bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reproductive challenges of a rare grass, Calamagrostis porteri subsp. insperata (Swallen) C. Greene: implications for habitat restoration
Authors: Gibson David J. , Delong Michael , Chandy Shibi , Honu Yohanes A. K. 
Published: March 2009

AbstractBackground: Habitat management for reproductively challenged rare species is a problem when there is insufficient knowledge of their autecology. This study investigated reproductive failure in the rare grass Calamagrostis porteri ssp. insperata (Swallen) C. Greene (Reed bentgrass). Does the management recommendation of high light stimulate clonal growth, flowering, and seed production?Location: Shawnee National Forest, IL, USA, and in a greenhouse and an experimental garden at Southern Illinois University, Carbondale, IL, USA.Methods: Clones obtained from the three known Illinois populations were grown in a glasshouse under experimental light and soil moisture treatments. After 3 years, plants from the high light treatment were planted outside in an experimental garden where the light treatments were maintained for two more years. In the field, vegetative and flowering tiller density, canopy cover, and associated biotic and abiotic variables including abundance of co‐occurring plant species were monitored for 5 years. The overhead tree canopy was cleared over a portion of one population.Results: In the glasshouse, plants increased in size under high light and moist soil, and there were size differences among populations. Sixty‐six per cent (20 of 30) of the genets flowered when planted outdoors under full sunlight but did not produce seed. In the field, flowering only occurred in Calamagrostis growing in the cleared area, but no seed were produced. The plants in the flowering population were smaller than plants in the other two populations. The herbaceous community associated with Calamagrostis in the open diverged from the communities remaining under the shade.Conclusions: This study highlights the difficulty of managing reproductively challenged rare species. Calamagrostis populations can be managed to enhance clonal growth, but establishment of new populations would require translocation of vegetative material as it is highly unlikely that seed can be obtained.
Oxidative Stress in COPD and Its Measurement through Exhaled Breath Condensate
Authors: Lee Wei , Thomas Paul S. 
Published: March 2009

AbstractOxidative stress and airway inflammation together form a vicious cycle, which is responsible for the disease progression in chronic pulmonary obstructive disease (COPD). The damaging effects of oxidative stress accumulate over the years, causing increased bronchial hyperresponsiveness and inflammation and destruction of airway epithelial cells and impairing the functions of antiproteases and surfactant. Although the lung expresses a number of antioxidants, cigarette smoking and recurrent infections associated with this disease overwhelm this protective mechanism. Studies of antioxidants in COPD have yielded conflicting results, probably due to the compartmentalization of these mediators, and because of the fact that the lung is a difficult organ to sample. Chronic exposure to oxidants upregulates the production of antioxidants, which become depleted during acute exacerbations. Future studies of the pathogenesis of COPD require a noninvasive yet accurate sampling procedure, of which exhaled breath condensate (EBC) is a good candidate. EBC samples the epithelial lining fluid, which contains the local oxidative stress markers in the lung. Oxidative stress markers such as hydrogen ions, hydrogen peroxide, 8‐isoprostanes, thiobarbituric acid reactive products, nitrosothiols, and nitrite/nitrate have been identified in EBC of COPD patients, whereas many other markers of the oxidative‐antioxidative balance have yet to be investigated.
Hematology of healthy Florida manatees (Trichechus manatus)
Authors: Harvey John W. , Harr Kendal E. , Murphy David , Walsh Michael T. , Nolan Elizabeth C. , Bonde Robert K. , Pate Melanie G. , Deutsch Charles J. , Edwards Holly H. , Clapp William L. 
Published: March 2009

Background: Hematologic analysis is an important tool in evaluating the general health status of free‐ranging manatees and in the diagnosis and monitoring of rehabilitating animals.Objectives: The purpose of this study was to evaluate diagnostically important hematologic analytes in healthy manatees (Trichechus manatus) and to assess variations with respect to location (free ranging vs captive), age class (small calves, large calves, subadults, and adults), and gender.Methods: Blood was collected from 55 free‐ranging and 63 captive healthy manatees. Most analytes were measured using a CELL‐DYN 3500R; automated reticulocytes were measured with an ADVIA 120. Standard manual methods were used for differential leukocyte counts, reticulocyte and Heinz body counts, and plasma protein and fibrinogen concentrations.Results: Rouleaux, slight polychromasia, stomatocytosis, and low numbers of schistocytes and nucleated RBCs (NRBCs) were seen often in stained blood films. Manual reticulocyte counts were higher than automated reticulocyte counts. Heinz bodies were present in erythrocytes of most manatees. Compared with free‐ranging manatees, captive animals had slightly lower MCV, MCH, and eosinophil counts and slightly higher heterophil and NRBC counts, and fibrinogen concentration. Total leukocyte, heterophil, and monocyte counts tended to be lower in adults than in younger animals. Small calves tended to have higher reticulocyte counts and NRBC counts than older animals.Conclusions: Hematologic findings were generally similar between captive and free‐ranging manatees. Higher manual reticulocyte counts suggest the ADVIA detects only reticulocytes containing large amounts of RNA. Higher reticulocyte and NRBC counts in young calves probably reflect an increased rate of erythropoiesis compared with older animals.
High Sensitivity and Specificity of Acid-Fast Microscopy for Diagnosis of Pulmonary Tuberculosis in an African Population with a High Prevalence of Human Immunodeficiency Virus
Authors: Shea Yvonne R. , Davis J. Lucian , Huang Laurence , Kovacs Joseph A. , Masur Henry , Mulindwa Francis , Opus Sally , Chow Yuenwah , Murray Patrick R. 
Published: March 2009

ABSTRACT
Laboratories in low-income countries report that acid-fast microscopy is insensitive and nonspecific. We demonstrate that for a Ugandan population with high prevalences of tuberculosis and human immunodeficiency virus infection, acid-fast microscopy is highly sensitive (93.1%) and specific (100%) when performed by trained technologists in a carefully controlled manner using established techniques.
Impact of Discrepancies between the Abbott RealTime and Cobas TaqMan Assays for Quantification of Human Immunodeficiency Virus Type 1 Group M Non-B Subtypes
Authors: Wirden M. , Tubiana R. , Marguet F. , Leroy I. , Simon A. , Bonmarchand M. , Ait-Arkoub Z. , Murphy R. , Marcelin A. G. , Katlama C. , Calvez V. 
Published: March 2009

ABSTRACT
Viral loads in 249 clinical samples from individual patients infected with human immunodeficiency virus type 1 non-B subtypes were determined with both the Abbott RealTime and Cobas TaqMan assays. The differences exceeded 0.5 log for about 20% of samples and 1 log for 3%, with higher values always from the Abbott assay in the latter cases.
A Common Variant of Staphylococcal Cassette Chromosome
mec
Type IVa in Isolates from Copenhagen, Denmark, Is Not Detected by the BD GeneOhm Methicillin-Resistant
Staphylococcus aureus
Assay
Authors: Bartels Mette Damkjaer , Boye Kit , Rohde Susanne Mie , Larsen Anders Rhod , Torfs Herbert , Bouchy Peggy , Skov Robert , Westh Henrik 
Published: March 2009

ABSTRACT

Rapid tests for detection of methicillin-resistant
Staphylococcus aureus
(MRSA) carriage are important to limit the transmission of MRSA in the health care setting. We evaluated the performance of the BD GeneOhm MRSA real-time PCR assay using a diverse collection of MRSA isolates, mainly from Copenhagen, Denmark, but also including international isolates, e.g., USA100-1100. Pure cultures of 349 MRSA isolates representing variants of staphylococcal cassette chromosome
mec
(SCC
mec
) types I to V and 103 different staphylococcal protein A (
spa
) types were tested. In addition, 53 methicillin-susceptible
Staphylococcus aureus
isolates were included as negative controls. Forty-four MRSA isolates were undetectable; of these, 95% harbored SCC
mec
type IVa, and these included the most-common clone in Copenhagen,
spa
t024-sequence type 8-IVa. The false-negative MRSA isolates were tested with new primers (analyte-specific reagent [ASR] BD GeneOhm MRSA assay) supplied by Becton Dickinson (BD). The ASR BD GeneOhm MRSA assay detected 42 of the 44 isolates that were false negative in the BD GeneOhm MRSA assay. Combining the BD GeneOhm MRSA assay with the ASR BD GeneOhm MRSA assay greatly improved the results, with only two MRSA isolates being false negative. The BD GeneOhm MRSA assay alone is not adequate for MRSA detection in Copenhagen, Denmark, as more than one-third of our MRSA isolates would not be detected. We recommend that the BD GeneOhm MRSA assay be evaluated against the local MRSA diversity before being established as a standard assay, and due to the constant evolution of SCC
mec
cassettes, a continuous global surveillance is advisable in order to update the assay as necessary.
Characterization of a Novel Golgi Apparatus-Localized Latency Determinant Encoded by Human Cytomegalovirus
Authors: Petrucelli Alex , Rak Michael , Grainger Lora , Goodrum Felicia 
Published: March 2009

ABSTRACTHuman cytomegalovirus (HCMV) exists indefinitely in infected individuals by a yet poorly characterized latent infection in hematopoietic cells. We previously demonstrated a requirement for the putativeUL138open reading frame (ORF) in promoting a latent infection in CD34+hematopoietic progenitor cells (HPCs) infected in vitro. In our present study, we have identified two coterminal transcripts of 2.7 and 3.6 kb and a 21-kilodalton (kDa) protein (pUL138) that are derived from theUL138locus with early-late gene kinetics during productive infection. TheUL138transcripts and protein are detected in both fibroblasts and HPCs. A recombinant virus, FIX-UL138STOP, that synthesizes theUL138transcripts but not the protein exhibited a partial loss-of-latency phenotype in HPCs, similar to the phenotype observed for theUL138-null recombinant virus. This finding suggests that the UL138 protein is required for latency, but it does not exclude the possibility that theUL138transcripts or other ORFs also contribute to latency. The mechanisms by which pUL138 contributes to latency remain unknown. While the 86- and 72-kDa immediate-early proteins were not detected in HPCs infected with HCMV in vitro, pUL138 did not function directly to suppress expression from the major immediate-early promoter in reporter assays. Interestingly, pUL138 localizes to the Golgi apparatus in infected cells but is not incorporated into virus particles. The localization of pUL138 to the Golgi apparatus suggests that pUL138 contributes to HCMV latency by a novel mechanism. pUL138 is the first HCMV protein demonstrated to promote an infection with the hallmarks of latency in CD34+HPCs.
Probing the Transcription Mechanisms of Reovirus Cores with Molecules That Alter RNA Duplex Stability
Authors: Demidenko Alexander A. , Nibert Max L. 
Published: March 2009

ABSTRACT
The mammalian reovirus (MRV) genome comprises 10 double-stranded RNA (dsRNA) segments, packaged along with transcriptase complexes inside each core particle. Effects of four small molecules on transcription by MRV cores were studied for this report, chosen for their known capacities to alter RNA duplex stability. Spermidine and spermine, which enhance duplex stability, inhibited transcription, whereas dimethyl sulfoxide and trimethylglycine, which attenuate duplex stability, stimulated transcription. Different mechanisms were identified for inhibition or activation by these molecules. With spermidine, one round of transcription occurred normally, but subsequent rounds were inhibited. Thus, inhibition occurred at the transition between the end of elongation in one round and initiation in the next round of transcription. Dimethyl sulfoxide or trimethylglycine, on the other hand, had no effect on transcription by a constitutively active fraction of cores in each preparation but activated transcription in another fraction that was otherwise silent for the production of elongated transcripts. Activation of this other fraction occurred at the transition between transcript initiation and elongation, i.e., at promoter escape. These results suggest that the relative stability of RNA duplexes is most important for certain steps in the particle-associated transcription cycles of dsRNA viruses and that small molecules are useful tools for probing these and probably other steps.
The Respiratory Syncytial Virus Matrix Protein Possesses a Crm1-Mediated Nuclear Export Mechanism
Authors: Ghildyal Reena , Ho Adeline , Dias Manisha , Soegiyono Lydia , Bardin Phillip G. , Tran Kim C. , Teng Michael N. , Jans David A. 
Published: March 2009

ABSTRACT
The respiratory syncytial virus (RSV) matrix (M) protein is localized in the nucleus of infected cells early in infection but is mostly cytoplasmic late in infection. We have previously shown that M localizes in the nucleus through the action of the importin β1 nuclear import receptor. Here, we establish for the first time that M's ability to shuttle to the cytoplasm is due to the action of the nuclear export receptor Crm1, as shown in infected cells, and in cells transfected to express green fluorescent protein (GFP)-M fusion proteins. Specific inhibition of Crm1-mediated nuclear export by leptomycin B increased M nuclear accumulation. Analysis of truncated and point-mutated M derivatives indicated that Crm1-dependent nuclear export of M is attributable to a nuclear export signal (NES) within residues 194 to 206. Importantly, inhibition of M nuclear export resulted in reduced virus production, and a recombinant RSV carrying a mutated NES could not be rescued by reverse genetics. That this is likely to be due to the inability of a nuclear export deficient M to localize to regions of virus assembly is indicated by the fact that a nuclear-export-deficient GFP-M fails to localize to regions of virus assembly when expressed in cells infected with wild-type RSV. Together, our data suggest that Crm1-dependent nuclear export of M is central to RSV infection, representing the first report of such a mechanism for a paramyxovirus M protein and with important implications for related paramyxoviruses.
RecombinantMycobacterium bovisBCG Prime-Recombinant Adenovirus Boost Vaccination in Rhesus Monkeys Elicits Robust Polyfunctional Simian Immunodeficiency Virus-Specific T-Cell Responses
Authors: Cayabyab Mark J. , Korioth-Schmitz Birgit , Sun Yue , Carville Angela , Balachandran Harikrishnan , Miura Ayako , Carlson Kevin R. , Buzby Adam P. , Haynes Barton F. , Jacobs William R. , Letvin Norman L. 
Published: March 2009

ABSTRACTWhile mycobacteria have been proposed as vaccine vectors because of their persistence and safety, little has been done systematically to optimize their immunogenicity in nonhuman primates. We successfully generated recombinantMycobacterium bovisBCG (rBCG) expressing simian immunodeficiency virus (SIV) Gag and Pol as multigenic, nonintegrating vectors, but rBCG-expressing SIV Env was unstable. A dose and route determination study in rhesus monkeys revealed that intramuscular administration of rBCG was associated with local reactogenicity, whereas intravenous and intradermal administration of 106to 108CFU of rBCG was well tolerated. After single or repeat rBCG inoculations, monkeys developed high-frequency gamma interferon enzyme-linked immunospot responses against BCG purified protein derivative. However, the same animals developed only modest SIV-specific CD8+T-cell responses. Nevertheless, high-frequency SIV-specific cellular responses were observed in the rBCG-primed monkeys after boosting with recombinant adenovirus 5 (rAd5) expressing the SIV antigens. These cellular responses were of greater magnitude and more persistent than those generated after vaccination with rAd5 alone. The vaccine-elicited cellular responses were predominantly polyfunctional CD8+T cells. These findings support the further exploration of mycobacteria as priming vaccine vectors.
Varicella-Zoster Virus Infection Induces Autophagy in both Cultured Cells and Human Skin Vesicles
Authors: Takahashi Marie-Noëlle , Jackson Wallen , Laird Donna T. , Culp Timothy D. , Grose Charles , Haynes John I. , Benetti Luca 
Published: March 2009

ABSTRACT
When grown in cultured cells, varicella-zoster virus (VZV) forms many aberrant light particles and produces low titers. Various studies have explored the reasons for such a phenotype and have pointed to impaired expression of specific late genes and at lysosomal targeting of egressing virions as possible causes. In the studies presented here, we report that the autophagic degradation pathway was induced at late time points after VZV infection of cultured cells, as documented by immunoblot analysis of the cellular proteins LC3B and p62/SQSTM1, along with electron microscopy analysis, which demonstrated the presence of both early autophagosomes and late autophagic compartments. Autophagy was induced in infected cells even in the presence of phosphonoacetic acid, an inhibitor of viral late gene expression, thus suggesting that accumulation of immediate-early and early viral gene products might be the major stimulus for its induction. We also showed that the autophagic response was not dependent on a specific cell substrate, virus strain, or type of inoculum. Finally, using immunofluorescence imaging, we demonstrated autophagosome-specific staining in human zoster vesicles but not in normal skin. Thus, our results document that this innate immune response pathway is a component of the VZV infectious cycle in both cultured cells and the human skin vesicle, the final site of virion formation in the infected human host.
Differential Effects of Hepatitis C Virus JFH1 on Human Myeloid and Plasmacytoid Dendritic Cells
Authors: Liang Hua , Russell Rodney S. , Yonkers Nicole L. , McDonald David , Rodriguez Benigno , Harding Clifford V. , Anthony Donald D. 
Published: March 2009

ABSTRACTDendritic cells (DCs) are reported to be functionally deficient during chronic hepatitis C virus (HCV) infection. Differing results have been reported on direct effects of intact replicative-form HCV on DC function. To better understand the effect of HCV on DC function, we treated freshly purified human myeloid DCs (mDCs) and plasmacytoid DCs (pDCs) with HCV JFH1. We found that HCV upregulated mDC maturation marker (CD83, CD86, and CD40) expression and did not inhibit Toll-like receptor 3 (TLR3) ligand [poly(I:C)]-induced mDC maturation, a finding consistent with the phenotype of DCs from HCV-infected subjects. At the same time, HCV JFH1 inhibited the ability of poly(I:C)-treated mDCs to activate naive CD4 T cells. In contrast, although there was no direct effect of virus on pDC maturation, HCV JFH1 inhibited TLR7 ligand (R848)-induced pDC CD40 expression, and this was associated with impaired ability to activate naive CD4 T cells. Parallel experiments with recombinant HCV proteins indicated HCV core protein may be responsible for a portion of the activity. Furthermore, HCV-mediated mDC maturation was dependent upon CD81-E2 interaction and, in part, TLR2. Using UV-treated HCV, we show that HCV-mediated mDC and pDC maturation is virus replication independent and, using strand specific PCR, we found no evidence for HCV replication within DCs. Because these effects of HCV on DC subset maturation and function in part recapitulate direct ex vivo analysis of DCs in chronic HCV infection, the mechanisms described here likely account for a portion of the DC subset defects observed in vivo.
Hip flexibility and strength measures: reliability and association with athletic groin pain
Authors: Malliaras P , Hogan A , Nawrocki A , Crossley K , Schache A 
Published: March 2009

Objective:Groin pain commonly affects football players and can be associated with prolonged recovery periods. Understanding the relationship between groin pain and reliable measures of hip flexibility and strength may facilitate the development of optimal rehabilitation and prevention strategies. In this study, the reliability and association with athletic groin pain of hip flexibility and strength measures were investigated.Methods:A cohort of 29 football players (15–21 years) participating in junior elite competitions (Australian Rules football and soccer) were recruited. The intra-rater reliability (n  =  13) and inter-rater reliability (n  =  12) of various hip flexibility (bent knee fall out test, hip internal rotation, hip external rotation) and strength (hip abduction, hip internal rotation, hip external rotation, hip adduction (squeeze test)) measures were investigated using intraclass correlation coefficients (ICC). Reliable hip flexibility and strength measures were compared between football players with (n  =  10) and without (n  =  19) groin pain.Results:The bent knee fall out test, hip internal rotation flexibility and the squeeze test demonstrated acceptable (ICC>0.75) intra-rater and inter-rater reliability, while hip external rotation flexibility and hip abduction strength demonstrated acceptable intra-rater but not inter-rater reliability. Hip internal and external rotation strength tests were not found to be reliable. Football players with groin pain had significantly reduced force production on the squeeze test (p>0.05).Conclusion:Several hip flexibility and strength measures were found to be reliable. Only the squeeze test discriminated between football players with and without groin pain.
HIGH-ORDER DESCRIPTION OF THE DYNAMICS IN FFAGs AND RELATED ACCELERATORS
Authors: MAKINO KYOKO , BERZ MARTIN , SNOPOK PAVEL , JOHNSTONE CAROL 
Published: March 2009

In this paper, we describe newly developed tools for the study and analysis of the dynamics in FFAG accelerators based on transfer map methods unique to the code COSY INFINITY. With these new tools, closed orbits, transverse amplitude dependencies and dynamic aperture are determined inclusive of full nonlinear fields and kinematics to arbitrary order. The dynamics are studied at discrete energies, via a high-order energy-dependent transfer map.The order-dependent convergence in the calculated maps allows precise determination of dynamic aperture and detailed particle dynamics. Using normal form methods, and minimal impact symplectic tracking, amplitude- and energy-dependent tune shifts and resonance strengths are extracted. Optimization by constrained global optimization methods further refine and promote robust machine attributes.Various methods of describing the fields will be presented, including representation of fields in radius-dependent Fourier modes, which include complex magnet edge contours and superimposed fringe fields, as well as the capability to interject calculated or measured field data from a magnet design code or actual components, respectively.
CONCEPTUAL DESIGN OF A SUPERCONDUCTING QUADRUPOLE WITH ELLIPTICAL ACCEPTANCE AND TUNABLE HIGHER ORDER MULTIPOLES
Authors: MANIKONDA SHASHIKANT , NOLEN JERRY , BERZ MARTIN , MAKINO KYOKO 
Published: March 2009

For charged particle beams that are wider in the dispersive plane compared to the transverse plane it is cost efficient to utilize magnets that accept beams with elliptic cross section. In this paper we presents the conceptual design of a quadrupole magnet with elliptic cross section and with tunable higher order multipoles. The design consists of 18 superconducting race-track coils placed on two hollow concentric rhombic prism support structures. To compute the magnetic field for the proposed design a new method of calculating 2D and 3D fields for the air core magnets based on differential algebra (DA) techniques is developed. We will present the new method and discuss its implementation of new numerical tools based on this method in the code COSY Infinity.