bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response of Humidity and Clouds to Tropical Deep Convection
Authors: Zelinka Mark D. , Hartmann Dennis L. 
Published: December 2008

Abstract
Currently available satellite data can be used to track the response of clouds and humidity to intense precipitation events. A compositing technique centered in space and time on locations experiencing high rain rates is used to detail the characteristic evolution of several quantities measured from a suite of satellite instruments. Intense precipitation events in the convective tropics are preceded by an increase in low-level humidity. Optically thick cold clouds accompany the precipitation burst, which is followed by the development of spreading upper-level anvil clouds and an increase in upper-tropospheric humidity over a broader region than that occupied by the precipitation anomalies. The temporal separation between the convective event and the development of anvil clouds is about 3 h. The humidity increase at upper levels and the associated decrease in clear-sky longwave emission persist for many hours after the convective event. Large-scale vertical motions from reanalysis show a coherent evolution associated with precipitation events identified in an independent dataset: precipitation events begin with stronger upward motion anomalies in the lower troposphere, which then evolve toward stronger upward motion anomalies in the upper troposphere, in conjunction with the development of anvil clouds. Greater upper-tropospheric moistening and cloudiness are associated with larger-scale and better-organized convective systems, but even weaker, more isolated systems produce sustained upper-level humidity and clear-sky outgoing longwave radiation anomalies.
Parameter Sensitivity in LSMs: An Analysis Using Stochastic Soil Moisture Models and ELDAS Soil Parameters
Authors: Teuling Adriaan J. , Uijlenhoet Remko , van den Hurk Bart , Seneviratne Sonia I. 
Published: December 2008

Abstract
Integration of simulated and observed states through data assimilation as well as model evaluation requires a realistic representation of soil moisture in land surface models (LSMs). However, soil moisture in LSMs is sensitive to a range of uncertain input parameters, and intermodel differences in parameter values are often large. Here, the effect of soil parameters on soil moisture and evapotranspiration are investigated by using parameters from three different LSMs participating in the European Land Data Assimilation System (ELDAS) project. To prevent compensating effects from other than soil parameters, the effects are evaluated within a common framework of parsimonious stochastic soil moisture models. First, soil parameters are shown to affect soil moisture more strongly than the average evapotranspiration. In arid climates, the effect of soil parameters is on the variance rather than the mean, and the intermodel flux differences are smallest. Soil parameters from the ELDAS LSMs differ strongly, most notably in the available moisture content between the wilting point and the critical moisture content, which differ by a factor of 3. The ELDAS parameters can lead to differences in mean volumetric soil moisture as high as 0.10 and an average evapotranspiration of 10%–20% for the investigated parameter range. The parsimonious framework presented here can be used to investigate first-order parameter sensitivities under a range of climate conditions without using full LSM simulations. The results are consistent with many other studies using different LSMs under a more limited range of possible forcing conditions.
On the Correction of Partial Beam Blockage in Polarimetric Radar Data
Authors: Lang Timothy J. , Nesbitt Stephen W. , Carey Lawrence D. 
Published: December 2008

Abstract
Three methodologies for correcting the radar reflectivity factor (ZH) in the presence of partial beam blockage are implemented, compared, and evaluated using a polarimetric radar dataset from the North American Monsoon Experiment (NAME) in northwestern Mexico. One methodology uses simulated interactions between radar beams and digital terrain maps, while the other two invoke the self-consistency of polarimetric radar measurands in rainfall, and the relative insensitivity of a specific differential phase to beam blockage. While the different methodologies often agree to within 1–2 dB, significant disagreements can occur in regions of sharp azimuthal gradients in beam blockage patterns, and in areas where the terrain-caused radar clutter map is complex. These disagreements may be mitigated by the use of additional radar data to develop the polarimetric correction techniques, by a more sophisticated terrain-beam interaction model, or by a higher-resolution digital terrain map. Intercomparisons between ground radar data and Tropical Rainfall Measuring Mission satellite overpasses suggest that all of the methodologies can correct mean ZH to within the expected uncertainty of such intercomparisons (1–1.5 dB). The polarimetric correction methods showed good results even in severely blocked regions (&gt;10 dB reduction). The results suggest the possibility that all of the techniques may be valid approaches to correcting partial beam blockage, and within that context relative advantages and disadvantages of each technique are discussed. However, none of the techniques can correct radar data when weak echoes are reduced to noise by strong blocks, thus leading to biases in corrected ZH and rainfall climatologies.
A Variational Method for Computation of Sensible Heat Flux over the Arctic Sea Ice
Authors: Cao Zuohao , Ma Jianmin 
Published: December 2008

Abstract
In this study, a variational approach was employed to compute surface sensible heat flux over the Arctic sea ice. Because the variational approach is able to take into account information from the Monin–Obukhov similarity theory (MOST) as well as the observed meteorological information, it is expected to improve the pure MOST-based approach in computation of sensible heat flux. Verifications using the direct eddy-correlation measurements over the Arctic sea ice during the Surface Heat Budget of the Arctic Ocean (SHEBA) experiment period of 1997/98 show that the variational method yields good agreement between the computed and the measured sensible heat fluxes. The variational method is also shown to be more accurate than the traditional MOST method in the computation of sensible heat flux over the Arctic sea ice.
A Comparison of Variational and Ensemble-Based Data Assimilation Systems for Reanalysis of Sparse Observations
Authors: Whitaker Jeffrey S. , Compo Gilbert P. , Thépaut Jean-Noël 
Published: December 2008

Abstract
An observing system experiment, simulating a surface-only observing network representative of the 1930s, is carried out with three- and four-dimensional variational data assimilation systems (3D-VAR and 4D-VAR) and an ensemble-based data assimilation system (EnsDA). It is found that 4D-VAR and EnsDA systems produce analyses of comparable quality and that both are much more accurate than the analyses produced by the 3D-VAR system. The EnsDA system also produces useful estimates of analysis error, which are not directly available from the variational systems.
Influence of section size on dual phase ADI microstructure and properties: Comparison with fully ferritic and fully ausferritic matrices
Authors: Basso A. , Martínez R. , Sikora J. 
Published: December 2008

The present work aims to evaluate and compare the influence that section size has on the microstructure and properties of fully ferritic, fully ausferritic and dual phase ADI matrices. Samples taken from ‘Y’ blocks of 25, 50 and 75 mm thickness were used to perform metallographic studies and mechanical tests. Cooling rate differences arising from changes in section size promote different microsegregation characteristics affecting solid state transformations and, consequently, the final microstructure and properties. When the section size increases, some properties decrease. The strongest deleterious effect was ascribed to the elongation and impact of ADI samples, where drops of nearly 40% were reached when specimens taken from the thinnest ‘Y’ blocks were compared to those taken from the thickest ones. Regarding fracture toughness, ferritic matrices exhibited the most noticeable detrimental effect. Dual phase ADI samples, on the other hand, presented the least deleterious section size effect on all the studied properties.
Naturally occurring regulatory T cells show reduced sensitivity toward oxidative stress–induced cell death
Authors: Mougiakakos Dimitrios , Johansson C. Christian , Kiessling Rolf 
Published: December 2008

Abstract
Although the authors of several studies report elevated numbers of immunosuppressive regulatory T cells (Tregs) in hematologic and solid malignancies, the underlying mechanism is not fully clarified. Cancer is associated with oxidative stress mediated through reactive oxygen species produced by malignant cells, granulocytes, tumor-associated macrophages, and myeloid-derived suppressor cells. Oxidative stress is known to have detrimental effects on natural killer (NK) and T cells during chronic inflammatory conditions and cancer. Paradoxically, greater numbers of Tregs can be detected at tumor sites, indicating that Tregs can persist in this environment of increased oxidative stress. We demonstrate that Tregs, especially naive CD45RA+, exhibit reduced sensitivity to oxidative stress–induced cell death and maintain their suppressive function, a phenomenon that may be attributed to their observed high antioxidative capacity. This newly described characteristic could explain their enrichment in malignancies associated with increased levels of oxidative stress.
Differential diagnosis and management of focal ground-glass opacities
Authors: Infante M. , Lutman R. F. , Imparato S. , Di Rocco M. , Ceresoli G. L. , Torri V. , Morenghi E. , Minuti F. , Cavuto S. , Bottoni E. , Inzirillo F. , Cariboni U. , Errico V. , Incarbone M. A. , Ferraroli G. , Brambilla G. , Alloisio M. , Ravasi G. 
Published: December 2008

Focal pulmonary ground-glass opacities (GGOs) can be associated with bronchioloalveolar carcinoma. The present retrospective study aimed to test the validity of a multistep approach to discriminate malignant from benign localised (focal) GGOs, identifies useful diagnostic features on computed tomography (CT), and suggests appropriate management guidelines.A stepwise approach, including oral antibiotics, follow-up high-resolution CT (HRCT) 40–60 days later and CT-guided core biopsy, was used. All cases with localised GGOs detected since 2001 were reviewed. CT features were described according to a structured scheme. In total, 40 patients were evaluated. Of these, 11 patients were diagnosed with benign GGOs, 19 patients had lung cancer and 10 were undetermined.Nonpolygonal shape, apparent radial growth and clear-cut margins were associated with a malignant histology. The specificity of CT findings was low. Diagnostic accuracy increased after oral antibiotics, follow-up HRCT and percutaneous core biopsy. Overall, 18 patients underwent surgery for lung cancer.In conclusion, malignant ground-glass opacities have a fairly typical appearance, but some benign lesions closely mimic their malignant counterparts. The stepwise approach adopted in the present study increased the diagnostic specificity and reduced time to definitive diagnosis. Segmentectomy might be the ideal resection volume for such tumours.
Diagnostic value of interleukin-12 p40 in tuberculous pleural effusions
Authors: Valdés L. , San José E. , Álvarez Dobaño J. M. , Golpe A. , Valle J. M. , Penela P. , González Barcala F. J. 
Published: December 2008

The diagnosis of tuberculous pleural effusion (TBPE) is frequently problematic. Several markers of TBPE in pleural fluid have been evaluated, with different results.Pleural effusions from 96 patients were classified on the basis of definitive diagnosis as tuberculous (n = 39), neoplastic (n = 42) or parapneumonic (n = 15). Adenosine deaminase (ADA), ADA isoform ADA-2, interferon (IFN)-γ, CD3+/DR+T-lymphocytes and interleukin (IL)-12 p40 were determined in all 96 effusions. The efficiency of IL-12 p40 for diagnosis of TBPEs was evaluated, in comparison with those of the other parameters, by comparing the areas under their receiver operating characteristics.With the threshold value of 550 pg·mL−1, IL-12 p40 had a sensitivity of 92.3% (36 out of 39) and specificity of 70.2% (17 false positives). The misclassification rate of IL-12 p40 was significantly greater than those of ADA-2 and ADA. Among TBPEs, ADA correlated significantly with ADA-2, and IFN-γ with ADA and IL-12 p40.Although tuberculous pleural effusions show values of interleukin-12 p40 that are significantly higher than neoplastic and parapneumonic fluids, this parameter is less efficient than adenosine deaminase, adenosine deaminase isoform 2 and interferon-γ. Its routine determination is, accordingly, not justified.
QuantiFERON-TB Gold and the TST are both useful for latent tuberculosis infection screening in autoimmune diseases
Authors: Bartalesi F. , Vicidomini S. , Goletti D. , Fiorelli C. , Fiori G. , Melchiorre D. , Tortoli E. , Mantella A. , Benucci M. , Girardi E. , Cerinic M. M. , Bartoloni A. 
Published: December 2008

Screening for active tuberculosis (TB) and latent TB infection (LTBI) is mandatory prior to the initiation of tumour necrosis factor-α inhibitor therapy. However, no agreement exists on the best strategy for detecting LTBI in this population. The aim of the present study was to analyse the performance of the tuberculin skin test (TST) and QuantiFERON®-TB Gold in-tube (QFT-GIT) on LTBI detection in subjects with immunomediated inflammatory diseases (IMID).The TST and QFT-GIT were prospectively performed in 398 consecutive IMID subjects, 310 (78%) on immunosuppressive therapy and only 16 (4%) had been bacillus Calmette–Guérin (BCG) vaccinated.Indeterminate results to QFT-GIT were found in five (1.2%) subjects. Overall, 74 (19%) out of 393 subjects were TST-positive and 52 (13%) were QFT-GIT-positive. Concordance between TST and QFT-GIT results was good (87.7%): 13 were QFT-GIT-positive/TST-negative and 35 QFT-GIT-negative/TST-positive. By multivariate analysis both tests were significantly associated with older age. Only the TST was associated with BCG vaccination and radiological lesions of past TB. Use of immunosuppressive drugs differently modulated QFT-GIT or TST scoring.Use of the QuantiFERON®-TB Gold in-tube, as a screening tool for latent tuberculosis among immunomediated inflammatory disease subjects, is feasible. Until further data will elucidate discordant tuberculin skin test/QuantiFERON®-TB Gold in-tube results, a strategy of simultaneous tuberculin skin and QuantiFERON®-TB Gold in-tube testing in a low prevalence bacillus Calmette–Guérin vaccinated population, should maximise potentials of latent tuberculosis diagnosis.
Comparison of methods for estimating the nucleotide substitution matrix
Authors: Oscamou Maribeth , McDonald Daniel , Yap Von Bing , Huttley Gavin A , Lladser Manuel E , Knight Rob 
Published: December 2008

Abstract

Background
The nucleotide substitution rate matrix is a key parameter of molecular evolution. Several methods for inferring this parameter have been proposed, with different mathematical bases. These methods include counting sequence differences and taking the log of the resulting probability matrices, methods based on Markov triples, and maximum likelihood methods that infer the substitution probabilities that lead to the most likely model of evolution. However, the speed and accuracy of these methods has not been compared.

Results
Different methods differ in performance by orders of magnitude (ranging from 1 ms to 10 s per matrix), but differences in accuracy of rate matrix reconstruction appear to be relatively small. Encouragingly, relatively simple and fast methods can provide results at least as accurate as far more complex and computationally intensive methods, especially when the sequences to be compared are relatively short.

Conclusion
Based on the conditions tested, we recommend the use of method of Gojobori et al. (1982) for long sequences (> 600 nucleotides), and the method of Goldman et al. (1996) for shorter sequences (< 600 nucleotides). The method of Barry and Hartigan (1987) can provide somewhat more accuracy, measured as the Euclidean distance between the true and inferred matrices, on long sequences (> 2000 nucleotides) at the expense of substantially longer computation time. The availability of methods that are both fast and accurate will allow us to gain a global picture of change in the nucleotide substitution rate matrix on a genomewide scale across the tree of life.
Genomic complexity of the variable region-containing chitin-binding proteins in amphioxus
Authors: Dishaw Larry J , Mueller M Gail , Gwatney Natasha , Cannon John P , Haire Robert N , Litman Ronda T , Amemiya Chris T , Ota Tatsuya , Rowen Lee , Glusman Gustavo , Litman Gary W 
Published: December 2008

Abstract

Background
The variable region-containing chitin-binding proteins (VCBPs) are found in protochordates and consist of two tandem immunoglobulin variable (V)-type domains and a chitin-binding domain. We previously have shown that these polymorphic genes, which primarily are expressed in the gut, exhibit characteristics of immune genes. In this report, we describe VCBP genomic organization and characterize adjacent and intervening genetic features which may influence both their polymorphism and complex transcriptional repertoire.

Results
VCBP genes 1, 2, 4, and 5 are encoded in a single contiguous gene-rich chromosomal region and VCBP3 is encoded in a separate locus. The VCBPs exhibit extensive haplotype variation, including copy number variation (CNV), indel polymorphism and a markedly elevated variation in repeat type and density. In at least one haplotype, inverted repeats occur more frequently than elsewhere in the genome. Multi-animal cDNA screening, as well as transcriptional profilingusing a novel transfection system, suggests that haplotype-specific transcriptional variants may contribute to VCBP genetic diversity.

Conclusion
The availability of the Branchiostoma floridae genome (Joint Genome Institute, Brafl1), along with BAC and PAC screening and sequencing described here, reveal that the relatively limited number of VCBP genes present in the amphioxus genome exhibit exceptionally high haplotype variation. These VCBP haplotypes contribute a diverse pool of allelic variants, which includes gene copy number variation, pseudogenes, and other polymorphisms, while contributing secondary effects on gene transcription as well.
Probing of Actinobacillus pleuropneumoniae ApxIIIA toxin-dependent cytotoxicity towards mammalian peripheral blood mononucleated cells
Authors: Vanden Bergh Philippe GAC , Zecchinon Laurent LM , Fett Thomas , Desmecht Daniel 
Published: December 2008

AbstractBackgroundActinobacillus pleuropneumoniae, the causative bacterial agent of porcine pleuropneumonia, produces Apx toxins which belong to RTX toxin family and are recognized as the major virulence factors. So far, their target receptor(s) has not been identified and the disease cytopathogenesis remains poorly understood. Production of an active Apx toxin and characterization of its toxic activity constitute the premises necessary to the description of its interaction with a potential receptor. From this point of view, we produced an active recombinant ApxIIIA toxin in order to characterize its toxicity on peripheral blood mononucleated cells (PBMCs) isolated from several species.FindingsToxin preparation exercises a strong cytotoxic action on porcine PBMCs which is directly related to recombinant ApxIIIA since preincubation with polymyxin B does not modify the cytotoxicity rate while preincubation with a monospecific polyclonal antiserum directed against ApxIIIA does. The cell death process triggered by ApxIIIA is extremely fast, the maximum rate of toxicity being already reached after 20 minutes of incubation. Moreover, ApxIIIA cytotoxicity is species-specific because llama, human, dog, rat and mouse PBMCs are resistant. Interestingly, bovine and caprine PBMCs are slightly sensitive to ApxIIIA toxin too. Finally, ApxIIIA cytotoxicity is cell type-specific as porcine epithelial cells are resistant.ConclusionWe have produced an active recombinant ApxIIIA toxin and characterized its specific cytotoxicity on porcine PBMCs which will allow us to get new insights on porcine pleuropneumonia pathogenesis in the future.
An artificial intelligence tool to predict fluid requirement in the intensive care unit: a proof-of-concept study
Authors: Celi Leo Anthony , Hinske Christian L , Alterovitz Gil , Szolovits Peter 
Published: December 2008

Abstract
Introduction
The goal of personalised medicine in the intensive care unit (ICU) is to predict which diagnostic tests, monitoring interventions and treatments translate to improved outcomes given the variation between patients. Unfortunately, processes such as gene transcription and drug metabolism are dynamic in the critically ill; that is, information obtained during static non-diseased conditions may have limited applicability. We propose an alternative way of personalising medicine in the ICU on a real-time basis using information derived from the application of artificial intelligence on a high-resolution database. Calculation of maintenance fluid requirement at the height of systemic inflammatory response was selected to investigate the feasibility of this approach.

Methods
The Multi-parameter Intelligent Monitoring for Intensive Care II (MIMIC II) is a database of patients admitted to the Beth Israel Deaconess Medical Center ICU in Boston. Patients who were on vasopressors for more than six hours during the first 24 hours of admission were identified from the database. Demographic and physiological variables that might affect fluid requirement or reflect the intravascular volume during the first 24 hours in the ICU were extracted from the database. The outcome to be predicted is the total amount of fluid given during the second 24 hours in the ICU, including all the fluid boluses administered.

Results
We represented the variables by learning a Bayesian network from the underlying data. Using 10-fold cross-validation repeated 100 times, the accuracy of the model in predicting the outcome is 77.8%. The network generated has a threshold Bayes factor of seven representing the posterior probability of the model given the observed data. This Bayes factor translates into p < 0.05 assuming a Gaussian distribution of the variables.

Conclusions
Based on the model, the probability that a patient would require a certain range of fluid on day two can be predicted. In the presence of a larger database, analysis may be limited to patients with identical clinical presentation, demographic factors, co-morbidities, current physiological data and those who did not develop complications as a result of fluid administration. By better predicting maintenance fluid requirements based on the previous day's physiological variables, one might be able to prevent hypotensive episodes requiring fluid boluses during the course of the following day.