bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autosomal and sex‐linked microsatellite loci in the green oak leaf roller Tortrix viridana L. (Lepidoptera, Tortricidae)
Authors: SCHROEDER H. , ARENS P. , SMULDERS M. J. M. 
Published: January 2009

AbstractEight microsatellite markers were developed for the lepidopteran species Tortrix viridana using an enrichment protocol. The loci were highly variable with number of alleles ranging from four to 38. Six of the eight loci were in Hardy–Weinberg equilibrium. The other two were linked to the Z‐chromosome. Values of observed heterozygosity ranged for the autosomal loci from 0.510 to 0.957. All loci will be useful to study dispersal and the autosomal loci, as well for phylogeographical studies.
Chloroplast simple sequence repeat markers for evolutionary studies in the sexually deceptive orchid genus Chiloglottis
Authors: EBERT DANIEL , HAYES CHRISTINE , PEAKALL ROD 
Published: January 2009

AbstractThe orchids in the genus Chiloglottis are pollinated exclusively by sexual deception. Extensive sequencing (> 19.5 kb) of noncoding chloroplast DNA revealed that simple sequence repeats (cpSSRs) were abundant, enabling a set of 41 cpSSR markers to be developed. All markers were polymorphic across the genus. Polymorphism reflected variation at both mononucleotide repeats and indels. For a subset of four taxa with 40 samples each, locus polymorphism varied from 46 to 81%, while the number of haplotypes ranged from seven to 21 per taxon. Extensive differentiation among the taxa was detected. These cpSSRs markers will enable novel insights into the evolution of this unique genus.
Effects of storage type and time on DNA amplification success in tropical ungulate faeces
Authors: SOTO‐CALDERÓN IVÁN D. , NTIE STEPHAN , MICKALA PATRICK , MAISELS FIONA , WICKINGS ELIZABETH J. , ANTHONY NICOLA M. 
Published: January 2009

AbstractThe present study compares the effect of three storage media (silica, RNAlater®, ethanol) and time to extraction (1 week, 1 month and 3 months) on mitochondrial and nuclear marker amplification success in faecal DNA extracts from a sympatric community of small to medium‐sized Central African forest ungulates (genera Cephalophus, Tragelaphus, Hyemoschus). The effect of storage type and time on nuclear DNA concentrations, genotyping errors and percentage recovery of consensus genotypes was also examined. Regardless of storage method, mitochondrial and nuclear amplification success was high in DNA extracted within the first week after collection. Over longer storage periods, RNAlater yielded better amplification success rates in the mitochondrial assay. However, samples stored on silica showed (i) highest nuclear DNA concentrations, (ii) best microsatellite genotyping success, (iii) lowest genotyping errors, and (iv) greatest percentage recovery of the consensus genotype. The quantity of nuclear DNA was generally a good predictor of microsatellite performance with 83% amplification success or greater achieved with sample DNA concentrations of ≥ 50 pg/µL. If faecal DNA samples are to be used for nuclear microsatellite analyses, we recommend silica as the best storage method. However, for maximum mitochondrial amplification success, RNAlater appears to be the best storage medium. In contrast, ethanol appeared inferior to the other two methods examined here and should not be used to store tropical ungulate faeces. Regardless of storage method, samples should be extracted as soon as possible after collection to ensure optimal recovery of DNA.
Prevalence of Anti-Varicella-Zoster Virus Antibodies in French Infants under 15 Months of Age
Authors: Pinquier Didier , Gagneur Arnaud , Balu Laurent , Brissaud Olivier , Gras Le Guen Christèle , Hau-Rainsard Isabelle , Mory Olivier , Picherot Georges , De Pontual Loïc , Stephan Jean-Louis , Maple Peter , Breuer Judith , Aubert Marie , Caulin Evelyne , Sana Claudine , Pradat Pierre , Soubeyrand Benoît , Reinert Philippe 
Published: January 2009

ABSTRACTVaricella is a widespread disease of childhood resulting from primary infection with varicella-zoster virus (VZV). The objective of this study was to determine the kinetics of the decline of maternal anti-VZV antibodies in French infants between birth and the age of 15 months in order to estimate the duration of passively acquired maternal anti-VZV immunoglobulin G (IgG). This prospective multicenter study was conducted between October 2005 and January 2007 in the pediatric wards and/or pediatric emergency units of seven French hospitals scattered throughout the country. The level of anti-VZV IgG antibodies in serum was measured by a time-resolved fluorescence immunoassay (TRFIA) (the threshold considered positive is 150 mIU/ml). A total of 345 infants were included. Seventy-seven percent of mothers reported a history of varicella. A rapid decline in the prevalence of anti-VZV antibodies was observed during the first few months of life, with the mean antibody titer decreasing from 536 mIU/ml at birth and through 1 month to below the 150-mIU/ml threshold at 3 to 4 months. The half-life of passively acquired maternal immunoglobulins was around 6 weeks. Based on a large number of subjects, this study clearly demonstrated, for the first time in France, high levels of passively acquired maternal antibodies during the neonatal period, and it allowed us to estimate the duration of passively acquired maternal anti-VZV IgG in French infants. After 4 to 5 months, infants had very low levels of maternal anti-VZV IgG, below the 150-mIU/ml cutoff of the VZV IgG TRFIA.
From Genome-Based In Silico Predictions to Ex Vivo Verification of Leprosy Diagnosis
Authors: Geluk Annemieke , Spencer John S. , Bobosha Kidist , Pessolani Maria C. V. , Pereira Geraldo M. B. , Banu Sayera , Honoré Nadine , Reece Stephen T. , MacDonald Murdo , Sapkota Bishwa Raj , Ranjit Chaman , Franken Kees L. M. C. , Zewdie Martha , Aseffa Abraham , Hussain Rabia , Stefani Mariane M. , Cho Sang-Nae , Oskam Linda , Brennan Patrick J. , Dockrell Hazel M. 
Published: January 2009

ABSTRACT

The detection of hundreds of thousands of new cases of leprosy every year suggests that transmission of
Mycobacterium leprae
infection still continues. Unfortunately, tools for identification of asymptomatic disease and/or early-stage
M. leprae
infection (likely sources of transmission) are lacking. The recent identification of
M. leprae
-unique genes has allowed the analysis of human T-cell responses to novel
M. leprae
antigens. Antigens with the most-promising diagnostic potential were tested for their ability to induce cytokine secretion by using peripheral blood mononuclear cells from leprosy patients and controls in five different areas where leprosy is endemic; 246 individuals from Brazil, Nepal, Bangladesh, Pakistan, and Ethiopia were analyzed for gamma interferon responses to five recombinant proteins (ML1989, ML1990, ML2283, ML2346, and ML2567) and 22 synthetic peptides. Of these, the
M. leprae
-unique protein ML1989 was the most frequently recognized and ML2283 the most specific for
M. leprae
infection/exposure, as only a limited number of tuberculosis patients responded to this antigen. However, all proteins were recognized by a significant number of controls in areas of endemicity. T-cell responses correlated with in vitro response to
M. leprae
, suggesting that healthy controls in areas where leprosy is endemic are exposed to
M. leprae
. Importantly, 50% of the healthy household contacts and 59% of the controls in areas of endemicity had no detectable immunoglobulin M antibodies to
M. leprae
-specific PGL-I but responded in T-cell assays to ≥1
M. leprae
protein. T-cell responses specific for leprosy patients and healthy household contacts were observed for ML2283- and ML0126-derived peptides, indicating that
M. leprae
peptides hold potential as diagnostic tools. Future work should concentrate on the development of a sensitive and field-friendly assay and identification of additional peptides and proteins that can induce
M. leprae
-specific T-cell responses.
Immune Responses and Protection against Experimental Challenge after Vaccination of Bison withBrucella abortusStrain RB51 or RB51 Overexpressing Superoxide Dismutase and Glycosyltransferase Genes
Authors: Olsen S. C. , Boyle S. M. , Schurig G. G. , Sriranganathan N. N. 
Published: January 2009

ABSTRACTVaccination is a tool that could be beneficial in managing the high prevalence of brucellosis in free-ranging bison in Yellowstone National Park. In this study, we characterized immunologic responses and protection against experimental challenge after vaccination of bison withBrucella abortusstrain RB51 (RB51) or a recombinant RB51 strain overexpressing superoxide dismutase (sodC) and glycosyltransferase (wboA) genes (RB51+sodC,wboA). Bison were vaccinated with saline only or with 4.6 × 1010CFU of RB51 or 7.4 × 1010CFU of RB51+sodC,wboA(n= eight animals/treatment). Bison vaccinated with RB51 or RB51+sodC,wboAhad greater (P< 0.05) antibody responses, proliferative responses, and production of gamma interferon to RB51 after vaccination than did nonvaccinates. However, bison vaccinated with RB51+sodC,wboAcleared the vaccine strain from draining lymph nodes faster than bison vaccinated with the parental RB51 strain. Immunologic responses of bison vaccinated with RB51+sodC,wboAwere similar to responses of bison vaccinated with RB51. Pregnant bison were intraconjunctivally challenged in midgestation with 107CFU ofB. abortusstrain 2308. Bison vaccinated with RB51, but not RB51+sodC,wboAvaccinates, had greater protection from abortion, fetal/uterine, mammary, or maternal infection than nonvaccinates. Our data suggest that the RB51+sodC,wboAstrain is less efficacious as a calfhood vaccine for bison than the parental RB51 strain. Our data also suggest that the RB51 vaccine is a currently available management tool that could be utilized to help reduce brucellosis in free-ranging bison.
Identification of Functional Domains in Reovirus Replication Proteins μNS and μ2
Authors: Kobayashi Takeshi , Ooms Laura S. , Chappell James D. , Dermody Terence S. 
Published: January 2009

ABSTRACT
Mammalian reoviruses are nonenveloped particles containing a genome of 10 double-stranded RNA (dsRNA) gene segments. Reovirus replication occurs within viral inclusions, which are specialized nonmembranous cytoplasmic organelles formed by viral nonstructural and structural proteins. Although these structures serve as sites for several major events in the reovirus life cycle, including dsRNA synthesis, gene segment assortment, and genome encapsidation, biochemical mechanisms of virion morphogenesis within inclusions have not been elucidated because much remains unknown about inclusion anatomy and functional organization. To better understand how inclusions support viral replication, we have used RNA interference (RNAi) and reverse genetics to define functional domains in two inclusion-associated proteins, μNS and μ2, which are interacting partners essential for inclusion development and viral replication. Removal of μNS N-terminal sequences required for association with μ2 or another μNS-binding protein, σNS, prevented the capacity of μNS to support viral replication without affecting inclusion formation, indicating that μNS-μ2 and μNS-σNS interactions are necessary for inclusion function but not establishment. In contrast, introduction of changes into the μNS C-terminal region, including sequences that form a putative oligomerization domain, precluded inclusion formation as well as viral replication. Mutational analysis of μ2 revealed a critical dependence of viral replication on an intact nucleotide/RNA triphosphatase domain and an N-terminal cluster of basic amino acid residues conforming to a nuclear localization motif. Another domain in μ2 governs the capacity of viral inclusions to affiliate with microtubules and thereby modulates inclusion morphology, either globular or filamentous. However, viral variants altered in inclusion morphology displayed equivalent replication efficiency. These studies reveal a modular functional organization of inclusion proteins μNS and μ2, define the importance of specific amino acid sequences and motifs in these proteins for viral replication, and demonstrate the utility of complementary RNAi-based and reverse genetic approaches for studies of reovirus replication proteins.
Noncytolytic Clearance of Sindbis Virus Infection from Neurons by Gamma Interferon Is Dependent on Jak/Stat Signaling
Authors: Burdeinick-Kerr Rebeca , Govindarajan Dhanasekaran , Griffin Diane E. 
Published: January 2009

ABSTRACTThe alphavirus Sindbis virus (SINV) causes encephalomyelitis in mice by infecting neurons of the brain and spinal cord. The outcome is age dependent. Young animals develop fatal disease, while older animals recover from infection. Recovery requires noncytolytic clearance of SINV from neurons, and gamma interferon (IFN-γ) is an important contributor to clearance in vivo. IFN-γ-dependent clearance has been studied using immortalized CSM14.1 rat neuronal cells that can be differentiated in vitro. Previous studies have shown that differentiated, but not undifferentiated, cells develop prolonged SINV replication and respond to IFN-γ treatment with noncytolytic clearance of virus preceded by suppression of genomic viral RNA synthesis and reactivation of cellular protein synthesis. To determine the signaling mechanisms responsible for clearance, the responses of SINV-infected differentiated neurons to IFN-γ were examined. IFN-γ treatment of SINV-infected differentiated CSM14.1 cells, AP-7 olfactory neuronal cells, and primary dorsal root ganglia neurons triggered prolonged Stat-1 Tyr701phosphorylation, Stat-1 Ser727phosphorylation, and transient Stat-5 phosphorylation. Inhibition of Jak kinase activity with Jak inhibitor I completely reversed the neuroprotective and antiviral activities of IFN-γ in differentiated cells. We conclude that activation of the Jak/Stat pathway is the primary mechanism for IFN-γ-mediated clearance of SINV infection from mature neurons.
Non-Cleavage Site Gag Mutations in Amprenavir-Resistant Human Immunodeficiency Virus Type 1 (HIV-1) Predispose HIV-1 to Rapid Acquisition of Amprenavir Resistance but Delay Development of Resistance to Other Protease Inhibitors
Authors: Aoki Manabu , Venzon David J. , Koh Yasuhiro , Aoki-Ogata Hiromi , Miyakawa Toshikazu , Yoshimura Kazuhisa , Maeda Kenji , Mitsuya Hiroaki 
Published: January 2009

ABSTRACTIn an attempt to determine whether mutations in Gag in human immunodeficiency virus type 1 (HIV-1) variants selected with a protease inhibitor (PI) affect the development of resistance to the same or a different PI(s), we generated multiple infectious HIV-1 clones carrying mutated Gag and/or mutated protease proteins that were identified in amprenavir (APV)-selected HIV-1 variants and examined their virological characteristics. In an HIV-1 preparation selected with APV (33 passages, yielding HIVAPVp33), we identified six mutations in protease and six apparently critical mutations at cleavage and non-cleavage sites in Gag. An infectious recombinant clone carrying the six protease mutations but no Gag mutations failed to replicate, indicating that the Gag mutations were required for the replication of HIVAPVp33. An infectious recombinant clone that carried wild-type protease and a set of five Gag mutations (rHIVWTpro12/75/219/390/409gag) replicated comparably to wild-type HIV-1; however, when exposed to APV, rHIVWTpro12/75/219/390/409gagrapidly acquired APV resistance. In contrast, the five Gag mutations significantly delayed the acquisition of HIV-1 resistance to ritonavir and nelfinavir (NFV). Recombinant HIV-1 clones containing NFV resistance-associated mutations, such as D30N and N88S, had increased susceptibilities to APV, suggesting that antiretroviral regimens including both APV and NFV may bring about favorable antiviral efficacy. The present data suggest that the preexistence of certain Gag mutations related to PI resistance can accelerate the emergence of resistance to the PI and delay the acquisition of HIV resistance to other PIs, and these findings should have clinical relevance in the therapy of HIV-1 infection with PI-including regimens.
Foot-and-Mouth Disease Virus Can Induce a Specific and Rapid CD4+T-Cell-Independent Neutralizing and Isotype Class-Switched Antibody Response in Naïve Cattle
Authors: Juleff Nicholas , Windsor Miriam , Lefevre Eric A. , Gubbins Simon , Hamblin Pip , Reid Elizabeth , McLaughlin Kerry , Beverley Peter C. L. , Morrison Ivan W. , Charleston Bryan 
Published: January 2009

ABSTRACTThe role of T-lymphocyte subsets in recovery from foot-and-mouth disease virus (FMDV) infection in calves was investigated by administering subset-specific monoclonal antibodies. The depletion of circulating CD4+or WC1+γδ T cells was achieved for a period extending from before challenge to after resolution of viremia and peak clinical signs, whereas CD8+cell depletion was only partial. The depletion of CD4+cells was also confirmed by analysis of lymph node biopsy specimens 5 days postchallenge. Depletion with anti-WC1 and anti-CD8 antibodies had no effect on the kinetics of infection, clinical signs, and immune responses following FMDV infection. Three of the four CD4+T-cell-depleted calves failed to generate an antibody response to the nonstructural polyprotein 3ABC but generated a neutralizing antibody response similar to that in the controls, including rapid isotype switching to immunoglobulin G antibody. We conclude that antibody responses to sites on the surface of the virus capsid are T cell independent, whereas those directed against the nonstructural proteins are T cell dependent. CD4 depletion was found to substantially inhibit antibody responses to the G-H peptide loop VP1135-156on the viral capsid, indicating that responses to this particular site, which has a more mobile structure than other neutralizing sites on the virus capsid, are T cell dependent. The depletion of CD4+T cells had no adverse effect on the magnitude or duration of clinical signs or clearance of virus from the circulation. Overall, we conclude that CD4+T-cell-independent antibody responses play a major role in the resolution of foot-and-mouth disease in cattle.
Certainty closure
Authors: Yorke-Smith Neil , Gervet Carmen 
Published: January 2009

Constraint Programming (CP) has proved an effective paradigm to model and solve difficult combinatorial satisfaction and optimization problems from disparate domains. Many such problems arising from the commercial world are permeated by data uncertainty. Existing CP approaches that accommodate uncertainty are less suited to uncertainty arising due to incomplete and erroneous data, because they do not build reliable models and solutions guaranteed to address the user's genuine problem as she perceives it. Other fields such as reliable computation offer combinations of models and associated methods to handle these types of uncertain data, but lack an expressive framework characterizing the resolution methodology independently of the model.We present a unifying framework that extends the CP formalism in both model and solutions, to tackle ill-defined combinatorial problems with incomplete or erroneous data. Thecertainty closure frameworkbrings together modeling and solving methodologies from different fields into the CP paradigm to provide reliable and efficient approches for uncertain constraint problems. We demonstrate the applicability of the framework on a case study in network diagnosis. We define resolution forms that give generic templates, and their associated operational semantics, to derive practical solution methods for reliable solutions.
From the chair
Authors: Sipior Janice C. , Lending Diane , Amoroso Donald L. , Shayo Conrad , Vowels Susan A. 
Published: January 2009

Happy New Year! I hope 2009 brings us all health, happiness, and prosperity!
"The Eighth Annual ACM-SIGMIS Reception," held at the International Conference on Information Systems (ICIS2008) in Paris, France was a delightful and successful networking event. Thanks to everyone who attended for encouraging guests to join SIGMIS! Next year's reception is planned for Saturday, December 14, 2009, from 5:30 -- 7:00pm, prior to ICIS2009 to be held in Phoenix, Arizona USA, December 15-18, 2009.

Please plan on attending our forthcoming:
Conference:
ACM-SIGMIS CPR (Computer Personnel Research) 2009 Conference and Doctoral Student Consortiumd
Theme:
"New Concepts and Practices in Preparing, Recruiting, and Retaining IS Professionals in the Global Context"
When:
May 28-30, 2009 (Doctoral Consortium: May 28, 2009)
Where:
University of Limerick Campus, Limerick, Ireland
URL:
http://www.sigmis.org/CPR_2009_Home_Page.htm.

For more information regarding ACM-SIGMIS CPR2009, please contact the Conference Co-Chairs: Norah Power, University of Limerick, norah.power@ul.ie Kate Kaiser, Marquette University, kate.kaiser@mu.edu.
For information regarding the Doctoral Consortium, please contact the Doctoral Consortium Co-Chairs: Deb Armstrong, Florida State University, djarmstrong@cob.fsu.edu Cindy Riemenschneider, University of Arkansas, cindy_riemenschneider@baylor.edu.
The refereed conference proceedings will be published by ACM and distributed at the conference. Additionally, an award for best doctoral consortium paper will be presented. We invite you to consider hosting a future SIGMIS CPR (Computer Personnel Research) Conference. Those interested should email Conrad Shayo at cshayo@csusb.edu) or me at janice.sipior@villanova.edu. Our astute Data Base editorial team, including Editor-in-Chief Tom Stafford, University of Memphis; Global Co-Editor Patrick Y.K. Chau, The University of Hong Kong; Managing Editor Colleen Schwarz, Louisiana State University; and Technical Editor Loel Kim, University of Memphis, has been doing an excellent job in maintaining the high quality and furthering the respected reputation of this quarterly ref-ereed publication. I invite you to send your best research to Data Base at: http://the-database.org.
Finally, I encourage you to vote in the 2009 SIGMIS elections this spring. I would like to thank Deb Armstrong, Florida State University, for serving as Chair of the Nominating Committee. The elections will be conducted electronically. Watch for the election announcement and visit the electronic voting site to review biographical information of candidates and cast your vote.
Thanks for your continued support of SIGMIS. Your participation, comments, and suggestions are always welcome.
We look forward to seeing you at SIGMIS CPR'09 in Limerick!