bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is oil palm agriculture really destroying tropical biodiversity?
Authors: Koh Lian Pin , Wilcove David S. 
Published: May 2008

AbstractOil palm is one of the world's most rapidly expanding equatorial crops. The two largest oil palm‐producing countries—Indonesia and Malaysia—are located in Southeast Asia, a region with numerous endemic, forest‐dwelling species. Oil palm producers have asserted that forests are not being cleared to grow oil palm. Our analysis of land‐cover data compiled by the United Nations Food and Agriculture Organization suggests that during the period 1990–2005, 55%–59% of oil palm expansion in Malaysia, and at least 56% of that in Indonesia occurred at the expense of forests. Using data on bird and butterfly diversity in Malaysia's forests and croplands, we argue that conversion of either primary or secondary (logged) forests to oil palm may result in significant biodiversity losses, whereas conversion of pre‐existing cropland (rubber) to oil palm results in fewer losses. To safeguard the biodiversity in oil palm‐producing countries, more fine‐scale and spatially explicit data on land‐use change need to be collected and analyzed to determine the extent and nature of any further conversion of forests to oil palm; secondary forests should be protected against conversion to oil palm; and any future expansion of oil palm agriculture should be restricted to pre‐existing cropland or degraded habitats.
Rapid and Simple Diagnosis of
Chlamydophila pneumoniae
Pneumonia by an Immunochromatographic Test for Detection of Immunoglobulin M Antibodies
Authors: Miyashita Naoyuki , Ouchi Kazunobu , Kishi Fumio , Tabuchi Mitsuaki , Tsumura Naoki , Bannai Hisaichi , Iwata Satoshi , Tanaka Toshihiro , Oka Mikio 
Published: May 2008

ABSTRACT

To evaluate a newly developed immunochromatographic test (the MySet test) for the detection of
Chlamydophila pneumoniae
-specific immunoglobulin M antibodies, the results obtained by the MySet test were compared with those obtained by two serological tests. The sensitivity and specificity of the MySet test were 100% and 92.9%, respectively. The MySet test is rapid and simple to use and is thought to be a useful tool for the selection of appropriate antibiotic therapy.
Modified Caspase-3 Assay Indicates Correlation of Caspase-3 Activity with Immunity of Nonhuman Primates to
Yersinia pestis
Infection
Authors: Welkos Susan , Norris Sarah , Adamovicz Jeffrey 
Published: May 2008

ABSTRACT

Defined candidate human vaccines for treating infection by
Yersinia pestis
, the agent of plague, have been developed. To facilitate evaluation of the vaccines' efficacy, the in vitro caspase-3 assay for cytotoxicity-neutralizing activity was modified and reevaluated. Immune serum-mediated caspase-3 neutralizing activity correlated with protection against infection in a nonhuman primate vaccine model of plague immunity.
Genetic and Antigenic Diversities of Major Immunoreactive Proteins in Globally DistributedEhrlichia canisStrains
Authors: Zhang Xiaofeng , Luo Tian , Keysary Avi , Baneth Gad , Miyashiro Simone , Strenger Carmela , Waner Trevor , McBride Jere W. 
Published: May 2008

ABSTRACTThe extent of knowledge regarding the diversity of globally distributedEhrlichia canisstrains has been limited to information gained from a few evolutionarily conserved genes. In this study,E. canisstrains from the United States (strain Jake [US]), Brazil (strain São Paulo [BR]), and Israel (strain 611 [IS] and Ranana [IS-R]) were used to examine the antigenic and genetic diversities of four well-characterized major immunoreactive protein genes/proteins. gp36 and gp200 were the most divergent genes, and nucleotide substitutions in the gp36 tandem repeat region of the IS strain, but not the IS-R strain, resulted in two amino acid differences (S→P and P→T) in each nine-amino-acid repeat (epitope-containing region). DNA sequences of gp19 and gp140 were completely conserved in the US and BR strains, but differences were found in the Israeli strains, including two fewer tandem repeats in gp140 and a single amino acid substitution in gp19 from the IS strain.E. caniswhole-cell lysates from each isolate were examined by Western immunoblotting using sera from naturally infected dogs from each country, and four major immunoreactive proteins (gp19, gp36, gp140, and gp200) were identified in each strain using protein-specific antisera. The US and BR strains exhibited highly conserved immunoreactive protein profiles, while some differences were identified in the IS strain. Sera from naturally infected Israeli dogs confirmed gene sequencing information, which demonstrated two distinctE. canisstrains, defined by the gp36 gene. Conversely, gp19 was strongly reactive and present in allE. canisisolates. gp140 and gp200 were also present in all strains, although gp140 in the IS strain had two fewer tandem repeats and exhibited a smaller mass.
LDBio-Toxo II Immunoglobulin G Western Blot Confirmatory Test for Anti-
Toxoplasma
Antibody Detection
Authors: Franck Jacqueline , Garin Yves Jean-François , Dumon Henri 
Published: May 2008

ABSTRACT

Tests commonly used for routine determination of anti-
Toxoplasma gondii
immunoglobulin G (IgG) antibodies show a high level of consistency. However, considerable variations between commercial screening tests are still observed in detecting antibodies present at low concentrations, leading to a number of discrepant and/or equivocal results. It is therefore important to use a reference test to confirm borderline results. In this study, we evaluated the use of a new qualitative test based on Western blot analysis—the LDBio-Toxo II IgG test—as a confirmatory test for at-risk patients. The study was performed retrospectively, using 569 serum samples with “low-positive” (2 to 32 international units) anti-
Toxoplasma
IgG levels from 375 patients. These samples were either sera collected during the routine screening of pregnant women, from patients with unrelated infections, or from immunocompromised patients or sequential sera taken from pregnant women with acquired
Toxoplasma
infection or from their newborns during follow-up. The LDBio-Toxo II IgG test was compared to several commercial tests commonly used for anti-
Toxoplasma
IgG screening. The Sabin-Feldman dye test was used as a reference test. In this study, the results of the LDBio-Toxo II IgG test appeared to be consistent with those of the dye test; the LDBio-Toxo II IgG test had a specificity of 100% and a sensitivity of 99.2%. Our findings suggest that the LDBio-Toxo II IgG test is a useful serological tool in cases in which the presence or absence of
Toxoplasma
antibodies needs to be reliably determined, for example, for the follow-up of pregnant women and their newborns or for subjects with immune deficiencies following human immunodeficiency virus infection, hematological malignancies, or transplantation.
Time to Blood Culture Positivity as a Marker for Catheter-Related Candidemia
Authors: Ben-Ami Ronen , Weinberger Miriam , Orni-Wasserlauff Ruth , Schwartz David , Itzhaki Avraham , Lazarovitch Tzipora , Bash Edna , Aharoni Yuval , Moroz Irina , Giladi Michael 
Published: May 2008

ABSTRACT

Candida
spp. are important causes of nosocomial bloodstream infections. Around 80% of patients with candidemia have an indwelling central venous catheter (CVC). Determining whether the CVC is the source of candidemia has implications for patient management. We assessed whether the time to detection of
Candida
species in peripheral blood (time to positivity [TTP]) can serve as a marker for catheter-related candidemia. Prospective surveillance of
Candida
bloodstream infection was conducted in two medical centers. TTP was recorded by the BacT/Alert automated system. Sixty-four candidemia episodes were included. Fifty patients (78%) had an indwelling CVC. Thirteen patients (20.3%) had definite catheter-related candidemia. TTP was shorter for definite catheter-related candidemia (17.3 ± 2 h) than that for candidemia from other sources (38.2 ± 3 h;
P
< 0.001). A TTP cutoff of 30 h was 100% sensitive and 51.4% specific for catheter-related candidemia (area under the receiver-operator characteristic curve of 0.76). We conclude that TTP in peripheral blood is a sensitive but nonspecific marker for catheter-related candidemia and that a TTP of more than 30 h can help exclude an intravascular catheter as the possible source of candidemia.
Microbiological Characteristics, Presumptive Identification, and Antibiotic Susceptibilities of
Staphylococcus lugdunensis
Authors: Tan Thean Yen , Ng Siew Yong , He Jie 
Published: May 2008

ABSTRACT

This study validated abbreviated methods for the presumptive identification of
Staphylococcus lugdunensis
and studied the antibiotic susceptibilities of 106 isolates. The combination of positive responses to ornithine and pyrrolidonyl arylamidase identified all
S. lugdunensis
isolates. Resistance to penicillin and methicillin was detected in 27 and 5% of isolates, respectively.
Difficulties in Diagnosing Group O Human Immunodeficiency Virus Type 1 Acute Primary Infection
Authors: Henquell Cécile , Jacomet Christine , Antoniotti Odile , Chaib Abdelhak , Regagnon Christel , Brunet Sylvie , Peigue-Lafeuille Hélène , Barin Francis 
Published: May 2008

ABSTRACT
We report a rare case of acute human immunodeficiency virus (HIV) type 1 group O infection in a French Caucasian woman. Her sexual partner was secondarily diagnosed with HIV infection, and transmission was confirmed by phylogenetic analysis. The unequal performance of many of the serologic and molecular assays commercially available leads to delays in diagnosis and affects patient management.
Real-Time PCR Method for Detection of Zygomycetes
Authors: Hata D. Jane , Buckwalter Seanne P. , Pritt Bobbi S. , Roberts Glenn D. , Wengenack Nancy L. 
Published: May 2008

ABSTRACT

Zygomycete infections can be devastating in immunocompromised hosts. Difficulties in the histopathologic differentiation of this class from other filamentous fungi (e.g.,
Aspergillus
spp.,
Fusarium
spp.) may lead to delays in diagnosis and initiation of appropriate treatment, thereby significantly affecting patient outcome. A real-time PCR assay was developed to detect species of the zygomycete genera
Absidia
,
Apophysomyces
,
Cunninghamella
,
Mucor
,
Rhizopus
, and
Saksenaea
in culture and tissue samples. Primers and fluorescence resonance energy transfer hybridization probes were designed to detect a 167-bp conserved region of the multicopy zygomycete cytochrome
b
gene. A plasmid containing target sequence from
Mucor racemosus
was constructed as a positive control. The analytical sensitivity of the assay is 10 targets/μl, and a specificity panel consisting of other filamentous fungi, yeasts (
Candida
spp.), and bacteria demonstrated no cross-reactivity in the assay. The clinical sensitivity and specificity of the assay from culture isolates were 100% (39/39) and 92% (59/64), respectively. Sensitivity and specificity determined using a limited number of fresh tissue specimens were both 100% (2/2). The sensitivity seen with formalin-fixed, paraffin-embedded tissues was 56% (35/62), and the specificity was 100% (19/19). The speed, sensitivity, and specificity of the PCR assay indicate that it is useful for the rapid and accurate detection of zygomycetes.
Cross-Reactive Human Immunodeficiency Virus Type 1-Neutralizing Human Monoclonal Antibody That Recognizes a Novel Conformational Epitope on gp41 and Lacks Reactivity against Self-Antigens
Authors: Zhang Mei-Yun , Vu Bang K. , Choudhary Anil , Lu Hong , Humbert Michael , Ong Helena , Alam Munir , Ruprecht Ruth M. , Quinnan Gerald , Jiang Shibo , Montefiori David C. , Mascola John R. , Broder Christopher C. , Haynes Barton F. , Dimitrov Dimiter S. 
Published: May 2008

ABSTRACT
Broadly cross-reactive human immunodeficiency virus (HIV)-neutralizing antibodies are infrequently elicited in infected humans. The two best-characterized gp41-specific cross-reactive neutralizing human monoclonal antibodies, 4E10 and 2F5, target linear epitopes in the membrane-proximal external region (MPER) and bind to cardiolipin and several other autoantigens. It has been hypothesized that, because of such reactivity to self-antigens, elicitation of 2F5 and 4E10 and similar antibodies by vaccine immunogens based on the MPER could be affected by tolerance mechanisms. Here, we report the identification and characterization of a novel anti-gp41 monoclonal antibody, designated m44, which neutralized most of the 22 HIV type 1 (HIV-1) primary isolates from different clades tested in assays based on infection of peripheral blood mononuclear cells by replication-competent virus but did not bind to cardiolipin and phosphatidylserine in an enzyme-linked immunosorbent assay and a Biacore assay nor to any protein or DNA autoantigens tested in Luminex assays. m44 bound to membrane-associated HIV-1 envelope glycoproteins (Envs), to recombinant Envs lacking the transmembrane domain and cytoplasmic tail (gp140s), and to gp41 structures containing five-helix bundles and six-helix bundles, but not to N-heptad repeat trimers, suggesting that the C-heptad repeat is involved in m44 binding. In contrast to 2F5, 4E10, and Z13, m44 did not bind to any significant degree to denatured gp140 and linear peptides derived from gp41, suggesting a conformational nature of the epitope. This is the first report of a gp41-specific cross-reactive HIV-1-neutralizing human antibody that does not have detectable reactivity to autoantigens. Its novel conserved conformational epitope on gp41 could be helpful in the design of vaccine immunogens and as a target for therapeutics.
Mutational Analysis of Plant Cap-Binding Protein eIF4E Reveals Key Amino Acids Involved in Biochemical Functions and Potyvirus Infection
Authors: German-Retana Sylvie , Walter Jocelyne , Doublet Bénédicte , Roudet-Tavert Geneviève , Nicaise Valérie , Lecampion Cécile , Houvenaghel Marie-Christine , Robaglia Christophe , Michon Thierry , Le Gall Olivier 
Published: May 2008

ABSTRACTThe eukaryotic translation initiation factor 4E (eIF4E) (the cap-binding protein) is involved in natural resistance against several potyviruses in plants. In lettuce, the recessive resistance genesmo11andmo12againstLettuce mosaic virus(LMV) are alleles coding for forms of eIF4E unable, or less effective, to support virus accumulation. A recombinant LMV expressing the eIF4E of a susceptible lettuce variety from its genome was able to produce symptoms inmo11ormo12varieties. In order to identify the eIF4E amino acid residues necessary for viral infection, we constructed recombinant LMV expressing eIF4E with point mutations affecting various amino acids and compared the abilities of these eIF4E mutants to complement LMV infection in resistant plants. Three types of mutations were produced in order to affect different biochemical functions of eIF4E: cap binding, eIF4G binding, and putative interaction with other virus or host proteins. Several mutations severely reduced the ability of eIF4E to complement LMV accumulation in a resistant host and impeded essential eIF4E functions in yeast. However, the ability of eIF4E to bind a cap analogue or to fully interact with eIF4G appeared unlinked to LMV infection. In addition to providing a functional mutational map of a plant eIF4E, this suggests that the role of eIF4E in the LMV cycle might be distinct from its physiological function in cellular mRNA translation.
Humanized Monoclonal Antibodies Derived from Chimpanzee Fabs Protect against Japanese Encephalitis Virus In Vitro and In Vivo
Authors: Goncalvez Ana P. , Chien Cheng-Hsin , Tubthong Kamolchanok , Gorshkova Inna , Roll Carrie , Donau Olivia , Schuck Peter , Yoksan Sutee , Wang Sy-Dar , Purcell Robert H. , Lai Ching-Juh 
Published: May 2008

ABSTRACTJapanese encephalitis virus (JEV)-specific Fab antibodies were recovered by repertoire cloning from chimpanzees initially immunized with inactivated JE-VAX and then boosted with attenuated JEV SA14-14-2. From a panel of 11 Fabs recovered by different panning strategies, three highly potent neutralizing antibodies, termed Fabs A3, B2, and E3, which recognized spatially separated regions on the virion, were identified. These antibodies reacted with epitopes in different domains: the major determinant for Fab A3 was Lys179(domain I), that for Fab B2 was Ile126(domain II), and that for Fab E3 was Gly302(domain III) in the envelope protein, suggesting that these antibodies neutralize the virus by different mechanisms. Potent neutralizing antibodies reacted with a low number of binding sites available on the virion. These three Fabs and derived humanized monoclonal antibodies (MAbs) exhibited high neutralizing activities against a broad spectrum of JEV genotype strains. Demonstration of antibody-mediated protection of JEV infection in vivo is provided using the mouse encephalitis model. MAb B2 was most potent, with a 50% protective dose (ED50) of 0.84 μg, followed by MAb A3 (ED50of 5.8 μg) and then MAb E3 (ED50of 24.7 μg) for a 4-week-old mouse. Administration of 200 μg/mouse of MAb B2 1 day after otherwise lethal JEV infection protected 50% of mice and significantly prolonged the average survival time compared to that of mice in the unprotected group, suggesting a therapeutic potential for use of MAb B2 in humans.
Intersubunit Disulfide Isomerization Controls Membrane Fusion of Human T-Cell Leukemia Virus Env
Authors: Li Kejun , Zhang Shujing , Kronqvist Malin , Wallin Michael , Ekström Maria , Derse David , Garoff Henrik 
Published: May 2008

ABSTRACT

Human T-cell leukemia virus (HTLV-1) Env carries a typical disulfide isomerization motif, C
225
XXC, in the C-terminal domain SU. Here we have tested whether this motif is used for isomerization of the intersubunit disulfide of Env and whether this rearrangement is required for membrane fusion. We introduced the C225A and C228A mutations into Env and found that the former but not the latter mutant matured into covalently linked SU-TM complexes in transfected cells. Next, we constructed a secreted Env ectodomain and showed that it underwent incubation-dependent intersubunit disulfide isomerization on target cells. However, the rearrangement was blocked by the C225A mutation, suggesting that C
225
carried the isomerization-active thiol. Still, it was possible to reduce the intersubunit disulfide of the native C225A ectodomain mutant with dithiothreitol (DTT). The importance of the CXXC-mediated disulfide isomerization for infection was studied using murine leukemia virus vectors pseudotyped with wild-type or C225A HTLV-1 Env. We found that the mutant Env blocked infection, but this could be rescued with DTT. The fusion activity was tested in a fusion-from-within assay using a coculture of rat XC target and transfected BHK-21 effector cells. We found that the mutation blocked polykaryon formation, but this could be reversed with DTT. Similar DTT-reversible inhibition of infection and fusion was observed when a membrane-impermeable alkylator was present during the infection/fusion incubation. We conclude that the fusion activity of HTLV-1 Env is controlled by an SU CXXC-mediated isomerization of the intersubunit disulfide. Thus, this extends the applicability of the isomerization model from gammaretroviruses to deltaretroviruses.
Qualitative and Quantitative Characteristics of Rotavirus-Specific CD8 T Cells Vary Depending on the Route of Infection
Authors: Jiang Janina Q. , He Xiao-Song , Feng Ningguo , Greenberg Harry B. 
Published: May 2008

ABSTRACT

CD8 T-cell response provides an important defense against rotavirus, which infects a variety of systemic locations in addition to the gut. Here we investigated the distribution, phenotype, and function of rotavirus-specific CD8 T cells in multiple organs after rotavirus infection initiated via the intranasal, oral, or intramuscular route. The highest level of virus-specific CD8 T cells was observed in the Peyer's patches of orally infected mice and in the lungs of intranasally infected animals. Very low levels of virus-specific CD8 T cells were detected in peripheral blood or spleen irrespective of the route of infection. Rotavirus-specific CD8 T cells from Peyer's patches of orally infected mice expressed high levels of CCR9, while CXCR6 and LFA-1 expression was associated with virus-specific CD8 T cells in lungs of intranasally infected mice. Oral infection induced the highest proportion of gamma interferon
−
CD107a/b
+
CD8 T cells in Peyer's patches. When equal numbers of rotavirus-specific CD8 T cells were transferred into Rag-1 knockout mice chronically infected with rotavirus, the donor cells derived from Peyer's patches of orally infected mice were more efficient than those derived from lungs of intranasally infected animals in clearing intestinal infection. These results suggest that different routes of infection induce virus-specific CD8 T cells with distinct homing phenotypes and effector functions as well as variable abilities to clear infection.
Biodistribution and Safety Profile of Recombinant Adeno-Associated Virus Serotype 6 Vectors following Intravenous Delivery
Authors: Stone Daniel , Liu Ying , Li Zong-Yi , Strauss Robert , Finn Eric E. , Allen James M. , Chamberlain Jeffrey S. , Lieber André 
Published: May 2008

ABSTRACT
Recombinant adeno-associated virus vectors based on serotype 6 (rAAV6) efficiently transduce skeletal muscle after intravenous administration and have shown efficacy in the mdx model of muscular dystrophy. As a prelude to future clinical studies, we investigated the biodistribution and safety profile of rAAV6 in mice. Although it was present in all organs tested, rAAV6 was sequestered mainly in the liver and spleen. rAAV6 had a minimal effect on circulating blood cells and caused no apparent hepatotoxicity or coagulation activation. rAAV6 caused some neutrophil infiltration into the liver, with a transient elevation in cytokine and chemokine transcription/secretion. In summary, rAAV6 induces transient toxicity that subsides almost completely within 72 h and causes no significant side effects.
R5X4 Viruses Are Evolutionary, Functional, and Antigenic Intermediates in the Pathway of a Simian-Human Immunodeficiency Virus Coreceptor Switch
Authors: Tasca Silvana , Ho Siu-Hong , Cheng-Mayer Cecilia 
Published: May 2008

ABSTRACT

To examine the pathway of the coreceptor switching of CCR5-using (R5) virus to CXCR4-using (X4) virus in simian-human immunodeficiency virus SHIV
SF162P3N
-infected rhesus macaque BR24, analysis was performed on variants present at 20 weeks postinfection, the time when the signature gp120 V3 loop sequence of the X4 switch variant was first detected by PCR. Unexpectedly, circulating and tissue variants with His/Ile instead of the signature X4 V3 His/Arg insertions predominated at this time point. Phylogenetic analysis of the sequences of the C2 conserved region to the V5 variable loop of the envelope (Env) protein showed that viruses bearing HI insertions represented evolutionary intermediates between the parental SHIV
SF162P3N
and the final X4 HR switch variant. Functional analyses demonstrated that the HI variants were phenotypic intermediates as well, capable of using both CCR5 and CXCR4 for entry. However, the R5X4 intermediate virus entered CCR5-expressing target cells less efficiently than the parental R5 strain and was more sensitive to both CCR5 and CXCR4 inhibitors than either the parental R5 or the final X4 virus. It was also more sensitive than the parental R5 virus to antibody neutralization, especially to agents directed against the CD4 binding site, but not as sensitive as the late X4 virus. Significantly, the V3 loop sequence that determined CXCR4 use also conferred soluble CD4 neutralization sensitivity. Collectively, the data illustrate that, similar to human immunodeficiency virus type 1 (HIV-1) infection in individuals, the evolution from CCR5 to CXCR4 usage in BR24 transitions through an intermediate phase with reduced virus entry and coreceptor usage efficiencies. The data further support a model linking an open envelope gp120 conformation, better CD4 binding, and expansion to CXCR4 usage.