bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome of Deerpox Virus
Authors: Afonso C. L. , Delhon G. , Tulman E. R. , Lu Z. , Zsak A. , Becerra V. M. , Zsak L. , Kutish G. F. , Rock D. L. 
Published: December 2004

ABSTRACTDeerpox virus(DPV), an uncharacterized and unclassified member of thePoxviridae, has been isolated from North American free-ranging mule deer (Odocoileus hemionus) exhibiting mucocutaneous disease. Here we report the genomic sequence and comparative analysis of two pathogenic DPV isolates, W-848-83 (W83) and W-1170-84 (W84). The W83 and W84 genomes are 166 and 170 kbp, containing 169 and 170 putative genes, respectively. Nucleotide identity between DPVs is 95% over the central 157 kbp. W83 and W84 share similar gene orders and code for similar replicative, structural, virulence, and host range functions. DPV open reading frames (ORFs) with putative virulence and host range functions include those similar to cytokine receptors (R), including gamma interferon receptor (IFN-γR), interleukin 1 receptor (IL-1R), and type 8 CC-chemokine receptors; cytokine binding proteins (BP), including IL-18BP, IFN-α/βBP, and tumor necrosis factor binding protein (TNFBP); serpins; and homologues of vaccinia virus (VACV) E3L, K3L, and A52R proteins. DPVs also encode distinct forms of major histocompatibility complex class I, C-type lectin-like protein, and transforming growth factor β1 (TGF-β1), a protein not previously described in a mammalian chordopoxvirus. Notably, DPV encodes homologues of cellular endothelin 2 and IL-1R antagonist, novel poxviral genes also likely involved in the manipulation of host responses. W83 and W84 differ from each other by the presence or absence of five ORFs. Specifically, homologues of a CD30 TNFR family protein, swinepox virus SPV019, and VACV E11L core protein are absent in W83, and homologues of TGF-β1 and lumpy skin disease virus LSDV023 are absent in W84. Phylogenetic analysis indicates that DPVs are genetically distinct from viruses of other characterized poxviral genera and that they likely comprise a new genus within the subfamilyChordopoxvirinae.
Analysis of Translational Initiation in Coxsackievirus B3 Suggests an Alternative Explanation for the High Frequency of R
+4
in the Eukaryotic Consensus Motif
Authors: Harkins Stephanie , Cornell Christopher T. , Whitton J. Lindsay 
Published: December 2004

ABSTRACT

Translational initiation of most eukaryotic mRNAs occurs when a preinitiation complex binds to the 5′ cap, scans the mRNA, and selects a particular AUG codon as the initiation site. Selection of the correct initiation codon relies, in part, on its flanking residues; in mammalian cells, the core of the “Kozak” consensus is R
−3
CCAUGG
+4
(R = purine; the A residue is designated position +1). The R
−3
is considered the most important flanking residue, followed by G
+4
. Picornaviral mRNAs differ from most cellular mRNAs in several ways; they are uncapped, and they contain an internal ribosome entry site that allows the ribosome to bind near the initiation codon. The initiation codon of coxsackievirus B3 (CVB3) is flanked by both R
−3
and G
+4
(AAAATGG). Here, we report the construction of full-length CVB3 genomes that vary at these two positions, and we evaluate the effects of these variant sequences in vitro, in tissue culture cells, and in vivo. A virus with an A→C transversion at position −3 replicates as well as wild-type CVB3, both in tissue culture and in vivo. This virus is highly pathogenic, and its sequence is stable throughout the course of an in vivo infection. Furthermore, the in vitro translation products from this RNA are very similar to the wild type. Thus, R
−3
—thought to be the most functionally important component of the Kozak consensus—appears to be dispensable in CVB3. In contrast, a G-to-C transversion at G
+4
is lethal; RNAs carrying this mutation fail to generate infectious virus either in tissue culture or in vivo. However, in vitro analysis indicates that G
+4
has only a marginal effect on translational initiation, especially if R
−3
is present; instead, the G
+4
is required mainly because the second triplet of the polyprotein open reading frame must encode glycine, without which infectious virus production cannot proceed. In summary, our data indicate that CVB3 remains viable, even in vivo, in the absence of R
−3
, and we propose that the most important factor contributing to the high frequency of G
+4
—not only in CVB but also in other eukaryotic mRNAs, and thus in the consensus motif itself—may be the constraint upon the second amino acid rather than the requirements for translational initiation.
Intensive education combined with low tech ergonomic intervention does not prevent low back pain in nurses
Authors: Hartvigsen J , Lauritzen S , Lings S , Lauritzen T 
Published: December 2004

Aims:To evaluate the effectiveness of an intensive educational and low-tech ergonomic intervention programme aimed at reducing low back pain (LBP) among home care nurses and nurses’ aids.Methods:In 1999, 345 home care nurses and nurses’ aids in four Danish municipalities were studied. Participants in two municipalities constituted the intervention group and participants in the other two served as the control group. In the intervention group, participants were divided into small groups, each of which was assigned one specially trained instructor. During weekly meetings participants were educated in body mechanics, patient transfer, and lifting techniques, and use of low-tech ergonomic aids. In the control group, participants attended a one time only three hour instructional meeting. Information on LBP was collected using the Standardised Nordic Questionnaire supplemented with information on number of episodes of LBP and care seeking due to LBP during the past year.Results:A total of 309 nurses and nurses’ aids returned the questionnaire at baseline and 255 at follow up in August 2001. At follow up, no significant differences were found between the two groups for any of the LBP variables, and both groups thought that education in patient transfer techniques had been helpful. Within group changes in LBP status was not related to the intervention or to satisfaction with participating in the project.Conclusions:Intensive weekly education in body mechanics, patient transfer techniques, and use of low-tech ergonomic equipment was not superior to a one time only three hour instructional meeting for home care nurses and nurses’ aids.
Employment characteristics and job loss in patients awaiting surgery on the hip or knee
Authors: Palmer K T , Milne P , Poole J , Cooper C , Coggon D 
Published: December 2004

Aims:To investigate the factors, including size of organisation, associated with job loss in patients awaiting surgery to the hip or knee joint.Methods:A questionnaire was mailed to 498 consecutive patients of working age listed at a district general hospital for major joint replacement, knee arthroscopy, or periacetabular osteotomy. Questions were asked about level of physical disability, duration of symptoms, employment circumstances at the time the joint problem began, and job changes since the onset of symptoms with their reasons. Analysis focused on those in work when their health problem began. Cox regression was used to examine risk factors for job loss related and unrelated to the joint problem, and results were summarised as adjusted hazard ratios (HRs) with 95% confidence intervals (95% CI).Results:Responses came from 370 (74%) of those mailed, including 278 who were in work when their joint problem began. Of these, 82 (30%) had left their original job mainly or partly because of their joint disorder. Such job loss was more common in those employed in small businesses (HR for <10v⩾10 employees: 1.9, 95% CI 1.2–3.0) and those whose work involved standing for >2 hours per day (HR 2.7, 95% CI 1.2–6.1) No similar associations were found when jobs were left for other reasons. After adjustment for non-sedentary work the association with small business employment remained but was weaker (HR 1.5, 95% CI 0.9–2.5). Modifications to work and access to occupational health advice were not associated with better job retention.Conclusions:In subjects with disabling hip or knee disease, job retention is poorer in those from small companies—a matter of concern given the rising prevalence of serious joint disease in the British workforce and the tendency of businesses to downsize and subcontract services to smaller enterprises.
Task based exposure assessment in ergonomic epidemiology: a study of upper arm elevation in the jobs of machinists, car mechanics, and house painters
Authors: Svendsen S W , Mathiassen S E , Bonde J P 
Published: December 2004

Aims:To explore the precision of task based estimates of upper arm elevation in three occupational groups, compared to direct measurements of job exposure.Methods:Male machinists (n = 26), car mechanics (n = 23), and house painters (n = 23) were studied. Whole day recordings of upper arm elevation were obtained for four consecutive working days, and associated task information was collected in diaries. For each individual, task based estimates of job exposure were calculated by weighting task exposures from a collective database by task proportions according to the diaries. These estimates were validated against directly measured job exposures using linear regression. The performance of the task based approach was expressed through the gain in precision of occupational group mean exposures that could be obtained by adding subjects with task based estimates to a group of subjects with measured job exposures in a “validation” design.Results:In all three occupations, tasks differed in mean exposure, and task proportions varied between individuals. Task based estimation proved inefficient, with squared correlation coefficients only occasionally exceeding 0.2 for the relation between task based and measured job exposures. Consequently, it was not possible to substantially improve the precision of an estimated group mean by including subjects whose job exposures were based on task information.Conclusions:Task based estimates of mechanical job exposure can be very imprecise, and only marginally better than estimates based on occupation. It is recommended that investigators in ergonomic epidemiology consider the prospects of task based exposure assessment carefully before placing resources at obtaining task information. Strategies disregarding tasks may be preferable in many cases.
Simulation of Effects of Atmospheric Aerosols on Deep Turbulent Convective Clouds Using a Spectral Microphysics Mixed-Phase Cumulus Cloud Model. Part II: Sensitivity Study
Authors: Khain A. , Pokrovsky A. 
Published: December 2004

Abstract
Effects of different size distributions of cloud condensational nuclei (CCN) on the evolution of deep convective clouds under dry unstable continental thermodynamic conditions are investigated using the spectral microphysics Hebrew University Cloud Model (HUCM). In particular, high supercooled water content just below the level of homogeneous freezing, as well as an extremely high concentration of ice crystals above the level, observed recently by Rosenfeld and Woodley at the tops of growing clouds in Texas, were successfully reproduced.
Numerical experiments indicate a significant decrease in accumulated precipitation in smoky air. The fraction of warm rain in the total precipitation amount increases with a decrease in the CCN concentration. The fraction is low in smoky continental air and is dominating in clean maritime air. As warm rain is a smaller fraction of total precipitation, the decrease in the accumulated rain amount in smoky air results mainly from the reduction of melted precipitation.
It is shown that aerosols significantly influence cloud dynamics leading to the elevation of the level of precipitating particle formation. The falling down of these particles through dry air leads to a loss in precipitation. Thus, close coupling of microphysical and dynamical aerosol effects leads to the rain suppression from clouds arising in dry smoky air.
The roles of freezing, CCN penetration through lateral cloud boundaries, and turbulent effects on cloud particles collisions are evaluated.
Results, obtained using spectral microphysics, were compared with those obtained using two well-known schemes of bulk parameterization. The results indicate that the bulk parameterization schemes do not reproduce well the observed cloud microstructure.
Solar Radiation Budget from the MRI Radiometers for Clear and Cloudy Air Columns within ARESE II
Authors: Asano Shoji , Uchiyama Akihiro , Yamazaki Akihiro , Kuchiki Katsuyuki 
Published: December 2004

Abstract
As an international collaborative research activity within the Japanese Cloud-Climate Study (JACCS) program, the authors participated in the second Atmospheric Radiation Measurement (ARM) Enhanced Shortwave Experiment (ARESE II) using the Meteorological Research Institute (MRI) radiometers. This paper describes results of ARESE II, as well as specifications and calibration of the MRI radiometers. The solar radiation budget for 2 days of typical clear sky (27 February and 20 March 2000) and overcast sky (3 and 21 March 2000) has been analyzed using spatially collocated, total-band solar irradiances measured by the MRI pyranometers (Kipp & Zonen CM21). These were installed on a Twin Otter aircraft, and deployed at the ARM Southern Great Planes Central Facility site. On average, the clear-sky and overcast-sky air columns between the surface and the Twin Otter flight level of 7 km absorbed about 13% ± 2% and 20% ± 3%, respectively, of the total-band solar radiation incident on the column top. The measured solar radiation budgets agree well with those computed for models of clear and cloudy atmospheres. The present results indicate no evidence of anomalous solar absorption for either the clear- or cloudy-sky cases. It is suggested that about half of the observed absorption enhancement of 7% for the overcast-sky cases could be caused by the presence of larger water vapor, compared with the clear-sky cases, and that the other half could be caused by increased absorption within and above the rather low cloud layers.
Mixing Layer Formation near the Tropopause Due to Gravity Wave–Critical Level Interactions in a Cloud-Resolving Model
Authors: Moustaoui Mohamed , Joseph Binson , Teitelbaum Hector 
Published: December 2004

Abstract
A plausible mechanism for the formation of mixing layers in the lower stratosphere above regions of tropical convection is demonstrated numerically using high-resolution, two-dimensional (2D), anelastic, nonlinear, cloud-resolving simulations. One noteworthy point is that the mixing layer simulated in this study is free of anvil clouds and well above the cloud anvil top located in the upper troposphere. Hence, the present mechanism is complementary to the well-known process by which overshooting cloud turrets causes mixing within stratospheric anvil clouds. The paper is organized as a case study verifying the proposed mechanism using atmospheric soundings obtained during the Central Equatorial Pacific Experiment (CEPEX), when several such mixing layers, devoid of anvil clouds, had been observed. The basic dynamical ingredient of the present mechanism is (quasi stationary) gravity wave–critical level interactions, occurring in association with a reversal of stratospheric westerlies to easterlies below the tropopause region. The robustness of the results is shown through simulations at different resolutions. The insensitivity of the qualitative results to the details of the subgrid scheme is also evinced through further simulations with and without subgrid mixing terms. From Lagrangian reconstruction of (passive) ozone fields, it is shown that the mixing layer is formed kinematically through advection by the resolved-scale (nonlinear) velocity field.
Effects of Large Eddies on the Structure of the Marine Boundary Layer under Strong Wind Conditions
Authors: Ginis Isaac , Khain Alexander P. , Morozovsky Elena 
Published: December 2004

AbstractA model of the atmospheric boundary layer (BL) is presented that explicitly calculates a two-way interaction of the background flow and convective motions. The model is utilized for investigation of the formation of large eddies (roll vortices) and their effects on the structure of the marine boundary layer under conditions resembling those of tropical cyclones. It is shown that two main factors controlling the formation of large eddies are the magnitude of the background wind speed and air humidity, determining the cloud formation and latent heat release. When the wind speed is high enough, a strong vertical wind shear develops in the lower part of the BL, which triggers turbulent mixing and the formation of a mixed layer. As a result, the vertical profiles of velocity, potential temperature, and mixing ratio in the background flow are modified to allow for the development of large eddies via dynamic instability. Latent heat release in clouds was found to be the major energy source of large eddies. The cloud formation depends on the magnitude of air humidity.The most important manifestation of the effects of large eddies is a significant increase of the near-surface wind speed and evaporation from the sea surface. For strong wind conditions, the increase of the near-surface speed can exceed 10 m s−1 and evaporation from the sea surface can double. These results demonstrate an important role large eddies play in the formation of BL structure in high wind speeds. Inclusion of these effects in the BL parameterizations of tropical cyclone models may potentially lead to substantial improvements in the prediction of storm intensity.
A New Heuristic Lagrangian Marine Boundary Layer Cloud Model
Authors: Park Sungsu , Leovy Conway B. , Rozendaal Margaret A. 
Published: December 2004

Abstract
A new heuristic model of stratocumulus cloudiness in the inversion-capped marine boundary layer is developed and tested. The essential ingredient is a new method for predicting the statistical distribution of temperature and specific humidity at the inversion base under partially decoupled conditions along steady-state marine boundary layer (MBL) trajectories. MBL decoupling is parameterized as an increasing function of the height difference between the inversion base and lifting condensation level (LCL) of the mixed-layer air. Required inputs are sea surface temperature (SST), free air (above inversion) temperature and humidity, subsidence velocity, and mean boundary layer wind speed. Upstream boundary conditions must also be specified but have little influence at sufficient downstream distances (&gt;2000 km).
The model is applied to the cold advection regime of the northeastern subtropical Pacific and to both warm and cold advection regimes of the eastern equatorial Pacific Ocean. The model is conceptually simple and avoids explicit calculation of several important physical processes. Nevertheless, it is at least qualitatively successful in predicting both the climatological mean properties and climate anomaly variations of MBL stratocumulus in both regions. These results suggest that, regardless of other properties, successful MBL stratocumulus models will need to accurately predict inversion base height and the LCL and they will have to account for downstream memory effects.
Simulation of Effects of Atmospheric Aerosols on Deep Turbulent Convective Clouds Using a Spectral Microphysics Mixed-Phase Cumulus Cloud Model. Part I: Model Description and Possible Applications
Authors: Khain A. , Pokrovsky A. , Pinsky M. , Seifert A. , Phillips V. 
Published: December 2004

Abstract
An updated version of the spectral (bin) microphysics cloud model developed at the Hebrew University of Jerusalem [the Hebrew University Cloud Model (HUCM)] is described. The model microphysics is based on the solution of the equation system for size distribution functions of cloud hydrometeors of seven types (water drops, plate-, columnar-, and branch-like ice crystals, aggregates, graupel, and hail/frozen drops) as well as for the size distribution function of aerosol particles playing the role of cloud condensational nuclei (CCN). Each size distribution function contains 33 mass bins.
The conditions allowing numerical reproduction of a narrow droplet spectrum up to the level of homogeneous freezing in deep convective clouds developed in smoky air are discussed and illustrated using as an example Rosenfeld and Woodley's case of deep Texas clouds.
The effects of breakup on precipitation are illustrated by the use of a new collisional breakup scheme. Variation of the microphysical structure of a melting layer is illustrated by using the novel melting procedure.
It is shown that an increase in the aerosol concentration leads to a decrease in precipitation from single clouds both under continental and maritime conditions. To provide similar precipitation, a cloud developed in smoky air should have a higher top height. The mechanisms are discussed through which aerosols decrease precipitation efficiency. It is shown that aerosols affect the vertical profile of the convective heating caused by latent heat release.
Mechanisms of Up-Valley Winds
Authors: Rampanelli Gabriele , Zardi Dino , Rotunno Richard 
Published: December 2004

Abstract
The basic physical mechanisms governing the daytime evolution of up-valley winds in mountain valleys are investigated using a series of numerical simulations of thermally driven flow over idealized three-dimensional topography. The three-dimensional topography used in this study is composed of two, two-dimensional topographies: one a slope connecting a plain with a plateau and the other a valley with a horizontal floor. The present two-dimensional simulations of the valley flow agree with results of previous investigations in that the heated sidewalls produce upslope flows that require a compensating subsidence in the valley core bringing down potentially warmer air from the stable free atmosphere. In the context of the three-dimensional valley–plain simulations, the authors find that this subsidence heating in the valley core is the main contributor to the valley– plain temperature contrast, which, under the hydrostatic approximation, is the main contributor to the valley– plain pressure difference that drives the up-valley wind.
Effects of Administration of Exogenous Growth Factors on Biomechanical Properties of the Elongation-type Anterior Cruciate Ligament Injury with Partial Laceration
Authors: Kondo Eiji , Yasuda Kazunori , Yamanaka Masanori , Minami Akio , Tohyama Harukazu 
Published: December 2004

Background No studies have been conducted to clarify the in vivo effect of growth factor application on healing in the injured anterior cruciate ligament. Hypothesis Administration of exogenous growth factors significantly increases the structural properties of the injured anterior cruciate ligament. Study Design Controlled laboratory study. Methods Thirty-six rabbits were randomly divided into 4 groups of 9 animals each after an overstretched injury was made in the right anterior cruciate ligament. In group 1, no treatment was applied around the injured anterior cruciate ligament. In group 2, 0.2 mL fibrin sealant was applied around it. In group 3, 4 ng transforming growth factor–β1 mixed with 0.2 mL fibrin sealant was applied. In group 4, 20 μg platelet-derived growth factor–BB mixed with 0.2 mL fibrin sealant was applied. Each rabbit was sacrificed at 12 weeks after the surgery. In addition, 9 knees randomly harvested from all the left knees were used to obtain normal control data. The femur–anterior cruciate ligament–tibia complex specimens were biomechanically and histologically evaluated. Results Concerning the maximum load and the stiffness, group 3 was significantly greater than groups 1 and 2, whereas there were no significant differences among groups 1, 2, and 4. Groups 1, 2, 3, and 4 were significantly lower than the control group. Conclusions The application of 4 ng transforming growth factor–β1 significantly enhances healing in the injured anterior cruciate ligament. Clinical Relevance Administration of certain growth factors is of value to be studied as one of the future therapeutic options for the overstretched anterior cruciate ligament injury.