bluuebunny/crossref_metadata_2025 huggingface dataset:
Topographic differences in adult neurogenesis in the mouse hippocampus: A stereology‐based study using endogenous markers
Authors: Jinno Shozo
Published: January 2010

The hippocampus plays a critical role in various cognitive and affective functions. Increasing evidence shows that these functions are topographically distributed along the dorsoventral (septotemporal) and transverse axes of the hippocampus. For instance, dorsal hippocampus is involved in spatial memory and learning whereas ventral hippocampus is related to emotion. Here, we examined the topographic differences (dorsal vs. ventral; suprapyramidal vs. infrapyramidal) in adult neurogenesis in the mouse hippocampus using endogenous markers. The optical disector was applied to estimate the numerical densities (NDs) of labeled cells in the granule cell layer. The NDs of radial glia‐like progenitors labeled by brain lipid binding protein were significantly lower in the infrapyramidal blade of the ventral DG than in other subdivisions. The NDs of doublecortin‐expressing cells presumed neural progenitors and immature granule cells were significantly higher in the suprapyramidal blade of the dorsal DG than in the other subdivisions. The NDs of calretinin‐expressing cells presumed young granule cells at the postmitotic stage were significantly higher in the suprapyramidal blade than in the infrapyramidal blade in the dorsal DG. No significant regional differences were detected in the NDs of dividing cells identified by proliferating cell nuclear antigen. Taken together, these findings suggest that a larger pool of immature granule cells in dorsal hippocampus might be responsible for spatial learning and memory, whereas a smaller pool of radial glia‐like progenitors in ventral hippocampus might be associated with the susceptibility to affective disorders. Cell number estimation using a 300‐μm‐thick hypothetical slice indicates that regional differences in immature cells might contribute to the formation of topographic gradients in mature granule cells in the adult hippocampus. Our data also emphasizes the importance of considering such differences when evaluating changes in adult neurogenesis in pathological conditions and following experimental procedures. © 2010 Wiley‐Liss, Inc.
Parvovirus H1 selectively induces cytotoxic effects on human neuroblastoma cells
Authors: Lacroix Jeannine , Leuchs Barbara , Li Junwei , Hristov Georgi , Deubzer Hedwig E. , Kulozik Andreas E. , Rommelaere Jean , Schlehofer Jörg R. , Witt Olaf
Published: January 2010

Despite multimodal therapeutic concepts, advanced localized and high‐risk neuroblastoma remains a therapeutic challenge with a long‐term survival rate below 50%. Consequently, new modalities for the treatment of neuroblastoma, e.g., oncolytic virotherapy are urgently required. H‐1PV is a rodent parvovirus devoid of relevant pathogenic effects in infected adult animals. In contrast, the virus has oncolytic properties and is particularly cytotoxic for transformed or tumor‐derived cells of various species including cells of human origin. Here, a preclinical in vitro assessment of the application of oncolytic H‐1PV for the treatment of neuroblastoma cells was performed. Infection efficiency, viral replication and lytic activity of H‐1PV were analyzed in 11 neuroblastoma cell lines with different MYCN status. Oncoselectivity of the virus was confirmed by the infection of short term cultures of nonmalignant infant cells of different origin. In these nontransformed cells, no effect of H‐1PV on viability or morphology of the cells was observed. In contrast, a lytic infection was induced in all neuroblastoma cell lines examined at MOIs between 0.001 and 10 pfu/cell. H‐1PV actively replicated with virus titres increasing up to 5,000‐fold within 48–96 hr after infection. The lytic effect of H‐1PV was observed independent of MYCN oncogene amplification or differentiation status. Moreover, a significant G2‐arrest and induction of apoptosis could be demonstrated. Infection efficiency, rapid virus replication and exhaustive lytic effects on neuroblastoma cells together with the low toxicity of H‐1PV for nontransformed cells, render this parvovirus a promising candidate for oncolytic virotherapy of neuroblastoma.
Histone deacetylase inhibitor‐induced sensitization to TNFα/TRAIL‐mediated apoptosis in cervical carcinoma cells is dependent on HPV oncogene expression
Authors: Darvas Katalin , Rosenberger Simone , Brenner Dirk , Fritsch Cornelius , Gmelin Nadine , Krammer Peter H. , Rösl Frank
Published: January 2010

Histone‐deacetylase (HDAC) inhibitors (HDACi) can block proliferation and induce intrinsic apoptosis in human papillomavirus (HPV)‐positive cervical carcinoma cells, independently of copy number and integration locus of the viral DNA. Using HPV18‐positive HeLa cells as model systems, we provide evidence that HDAC inhibition leads to transcriptional suppression of c‐FLIP, which negatively regulates extrinsic apoptosis by preventing the recruitment of caspase‐8 to the death‐inducing signaling complex. Consequently, HDACi pretreatment renders cervical cancer cells sensitive to TNFα and TRAIL‐induced apoptosis. Already 5‐hr incubation with TNFα or TRAIL was sufficient to eradicate more than 40% of pretreated cells, which are normally completely refractory against respective death‐ligands alone even under long‐term incubation. Ectopic expression of either short or long splicing variant of c‐FLIP, c‐FLIPs and c‐FLIPL, abrogates sensitization. Notably, combined HDACi/death ligand treatment did not result in eradication of HPV‐negative cells, despite the fact that both c‐FLIP isoforms were also downregulated. However, knocking down HPV18 E6/E7 transcription by siRNA prevents HDACi/death‐ligand mediated apoptosis, indicating that continued viral oncogene expression favors sensitization. Here, the viral oncoprotein E7 seems to play a functional role, since only HPV16 E7‐immortalized human keratinocytes underwent significant apoptosis on HDACi/TNFα treatment, whereas keratinocytes expressing only HPV16 E6 or primary keratinocytes were refractory under the same experimental conditions. Taken together, HDACi can be considered as an alternative therapeutic option in the treatment of premalignant and malignant lesions.
Atomistic insight into chondroitin‐6‐sulfate glycosaminoglycan chain through quantum mechanics calculations and molecular dynamics simulation
Authors: Cilpa G. , Hyvönen M. T. , Koivuniemi A. , Riekkola M.‐L.
Published: January 2010

Chondroitin‐6‐sulfate (C6S) is a glycosaminoglycan (GAG) constituent in the extracellular matrix, which participates actively in crucial biological processes, as well as in various pathological conditions, such as atherosclerosis and cancer. Molecular interactions involving the C6S chain are therefore of considerable interest. A computational model for atomistic simulation was built. This work describes the design and validation of a force field for a C6S dodecasaccharide chain. The results of an extensive molecular dynamics simulation performed with the new force field provide a novel insight into the structure and dynamics of the C6S chain. The intramolecular H‐bonds in the disaccharide linkage region are suggested to play a major role in determining the chain structural dynamics. Moreover, the unravelling of an additional H‐bond involving the sulfate groups in C6S is interesting as changes in sulfation have been claimed to be an important factor in several diseases. The force field will prove useful for future studies of crucial interactions between C6S and various nanoassemblies. It can also be used as a basis for modeling of other GAGs. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
Protein‐protein docking by shape‐complementarity and property matching
Authors: Geppert Tim , Proschak Ewgenij , Schneider Gisbert
Published: January 2010

We present a computational approach to protein‐protein docking based on surface shape complementarity (“ProBinder”). Within this docking approach, we implemented a new surface decomposition method that considers local shape features on the protein surface. This new surface shape decomposition results in a deterministic representation of curvature features on the protein surface, such as “knobs,” “holes,” and “flats” together with their point normals. For the actual docking procedure, we used geometric hashing, which allows for the rapid, translation‐, and rotation‐free comparison of point coordinates. Candidate solutions were scored based on knowledge‐based potentials and steric criteria. The potentials included electrostatic complementarity, desolvation energy, amino acid contact preferences, and a van‐der‐Waals potential. We applied ProBinder to a diverse test set of 68 bound and 30 unbound test cases compiled from the Dockground database. Sixty‐four percent of the protein‐protein test complexes were ranked with an root mean square deviation (RMSD) < 5 Å to the target solution among the top 10 predictions for the bound data set. In 82% of the unbound samples, docking poses were ranked within the top ten solutions with an RMSD < 10 Å to the target solution. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
Lectin affinity electrophoresis of serum alkaline phosphatase in metastasized breast cancer
Authors: Le Bricon Thierry , Gay‐Bellile Cécile , Cottu Paul , Benlakehal Mourad , Guillon Hélène , Houzé Pascal
Published: January 2010

The use of serum alkaline phosphatase (ALP) isoenzymes as markers of breast cancer metastases and treatment efficacy has received little attention. Twenty‐six breast cancer women (56±13 years, all post‐menopausal) were prospectively evaluated during their first and third course of chemotherapy (4‐week interval). Serum samples were analyzed for ALP isoenzymes (bone, liver, and intestine) using a lectin affinity electrophoresis kit (Hydragel 15 ISO‐PAL®, Sebia) adapted on a semi‐automated Hydrasys® system (Sebia). Results were compared with imaging techniques for the presence of metastases; bone ALP isoenzyme (B‐ALP) results werecompared with C‐Terminal degradation products of type I collagen (S‐CTX) (CrossLaps®, IDS Nordic). Serum B‐ALP, but not S‐CTX, confirmed the presence of bone metastases (BM) (n=15) with 67/100% sensitivity/specificity (using a 69 UI/L ROC cut‐off); ROC AUC was 0.806 (P=0.0004) (NS for S‐CTX). Chemotherapy reduced serum B‐ALP by 24% over 4 weeks (P=0.0012); there was no change for S‐CTX. There was no specific clinical pattern for other ALP isoenzymes (liver and intestine). In conclusion, serum B‐ALP, but not S‐CTX, could help confirm the presence of BM in breast cancer patients. J. Clin. Lab. Anal. 24:20–24, 2010. © 2010 Wiley‐Liss, Inc.
Platelets oxidative stress in Indian patients with ischemic heart disease
Authors: Garelnabi Mahdi , Gupta Vinod , Mallika Venkatesan , Bhattacharjee Jayashree
Published: January 2010

Background: Oxidative stress has been implicated in the development of atherosclerosis and vascular tissue injury. Both platelet activation and lipid peroxidation are known to play major role in ischemic heart disease. The purpose of this study was to investigate the status of platelets oxidative stress in Indian patients with ischemic heart disease. Methods: We measured platelets aggregation, malonyldialdehyde (MDA), plasma‐ionized Ca2+, and antioxidant enzymes, i.e., glutathione peroxidase and superoxide dismutase in healthy volunteers and patients with myocardial infarction, unstable and stable angina 40 subjects each. Results: Platelets aggregation, MDA, and plasma‐ionized Ca2+ have increased significantly across the patients groups compared with controls, this increase was accompanied by an overall decrease in the antioxidant enzymes activity; except for the slight increases in the glutathione peroxidase levels among the myocardial infarction patients. Conclusions: The current results suggest that platelet lipid peroxidation as marked by increased MDA level is augmented in ischemic heart diseases. The increased oxidative stress seen in these patients was accompanied by platelet activation and impaired antioxidant enzymes activity. J. Clin. Lab. Anal. 24:49–54, 2010. © 2010 Wiley‐Liss, Inc.
Influence of acceleration voltage on scanning electron microscopy of human blood platelets
Authors: Pretorius E.
Published: January 2010

Scanning electron microscopy (SEM) is used to view a variety of surface structures, molecules, or nanoparticles of different materials, ranging from metals, dental and medical instruments, and chemistry (e.g. polymer analysis) to biological material. Traditionally, the operating conditions of the SEM are very important in the material sciences, particularly the acceleration voltage. However, in biological sciences, it is not typically seen as an important parameter. Acceleration voltage allows electrons to penetrate the sample; thus, the higher the acceleration voltage the more penetration into the sample will occur. As a result, ultrastructural information from deeper layers will interfere with the actual surface morphology that is seen. Therefore, ultimately, if acceleration voltage is lower, a better quality of the surface molecules and structures will be produced. However, in biological sciences, this is an area that is not well‐documented. Typically, acceleration voltages of between 5 and 20 kV are used. This manuscript investigates the influence of acceleration voltages ranging from 5 kV to as low as 300 V, by studying surface ultrastructure of a human platelet aggregate. It is concluded that, especially at higher magnifications, much more surface detail is visible in biological samples when using an acceleration voltage between 2 kV and 300 V. Microsc. Res. Tech., 2010. © 2010 Wiley‐Liss, Inc.
Automated synthesis of 18F‐labelled analogs of metomidate, vorozole and harmine using commercial platform
Authors: Rahman Obaidur , Erlandsson Maria , Blom Elisabeth , Långström Bengt
Published: January 2010

Three 18F‐labelled PET tracers, 2‐[18F]fluoroethyl 1‐[(1R)‐1‐phenylethyl]‐1H‐imidazole‐5‐carboxylate ([18F]FETO), 6‐[(S)‐(4‐chlorophenyl)‐(1H)‐1,2,4‐triazol‐1‐yl)methyl]‐1‐(2‐[18F]fluoroethyl)‐1H‐benzotriazole ([18F]FVOZ) and 7‐[2‐(2‐[18F]fluoroethoxy)ethoxy]‐1‐9H‐β‐carboline ([18F]FHAR) were synthesized by a one‐step nucleophilic fluorination using the automated commercial platform TRACERLab FXFN. The labelled products were obtained with 16–20% isolated decay corrected radiochemical yields after 70–75 min synthesis time. The radiochemical and chemical purities were more than 98% in all cases. The synthesis using commercial platform may make these tracers more accessible for clinical research. Copyright © 2010 John Wiley & Sons, Ltd.
Virus clearance reduces bone fracture in postmenopausal women with osteoporosis and chronic liver disease caused by hepatitis C virus
Authors: Arase Yasuji , Suzuki Fumitaka , Suzuki Yoshiyuki , Akuta Norio , Kobayashi Masahiro , Sezaki Hitomi , Hosaka Tetsuya , Kawamura Yusuke , Yatsuji Hiromi , Hirakawa Miharu , Ikeda Kenji , Hsieh Shiun Dong , Oomoto Yuki , Amakawa Kazuhisa , Kato Hisahito , Kazawa Tamae , Tsuji Hiroshi , Kobayashi Tetsuro , Kumada Hiromitsu
Published: January 2010

Osteoporosis is often present in postmenopausal women. The aim of this retrospective cohort study was to assess the cumulative incidence and predictive factors for bone fracture after cessation of interferon (IFN) in postmenopausal women with osteoporosis and chronic liver disease caused by hepatitis C virus (HCV). A total of 420 postmenopausal women treated with IFN monotherapy were enrolled. The mean observation period was 7.2 years. The primary goal was the development of bone fracture. Evaluation was carried out by using the Kaplan–Meier method and the Cox proportional hazards analysis. Thirty‐one out of 420 patients sustained bone fracture. The cumulative development rate of bone fracture was 3.6% at 5th year, 9.2% at 10th year, and 17.4% at 15th year. Multivariate Cox proportional hazards analysis showed that bone fracture after cessation of IFN therapy occurred when histological staging of the liver was advanced (hazard ratio (HR): 2.54; 95% confidence interval (CI) = 1.21–5.31; P = 0.013), serum albumin level was < 3.5g/dl (HR: 2.25; 95% CI = 1.10–4.59; P = 0.026), and virus clearance was not achieved (HR: 3.65; 95% CI = 1.11–12.05; P = 0.033). The results indicate that virus clearance causes a reduction of two‐thirds in the risk of bone fracture after cessation of IFN therapy in postmenopausal women with osteoporosis and chronic liver disease caused by HCV. J. Med. Virol. 82:390–395, 2010. © 2010 Wiley‐Liss, Inc.
Zymosan enhances the mucosal adjuvant activity of poly(I:C) in a nasal influenza vaccine
Authors: Ainai Akira , Ichinohe Takeshi , Tamura Shin‐ichi , Kurata Takeshi , Sata Tetsutaro , Tashiro Masato , Hasegawa Hideki
Published: January 2010

The synthetic double‐stranded RNA polyriboinocinic polyribocytidylic acid [poly(I:C)] is a potent mucosal adjuvant in mice immunized intranasally with an inactivated influenza vaccine. In an attempt, to increase the effectiveness of a nasal poly(I:C)‐combined vaccine, the effect of zymosan, a cell wall extract from Saccharomyces cervisiae was investigated, on the adjuvant activity of poly(I:C) in BALB/c mice. The addition of zymosan (10 µg) as an adjuvant in mice which were immunized intranasally with a poly(I:C) (1–5 µg)‐combined vaccine (1 µg) enhanced the ability of the mice to mount an effective immune response to a lethal dose of influenza virus, and resulted in a synergistic increase in secretory IgA and serum IgG antibody levels. To define the mechanism by which zymosan enhanced the adjuvant activity of poly(I:C), bone marrow‐derived dendritic cells (BM‐DCs) were cultured in the presence of poly(I:C) and/or zymosan. There was a synergistic increase in cytokine production (TNF‐α, IL‐6, IL‐10, and IFN‐β) in BM‐DCs, together with an increase in the expression of co‐stimulatory molecules (CD86 and CD40) in response to co‐treatment with poly(I:C) and zymosan. This synergistic effect on cytokine production was mimicked by co‐treatment with poly(I:C) and a Toll‐like receptor 2 (TLR2) ligand, which represented one of the components of zymosan. The results of the current study suggest that one of the mechanisms by which zymosan enhances the adjuvant activity of poly(I:C) is through increased cytokine production by DCs involving the synergistic activation of poly(I:C)‐induced TLR3‐ and zymosan‐induced TLR2‐mediated signaling pathways. J. Med. Virol. 82:476–484, 2010. © 2010 Wiley‐Liss, Inc.
Elevated Epstein–Barr virus loads and lower antibody titers in competitive athletes
Authors: Hoffmann Dieter , Wolfarth Bernd , Hörterer Hubert G. , Halle Martin , Reichhuber Christine , Nadas Korinna , Tora Catrin , Erfle Volker , Protzer Ulrike , Schätzl Hermann M.
Published: January 2010

Epstein–Barr virus (EBV) is a persisting herpesvirus which is controlled by the adaptive immune response after primary infection and maintained in a latent state. However, reactivation or persistent replication is observed in situations where the immune response is compromised. Since intensive physical training has been reported to diminish immune function, increased EBV load may be a cause of reduced performance and decreased ability to sustain high training loads in competitive athletes. Samples drawn from 209 athletes during their regular follow‐up appointments were tested. One hundred sixty‐five individuals of similar age not active in competitive sports served as case–controls. EBV load was quantified in peripheral blood leucocytes (PBLs) by real‐time PCR, and EBV antibodies were detected in plasma by ELISA and immunoblot analysis. EBV DNA was detectable in 25 of 209 athletes and in 26 of 165 controls. Of note, the EBV load per 105 PBLs was 6.44 ± 1.75 in the case and 1.67 ± 0.44 copies in the controls, yielding a high significant difference (P < 0.0001). However, EBV‐specific IgG titers were significantly lower in athletes (150.4 ± 10.73 U ml−1 vs. 241.6 ± 18.59 U ml−1). As monitored by immunoblotting, primary infections were detected with low prevalence, three in the case group and one in the control group. These findings demonstrate that EBV is present at higher levels in athletes, but the antibody response is lower in athletes than in the controls. J. Med. Virol. 82:446–451, 2010. © 2010 Wiley‐Liss, Inc.
Difference in susceptibility to MxA protein between a coxsackievirus B1 isolate and prototype, impact of serial cell culture passage
Authors: Chehadeh Wassim , Abdulkareem Hayfaa A.
Published: January 2010

Human enteroviruses (EVs) cause a broad spectrum of acute and chronic diseases including meningitis and myocarditis. The type I interferon‐induced MxA protein has been shown to inhibit the replication of an EV, coxsackievirus B4 (CVB4), but not cardioviruses such as encephalomyocarditis virus and mengo virus, members of the Picornaviridae family. EVs consist of more than 60 distinct serotypes against which the antiviral activity of MxA was not investigated yet. The main aim of this study was to explore the antiviral activity of MxA protein against a clinical CVB1 isolate and other EV prototypes. Vero cells expressing constituvely MxA protein were infected with EVs, and the percentage of inhibiton of expression of enteroviral RNA and capsid VP1 protein was determined. Following infection of MxA‐transfected Vero cells with EVs, the expression of enteroviral RNA was inhibited by up to 99%, and that of VP1 protein by up to 85%. However, there was a difference in the percentage of MxA inhibition of EV replication between the different EV prototypes. This difference in MxA sensitivity was not due to a difference in the viral replication rates. The MxA protein was inactive against the clinical CVB1 isolate, and the replication rate of CVB1 isolate in MxA‐transfected Vero cells was higher than that in mock‐transfected Vero cells. A serial passage of the clinical CVB1 isolate and other EV prototypes resulted in an increase in their susceptibility to MxA protein. These results suggest the presence of MxA‐resistant EV variants that may escape innate immunity and cause disease. J. Med. Virol. 82:424–432, 2010. © 2010 Wiley‐Liss, Inc.
Impact of changes in antigen level on CD38/PD‐1 co‐expression on HIV‐specific CD8 T cells in chronic, untreated HIV‐1 infection
Authors: Vollbrecht Thomas , Brackmann Heike , Henrich Nadja , Roeling Joerg , Seybold Ulrich , Bogner Johannes R. , Goebel Frank D. , Draenert Rika
Published: January 2010

Excessive immune activation is a hallmark of chronic uncontrolled HIV infection. During the past years, growing evidence suggests that immune inhibitory signals also play an important role in progressive disease. However, the relationship between positive and negative immune signals on HIV‐specific CD8 T cells has not been studied in detail so far in chronic HIV‐1 infection. In this study, the expression of markers of positive (CD38) and negative (PD‐1) immune signals on virus‐specific CD8 T cells in chronic, untreated HIV‐1 infection was evaluated using intracellular cytokine staining. Viral escape mutations were assessed by autologous virus sequence analysis and subsequent peptide titration assays. Single‐epitope CD8 T‐cell responses toward Gag, Pol, and Nef were compared in 12 HIV‐1 controllers (viral load <5,000 cp/ml) and 12 HIV‐1 progressors (viral load >50,000 cp/ml) and a highly significant increase of CD38/PD‐1 co‐expression on virus‐specific CD8 T cells in progressors was found (P < 0.0001). The level of CD38/PD‐1 co‐expression was independent of epitope specificity. Longitudinal follow‐up revealed a clear drop in CD38/PD‐1 co‐expression on virus‐specific CD8 T cells after the suppression of antigen following either viral escape mutation or the initiation of HAART (P = 0.004). Antigen persistence with a fluctuating viral load revealed stable levels of CD38/PD‐1 co‐expression whereas significant rises in viral load were accompanied or even preceded by substantial increases in CD38/PD‐1 co‐expression. The CD38/PD‐1 phenotype clearly distinguishes HIV‐specific CD8 T‐cell responses between controllers and progressors. Whether it plays a causative role in disease progression remains debatable. J. Med. Virol. 82:358–370, 2010. © 2010 Wiley‐Liss, Inc.
Ex vivo monitoring of human cytomegalovirus‐specific CD8+ T‐Cell responses using the QuantiFERON®‐CMV assay in allogeneic hematopoietic stem cell transplant recipients attending an Irish hospital
Authors: Fleming T. , Dunne J. , Crowley B.
Published: January 2010

Reconstitution of human cytomegalovirus (HCMV) T‐cell immunity is crucial in hematopoietic stem cell transplant (HSCT) recipients. The QuantiFERON®‐CMV assay for cellular HCMV‐specific immunity was evaluated in allogeneic HSCT recipients (n = 43) and patients with hematological malignancies (n = 29) attending a tertiary‐care Irish hospital. An intracellular cytokine (ICC) assay correlated with the QuantiFERON®‐CMV assay. Although there was agreement between HCMV seropositivity and QuantiFERON®‐CMV assay, six HCMV seropositive immunosuppressed patients with hematological malignancy had negative QuantiFERON®‐CMV results. The 43 HSCT recipients were classified as high risk (D−/R+) (n = 18), intermediate risk (D+/R+ and D+/R−) (n = 17), and low risk (D−/R−) (n = 8). During episodes of HCMV DNAemia no evidence of HCMV‐specific immunity was found using the QuantiFERON®‐CMV assay. Furthermore, the recovery of HCMV‐specific CD8+ T‐cell responses in high‐risk seropositive recipients of matched unrelated donors was severely delayed, a mean of 200 (SD = 117) days compared to 58 (SD = 23) days for sibling donors (P ≤ 0.028). In addition, three patients with late HCMV infection (infection >100 days post‐transplant) had delayed reconstitution of HCMV‐specific CD8+ T cells. Interestingly, two recipients (R+/D−) developed rapid immune reconstitution by days 15 and 36 post‐HSCT, suggesting HCMV‐specific T‐cell lymphopoiesis of recipient origin. Levels of CD8+ T‐cell immunity in HCMV seropositive HSCT recipients were lowest following HSCT. A high number (33%) of indeterminate results was observed immediately after transplantation. Patients with indeterminate QuantiFERON®‐CMV results had low levels of HCMV‐specific CD8+ T cells. J. Med. Virol. 82:433–440, 2010. © 2010 Wiley‐Liss, Inc.
Enantioselective analysis of mirtazapine, demethylmirtazapine and 8‐hydroxy mirtazapine in human urine after solid‐phase microextraction
Authors: de Santana Fernando José Malagueño , Jabor Valquíria Aparecida Polisel , Cesarino Evandro José , Lanchote Vera Lúcia , Bonato Pierina Sueli
Published: January 2010

A selective and reproducible off‐line solid‐phase microextraction procedure was developed for the simultaneous enantioselective determination of mirtazapine (MRT), demethylmirtazapine and 8‐hydroxymirtazapine in human urine. CE was used for optimization of the extraction procedure whereas LC‐MS was used for method validation and application. The influence of important factors in the solid‐phase microextraction efficiency is discussed, such as the fiber coatings, extraction time, pH, ionic strength, temperature and desorption time. Before extraction, human urine samples were submitted to enzymatic hydrolysis at 37°C for 16 h. Then, the enzyme was precipitated with trichloroacetic acid and the pH was adjusted to 8 with 1 mol/L pH 11 phosphate buffer solution. In the extraction, the analytes were transferred from the aqueous solution to the polydimethylsiloxane‐divinylbenzene fiber coating and then desorbed in methanol. The mean recoveries were 5.4, 1.7 and 1.0% for MRT, demethylmirtazapine and 8‐hydroxymirtazapine enantiomers, respectively. The method was linear over the concentration range of 62–1250 ng/mL. The within‐day and between‐day assay precision and accuracy were lower than 15%. The method was successfully employed in a preliminary cumulative urinary excretion study after administration of racemic MRT to a healthy volunteer.
A new thermally immobilized fluorinated stationary phase for RP‐HPLC
Authors: Maldaner Liane , Jardim Isabel C. S. F.
Published: January 2010

A new fluorinated stationary phase was prepared through thermal immobilization of poly(methyl‐3,3,3‐trifluoropropylsiloxane) onto 5 μm Kromasil silica particles. The best conditions of immobilization time and temperature were determined through a central composite design and response surface methodologies. Physical–chemical characterization using solid‐state 29Si NMR measurements, infrared spectroscopy and elemental analysis showed that the immobilization process was effective to promote a coating of the support that corresponds to a monolayer of polymer. The stationary phase presents selectivity for positional isomers and good peak shape for basic compounds.
Knowledge discovery in metabolomics: An overview of MS data handling
Authors: Boccard Julien , Veuthey Jean‐Luc , Rudaz Serge
Published: January 2010

While metabolomics attempts to comprehensively analyse the small molecules characterising a biological system, MS has been promoted as the gold standard to study the wide chemical diversity and range of concentrations of the metabolome. On the other hand, extracting the relevant information from the overwhelming amount of data generated by modern analytical platforms has become an important issue for knowledge discovery in this research field. The appropriate treatment of such data is therefore of crucial importance in order, for the data, to provide valuable information. The aim of this review is to provide a broad overview of the methodologies developed to handle and process MS metabolomic data, compare the samples and highlight the relevant metabolites, starting from the raw data to the biomarker discovery. As data handling can be further separated into data processing, data pre‐treatment and data analysis, recent advances in each of these steps are detailed separately.
Residue analysis of multi‐class pesticides in watermelon by LC‐MS/MS
Authors: Park Semin , Lee Sung Joong , Kim Hae Gyeong , Jeong Won Young , Shim Jae‐Han , Abd El‐Aty A. M. , Jeong Sung Woo , Lee Won Sup , Kim Soo Taek , Shin Sung Chul
Published: January 2010

As watermelon is farmed primarily by protected and successive cultivation techniques, a number of pesticides are required for the control of pests and diseases. To evaluate the harmful effects of pesticides in watermelon and to guarantee consumers' safety, a rapid screening process for pesticides is required. A LC‐MS/MS method was applied for the direct quantitation of 44 pesticide residues in watermelon. A Zorbax XDB‐C18 column was selected for analysis, with a mobile phase consisting of a gradient system of water and 5 mM methanolic ammonium formate. MS/MS experiments were performed in ESI positive ion and multiple reaction monitoring modes. The LOQs were in the range of 1–26 μg/kg, thereby indicating good sensitivity. Most of the recoveries ranged between 70–131% with RSDs≤20%. We suggested that the amount of pesticide residues such as pyroquilon (pyn), boscalid (bd), and dimethomorph (di) in amides (AM) and cinosulfuron (ci) in ureas (UR) may have been overestimated for the pesticides owing to increased α‐error risk, whereas the amounts of pesticide residues, such as imibenconazole (ie) in the triazoles (TR) and fenpyroximate (fee) in the imidazoles (IM), may have been underestimated as the result of increased β‐error risk. The current method allowed for the rapid quantitation and identification of low pesticide levels in the watermelon samples. No pesticide residues were detected in any of the surveyed watermelons obtained from eight local markets in the Republic of Korea. Statistical analysis of the recoveries classified the 44 pesticides into nine groups and three overall categories.
Dual hydrophilic interaction‐RP retention mechanism on polar columns: Structural correlations and implementation for 2‐D separations on a single column
Authors: Jandera Pavel , Hájek Tomáš , Škeříková Veronika , Soukup Jan
Published: January 2010

We investigated the retention of phenolic acid and flavone antioxidants on five polar columns in buffered aqueous ACN mobile phases. All columns show mixed retention mechanism: RP in highly aqueous mobile phases and normal phase (hydrophilic interaction LC, HILIC) in mobile phases with high concentration of ACN. The Silica Hydride and the ZIC HILIC sulfobetaine zwitterionic columns show rather limited retention in the RP mode. The Luna HILIC column shows higher retention in both the HILIC and the RP modes in comparison to the PEG and DIOL columns. We characterized the selectivity of various HILIC systems using linear solvation energy relationship model with molecular structure descriptors characterizing selective molecular size, dipole–dipole and proton–donor/proton–acceptor interactions and we investigated the effects of the mobile phase composition on the linear solvation energy relationship characteristics of the separation phase systems to select suitable conditions for orthogonal HILIC separations in combination with RP systems. Dual retention mechanism offers possibilities for using complementary selectivity in the HILIC and the RP modes for sequential 2‐D separations of natural antioxidants on a single Luna HILIC column. Column equilibration time of 15 min between alternating RP and HILIC gradient runs is sufficient for reproducible results.
Photon transport in a time‐dependent interstellar cloud
Authors: Belleni‐Morante Aldo , Monaco Roberto , Pieraccini Sandra
Published: January 2010

Photon transport is studied in an interstellar cloud occupying a time‐dependent region V(t)⊂ℝ3. First, under the assumption that the surface ∂V(t) is a known function of t∈[0, tmax], a direct problem is set and proof of well‐posedness is sketched. Then, an inverse problem is examined, under the assumptions that the time behaviour of ∂V(t) is unknown and the photon distribution function is measured at a location far from the cloud. Some numerical experiments are then provided. Copyright © 2010 John Wiley & Sons, Ltd.
The demographic, socio‐economic and temporal contextualisation of the Universitat Autònoma de Barcelona collection of identified human skeletons (UAB collection)
Authors: Rissech C. , Steadman D. W.
Published: January 2010

Identified human skeletal collections are those in which basic demographic data (sex, age and biological origin) are known and are crucial for developing and testing osteological methodologies. It is important that the identified collection be contextualised, and in this way the collection will be considered a reference collection. To contextualise a collection requires documentation of the basic demographic data of the individuals (sex, age, year of birth, geographical area) as well as information concerning the socio‐economic and temporal context in which the individuals lived. The contextualisation of an identified collection is very important so the researchers can understand the ‘point of reference’ when applying a method to it or developing a new method. The purpose of this study is to contextualise the identified skeletal collection of the Universitat Autónoma de Barcelona (UAB) which currently contains 35 adult skeletons of both sexes. To carry out the objectives of the present study, the information about the individuals was collected from cemetery registers and compared with the information of the demographic and statistic public institutions of Spain. The results indicate that the UAB collection is formed only by Spanish nationals who mainly lived during the 20th century in Granollers (Barcelona, Spain). Both sexes are equally represented and all of the individuals are adults. They reflect the most current adult population structure of Catalonia and be treated as a Catalan reference sample of adults living in the 20th century. This collection offers special opportunities for demographic analysis, including validation studies of skeletal ageing and sexing methods that target adult individuals. The collection can also be used in conjunction with other reference samples to investigate secular and populational change in cranial form, sexual dimorphism and stature. Copyright © 2010 John Wiley & Sons, Ltd.
The prognostic role of immunohistochemical chromogranin a expression in prostate cancer patients is significantly modified by androgen‐deprivation therapy
Authors: Berruti Alfredo , Bollito Enrico , Cracco Cecilia M. , Volante Marco , Ciccone Giovannino , Porpiglia Francesco , Papotti Mauro , Scarpa Roberto Mario , Dogliotti Luigi
Published: January 2010

BACKGROUND

Several data suggest that neuroendocrine (NE) differentiation in prostate cancer is implicated in the development of resistance to androgen‐deprivation therapy (ADT). This study was undertaken to assess the prognostic role of tissue chromogranin A (CgA) expression in patients addressed to ADT as opposed to those who did not.

METHODS

Four hundred fourteen newly diagnosed prostate cancer patients, consecutively recruited in a single institution, entered the study. Two hundred fourteen patients received ADT early after diagnosis, 200 did not. Median follow‐up was 85 months. CgA expression was evaluated immunohistochemically in prostate cancer needle biopsies.

RESULTS

In multivariate analysis after adjusting for Gleason score, serum PSA, disease stage and local treatments, tissue CgA expression in overall cases was significantly associated with a shorter survival (P = 0.009) but failed to be associated with PSA progression (P = 0.10). Dividing patients according to whether they received immediate ADT or not, tissue CgA was associated with a shorter time to PSA progression in ADT‐treated patients (hazard ratios (HR) 1.96, 95% confidence interval (CI): 1.37–2.81, P = 0.0001), but failed to be associated in those who did not (HR 0.87, 95% CI: 0.58–1.30, P = 0.49), interaction test P = 0.007. Conversely the survival effect of tissue CgA was not modified by ADT (interaction test, P = 0.41).

CONCLUSIONS

Tissue CgA expression, evaluated in prostate cancer needle biopsies at diagnosis, is an independent prognostic factor of survival in prostate cancer patients. The negative influence of NE differentiation on time to progression confined in ADT‐treated patients suggests a role of NE differentiation in predicting endocrine resistance that deserves validation. Prostate 70: 718–726, 2010. © 2010 Wiley‐Liss, Inc.
The impact of GPS radio occultation assimilation at the Met Office
Authors: Rennie M. P.
Published: January 2010

Monitoring of global positioning system radio occultation (GPSRO) data was performed. By comparisons between coincident GRAS and FORMOSAT‐3/COSMIC occultations and coincident GPSRO refractivity and Vaisala RS92 radiosonde‐derived refractivity data, we show the consistency of GPSRO data from independent missions (and differing processing methods) and with independent insitu observation data. It was found that the bending angle and refractivity data from COSMIC is positively biased relative to that of GRAS by 0.2–0.5% in the stratosphere, which is where the GRAS refractivity agreed better with the RS92 radiosonde‐derived refractivity than COSMIC.

Forecast impact experiments using GPSRO refractivity and bending angle measurements were conducted (using 1D operators). It is shown that refractivity data (from FORMOSAT‐3/COSMIC, GRAS, CHAMP and GRACE‐A) provided a large positive impact, with the greatest improvements in the Southern Hemisphere extratropics, where r.m.s. fit to radiosondes improved by up to 10% at 250 hPa. A refractivity to bending angle assimilation comparison was made. We found that bending angle assimilation (1D operator) generally provides a greater positive impact than refractivity, with a notable improvement in the Northern Hemisphere extratropics, where a ∼1% improvement in r.m.s. fit to radiosonde temperatures, geopotential heights and winds in the lower stratosphere was seen. © Crown Copyright 2010. Published by John Wiley & Sons, Ltd.
Diagnosis of systematic analysis increments by using normal modes
Authors: Žagar N. , Tribbia J. , Anderson J. L. , Raeder K. , Kleist D. T.
Published: January 2010

This paper applies the normal‐mode functions for the three‐dimensional diagnosis of systematic analysis increments in the operational systems of ECMWF and NCEP, in the NCEP/NCAR reanalyses and in the ensemble data assimilation system DART/CAM which is developed at NCAR. Non‐zero systematic increments are interpreted as the analysis system bias. The main region of tropospheric biases in all systems is the Tropics; most of the large‐scale tropical bias resides in the unbalanced (inertio‐gravity) motion with the eastward‐propagating component being dominant in some datasets. The magnitudes of tropospheric wind‐field biases in July 2007 were in the range between 1 ms−1 and 2 ms−1, illustrating the importance of diagnosing analysis systems in the Tropics where magnitudes of the large‐scale variability are of the same order. The systematic increments integrated over the whole models' atmosphere appear predominantly balanced; this balance is associated with biases in the zonally averaged balanced state and, in case of ECMWF and NCEP, with the biases at the model top levels. Spectra of analysis increments averaged over one month show that, on average, 20% to 45% of total energy in increment fields belongs to the inertio‐gravity motions. Copyright © 2010 Royal Meteorological Society
A very simple model for the water vapour feedback on climate change
Authors: Ingram William
Published: January 2010

Climate sensitivity is often said to be doubled by water vapour feedback. We expect the distribution of relative humidity to change little under climate change from simple physical arguments, which are confirmed by the most detailed physical models we have, and consistent with the limited observational evidence. A substantial positive feedback on climate change is then to be expected, and an approximate doubling is well established numerically. However, a physical explanation for the size of this effect is conspicuously lacking.

We consider an idealized numerical model of Simpson's. Its counter‐intuitive result –that OLR does not change as climate warms –is shown to be more general than often thought, though clearly not applicable to our planet as it stands. However, with certain physical approximations a ‘partly‐Simpsonian’ generalization can be derived: that the component radiated by water vapour does not change as the climate system warms, while that radiated by everything else increases following Planck's Law. While still not quantitatively accurate, this does provide a physical explanation for the general size of the water vapour feedback, as well as for its robustness in GCMs.

The partly‐Simpsonian approach also provides a physical explanation for the well‐established fact that, in water‐vapour‐dominated regions of the spectrum, the heat radiated by the climate system is a function primarily of relative humidity, not temperature. © Crown Copyright 2010. Published by John Wiley & Sons, Ltd.
A nudging scheme to assimilate satellite brightness temperature in a meteorological model: Impact on representation of African mesoscale convective systems
Authors: Orlandi E. , Fierli F. , Davolio S. , Buzzi A. , Drofa O.
Published: January 2010

The study presents the implementation of a nudging procedure in a mesoscale meteorological model, and its evaluation in improving the representation of mesoscale convective systems in the region of West Africa. The generation and development of convection are related to processes with different spatial scales, making it often difficult for meteorological models to reproduce their dynamics.

The assimilation approach is based on the continuous assimilation of METEOSAT infrared brightness temperatures within the model in order to trigger convection, where observations show the presence of large convective systems. The nudging also inhibits convection, when the model reproduces unrealistic convective precipitation and coherently modifies the dynamical fields.

Model sensitivity to the nudging scheme has been tested to evaluate the role of the forcing term. The nudging improves the geographical distribution and time evolution of mesoscale convective systems reproduced by the model; the impact of assimilation is positive up to 13 h after the end of the nudging period. It is also shown that the nudging improves the simulated amount and spatial distribution of precipitation.

Finally, the assimilation is performed throughout the entire simulation, showing how the proposed approach can be used to improve meteorological analyses in terms of convective activity and rainfall. Copyright © 2010 Royal Meteorological Society
Reliability diagrams for non‐parametric density forecasts of continuous variables: Accounting for serial correlation
Authors: Pinson Pierre , McSharry Patrick , Madsen Henrik
Published: January 2010

Reliability is seen as a primary requirement when verifying probabilistic forecasts, since a lack of reliability would introduce a systematic bias in subsequent decision‐making. Reliability diagrams comprise popular and practical diagnostic tools for the reliability evaluation of density forecasts of continuous variables. Such diagrams relate to the assessment of the unconditional calibration of probabilistic forecasts. A reason for their appeal is that deviations from perfect reliability can be visually assessed based on deviations from the diagonal. Deviations from the diagonal may, however, be caused by both sampling effects and serial correlation in the forecast‐verification pairs. We build on a recent proposal, consisting of associating reliability diagrams with consistency bars that would reflect the deviations from the diagonal that are potentially observable even if density forecasts are perfectly reliable. Our consistency bars, however, reflect potential deviations originating from the combined effects of limited counting statistics and serial correlation in the forecast‐verification pairs. They are generated based on an original surrogate consistency resampling method. Its ability to provide consistency bars with a significantly better coverage against the independent and identically distributed (i.i.d.) resampling alternative is shown from simulations. Finally, a practical example of the reliability assessment of non‐parametric density forecasts of short‐term wind‐power generation is given. Copyright © 2010 Royal Meteorological Society
A nonstationary Markov transition model for computing the relative risk of dementia before death
Authors: Yu Lei , Griffith William S. , Tyas Suzanne L. , Snowdon David A. , Kryscio Richard J.
Published: January 2010

This paper investigates the long‐term behavior of the k‐step transition probability matrix for a nonstationary discrete‐time Markov chain in the context of modeling transitions from intact cognition to dementia with mild cognitive impairment and global impairment as intervening cognitive states. The authors derive formulas for the following absorption statistics: (1) the relative risk of absorption between competing absorbing states and (2) the mean and variance of the number of visits among the transient states before absorption. As absorption is not guaranteed, sufficient conditions are discussed to ensure that the substochastic matrix associated with transitions among transient states converges to zero in limit. Results are illustrated with an application to the Nun Study, a cohort of 678 participants, 75–107 years of age, followed longitudinally with up to 10 cognitive assessments over a 15‐year period. Copyright © 2010 John Wiley & Sons, Ltd.
Bayesian adjustment for exposure misclassification in case–control studies
Authors: Chu Rong , Gustafson Paul , Le Nhu
Published: January 2010

Poor measurement of explanatory variables occurs frequently in observational studies. Error‐prone observations may lead to biased estimation and loss of power in detecting the impact of explanatory variables on the response. We consider misclassified binary exposure in the context of case–control studies, assuming the availability of validation data to inform the magnitude of the misclassification. A Bayesian adjustment to correct the misclassification is investigated. Simulation studies show that the Bayesian method can have advantages over non‐Bayesian counterparts, particularly in the face of a rare exposure, small validation sample sizes, and uncertainty about whether exposure misclassification is differential or non‐differential. The method is illustrated via application to several real studies. Copyright © 2010 John Wiley & Sons, Ltd.