bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Characteristics of Key Analysis Errors. Part III: A Diagnosis of Their Evolution
Authors: Caron Jean-François , Yau M. K. , Laroche Stéphane 
Published: July 2007

Abstract
This paper presents a diagnostic study of the evolution of initial corrections obtained from the key analysis error algorithm that minimizes the short-range (24 h) forecast errors for four specific events poorly forecasted over the eastern part of North America. A potential vorticity (PV) perspective is employed. It is shown that the modification to the low-level structure at the initial time is mainly attributed to the modification of the low-level PV distribution, while changes in the upper-level structure are attributed to the modification of the upper-level PV distribution. The low-level corrections grow mainly through background surface potential temperature advection by the wind corrections attributable to the interior PV corrections. Changes in the diabatic processes and the vertical alignment of low-level PV corrections by differential PV advection also increase the magnitude of the low-level corrections with time. The upper-level corrections grow by advection of background PV from wind corrections. However, the cause of these latter wind corrections responsible for upper-level background PV advection varies from case to case. An investigation of the relative importance of the low-level and of the upper-level initial corrections to produce the final-time corrections also reveals strong variability between cases. Finally, comparison of two cases in which the key analysis errors propagate vertically with two others without significant vertical propagation shows how the relative position of the key analysis errors with respect to the structure of the background flow can influence the evolution of the initial corrections.
Factors associated with depressive distress among Taiwanese family caregivers of cancer patients at the end of life
Authors: Siew Tzuh Tang  , Li Chung-Yi , Liao Yen-Chi 
Published: July 2007

Family caregivers in East Asian countries are known to have a strong sense of filial piety and a traditional caregiving ideology. They are generally presumed to be protected from psychological distress arising from caregiving. However, there is scant information regarding the impact of caregiving on Chinese/Taiwanese families. The purpose of this study was aimed at identifying those family caregivers of Taiwanese terminally ill cancer patients who are at risk of experiencing depressive distress from the following three categories of predisposing factors: 1) contextual factors; 2) stressors; and 3) appraisal of the caregiving situation. Of the 170 Taiwanese family caregivers of terminally ill cancer patients that participated in this survey, 129 (75.9%) were at an extraordinarily high risk of being distressed because of depressive symptoms (CES-D > 15). Results indicated that family caregivers were vulnerable to clinically depressive distress if they were the patient's spouse (adjusted odds ratio (AOR): 2.89; 95% confidence interval (CI): 1.19—7.01), or evaluated caregiving as imposing a greater negative impact on their own health (AOR: 1.27; 95% CI: 1.09—1.47). In contrast, if family caregivers felt very confident in their knowledge of how to take care of the patient at home (AOR: 0.35; 95% CI: 0.15—0.81), or were sufficiently aware of the patient's thoughts and feelings about disease experiences and symptoms (AOR: 0.47; 95% CI: 0.25—0.88), they were less likely to suffer from depressive distress. These finding have significant clinical implications when they are put into the context of Confucian cultures which place great emphasis on filial piety and familism. Interventions and policy should be developed to target spousal caregivers to enhance their confidence in caregiving and understanding of the patient's disease experiences. This will reduce the negative caregiving impact on the caregiver's health, which in turn may prevent the development of depressive distress among family caregivers. Palliative Medicine 2007; 21: 249—257
A procedure for identifying homologous alternative splicing events
Authors: Talavera David , Hospital Adam , Orozco Modesto , de la Cruz Xavier 
Published: July 2007

Abstract

Background
The study of the functional role of alternative splice isoforms of a gene is a very active area of research in biology. The difficulty of the experimental approach (in particular, in its high-throughput version) leaves ample room for the development of bioinformatics tools that can provide a useful first picture of the problem. Among the possible approaches, one of the simplest is to follow classical protein function annotation protocols and annotate target alternative splice events with the information available from conserved events in other species. However, the application of this protocol requires a procedure capable of recognising such events. Here we present a simple but accurate method developed for this purpose.

Results
We have developed a method for identifying homologous, or equivalent, alternative splicing events, based on the combined use of neural networks and sequence searches. The procedure comprises four steps: (i) BLAST search for homologues of the two isoforms defining the target alternative splicing event; (ii) construction of all possible candidate events; (iii) scoring of the latter with a series of neural networks; and (iv) filtering of the results. When tested in a set of 473 manually annotated pairs of homologous events, our method showed a good performance, with an accuracy of 0.99, a precision of 0.98 and a sensitivity of 0.93. When no candidates were available, the specificity of our method varied between 0.81 and 0.91.

Conclusion
The method described in this article allows the identification of homologous alternative splicing events, with a good success rate, indicating that such method could be used for the development of functional annotation of alternative splice isoforms.
Staffing level: a determinant of late-onset ventilator-associated pneumonia
Authors: Hugonnet Stéphane , Uçkay Ilker , Pittet Didier 
Published: July 2007

Abstract
Introduction
The clinical and economic burden of ventilator-associated pneumonia (VAP) is uncontested. We conducted the present study to determine whether low nurse-to-patient ratio increases the risk for VAP and whether this effect is similar for early-onset and late-onset VAP.

Methods
This prospective, observational, single-centre cohort study was conducted in the medical intensive care unit (ICU) of the University of Geneva Hospitals. All patients who were at risk for ICU-acquired infection admitted from January 1999 to December 2002 were followed from admission to discharge. Collected variables included patient characteristics, admission diagnosis, Acute Physiology and Chronic Health Evaluation II score, co-morbidities, exposure to invasive devices, daily number of patients and nurses on duty, nurse training level and all-site ICU-acquired infections. VAP was diagnosed using standard definitions.

Results
Among 2,470 patients followed during their ICU stay, 262 VAP episodes were diagnosed in 209/936 patients (22.3%) who underwent mechanical ventilation. Median duration of mechanical ventilation was 3 days (interquartile range 2 to 6 days) among patients without VAP and 11 days (6 to 19 days) among patients with VAP. Late-onset VAP accounted for 61% of all episodes. The VAP rate was 37.6 episodes per 1,000 days at risk (95% confidence interval 33.2 to 42.4). The median daily nurse-to-patient ratio over the study period was 1.9 (interquartile range 1.8 to 2.2). By multivariate Cox regression analysis, we found that a high nurse-to-patient ratio was associated with a decreased risk for late-onset VAP (hazard ratio 0.42, 95% confidence interval 0.18 to 0.99), but there was no association with early-onset VAP.

Conclusion
Lower nurse-to-patient ratio is associated with increased risk for late-onset VAP.
A semi-quantitative GeLC-MS analysis of temporal proteome expression in the emerging nosocomial pathogen Ochrobactrum anthropi
Authors: Graham Robert Leslie James , Sharma Mohit K , Ternan Nigel G , Weatherly D Brent , Tarleton Rick L , McMullan Geoff 
Published: July 2007

Abstract
Background
The α-Proteobacteria are capable of interaction with eukaryotic cells, with some members, such as Ochrobactrum anthropi, capable of acting as human pathogens. O. anthropi has been the cause of a growing number of hospital-acquired infections; however, little is known about its growth, physiology and metabolism. We used proteomics to investigate how protein expression of this organism changes with time during growth.

Results
This first gel-based liquid chromatography-mass spectrometry (GeLC-MS) temporal proteomic analysis of O. anthropi led to the positive identification of 131 proteins. These were functionally classified and physiochemically characterized. Utilizing the emPAI protocol to estimate protein abundance, we assigned molar concentrations to all proteins, and thus were able to identify 19 with significant changes in their expression. Pathway reconstruction led to the identification of a variety of central metabolic pathways, including nucleotide biosynthesis, fatty acid anabolism, glycolysis, TCA cycle and amino acid metabolism. In late phase growth we identified a number of gene products under the control of the oxyR regulon, which is induced in response to oxidative stress and whose protein products have been linked with pathogen survival in response to host immunity reactions.

Conclusion
This study identified distinct proteomic profiles associated with specific growth points for O. anthropi, while the use of emPAI allowed semi-quantitative analyses of protein expression. It was possible to reconstruct central metabolic pathways and infer unique functional and adaptive processes associated with specific growth phases, thereby resulting in a deeper understanding of the physiology and metabolism of this emerging pathogenic bacterium.
Differential effects ofFrancisella tularensislipopolysaccharide on B lymphocytes
Authors: Rahhal Riad M , Vanden Bush Tony J , McLendon Molly K , Apicella Michael A , Bishop Gail A 
Published: July 2007

AbstractFrancisella tularensis, a designated Category A biological agent, can cause severe infection in humans. Previous studies have demonstrated a significant immunoprotective role for B lymphocytes in animal models, but the responses of human B lymphocytes to F. tularensis components are largely unknown. The LPS of F. tularensis is atypical and has been reported to lack biological activity on myeloid cells and mouse B cells. Our study characterized the immunological effects of highly purified LPS from different stains of F. tularensis on human B lymphocytes and compared these effects with those on mouse B cells and human monocyte-derived macrophages. Results indicate that marked differences exist between cell type and species in specific responses to this interesting bacterial component. In sharp contrast to responses of mouse splenic B cells or human macrophages, human peripheral B cells showed reproducibly elevated IL-6, TNF-α, and antibody production in response to F. tularensis LPS. Data also indicated that these activated human B lymphocytes may subsequently promote the activation of other immune cell types by direct cell–cell interaction. Further investigation into the potential usefulness of F. tularensis LPS as an adjuvant component of a more optimal subunit vaccine is warranted, as it is now clear that it is not biologically inactive, as assumed previously.
Bacterial Community Changes during Plant Establishment at the San Pedro River Mine Tailings Site
Authors: Rosario Karyna , Iverson Sadie L. , Henderson David A. , Chartrand Shawna , McKeon Casey , Glenn Edward P. , Maier Raina M. 
Published: July 2007

AbstractMine tailings are moderately to severely impacted sites that lack normal plant cover, soil structure and development, and the associated microbial community. In arid and semiarid environments, tailings and their associated contaminants are prone to eolian dispersion and water erosion, thus becoming sources of metal contamination. One approach to minimize or eliminate these processes is to establish a permanent vegetation cover on tailings piles. Here we report a revegetation trial conducted at a moderately impacted mine tailings site in southern Arizona. A salt and drought‐tolerant plant, four‐wing saltbush [Atriplex canescens (Pursh) Nutt.], was chosen for the trial. A series of 3 by 3 m plots were established in quadruplicate on the test site to evaluate growth of four‐wing saltbush transplants alone or with compost addition. Results show that >80% of the transplanted saltbush survived after 1.5 yr in both treatments. Enumeration of heterotrophs and community structure analysis were conducted to monitor bacterial community changes during plant establishment as an indicator of plant and soil health. The bacterial community was evaluated using denaturing gradient gel electrophoresis (DGGE) analysis of 16S rDNA PCR gene products from tailings samples taken beneath transplant canopies. Significant differences in heterotrophic counts and community composition were observed between the two treatments and unplanted controls throughout the trial, but treatment effects were not observed. The results suggest that compost is not necessary for plant establishment at this site and that plants, rather than added compost, is the primary factor enhancing bacterial heterotrophic counts and affecting community composition.
Colloid Mobilization and Arsenite Transport in Soil Columns: Effect of Ionic Strength
Authors: Zhang Hua , Selim H.M. 
Published: July 2007

AbstractColloid generation and transport in soils is of significance because of suspected colloid‐facilitated transport of contaminants to the groundwater. In this study, colloid mobilization and its effect on the transport of arsenite [As(III)] were investigated in Olivier (fine‐silty, mixed, active, thermic Aquic Fraglossudalfs) and Windsor (mixed, mesic typic Udipsamments) soil columns. Input solution of 10 mg L−1As(III) in 0.01MNaCl was applied to water‐saturated columns, and followed by leaching with deionized water (DIW). Flow interruptions were performed during the As(III) input and DIW leaching phases. Turbidity, electrical conductivity (EC), and pH of column effluents were monitored with time. Total and dissolved concentrations of As, Fe, and Al were analyzed. Effluent results demonstrated that colloid‐facilitated transport contributed little to arsenic movement when the solution ionic strength was maintained constant. Mobilization of colloidal amorphous material and enhanced transport of As(III) were observed as a result of changes in ionic strength of the input solution. The peak of colloid generation coincided with peak concentrations of Fe, suggesting mobilization of Fe oxides and facilitated transport of As(III) adsorbed on oxide surfaces. Colloid mobilization was enhanced due to flow interruption in the Olivier column, which suggests slow dissociation of aggregated colloidal particles. Moreover, effluent results indicate significant effect of organic matter in stabilizing aggregates of colloidal particles.
The Contribution of Ice Cover to Sediment Resuspension in a Shallow Temperate Lake: Possible Effects of Climate Change on Internal Nutrient Loading
Authors: Niemistö Juha P. , Horppila Jukka 
Published: July 2007

AbstractThe effect of ice cover on sediment resuspension and internal total P (Tot‐P) loading was studied in the northern temperate Kirkkojärvi basin in Finland. The gross sedimentation and resuspension rates were estimated with sediment traps during ice‐cover and ice‐free periods. After ice break, the average gross sedimentation rate increased from 1.4 to 30.0 g dw m−2 d−1 Resuspension calculations showed clearly higher values after ice break as well. Under ice cover, resuspension ranged from 50 to 78% of the gross sedimentation while during the ice‐free period it constituted from 87 to 97% of the gross sedimentation. Consequently, the average resuspension rate increased from 1.0 g dw m−2 d−1 under ice‐cover to 27.0 g dw m−2 d−1 after thaw, indicating the strong effect of ice cover on sediment resuspension. To estimate the potential effect of climate change on internal P loading caused by resuspension we compared the Tot‐P loading calculations between the present climate and the climate with doubled atmospheric CO2 concentration relative to the present day values (ice cover reduced from current 165 to 105 d). The annual load increased from 7.4 to 9.4 g m−2 In conclusion, the annual internal Tot‐P loading caused by resuspension will increase by 28% in the Kirkkojärvi basin if the 2 × CO2 climate scenario comes true.
Diet Modification to Reduce Phosphorus Surpluses: A Mass Balance Approach
Authors: Maguire R. O. , Crouse D. A. , Hodges S. C. 
Published: July 2007

AbstractDiet modification to reduce phosphorus (P) concentrations in manures has been developed in response to environmental concerns over P losses from animal agriculture to surface waters. We used USDA‐NASS statistics on animal numbers and crop production to calculate county scale mass balances for manure P production, P removed in harvested portion of crops, and the potential effects of diet modification. Although spreading manure evenly over all crop acreage within a county is unlikely to occur, these calculations give a good indication as to the impact diet modification to reduce P can have at a regional or national scale. There was a high degree of regional variability in manure P surpluses (e.g., with the large crop acreages in the grain belt leading to large P offtake in crops preventing most P surpluses). In 89% of counties, there was a deficit of manure P relative to crop P removal; therefore there was a manure P surplus in 11% of counties. Diet modification decreased the percentage of states with a manure P surplus from 11 to 8%, a decrease of approximately 27%. Diet modification decreased the percentage of counties with the greatest surpluses of manure P (>30 kg ha−1) from 3% of all counties to 1%. Diet modification to decrease manure P is an important part of strategies to alleviate environmental concerns associated with surplus manure P in many areas, but additional strategies to deal with manure P surpluses are needed in some areas.
A Stochastic Model for Colloid Transport and Deposition
Authors: Bradford S. A. , Toride N. 
Published: July 2007

AbstractProfiles of retained colloids in porous media have frequently been observed to be hyper‐exponential or non‐monotonic with transport depth under unfavorable attachment conditions, whereas filtration theory predicts an exponential profile. In this work we present a stochastic model for colloid transport and deposition that allows various hypotheses for such deviations to be tested. The model is based on the conventional advective dispersion equation that accounts for first‐order kinetic deposition and release of colloids. One or two stochastic parameters can be considered in this model, including the deposition coefficient, the release coefficient, and the average pore water velocity. In the case of one stochastic parameter, the probability density function (PDF) is characterized using log‐normal, bimodal log‐normal, or a simple two species/region formulation. When two stochastic parameters are considered, then a joint log‐normal PDF is employed. Simulation results indicated that variations in the deposition coefficient and the average pore water velocity can both produce hyper‐exponential deposition profiles. Bimodal formulations for the PDF were also able to produce hyper‐exponential profiles, but with much lower variances in the deposition coefficient. The shape of the deposition profile was found to be very sensitive to the correlation of deposition and release coefficients, and to the correlation of pore water velocity and deposition coefficient. Application of the developed stochastic model to a particular set of colloid transport and deposition data indicated that chemical heterogeneity of the colloid population could not fully explain the observed behavior. Alternative interpretations were therefore proposed based on variability of the pore size and the water velocity distributions.
Pyrene Mineralization by Mycobacterium sp. Strain KMS in a Barley Rhizosphere
Authors: Child R. , Miller C. D. , Liang Y. , Sims R. C. , Anderson A. J. 
Published: July 2007

AbstractTo determine whether the soil Mycobacterium isolate KMS would mineralize pyrene under rhizosphere conditions, a microcosm system was established to collect radioactive carbon dioxide released from the labeled polycyclic aromatic hydrocarbon. Microcosms were designed as sealed, flow‐through systems that allowed the growth of plants. Experiments were conducted to evaluate mineralization of 14C‐labeled pyrene in a sand amended with the polycyclic aromatic hydrocarbons degrading Mycobacterium isolate KMS, barley plants, or barley plants with roots colonized by isolate KMS. Mineralization was quantified by collecting the 14CO2 produced from 14C‐labeled pyrene at intervals during the 10‐d incubation period. Roots and foliar tissues were examined for 14C incorporation. Mass balances for microcosms were determined through combustion of sand samples and collection and quantification of 14CO2 evolved from radiolabeled pyrene. No pyrene mineralization was observed in the sterile control systems. Greater release of 14CO2 was observed in the system with barley colonized by KMS than in microcosms containing just the bacterium inoculum or sterile barley plants. These findings suggest that phytostimulation of polycyclic aromatic hydrocarbons mineralization could be applied in remediation schemes.
Determination of field‐incurred pyrimethanil residues in persimmon (Diospyros kaki Linn) by liquid chromatography
Authors: Shim Jae‐Han , Abd El‐Aty A. M. , Choi Jeong‐Heui , Kang Cheol‐Ah 
Published: July 2007

AbstractField trials have been carried out to determine the residues of the fungicide pyrimethanil in persimmon (Diospyros kaki Linn) after field treatment. Three treatments using pyrimethanil (PYR 30% WP) were carried out on persimmon trees at a recommended dose rate: the former was sprayed at two different times at 30 and 21 days prior to harvesting; the second was sprayed three times at 40, 30 and 21 days prior to harvesting; and the third was sprayed four times at 40, 30, 21 and 14 days prior to harvesting. The analysis was based on liquid–liquid extraction and solid‐phase extraction followed by liquid chromatography with ultraviolet detection at 268 nm. Pyrimethanil was confirmed by high‐performance liquid chromatography–mass spectrometry HPLC‐MS in the selected ion monitoring mode. The method was validated with spiked fruit samples at concentrations of 0.1 and 0.4 ppm. Average recoveries (three replicates) ranged from 87.1 to 92.1% with relative standard deviations between 4.5 and 11.98%. The calculated limit of detection was 0.02 ppm and the limit of quantitation was 0.07 ppm. After two, three or four applications, pyrimethanil residues on persimmon averaged 0.44, 0.48 or 0.53 ppm, respectively; all of these values were below the maximum residue level established by the Korean Food and Drug Administration (5.0 ppm). This indicates that pyrimethanil residues declined to a level well below the maximum residue level within the 14 day period between the last application and harvesting. Copyright © 2007 John Wiley & Sons, Ltd.
Rhodium‐Catalyzed [2+2+1+1] Cyclocarbonylative Coupling of Alkynes with Carbon Monoxide Affording Tetrasubstituted p‐Benzoquinones
Authors: Huang Qiufeng , Hua Ruimao 
Published: July 2007

AbstractIn this strategy, the tetrasubstituted benzoquinones have been prepared directly by a [2+2+1+1] cyclocarbonylative coupling reaction of internal alkynes with CO in the presence of [RhCl(CO)2]2. The low concentration of CO in the reaction is the crucial point for the chemoselective formation of tetrasubstituted benzoquinones in good to high yields. Functional groups such as chloro, methoxy, cyano, vinyl, fluoro, and carboxylate are tolerated under the reaction conditions.