bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for Enhanced Eddy Mixing at Middepth in the Southern Ocean
Authors: Smith K. Shafer , Marshall John 
Published: June 2008

Abstract
Satellite altimetric observations of the ocean reveal surface pressure patterns in the core of the Antarctic Circumpolar Current (ACC) that propagate downstream (eastward) but slower than the mean surface current by about 25%. The authors argue that these observations are suggestive of baroclinically unstable waves that have a steering level at a depth of about 1 km. Detailed linear stability calculations using a hydrographic atlas indeed reveal a steering level in the ACC near the depth implied by the altimetric observations. Calculations using a nonlinear model forced by the mean shear and stratification observed close to the core of the ACC, coinciding with a position where mooring data and direct eddy flux measurements are available, reveal a similar picture, albeit with added details. When eddy fluxes are allowed to adjust the mean state, computed eddy kinetic energy and eddy stress are close to observed magnitudes with steering levels between 1 and 1.5 km, broadly consistent with observations.
An important result of this study is that the vertical structure of the potential vorticity (PV) eddy diffusivity is strongly depth dependent, implying that the diffusivity for PV and buoyancy are very different from one another. It is shown that the flow can simultaneously support a PV diffusivity peaking at 5000 m2 s−1 or so near the middepth steering level and a buoyancy diffusivity that is much smaller, of order 1000 m2 s−1, exhibiting less vertical structure. An effective diffusivity calculation, using an advected and diffused tracer transformed into area coordinates, confirms that the PV diffusivity more closely reflects the mixing properties of the flow than does the buoyancy diffusivity, and points explicitly to the need for separating tracer and buoyancy flux parameterizations in coarse-resolution general circulation models. Finally, implications for the eddy-driven circulation of the ACC are discussed.
The Statistical Theory of Breaking Entrainment Depth and Surface Whitecap Coverage of Real Sea Waves
Authors: Yuan Yeli , Han Lei , Hua Feng , Zhang Shuwen , Qiao Fangli , Yang Yongzeng , Xia Changshui 
Published: June 2008

Abstract
Some basic statistics for wave breaking have been derived based on the statistical model of real sea waves. The analytic expressions of breaking entrainment depth and surface whitecap coverage involved with both sea wave characteristics and surface wind velocity have been derived on the basis of the whitecap formation model. The concept of the upper envelope for all the whitecap coverage data versus wind speed has been proposed, and it is assumed to correspond to the whitecap coverage in the case of the infinite wind duration and fetch to determine the model constants. The analytic expressions of breaking entrainment depth and whitecap coverage have been compared with the observations in several ways, and consistently favorable agreement can be found for most observations.
An Analysis of Errors in Drop Size Distribution Retrievals and Rain Bulk Parameters with a UHF Wind Profiling Radar and a Two-Dimensional Video Disdrometer
Authors: Kanofsky Laura , Chilson Phillip 
Published: June 2008

Abstract
Vertically pointed wind profiling radars can be used to obtain measurements of the underlying drop size distribution (DSD) for a rain event by means of the Doppler velocity spectrum. Precipitation parameters such as rainfall rate, radar reflectivity factor, liquid water content, mass-weighted mean drop diameter, and median volume drop diameter can then be calculated from the retrieved DSD. The DSD retrieval process is complicated by the presence of atmospheric turbulence, vertical ambient air motion, selection of fall speed relationships, and velocity thresholding. In this note, error analysis is presented to quantify the effect of each of those factors on rainfall rate. The error analysis results are then applied to two precipitation events to better interpret the rainfall-rate retrievals.
It was found that a large source of error in rain rate is due to unaccounted-for vertical air motion. For example, in stratiform rain with a rainfall rate of R = 10 mm h−1, a mesoscale downdraft of 0.6 m s−1 can result in a 34% underestimation of the estimated value of R. The fall speed relationship selection and source of air density information both caused negligible errors. Errors due to velocity thresholding become more important in the presence of significant contamination near 0 m s−1, such as ground clutter. If particles having an equivalent volume diameter of 0.8 mm and smaller are rejected, rainfall rate errors from −4% to −10% are possible, although these estimates depend on DSD and rainfall rate.
Well-Posed Lateral Boundary Conditions for Spectral Semi-Implicit Semi-Lagrangian Schemes: Tests in a One-Dimensional Model
Authors: Voitus F. , Termonia P. , Bénard P. 
Published: June 2008

Abstract
The aim of this paper is to investigate the feasibility of well-posed lateral boundary conditions in a Fourier spectral semi-implicit semi-Lagrangian one-dimensional model. Two aspects are analyzed: (i) the complication of designing well-posed boundary conditions for a spectral semi-implicit scheme and (ii) the implications of such a lateral boundary treatment for the semi-Lagrangian trajectory computations at the lateral boundaries.
Straightforwardly imposing boundary conditions in the gridpoint-explicit part of the semi-implicit time-marching scheme leads to numerical instabilities for time steps that are relevant in today’s numerical weather prediction applications. It is shown that an iterative scheme is capable of curing these instabilities. This new iterative boundary treatment has been tested in the framework of the one-dimensional shallow-water equations leading to a significant improvement in terms of stability.
As far as the semi-Lagrangian part of the time scheme is concerned, the use of a trajectory truncation scheme has been found to be stable in experimental tests, even for large values of the advective Courant number. It is also demonstrated that a well-posed buffer zone can be successfully applied in this spectral context. A promising (but not easily implemented) alternative to these three above-referenced schemes has been tested and is also presented here.
On the Improvement of COAMPS Weather Forecasts Using an Advanced Radiative Transfer Model
Authors: Liu Ming , Nachamkin Jason E. , Westphal Douglas L. 
Published: June 2008

Abstract
Fu–Liou’s delta-four-stream (with a two-stream option) radiative transfer model has been implemented in the U.S. Navy’s Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS)1 to calculate solar and thermal infrared fluxes in 6 shortwave and 12 longwave bands. The model performance is evaluated at high resolution for clear-sky and overcast conditions against the observations from the Southern Great Plains of the Atmospheric Radiation Measurement Program. In both cases, use of the Fu–Liou model provides significant improvement over the operational implementation of the standard Harshvardhan radiation parameterization in both shortwave and longwave fluxes. A sensitivity study of radiative flux on clouds reveals that the choices of cloud effective radius schemes for ice and liquid water are critical to the flux calculation due to the effects on cloud optical properties. The sensitivity study guides the selection of optimal cloud optical properties for use in the Fu–Liou parameterization as implemented in COAMPS. The new model is then used to produce 3-day forecasts over the continental United States for a winter and a summer month. The verifications of parallel runs using the standard and new parameterizations show that Fu–Liou dramatically reduces the model’s systematic warm bias in the upper troposphere in both winter and summer. The resultant cooling modifies the atmospheric stability and moisture transport, resulting in a significant reduction in the upper-tropospheric wet bias. Overall ice and liquid water paths are also reduced. At the surface, Fu–Liou reduces the negative temperature and sea level pressure biases by providing more accurate radiative heating rates to the land surface model. The error reductions increase with forecast length as the impact of improved radiative fluxes accumulates over time. A combination of the two- and four-stream options results in major computational efficiency gains with minimal loss in accuracy.
Good death study of elderly patients with terminal cancer in Taiwan
Authors: Cheng SY , Hu WY , Liu WJ , Yao CA , Chen CY , Chiu TY 
Published: July 2008

Objectives: Over half of all terminal cancer patients in Taiwan are 65 or older, thus demonstrating the importance of terminal care for elderly people. This study investigates the good death status of elderly patients with terminal cancer, comparing the differences in the degree of good death among elderly and younger groups, and exploring the factors related to the good death score. Methods: Three hundred and sixty-six patients with terminal cancer admitted to a palliative care unit were enrolled. Two structured measurements, the good death scale and the audit scale for good death services, were used as the instruments in the study. Results: The scores of individual items and of the good death scale were increased significantly in both elderly ( n = 206, 56.3%) and younger ( n = 160, 43.7%) groups from the time of admission to just prior to death. However, the elderly group had significantly lower scores in ‘awareness’ ( t = −3.76, P < 0.001), ‘propriety’ ( t = −2.92, P < 0.01) and ‘timeliness’ ( t = −2.91, P < 0.01) than the younger group prior to death. Furthermore, because of a lack of truth-telling, the elderly group also had significantly lower scores than the younger group in both ‘respect for autonomy’ and ‘decision-making participation’ ( t = –2.17, P < 0.05; t = –2.21, P < 0.05, respectively). Multiple regression analysis revealed that ‘respect for autonomy’ (OR = 1.22, 95% CI = 0.76–1.67) and ‘verbal support ‘(OR = 0.93, 95% CI = 0.34–1.51) were two independent correlates of the good death score in the elderly group. Conclusion: The dilemma of truth-telling compromises the autonomy of the elderly patients with terminal cancer and consequently affects their good death scores. The palliative care team should emphasize the issue of truth-telling in the process of caring for terminally ill cancer patients, especially elderly patients.
The response of a Swiss university hospital’s palliative care consult team to assisted suicide within the institution
Authors: Pereira J , Laurent P , Cantin B , Petremand D , Currat T 
Published: July 2008

In January 2006 the Centre Hospitalier Universitaire Vaudois (CHUV), a large university hospital in Lausanne, Switzerland, became the first hospital in Switzerland to allow assisted suicide (AS) in exceptional cases within its walls. However, euthanasia is illegal. This decision has posed several ethical and practical dilemmas for the hospital’s palliative care consult service. To address these, the team embarked on a formal process of open dialogue amongst its members with the goal of identifying a collective response and position. This process involved meetings every 4 to 6 weeks over the course of 10 months. An iterative process unfolded. One of the principal dilemmas relates to finding a balance between the team’s position against AS and the patient’s autonomy and the institution’s directive. Although all team members expressed opposition to AS, there were mixed opinions as to whether or not the team members should be present during the act if requested so by patients. Some thought this could be misinterpreted as complicity in the act and could send out mixed messages to the public and other health professionals about palliative care. Others felt that the team’s commitment to nonabandonment obliged them to be present even if they did not provide the drug or give any advice or assistance. The implications of nonabandonment are explored, as are several other questions such as whether or not the teams are obliged to provide detailed information on AS when requested by patients.
Phosphodiesterase inhibitors for the treatment of pulmonary hypertension
Authors: Wilkins M. R. , Wharton J. , Grimminger F. , Ghofrani H. A. 
Published: June 2008

The pulmonary vascular bed is both a source of and target for a number of vasoactive factors. Among the most important for pulmonary vascular homeostasis are factors that utilise cyclic guanosine monophosphate (cGMP) as an intracellular second messenger. These include nitric oxide and the natriuretic peptide family (atrial, brain and C-type natriuretic peptides). In the search for therapeutic strategies that engage the cGMP signalling pathway for the treatment of pulmonary arterial hypertension (PAH), inhibition of cGMP metabolism by phosphodiesterase type 5 (PDE5)-targeted compounds has proven most successful to date. One PDE5 inhibitor, sildenafil, has been shown to improve pulmonary haemodynamics and exercise capacity in patients with PAH and is now an approved treatment. Others are under investigation.An interesting, although still tentative, observation is the potential of sildenafil to reduce pulmonary vascular resistance without adversely affecting ventilation–perfusion matching. Another is the expression of phosphodiesterase type 5 in the hypertrophied right ventricle. These data suggest that phosphodiesterase type 5 inhibitors may have effects that distinguish them from other treatments for pulmonary hypertension and merit further study.
Re-activation of bovine tuberculosis in a patient treated with infliximab: Table 1—
Authors: Larsen M. V. , Sørensen I. J. , Thomsen V. Ø. , Ravn P. 
Published: June 2008

Treatment with tumour necrosis factor-α inhibitors increases the risk of tuberculosis (TB). Screening for latent TB infection (LTBI) and prophylactic treatment has become mandatory.A 79-yr-old female with a history of severe erosive sero-positive rheumatoid arthritis was screened for LTBI before initiation of treatment with infliximab. The tuberculin skin test (TST) was negative, chest radiography was normal and she had no known risk factors for TB. After 4 months of treatment with infliximab, the patient developed ascites caused byMycobacterium bovis. The TST was repeatedly negative. QuantiFERON®-TB (QFT) testing performed during screening and immunosuppressive treatment was indeterminate, whereas the QFT test performed at the time of ascites puncture was positive.The patient history revealed previous work at a dairy, with probable exposure to unpasteurised milk fromM. bovis-infected cattle.Re-activation of bovine tuberculosis is a risk in people with recent or previous exposure to unpasteurised dairy products. The QuantiFERON®-TB test has the potential to detectMycobacterium bovisinfection. Indeterminate test results reflect either anergy, due to poor immunity, or technical problems and should be cautiously interpreted and as a minimum be repeated. Studies are ongoing to determine the role of QuantiFERON®-TB testing in the screening for latent tuberculosis infection.
Nonpharmacological treatment and relief of symptoms in COPD: Table 1—
Authors: Clini E. M. , Ambrosino N. 
Published: June 2008

Evidence-based guidelines for chronic obstructive pulmonary disease (COPD) have recently been developed.Nonpharmacological treatments have evolved rapidly as an essential part of COPD therapy. They are especially important as complementary interventions in severe or very severe disease, when there is loss in function, a reduction in quality of life and when psychological impairments further complicate the disease.The present article discusses the most used nonpharmacological treatments for severe COPD patients (rehabilitation, long-term oxygen therapy, surgery, noninvasive positive pressure ventilation and supportive nutrition) and their evidence-based usefulness in promoting strategies that relieve symptoms.All of these interventions are used during end-stage disease, to promote self-efficacy, relieve symptoms and prevent further deterioration. These therapeutic options support physicians and allied professionals in improving symptom management for their patients.
Statistical analysis of exacerbation rates in COPD: TRISTAN and ISOLDE revisited
Authors: Keene O. N. , Calverley P. M. A. , Jones P. W. , Vestbo J. , Anderson J. A. 
Published: June 2008

Various statistical methods have been used to measure the impact of treatment on chronic obstructive pulmonary disease (COPD) exacerbations. Poisson regression has recently been recommended as the appropriate method but the model does not satisfactorily account for variability between patients. In contrast, use of a negative binomial model, which corresponds to assuming a separate Poisson parameter for each patient, offers a more appealing approach.The present paper reviews analysis methods, with particular focus on the negative binomial model. To illustrate the differences that arise from using different analysis methods, we have reanalysed data from two large studies which, among other objectives, investigated the effectiveness of inhaled corticosteroids in reducing COPD exacerbation rates.Using the negative binomial model to reanalyse data from the TRISTAN and ISOLDE studies, the overall estimates of exacerbation rates on each treatment arm are higher and the confidence intervals for comparisons between treatments are wider, but the overall conclusions of TRISTAN and ISOLDE regarding reduction of exacerbations remain unchanged.The negative binomial approach appears to provide a better fit to the distribution of the data than earlier methods and is currently the method of choice. Research needs to continue on further methods to improve the analysis of exacerbation data.
The ORFeome of Staphylococcus aureus v 1.1
Authors: Brandner Christina J , Maier Richard H , Henderson Daryl S , Hintner Helmut , Bauer Johann W , Önder Kamil 
Published: July 2008

Abstract

Background
The bacterium Staphylococcus aureus causes significant morbidity and mortality in humans, primarily due to the emergence of strains that are resistant to antibiotics – notably methicillin-resistant S. aureus (MRSA) isolates. Development of effective strategies for the control and treatment of MRSA infections may best be achieved through 'omics' approaches, which first requires cloning the entire set of S. aureus' protein-encoding open reading frames (ORFs), or ORFeome.

Results
The complete genome sequence of S. aureus strain Mu50 has 2697 predicted protein-coding ORFs. Based on the sequence of this strain we designed PCR primers to construct from an S. aureus (non-MRSA) clinical isolate an ORFeome library that contains 2562 unique Gateway® entry clones (95% coverage), each corresponding to a defined ORF. The high quality of the ORFeome library was verified by DNA sequencing and PCR amplification, and its functionality was demonstrated by expressing recombinant proteins and observing protein interactions in a yeast 2-hybrid homodimerization screen.

Conclusion
This first ORFeome library for S. aureus provides an essential new tool for investigating the systems biology of this important pathogen.
Laparoscopic partial gastric transection and devascularization in order to enhance its flow
Authors: Cuenca-Abente Federico , Assalia Ahmad , del Genio Gianmattia , Rogula Tomasz , Nocca David , Ueda Kazuki , Gagner Michel 
Published: July 2008

Abstract

Background
Esophagogastric fistula following an esophagectomy for cancer is very common. One of the most important factors that leads to its development is gastric isquemia. We hypothesize that laparoscopic gastric devascularization and partial transection is a safe operation that will enhance the vascular flow of the fundus of the stomach.

Method
Our study included eight pigs. Each animal had two operations. In the first one, a laparoscopic gastric devascularization and mobilization took place. Vascular flow was measured previous to the procedure and immediately after it with a laser doppler (endoscopic probe). After three weeks, a second operation took place. We re-measured the vascular flow and sent a sample of gastric fundus for histopathologic evaluation.

Results
The gastric fundus showed signs of neovascularization after both macroscopic and microscopic evaluation. These findings correlated with laser doppler measurements.

Conclusion
Laparoscopic gastric devascularization and partial transection is a safe procedure that increases the vascular flow of the stomach in a three week period. This finding can have a positive impact in terms of decreasing fistula formation.
Protein structure protection commits gene expression patterns
Authors: Chen Jianping , Liang Han , Fernández Ariel 
Published: July 2008

Abstract
Background
Gene co-expressions often determine module-defining spatial and temporal concurrences of proteins. Yet, little effort has been devoted to tracing coordinating signals for expression correlations to the three-dimensional structures of gene products.

Results
We performed a global structure-based analysis of the yeast and human proteomes and contrasted this information against their respective transcriptome organizations obtained from comprehensive microarray data. We show that protein vulnerability quantifies dosage sensitivity for metabolic adaptation phases and tissue-specific patterns of mRNA expression, determining the extent of co-expression similarity of binding partners. The role of protein intrinsic disorder in transcriptome organization is also delineated by interrelating vulnerability, disorder propensity and co-expression patterns. Extremely vulnerable human proteins are shown to be subject to severe post-transcriptional regulation of their expression through significant micro-RNA targeting, making mRNA levels poor surrogates for protein-expression levels. By contrast, in yeast the expression of extremely under-wrapped proteins is likely regulated through protein aggregation. Thus, the 85 most vulnerable proteins in yeast include the five confirmed prions, while in human, the genes encoding extremely vulnerable proteins are predicted to be targeted by microRNAs. Hence, in both vastly different organisms protein vulnerability emerges as a structure-encoded signal for post-transcriptional regulation.

Conclusion
Vulnerability of protein structure and the concurrent need to maintain structural integrity are shown to quantify dosage sensitivity, compelling gene expression patterns across tissue types and temporal adaptation phases in a quantifiable manner. Extremely vulnerable proteins impose additional constraints on gene expression: They are subject to high levels of regulation at the post-transcriptional level.
Pitfalls and potential dangers in the referral process to a specialist brain injury unit
Authors: Kuruvatti Jay , Fleminger Simon 
Published: June 2008

Aims and MethodsWe looked retrospectively at referrals over 1 year and determined the length of time from receipt of the referral to the date when authorisation to see the patient was given, and the time from authorisation to first contact. For in-patients we determined the time from the recommendation for admission to the time authorisation was granted, and the time from authorisation to admission.ResultsOf the 108 referrals, 80 (74%) were seen within 13 weeks (mean=53 days); 7 patients (6%) had to wait over 13 weeks, usually because of delays in authorisation; 10 patients were admitted; 14 were never admitted (although we had recommended admission). The time from recommendation to admit to authorisation of admission, 27 days, was the same as the time they waited for a bed once authorisation had been given.Clinical ImplicationsWaiting for authorisation seemed in some patients to delay their access to tertiary services. Any advantage of using panels to authorise referrals, like ensuring better use of local resources, may be outweighed by patients taking longer to get the care that best meets their needs.