bluuebunny/crossref_metadata_2025_split huggingface dataset:
A High-resolution diatom-inferred palaeoconductivity and lake level record of the Aral Sea for the Last 1600 yr
Authors: Austin Patrick , Mackay Anson , Palagushkina Olga , Leng Melanie 
Published: March 2007

AbstractFormerly the world's fourth largest lake by area, the Aral Sea is presently undergoing extreme desiccation due to large-scale irrigation strategies implemented in the Soviet era. As part of the INTAS-funded CLIMAN project into Holocene climatic variability and the evolution of human settlement in the Aral Sea basin, fossil diatom assemblages contained within a sediment core obtained from the Aral Sea have been applied to a diatom-based inference model of conductivity (r2= 0.767, RMSEP = 0.469 log10μS cm− 1). This has provided a high-resolution record of conductivity and lake level change over the last ca. 1600 yr. Three severe episodes of lake level regression are indicated at ca. AD 400, AD 1195–1355 and ca. AD 1780 to the present day. The first two regressions may be linked to the natural diversion of the Amu Darya away from the Aral Sea and the failure of cyclones formed in the Mediterranean to penetrate more continental regions. Human activity, however, and in particular the destruction of irrigation facilities are synchronous with these early regressions and contributed to the severity of the observed low stands.
The kinetics of exsheathment of infective nematode larvae is disturbed in the presence of a tannin-rich plant extract (sainfoin) both in vitro and in vivo
Authors: BRUNET S. , AUFRERE J. , El BABILI F. , FOURASTE I. , HOSTE H. 
Published: March 2007

SUMMARYThe mode of action of bioactive plants on gastrointestinal nematodes remains obscure. Previous in vitro studies showed that exsheathment was significantly disturbed after contact with tannin-rich extracts. However, the role of important factors (extract concentration, parasite species) has not been assessed and no information is available on the occurrence in vivo. These questions represent the objectives of this study. The model incorporated the parasites Haemonchus contortus and Trichostrongylus colubriformis with sainfoin as the bioactive plant. A set of in vitro assays was performed, measuring the changes observed, after 3 h of contact with increasing concentrations of sainfoin, on the rate of artificial exsheathment. The results indicated that sainfoin extracts interfered with exsheathment in a dose-dependent manner and the process overall was similar for both nematodes. The restoration of control values observed after adding PEG to extracts confirms a major role for tannins. A second study was performed in vivo on rumen-cannulated sheep fed with different proportions of sainfoin in the diet to verify these in vitro results. The consumption of a higher proportion of sainfoin was indeed associated with significant delays in Haemonchus exsheathment. Overall, the results confirmed that interference with the early step of nematode infection might be one of the modes of action that contributes to the anthelmintic properties of tanniniferous plants.
The relationship of meteorological conditions to the epidemic activity of respiratory syncytial virus
Authors: YUSUF S. , PIEDIMONTE G. , AUAIS A. , DEMMLER G. , KRISHNAN S. , VAN CAESEELE P. , SINGLETON R. , BROOR S. , PARVEEN S. , AVENDANO L. , PARRA J. , CHAVEZ-BUENO S. , DE SIERRA T. MURGUÍA , SIMOES E. A. F. , SHAHA S. , WELLIVER R. 
Published: March 2007

SUMMARYOur aim was to obtain knowledge of how meteorological conditions affect community epidemics of respiratory syncytial virus (RSV) infection. To this end we recorded year-round RSV activity in nine cities that differ markedly in geographic location and climate. We correlated local weather conditions with weekly or monthly RSV cases. We reviewed similar reports from other areas varying in climate. Weekly RSV activity was related to temperature in a bimodal fashion, with peaks of activity at temperatures above 24–30°C and at 2–6°C. RSV activity was also greatest at 45–65% relative humidity. RSV activity was inversely related to UVB radiance at three sites where this could be tested. At sites with persistently warm temperatures and high humidity, RSV activity was continuous throughout the year, peaking in summer and early autumn. In temperate climates, RSV activity was maximal during winter, correlating with lower temperatures. In areas where temperatures remained colder throughout the year, RSV activity again became nearly continuous. Community activity of RSV is substantial when both ambient temperatures and absolute humidity are very high, perhaps reflecting greater stability of RSV in aerosols. Transmission of RSV in cooler climates is inversely related to temperature possibly as a result of increased stability of the virus in secretions in the colder environment. UVB radiation may inactivate virus in the environment, or influence susceptibility to RSV by altering host resistance.
Pooling mRNA in microarray experiments and its effect on power
Authors: Zhang Wuyan , Carriquiry Alicia , Nettleton Dan , Dekkers Jack C.M. 
Published: March 2007

AbstractMotivation: Microarrays can simultaneously measure the expression levels of many genes and are widely applied to study complex biological problems at the genetic level. To contain costs, instead of obtaining a microarray on each individual, mRNA from several subjects can be first pooled and then measured with a single array. mRNA pooling is also necessary when there is not enough mRNA from each subject. Several studies have investigated the impact of pooling mRNA on inferences about gene expression, but have typically modeled the process of pooling as if it occurred in some transformed scale. This assumption is unrealistic.Results: We propose modeling the gene expression levels in a pool as a weighted average of mRNA expression of all individuals in the pool on the original measurement scale, where the weights correspond to individual sample contributions to the pool. Based on these improved statistical models, we develop the appropriate F statistics to test for differentially expressed genes. We present formulae to calculate the power of various statistical tests under different strategies for pooling mRNA and compare resulting power estimates to those that would be obtained by following the approach proposed by Kendziorski et al. (2003). We find that the Kendziorski estimate tends to exceed true power and that the estimate we propose, while somewhat conservative, is less biased. We argue that it is possible to design a study that includes mRNA pooling at a significantly reduced cost but with little loss of information.Contact: alicia@iastate.edu
Humoral Immune Response after Primary Rubella Virus Infection and after Vaccination
Authors: Vauloup-Fellous C. , Grangeot-Keros L. 
Published: March 2007

ABSTRACT
We measured rubella virus immunoglobulin G (IgG) and IgM levels, as well as IgG avidity indexes, in serum samples taken before or after 6 months either after infection or after vaccination. The results obtained indicate that humoral immune responses are different after primary infection and after vaccination. This may have important consequences on the serological diagnosis of rubella virus infection.
Histoplasmosis-Associated Cross-Reactivity in the BioRad Platelia
Aspergillus
Enzyme Immunoassay
Authors: Wheat L. Joseph , Hackett Emily , Durkin Michelle , Connolly Patricia , Petraitiene Ruta , Walsh Thomas J. , Knox Kenneth , Hage Chadi 
Published: March 2007

ABSTRACT

We observed false-positive results in the Platelia
Aspergillus
enzyme-linked immunoassay (EIA) for specimens from patients with histoplasmosis and mice with experimental infection. Platelia
Aspergillus
EIA-positive specimens were negative in the second-generation
Histoplasma
antigen EIA. Care must be taken to exclude histoplasmosis for patients with positive Platelia
Aspergillus
EIA results.
Use of Serum or Buffer-Changed EDTA-Plasma in a Rapid, Inexpensive, and Easy-To-Perform Hemolytic Complement Assay for Differential Diagnosis of Systemic Lupus Erythematosus and Monitoring of Patients with the Disease
Authors: Ekdahl Kristina N. , Norberg Dan , Bengtsson Anders A. , Sturfelt Gunnar , Nilsson Ulf R. , Nilsson Bo 
Published: March 2007

ABSTRACTWe previously described a simplified quantitative hemolytic assay for classical pathway (CP) hemolytic function in serum that has been shown to correlate with the 50% hemolytic complement (CH50) assay. In the present study, we used this assay to compare CP functions; plasma levels of C3, C4, and C3dg; and ratios of C3dg to C3 in healthy individuals and patients with systemic lupus erythematosus (SLE) or rheumatoid arthritis (RA) with different degrees of complement activation. A significant depression in CP function and levels of C4 and C3 and increased C3dg levels and C3dg/C3 ratios were observed in the SLE patients. In patients with RA, CP function was normal, whereas C3, C4, and C3dg levels and the C3dg/C3 ratio were elevated. The SLE results are compatible with systemic complement consumption, whereas the RA data suggest an acute-phase reaction with a normal C3 catabolic rate. To facilitate the handling of patient samples, we also developed a method to restore the hemolytic function of EDTA-plasma by transferring it to Veronal-buffered saline containing the thrombin inhibitor lepirudin. This process inhibits coagulation and enables complement activation, allowing a longer time lag between sample harvesting and testing. These results, combined with previous correlation studies, suggest that the CP hemolytic assay can effectively replace the CH50assay for routine SLE differential diagnosis and monitoring of disease activity.
Genotypes and Related Factors Reflecting Macrolide Resistance in Pneumococcal Pneumonia Infections in Japan
Authors: Isozumi Rie , Ito Yutaka , Ishida Tadashi , Osawa Makoto , Hirai Toyohiro , Ito Isao , Maniwa Ko , Hayashi Michio , Kagioka Hitoshi , Hirabayashi Masataka , Onari Koichi , Tomioka Hiromi , Tomii Keisuke , Gohma Iwao , Imai Seiichiro , Takakura Shunji , Iinuma Yoshitsugu , Ichiyama Satoshi , Mishima Michiaki 
Published: March 2007

ABSTRACT

Although macrolide-resistant
Streptococcus pneumoniae
strains possessing either the
ermB
or
mefA
gene are very common in Japan, clinical and microbial factors in community-acquired pneumonia (CAP) caused by different macrolide resistance genotypes have not been evaluated. A multicenter study of CAP caused by
S. pneumoniae
was performed in Japan from 2003 to 2005. A total of 156 isolates were tested for susceptibility to antibiotics correlated with
ermB
and
mefA
genotyping. Independent relationships between tested variables and possession of either the
ermB
or the
mefA
gene were identified. Of 156 isolates, 127 (81.4%) were resistant to erythromycin, with the following distribution of resistance genotypes:
ermB
alone (50.0%),
mefA
alone (23.7%), and both
ermB
and
mefA
(7.1%). All isolates were susceptible to telithromycin. By multivariate analysis, oxygen saturation of <90% on admission increased the risk for
ermB
-positive pneumococcal pneumonia (odds ratio [OR] = 11.1; 95% confidence interval [CI] = 1.30 to 95.0;
P
= 0.03), but there were no associations with
mefA
or with
ermB mefA
positivity. Penicillin nonsusceptibility was associated with
mefA
-positive and with
ermB
- and
mefA
-positive isolates (OR = 14.2; 95% CI = 4.27 to 46.9;
P
< 0.0001 and
P
< 0.0001, respectively) but not with
ermB
-positive isolates. The overall patient mortality was 5.1%. Mortality, the duration of hospitalization, and the resolution of several clinical markers were not associated with the different erythromycin resistance genotypes. In Japan,
S. pneumoniae
with erythromycin resistance or possession of
ermB
,
mefA
, or both genes was highly prevalent in patients with CAP. The risk factors for
ermB
-positive,
mefA
-positive, and double
ermB
-
mefA
-positive pneumococcal pneumonia were different, but the clinical outcomes did not differ.
Clostridium glycolicum
Bacteremia in a Bone Marrow Transplant Patient
Authors: Elsayed Sameer , Zhang Kunyan 
Published: March 2007

ABSTRACT

We describe a case of
Clostridium glycolicum
bacteremia and septic shock in an adult woman with a recent bone marrow transplant for relapsed Hodgkin's disease. The bacterium was identified by 16S rRNA gene sequencing. This is the first published report of the recovery of this organism from human clinical material.
Human Cytomegalovirus Downregulates Expression of Receptors for Platelet-Derived Growth Factor by Smooth Muscle Cells
Authors: Gredmark Sara , Strååt Klas , Homman-Loudiyi Mohammed , Kannisto Katja , Söderberg-Nauclér Cecilia 
Published: March 2007

ABSTRACT
Infection by human cytomegalovirus (HCMV) is associated with the development of vascular diseases and may cause severe brain damage in infected fetuses. Platelet-derived growth factor receptors alpha and beta (PDGFR-α and -β) control important cellular processes associated with atherosclerosis and fetal development. In the present investigation, our goal was to determine whether infection by HCMV can influence the expression of PDGFR-α and -β in human smooth muscle cells (SMCs). In connection with HCMV infection in vitro the levels of PDGFR-α and -β at the cell surface and in the total cellular protein of SMCs were reduced in parallel with decreases in the levels of the corresponding mRNAs. These effects were dependent on immediate-early (IE) or early (E) HCMV gene products, since inhibition of late genes did not prevent HCMV from affecting the expression of PDGFR-α and -β. The downregulation of PDGFR caused by HCMV was dose dependent. Furthermore, confocal microscopy revealed that the localization of PDGFR-β was altered in HCMV-infected cells, in which this protein colocalized with proteins associated with endosomes (Rab4 and -5) and lysosomes (Lamp1 and -2), indicating entrance into pathways for protein degradation. Altogether these observations indicate that an IE and/or E HCMV protein(s) downregulates the expression of PDGFR-α and -β in SMCs. This phenomenon may disrupt cellular processes of importance in connection with cellular differentiation, migration, and/or proliferation. These observations may explain why congenital infection with HCMV can cause fetal brain damage.
Antiviral Effects of Antisense Morpholino Oligomers in Murine Coronavirus Infection Models
Authors: Burrer Renaud , Neuman Benjamin W. , Ting Joey P. C. , Stein David A. , Moulton Hong M. , Iversen Patrick L. , Kuhn Peter , Buchmeier Michael J. 
Published: March 2007

ABSTRACT
The recent emergence of novel pathogenic human and animal coronaviruses has highlighted the need for antiviral therapies that are effective against a spectrum of these viruses. We have used several strains of murine hepatitis virus (MHV) in cell culture and in vivo in mouse models to investigate the antiviral characteristics of peptide-conjugated antisense phosphorodiamidate morpholino oligomers (P-PMOs). Ten P-PMOs directed against various target sites in the viral genome were tested in cell culture, and one of these (5TERM), which was complementary to the 5′ terminus of the genomic RNA, was effective against six strains of MHV. Further studies were carried out with various arginine-rich peptides conjugated to the 5TERM PMO sequence in order to evaluate efficacy and toxicity and thereby select candidates for in vivo testing. In uninfected mice, prolonged P-PMO treatment did not result in weight loss or detectable histopathologic changes. 5TERM P-PMO treatment reduced viral titers in target organs and protected mice against virus-induced tissue damage. Prophylactic 5TERM P-PMO treatment decreased the amount of weight loss associated with infection under most experimental conditions. Treatment also prolonged survival in two lethal challenge models. In some cases of high-dose viral inoculation followed by delayed treatment, 5TERM P-PMO treatment was not protective and increased morbidity in the treated group, suggesting that P-PMO may cause toxic effects in diseased mice that were not apparent in the uninfected animals. However, the strong antiviral effect observed suggests that with further development, P-PMO may provide an effective therapeutic approach against a broad range of coronavirus infections.
Artificial MicroRNA-Mediated Virus Resistance in Plants
Authors: Qu Jing , Ye Jian , Fang Rongxiang 
Published: March 2007

ABSTRACT

RNA silencing in plants is a natural defense system against foreign genetic elements including viruses. This natural antiviral mechanism has been adopted to develop virus-resistant plants through expression of virus-derived double-stranded RNAs or hairpin RNAs, which in turn are processed into small interfering RNAs (siRNAs) by the host's RNA silencing machinery. While these virus-specific siRNAs were shown to be a hallmark of the acquired virus resistance, the functionality of another set of the RNA silencing-related small RNAs, microRNAs (miRNAs), in engineering plant virus resistance has not been extensively explored. Here we show that expression of an artificial miRNA, targeting sequences encoding the silencing suppressor 2b of
Cucumber mosaic virus
(CMV), can efficiently inhibit 2b gene expression and protein suppressor function in transient expression assays and confer on transgenic tobacco plants effective resistance to CMV infection. Moreover, the resistance level conferred by the transgenic miRNA is well correlated to the miRNA expression level. Comparison of the anti-CMV effect of the artificial miRNA to that of a short hairpin RNA-derived small RNA targeting the same site revealed that the miRNA approach is superior to the approach using short hairpin RNA both in transient assays and in transgenic plants. Together, our data demonstrate that expression of virus-specific artificial miRNAs is an effective and predictable new approach to engineering resistance to CMV and, possibly, to other plant viruses as well.
Preferential Selection of Human T-Cell Leukemia Virus Type 1 Provirus Lacking the 5′ Long Terminal Repeat during Oncogenesis
Authors: Miyazaki Maki , Yasunaga Jun-Ichirou , Taniguchi Yuko , Tamiya Sadahiro , Nakahata Tatsutoshi , Matsuoka Masao 
Published: March 2007

ABSTRACTIn adult T-cell leukemia (ATL) cells, a defective human T-cell leukemia virus type 1 (HTLV-1) provirus lacking the 5′ long terminal repeat (LTR), designated type 2 defective provirus, is frequently observed. To investigate the mechanism underlying the generation of the defective provirus, we sequenced HTLV-1 provirus integration sites from cases of ATL. In HTLV-1 proviruses retaining both LTRs, 6-bp repeat sequences were adjacent to the 5′ and 3′ LTRs. In 8 of 12 cases with type 2 defective provirus, 6-bp repeats were identified at both ends. In five of these cases, a short repeat was bound to CA dinucleotides of thepolandenvgenes at the 5′ end, suggesting that these type 2 defective proviruses were formed before integration. In four cases lacking the 6-bp repeat, short (6- to 26-bp) deletions in the host genome were identified, indicating that these defective proviruses were generated after integration. Quantification indicated frequencies of type 2 defective provirus of less than 3.9% for two carriers, which are much lower than those seen for ATL cases (27.8%). In type 2 defective proviruses, the second exons of thetax,rex, andp30genes were frequently deleted, leaving Tax unable to activate NF-κB and CREB pathways. TheHTLV-1 bZIP factorgene, located on the minus strand, is expressed in ATL cells with this defective provirus, and its coding sequences are intact, suggesting its significance in oncogenesis.
Fitness Declines in
Tobacco Etch Virus
upon Serial Bottleneck Transfers
Authors: de la Iglesia Francisca , Elena Santiago F. 
Published: March 2007

ABSTRACT

It has been well established that populations of RNA viruses transmitted throughout serial bottlenecks suffer from significant fitness declines as a consequence of the accumulation of deleterious mutations by the onset of Muller's ratchet. Bottlenecks are unavoidably linked to different steps of the infectious cycle of most plant RNA viruses, such as vector-mediated transmissions and systemic colonization of new leaves. Here we report evidence for fitness declines by the accumulation of deleterious mutations in the potyvirus
Tobacco etch virus
(TEV). TEV was inoculated into the nonsystemic host
Chenopodium quinoa
, and local lesions were isolated and used to initiate 20 independent mutation accumulation lineages. Weekly, a random lesion from each lineage was isolated and used to inoculate the next set of plants. At each transfer, the Malthusian growth rate was estimated. After 11 consecutive transfers, all lineages suffered significant fitness losses, and one even became extinct. The average rate of fitness decline was 5% per day. The average pattern of fitness decline was consistent with antagonistic epistasis between deleterious mutations, as postulated for antiredundant genomes. Temporal fitness fluctuations were not explained by random noise but reflected more complex underlying processes related to emergence and self-organization phenomena.
Multifunctional Human Immunodeficiency Virus (HIV) Gag-Specific CD8+T-Cell Responses in Rectal Mucosa and Peripheral Blood Mononuclear Cells during Chronic HIV Type 1 Infection
Authors: Critchfield J. William , Lemongello Donna , Walker Digna H. , Garcia Juan C. , Asmuth David M. , Pollard Richard B. , Shacklett Barbara L. 
Published: March 2007

ABSTRACTThe intestinal tract is a lymphocyte-rich site that undergoes severe depletion of memory CD4+T cells within days of simian immunodeficiency virus or human immunodeficiency virus type 1 (HIV-1) infection. An ensuing influx of virus-specific CD8+T cells, which persist throughout the chronic phase of infection, has also been documented in the gastrointestinal tract. However, little is known of the functionality of these effector cells or their relationship to the disease course. In this study, we measured CD8+T-cell responses to HIV-1 peptides in paired rectal and blood samples from chronically infected patients. In both blood and rectum, there was an immunodominant CD8+T-cell response to HIV Gag compared to Pol and Env (P< 0.01). In contrast, cytomegalovirus pp65 peptides elicited gamma interferon (IFN-γ) secretion strongly in peripheral blood mononuclear cells (PBMC) but weakly in rectal CD8+T cells (P= 0.015). Upon stimulation with HIV peptides, CD8+T cells from both sites were capable of mounting complex responses including degranulation (CD107 expression) and IFN-γ and tumor necrosis factor alpha (TNF-α) production. In rectal tissue, CD107 release was frequently coupled with production of IFN-γ or TNF-α. In patients not on antiretroviral therapy, the magnitude of Gag-specific responses, as a percentage of CD8+T cells, was greater in the rectal mucosa than in PBMC (P= 0.054); however, the breakdown of responding cells into specific functional categories was similar in both sites. These findings demonstrate that rectal CD8+T cells are capable of robust and varied HIV-1-specific responses and therefore likely play an active role in eliminating infected cells during chronic infection.