bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vacuolar Protein Sorting Pathway Contributes to the Release of Marburg Virus
Authors: Kolesnikova Larissa , Strecker Thomas , Morita Eiji , Zielecki Florian , Mittler Eva , Crump Colin , Becker Stephan 
Published: December 2008

ABSTRACT
VP40, the major matrix protein of Marburg virus, is the main driving force for viral budding. Additionally, cellular factors are likely to play an important role in the release of progeny virus. In the present study, we characterized the influence of the vacuolar protein sorting (VPS) pathway on the release of virus-like particles (VLPs), which are induced by Marburg virus VP40. In the supernatants of HEK 293 cells expressing VP40, different populations of VLPs with either a vesicular or a filamentous morphology were detected. While the filaments were almost completely composed of VP40, the vesicular particles additionally contained considerable amounts of cellular proteins. In contrast to that in the vesicles, the VP40 in the filaments was regularly organized, probably inducing the elimination of cellular proteins from the released VLPs. Vesicular particles were observed in the supernatants of cells even in the absence of VP40. Mutation of the late-domain motif in VP40 resulted in reduced release of filamentous particles, and likewise, inhibition of the VPS pathway by expression of a dominant-negative (DN) form of VPS4 inhibited the release of filamentous particles. In contrast, the release of vesicular particles did not respond significantly to the expression of DN VPS4. Like the budding of VLPs, the budding of Marburg virus particles was partially inhibited by the expression of DN VPS4. While the release of VLPs from VP40-expressing cells is a valuable tool with which to investigate the budding of Marburg virus particles, it is important to separate filamentous VLPs from vesicular particles, which contain many cellular proteins and use a different budding mechanism.
Identification of human enteric pathogens in gull feces at Southwestern Lake Michigan bathing beaches
Authors: Kinzelman Julie , McLellan Sandra L. , Amick Ashley , Preedit Justine , Scopel Caitlin O. , Olapade Ola , Gradus Steve , Singh Ajaib , Sedmak Gerald 
Published: December 2008

Ring-billed ( Larus delawarensis Ord, 1815) and herring ( Larus argentatus Pontoppidan, 1763) gulls are predominant species of shorebirds in coastal areas. Gulls contribute to the fecal indicator burden in beach sands, which, once transported to bathing waters, may result in water quality failures. The importance of these contamination sources must not be overlooked when considering the impact of poor bathing water quality on human health. This study examined the occurrence of human enteric pathogens in gull populations at Racine, Wisconsin. For 12 weeks in 2004 and 2005, and 7 weeks in 2006, 724 gull fecal samples were examined for pathogen occurrence on traditional selective media (BBL CHROMagar-Salmonella, Remel Campy-BAP, 7% horse blood agar) or through the use of novel isolation techniques ( Campylobacter , EC FP5-funded CAMPYCHECK Project), and confirmed using polymerase chain reaction (PCR) for pathogens commonly harbored in gulls. An additional 226 gull fecal samples, collected in the same 12-week period in 2004, from a beach in Milwaukee, Wisconsin, were evaluated with standard microbiological methods and PCR. Five isolates of Salmonella (0.7%), 162 (22.7%) isolates of Campylobacter, 3 isolates of Aeromonas hydrophila group 2 (0.4%), and 28 isolates of Plesiomonas shigelloides (3.9%) were noted from the Racine beach. No occurrences of Salmonella and 3 isolates of Campylobacter (0.4%) were found at the Milwaukee beach. A subset of the 2004 samples was also examined for Giardia and Cryptosporidium and was found to be negative. Information as to the occurrence of human pathogens in beach ecosystems is essential to design further studies assessing human health risk and to determine the parameters influencing the fate and transport of pathogens in the nearshore environment.
Initial tree mortality and insect and pathogen response to fire and thinning restoration treatments in an old-growth mixed-conifer forest of the Sierra Nevada, California
Authors: Maloney Patricia E. , Smith Thomas F. , Jensen Camille E. , Innes Jim , Rizzo David M. , North Malcolm P. 
Published: December 2008

Fire and thinning restoration treatments in fire-suppressed forests often damage or stress leave trees, altering pathogen and insect affects. We compared types of insect- and pathogen-mediated mortality on mixed-conifer trees 3 years after treatment. The number of bark beetle attacked trees was greater in burn treatments compared with no-burn treatments, and in some cases, larger pine trees were preferentially attacked. Restoration treatments are not expected to change the trajectory of spread and intensification of dwarf mistletoe. Thinning treatments may have provided a sanitation effect in which large leave trees have lower levels of dwarf mistletoe. Although thinning treatments are known to exacerbate root disease, <12% of cut stumps were infected with root pathogens ( Armillaria gallica and Heterobasidion annosum ). Treatments increased Ribes (alternate host for white pine blister rust) frequency and abundance, which may have very localized impacts on white pine blister rust dynamics. In some instances, fire, insects, and pathogens appear to conflict with forest restoration goals by reducing the percentage of pine and producing proportionally higher rates of tree mortality in large-diameter size classes. To better understand the long-term effects of restoration treatments on pathogens and insects, continued monitoring over the course of varying climatic conditions will be needed.
Viscosity Approximation Methods for Generalized Mixed Equilibrium Problems and Fixed Points of a Sequence of Nonexpansive Mappings
Authors: Zeng Wei-You , Huang Nan-Jing , Zhao Chang-Wen 
Published: December 2008

AbstractWe introduce an iterative scheme by the viscosity approximation method for finding a common element of the set of common solutions for generalized mixed equilibrium problems and the set of common fixed points of a sequence of nonexpansive mappings in Hilbert spaces. We show a strong convergence theorem under some suitable conditions.
Trade-Offs between Measurement Accuracy and Resolutions in Configuring Phased-Array Radar Velocity Scans for Ensemble-Based Storm-Scale Data Assimilation
Authors: Lu Huijuan , Xu Qin 
Published: December 2008

Abstract
Assimilation experiments are carried out with simulated radar radial-velocity observations to examine the impacts of observation accuracy and resolutions on storm-scale wind assimilation with an ensemble square root filter (EnSRF) on a storm-resolving grid (Δx = 2 km). In this EnSRF, the background covariance is estimated from an ensemble of 40 imperfect-model predictions. The observation error includes both measurement error and representativeness error, and the error variance is estimated from the simulated observations against the simulated “truth.” The results show that the analysis is not significantly improved when the measurement error is overly reduced (from 4 to 1 m s−1) and becomes smaller than the representativeness error. The analysis can be improved by properly coarsening the observation resolution (to 2 km in the radial direction) with an increase in measurement accuracy and further improved by properly enhancing the temporal resolution of radar volume scans (from every 5 to 2 or 1 min) with a decrease in measurement accuracy. There can be an optimal balance or trade-off between measurement accuracy and resolutions (in space and time) for configuring radar scans, especially phased-array radar scans, to improve storm-scale radar wind analysis and assimilation.
Internal Waves at an Interface between Two Layers of Differing Stability
Authors: McHugh John 
Published: December 2008

Abstract
Internal waves in a two-layer fluid are considered. The layers have different values of the buoyancy frequency, assumed to be constant in each layer. The density profile is chosen to be continuous across the interface and the flow is Boussinesq. The solution is an expansion in the wave amplitude, similar to a Stokes expansion for free surface waves. The results show that the nonlinear terms in the interfacial boundary conditions require higher harmonics and result in nonlinear wave steepening at the interface. The first few harmonics are scattered by the interface, whereas the higher harmonics are evanescent in the vertical. The second-order correction to the wave speed is negative, similar to previous results with a rigid upper boundary.
Variations in the Three-Dimensional Structure of the Atmospheric Circulation with Different Flavors of El Niño
Authors: Trenberth Kevin E. , Smith Lesley 
Published: December 2008

Abstract
Two rather different flavors of El Niño are revealed when the full three-dimensional spatial structure of the temperature field and atmospheric circulation monthly mean anomalies is analyzed using the Japanese Reanalysis (JRA-25) temperatures from 1979 through 2004 for a core region of the tropics from 30°N to 30°S, with results projected globally onto various other fields. The first two empirical orthogonal functions (EOFs) both have primary relationships to El Niño–Southern Oscillation (ENSO) but feature rather different vertical and spatial structures. By construction the two patterns are orthogonal, but their signatures in sea level pressure, precipitation, outgoing longwave radiation (OLR), and tropospheric diabatic heating are quite similar. Moreover, they are significantly related, with EOF-2 leading EOF-1 by about 4–6 months, indicating that they play complementary roles in the evolution of ENSO events, and with each mode playing greater or lesser roles in different events and seasons.
The dominant pattern (EOF-1) in its positive sign features highly coherent zonal mean warming throughout the tropical troposphere from 30°N to 30°S that increases in magnitude with height to 200 hPa, drops to zero about 100 hPa at the tropopause, and has reverse sign to 30 hPa with peak values at 70 hPa. It correlates strongly with global mean surface temperatures. EOF-2 emphasizes off-equatorial centers of action and strong Rossby wave temperature signatures that are coherent throughout the troposphere, with the strongest values in the Pacific that extend into the extratropics and a sign reversal at and above 150 hPa. Near the surface, both patterns feature boomerang-shaped opposite temperatures in the western tropical and subtropical Pacific, with similar sea level pressure patterns, but with EOF-1 more focused in equatorial regions. Both patterns are strongest during the boreal winter half-year when anomalous precipitation in the tropics and associated latent heating drive teleconnections throughout the world. For El Niño in northern winter EOF-1 has more precipitation in the eastern tropical Pacific, while EOF-2 has much drier conditions over northern Australia and the Indian Ocean. In northern summer, the main differences are in the South Pacific and Indian Ocean. Differences in teleconnections suggest great sensitivity to small changes in forcings in association with seasonal variations in the mean state.
Varus Alignment Leads to Increased Forces in the Anterior Cruciate Ligament
Authors: Jan van de Pol Gerrit , Arnold Markus P. , Verdonschot Nico , van Kampen Albert 
Published: December 2008

Background Varus thrust of the knee is a dynamic increase of an often preexisting varus angle and it is suspected to be a major reason for failure of anterior cruciate ligament reconstructions. However, it is not known if a direct relationship exists between varus thrust and forces in the anterior cruciate ligament. Hypothesis Forces in the anterior cruciate ligament increase with increasing varus alignment, and consequently an anterior cruciate ligament deficiency in a varus-aligned leg leads to more lateral tibiofemoral joint opening. Study Design Controlled laboratory study. Methods Six human cadaver legs were axially loaded with 3 different weightbearing lines—a neutral weightbearing line, a weightbearing line that passes through the middle of the medial tibial plateau (50% varus), and a line passing the edge of the medial tibial plateau (100% varus)—that were used to create a varus moment. The resulting lateral tibiofemoral joint opening and corresponding anterior cruciate ligament tension were measured. The tests were repeated with and without the anterior cruciate ligament in place. Results In the neutral aligned legs, there was no apparent lateral joint opening, and no anterior cruciate ligament tension change was noted. The lateral joint opening increased when the weightbearing line increased from 0% to 50% to 100%. The lateral joint opening was significantly higher in 10° of knee flexion compared with knee extension. In the 100% varus weightbearing line, the anterior cruciate ligament tension was significantly higher (53.9 N) compared with neutral (31 N) or the 50% weightbearing line (37.9 N). A thrust could only be observed in the 100% weightbearing line tests. In the absence of an anterior cruciate ligament, there was more lateral joint opening, although this was only significant in the 100% weightbearing line. Conclusion There is a direct relationship between varus alignment and anterior cruciate ligament tension. In the absence of an anterior cruciate ligament, the amount of lateral opening tends to increase. With increasing lateral opening, a thrust can sometimes be experimentally observed. Clinical Relevance A varus alignment in an anterior cruciate ligament—deficient knee does not necessarily lead to a varus thrust and therefore does not always need operative varus alignment correction. However, in an unstable anterior cruciate ligament—deficient knee with a varus thrust, it might be safer to perform a high valgus tibial osteotomy to minimize the risk of an anterior cruciate ligament reconstruction failure.
Can rate of brain atrophy in multiple sclerosis be explained by clinical and MRI characteristics?
Authors: Korteweg T , Rovaris M , Neacsu V , Filippi M , Comi G , Uitdehaag BM , Knol DL , Polman CH , Barkhof F , Vrenken H ,   On behalf of the MAGNIMS collaboration
Published: December 2008

Introduction Multiple sclerosis (MS) is characterized, besides focal lesions, by brain atrophy. The determinants of atrophy rates in individual patients are poorly understood. Aim This study investigated the predictive value of clinical and magnetic resonance imaging (MRI) factors, including short-term changes thereof, for concurrent and future atrophy evolution using Spearman’s rank correlations and stepwise multiple linear regression. Methods We retrospectively identified a group of 115 active, early relapsing-remitting (RR) patients relatively homogeneous in terms of disease course and MRI activity compared to a second group of 96 patients with broader spectrum of MS phenotypes and inactive scans. All patients had undergone three MRI investigations with interscan intervals of at least 12 and 24 months, respectively. Results In the RR patients, 23% of variance in concurrent atrophy rates (over the first interval) could be explained by the combination of baseline T2 lesion volume and change in EDSS score over the first interval, whereas only 6% in future atrophy rates (over the second interval) was explained. In the heterogeneous group, 20.2% of the variance in future atrophy rates could be explained, but slightly less in concurrent atrophy rates (16.2%). Conclusion We concluded that variance in brain atrophy rates can partially be explained by clinical and MRI measures of disease. Future atrophy rates in individual MS patients are difficult to predict even when including previous atrophy rates.
Retention of Irish skills: A longitudinal study of a school-acquired second language
Authors: Murtagh Lelia , van der Slik Frans 
Published: December 2008

This paper describes a study of retention of school-acquired Irish among school leavers. The initial group selected represented final year secondary school students from three different instructional categories: ordinary level Irish, advanced level Irish and immersion school students. Participants were interviewed and their language skills assessed as they completed their study of Irish and again 18 months after they had left secondary school. Proficiency was measured in terms of scores on a communicative test of spoken Irish and a C-test in Irish. Background information collected included participants' self-assessed ability in spoken Irish, attitude/motivation in relation to learning Irish and their out-of-school use of Irish. Test results did not indicate any attrition of Irish language skills over time, despite participants' general feelings of loss. This outcome matches findings from similar studies of second language attrition elsewhere, for example, Weltens, 1989. The results also indicated a general decline in opportunity to use Irish among participants from all three instructional backgrounds. The ex-immersion school participants, however, were the most likely to continue speaking the language. A small but significant gain on one particular Irish speaking subtest which was noted in this ex-immersion group may be attributed, in part at least, to these participants' greater access to Irish language-speaking networks.
Living with cystic fibrosis-related diabetes or type 1 diabetes mellitus: a comparative study exploring health-related quality of life and patients' reported experiences of hypoglycaemia
Authors: Tierney Stephanie , Webb Kevin , Jones Andrew , Dodd Mary , Mckenna Diane , Rowe Rachel , Whitehouse Joanna , Deaton Christi 
Published: December 2008

Objectives: To compare patients with type 1 diabetes mellitus (T1DM) or cystic fibrosis-related diabetes (CFRD) on frequency and severity of symptoms suggestive of hypoglycaemia and diabetes-specific health-related quality of life (HRQoL). Methods: This was a cross-sectional comparison study. Participants with T1DM or CFRD completed a questionnaire that assessed symptoms suggestive of hypoglycaemia and diabetes-specific HRQoL, and recorded episodes of low blood sugars in a prospective diary. Comparisons of responses were conducted, and Pearson product correlations were determined between HRQoL scores and other continuous variables. HRQoL scores were compared between the groups after adjusting for confounding factors. Results: Diabetes in cystic fibrosis (CF) patients had a less negative impact on HRQoL than in T1DM patients. Both groups experienced hypoglycaemia, but loss of consciousness or needing help was more common in T1DM patients. Symptoms suggestive of hypoglycaemia were less of a problem for CFRD patients in terms of severity, with T1DM patients having more neuroglycopenic symptoms. Discussion: Although the same percentage of patients in both groups reported experiencing hypoglycaemia, severity (e.g. symptoms and loss of consciousness) was higher for those with T1DM. Symptoms of hypoglycaemia appear to have a significant impact on HRQoL, and could account for the worse HRQoL in T1DM patients.
The Arabic version of Diabetes-39: psychometric properties and validation
Authors: Khader Yousef S. , Bataineh Safaa , Batayha Waleed 
Published: December 2008

Objective: To translate Diabetes-39 (D-39) into Arabic language and assess its psychometric properties among patients with type 2 diabetes in Jordan. Methods: A sample of 368 subjects (162 men and 206 women) was randomly selected from patients with type 2 diabetes attending outpatient clinics in King Abdullah University Hospital (KAUH). D-39 was translated using backward forward translation method. Individual D-39 items were recoded, summed and transformed to a 0 to 100-scale. Acceptability, item level validity, scale level validity and reliability were evaluated. Results: The mean (SD) of D-39 subscales ranged from 26.9 (22.4) for `Social burden' to 50.5 (21.1) for `Energy and Mobility'. Inter item correlations within each scale were moderate to strong. All item-scale correlations exceeded the minimum correlation of 0.40 for adequate item internal consistency. Item discriminat validity was demonstrated since items correlated higher with their own scale than with other scales. For all scales, Cronbach's alpha coefficient exceeded the minimum criterion of 0.7. Conclusions: Arabic version of D-39 is a reliable and valid instrument to measure quality of life among patients with diabetes in Jordan.
VEGF-mediated cross-talk within the neonatal murine thymus
Authors: Cuddihy Andrew R. , Ge Shundi , Zhu Judy , Jang Julie , Chidgey Ann , Thurston Gavin , Boyd Richard , Crooks Gay M. 
Published: December 2008

AbstractAlthough the mechanisms of cross-talk that regulate the hematopoietic and epithelial compartments of the thymus are well established, the interactions of these compartments with the thymic endothelium have been largely ignored. Current understanding of the thymic vasculature is based on studies of adult thymus. We show that the neonatal period represents a unique phase of thymic growth and differentiation, marked by endothelium that is organized as primitive, dense networks of capillaries dependent on vascular endothelial growth factor (VEGF). VEGF dependence in neonates is mediated by significantly higher levels of both VEGF production and endothelial VEGF receptor 2 (VEGF-R2) expression than in the adult thymus. VEGF is expressed locally in the neonatal thymus by immature, CD4−CD8− “double negative” (DN) thymocytes and thymic epithelium. Relative to adult thymus, the neonatal thymus has greater thymocyte proliferation, and a predominance of immature thymocytes and cortical thymic epithelial cells (cTECs). Inhibition of VEGF signaling during the neonatal period results in rapid loss of the dense capillaries in the thymus and a marked reduction in the number of thymocytes. These data demonstrate that, during the early postnatal period, VEGF mediates cross-talk between the thymocyte and endothelial compartments of the thymus.
Barcodes for genomes and applications
Authors: Zhou Fengfeng , Olman Victor , Xu Ying 
Published: December 2008

Abstract

Background
Each genome has a stable distribution of the combined frequency for each k-mer and its reverse complement measured in sequence fragments as short as 1000 bps across the whole genome, for 1<k<6. The collection of these k-mer frequency distributions is unique to each genome and termed the genome's barcode.

Results
We found that for each genome, the majority of its short sequence fragments have highly similar barcodes while sequence fragments with different barcodes typically correspond to genes that are horizontally transferred or highly expressed. This observation has led to new and more effective ways for addressing two challenging problems: metagenome binning problem and identification of horizontally transferred genes. Our barcode-based metagenome binning algorithm substantially improves the state of the art in terms of both binning accuracies and the scope of applicability. Other attractive properties of genomes barcodes include (a) the barcodes have different and identifiable characteristics for different classes of genomes like prokaryotes, eukaryotes, mitochondria and plastids, and (b) barcodes similarities are generally proportional to the genomes' phylogenetic closeness.

Conclusion
These and other properties of genomes barcodes make them a new and effective tool for studying numerous genome and metagenome analysis problems.