bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic and Genotypic Characterization of
Streptococcus pneumoniae
Strains Colonizing Children Attending Day-Care Centers in Norway
Authors: Vestrheim Didrik F. , Høiby E. Arne , Aaberge Ingeborg S. , Caugant Dominique A. 
Published: June 2008

ABSTRACT

A cross-sectional study of nasopharyngeal colonization with
Streptococcus pneumoniae
was performed among 573 children attending 29 day-care centers (DCCs) in Norway prior to the start of mass vaccination with the heptavalent pneumococcal conjugate vaccine (PCV-7). A sensitive sampling method was employed, including transport in an enrichment broth and serotyping of pneumococci directly from the broth, in addition to traditional single-colony isolation from blood agar plates. The prevalence of carriage was high, peaking at 88.7% in 2-year-olds. More than one serotype was isolated from 12.7% of the carriers. Of 509 isolates obtained, 227 (44.6%) belonged to the PCV-7 serotypes. Penicillin nonsusceptibility was rare (1.8% of the isolates). Nonsusceptibility to erythromycin (5.9%), clindamycin (2.0%), and tetracycline (5.5%) was associated with PCV-7 serotypes (
P
< 0.001). Multilocus sequence typing was performed on the whole strain collection, revealing 102 sequence types (STs), of which 31 (30.4%) were novel. Eleven isolates (2.2%) belonged to the England
14
-9 clone, and 19 isolates (3.7%) belonged to, or were single-locus variants of, the Portugal
19F
-21 clone. The pneumococcal populations within the DCCs were composed of a majority of isolates with STs shared between the DCCs and a minority of isolates with STs unique for each DCC. The highest numbers of different STs, including novel STs, were found within the most frequent serotypes. Our study indicates that carriage of
S. pneumoniae
is highly prevalent among children in Norwegian DCCs, with a genetically diverse pneumococcal population consisting of unique microepidemic DCC populations.
Real-Time PCR Assays To Address Genetic Diversity among Strains ofMycoplasma hyopneumoniae
Authors: Strait Erin L. , Madsen Melissa L. , Minion F. Chris , Christopher-Hennings Jane , Dammen Matthew , Jones Katherine R. , Thacker Eileen L. 
Published: June 2008

ABSTRACTMycoplasma hyopneumoniaeis an important cause of pneumonia in pigs around the world, but confirming its presence in (or absence from) pigs can be difficult. Culture for diagnosis is impractical, and seroconversion is often delayed after natural infection, limiting the use of serology. Numerous PCR assays for the detection ofM.hyopneumoniaehave been developed, targeting several different genes. Recently, genetic diversity among strains ofM.hyopneumoniaewas demonstrated. The effect of this diversity on the accuracy and sensitivity of theM.hyopneumoniaePCR assays could result in false-negative results in current PCR tests. In this study, a panel of isolates ofM.hyopneumoniae,M. flocculare,M. hyorhinis, andM. hyosynoviaewere tested with a number ofM.hyopneumoniae-specific PCR assays. SomeM.hyopneumoniaePCR assays tested did not detect all isolates ofM.hyopneumoniae. To increase the efficiency of PCR testing, two new real-time PCR assays that are specific and capable of detecting all of theM.hyopneumoniaeisolates used in this study were developed.
In Vivo Potential Effects of Adenovirus Type 5
E1A
and
E1B
on Lung Carcinogenesis and Lymphoproliferative Inflammation
Authors: Yang Yongping , McKerlie Colin , Lu Zhan , Wang Lena , Buchwald Manuel 
Published: June 2008

ABSTRACT

Triggering uncontrolled cellular proliferation, chronic inflammation, and/or disruption of p53 activity is critical for tumorigenesis initiated by latent viral oncogenes. The adenovirus type 5 (Ad5) early genes
E1A
and
E1B
can maintain lifelong latency in the lungs of patients with chronic pulmonary diseases. To determine the in vivo effects of the latent Ad5
E1A
and
E1B
oncogenes, we have examined the influence of Ad5
E1A
and
E1B
gene products on mouse lung carcinogenesis and inflammation by generation and characterization of lung-specific transgenic mouse models. Here, we show that either the Ad5 E1A 243-amino-acid (aa) protein or the E1B 58-kDa protein was dominantly expressed in the transgenic lung. Preferential expression of Ad5 E1A 243-aa protein alone was not sufficient to induce lung carcinogenesis but resulted in low-grade cellular proliferation and high-grade lymphoproliferative inflammation in the lung. The presence of Ad5
E1B
dramatically enhanced the expression of the E1A 243-aa protein, in addition to impairing p53 and apoptosis response, resulting in uncontrolled cellular proliferation, lymphoproliferative inflammation, and metastatic carcinomas in the lung after a period of latency. Our studies may provide clues to understanding the potential in vivo biological effects of Ad5
E1A
and
E1B
latent in the lung and a new scope for assessing in vivo functions of viral genes latent in the infection target tissue.
Properties of Subviral Particles of Hepatitis B Virus
Authors: Chai Ning , Chang Ho Eun , Nicolas Emmanuelle , Han Ziying , Jarnik Michal , Taylor John 
Published: June 2008

ABSTRACT
In the sera of patients infected with hepatitis B virus (HBV), in addition to infectious particles, there is an excess (typically 1,000- to 100,000-fold) of empty subviral particles (SVP) composed solely of HBV envelope proteins in the form of relatively smaller spheres and filaments of variable length. Hepatitis delta virus (HDV) assembly also uses the envelope proteins of HBV to produce an infectious particle. Rate-zonal sedimentation was used to study the particles released from liver cell lines that produced SVP only, HDV plus SVP, and HBV plus SVP. The SVP made in the absence of HBV or HDV were further examined by electron microscopy. They bound efficiently to heparin columns, consistent with an ability to bind cell surface glycosaminoglycans. However, unlike soluble forms of HBV envelope protein that were potent inhibitors, the SVP did not inhibit the ability of HBV and HDV to infect primary human hepatocytes.
Tegument Proteins of Human Cytomegalovirus
Authors: Kalejta Robert F. 
Published: June 2008

SUMMARY
Human cytomegalovirus (HCMV) is a common, medically relevant human herpesvirus. The tegument layer of herpesvirus virions lies between the genome-containing capsids and the viral envelope. Proteins within the tegument layer of herpesviruses are released into the cell upon entry when the viral envelope fuses with the cell membrane. These proteins are fully formed and active and control viral entry, gene expression, and immune evasion. Most tegument proteins accumulate to high levels during later stages of infection, when they direct the assembly and egress of progeny virions. Thus, viral tegument proteins play critical roles at the very earliest and very last steps of the HCMV lytic replication cycle. This review summarizes HCMV tegument composition and structure as well as the known and speculated functions of viral tegument proteins. Important directions for future investigation and the challenges that lie ahead are identified and discussed.
Colonization and decomposition of salal (Gaultheria shallon) leaf litter by saprobic fungi in successional forests on coastal British Columbia
Authors: Osono Takashi , Iwamoto Susumu , Trofymow John A. 
Published: June 2008

The colonization of leaf litter by saprobic fungi was studied in old-growth and post-harvest successional Douglas-fir forests on southeast Vancouver Island, British Columbia. This study focused on leaf litter of salal ( Gaultheria shallon Pursh.), a dominant understory shrub in all stands. Salal litter is characterized by the occurrence of bleached portions attributable to fungal colonization of the litter and to the variable decomposition of recalcitrant compounds, such as lignin. Analyses of proximate chemical fractions, fungal assemblages on the bleached leaf area, and pure culture decomposition assays indicated that Marasmius sp. and Coccomyces sp. were responsible for rapid decomposition and bleaching of salal leaf litter. The bleached area accounted for 17%–22% of total area of salal leaf litter collected in immature (40–60 years old), mature (85–105 years old), and old-growth (more than 290 years old) stands, but for only 2% in regeneration (5–15 years old) stands. The reduction of bleached leaf area occupied by Marasmius sp. and Coccomyces sp. in regeneration stands could be due to the changes in microenvironmental conditions on the forest floor, in litter quality, or in food-web structure in soils. The decrease of fungi able to decay recalcitrant compounds may lead to a reduction of salal decomposition rates in clear-cut sites that would persist until canopy closure occurs.
The succinate:menaquinone reductase of Bacillus cereus — characterization of the membrane-bound and purified enzyme
Authors: García L.M. , Contreras-Zentella M.L. , Jaramillo R. , Benito-Mercadé M.C. , Mendoza-Hernández G. , del Arenal I.P. , Membrillo-Hernández J. , Escamilla J.E. 
Published: June 2008

Utilization of external succinate by Bacillus cereus and the properties of the purified succinate:menaquinone-7 reductase (SQR) were studied. Bacillus cereus cells showed a poor ability for the uptake of and respiratory utilization of exogenous succinate, thus suggesting that B. cereus lacks a specific succinate uptake system. Indeed, the genes coding for a succinate–fumarate transport system were missing from the genome database of B. cereus. Kinetic studies of membranes indicated that the reduction of menaquinone-7 is the rate-limiting step in succinate respiration. In accordance with its molecular characteristics, the purified SQR of B. cereus belongs to the type-B group of SQR enzymes, consisting of a 65-kDa flavoprotein (SdhA), a 29-kDa iron–sulphur protein (SdhB), and a 19-kDa subunit containing 2 b-type cytochromes (SdhC). In agreement with this, we could identify the 4 conserved histidines in the SdhC subunit predicted by the B. cereus genome database. Succinate reduced half of the cytochrome b content. Redox titrations of SQR-cytochrome b-557 detected 2 components with apparent midpoint potential values at pH 7.6 of 79 and –68 mV, respectively; the components were not spectrally distinguishable by their maximal absorption bands as those of Bacillus subtilis . The physiological properties and genome database analyses of B. cereus are consistent with the cereus group ancestor being an opportunistic pathogen.
Targeting of sonic hedgehog-GLI signaling: a potential strategy to improve therapy for mantle cell lymphoma
Authors: Hegde Ganapati V. , Munger Corey M. , Emanuel Katy , Joshi Avadhut D. , Greiner Timothy C. , Weisenburger Dennis D. , Vose Julie M. , Joshi Shantaram S. 
Published: June 2008

Abstract
Mantle cell lymphoma (MCL) has one of the worst clinical outcomes among the B-cell lymphomas, with a median survival of only 3 to 4 years. Therefore, a better understanding of the underlying mechanisms that regulate MCL proliferation/survival is needed to develop an effective therapy. Because sonic hedgehog (Shh)-GLI signaling has been shown to be important in the proliferation and survival of several cancers, and no such information is available for MCL, this study was undertaken. Our results show that the molecules associated with Shh-GLI signaling, such as PTCH and SMO receptors, and GLI1 and GLI2 target transcription factors were expressed in the human MCL cell lines and primary MCL cells from patients. Perturbation of this signaling in the presence of exogenous Shh/cyclopamine significantly (P &lt; 0.001) influenced the proliferation of JVM2 MCL cells. Furthermore, down-regulation of GLI transcription factors using antisense oligonucleotides not only resulted in significantly (P &lt; 0.001) decreased proliferation of the MCL cells but also significantly (P &lt; 0.05) increased their susceptibility to chemotherapeutic drug, doxorubicin. Also, down-regulation of GLI decreased cyclin D1 and BCL2 transcript levels, which suggests that these key molecules might be regulated by GLI in MCL. Thus, our results indicate a significant role for Shh-GLI signaling in the proliferation of MCL, and molecular targeting of GLI is a potential therapeutic approach to improve the treatment for MCL. [Mol Cancer Ther 2008;7(6):1450–60]
Classification of Tropical Precipitating Systems Using Wind Profiler Spectral Moments. Part I: Algorithm Description and Validation
Authors: Rao T. Narayana , Kirankumar N. V. P. , Radhakrishna B. , Rao D. Narayana , Nakamura K. 
Published: June 2008

Abstract
The lower atmospheric wind profiler (LAWP) measurements made at Gadanki, India, have been used to develop an objective algorithm to classify the tropical precipitating systems. A detailed investigation on the existing classification scheme reveals major shortcomings in the scheme. In the present study, it is shown with examples that the Doppler velocity gradient (DVG) criterion is a necessary but certainly not a sufficient condition to identify the radar bright band. Such gradients in Doppler velocity can exist in other types of rain systems, for example, in convection, due to the modulation of Doppler velocity of hydrometeors by vertical air motion. The approach of the new classification scheme deviates considerably from that of existing algorithms. For instance, the new algorithm, in contrast to identifying the stratiform rain and assuming the remaining rain as convection, identifies first convection and later stratiform precipitation based on their specific characteristics. The other interesting feature in this algorithm is that it was built on the strengths of other potential classification schemes and theoretically accepted thresholds for classification of the precipitation. The performance of the new algorithm has been verified with the help of time–height maps of profiler moments and corresponding surface rainfall patterns.
Classification of Tropical Precipitating Systems Using Wind Profiler Spectral Moments. Part II: Statistical Characteristics of Rainfall Systems and Sensitivity Analysis
Authors: Rao T. Narayana , Kirankumar N. V. P. , Radhakrishna B. , Rao D. Narayana , Nakamura K. 
Published: June 2008

Abstract
An automated precipitation algorithm to classify tropical precipitating systems has been described in a companion paper (Part I). In this paper, the algorithm has been applied to 18 months of lower atmospheric wind profiler measurements to study the vertical structure and statistical features of different types of tropical precipitating systems over Gadanki, India. The shallow precipitation seems to be an important component of tropical precipitation, because it is prevalent for about 23% of the observations, with a rainfall fraction of 16%. As expected, the deep convective systems contribute maximum (60%) to the total rainfall, followed by transition and stratiform precipitation. Nonprecipitating clouds (clouds associated with no surface rainfall) are predominant in transition category, indicating that evaporation of precipitation is significant in this region. The quantitative rainfall statistics in different precipitation regimes are compared and contrasted between themselves and also with those reported at different geographical locations obtained with a wide spectrum of instruments, from rain gauges to profilers and scanning radars. The results herein agree with the reports based on scanning radar measurements but differ from profiler-based statistics. The discrepancies are discussed in light of differences in classification schemes, variation in geographical conditions, etc. The sensitivity of the algorithm on the choice of thresholds for identifying different types of precipitating systems is also examined.
Optimal Compression of High Spectral Resolution Satellite Data via Adaptive Vector Quantization with Linear Prediction
Authors: Huang Bormin , Ahuja Alok , Huang Hung-Lung 
Published: June 2008

AbstractContemporary and future high spectral resolution sounders represent a significant technical advancement for environmental and meteorological prediction and monitoring. Given their large volume of spectral observations, the use of robust data compression techniques will be beneficial to data transmission and storage. In this paper, a novel adaptive vector quantization (VQ)-based linear prediction (AVQLP) method for lossless compression of high spectral resolution sounder data is proposed. The AVQLP method optimally adjusts the quantization codebook sizes to yield the maximum compression on prediction residuals and side information. The method outperforms the state-of-the-art compression methods [Joint Photographic Experts Group (JPEG)-LS, JPEG2000 Parts 1 and 2, Consultative Committee for Space Data Systems (CCSDS) Image Data Compression (IDC) 5/3, Context-Based Adaptive Lossless Image Coding (CALIC), and 3D Set Partitioning in Hierarchical Trees (SPIHT)] and achieves a new high in lossless compression for the standard test set of 10 NASA Atmospheric Infrared Sounder (AIRS) granules. It also compares favorably in terms of computational efficiency and compression gain to recently reported adaptive clustering methods for lossless compression of high spectral resolution data. Given its superior compression performance, the AVQLP method is well suited to ground operation of high spectral resolution satellite data compression for rebroadcast and archiving purposes.
Application of the Sequential Three-Dimensional Variational Method to Assimilating SST in a Global Ocean Model
Authors: He Zhongjie , Xie Yuanfu , Li Wei , Li Dong , Han Guijun , Liu Kexiu , Ma Jirui 
Published: June 2008

Abstract
A recursive filter or parameterized curve fitting technique is usually used in a three-dimensional variational data assimilation (3DVAR) scheme to approximate the background error covariance, which can only represent the errors of an ocean field over a predetermined scale. Without an accurate flow-dependent error covariance that is also local and time dependent, a 3DVAR system may not provide good analyses because it is optimal only under the assumption of an accurate covariance. In this study, a sequential 3DVAR (S3DVAR) is formulated in model grid space to examine if there is useful information that can be extracted from the observation. This formulation is composed of a series of 3DVARs, each of which uses recursive filters with different length scales. It can provide an inhomogeneous and anisotropic analysis for the wavelengths that can be resolved by the observation network, just as with the conventional Barnes analysis or successive corrections. Being a variational formulation, S3DVAR can deal with data globally with an explicit specification of the observation errors; explicit physical balances or constraints; and advanced datasets, such as satellite and radar. Even though the S3DVAR analysis can be viewed as a set of isotropic functions superpositioned together, this superposition is not prespecified as in a single 3DVAR approach but is determined by the information that can be resolved by observation. The S3DVAR is adopted in a global sea surface temperature (SST) data assimilation system, into which the shipboard SSTs and the 4-km Advanced Very High Resolution Radiometer (AVHRR) Pathfinder daily SSTs are assimilated, respectively. The results demonstrate that the proposed S3DVAR works better in practice than a single 3DVAR.
Alongfront Variability of Precipitation Associated with a Midlatitude Frontal Zone: TRMM Observations and MM5 Simulation
Authors: Han Mei , Braun Scott A. , Persson P. Ola G. , Bao Jian-Wen 
Published: June 2008

Abstract
On 19 February 2001, the Tropical Rainfall Measuring Mission (TRMM) satellite observed complex alongfront variability in the precipitation structure of an intense cold-frontal rainband. The TRMM Microwave Imager brightness temperatures suggested that, compared to the northern and southern ends of the rainband, a greater amount of precipitation ice was concentrated in the middle portion of the rainband where the front bowed out. A model simulation conducted using the fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5) is examined to explain the distribution of precipitation associated with the cold-frontal rainband. The simulation reveals that the enhanced precipitation ice production and the implied mean ascent along the central part of the front were associated with a synergistic interaction between a low-level front and an upper-level front associated with an intrusion of high-PV stratospheric air. The low-level front contributed to an intense bow-shaped narrow cold-frontal rainband (NCFR). The upper-level front was dynamically active only along the central to northern portion of the NCFR, where the upper-level PV advection and Q-vector convergence were most prominent. The enhanced mean ascent associated with the upper-level front contributed to a wide cold-frontal rainband (WCFR) that trailed or overlapped with the NCFR along its central to northern segments. Because of the combination of the forcing from both lower- and upper-level fronts, the ascent was deepest and most intense along the central portion of the front. Thus, a large concentration of precipitation ice, attributed to both the NCFR and WCFR, was produced.
New bench test for venous cannula performance assessment
Authors: Abdel-Sayed S , Favre J , Horisberger J , Taub S , Hayoz D , von Segesser LK 
Published: June 2008

Cannula design is of prime importance for venous drainage during cardiopulmonary bypass (CPB). To evaluate cannulas intended for CPB, an in vitro circuit was set up with silicone tubing between the test cannula encased in a movable preload reservoir and another static reservoir. The pressure-drop ( ΔP) value (P-drainage – P-preload) was measured using Millar pressure transducers. Flow rate ( Q) was measured using an ultrasound flowmeter. Data display and data recording were controlled using a LabView application, custom made particularly for our experiments. Our results demonstrated that ΔP, Q, and cannula resistance ( ΔP/Q) values were significantly decreased when the cannula diameter was increased for Smart and Medtronic cannulas. Smartcanula® showed 36% and 43% less resistance compared to Medtronic venous and Medtronic femoral cannulas, respectively. The cannula shape (straight- or curved-tips) did not affect the DLP cannula resistance. Out of five cannulas tested, the Smartcanula® outperforms the other commercially available cannulas. The mean ( ΔP/Q) values were 3.3 ± 0.08, 4.07 ± 0.08, 5.58 ± 0.10, 5.74 ± 0.15, and 6.45 ± 0.15 for Smart, Medtronic, Edwards, Sarns, and Gambro cannulas, respectively (two-way ANOVA, p < 0.0001). In conclusion, the present assay allows discrimination between different forms of cannula with high or low lumen resistance.
Influence of Cut-Out Variables on Buckling Behavior of Composite Plates
Authors: Yazici Murat 
Published: June 2008

Cut-outs are often found in composite structures. These are provided with structural components for ventilation and sometimes to lighten the structure. This article addresses the effects of a cut-out on the buckling behavior of rectangular plates made of polymer matrix composites. While the loaded edges are modeled in simply supported boundary conditions, the unloaded edges are taken as free. Finite element analysis is also performed to predict the effects of cut-outs on the buckling behavior of these plates. Several key findings and behavioral characteristics are discussed. These findings include the effects of cut-out size, cut-out orientation, and corner fillet radius conditions. Some overall important findings of these studies are that the critical buckling loads are not changed by increasing cut-out orientation angle and hole corner fillet radius. The maximum variation was obtained as 5.91% by increasing the hole orientation angle in the buckling loads.