bluuebunny/crossref_metadata_2025 huggingface dataset:
Mass spectrometry in biodefense
Authors: Demirev Plamen A. , Fenselau Catherine
Published: August 2008

Potential agents for biological attacks include both microorganisms and toxins. In mass spectrometry (MS), rapid identification of potential bioagents is achieved by detecting the masses of unique biomarkers, correlated to each agent. Currently, proteins are the most reliable biomarkers for detection and characterization of both microorganisms and toxins, and MS‐based proteomics is particularly well suited for biodefense applications. Confident identification of an organism can be achieved by top‐down proteomics following identification of individual protein biomarkers from their tandem mass spectra. In bottom‐up proteomics, rapid digestion of intact protein biomarkers is again followed by MS/MS to provide unambiguous bioagent identification and characterization. Bioinformatics obviates the need for culturing and rigorous control of experimental variables to create and use MS fingerprint libraries for various classes of bioweapons. For specific applications, MS methods, instruments and algorithms have also been developed for identification based on biomarkers other than proteins and peptides. Copyright © 2008 John Wiley & Sons, Ltd.
Genetic diversity of norovirus, sapovirus, and astrovirus isolated from children hospitalized with acute gastroenteritis in Chiang Mai, Thailand
Authors: Malasao Rungnapa , Maneekarn Niwat , Khamrin Pattara , Pantip Chansom , Tonusin Supin , Ushijima Hiroshi , Peerakome Supatra
Published: August 2008

Norovirus (NV), sapovirus (SV), and human astrovirus (HAstV) are important causes of acute gastroenteritis in infants and young children. This study investigated the prevalence of NV, SV, and HAstV infections in children hospitalized with acute gastroenteritis in Chiang Mai, Thailand from May 2000 to March 2002. Fecal specimens were tested for NV, SV, and HAstV by reverse transcription polymerase chain reaction (RT‐PCR) using degenerate specific primers. These viruses were characterized further by sequence and phylogenetic analyses of the partial capsid gene. From 296 fecal specimens tested, 13.5% (40 of 296) were positive for NV, SV, and HAstV. Of these, NV most predominant, with a prevalence of 60% (24 of 40), of which 17.5% were NVGI and 42.5% were NVGII. Of note, one specimen was positive for both NVGI and SV. SV was detected in 25%, while HAstV was detected in 17.5%. Analysis of nucleotide and amino acid sequences revealed that NVGI strains comprised GI/3, GI/4, GI/6, GI/7, and GI/13 genotypes. Among NVGII strains, approximately half of them belonged to genotype GII/4 (Lordsdale virus cluster), followed by GII/3, GII/10, GII/1, GII/6, GII/8, and GII/15. Analysis of SV sequences revealed that SVGI (Manchester virus) was more common than SVGII (London virus). The SV genotypes detected in this study belonged to SVGI/1, SVGI/4, SVGI/5, SVGII/1, and SVGII/2, whereas the HAstV belonged to genotypes HAstV‐1, HAstV‐2, HAstV‐3, and HAstV‐5. The findings suggest that NV, SV, and HAstV are important enteric viruses cocirculating among hospitalized children in Chiang Mai, Thailand. J. Med. Virol. 80:1749–1755, 2008. © 2008 Wiley‐Liss, Inc.
Immune suppression leading to hepatitis C virus re‐emergence after sustained virological response
Authors: Lin Amy , Thadareddy Anupama , Goldstein Michael J. , Lake‐Bakaar Gerond
Published: August 2008

Sustained virological response SVR is defined as undetectable HCV RNA in plasma 6 months after therapy has been discontinued. Relapse or re‐emergence of viremia after SVR is rare. We report two patients that relapsed when immune suppressive therapy was given within a few weeks of achieving SVR. Patient 1 received prednisone for bronchitis and patient 2 relapsed soon after immune suppression was started post renal transplantation. These data suggest that the early phase of SVR might be associated with incomplete protective immunity. They suggest that sterilizing immunity with complete elimination of virus is unlikely. The cases also caution against the use of immune suppressive therapy in the immediate aftermath of SVR. J. Med. Virol. 80:1720–1722, 2008. © 2008 Wiley‐Liss, Inc.
Seroprevalence of human T‐lymphotropic virus type 1 and 2 in Korean blood donors
Authors: Kwon So‐Yong , Lim A Hyun , Park Ji Young , Han Seung Hee , Cho Nam‐Sun
Published: August 2008

The seroprevalence rate of human T‐lymphotropic virus (HTLV) among the Korean blood donor population was studied to determine whether screening for HTLV should be implemented. A total of 15,173 serum samples collected from June to July 2006 at five Blood Centers which are located closely to Japan geographically, where the prevalence of HTLV is known to be high, were tested. Serological screening was done by a chemiluminescence method. Samples reactive repeatedly on serological screening were confirmed further by Western blot, line immunoassay, nested polymerase chain reaction and sequencing of proviral DNA. Six samples tested reactive with the serological assay showing a reactive rate of 0.004%. Among the six samples, one sample was confirmed as HTLV‐1 positive, giving a confirmed reactive rate of 0.007%. Based on the results of this study, an extended study will be conducted to evaluate whether introduction of HTLV screening is necessary in Korea. J. Med. Virol. 80:1864–1867, 2008. © 2008 Wiley‐Liss, Inc.
Evidence of intrafamilial transmission of rotavirus in a birth cohort in South India
Authors: Banerjee Indrani , Primrose Gladstone Beryl , Iturriza‐Gomara Miren , Gray James J. , Brown David W. , Kang Gagandeep
Published: August 2008

Transmission of rotavirus infection was studied in a birth cohort of children based in an urban slum in Vellore and their familial contacts. Contemporaneous samples from index patients and their familial contacts were collected for analysis in three different settings. Firstly, samples were collected from familial contacts during a period of rotavirus infection in children from the cohort. Secondly, on occasions when a family member had rotavirus diarrhea, samples from the cohort child were taken for analysis. Lastly, asymptomatic surveillance samples collected at predetermined time points from both the cohort child and familial contacts were analyzed. From 560 samples collected from family members during symptomatic and asymptomatic rotavirus infections in these children, three rotavirus transmissions were identified, accounting for a secondary attack rate of 0.54%. In four instances of rotavirus diarrhea in a family member, one infection was transmitted to the cohort child. Nucleotide sequence and phylogenetic analysis demonstrated a high degree of similarity in all these pairs ranging between 99% and 100% at both the nucleotide and the deduced amino acid levels, highly suggestive of person‐to‐person transmission of rotavirus infection. There was complete concordance of rotavirus genotyping between these pairs. No transmission events were noted from 14 asymptomatic rotavirus infections identified during routine surveillance of family members. This study is the first to use phylogenetic analysis to study the intrafamilial spread of rotavirus infection. J. Med. Virol. 80:1858–1863, 2008. © 2008 Wiley‐Liss, Inc.
First report on fatal myocarditis associated with adenovirus infection in Cuba
Authors: Valdés Odalys , Acosta Belsy , Piñón Alexander , Savón Clara , Goyenechea Angel , Gonzalez Grehete , Gonzalez Guelsys , Palerm Lidice , Sarmiento Luis , Pedro Mas Lago , Martínez Pedro A. , Rosario Delfina , Kourí Vivian , Guzmán María Guadalupe , Llop Alina , Casas Inmaculada , Perez Breña Ma. Pilar
Published: August 2008

Myocarditis is caused frequently by viral infections of the myocardium. In the past, enteroviruses (EV) were considered the most common cause of myocarditis in all age groups. Other viruses that cause myocarditis are adenovirus and influenza viruses. Parvovirus B19 infection is associated sometimes with myocarditis. Members of the Herpesviridae family, cytomegalovirus (CMV), and human herpesvirus 6 (HHV‐6) have been associated occasionally with myocarditis. During an atypical outbreak of acute febrile syndrome, eight children, with ages from 5 months to 15 years, died in cardiogenic shock due to myocarditis in July–August 2005, in the city of Havana, Cuba. Nested polymerase chain reaction (nPCR) and nested reverse transcription‐PCR (nRT‐PCR) were carried out on fresh heart muscle and lung tissue to analyze the genomic sequences of adenovirus, CMV, HHV‐6, herpes simplex virus, Epstein–Barr virus (EBV), varizella zoster virus, influenza virus A, B, C, respiratory syncytial virus (RSV) A and B, parainfluenza viruses, rhinoviruses, coronavirus, flaviruses and enteroviruses. Evidence was for the presence of the adenovirus genome in 6 (75%) of the children. Phylogenetic analyses of a conserved hexon gene fragment in four cases showed serotype 5 as the causal agent. No others viruses were detected. Histological examination was undertaken to detect myocardial inflammation. After exclusion of other possible causes of death, the results indicated that viral myocarditis was the cause of death in patients with adenovirus infection. J. Med. Virol. 80:1756–1761, 2008. © 2008 Wiley‐Liss, Inc.
Case Report: Persistent cytomegalovirus (CMV) infection after haploidentical hematopoietic stem cell transplantation using in vivo alemtuzumab: emergence of resistant CMV due to mutations in the UL97 and UL54 genes
Authors: Oshima Kumi , Kanda Yoshinobu , Kako Shinichi , Asano‐Mori1 Yuki , Watanabe Takuro , Motokura Toru , Chiba Shigeru , Shiraki Kimiyasu , Kurokawa Mineo
Published: August 2008

Addition of in vivo alemtuzumab to the conditioning regimen enabled 2‐ or 3‐locus‐mismatched hematopoietic stem cell transplantation with an acceptable incidence of graft‐versus‐host‐disease. However, the procedure was associated with a high incidence of cytomegalovirus (CMV) reactivation. Although preemptive therapy with ganciclovir prevented successfully severe CMV diseases and CMV‐related mortality, a patient developed persistent positive CMV antigenemia for more than 1 year after transplantation and CMV disease, despite the use of ganciclovir and foscarnet. The in vitro susceptibility assay showed that the clinical isolate was resistant to foscarnet, moderately resistant to ganciclovir, but sensitive to cidofovir. Therefore, cidofovir was administered. CMV antigenemia became negative within 2 weeks and never developed again. Nucleotide sequence of the UL54 and UL97 of the clinical isolate showed 4 amino acid substitutions (V11L, Q578H, S655L, and G874R) in UL54 and 2 mutations (A140V and A594V) in UL97 compared with the Towne and AD169 strains. Ganciclovir resistance was suspected to be caused by both A594V of UL97 and Q578H of UL54, whereas foscarnet resistance was due mainly to Q578H of UL54. In conclusion, the in vitro susceptibility assay as well as nucleotide sequence of clinical isolate is important to choose appropriate antiviral agents for patients who have persistent CMV reactivation after stem cell transplantation. J. Med. Virol. 80:1769–1775, 2008. © 2008 Wiley‐Liss, Inc.
Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories
Authors: Luo C. , Bueno M. , Kant J. , Randhawa P.
Published: August 2008

Data on polyomavirus genomic diversity has greatly expanded in the past few years. The implications of viral DNA sequence variation on the performance of molecular diagnostic assays have not been systematically examined. 716 BK, 1626 JC, and 73 SV40 virus sequences available in GenBank were aligned using Clustal‐X. Five different published BKV PCR assays currently in use at major medical centers were evaluated for primer and probe mismatches with available GenBank sequences. Coverage of naturally occurring BKV strains varied amongst different assay methods. Targeted viral sequences showed major mismatch with primer or probe sequence in up to 30.7% of known BKV strains. BKV subtypes IVa, IVb, and IVc were more prone to this problem, reflecting common use of Type I Dun sequence for assay design. Despite the known polymorphism of this gene, 484 VP‐1 sequences with conserved areas potentially suitable for PCR assay design are available. Assay targets in the Large T‐antigen and agnogene are less subject to genetic variation, but sequence information corresponding to the latter two genes is available only for 164 and 174 published strains, respectively. Cross reactivity of appropriately selected BKV primers with JCV and SV40 sequences available in current databases was not a significant problem. J. Med. Virol. 80:1850–1857, 2008. © 2008 Wiley‐Liss, Inc.
Brief Report: acute viral hepatitis and poor maternal and perinatal outcomes in pregnant Sudanese women
Authors: Ahmed Rihab E. , Karsany Mubarak S. , Adam Ishag
Published: August 2008

Sixteen pregnant women presented at the three main hospitals in Khartoum province, Sudan during the period of March–September 2007 with features of acute viral hepatitis. Their mean (SD) gestational age was 28.0(6.7) weeks. The etiology of acute viral hepatitis was hepatitis B virus in five women (31.3%), hepatitis C virus in one woman (6.3%), hepatitis E virus in eight women (50%), and hepatitis non‐A‐to‐E virus in two women (12.5%). There were four (25%) maternal deaths and three (18.7%) intrauterine fetal deaths. Three of these maternal deaths were due to hepatitis E virus and the fourth was due to hepatitis B virus. J. Med. Virol. 80:1747–1748, 2008. © 2008 Wiley‐Liss, Inc.
Complete genome sequencing and phylogenetic analysis of HCV isolates from China reveals a new subtype, designated 6u
Authors: Xia Xueshan , Zhao Wenhua , Tee Kok Keng , Feng Yue , Takebe Yutaka , Li Qihan , Pybus Oliver G. , Lu Ling
Published: August 2008

Full length genome sequences were characterized for three novel hepatitis C virus (HCV) isolates (here named DH012, DH014, and DH028). The complete genomes were all isolated from injecting drug users (IDUs) who were co‐infected with HIV‐1 and lived in Dehong prefecture, Yunnan Province, China, which neighbors Myanmar. The three genomes are 9,443–9,470 nt in length and each contains a single open reading frame (ORF) of 9,069 nt long. Pairwise comparisons indicated nucleotide similarities of 97.9–98.6% among the three isolates, and similarities of 72.4–75.0% between the three isolates and 20 reference strains (representing HCV subtypes 6a–6q and 6t plus two unassigned genotype 6 isolates km41 and gz52557). Phylogenetic analyses demostrated that the three isolates formed a tight and well‐supported monophyletic cluster in the genotype 6 clade. No evidence of viral recombination was found using similarity plots and bootscanning analyses. Based on the current HCV classification criteria, we have assigned the three isolates to a new subtype, 6u. Although another “6u” isolate D83 has been reported very recently, it is subtypically distinct from the three isolates we described here. Because its designation does not meet the criteria described in the updated HCV nomenclature proposal, this “6u” isolate should be reclassified. J. Med. Virol. 80:1740–1746, 2008. © 2008 Wiley‐Liss, Inc.
Multiple outbreaks of acute hemorrhagic conjunctivitis due to a variant of coxsackievirus A24: Guangdong, China, 2007
Authors: Wu De , Ke Chang‐Wen , Mo Yan‐Ling , Sun Li‐Mei , Li Hui , Chen Qiu‐Xia , Zou Li‐Rong , Fang Ling , Huang Ping , Zhen Huan‐ying
Published: August 2008

Acute hemorrhagic conjunctivitis (AHC) is usually caused by enterovirus 70, coxsackievirus A24(CA24v) and adenoviruses. Several outbreaks of AHC caused by a CA24v have occurred since it was imported into China in 1971. Multiple outbreaks of AHC reappeared in 10 cities of Guangdong during June to November in 2007. The epidemic began in the June, and spread extensively, with a peak in the September. A total of 31,659 cases were reported to center for disease control and prevention of Guangdong, it was estimated that the number of actual AHC was >200 thousands. Forty conjunctival swab specimens were collected from the cases diagnosed clinically with AHC. (RT)‐PCR testing on these conjunctival specimens revealed the presence of an enterovirus, and this was confirmed by 16 isolates. We demonstrated the most likely etiological agent for the multiple outbreaks was a variant of coxsackievirus A24 by molecular typing using a partial VP1 sequence. Sequence comparison and phylogenetic analyses of the VP1 and 3Cpro gene regions were performed by Neighbor‐joining method, the strains from different outbreaks and different geographical areas within Guangdong had no sequence divergence in 2007. The representative isolates from mainland of China including Hangzhou, Ningbo, Beijing, Yunnan, Liaoning, and Henan were analyzed in this study. Phylogenetic analysis revealed theses isolates were located in different clusters, a close phylogenetic and chronological relationship with Singaporean, South Korean and Thailand isolates had been observed. This confirms CA24v circulated in China's mainland has not evolved independently, but co‐evolved with the isolates of Southeast Asia. J. Med. Virol. 80:1762–1768, 2008. © 2008 Wiley‐Liss, Inc.
Prevalence of HBV genotypes in Central and Eastern Europe
Authors: Deterding Katja , Constantinescu Ileana , Nedelcu Filofteia Daniela , Gervain Judit , Nĕmeček Vratislav , Srtunecky Otakar , Vince Adriana , Grgurevic Ivica , Bielawski Krzysztof P. , Zalewska Małgorzata , Bock Thomas , Ambrozaitis Arvydas , Stanczak Janusz , Takács Mária , Chulanov Vladimir , Slusarczyk Janusz , Dražd'áková Marcela , Wiegand Johannes , Cornberg Markus , Manns Michael P. , Wedemeyer Heiner
Published: August 2008

The importance of hepatitis B virus (HBV) genotypes for disease progression and response to interferon‐alpha‐based treatment is well established. While almost all patients in the Mediterranean area are infected with HBV genotype D, HBV genotype A is dominant in Northern Europe. However, the distribution of HBV genotypes is unknown for several Central and Eastern European countries. Data are described of 1313 HBsAg‐positive patients recruited at 14 referral centers in eight countries. There were only very few cases of HBV genotype B, C, E, F, and H infection while HBV genotypes A and D were found in 42% and 48% of patients, respectively. Eight percent of patients had positive bands for more than one genotype using the hybridization assay. The frequency of genotype A was higher in Poland (77%) and the Czech Republic (67%) as compared to Hungary (47%), Lithuania (41%), Croatia (8%), and Germany (32%). In contrast, HBV genotype D was most frequent in Croatian, Romanian, and Russian patients with 80%, 67%, and 93% of cases, respectively. In conclusion, HBV genotype A versus D showed significantly different distribution patterns in Central and Eastern Europe which deserves consideration for national guidelines and treatment decisions. J. Med. Virol. 80:1707–1711, 2008. © 2008 Wiley‐Liss, Inc.
Identification and in vitro characterisation of Lactobacillus plantarum strains from artisanal Bulgarian white brined cheeses
Authors: Georgieva Ralitsa N. , Iliev Ilia N. , Chipeva Valentina A. , Dimitonova Silvia P. , Samelis John , Danova Svetla T.
Published: August 2008

Lactobacillus plantarum strains were isolated from fully ripened, white brined Bulgarian home‐made cheeses. Strains were derived from phenotypically homogenous Lactobacillus group and were identified as L. plantarum based on both phenotypic and molecular identification (species‐specific and multiplex PCR) methods. Heterogeneity of L. plantarum isolates was evaluated by Rep‐PCR analysis.

Further antimicrobial activity, antibiotic susceptibility and transit tolerance of the strains were evaluated. Most of them showed broad spectrum of activity against Gram‐negative bacteria (including human pathogens) independent on the presence of organic acids or hydrogen peroxide.

All strains were sensitive to amoxicillin and sulfamethoxazole/trimethoprim, resistant to clinically relevant β ‐lactame antibiotics (penicillin and ampicillin) and to nalidixic acid, ciprofloxacin, streptomycin, and vancomycin. Significant variability in the sensitivity to tetracycline was noted.

The tolerance to low pH, bile salts, pepsin and pancreatin at concentrations similar to those in the gastrointestinal tract was strain‐dependent. The exposure to bile salts was less destructive than exposure to pH 2.0 for all tested strains. Based on their combined responses to the above selection criteria, four L. plantarum strains, RL29, RL34, RL36 and RL37, were selected as potential probiotics for in vivo studies. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Efflux genes and active efflux activity detection in Malaysian clinical isolates of methicillin‐resistant Staphylococcus aureus (MRSA)
Authors: Saiful Azmi Johari , Mastura Mohtar , Zarizal Suhaili , Mazurah Mohamed Isa , Shuhaimi Mustafa , Ali Abdul Manaf
Published: August 2008

Efflux‐mediated resistance has been recognized as an important contributor of antibiotic resistance in bacteria, especially in methicillin‐resistant Staphylococcus aureus (MRSA) isolates. This study was carried out to detect and analyze efflux genes (norA and mdeA) and active efflux activity in a collection of Malaysian MRSA and methicillin‐sensitive S. aureus (MSSA) clinical isolates. Nineteen isolates including three ATCC S. aureus reference strains were subjected to PCR detection and DNA sequence analysis for norA and mdeA and active efflux detection using modified minimum inhibitory concentration (MIC) assay. From the 19 isolates, 18 isolates harboured the mdeA gene while 16 isolates contained norA gene. DNA sequence analysis reveals 98–100% correlation between the PCR product and the published DNA sequences in GenBank. In addition, 16 isolates exhibited active efflux activity using the ethidium bromide (EtBr)‐reserpine combination MIC assay. To our knowledge, this is the first report on the detection of efflux genes and active efflux activity amongst Malaysian clinical isolates of MRSA/MSSA. Detection of active efflux activity may explain the previous report on efflux‐mediated drug resistance profile amongst the local clinical isolates. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
In vitro antifungal activity and mechanism of action of chitinase against four plant pathogenic fungi
Authors: Yan RuiXiang , Hou JianHua , Ding DongFeng , Guan WenQqiang , Wang CuiYan , Wu ZhiQiang , Li MingGang
Published: August 2008

To determine why chitinase has different antifungal activity on different pathogenic fungi in vitro, we purified recombinant rice chitinase from Pichia pastoris and investigated its antifungal activity against four fungi – Rhizopus stolonifer (Ehrenb. et Fr.) Vuill, Botrytis squamosa Walker, Pythium aphanidermatum (eds.) Fitzp, and Aspergillus niger van Tiegh. Scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR) were used to analyze the surface microstructure and proportion of chitin in the cell wall of the four fungi, respectively. The results showed that the chitinase exhibited different antifungal activities against the four fungi, which was directly correlated to the surface microstructure and the proportion of chitin in the fungal cell wall. It will help understanding the antifungal mechanism of the recombinant chitinase and further determining its application scope on crop protection and post‐harvest storage of fruits and vegetables. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Inducible nature of the enzymes involved in catabolism of caffeine and related methylxanthines
Authors: Dash Swati Sucharita , Gummadi Sathyanarayana N.
Published: August 2008

Previously isolated strain of Pseudomonas sp. has the capability of utilizing caffeine as the sole source of carbon and nitrogen and degrading caffeine at higher concentrations (>10 g l–1). In this study, an assay has been developed to study the enzymatic conversion of caffeine to subsequent methylxanthines by cell free extracts of Pseudomonas sp., the activity of which has been stabilized by use of stabilizers in the lysis buffer. Growth of the strain in various methylxanthines and later enzyme assay demonstrated that the enzyme(s) involved in degradation of caffeine and other methylxanthines were inducible in nature. The results also indicated that more than one enzyme are involved in degradation of caffeine to xanthine, which constitute the primary steps in bacterial caffeine catabolism. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Metabolic adaptation and oxaloacetate homeostasis in P. fluorescens exposed to aluminum toxicity
Authors: Lemire Joseph , Kumar Puja , Mailloux Ryan , Cossar Kathyrn , Appanna Vasu D.
Published: August 2008

Microbial systems are known to elaborate intricate metabolic strategies in an effort to fend the toxic impact of numerous metals. In this study, we show that the exposure of Pseudomonas fluorescens to aluminum (Al) resulted in a metabolic shift aimed at diverting oxaloacetate towards the biogenesis of an aluminophore. This metabolic alteration was characterized by uncoupling of two gluconeogenic enzymes, namely pyruvate carboxylase (PC) and phosphoenolpyruvate carboxykinase (PEPCK). While PC displayed a sharp increase in activity and expression, PEPCK was severely diminished. Malic enzyme (ME) and NAD kinase (NADK), two enzymes involved in maintaining a reductive environment, were markedly increased in the Al‐stressed cells. Hence, Al‐exposed Pseudomonas fluorescens evoked a metabolic response aimed at generating oxaloacetate and promoting an intracellular reductive environment. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Direct detection of Kitasatospora species with a chaperone oligonucleotide microarray method lacking PCR amplification
Authors: Guenther Sebastian , Groth Ingrid , Schierack Peter , Grabley Susanne , Munder Thomas
Published: August 2008

Identification of members of the genus Kitasatospora from soil samples has been introduced to evaluate occurrence of potential natural compound producers in different habitats. The microarray hybridization usually involves PCR amplification of the target DNA. Since PCR might lead to biased amplification, a diagnostic Kitasatospora microarray technique was improved by a protocol lacking PCR amplification prior to hybridization. The described advanced hybridization method used chaperone oligonucleotides for direct co‐hybridization with genomic DNA on an oligonuclotide microarray with optical readout. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
HIV entry inhibitors and their potential in HIV therapy
Authors: Qian Keduo , Morris‐Natschke Susan L. , Lee Kuo‐Hsiung
Published: August 2008

This review discusses recent progress in the development of anti‐HIV agents targeting the viral entry process. The three main classes (attachment inhibitors, co‐receptor binding inhibitors, and fusion inhibitors) are further broken down by specific mechanism of action and structure. Many of these inhibitors are in advanced clinical trials, including the HIV maturation inhibitor bevirimat, from the authors' laboratories. In addition, the CCR5 inhibitor maraviroc has recently been FDA‐approved. Possible roles for these agents in anti‐HIV therapy, including treatment of virus resistant to current drugs, are also discussed. © 2008 Wiley Periodicals, Inc. Med Res Rev, 29, No. 2, 369–393, 2009
Heteronuclear dipolar decoupling effects on multiple‐quantum and satellite‐transition magic‐angle spinning NMR spectra
Authors: Ganapathy S. , Delevoye L. , Amoureux J. P. , Madhu P. K.
Published: August 2008

We here report on the influence of heteronuclear dipolar decoupling on the 27Al 3QMAS, 5QMAS, and the double‐quantum filter–satellite‐transition magic‐angle spinning (DQF‐STMAS) spectra of a strongly dipolar‐coupled system, gibbsite. The requirements for heteronuclear dipolar decoupling increase with the order of coherence evolving in the indirect dimension of a two‐dimensional (2D) experiment. The isotropic line width of the high‐resolution 2D spectra, in samples like gibbsite, is composed of four parts: the distribution of isotropic shifts (δISO, δQIS), the homogeneous broadening related to the proton–proton flip‐flop terms, the 27Al27Al homonulcear dipolar couplings, and the 1H27Al heteronuclear dipolar couplings. It is shown that, even in the case of gibbsite, where a strong proton–proton bath exists, the main resolution limiting factor in these experiments resides in the 1H27Al dipolar interaction. Copyright © 2008 John Wiley & Sons, Ltd.
DFT/NMR integrated approach: a valid support to the total synthesis of chiral molecules
Authors: Chini Maria Giovanna , Riccio Raffaele , Bifulco Giuseppe
Published: August 2008

The analysis of the configuration of kedarcidin chromophore and palau'amine through quantum chemical calculation of Js and chemical shifts suggests a fast and convenient quantum chemical approach that can be applied prior to proceeding to the total synthesis of complex natural compounds in order to avoid loss of time and resources employed in the total synthesis of wrong diastereoisomers. Copyright © 2008 John Wiley & Sons, Ltd.
Deposition of Barrier Coatings from Vinyltrimethylsilane‐Fed Glow Discharges
Authors: Francescangeli Adriano , Palumbo Fabio , d'Agostino Riccardo
Published: August 2008

Radio‐frequency glow discharges fed with vinyltrimethylsilane have been studied for the deposition of barrier coatings onto polymer substrates as single or multiple layers. The deposition process has been investigated considering both the chemistry of the coatings and the spectroscopic analysis of the gas phase. It has been shown that RF power and oxygen addition allow one to switch from organosilane films to silica‐like inorganic, dense, barrier films. A deposition mechanism is suggested for the interpretation of the deposition kinetics. Furthermore, it has been shown that vinyltrimethylsilane can be conveniently exploited as single monomer for the deposition of organic/inorganic multistacks with high barrier performances.

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Superionic transition of the NaI–AgI system
Authors: Lozano Z. C. A. , Correa H. , Lara D. Peña , Vargas R. A.
Published: August 2008

The solid electrolyte transition in NaI–AgI was studied by electrical conductivity measurements in the temperature range between 323 K and 523 K. Although NaI does not dissolve in AgI, the addition of NaI led to a stable α–β‐phase boundary of AgI at 420 K, decreased the total ionic conductivity in the α‐phase and caused a smaller step change of conductivity between the values above (α‐phase) and below (β‐phase) 420 K. The conductivity data were analyzed by considering that the ionic carrier density is the main source of the sudden increase in the ionic conductivity through this solid electrolyte transition; therefore, we propose a modified version of the Welch–Dienes trial model free energy density in which the quadratic terms for energy are conserved. In this model three terms were considered: the first one associated with the activation energy (Ui) to promote an atom toward an interstitial site; the second one associated with the attractive interaction due to the Frenkel pair (U) and the last one due to the configurational entropy. It was found that the observed step change in conductivity is mainly due to the carrier density ni The trial free energy function admits at least three solutions for given parameter values, but the equilibrium configuration is that in which ni = $ \bar n $i gives the minimum value at a given temperature. In this way, we were able to reproduce the conductivity changes observed in the NaI–AgI system at 420 K. The phase transition is expected to be first order because the order parameter (n) changes abruptly. The activation energy Ui associated with this anomaly was of the order of 0.3 eV, and the best fitting parameters were Γ = 2.81, x = 0.77 and γ = 5.49. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Excitonic imaging spectroscopy of single‐walled carbon nanotubes
Authors: Lefebvre Jacques , Austing David G. , Finnie Paul
Published: August 2008

We show how photoluminescence (PL) imaging can be used to gain fundamental spectroscopic information on the optical excitations in single‐walled carbon nanotubes (SWNTs). Individual SWNTs are identified, and emission and excitation (PLE) spectra are obtained. In addition to the dominant E11 and E22 transitions, we observe several resonances including the transverse E12 exciton, and up to three excited excitonic bands. The (n,m) family dependence is obtained for some 25 species in the 1.1 to 1.6 µm emission range. We provide simple power series expansion to facilitate (n,m) assignment of all these peaks. This paper complements recently published work. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Carbon nanotubes for interconnects in VLSI integrated circuits
Authors: Robertson J. , Zhong G. , Telg H. , Thomsen C. , Warner J. M. , Briggs G. A. D. , Detlaff U. , Roth S. , Dijon J.
Published: August 2008

The paper reviews the requirements for carbon nanotubes to be used as interconnects in VLSI integrated circuits. It describes the production by chemical vapour deposition of high density arrays of nanotubes suitable for use as interconnects, and describes their characterisation by Raman and transmission electron microscopy. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Improving separation techniques for single‐walled carbon nanotubes: Towards monodisperse samples
Authors: Hennrich F. , Lebedkin S. , Kappes Manfred M.
Published: August 2008

We describe novel procedures which allow the facile production of monochiral single wall carbon nanotube suspensions using either density gradient centrifugation or selective dispersion with special organic polymers. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Growth of carbon nanotubes as horizontal interconnects
Authors: Zhang Can , Cott Daire , Chiodarelli Nicolo , Vereecken Philippe , Robertson John , Whelan Caroline M.
Published: August 2008

In this study, we evaluate the possibility of achieving horizontal carbon nanotube (CNT) growth for application as global interconnects in VLSI integrated circuits. A test structure suitable for electrical characterization has been designed and fabricated to assess horizontal CNT growth. Catalyst placement on the vertical electrode surface was realized by either physical vapour deposition or electroless deposition of Ni. The resulting yield of nanotubes grown by a chemical vapour deposition method is found to be low and randomly oriented, most likely due to low density of the catalyst particles deposited on the HGTS. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Infrared microreflectance study of the pressure effect on the structural properties of magnetically aligned single‐wall carbon nanotubes
Authors: Kuntscher C. A. , Thirunavukkuarasu K. , Kamarás K. , Simon F. , Walters D. A.
Published: August 2008

The optical response of magnetically aligned singlewall carbon nanotube films was studied by polarizationdependent reflectance measurements in the infrared and visible frequency range as a function of external pressure. At ambient pressure the optical properties are anisotropic and show the characteristic excitations (broad infrared peak and optical transitions).

The pressure‐induced shift of the optical transitions reveals an anomaly at a critical pressure Pc≈2.7 GPa. This anomaly can be attributed to the circular‐to‐oval structural phase transition in the nanotubes. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Inkjet printed resistive and chemical‐FET carbon nanotube gas sensors
Authors: Mäklin Jani , Mustonen Tero , Halonen Niina , Tóth Géza , Kordás Krisztián , Vähäkangas Jouko , Moilanen Hannu , Kukovecz Ákos , Kónya Zoltán , Haspel Henrik , Gingl Zoltán , Heszler Péter , Vajtai Robert , Ajayan Pulickel M.
Published: August 2008

Aqueous solutions of carboxyl functionalized single‐wall carbon nanotube (SWCNT) films are deposited on silicon chips by the inkjet printing technique. By varying the film thickness it is possible to obtain low‐ or high density networks of SWCNTs, having either nonlinear or linear current‐voltage characteristics, respectively. The electrical transport in the low‐density films is gate‐controllable and utilized as chemical field‐effect transistor sensors; whereas the high‐density SWCNT networks of nearly Ohmic behaviour are used as conventional resistive gas sensors. The response of both types of sensors is studied for hydrogen sulfide (H2S) analyte. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Dielectrophoretically assembled carbon nanotube‐metal hybrid structures with reduced contact resistance
Authors: Ranjan Nitesh , Mertig Michael
Published: August 2008

We report the bottom‐up assembly of single‐walled carbon nanotube interconnects between micro‐fabricated gold electrodes by dielectrophoresis followed by a post‐dielectrophoretic deposition of metal from an aqueous Pd salt solution. The dielectrophoretic metal deposition along interconnects takes preferentially place at sites where high contact resistances occur. These create sufficiently high voltage drops, and thus, large field gradients which lead to a local deposition of met al. Since in turn the metal deposition leads to a reduction of the local resistances, the reported post‐treatment process is self‐regulating, that is, the deposition of metal stops when the contact resistances become sufficiently reduced. Applying this process to single interconnects of carbon nanotubes a reduction of the overall resistance below 1 MΩ has been achieved. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
New phase of polymeric C60: double chains via [2+2] cycloaddition
Authors: Artyukhov Vasilii I. , Belova Elena E. , Chernozatonskii Leonid A.
Published: August 2008

We investigate the structure of a new phase of one‐dimensional polymeric C60 that has recently been demonstrated to form from the orthorhombic phase of polymeric C60 as a result of pressure‐driven photopolymerization, using ab initio calculations at the density‐functional theory level. The transition to the new phase proceeds via formation of additional [2+2] bonds between neighbouring C60 chains of the O phase, resulting in double chains of C60 units along the [100] crystallographic direction. The new phase is a semiconductor, like the original O phase, but with a narrower band gap. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Gas chromatography/time‐of‐flight mass spectrometry based metabonomic approach to differentiating hypertension‐ and age‐related metabolic variation in spontaneously hypertensive rats
Authors: Lu Yihong , A Jiye , Wang Guangji , Hao Haiping , Huang Qing , Yan Bei , Zha Weibin , Gu Shenghua , Ren Hongcan , Zhang Ying , Fan Xialei , Zhang Mei , Hao Kun
Published: August 2008

Metabonomics is a systematic approach to the study of in vivo metabolic profiles and therefore allows deep insight into and a better understanding of the pathogenesis of disease. To characterize the development of hypertension, a hypertensive animal model, the spontaneously hypertensive rat (SHR), and its normotensive control, the Wistar Kyoto (WKY) rat, were investigated and their blood plasma analyzed using the high‐throughput metabolomic tool, gas chromatography/time‐of‐flight mass spectrometry (GC/TOFMS). A total of 187 peaks were quantitatively determined after deconvolution, and 78 of them were identified. Principal components analysis (PCA) and projection to latent structure partial least‐squares discriminant analysis (PLS‐DA) were used to process the GC/TOFMS data. The resulting mathematical models were further validated by cross‐validation. Plasma compositional differences of many identified compounds showed hypertension‐related variation between SHR and WKY rats, and age‐related changes from 10 to 18 weeks for both the SHR and WKY rats. These compositional changes involved compounds such as hexadecanoic acid, linoleic acid, oleic acid, stearic acid, 3‐hydroxybutyric acid, citric acid, threonic acid, tyrosine, tryptophan, threonine, phenylalanine, serine, ornithine, methionine, 3‐hydroxyproline, creatinine, erythrose, myo‐inositol, D‐methylglucopyranoside, tocopherol, sitosterol, and nonesterified cholesterol. Significantly elevated free fatty acids (FFA) were observed in SHR relative to those in WKY rats, and their levels increased as the SHR aged from 10 to 18 weeks. The close correlation between FFA and hypertension suggests that FFA are potential biomarker candidates for hypertension and they may play an important role in the development of hypertension in SHR. It is also indicated that GC/TOFMS‐based metabonomics is a powerful approach to identifying potential biomarkers and investigating the pathological processes of hypertension and the physiological developments of aging. Copyright © 2008 John Wiley & Sons, Ltd.
Applications of silver nanoparticles capped with different functional groups as the matrix and affinity probes in surface‐assisted laser desorption/ionization time‐of‐flight and atmospheric pressure matrix‐assisted laser desorption/ionization ion trap mass spectrometry for rapid analysis of sulfur drugs and biothiols in human urine
Authors: Shrivas Kamlesh , Wu Hui‐Fen
Published: August 2008

A strategy is presented for the analysis of sulfur drugs and biothiols using silver nanoparticles (AgNPs) capped with different functional groups as the matrix and affinity probes in surface‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (SALDI‐TOF MS) and atmospheric pressure‐matrix assisted laser desorption/ionization ion trap mass spectrometry (AP‐MALDI‐ITMS). Biothiols adsorbed on the surface of AgNPs through covalent bonding were subjected to ultraviolet (UV) radiation that enabled desorption and ionization due to the excellent photochemical property of NPs. The proposed method has been successfully applied for the determination of cysteine and homocysteine in human urine samples using an internal standard. The limit of detection (LOD) and limit of quantification (LOQ) for cysteine and homocysteine in urine sample are 7 and 22 nM, respectively, with a relative standard deviation (RSD) of <10%. The advantages of the present method compared with the methods reported in the literature for biothiol analysis are simplicity, rapidity and sensitivity without the need for time‐consuming separation and tedious preconcentration processes. Additionally, we also found that the bare AgNPs can be directly used as the matrix in MALDI‐TOF MS for the analysis of sulfur drugs without the addition of an extra proton source. Copyright © 2008 John Wiley & Sons, Ltd.
Correction
Authors: Harel Ofer , (Andrew) Zhou X. H.
Published: August 2008

‘Multiple imputation for correcting verification bias’ by Harel O, Zhou XH (Statistics in Medicine 2006; 25:3769–3786) and ‘Rejoinder to Multiple imputation for correcting verification bias’ (Statistics in Medicine 2007; 26:3047–3050). A calculation error in the breast cancer example using diaphanography data presented in our paper was recently brought to our attention. In this example, the code calculating the sensitivity and specificity for the multiple imputation (MI) techniques had a typo resulting in column summation instead of row summation. As a result, the reported sensitivity and specificity were actually positive predictive and negative predictive values. The reported values for the methods not requiring MI (Naive 1 and B&G 2) were correct. The corrected table is reported in Table I.

We want to emphasize that the conclusions in Harel and Zhou 1 are still valid. The conclusions were based on a simulation study for which their results are valid.

We apologize for any inconvenience caused to Statistics in Medicine readers.

Results comparing five MI methods, the B&G as existing method and naive method of sensitivity and specificity—diaphanography data for breast cancer.

Sensitivity
Specificity

Procedure
Est
SE
CI
Est
SE
CI

Naive
0.788
0.071
(0.649, 0.927)
0.800
0.054
(0.694, 0.906)

B&G
0.292
0.080
(0.134, 0.449)
0.973
0.008
(0.958, 0.988)

Logit B&G
0.292
0.388
(0.161, 0.469)
0.973
0.288
(0.954, 0.985)

A&C
0.304
0.075
(0.145, 0.462)
0.972
0.007
(0.959, 0.985)

Rubin
0.297
0.079
(0.165, 0.475)
0.974
0.007
(0.957, 0.984)

Wilson
0.292
0.035
(0.223, 0.361)
0.972
0.006
(0.960, 0.983)

Jeffrey
0.299
—
(0.222, 0.359)
0.974
—
(0.961, 0.984)

Z&L
0.301
—
(0.235, 0.373)
0.973
—
(0.960, 0.983)
Correction
Authors: Young Linda J.
Published: August 2008

In ‘Assessing the association between environmental impacts and health outcomes: A case study from Florida’, by Young, Gotway, Yang, Kearney, and DuClos (DOI: 10.1002/sim.3249), Reference [33] is incorrect and should be

33. Müller WG. Collecting Spatial Data: Optimum Design of Experiments for Random Fields. Physica‐Verlag: Heidelberg, 1998.
High‐Fidelity Formation of a Molecular‐Junction Device Using a Thickness‐Controlled Bilayer Architecture
Authors: Bang Gyeong Sook , Chang Hojong , Koo Ja‐Ryong , Lee Takhee , Advincula Rigoberto C. , Lee Hyoyoung
Published: August 2008

The device yield of molecular junctions has become a major issue for the practical application of molecular electronics based on a crossbar system of a metal–molecule–metal (MMM) junction. As the thickness of self‐assembled monolayers (SAMs) is typically 1–2 nm, it is difficult to avoid electrical shorts due to the penetration of top metal particles into the SAMs. A simple and effective strategy for the creation of a reliable molecular junction using a thickness‐controlled bilayer with a bifunctional heterostructure is presented. In the MMM device, the Au adlayer on the molecular layer is spontaneously formed with deposition of the top Au metals and the sandwiched molecular layer maintains the quality of the SAMs. This method greatly reduces electrical shorts by preventing the diffusion of the top metal electrode and offsetting the surface roughness of the bottom metal electrode, resulting in a device yield of more than 90%.
Glutamate receptor subunits expression in memory‐associated brain structures: Regional variations and effects of aging
Authors: Liu Ping , Smith Paul F. , Darlington Cynthia L.
Published: August 2008

We investigated regional variations and the effects of aging on the expression of the N‐methyl‐D‐aspartate (NMDA) and α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazole (AMPA) receptor subunits in several memory‐associated structures using Western blotting. In young adult rats, NR1, NR2A, and GluR2 levels varied between the hippocampus and parahippocampal region and between the subregions of the hippocampus. When a comparison was made between young (4‐month‐old) and aged (24‐month‐old) rats, significant decreases in NR1 expression were found in the aged ventral hippocampus and the entorhinal and postrhinal cortices. There were significant decreases in NR2A expression in the aged parahippocampal region, but not in the hippocampus. The expression of the GluR2 subunit was significantly reduced in the ventral hippocampus and the postrhinal cortex. A dramatic decrease in NR1 and GluR2 expression was found in the aged CA2/3 and CA1, respectively, but there were no significant age‐related changes in NR2A expression. All three subunits were expressed at a similar level in the two age groups in the prefrontal cortex. These results suggest differential expression and effects of aging on NMDA and AMPA receptor subunits in memory‐associated brain structures. Synapse 62:834–841, 2008. © 2008 Wiley‐Liss, Inc.
Dopamine modulating drugs influence striatal (+)‐[11C]DTBZ binding in rats: VMAT2 binding is sensitive to changes in vesicular dopamine concentration
Authors: Tong Junchao , Wilson Alan A. , Boileau Isabelle , Houle Sylvain , Kish Stephen J.
Published: August 2008

Binding of (+)‐[11C]DTBZ (dihydrotetrabenazine) to the striatal vesicular monoamine transporter (VMAT2) is widely considered to be a stable marker of dopamine neurone integrity. However, we now find that specific binding of a tracer dose of (+)‐[11C]DTBZ is modestly increased in rat striatum following dopamine depletion with α‐methyl‐p‐tyrosine (α‐MPT, +14%) or d‐amphetamine (d‐AMPH, 20 mg/kg, +12%) and decreased following dopamine elevation with γ‐hydroxybutyrate (GHB, −16%) or levodopa (−20%). We suggest that in vivo (+)‐[11C]DTBZ binding in imaging studies is subject to competition by vesicular dopamine and, in this respect, is not a “stable” dopamine biomarker as is generally assumed. Synapse 62:873–876, 2008. © 2008 Wiley‐Liss, Inc.