bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Cytomegalovirus Infection Alters the Expression of Cellular MicroRNA Species That Affect Its Replication
Authors: Wang Fu-Zhang , Weber Frank , Croce Carlo , Liu Chang-Gong , Liao Xudong , Pellett Philip E. 
Published: July 2008

ABSTRACT
The human genome encodes over 500 microRNAs (miRNAs), small RNAs (19 to 26 nucleotides [nt]) that regulate the expressions of diverse cellular genes. Many cellular processes are altered through a variety of mechanisms by human cytomegalovirus (HCMV) infection. We asked whether HCMV infection leads to changes in the expression of cellular miRNAs and whether HCMV-regulated miRNAs are important for HCMV replication. Levels of most miRNAs did not change markedly during infection, but some were positively or negatively regulated. Patterns of miRNA expression were linked to the time course of infection. Some similarly reregulated miRNAs share identical or similar seed sequences, suggesting coordinated regulation of miRNA species that have shared targets. miRNAs miR-100 and miR-101 were chosen for further analyses based on their reproducible changes in expression after infection and on the basis of having predicted targets in the 3′ untranslated regions (3′-UTR) of genes encoding components of the mammalian target of rapamycin (mTOR) pathway, which is important during HCMV infection. Reporter genes that contain the 3′-UTR of mTOR (predicted targets for miR-100 and miR-101) or raptor (a component of the mTOR pathway; predicted site for miR-100) were constructed. Mimics of miR-100 and miR-101 inhibited expression from the mTOR construct, while only miR-100 inhibited the raptor construct. Together, miR-100 and miR-101 reduced mTOR protein levels. While the miR-100 and miR-101 mimics individually modestly inhibited production of infectious progeny, much greater inhibition was achieved with a combination of both (33-fold). Our key finding is that HCMV selectively manipulates the expression of some cellular miRNAs to help its own replication.
Analysis of Natural Sequence Variation and Covariation in Human Immunodeficiency Virus Type 1 Integrase
Authors: Myers Richard E. , Pillay Deenan 
Published: July 2008

ABSTRACT
Human immunodeficiency virus type 1 (HIV-1) integrase inhibitors are in clinical trials, and raltegravir and elvitegravir are likely to be the first licensed drugs of this novel class of HIV antivirals. Understanding resistance to these inhibitors is important to maximize their efficacy. It has been shown that natural variation and covariation provide valuable insights into the development of resistance for established HIV inhibitors. Therefore, we have undertaken a study to fully characterize natural polymorphisms and amino acid covariation within an inhibitor-naïve sequence set spanning all defined HIV-1 subtypes. Inter- and intrasubtype variation was greatest in a 50-amino-acid segment of HIV-1 integrase incorporating the catalytic aspartic acid codon 116, suggesting that polymorphisms affect inhibitor binding and pathways to resistance. The critical mutations that determine the resistance pathways to raltegravir and elvitegravir (N155H, Q148K/R/H, and E92Q) were either rare or absent from the 1,165-sequence data set. However, 25 out of 41 mutations associated with integrase inhibitor resistance were present. These mutations were not subtype associated and were more prevalent in the subtypes that had been sampled frequently within the database. A novel modification of the Jaccard index was used to analyze amino acid covariation within HIV-1 integrase. A network of 10 covarying resistance-associated mutations was elucidated, along with a further 15 previously undescribed mutations that covaried with at least two of the resistance positions. The validation of covariation as a predictive tool will be dependent on monitoring the evolution of HIV-1 integrase under drug selection pressure.
Snow Cover Characteristics over the Main Russian River Basins as Represented by Reanalyses and Measured Data
Authors: Khan V. , Holko L. , Rubinstein K. , Breiling M. 
Published: July 2008

Abstract
Snow water equivalents (SWE) produced by the National Centers for Environmental Prediction–U.S. Department of Energy (NCEP–DOE) and 40-yr European Centre for Medium-Range Weather Forecasts (ERA-40) reanalyses and snow depths (SD) produced by the 25-yr Japanese “JRA-25” reanalysis over the main Russian river basins for 1979–2000 were examined against measured data. The analysis included comparisons of mean basin values and correlation of anomalies, as well as seasonal and interannual variabilities and trends. ERA-40 generally provided better estimates of mean SWE values for river basins than did the NCEP–DOE reanalysis. Mean SD values from the JRA-25 reanalysis were systematically underestimated. The best correlations among the anomalies were given by ERA-40, followed by JRA-25. All reanalyses reproduced seasonal variability well, although the differences in absolute values varied substantially. The highest differences were typically connected with the snowmelt period (April and May). Interannual variability confirmed the errors of ERA-40 and JRA-25 in 1992–94 and 1979–83, respectively. Otherwise, the reproduction of the interannual variability of SWE and SD was reasonable. Strong biases in SD data from JRA-25 that decrease with time induce artificial positive trends. Significant underestimations of SWE data by ERA-40 for 1991–94 influenced the values of the trends. NCEP–DOE reasonably represented the trend found in measured data. In general, the highest discrepancies between measured and reanalysis data were found for the northern European and eastern Asian rivers (Pechora, Lena, and Amur). The assessment of the quality of SWE and SD reanalysis data can help potential users in the selection of a particular reanalysis as being appropriate to the purpose of their studies.
Summertime Low-Level Jets over the High-Latitude Arctic Ocean
Authors: ReVelle Douglas O. , Nilsson E. Douglas 
Published: July 2008

Abstract
The application of a simple analytic boundary layer model developed by Thorpe and Guymer did not produce good agreement with observational data for oceanic low-level jet observations even though this model has worked well for the predictions of low-level jets over continental surfaces. This failure to properly predict the boundary layer wind maxima was very puzzling because more detailed numerical boundary layer models have properly predicted these low-level oceanic wind maxima. To understand the reasons for its failure to explain the ocean observations, the authors modified the frictional terms in the horizontal linear momentum equations of Thorpe and Guymer, using a standard eddy viscosity closure technique instead of the Rayleigh friction parameterization originally used. This improvement in the modeling of the dissipation terms, which has resulted in the use of an enhanced Rayleigh friction parameterization in the horizontal momentum equations, modified the boundary layer winds such that the continental predictions remained nearly identical to those predicted previously using the Thorpe and Guymer model while the oceanic predictions have now become more representative of the measured wind speed from recent Arctic expeditions.
On the Estimation of Trends in Annual Rainfall Using Paired Gauge Observations
Authors: Paldor Nathan 
Published: July 2008

Abstract
A method was recently proposed for evaluating the impact of a perturbation, such as air pollution or urbanization, on the precipitation at a location by calculating the ratio between the precipitation at the perturbed location and that at a location believed to be unperturbed. However, this method may be inappropriate because of the high degree of variability of precipitation at each of the stations. To explore the validity of this approach, noisy annual rainfall records are generated numerically in an upwind, unperturbed station and in a downwind, perturbed station, and the time series of ratio between the annual rainfalls in the two stations is analyzed. The noisy rainfall records are 50 yr long, and the imposed trend for the downwind, perturbed station is −2 mm yr−1 while at the upwind station the variations in annual rainfall are purely noisy. Many pairs of noisy rainfall records are numerically generated (each pair constitutes an experiment), and in every experiment the slope of the linear best fit to the rainfall ratio yields an estimate of the trend of rainfall at the perturbed station. In the absence of noise, the trend of the rainfall ratio is explicitly related to the trend of rainfall at the perturbed station, but the natural rainfall variation at the stations completely masks this explicit relationship. The results show that in some experiments the trend line of the rainfall ratio has the opposite sign to the imposed trend and that in only about one-half of the experiments does the ratio’s trend line lie within ±75% of the imposed trend. Trend estimates within ±25% of the imposed trend are obtained in less than one-quarter of the experiments. This result casts doubt on the generality and validity of using trends of rainfall ratio between two stations to estimate trends of precipitation in one of these stations.
Toward a Fully Parametric Retrieval of the Nonraining Parameters over the Global Oceans
Authors: Elsaesser Gregory S. , Kummerow Christian D. 
Published: July 2008

Abstract
In light of the upcoming launch of the Global Precipitation Measurement (GPM) mission, a parametric retrieval algorithm of the nonraining parameters over the global oceans is developed with the ability to accommodate all currently existing and planned spaceborne microwave window channel sensors and imagers. The physical retrieval is developed using all available sensor channels in a full optimal estimation inversion. This framework requires that retrieved parameters be physically consistent with all observed satellite radiances regardless of the sensor being used. The retrieval algorithm has been successfully applied to the Advanced Microwave Scanning Radiometer-Earth Observing System (AMSR-E), the Special Sensor Microwave Imager (SSM/I), and the Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI) with geophysical parameter retrieval results comparable to independent studies using sensor-optimized algorithms. The optimal estimation diagnostics characterize the retrieval further, providing errors associated with each of the retrieved parameters, indicating whether the retrieved state is physically consistent with observed radiances, and yielding information on how well simulated radiances agree with observed radiances. This allows for the quantitative assessment of potential calibration issues in either the model or sensor. In addition, there is an expected, consistent response of these diagnostics based on the scene being observed, such as in the case of a raining scene, allowing for the emergence of a rainfall detection scheme providing a new capability in rainfall identification for use in passive microwave rainfall and cloud property retrievals.
Source Inversion for Contaminant Plume Dispersion in Urban Environments Using Building-Resolving Simulations
Authors: Chow Fotini Katopodes , Kosović Branko , Chan Stevens 
Published: July 2008

AbstractThe ability to determine the source of a contaminant plume in urban environments is crucial for emergency-response applications. Locating the source and determining its strength based on downwind concentration measurements, however, are complicated by the presence of buildings that can divert flow in unexpected directions. High-resolution flow simulations are now possible for predicting plume evolution in complex urban geometries, where contaminant dispersion is affected by the flow around individual buildings. Using Bayesian inference via stochastic sampling algorithms with a high-resolution computational fluid dynamics model, an atmospheric release event can be reconstructed to determine the plume source and release rate based on point measurements of concentration. Event-reconstruction algorithms are applied first for flow around a prototype isolated building (a cube) and then using observations and flow conditions from Oklahoma City, Oklahoma, during the Joint Urban 2003 field campaign. Stochastic sampling methods (Markov chain Monte Carlo) are used to extract likely source parameters, taking into consideration measurement and forward model errors. In all cases the steady-state flow field generated by a 3D Navier–Stokes finite-element code (FEM3MP) is used to drive thousands of forward-dispersion simulations. To enhance computational performance in the inversion procedure, a reusable database of dispersion simulation results is created. It is possible to successfully invert the dispersion problems to determine the source location and release rate to within narrow confidence intervals even with such complex geometries. The stochastic methodology here is general and can be used for time-varying release rates and reactive flow conditions. The results of inversion indicate the probability of a source being found at a particular location with a particular release rate, thus inherently reflecting uncertainty in observed data or the lack of enough data in the shape and size of the probability distribution. A composite plume showing concentrations at the desired confidence level can also be constructed using the realizations from the reconstructed probability distribution. This can be used by emergency responders as a tool to determine the likelihood of concentration at a particular location being above a threshold value.
Using Thermal Time to Simulate Dormancy Depth and Bud-Burst of Vineyards in Korea for the Twentieth Century
Authors: Kwon Eun-Young , Jung Jea-Eun , Chung Uran , Yun Jin I. , Park Hee-Seung 
Published: July 2008

Abstract
A winter-season warming trend has been observed in eastern Asian countries during the last century. Significant effects on dormancy and the subsequent bud-burst of deciduous fruit trees are expected. However, phenological observations are scant in comparison with long-time climate records in the region. Chill-day accumulation, estimated from daily maximum and minimum temperature, is a reasonable proxy for dormancy depth of temperate-zone fruit trees. A selected chill-day model was parameterized for the Campbell Early grapevine, which is the major cultivar (grown virtually everywhere) in South Korea. To derive model parameters (threshold temperature for chilling and the chilling requirement for breaking dormancy), a controlled-environment experiment using field-sampled twigs of Campbell Early was conducted. The chill-day model to estimate bud-burst dates was adjusted by derived parameters and was applied using 1994–2004 daily temperature data obtained from the automated weather station in the vineyard at the National Horticultural Research Institute. The model gave consistently good performance in predicting bud-burst of Campbell Early (RMSE of 2.5 days). To simulate dormancy depth of Campbell Early at eight locations in South Korea for the last century, the model was applied using data obtained for each location from 1921 to 2004. Calculations showed that the chilling requirement for breaking endodormancy of Campbell Early can be satisfied by mid-January to late February in South Korea, and the date was delayed going either northward or southward from the Daegu–Jeonju line that crosses the middle of South Korea in the east–west direction. Maximum length of the cold tolerant period (the number of days between endodormancy release and the forced dormancy release) showed the same spatial pattern. Dormancy release for 1981–2004 advanced by as much as 15 days relative to that for 1921–50 at all locations except Jeju (located in the southernmost island with a subtropical climate), where an average 15-day delay was predicted. The cold-tolerant period diminished somewhat at six out of eight locations. As a result, bud-burst of Campbell Early in spring was advanced by 6–10 days at most locations, and interannual variation in bud-burst dates increased at all locations. The earlier bud-burst after the 1970s was due to 1) warming in winter that results in earlier dormancy release (Incheon, Mokpo, Gangneung, and Jeonju), 2) warming in early spring that enhances regrowth after breaking dormancy (Busan and Jeju), and 3) a combination of both (Seoul and Daegu).
Muscle Strength and Range of Motion in Adolescent Pitchers with Throwing-Related Pain
Authors: Trakis James E. , McHugh Malachy P. , Caracciolo Philip A. , Busciacco Lisa , Mullaney Michael , Nicholas Stephen J. 
Published: July 2008

Background A high prevalence of throwing-related shoulder and elbow pain has been documented in adolescent baseball pitchers. Hypothesis Pitchers with a history of throwing-related pain will have weakened dominant-arm posterior shoulder musculature and greater dominant-arm glenohumeral total range of motion (ROM) loss compared with pitchers without throwing-related pain. Study Design Controlled laboratory study. Methods Twenty-three adolescent pitchers (age 15.7 ±1.4 years) were tested. Twelve pitchers had throwing-related pain in the prior season and were currently symptom-free, while the remaining 11 pitchers had no such history of pain. Internal and external rotation ROM and muscle strength (lower trapezius, middle trapezius, rhomboids, latissimus dorsi, supraspinatus, internal rotators, external rotators) were measured bilaterally. Dominant versus nondominant differences in ROM and strength were compared between pitchers with and without throwing-related pain. Results As a whole, the group of 23 pitchers had a loss of internal rotation ROM (13° ± 10°, P < .001) and gain in external rotation ROM (11° ± 10°, P < .001) on the dominant versus nondominant arm, with no effect on total ROM (2° ± 7° loss, P = .14). There was no difference in bilateral comparison of total ROM between pitchers with and without throwing-related pain. Dominant versus nondominant muscle strength was lower ( P < .05) for the pain group versus nonpain group for the middle trapezius (7% ± 19% vs 22% ± 12%) and supraspinatus (−4% ± 27% vs 14% ± 14%) and higher (P < .05) for the internal rotators (19% ± 14% vs 6%±12%). Conclusion Throwing-related pain in this population may be due to the inability of weakened posterior shoulder musculature to tolerate stress imparted on it by adaptively strengthened propulsive muscles. Clinical Relevance Selective posterior shoulder strengthening may be indicated in rehabilitative and injury prevention programs for adolescent pitchers.
Biomechanical Comparison of Ulnar Collateral Ligament Reconstruction Techniques
Authors: Ruland Robert T. , Hogan Christopher J. , Randall Craig J. , Richards Andrew , Belkoff Stephen M. 
Published: July 2008

Background Incompetence of the ulnar collateral ligament (UCL) of the elbow is career-threatening for high-performance throwing athletes. Although multiple reconstructions have been described, a procedure that combines a larger graft with improved fixation may demonstrate more favorable loading characteristics than current techniques. Hypothesis Ulnar collateral ligament reconstructions utilizing a semitendinosus graft and interference knot fixation will be biomechanically superior to previously reported techniques. Study Design Controlled laboratory study. Methods Thirty cadaveric elbows were stripped of all medial soft tissue superficial to the UCL. The proximal humeri were mounted on a materials testing system with the elbows flexed 90°. The intact UCL was loaded to failure at 4.5 deg/s. The torsional failure moment, torsional stiffness, and mode of failure were recorded. Three groups of 10 specimens were created. Group 1 underwent reconstruction using a palmaris tendon graft secured with interference knot fixation. Group 2 reconstructions utilized a palmaris graft and the docking technique. Group 3 specimens were reconstructed using a semitendinosus graft and interference knot fixation. All specimens were loaded to failure and the same parameters recorded. Results The torsional failure moments for group 1 (13.28 Nm) and group 2 (12.81 Nm) reconstructions were significantly ( P < .05) inferior to that of their respective native values (21.3 Nm and 23.5 Nm). Semitendinosus reconstructions (20.5 Nm) were not significantly different ( P = .24) from their native UCLs (23.0 Nm). All reconstructions were torsionally less stiff (P < .001) than the native UCL. There were no statistically significant differences in stiffness between the groups ( P = .4). Conclusion Ulnar collateral ligament reconstruction utilizing semitendinosus graft and interference knot fixation restores the torsional strength of the intact UCL. Clinical Relevance Reconstructions using semitendinosus grafts may allow for accelerated rehabilitation and earlier return to competition.
Sexual dysfunction in newly diagnosed multiple sclerosis women
Authors: Tzortzis Vassilios , Skriapas Konstantinos , Hadjigeorgiou George , Mitsogiannis Iraklis , Aggelakis Konstantinos , Gravas Stavros , Poulakis Vassilios , Melekos Michael D 
Published: July 2008

Objectives The aim of the study was to evaluate female sexuality in a selective population of newly diagnosed multiple sclerosis (MS) women. Materials and methods In this clinic-based study, 63 newly diagnosed consecutive women affected by definite MS were admitted. Disability and depression were evaluated with the expanded disability status scale (EDSS) and Beck depression inventory, respectively. Sexual function was evaluated with the female sexual function index (FSFI). A group of 61 healthy female volunteers with the same baseline characteristics were used as controls. Postmenopausal women and patients with other major concomitant neurological, endocrinological, vascular, gynecological, psychiatric disorders, use of medicines that can cause female sexual dysfunction (FSD) and disease-modifying drugs were excluded from the study. Results All the evaluated patients were ambulant with no major neurological impairment (mean EDSS score 2.5, range 0—3.5). None of the patients were considered clinically depressed, but some of them were sad or worried. According to the sexual history and FSFI scores, sexual dysfunction was diagnosed in 22 (34.9%) out of the 63 patients and in 13 (21.31%) out of the 61 healthy females ( P > 0.05). Conclusions In the newly diagnosed MS patients, FSD represent an important issue even though disability and other concomitant disorders affecting sexual function were excluded. Multiple Sclerosis 2008; 14: 561—563. http://msj.sagepub.com
Questioning the Evidence for Service Assumptions
Authors: Reith Margaret , Lucas Caroline 
Published: July 2008

• Summary: This article reports an audit of people considered for transfer from a hospice to a nursing home for end-of-life care and discusses implications for patients, families and staff. • Findings: Moving patients to nursing homes at the end of their lives is often distressing for both patients and families and in many cases patients die within a short time of transfer. Few patients are actually transferred although many more are asked to face this possibility often creating unnecessary anxiety. This may have adverse consequences for family members' bereavement. • Applications : There is a weak evidence base for transferring patients from hospices to nursing homes. Palliative care services assume a short in-patient stay to ration an expensive scarce resource. Assessment with social work contributions identifying complex emotional, family and bereavement consequences may allow multidisciplinary teams to justify longer hospice stays by identifying more complex needs to justify better substantive equality between patients.