bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Urban Surface Energy Fluxes Using an Open-Air Scale Model
Authors: Pearlmutter D. , Berliner P. , Shaviv E. 
Published: May 2005

Abstract
The thermal behavior of an urban surface is crucial to understand, but it is difficult to predict using conventional measurement or modeling approaches. In this study, an integrated method is proposed for evaluating urban energy exchanges with an open-air scale model of a building–street canyon surface array. The technique, which potentially combines the flexibility of modeling with the reliability of empirical observation under natural turbulence and radiative loading, is tested in hot, arid summer conditions to gauge its ability for reproducing surface–atmosphere energy fluxes that are representative of diurnal patterns in actual urban settings. After identifying the inertial sublayer, which is created above the scaled roughness array at a point near its downwind edge, roughness parameters utilized in the calculation of turbulent sensible heat flux are determined for two different array configurations of varying frontal area density and compared with existing data from field studies and morphometric models. For each geometric configuration, the relative sharing of radiant energy between storage and turbulent fluxes is compared with published findings obtained by conventional methods, as is the diurnal pattern of each component flux. Roughness parameters that are obtained conform to the expected ranges, as do daytime and overall daily fluxes and flux ratios. Overall, radiation absorption and heat storage are higher in the array with deeper canyons, and in both arrays the share of sensible heat channeled into the atmosphere is both higher in magnitude and later in reaching its peak intensity than that which is stored within the scaled urban fabric. This thermal time lag, when evaluated by fitting data to a published model for parameterizing heat storage from net radiation, shows a high correlation with hysteresis behavior in actual cities.
Use of a Neurovariational Inversion for Retrieving Oceanic and Atmospheric Constituents from Ocean Color Imagery: A Feasibility Study
Authors: Jamet C. , Thiria S. , Moulin C. , Crepon M. 
Published: May 2005

AbstractThis paper presents a neurovariational method for inverting satellite ocean-color signals. The method is based on a combination of neural networks and classical variational inversion. The radiative transfer equations are modeled by neural networks whose inputs are the oceanic and atmospheric parameters, and outputs the top of the atmosphere reflectance at several wavelengths. The procedure consists in minimizing a quadratic cost function that is the distance between the satellite-observed reflectance and the computed neural-network reflectance, the control parameters being the oceanic and atmospheric parameters.First, a feasibility experiment using synthetic data is presented to show that chlorophyll-a can be retrieved with an error of 19.7% when the atmospheric parameters are known exactly. Then both atmospheric and oceanic parameters are relaxed. A first guess for the atmospheric parameters was provided by a direct inverse neural network whose inputs are at near-infrared wavelengths. Sensitivity experiments showed that these parameters can be retrieved with an adequate accuracy.An inversion of a composite SeaWiFS image is presented. Optical thickness and chlorophyll-a both give coherent spatial structures when a background term is added to the cost function. Finally, chlorophyll-a retrievals are compared with SeaWiFS product through in situ data. It shows a better estimation of the chlorophyll-a with the neurovariational inversion for the oligotrophic regions.
An Adaptive Moments Estimation Technique Applied to MST Radar Echoes
Authors: Anandan V. K. , Balamuralidhar P. , Rao P. B. , Jain A. R. , Pan C. J. 
Published: May 2005

Abstract
An adaptive spectral moments estimation technique has been developed for analyzing the Doppler spectra of the mesosphere–stratosphere–troposphere (MST) radar signals. The technique, implemented with the MST radar at Gadanki (13.5°N, 79°E), is based on certain criteria, set up for the Doppler window, signal-to-noise ratio (SNR), and wind shear parameters, which are used to adaptively track the signal in the range–Doppler spectral frame. Two cases of radar data, one for low and the other for high SNR conditions, have been analyzed and the results are compared with those from the conventional method based on the strongest peak detection in each range gate. The results clearly demonstrate that by using the adaptive method the height coverage can be considerably enhanced compared to the conventional method. For the low SNR case, the height coverage for the adaptive and conventional methods is about 22 and 11 km, respectively; the corresponding heights for the high SNR case are 24 and 13 km. To validate the results obtained through the adaptive method, the velocity profile is compared with global positioning system balloon sounding (GPS sonde) observations. The results of the adaptive method show excellent agreement with the GPS sonde measured wind speeds and directions throughout the height profile. To check the robustness and reliability of the adaptive algorithm, data taken over a diurnal cycle at 1-h intervals were analyzed. The results demonstrate the reliability of the algorithm in extracting wind profiles that are self-consistent in time. The adaptive method is thus found to be of considerable advantage over the conventional method in extracting information from the MST radar signal spectrum, particularly under low SNR conditions that are free from interference and ground clutter.
Retrieval of Arbitrarily Shaped Raindrop Size Distributions from Wind Profiler Measurements
Authors: Kobayashi Takahisa , Adachi Ahoro 
Published: May 2005

Abstract
An efficient iterative retrieval method for arbitrarily shaped raindrop size distributions (ITRAN) is developed for Doppler spectra measured with a wind profiler. A measured Doppler spectrum is a convolution of the precipitation spectrum and the turbulent spectrum. Deconvolution of the Doppler spectra is achieved through repeated convolutions. The developed method assumes no prior shape of drop size distributions and automatically obtains raindrop size distributions; additionally, it can be applied to large data volumes. Furthermore, it is insensitive to initial values. The method was applied to both simulated and observed spectra. Derived drop size distributions agree with simulated values. Narrower turbulent spectral widths yield better results. Integral values of median volume diameter (D0), liquid water content (LWC), and radar reflectivity factor are estimated with errors of less than 10%. Accurate vertical profiles of raindrop size distributions result when this method is applied to wind profiler data. The technique performed very well with most observed spectra. Some recovered spectra departed from the corresponding measured spectra, for cases in which a clear-air peak could not be accurately reproduced because of uncertainties in the location of the minimum position between the clear-air echo and the precipitation echo. Statistical relationships between LWC and integral rainfall parameters yield interesting features. The median volume diameter is statistically independent of the LWC and is associated with the large variability of the total number of drops, NT, between events. Vertical profiles from one event show a clear inverse relationship between NT and D0
Test of a Staggered PRT Scheme for the French Radar Network
Authors: Tabary P. , Perier L. , Gagneux J. , Parent-du-Chatelet J. 
Published: May 2005

Abstract
This paper describes the test of a staggered PRT scheme for the French radar network. The design of the staggered scheme has been done in the following context: 1) the scheme is meant to be implemented on existing C-band and S-band radars of the network, the PRF of which cannot, for technical reasons, be increased above their current values (300–400 Hz for C band and 250–300 Hz for S band); 2) the minimum expected Nyquist velocity should be around 30 m s−1; and 3) the Doppler information will essentially be used to retrieve a VAD wind profile and for data assimilation by operational nonhydrostatic numerical prediction models. An operational C-band radar of the network, located in Trappes, near Paris, has been modified in order to allow Doppler processing and a dual-PRT staggered scheme with two low PRFs (PRF1=310 and PRF2=360 Hz corresponding to a ratio of 6/7) has been implemented. Two months of data (July–August 2003) have been analyzed. The performance of the scheme is assessed qualitatively and quantitatively through the computation of the error structure of the various velocities: velocity at PRF1, velocity at PRF2, and combined velocity. The sensitivity of the error structure on the signal-to-noise ratio is documented. A 7 km × 7 km median filter is introduced to reduce dealiasing errors.
Measurement of Low Amounts of Precipitable Water Vapor Using Ground-Based Millimeterwave Radiometry
Authors: Racette Paul E. , Westwater Ed R. , Han Yong , Gasiewski Albin J. , Klein Marian , Cimini Domenico , Jones David C. , Manning Will , Kim Edward J. , Wang James R. , Leuski Vladimir , Kiedron Peter 
Published: May 2005

Abstract
Extremely dry conditions characterized by amounts of precipitable water vapor (PWV) as low as 1–2 mm commonly occur in high-latitude regions during the winter months. While such dry atmospheres carry only a few percent of the latent heat energy compared to tropical atmospheres, the effects of low vapor amounts on the polar radiation budget—both directly through modulation of longwave radiation and indirectly through the formation of clouds—are considerable. Accurate measurements of PWV during such dry conditions are needed to improve polar radiation models for use in understanding and predicting change in the climatically sensitive polar regions. To this end, the strong water-vapor absorption line at 183.310 GHz provides a unique means of measuring low amounts of PWV. Weighting function analysis, forward model calculations based upon a 7-yr radiosonde dataset, and retrieval simulations consistently predict that radiometric measurements made using several millimeter-wavelength (MMW) channels near the 183-GHz line, together with established microwave (MW) measurements near the 22.235-GHz water-vapor line and ∼31-GHz atmospheric absorption window can be used to determine within 5% uncertainty the full range of PWV expected in the Arctic. This combined capability stands in spite of accuracy limitations stemming from uncertainties due to the sensitivity of the vertical distribution of temperature and water vapor at MMW channels.
In this study the potential of MMW radiometry using the 183-GHz line for measuring low amounts of PWV is demonstrated both theoretically and experimentally. The study uses data obtained during March 1999 as part of an experiment conducted at the Department of Energy’s Cloud and Radiation Testbed (CART) site near Barrow, Alaska. Several radiometers from both NOAA and NASA were deployed during the experiment to provide the first combined MMW and MW ground-based dataset during dry Arctic conditions. Single-channel retrievals of PWV were performed using the MW and MMW data. Discrepancies in the retrieved values were found to be consistent with differences observed between measured brightness temperatures (TBs) and forward-modeled TBs based on concurrent radiosonde profiles. These discrepancies are greater than can be explained by radiometer measurement error alone; errors in the absorption models and uncertainty in the radiosonde measurements contribute to the discrepancies observed. The measurements, retrieval technique, and line model discrepancies are discussed, along with difficulties and potential of MMW/MW PWV measurement.
Intersatellite Radiance Biases for the High-Resolution Infrared Radiation Sounders (HIRS) on board NOAA-15, -16, and -17 from Simultaneous Nadir Observations
Authors: Cao Changyong , Xu Hui , Sullivan Jerry , McMillin Larry , Ciren Pubu , Hou Yu-Tai 
Published: May 2005

Abstract
Intersatellite radiance comparisons for the 19 infrared channels of the High-Resolution Infrared Radiation Sounders (HIRS) on board NOAA-15, -16, and -17 are performed with simultaneous nadir observations at the orbital intersections of the satellites in the polar regions, where each pair of the HIRS views the same earth target within a few seconds. Analysis of such datasets from 2000 to 2003 reveals unambiguous intersatellite radiance differences as well as calibration anomalies.
The results show that in general, the intersatellite relative biases are less than 0.5 K for most HIRS channels. The large biases in different channels differ in both magnitude and sign, and are likely to be caused by the differences and measurement uncertainties in the HIRS spectral response functions. The seasonal bias variation in the stratosphere channels is found to be highly correlated with the lapse rate factor approximated by the channel radiance differences. The method presented in this study works particularly well for channels sensing the stratosphere because of the relative spatial uniformity and stability of the stratosphere, for which the intercalibration accuracy and precision are mostly limited by the instrument noise. This method is simple and robust, and the results are highly repeatable and unambiguous. Intersatellite radiance calibration with this method is very useful for the on-orbit verification and monitoring of instrument performance, and is potentially useful for constructing long-term time series for climate studies.
High-sensitivity detection of BCR-ABL kinase domain mutations in imatinib-naive patients: correlation with clonal cytogenetic evolution but not response to therapy
Authors: Willis Stephanie G. , Lange Thoralf , Demehri Shadmehr , Otto Sandra , Crossman Lucy , Niederwieser Dietger , Stoffregen Eric P. , McWeeney Shannon , Kovacs Ines , Park Byung , Druker Brian J. , Deininger Michael W. 
Published: May 2005

Abstract
Mutations in the kinase domain (KD) of BCR-ABL are the leading cause of acquired imatinib resistance. In some cases, identical mutations were detected at relapse and in pretherapeutic specimens, consistent with selection of resistant clones in the presence of drug. However, the incidence of KD mutations in imatinibnaive patients, irrespective of response to therapy, is unknown. We studied mutation frequency in 66 patients with chronic myelogenous leukemia (CML), using cDNA sequencing and allele-specific oligonucleotide-polymerase chain reaction (ASO-PCR) assays for 8 common mutations. Thirteen patients were positive by ASO-PCR only, 1 by ASO-PCR and sequencing, and 1 by sequencing only (overall frequency, 22.7%). T315I was most frequent (12% of patients). Eleven of the 14 patients with positive ASO-PCR had follow-up samples available for sequencing. Wild-type sequence was detected in 6 of 11, 2 different mutations in 1 of 11, and identical mutations in 4 of 11 patients, 2 of whom had achieved major cytogenetic response. In multivariate analysis mutation detection was associated with clonal cytogenetic evolution, exposure to 6-Thioguanine, and a low platelet count, but not with response to imatinib, event-free survival, and overall survival. KD mutants present at low levels do not invariably lead to relapse, and additional factors are required to induce a fully drug-resistant phenotype. (Blood. 2005; 106:2128-2137)
Genome comparison without alignment using shortest unique substrings
Authors: Haubold Bernhard , Pierstorff Nora , Möller Friedrich , Wiehe Thomas 
Published: May 2005

Abstract
Background
Sequence comparison by alignment is a fundamental tool of molecular biology. In this paper we show how a number of sequence comparison tasks, including the detection of unique genomic regions, can be accomplished efficiently without an alignment step. Our procedure for nucleotide sequence comparison is based on shortest unique substrings. These are substrings which occur only once within the sequence or set of sequences analysed and which cannot be further reduced in length without losing the property of uniqueness. Such substrings can be detected using generalized suffix trees.

Results
We find that the shortest unique substrings in Caenorhabditis elegans, human and mouse are no longer than 11 bp in the autosomes of these organisms. In mouse and human these unique substrings are significantly clustered in upstream regions of known genes. Moreover, the probability of finding such short unique substrings in the genomes of human or mouse by chance is extremely small. We derive an analytical expression for the null distribution of shortest unique substrings, given the GC-content of the query sequences. Furthermore, we apply our method to rapidly detect unique genomic regions in the genome of Staphylococcus aureus strain MSSA476 compared to four other staphylococcal genomes.

Conclusion
We combine a method to rapidly search for shortest unique substrings in DNA sequences and a derivation of their null distribution. We show that unique regions in an arbitrary sample of genomes can be efficiently detected with this method. The corresponding programs shustring (SHortest Unique subSTRING) and shulen are written in C and available at http://adenine.biz.fh-weihenstephan.de/shustring/.
arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays
Authors: Menten Björn , Pattyn Filip , De Preter Katleen , Robbrecht Piet , Michels Evi , Buysse Karen , Mortier Geert , De Paepe Anne , van Vooren Steven , Vermeesch Joris , Moreau Yves , De Moor Bart , Vermeulen Stefan , Speleman Frank , Vandesompele Jo 
Published: May 2005

Abstract
Background
The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH). One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment.

Results
We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser.

Conclusion
ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at http://medgen.ugent.be/arrayCGHbase/.
Overview of BioCreAtIvE: critical assessment of information extraction for biology
Authors: Hirschman Lynette , Yeh Alexander , Blaschke Christian , Valencia Alfonso 
Published: May 2005

Abstract

Background
The goal of the first BioCreAtIvE challenge (Critical Assessment of Information Extraction in Biology) was to provide a set of common evaluation tasks to assess the state of the art for text mining applied to biological problems. The results were presented in a workshop held in Granada, Spain March 28–31, 2004. The articles collected in this BMC Bioinformatics supplement entitled "A critical assessment of text mining methods in molecular biology" describe the BioCreAtIvE tasks, systems, results and their independent evaluation.

Results
BioCreAtIvE focused on two tasks. The first dealt with extraction of gene or protein names from text, and their mapping into standardized gene identifiers for three model organism databases (fly, mouse, yeast). The second task addressed issues of functional annotation, requiring systems to identify specific text passages that supported Gene Ontology annotations for specific proteins, given full text articles.

Conclusion
The first BioCreAtIvE assessment achieved a high level of international participation (27 groups from 10 countries). The assessment provided state-of-the-art performance results for a basic task (gene name finding and normalization), where the best systems achieved a balanced 80% precision / recall or better, which potentially makes them suitable for real applications in biology. The results for the advanced task (functional annotation from free text) were significantly lower, demonstrating the current limitations of text-mining approaches where knowledge extrapolation and interpretation are required. In addition, an important contribution of BioCreAtIvE has been the creation and release of training and test data sets for both tasks. There are 22 articles in this special issue, including six that provide analyses of results or data quality for the data sets, including a novel inter-annotator consistency assessment for the test set used in task 2.
Data preparation and interannotator agreement: BioCreAtIvE Task 1B
Authors: Colosimo Marc E , Morgan Alexander A , Yeh Alexander S , Colombe Jeffrey B , Hirschman Lynette 
Published: May 2005

Abstract

Background
We prepared and evaluated training and test materials for an assessment of text mining methods in molecular biology. The goal of the assessment was to evaluate the ability of automated systems to generate a list of unique gene identifiers from PubMed abstracts for the three model organisms Fly, Mouse, and Yeast. This paper describes the preparation and evaluation of answer keys for training and testing. These consisted of lists of normalized gene names found in the abstracts, generated by adapting the gene list for the full journal articles found in the model organism databases. For the training dataset, the gene list was pruned automatically to remove gene names not found in the abstract; for the testing dataset, it was further refined by manual annotation by annotators provided with guidelines. A critical step in interpreting the results of an assessment is to evaluate the quality of the data preparation. We did this by careful assessment of interannotator agreement and the use of answer pooling of participant results to improve the quality of the final testing dataset.

Results
Interannotator analysis on a small dataset showed that our gene lists for Fly and Yeast were good (87% and 91% three-way agreement) but the Mouse gene list had many conflicts (mostly omissions), which resulted in errors (69% interannotator agreement). By comparing and pooling answers from the participant systems, we were able to add an additional check on the test data; this allowed us to find additional errors, especially in Mouse. This led to 1% change in the Yeast and Fly "gold standard" answer keys, but to an 8% change in the mouse answer key.

Conclusion
We found that clear annotation guidelines are important, along with careful interannotator experiments, to validate the generated gene lists. Also, abstracts alone are a poor resource for identifying genes in paper, containing only a fraction of genes mentioned in the full text (25% for Fly, 36% for Mouse). We found that there are intrinsic differences between the model organism databases related to the number of synonymous terms and also to curation criteria. Finally, we found that answer pooling was much faster and allowed us to identify more conflicting genes than interannotator analysis.