bluuebunny/crossref_metadata_2025_split huggingface dataset:
ANALYTICAL EXPRESSIONS FOR CORRECTION FACTORS FOR NOISE MEASUREMENTS WITH A FOUR-POINT PROBE
Authors: VANDAMME L. K. J. , LEROY G. 
Published: April 2006

The linear four-point probe method is useful to measure the resistivity, by passing a current I14 through the outer probes and by measuring the voltage V23 between the inner probes. The contacts are on a line and denoted by 1, 2, 3, 4, respectively. The sheet resistance for thin layers with thickness t is Rsh = ρ/t (Ω). The sheet resistance is measured as Rsh = (V23/I14). C23 where the correction factor is C23 = π/ln2 = 4.53 for t smaller than s, the distance between probe points. In order to characterize the 1/f noise of a film with a four-point probe we need noise correction factors for the calculation of the conductance noise from the voltage noise between the pair of points, where the current is not passed through. Our calculations of the noise correction factors are based on the general theory for conductance noise investigations with four arbitrarily shaped and placed electrodes. Analytical expressions for noise correction factors Fij and fij are derived and compared with experimental results for the three cases. The subscripts of F and f denote the voltage sensor contacts. The following cases are investigated: 1) I14 and V23, 2) I13 and V24 and 3) I12 and V34. The subscripts in I and V denote the current driver contacts and voltage sensor contacts, respectively. From the calculations and experimental results it follows that: i) case1 (I14 and V23) is the best choice in order to suppress a non-intentional noise contribution from the interface between probe tip and layer, ii) the reciprocity relation is applicable to voltage noise due to conductance fluctuations. The voltage noise SV23 that is observed by passing a constant current I14 through the pair of probes 1, 4 is equal to the voltage noise SV14 if we pass the same current through the contacts 2, 3. The four-point probe method with the noise correction factors can be recommended to investigate e.g., the conductance noise of conductive polymer layers even with an insulating top layer and without the preparation of rectangular samples with perfect noise-free line contacts. The four-point probe can punch an insulating top layer and allows the measurement of sheet resistance and noise. Several tests show that the noise contributions from the interface between probe tip and layer are negligible. The ratio of the conductance (1/f) noise, Cus, normalized for frequency and area and the sheet resistance gives an indication of the degree of percolation in composite conductive layers.
Modeling the Evolution of the Atmospheric Boundary Layer Coupled to the Land Surface for Three Contrasting Nights in CASES-99
Authors: Steeneveld G. J. , van de Wiel B. J. H. , Holtslag A. A. M. 
Published: April 2006

Abstract
The modeling and prediction of the stable boundary layer over land is a persistent, problematic feature in weather, climate, and air quality topics. Here, the performance of a state-of-the-art single-column boundary layer model is evaluated with observations from the 1999 Cooperative Atmosphere–Surface Exchange Study (CASES-99) field experiment. Very high model resolution in the atmosphere and the soil is utilized to represent three different stable boundary layer archetypes, namely, a fully turbulent night, an intermittently turbulent night, and a radiative night with hardly any turbulence (all at clear skies). Each archetype represents a different class of atmospheric stability. In the current model, the atmosphere is fully coupled to a vegetation layer and the underlying soil. In addition, stability functions (local scaling) are utilized based on in situ observations.
Overall it is found that the vertical structure, the surface fluxes (apart from the intermittent character) and the surface temperature in the stable boundary layer can be satisfactorily modeled for a broad stability range (at a local scale) with the current understanding of the physics of the stable boundary layer. This can also be achieved by the use of a rather detailed coupling between the atmosphere and the underlying soil and vegetation, together with high resolution in both the atmosphere and the soil. This is especially true for the very stable nights, when longwave radiative cooling is dominant. Both model outcome and observations show that in the latter case the soil heat flux is a dominant term of the surface energy budget.
Sensitivity Studies of the Importance of Dust Ice Nuclei for the Indirect Aerosol Effect on Stratiform Mixed-Phase Clouds
Authors: Lohmann U. , Diehl K. 
Published: April 2006

AbstractNew parameterizations of contact freezing and immersion freezing in stratiform mixed-phase clouds (with temperatures between 0° and −35°C) for black carbon and mineral dust assumed to be composed of either kaolinite (simulation KAO) or montmorillonite (simulation MON) are introduced into the ECHAM4 general circulation model. The effectiveness of black carbon and dust as ice nuclei as a function of temperature is parameterized from a compilation of laboratory studies. This is the first time that freezing parameterizations take the chemical composition of ice nuclei into account. The rather subtle differences between these sensitivity simulations in the present-day climate have significant implications for the anthropogenic indirect aerosol effect. The decrease in net radiation in these sensitivity simulations at the top of the atmosphere varies from 1 ± 0.3 to 2.1 ± 0.1 W m−2 depending on whether dust is assumed to be composed of kaolinite or montmorillonite. In simulation KAO, black carbon has a higher relevancy as an ice nucleus than in simulation MON, because kaolinite is not freezing as effectively as montmorillonite. In simulation KAO, the addition of anthropogenic aerosols results in a larger ice water path, a slightly higher precipitation rate, and a reduced total cloud cover. On the contrary, in simulation MON the increase in ice water path is much smaller and globally the decrease in precipitation is dominated by the reduction in warm-phase precipitation due to the indirect cloud lifetime effect.
A Method to Estimate Aerosol Radiative Forcing from Spectral Optical Depths
Authors: Satheesh S. K. , Srinivasan J. 
Published: April 2006

Abstract
Radiative forcing of aerosols is much more difficult to estimate than that of well-mixed gases due to the large spatial variability of aerosols and the lack of an adequate database on their radiative properties. Estimation of aerosol radiative forcing generally requires knowledge of its chemical composition, which is sparse. Ground-based sky radiance measurements [e.g., aerosol robotic network (AERONET)] can provide key parameters such as the single-scattering albedo, but in shipborne experiments over the ocean it is difficult to make sky radiance measurements and hence these experiments cannot provide parameters such as the single-scattering albedo. However, aerosol spectral optical depth data (cruise based as well as satellite retrieved) are available quite extensively over the ocean. Spectral optical depth measurements have been available since the 1970s, and spectral turbidity measurements (carried out at meteorological departments all over the world) have been available for several decades, while long-term continuous chemical composition information is not available. A new method to differentiate between scattering and absorbing aerosols is proposed here. This can be used to derive simple aerosol models that are optically equivalent and can simulate the observed aerosol optical properties and radiative fluxes, from spectral optical depth measurements. Thus, aerosol single-scattering albedo and, hence, aerosol radiative forcing can be estimated. Note that the proposed method is to estimate clear-sky aerosol radiative forcing (over regions where chemical composition data or sky radiance data are not available) and not to infer its exact chemical composition. Using several independent datasets from field experiments, it is demonstrated that the proposed method can be used to estimate aerosol radiative forcing (from spectral optical depths) with an accuracy of ±2 W m−2.
Origin of the Summertime Synoptic-Scale Wave Train in the Western North Pacific*
Authors: Li Tim 
Published: April 2006

Abstract
The origin of the summertime synoptic wave train in the western North Pacific is investigated with a multilevel, nonlinear baroclinic model. A realistic three-dimensional summer mean state is specified and eigenvectors are calculated by introducing small perturbation initially to the model. Numerical experiments indicate that the origin of the synoptic wave train may arise from instability of the summer mean flow in the presence of a convection–frictional convergence (CFC) feedback. In the lack of the CFC feedback, the summer mean flow supports only a least damped mode, characterized by a northwest–southeast-oriented wave train pattern with a zonal wavelength of 2500 km. In the presence of both the realistic summer mean flow and the CFC feedback, the model reproduces a fast growing mode, whose structure and propagation characters are similar to the observed.
Sensitivity experiments with different initial perturbation patterns indicate that the model solution is not sensitive to initial conditions. Further sensitivity experiments reveal that the basic-state vertical shear may affect the growth rate and propagation character of the wave train. An easterly shear may lead to a faster growth and northwestward phase propagation, whereas a westerly shear may favor a slower growth and southeastward phase propagation.
Seasonal Hydroclimate Variability over North America in Global and Regional Reanalyses and AMIP Simulations: Varied Representation
Authors: Nigam Sumant , Ruiz-Barradas Alfredo 
Published: April 2006

Abstract
The monotony of seasonal variability is often compensated by the complexity of its spatial structure—the case in North American hydroclimate. The structure of hydroclimate variability is analyzed to provide insights into the functioning of the climate system and climate models.
The consistency of hydroclimate representation in two global [40-yr ECMWF Re-Analysis (ERA-40) and NCEP] and one regional [North American Regional Reanalysis (NARR)] reanalysis is examined first, from analysis of precipitation, evaporation, surface air temperature (SAT), and moisture flux distributions. The intercomparisons benchmark the recently released NARR data and provide context for evaluation of the simulation potential of two state-of-the-art atmospheric models [NCAR's Community Atmospheric Model (CAM3.0) and NASA's Seasonal-to-Interannual Prediction Project (NSIPP) atmospheric model].
Intercomparisons paint a gloomy picture: great divergence in global reanalysis representations of precipitation, with the eastern United States being drier in ERA-40 and wetter in NCEP in the annual mean by up to a third in each case; model averages are like ERA-40. The annual means, in fact, mask even larger but offsetting seasonal departures.
Analysis of moisture transport shows winter fluxes to be more consistently represented. Summer flux convergence over the Gulf Coast and Great Plains, however, differs considerably between global and regional reanalyses. Flux distributions help in understanding the choice of rainy season, especially the winter one in the Pacific Northwest; stationary fluxes are key.
Land–ocean competition for convection is too intense in the models—so much so that the oceanic ITCZ in July is southward of its winter position in the both simulations! The overresponsiveness of land is also manifest in SAT; the winter-to-summer change over the Great Plains is 5–9 K larger than in observations, with implications for modeling of climate sensitivity.
The nature of atmospheric water balance over the Great Plains is probed, despite unbalanced moisture budgets in reanalyses and model simulations. The imbalance is smaller in NARR but still unacceptably large, resulting from excessive evaporation in spring and summer. Adjusting evaporation during precipitation assimilation could lead to a more balanced budget.
Global and regional reanalysis will remain of limited use for hydroclimate studies until they comply with the operative water and energy balance constraints.
Observed Vegetation–Climate Feedbacks in the United States*
Authors: Notaro M. , Liu Z. , Williams J. W. 
Published: April 2006

Abstract
Observed vegetation feedbacks on temperature and precipitation are assessed across the United States using satellite-based fraction of photosynthetically active radiation (FPAR) and monthly climate data for the period of 1982–2000. This study represents the first attempt to spatially quantify the observed local impact of vegetation on temperature and precipitation over the United States for all months and by season. Lead–lag correlations and feedback parameters are computed to determine the regions where vegetation substantially impacts the atmosphere and to quantify this forcing. Temperature imposes a significant instantaneous forcing on FPAR, while precipitation's impact on FPAR is greatest at one-month lead, particularly across the prairie. An increase in vegetation raises the surface air temperature by absorbing additional radiation and, in some cases, masking the high albedo of snow cover. Vegetation generally exhibits a positive forcing on temperature, strongest in spring and particularly across the northern states. The local impact of FPAR on precipitation appears to be spatially inhomogeneous and relatively weak, potentially due to the atmospheric transport of transpired water. The computed feedback parameters can be used to evaluate vegetation–climate interactions simulated by models with dynamic vegetation.
Hormonal regulation of alveolarization: structure-function correlation
Authors: Garber Samuel J , Zhang Huayan , Foley Joseph P , Zhao Hengjiang , Butler Stephan J , Godinez Rodolfo I , Godinez Marye H , Gow Andrew J , Savani Rashmin C 
Published: April 2006

Abstract

Background
Dexamethasone (Dex) limits and all-trans-retinoic acid (RA) promotes alveolarization. While structural changes resulting from such hormonal exposures are known, their functional consequences are unclear.

Methods
Neonatal rats were treated with Dex and/or RA during the first two weeks of life or were given RA after previous exposure to Dex. Morphology was assessed by light microscopy and radial alveolar counts. Function was evaluated by plethysmography at d13, pressure volume curves at d30, and exercise swim testing and arterial blood gases at both d15 and d30.

Results
Dex-treated animals had simplified lung architecture without secondary septation. Animals given RA alone had smaller, more numerous alveoli. Concomitant treatment with Dex + RA prevented the Dex-induced changes in septation. While the results of exposure to Dex + RA were sustained, the effects of RA alone were reversed two weeks after treatment was stopped. At d13, Dex-treated animals had increased lung volume, respiratory rate, tidal volume, and minute ventilation. On d15, both RA- and Dex-treated animals had hypercarbia and low arterial pH. By d30, the RA-treated animals resolved this respiratory acidosis, but Dex-treated animals continued to demonstrate blood gas and lung volume abnormalities. Concomitant RA treatment improved respiratory acidosis, but failed to normalize Dex-induced changes in pulmonary function and lung volumes. No differences in exercise tolerance were noted at either d15 or d30. RA treatment after the period of alveolarization also corrected the effects of earlier Dex exposure, but the structural changes due to RA alone were again lost two weeks after treatment.

Conclusion
We conclude that both RA- and corticosteroid-treatments are associated with respiratory acidosis at d15. While RA alone-induced changes in structure andrespiratory function are reversed, Dex-treated animals continue to demonstrate increased respiratory rate, minute ventilation, tidal and total lung volumes at d30. Concomitant treatment with Dex + RA prevents decreased septation induced by Dex alone and results in correction of hypercarbia. However, these animals continue to have abnormal pulmonary function and lung volumes. Increased septation as a result of RA treatment alone is reversed upon discontinuation of treatment. These data suggest that Dex + RA treatment results in improved gas exchange likely secondary to normalized septation.
Exploring supervised and unsupervised methods to detect topics in biomedical text
Authors: Lee Minsuk , Wang Weiqing , Yu Hong 
Published: April 2006

Abstract

Background
Topic detection is a task that automatically identifies topics (e.g., "biochemistry" and "protein structure") in scientific articles based on information content. Topic detection will benefit many other natural language processing tasks including information retrieval, text summarization and question answering; and is a necessary step towards the building of an information system that provides an efficient way for biologists to seek information from an ocean of literature.

Results
We have explored the methods of Topic Spotting, a task of text categorization that applies the supervised machine-learning technique naïve Bayes to assign automatically a document into one or more predefined topics; and Topic Clustering, which apply unsupervised hierarchical clustering algorithms to aggregate documents into clusters such that each cluster represents a topic. We have applied our methods to detect topics of more than fifteen thousand of articles that represent over sixteen thousand entries in the Online Mendelian Inheritance in Man (OMIM) database. We have explored bag of words as the features. Additionally, we have explored semantic features; namely, the Medical Subject Headings (MeSH) that are assigned to the MEDLINE records, and the Unified Medical Language System (UMLS) semantic types that correspond to the MeSH terms, in addition to bag of words, to facilitate the tasks of topic detection. Our results indicate that incorporating the MeSH terms and the UMLS semantic types as additional features enhances the performance of topic detection and the naïve Bayes has the highest accuracy, 66.4%, for predicting the topic of an OMIM article as one of the total twenty-five topics.

Conclusion
Our results indicate that the supervised topic spotting methods outperformed the unsupervised topic clustering; on the other hand, the unsupervised topic clustering methods have the advantages of being robust and applicable in real world settings.
More robust detection of motifs in coexpressed genes by using phylogenetic information
Authors: Monsieurs Pieter , Thijs Gert , Fadda Abeer A , De Keersmaecker Sigrid CJ , Vanderleyden Jozef , De Moor Bart , Marchal Kathleen 
Published: April 2006

Abstract

Background
Several motif detection algorithms have been developed to discover overrepresented motifs in sets of coexpressed genes. However, in a noisy gene list, the number of genes containing the motif versus the number lacking the motif might not be sufficiently high to allow detection by classical motif detection tools. To still recover motifs which are not significantly enriched but still present, we developed a procedure in which we use phylogenetic footprinting to first delineate all potential motifs in each gene. Then we mutually compare all detected motifs and identify the ones that are shared by at least a few genes in the data set as potential candidates.

Results
We applied our methodology to a compiled test data set containing known regulatory motifs and to two biological data sets derived from genome wide expression studies. By executing four consecutive steps of 1) identifying conserved regions in orthologous intergenic regions, 2) aligning these conserved regions, 3) clustering the conserved regions containing similar regulatory regions followed by extraction of the regulatory motifs and 4) screening the input intergenic sequences with detected regulatory motif models, our methodology proves to be a powerful tool for detecting regulatory motifs when a low signal to noise ratio is present in the input data set. Comparing our results with two other motif detection algorithms points out the robustness of our algorithm.

Conclusion
We developed an approach that can reliably identify multiple regulatory motifs lacking a high degree of overrepresentation in a set of coexpressed genes (motifs belonging to sparsely connected hubs in the regulatory network) by exploiting the advantages of using both coexpression and phylogenetic information.
GOPET: A tool for automated predictions of Gene Ontology terms
Authors: Vinayagam Arunachalam , del Val Coral , Schubert Falk , Eils Roland , Glatting Karl-Heinz , Suhai Sándor , König Rainer 
Published: April 2006

Abstract

Background
Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however, either apply to specific subsets, or their predictions are not formalised, or they do not provide precise confidence values for their predictions.

Description
We recently established a learning system for automated annotation, trained with a broad variety of different organisms to predict the standardised annotation terms from Gene Ontology (GO). Now, this method has been made available to the public via our web-service GOPET (Gene Ontology term Prediction and Evaluation Tool). It supplies annotation for sequences of any organism. For each predicted term an appropriate confidence value is provided. The basic method had been developed for predicting molecular function GO-terms. It is now expanded to predict biological process terms. This web service is available via http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar

Conclusion
Our web service gives experimental researchers as well as the bioinformatics community a valuable sequence annotation device. Additionally, GOPET also provides less significant annotation data which may serve as an extended discovery platform for the user.