bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotypic Diversity of Anaerobic Isolates from Bloodstream Infections
Authors: Simmon Keith E. , Mirrett Stanley , Reller L. Barth , Petti Cathy A. 
Published: March 2008

ABSTRACT

Accurate species determination for anaerobes from blood culture bottles has become increasingly important with the reemergence of anaerobic bacteremia and prevalence of multiple-drug-resistant microorganisms. Our knowledge of the taxonomical diversity of anaerobes that cause bloodstream infections is extremely limited, because identification historically has relied on conventional methods. Over a 5-year period, we profiled anaerobic bacteremia at a large tertiary care hospital with 16S rRNA gene sequencing to gain a better understanding of the taxonomical diversity of the bacteria. Of 316 isolates, 16S rRNA gene sequencing and phylogenetic analysis identified 316 (100%) to the genus or taxonomical group level and 289 (91%) to the species level. Conventional methods identified 279 (88%) to the genus level and 208 (66%) to the species level; 75 (24%) were misidentified at the species level, and 33 (10%) results were inconclusive. High intragenus variability was observed for
Bacteroides
and
Clostridium
species, and high intraspecies variability was observed for
Bacteroides thetaiotaomicron
and
Fusobacterium nucleatum
. Sequence-based identification has potential benefits in comparison to conventional methods, because it more accurately characterizes anaerobes within taxonomically related clusters and thereby may enable better correlation with specific clinical syndromes and antibiotic resistance patterns.
Influenza A Virus Neuraminidase Limits Viral Superinfection
Authors: Huang I-Chueh , Li Wenhui , Sui Jianhua , Marasco Wayne , Choe Hyeryun , Farzan Michael 
Published: March 2008

ABSTRACTEnveloped viruses use multiple mechanisms to inhibit infection of a target cell by more than one virion. These mechanisms may be of particular importance for the evolution of segmented viruses, because superinfection exclusion may limit the frequency of reassortment of viral genes. Here, we show that cellular expression of influenza A virus neuraminidase (NA), but not hemagglutinin (HA) or the M2 proton pump, inhibits entry of HA-pseudotyped retroviruses. Cells infected with H1N1 or H3N2 influenza A virus were similarly refractory to HA-mediated infection and to superinfection with a second influenza A virus. Both HA-mediated entry and viral superinfection were rescued by the neuraminidase inhibitors oseltamivir carboxylate and zanamivir. These inhibitors also prevented the removal of α-2,3- and α-2,6-linked sialic acid observed in cells expressing NA or infected with influenza A viruses. Our data indicate that NA alone among viral proteins limits influenza A virus superinfection.
Casein Kinase II Motif-Dependent Phosphorylation of Human Papillomavirus E7 Protein Promotes p130 Degradation and S-Phase Induction in Differentiated Human Keratinocytes
Authors: Genovese Nicholas J. , Banerjee N. Sanjib , Broker Thomas R. , Chow Louise T. 
Published: March 2008

ABSTRACT
The E7 proteins of human papillomaviruses (HPVs) promote S-phase reentry in differentiated keratinocytes of the squamous epithelia to support viral DNA amplification. In this study, we showed that nuclear p130 was present in the differentiated strata of several native squamous epithelia susceptible to HPV infection. In contrast, p130 was below the level of detection in HPV-infected patient specimens. In submerged and organotypic cultures of primary human keratinocytes, the E7 proteins of the high-risk mucosotrophic HPV-18, the benign cutaneous HPV-1, and, to a lesser extent, the low-risk mucosotropic HPV-11 destabilized p130. This E7 activity depends on an intact pocket protein binding domain and a casein kinase II (CKII) phosphorylation motif. Coimmunoprecipitation experiments showed that both E7 domains were important for binding to p130 in extracts of organotypic cultures. Metabolic labeling in vivo demonstrated that E7 proteins were indeed phosphorylated in a CKII motif-dependent manner. Moreover, the efficiencies of the E7 proteins of various HPV types or mutations to induce S-phase reentry in spinous cells correlated with their relative abilities to bind and to destabilize p130. Collectively, these data support the notion that p130 controls the homeostasis of the differentiated keratinocytes and is therefore targeted by E7 for degradation to establish conditions permissive for viral DNA amplification.
Importance of Protease Cleavage Sites within and Flanking Human Immunodeficiency Virus Type 1 Transframe Protein p6* for Spatiotemporal Regulation of Protease Activation
Authors: Ludwig Christine , Leiherer Andreas , Wagner Ralf 
Published: March 2008

ABSTRACT
The human immunodeficiency virus type 1 (HIV-1) protease (PR) has recently been shown to be inhibited by its propeptide p6* in vitro. As p6* itself is a PR substrate, the primary goal of this study was to determine the importance of p6* cleavage for HIV-1 maturation and infectivity. For that purpose, short peptide variants mimicking proposed cleavage sites within and flanking p6* were designed and analyzed for qualitative and quantitative hydrolysis in vitro. Proviral clones comprising the selected cleavage site mutations were established and analyzed for Gag and Pol processing, virus maturation, and infectivity in cultured cells. Amino-terminal cleavage site mutation caused aberrant processing of nucleocapsid proteins and delayed replication kinetics. Blocking the internal cleavage site resulted in the utilization of a flanking site at a significantly decreased hydrolysis rate in vitro, which however did not affect Gag-Pol processing and viral replication. Although mutations blocking cleavage at the p6* carboxyl terminus yielded noninfectious virions exhibiting severe Gag processing defects, mutations retarding hydrolysis of this cleavage site neither seemed to impact viral infectivity and propagation in cultured cells nor seemed to interfere with overall maturation of released viruses. Interestingly, these mutants were shown to be clearly disadvantaged when challenged with wild-type virus in a dual competition assay. In sum, we conclude that p6* cleavage is absolutely essential to allow complete activation of the PR and subsequent processing of the viral precursors.
A Novel Methyltransferase MethylatesCucumber Mosaic Virus1a Protein and Promotes Systemic Spread
Authors: Kim Min Jung , Huh Sung Un , Ham Byung-Kook , Paek Kyung-Hee 
Published: March 2008

ABSTRACTIn mammalian and yeast systems, methyltransferases have been implicated in the regulation of diverse processes, such as protein-protein interactions, protein localization, signal transduction, RNA processing, and transcription. TheCucumber mosaic virus(CMV) 1a protein is essential not only for virus replication but also for movement. Using a yeast two-hybrid system with tobacco plants, we have identified a novel gene encoding a methyltransferase that interacts with the CMV 1a protein and have designated this geneTcoi1(tobaccoCMV 1a-interacting protein1). Tcoi1 specifically interacted with the methyltransferase domain of CMV 1a, and the expression ofTcoi1was increased by CMV inoculation. Biochemical studies revealed that the interaction of Tcoi1 with CMV 1a protein was direct and that Tcoi1 methylated CMV 1a protein both in vitro and in vivo. The CMV 1a binding activity of Tcoi1 is in the C-terminal domain, which shows the methyltransferase activity. The overexpression of Tcoi1 enhanced the CMV infection, while the reduced expression of Tcoi1 decreased virus infectivity. These results suggest that Tcoi1 controls the propagation of CMV through an interaction with the CMV 1a protein.
“Where our women used to get the food”: cumulative effects and loss of ethnobotanical knowledge and practice; case study from coastal British ColumbiaThis paper was submitted for the Special Issue on Ethnobotany, inspired by the Ethnobotany Symposium organized by Alain Cuerrier, Montreal Botanical Garden, and held in Montreal at the 2006 annual meeting of the Canadian Botanical Association.
Authors: Turner Nancy J. , Turner Katherine L. 
Published: March 2008

Knowledge and practices of indigenous peoples relating to local plants used for food, medicine, materials, and other purposes are threatened in many parts of the world. The reasons for declining knowledge and use of traditional resources are complex and multifaceted. We review a series of case examples of culturally valued food plants in British Columbia and identify a suite of interacting social and environmental factors that have resulted in decreased use of and dwindling cultural knowledge about these plants over the past 150 years. Reasons for this loss include compounding influences of changing knowledge systems owing to religious conversion and residential schools, loss of indigenous languages, loss of time and opportunity for traditional practices owing to participation in the wage economy, increasing urbanization of indigenous populations, loss of access to traditional resources, restriction of management practices for sustaining these resources, and most recently, forces of globalization and industrialization. Efforts to renew and restore traditional practices and relationships with plants and environments must recognize the cumulative effects of these factors and find ways to retain and reinforce the knowledge and practices still held by individuals and communities, to reverse some of the negative influences on cultural retention, and to develop new, relevant, and effective ways to revitalize languages, cultures, and ethnobotanical knowledge within contemporary contexts.
Atmospheric nitrogen dioxide at ambient levels stimulates growth and development of horticultural plants
Authors: Adam Suaad E.H. , Shigeto Jun , Sakamoto Atsushi , Takahashi Misa , Morikawa Hiromichi 
Published: March 2008

We recently discovered that atmospheric nitrogen dioxide (NO2) at ambient levels acts as a signal to Nicotiana plumbaginifolia Viviani, causing these plants to double both their biomass and all of the cell contents. Herein, we addressed whether this effect of NO2 is also observed in various horticultural plants. Lettuce ( Lactuca sativa L.), sunflower ( Helianthus annuus L.), cucumber ( Cucumis sativus L.), and pumpkin ( Cucurbita moschata Duch. ex Lam.) were grown with 50, 200, 100, and 200 µL·L–1, respectively, of air supplemented with stable isotope-labelled (15N) NO2, for 5−6 weeks. Control plants were grown without NO2 (<5 µL·L–1). All plants were irrigated with nonlabelled nitrate. The presence of NO2 doubled both the aboveground and belowground biomass in sunflowers compared with their growth in the absence of NO2, whereas lettuce, cucumber, and pumpkin doubled in aboveground biomass only. Contents per shoot of carbon (C), nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg) were almost doubled during the “NO2-enhanced” growth in lettuce, but not in other plants. Mass spectrometry analysis of 15N/14N indicated that only a minor proportion (0.2%–14%) of total plant N was derived from NO2, implying that exogenous NO2 acts as a signal rather than a significant nutrient source in horticultural plants.
A Relaxed Eddy Accumulation System for Measuring Surface Fluxes of Total Gaseous Mercury
Authors: Bash Jesse O. , Miller David R. 
Published: March 2008

Abstract
A relaxed eddy accumulation (REA) system was designed to continuously measure total gaseous mercury (TGM) fluxes over a forest canopy. TGM concentration measurements were measured at 5-min intervals with a Tekran model 2537A mercury analyzer located above the forest canopy on a walk-up meteorological tower. Ten-minute averages for up- and downdraft mercury concentrations were used to calculate the flux. The multiresolution decomposition technique was used to determine day- and nighttime averaging periods for the turbulent statistics used in the REA technique. This paper documents the REA system for mercury flux measurements and its use over a forest canopy.
The REA system response to the averaging times for the turbulent statistics and corrections to up- and downdraft concentrations are major considerations when using the technique with the Tekran mercury analyzer over a forest canopy. TGM flux data collected from 18 August to 12 September 2005 are used here to demonstrate the capabilities of the REA system to measure both short- (1-h time periods) and long-term flux dynamics. During the demonstration period the TGM median flux was 21.9 ± 32.6 ng m−2 h−1 and the median atmospheric TGM concentrations were 1.34 ± 0.13 ng m−2 h−1. Maximum short-term TGM evasive fluxes occurred during the daylight hours with minimums during the nighttime. A consistent bimodal emission pattern was observed during the daytime emissions over the canopy. The first peak occurred immediately following the evaporation of the nighttime dew on the canopy and the second peak occurred in the late afternoon.
Application of Aerosondes to Melt-Pond Observations over Arctic Sea Ice
Authors: Inoue Jun , Curry Judith A. , Maslanik James A. 
Published: March 2008

Abstract
Continuous observation of sea ice using a small robotic aircraft called the Aerosonde was made over the Arctic Ocean from Barrow, Alaska, on 20–21 July 2003. Over a region located 350 km off the coast of Barrow, images obtained from the aircraft were used to characterize the sea ice and to determine the fraction of melt ponds on both multiyear and first-year ice. Analysis of the data indicates that melt-pond fraction increased northward from 20% to 30% as the ice fraction increased. However, the fraction of ponded ice was over 30% in the multiyear ice zone while it was about 25% in the first-year ice zone. A comparison with a satellite microwave product showed that the ice concentration derived from the Advanced Microwave Scanning Radiometer for the Earth Observing System (AMSR-E) has a negative bias of 7% due to melt ponds. These analyses demonstrate the utility of recent advances in unmanned aerial vehicle (UAV) technology for monitoring and interpreting the spatial variations in the sea ice with melt ponds.
The Hydroclimatology of Kuwait: Explaining the Variability of Rainfall at Seasonal and Interannual Time Scales
Authors: Marcella Marc P. , Eltahir Elfatih A. B. 
Published: March 2008

Abstract
This paper presents an analysis of the spatial, seasonal, and interannual variabilities of Kuwaiti rainfall. Based on an analysis of rain gauge, as well as satellite, datasets, it is estimated that about 110–190 mm of rainfall occurs annually in Kuwait, depending on the dataset sampled. The corresponding estimates for the standard deviations of the annual rainfall are about 40–70 mm. Discrepancies between values arise from the different techniques used in constructing each dataset. Moreover, the spatial distribution of annual rainfall features a gradual increase from the southwest to the northeast. A distinct rainy season occurs from November to April, with double peaks in January and March. In addition, the seasonal variability of rainfall is associated with shifts in patterns of midlatitude storm tracks, which propagate southward toward the Middle East during the winter and spring season. These trends are characterized using estimates of the spatial correlations of rainfall in Kuwait with the surrounding region. At the interannual time scale, significant correlation is found between the tropical El Niño–Southern Oscillation (ENSO) and annual rainfall anomalies. Similar weak correlations are found between midlatitude rainfall in Europe and rainfall in Kuwait. The weak connections observed with both tropical and midlatitude atmospheric systems are consistent with the fact that Kuwait is located in the transitional zone between the tropics and midlatitudes.
Propagation of Wind Energy into the Deep Ocean through a Fully Turbulent Mesoscale Eddy Field
Authors: Danioux Eric , Klein Patrice , Rivière Pascal 
Published: March 2008

Abstract
The authors analyze the 3D propagation of wind-forced near-inertial motions in a fully turbulent mesoscale eddy field with a primitive equation numerical model. Although the wind stress is uniform, the near-inertial motion field quickly becomes spatially heterogeneous, involving horizontal scales much smaller than the eddy scales. Analysis confirms that refraction by the eddy relative vorticity is the main mechanism responsible for the horizontal distortion of the near-inertial motions, which subsequently triggers their vertical propagation. An important result is the appearance of two maxima of near-inertial vertical velocity (both with rms values reaching 40 m day−1): one at a depth of 100 m and another unexpected one much below the main thermocline around 1700 m. The shallow maximum, captured by the highest vertical normal modes, involves near-inertial motions with a spatial heterogeneity close to the eddy vorticity gradient field. These characteristics match analytical results obtained with Young and Ben Jelloul’s approach. The deep maximum, captured by the lowest vertical normal modes, involves superinertial motions with a frequency of twice the inertial frequency and much smaller horizontal scales. Because of these characteristics, not anticipated by previous analytical studies, these superinertial motions may represent an energy source for small-scale mixing through a mechanism not taken into account in the present study: the parametric subharmonic instability (PSI). This reveals a pathway by which wind energy may have a significant impact on small-scale mixing in the deep interior. Further studies that explicitly take into account PSI are needed to estimate this potential impact.
On the Vertical Structure of Wind-Driven Sea Currents
Authors: Kudryavtsev Vladimir , Shrira Victor , Dulov Vladimir , Malinovsky Vladimir 
Published: March 2008

Abstract
The vertical structure of wind-driven sea surface currents and the role of wind-wave breaking in its formation are investigated by means of both field experiments and modeling. Analysis of drifter measurements of surface currents in the uppermost 5-m layer at wind speeds from 3 to 15 m s−1 is the experimental starting point of this study. The velocity gradients beneath the surface are found to be 2 to 5 times weaker than in the “wall” boundary layer. Surface wind drift (identified via drift of an artificial slick) with respect to 0.5-m depths is about 0.7%, which is even less than the velocity defect over the molecular sublayer in the wall boundary layer at a smooth surface. To interpret the data, a semiempirical model describing the effect of wave breaking on wind-driven surface currents and subsurface turbulence is proposed. The model elaborates on the idea of direct injection of momentum and energy from wave breaking (including microscale breaking) into the water body. Momentum and energy transported by breaking waves into the water significantly enhance the turbulent mixing and considerably decrease velocity shears as compared to the wall boundary layer. No “artificial” surface roughness scale is needed in the model. From the experimental fact of the existence of cool temperature skin at the sea surface, it is deduced that there is a molecular sublayer at the water side of the sea surface with a thickness that depends on turbulence intensity just beneath the surface. The model predictions are consistent with the reported and other available experimental data.
From Model-Based Parameterizations to Lookup Tables: An EOF Approach
Authors: Leoncini Giovanni , Pielke Roger A. , Gabriel Philip 
Published: March 2008

Abstract
The goal of this study is to transform the Harrington radiation parameterization into a transfer scheme or lookup table, which provides essentially the same output (heating rate profile and short- and longwave fluxes at the surface) at a fraction of the computational cost. The methodology put forth here does not introduce a new parameterization simply derived from the Harrington scheme but, rather, shows that given a generic parameterization it is possible to build an algorithm, largely not based on the physics, that mimics the outcome of the parent parameterization. The core concept is to compute the empirical orthogonal functions (EOFs) of all of the input variables of the parent scheme, run the scheme on the EOFs, and express the output of a generic input sounding exploiting the input–output pairs associated with the EOFs. The weights are based on the difference between the input and EOFs water vapor mixing ratios. A detailed overview of the algorithm and the development of a few transfer schemes are also presented. Results show very good agreement (r &gt; 0.91) between the different transfer schemes and the Harrington radiation parameterization with a very significant reduction in computational cost (at least 95%).
Crisis as change strategy in public organizations
Authors: Rochet Claude , Keramidas Olivier , Bout Lugdivine 
Published: March 2008

According to the common vision, the public sector is strongly change-resistant. Is this justified? In this research, we adopt the Northian distinction between institutions and organizations by focusing on the latter and their capability for change. We try to identify the strategically most effective lever to operate an organizational change in the public sector. We first review the literature on change strategies and their setting in the context of public organizations. Then, we synthesize the conclusions of four case studies around a question: `Is building public organizations capable of co-evolution with their environment feasible?' We will present some strategies of evolution for public organizations, in response to a state of crisis, constituting a vector of organizational change. We conclude on the interest of considering crisis as a vector of organizational change in public organizations. Points for practitioners The public sector is commonly said to be change-resistant. Through case studies we prove this opinion to be false and that change aptitudes are identical to other organizations. We emphasize crises that provide particular opportunities that allow us to offset the absence of performance evaluation and the lack of feedback from the market, and we underline possible change strategies.
Explaining change in the Mexican public sector: the limits of New Public Management
Authors: Cejudo Guillermo M. 
Published: March 2008

The Mexican public sector has undergone significant transformations in recent decades. This article argues against the view that these changes are the result of New Public Management-style reforms. Even though the Mexican government has applied some of the tools associated with this paradigm, the essential NPM doctrines — granting more autonomy to public agencies and government officials, and using market mechanisms to promote competition in the public sector — have been absent from the agenda. The Mexican experience exposes two erroneous assumptions in the international debate about NPM: that there is a global trend of similar national reforms and that every change in the public sector is part of this new paradigm. Instead, the changes in the Mexican public sector are the result of incremental adjustments to two broader domestic processes: economic liberalization and political democratization — which have led to a smaller and relatively more accountable administration. Points for practitioners This article suggests that not all reforms are the result of New Public Management initiatives. It points towards alternative explanations for change in the Mexican public sector and identifies political democratization and economic liberalization as the main sources of change. This view challenges existing accounts of public sector change in developing countries and suggests a more complex process of reform. The main lesson for practitioners is that, when analysing reform experiences, they should look at the underlying causal processes rather than at the official rhetoric. Moreover, the article reminds practitioners that NPM is only one among several sources of doctrines for changing the public administration.