the security of them must be scrutinized before being put forth into any real application. In this paper, we present two effective attacks, namelyde‐synchronization attackandfull‐disclosure attack, against an efficient ultra‐lightweight RFID mutual authentication protocol: LMAP2, which is recently proposed by Peris‐Lopezet al. These active attacks are so serious as they cannot only disable the authentication capability of an RFID tag by destroying synchronization between the tag and the RFID reader, but also disclose all secret values stored in the tag. We point out the design flaws of the protocol and based on that, we improve the protocol with a stateful variant (SLMAP). The improved protocol is more secure in sense of tag anonymity, man‐in‐the‐middle (MITM) resistance, and forgery prevention as shown in our analysis, and is more compact due to reduced operations and memory usage on implementing such a tag. Copyright © 2008 John Wiley & Sons, Ltd.
Designing fault tolerant networks to prevent poison message failure
Authors: Du Xiaojiang , Shayman Mark A. , Skoog Ronald A.
Published: February 2008

Poison message failure is a mechanism that has been responsible for large‐scale failures in both telecommunications and IP networks. We design a fault management framework that integrates passive diagnosis and active diagnosis to identify the poison message and prevent network instability. Passive diagnosis uses real‐time inference and reasoning techniques to analyze network information and generates a probability distribution of the poison message, and the probability distribution is used in active diagnosis for further failure identification. In active diagnosis, message filtering is used to block suspect message types. Blocking messages affects network performance and service. The tradeoff of message filtering is formulated as a Markov Decision Process (MDP). The large size of the state space makes it impractical to use traditional techniques to solve the MDP. Con sequently, we use a combination of reinforcement learning and feature‐based function approximation to obtain a suboptimal policy. Extensive simulations demonstrate the effectiveness of passive diagnosis, and show that the suboptimal policy performs significantly better than a well‐known heuristic policy. Copyright © 2008 John Wiley & Sons, Ltd.
Ultraviolet femtosecond laser ionization mass spectrometry
Authors: Imasaka Totaro
Published: February 2008

For this study, multiphoton ionization/mass spectrometry using an ultraviolet (UV) femtosecond laser was employed for the trace analysis of organic compounds. Some of the molecules, such as dioxins, contain several chlorine atoms and have short excited‐state lifetimes due to a “heavy atom” effect. A UV femtosecond laser is, then, useful for efficient resonance excitation and subsequent ionization. A technique of multiphoton ionization using an extremely short laser pulse (e.g., <10 fs), referred to as “impulsive ionization,” may have a potential for use in fragmentation‐free ionization, thus providing information on molecular weight in mass spectrometry. © 2008 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 8: 23–32; 2008: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20136
Polyisoprenoid alcohols—Recent results of structural studies
Authors: Skorupinska‐Tudek Karolina , Wojcik Jacek , Swiezewska Ewa
Published: February 2008

Polyisoprenoid alcohols (polyprenols and dolichols) are linear polymers of from several up to more than 100 isoprene units identified in almost all living organisms. Studies of their chemical structures have resulted in the discovery of new variants such as the recently described alloprenols with reversed configuration of the double bond in the α‐isoprene unit. In parallel, structural elucidation of metabolically labeled plant dolichols has indicated that both the mevalonate and methylerythritol phosphate pathways are involved in the biosynthesis of dolichols in roots, leading to the construction of a spatial model of their biosynthesis. According to this model, in root cells, synthesis of the dolichol molecule is initiated in the plastids, and the resulting intermediates, oligoprenyl diphosphates, are exported to the cytoplasm and are elongated up to the desired chain length. The metabolic consequences of this putative model are discussed in the context of the enzymatic machinery involved. © 2008 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 8: 33–45; 2008: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20137
Identification of an NADH‐dependent 5‐hydroxymethylfurfural‐reducing alcohol dehydrogenase in Saccharomyces cerevisiae
Authors: Laadan Boaz , Almeida João R. M. , Rådström Peter , Hahn‐Hägerdal Bärbel , Gorwa‐Grauslund Marie
Published: February 2008

We report on the identification and characterization of a mutated alcohol dehydrogenase 1 from the industrial Saccharomyces cerevisiae strain TMB3000 that mediates the NADH‐dependent reduction of 5‐hydroxymethylfurfural (HMF) to 2,5‐bis‐hydroxymethylfuran. The co‐factor preference distinguished this alcohol dehydrogenase from the previously reported NADPH‐dependent S. cerevisiae HMF alcohol dehydrogenase Adh6. The amino acid sequence revealed three novel mutations (S109P, L116S and Y294C) that were all predicted at the vicinity of the substrate binding site, which could explain the unusual substrate specificity. Increased biomass production and HMF conversion rate were achieved in a CEN.PK S. cerevisiae strain overexpressing the mutated ADH1 gene. Copyright © 2008 John Wiley & Sons, Ltd.