bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wild-Type MIC Distribution and Epidemiological Cutoff Values for
Aspergillus fumigatus
and Three Triazoles as Determined by the Clinical and Laboratory Standards Institute Broth Microdilution Methods
Authors: Pfaller M. A. , Diekema D. J. , Ghannoum M. A. , Rex J. H. , Alexander B. D. , Andes D. , Brown S. D. , Chaturvedi V. , Espinel-Ingroff A. , Fowler C. L. , Johnson E. M. , Knapp C. C. , Motyl M. R. , Ostrosky-Zeichner L. , Sheehan D. J. , Walsh T. J. 
Published: August 2009

ABSTRACT

Antifungal susceptibility testing of
Aspergillus
species has been standardized by both the Clinical and Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Recent studies suggest the emergence of strains of
A
spergillus fumigatus
with acquired resistance to azoles. The mechanisms of resistance involve mutations in the
cyp51A
(sterol demethylase) gene, and patterns of azole cross-resistance have been linked to specific mutations. Studies using the EUCAST broth microdilution (BMD) method have defined wild-type (WT) MIC distributions, epidemiological cutoff values (ECVs), and cross-resistance among the azoles. We tested a collection of 637 clinical isolates of
A. fumigatus
for which itraconazole MICs were ≤2 μg/ml against posaconazole and voriconazole using the CLSI BMD method. An ECV of ≤1 μg/ml encompassed the WT population of
A. fumigatus
for itraconazole and voriconazole, whereas an ECV of ≤0.25 μg/ml was established for posaconazole. Our results demonstrate that the WT distribution and ECVs for
A. fumigatus
and the mold-active triazoles were the same when determined by the CLSI or the EUCAST BMD method. A collection of 43 isolates for which itraconazole MICs fell outside of the ECV were used to assess cross-resistance. Cross-resistance between itraconazole and posaconazole was seen for 53.5% of the isolates, whereas cross-resistance between itraconazole and voriconazole was apparent in only 7% of the isolates. The establishment of the WT MIC distribution and ECVs for the azoles and
A. fumigatus
will be useful in resistance surveillance and is an important step toward the development of clinical breakpoints.
Differentiating Culture Samples Representing Coagulase-Negative Staphylococcal Bacteremia from Those Representing Contamination by Use of Time-to-Positivity and Quantitative Blood Culture Methods
Authors: Kassis Christelle , Rangaraj Gopi , Jiang Ying , Hachem Ray Y. , Raad Issam 
Published: August 2009

ABSTRACT

Differentiating true coagulase-negative staphylococcal infection from contamination has an important impact on therapeutic implications. Time to positivity reflects bacterial density and may help in the interpretation of blood cultures. We retrospectively reviewed the records of 272 patients from June 2005 to January 2008 for clinical characteristics, microbiological data, and therapeutic outcome. Four groups were identified. The first three groups, as follows, included patients with one positive quantitative blood culture: the low-colony-count group (<10 CFU/ml), the moderate-colony-count group (30 to 100 CFU/ml), and the high-colony-count group (>100 CFU/ml). The control group included patients with two positive quantitative blood cultures and definite coagulase-negative staphylococcal bloodstream infection. The high-colony-count group had shorter time to positivity (≤16 h) than did the low-colony-count group (
P
< 0.0001). The low-colony-count group had a significantly longer time to positivity, >20 h (
P
= 0.001), than did the moderate-colony-count group. Even though antibiotics were not provided in 71% of cases and central venous catheter was retained in 83%, the low-colony-count group had a favorable outcome, suggesting that <10 CFU/ml represents contamination. The high-colony-count group, similar to the positive control group, required antibiotics in 81% of cases and central venous catheter removal in 51% (
P
= 0.001). A time to positivity of ≤16 h reflects high-grade bacteremia with CFU of >100. Similar to the positive control group, these patients required an active therapeutic approach. A time to positivity of >20 h indicates possible contamination with a CFU of <10, and active therapy may not be required.
Impaired Plasmacytoid Dendritic Cell (PDC)-NK Cell Activity in Viremic Human Immunodeficiency Virus Infection Attributable to Impairments in both PDC and NK Cell Function
Authors: Conry Sara J. , Milkovich Kimberly A. , Yonkers Nicole L. , Rodriguez Benigno , Bernstein Helene B. , Asaad Robert , Heinzel Frederick P. , Tary-Lehmann Magdalena , Lederman Michael M. , Anthony Donald D. 
Published: August 2009

ABSTRACTHuman immunodeficiency virus (HIV) and hepatitis C virus (HCV) infections impair plasmacytoid dendritic cell (PDC) and natural killer (NK) cell subset numbers and functions, though little is known about PDC-NK cell interactions during these infections. We evaluated PDC-dependent NK cell killing and gamma interferon (IFN-γ) and granzyme B production, using peripheral blood mononuclear cell (PBMC)-based and purified cell assays of samples from HCV- and HIV-infected subjects. CpG-enhanced PBMC killing and IFN-γ and granzyme B activity (dependent on PDC and NK cells) were impaired in viremic HIV infection. In purified PDC-NK cell culture experiments, CpG-enhanced, PDC-dependent NK cell activity was cell contact and IFN-α dependent, and this activity was impaired in viremic HIV infection but not in HCV infection. In heterologous PDC-NK cell assays, impaired PDC-NK cell killing activity was largely attributable to an NK cell defect, while impaired PDC-NK cell IFN-γ-producing activity was attributable to both PDC and NK cell defects. Additionally, the response of NK cells to direct IFN-α stimulation was defective in viremic HIV infection, and this defect was not attributable to diminished IFN-α receptor expression, though IFN-α receptor and NKP30 expression was closely associated with killer activity in viremic HIV infection but not in healthy controls. These data indicate that during uncontrolled HIV infection, PDC-dependent NK cell function is impaired, which is in large part attributable to defective IFN-α-induced NK cell activity and not to altered IFN-α receptor, NKP30, NKP44, NKP46, or NKG2D expression.
Extension of Flavivirus Protein C Differentially Affects Early RNA Synthesis and Growth in Mammalian and Arthropod Host Cells
Authors: Schrauf Sabrina , Mandl Christian W. , Bell-Sakyi Lesley , Skern Tim 
Published: August 2009

ABSTRACT
The translation of flaviviral RNA genomes yields a single polyprotein that is processed into the mature proteins by viral and host cell proteases. Mature capsid protein C is freed from the polyprotein by the viral NS2B/3 protease, cleaving in the C-terminal region of protein C in front of the signal sequence for prM. Protein C has been shown to be involved in viral assembly and RNA packaging. To examine further the role of protein C and its production by proteolysis, we replaced the NS2B/3 capsid cleavage site in tick-borne encephalitis virus (TBEV) and West Nile virus (WNV) by the 2A protein of foot-and-mouth disease virus (TBEV-2A and WNV-2A). This obviated the need for NS2B/3 processing at the C terminus of mature protein C while simultaneously producing a 19-amino-acid extension on protein C. Infectious virions were generated with both viruses; the phenotype depended on the host cell. TBEV-2A replicated well in BHK-21 cells but was essentially incapable of replication in tick cells. In contrast, WNV-2A replicated well in mosquito cells but showed a small-plaque phenotype in Vero cells, with frequent production of larger plaques. Sequencing of viral RNA from the larger plaques showed substitutions in the signal sequence for prM, presumably improving coordinated protein processing at the C-prM junction. Furthermore, both TBEV-2A and WNV-2A were also defective in unpackaging and/or early RNA synthesis. Together, these results indicate a role for flavivirus protein C in both viral assembly and RNA replication, possibly by interacting with host cell factors required to set up the cell for RNA replication.
E1 Mutants Identify a Critical Region in the Trimer Interface of the Semliki Forest Virus Fusion Protein
Authors: Liu Catherine Y. , Kielian Margaret 
Published: August 2009

ABSTRACT
The alphavirus Semliki Forest virus (SFV) uses a membrane fusion reaction to infect host cells. Fusion of the virus and cell membranes is triggered by low pH in the endosome and is mediated by the viral membrane protein E1. During fusion, E1 inserts into the target membrane, trimerizes, and refolds into a hairpin conformation. Formation of the E1 homotrimer is critical to membrane fusion, but the mechanism of trimerization is not understood. The crystal structure of the postfusion E1 trimer shows that an aspartate residue, D188, is positioned in the central core trimer interface. D188 is conserved in all reported alphavirus E1 sequences. We tested the contribution of this amino acid to trimerization and fusion by replacing D188 with alanine (D188A) or lysine (D188K) in an SFV infectious clone. These mutations were predicted to disrupt specific interactions at this position and/or change their pH dependence. Our results indicated that the D188K mutation blocked SFV fusion and infection. At low pH, D188K E1 inserted into target membranes but was trapped as a target membrane-inserted monomer that did not efficiently form the stable core trimer. In contrast, the D188A mutant was infectious, although trimerization and fusion required a lower pH. While there are extensive contacts between E1 subunits in the homotrimer, the D188K mutant identifies an important “hot spot” for protein-protein interactions within the core trimer.
Coinfection of Ugandan Red Colobus (
Procolobus
[
Piliocolobus
]
rufomitratus tephrosceles
) with Novel, Divergent Delta-, Lenti-, and Spumaretroviruses
Authors: Goldberg Tony L. , Sintasath David M. , Chapman Colin A. , Cameron Kenneth M. , Karesh William B. , Tang Shaohua , Wolfe Nathan D. , Rwego Innocent B. , Ting Nelson , Switzer William M. 
Published: August 2009

ABSTRACT

Nonhuman primates host a plethora of potentially zoonotic microbes, with simian retroviruses receiving heightened attention due to their roles in the origins of human immunodeficiency viruses type 1 (HIV-1) and HIV-2. However, incomplete taxonomic and geographic sampling of potential hosts, especially the African colobines, has left the full range of primate retrovirus diversity unexplored. Blood samples collected from 31 wild-living red colobus monkeys (
Procolobus
[
Piliocolobus
]
rufomitratus tephrosceles
) from Kibale National Park, Uganda, were tested for antibodies to simian immunodeficiency virus (SIV), simian T-cell lymphotrophic virus (STLV), and simian foamy virus (SFV) and for nucleic acids of these same viruses using genus-specific PCRs. Of 31 red colobus tested, 22.6% were seroreactive to SIV, 6.4% were seroreactive to STLV, and 97% were seroreactive to SFV. Phylogenetic analyses of SIV polymerase (
pol
), STLV
tax
and long terminal repeat (LTR), and SFV
pol
and LTR sequences revealed unique SIV and SFV strains and a novel STLV lineage, each divergent from corresponding retroviral lineages previously described in Western red colobus (
Procolobus badius badius
) or black-and-white colobus (
Colobus guereza
). Phylogenetic analyses of host mitochondrial DNA sequences revealed that red colobus populations in East and West Africa diverged from one another approximately 4.25 million years ago. These results indicate that geographic subdivisions within the red colobus taxonomic complex exert a strong influence on retroviral phylogeny and that studying retroviral diversity in closely related primate taxa should be particularly informative for understanding host-virus coevolution.
Pop-ups and related damage in granite at the Medika Pluton in southeastern Manitoba
Authors: Everitt Richard A. 
Published: August 2009

Stress relief in the form of small displacements and a pop-up has occurred in a line-drilled, blast-free quarry in Archean granite 100 km east of Winnipeg. A 60 m by 19 m and up to 1.5 m thick block, forming the east wall of the quarry, has undergone deformation and displacement following quarrying. The pop-up base is a low-dipping exfoliation fracture that predates the quarry. Block movement is complex, with compressional, strike-slip, and extensional features observed around the damaged zone perimeter. Overall, block displacement and expansion are dominated by upslope thrusting. The northeast–southwest displacement of the postexcavation damage zone mimics that of a nearby pre-quarry pop-up. The orientation of the maximum horizontal in situ compressive stress, σh max, inferred from the postquarry pop-up is consistent with on-site overcoring results. The compressional origin of the quarry-induced low-dip thrust fault and pop-up and the predominant orientations of these structures are compatible with the ambient stress field in eastern North America. This indicates that, although the quarry initiated and localized the damage zone, the regional in situ stress field defines its geometry and relative displacement.
Experiments for alternative management of forest reserves: effects of partial cutting on stem growth and mortality of large oaks
Authors: Götmark Frank 
Published: August 2009

Although protected forests are usually kept as free of human disturbance as possible, careful cutting may favour biodiversity in such areas. However, the use of heavy machinery during cutting operations may have a negative impact on protected forests. The large oaks ( Quercus spp.) found in many temperate nature reserves have a rich associated biodiversity. In 25 conservation forests in Sweden, the basal area growth and mortality of 250 large oaks (31–110 cm DBH) were compared between plots that were partially cut to promote the growth and survival of oaks and undisturbed plots. Each forest had one treatment plot (1 ha) and one undisturbed reference plot (1 ha) with similar levels of canopy cover. In 2002–2003, about 25% of the basal area was harvested in treatment plots, thereby increasing canopy openness from 14% to 33%. Cutting increased the mean relative basal area growth of large oaks (49% by plot, 22% by tree) after four seasons (P = 0.026). However, in nine forests, the growth rate was not higher in the treated plot than in the reference plot. Mortality, apparently due to cutting, was recorded only in one forest, where 18 large oaks died. Tree condition (percentage of dead large branches in crown) was the best (negative) predictor of growth rate, and openness around oak crown was also a (positive) predictor. Partial cutting favoured the growth of oaks and may be recommended, but a “hands-off” policy is also effective for these conservation forests.
Biases in the estimation of size-dependent mortality models: advantages of a semiparametric approach
Authors: Vieilledent Ghislain , Courbaud Benoît , Kunstler Georges , Dhôte Jean-François , Clark James S. 
Published: August 2009

Mortality rate is thought to show a U-shape relationship to tree size. This shape could result from a decrease of competition-related mortality as diameter increases, followed by an increase of senescence and disturbance-related mortality for large trees. Modeling mortality rate as a function of diameter is nevertheless difficult, first because this relationship is strongly nonlinear, and second because data can be unbalanced, with few observations for large trees. Parametric functions, which are inflexible and sensitive to the distribution of observations, tend to introduce biases in mortality rate estimates. In this study we use mortality data for Abies alba Mill. and Picea abies (L.) Karst. to demonstrate that mortality rate estimates for extreme diameters were biased when using classical parametric functions. We then propose a semiparametric approach allowing a more flexible relationship between mortality and diameter. We show that the relatively shade-tolerant A. alba has a lower annual mortality rate (2.75%) than P. abies (3.78%) for small trees (DBH <15 cm). Picea abies, supposedly more sensitive to bark beetle attacks and windthrows, had a higher mortality rate (up to 0.46%) than A. alba (up to 0.30%) for large trees (DBH ≥50 cm).
Integration of soil moisture, xylem water potential, and fall–spring herbicide treatments to achieve the maximum growth response in newly planted Douglas-fir seedlings
Authors: Dinger Eric J. , Rose Robin 
Published: August 2009

Early in the establishment of Pacific Northwest Douglas-fir ( Pseudotsuga menziesii (Mirb.) Franco) plantations, herbaceous vegetation can decrease seedling growth through competition for soil moisture during the dry summer months. This study was designed to statistically quantify soil moisture, seedling xylem water potential (Ψ), vegetation community, and seedling growth response to six herbicide treatment regimes commonly applied over the first 2 years of establishment. When compared with the control, soil moisture and seedling Ψ increased in response to reductions in competitive cover, allowing seedlings to extend productive growing time from 28 to 80 days. As a result, seedling volume growth increased from 56 cm3 in the untreated control to greater than 250 cm3 for the most intensive herbicide treatment regimes. Vegetation surveys revealed that treatment regimes had the potential to provide a disturbance, which could shift community composition from native to introduced species as the relationship decreased from 10:1 to 2:1. The most intense herbicide treatment regime reduced cover below 20%, retained soil moisture >30%, maintained predawn seedling Ψ above –1.0 MPa, and decreased height to diameter ratio below 50, increasing the likelihood of successful plantation establishment.
Monoterpene persistence in the sapwood and heartwood of longleaf pine stumps: assessment of differences in composition and stability under field conditions
Authors: Eberhardt Thomas L. , Sheridan Philip M. , Mahfouz Jolie M. 
Published: August 2009

Monoterpenes in exudates, phloem, and sapwood have received considerable attention relative to the active defenses of pine trees. However, little is known about the composition and function of the heartwood monoterpenes. To address this deficiency, monoterpene contents and relative compositions were determined for sapwood and heartwood samples from longleaf pine ( Pinus palustris Mill.) stumps monitored in the field for a 1 year period postharvest. Gas chromatography – mass spectrometry analysis of sapwood and heartwood sample extracts showed the total monoterpene contents for both declined at essentially the same rate. For sapwood, α-pinene continued to comprise about 75% of all compounds detected, while the proportion of β-pinene declined with time (15%–7%). For the heartwood, lower proportions of both α- and β-pinenes (64% and 10%, respectively) were offset by higher proportions of other monoterpenes (e.g., limonene, α-terpineol, borneol). The low proportion of β-pinene in very old turpentine and lightwood stump samples further suggested the lower stability of this particular monoterpene. While it has not been specifically demonstrated that the monoterpenes have an active role in the decay resistance of longleaf pine stump heartwood, these compounds do persist for a very long time and thus are available should they serve this function.
Rapid capture of growing space by red maple
Authors: Fei Songlin , Steiner Kim C. 
Published: August 2009

Red maple ( Acer rubrum L.) is becoming increasingly dominant in forest stands throughout the eastern United States. To investigate the reasons for the increase, we examined the development of red maple and oak ( Quercus spp.) seedlings and stump sprouts following the harvest of oak-dominated stands. Within 7 years after harvest, red maple seedlings were present in far greater numbers and captured more growing space than all oaks combined. Growing space occupied by red maple stump sprouts exceeded oak sprouts by a ratio of 3.5:1. Through stump sprouts alone, red maple fully recaptured the amount of growing space it had previously occupied in the overstory 7 years after harvest. Results from similar but older stands show that red maple dominance is sustained into the third decade of stand development. Red maple surpassed all oaks combined in rapid site capture through both seed-origin and sprout-origin regeneration. Red maple’s superior ability to regenerate by sprouts is particularly favored by timber harvesting following a history of management and disturbance regimes that permit the accumulation of suppressed small-diameter red maple stems. Among the events and processes that promote stand conversion, timber harvesting may be the major proximal cause of the widespread, increasing dominance of red maple.
Seasonal fluctuation of root carbohydrates in hybrid aspen clones and its relationship to the sprouting efficiency of root cuttings
Authors: Stenvall N. , Piisilä M. , Pulkkinen P. 
Published: August 2009

We examined the relationship between root carbohydrates and sprouting efficiency in four hybrid aspen ( Populus tremula × Populus tremuloides ) clones. Our hypothesis was that the interclonal variation in sprouting efficiency is due to the concentration of carbohydrates. In addition to that relationship, we wanted to study seasonal fluctuation of carbohydrates and how the –18 °C storage conditions of stock plants affects the stability of carbohydrate content and thus sprouting ability of roots cuttings. Clones varied in root carbohydrate content, and sucrose showed the greatest variation throughout the year. Sucrose levels were highest in the clone with the highest sprouting efficiency and lowest in the clone with the lowest sprouting efficiency. Carbohydrate concentrations were highest in winter and lowest in early autumn. In general, root cuttings sprouted most efficiently when root carbohydrate levels peaked. Although root cuttings taken from frozen (–18 °C) stock plants sprouted poorly in summer and autumn, they had high and almost constant carbohydrate concentrations throughout the year.
Conifer seed predation in harvested and burned dry Douglas-fir forests in southern British Columbia
Authors: Huggard David J. , Arsenault André 
Published: August 2009

Consumption of seeds of Douglas-fir ( Pseudotsuga menziesii (Mirb.) Franco) and ponderosa pine ( Pinus ponderosa Dougl. ex P. & C. Laws.) was measured in dry Douglas-fir forest at the Opax Mountain Silvicultural Systems site and a nearby burned area as one component of understanding limited natural regeneration in these sites. Seeds were placed in plots surrounded by a physical barrier to invertebrates, enclosed in mesh impermeable to small mammals, covered by litter, or unprotected in clear-cut, partially harvested, uncut, and burned areas and monitored for three several-day sessions in 2 years. Daily survival rates of unprotected seeds of both species were equally low: 0.63 in uncut forest, 0.45 in partially harvested and clear-cut sites, and 0.03 in the burned area. Experimental reductions of coarse woody debris reduced seed predation moderately in patch cuts but not in uncut forest. Litter cover or selective exclosure of ground-dwelling invertebrates reduced seed losses only slightly, whereas small mammal exclosures eliminated most seed loss. Deer mice ( Peromyscus maniculatus Wagner) are likely the most important seed predators. High rates of seed predation in dry Douglas-fir forests likely limit natural regeneration in harvested and burned stands.
Numerical Treatment of Fixed Point Applied to the Nonlinear Fredholm Integral Equation
Authors: Berenguer M. I. , Fernández Muñoz M. V. , Garralda Guillem A. I. , Ruiz Galán M. 
Published: August 2009

AbstractThe authors present a method of numerical approximation of the fixed point of an operator, specifically the integral one associated with a nonlinear Fredholm integral equation, that uses strongly the properties of a classical Schauder basis in the Banach space "Equation missing".