bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polysomnography in Children Scheduled for Adenotonsillectomy
Authors: Weatherly Robert A. , Ruzicka Deborah L. , Marriott Deanna J. , Chervin Ronald D. 
Published: October 2004

OBJECTIVESeveral studies suggest that a reliable diagnosis of childhood sleep‐disordered breathing (SDB) requires polysomnography (PSG). We compared clinical and PSG‐based diagnoses in children scheduled for adenotonsillectomy (AT). Parent responses on a validated Pediatric Sleep Questionnaire were used to determine which symptoms could help identify children with clinical diagnoses of SDB but normal PSG.STUDY DESIGN AND SETTINGThirty‐four children aged 5.0 to 12.9 years and scheduled for AT to treat clinically diagnosed sleep‐disordered breathing underwent laboratory‐based PSG. Results were scored by 3 different criteria: 1) >1 obstructive apnea (2 breaths or longer) per hour of sleep; 2) >5 apneas or hypopneas per hour of sleep; or 3) >1 apnea, hypopnea, or respiratory event–related arousal per hour of sleep.RESULTSDepending on the criterion used, the PSG documented SDB from a minimum of 18/34 subjects (53%, for criterion I) to as many as 30/34 subjects (88%, for criterion III). Among symptoms studied, absence of daytime mouth breathing and habitual snoring were most helpful in identification of children who had no evidence of SDB on PSG, by criterion I (Chi‐square, P < 0.05). The absence of other common symptoms, such as “loud snoring” or “trouble breathing” at night, were not helpful.CONCLUSIONChildren with clinical diagnoses of SDB may not consistently meet PSG criteria for this disorder. Questions about daytime mouth breathing and habitual snoring might help clinicians recognize children who would not have SDB on objective testing.SIGNIFICANCEClinical identification of SDB confirmable on PSG could be improved. However, available outcome data do not yet clarify whether clinical or PSG criteria best identify children likely to suffer morbidity from SDB. EBM rating: C.
A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples
Authors: Ji Yuan , Tsui Kam-Wah , Kim KyungMann 
Published: October 2004

Abstract
Motivation: The classification of samples using gene expression profiles is an important application in areas such as cancer research and environmental health studies. However, the classification is usually based on a small number of samples, and each sample is a long vector of thousands of gene expression levels. An important issue in parametric modeling for so many gene expression levels is the control of the number of nuisance parameters in the model. Large models often lead to intensive or even intractable computation, while small models may be inadequate for complex data.
Methodology: We propose a two-step empirical Bayes classification method as a solution to this issue. At the first step, we use the model-based cluster algorithm with a non-traditional purpose of assigning gene expression levels to form abundance groups. At the second step, by assuming the same variance for all the genes in the same group, we substantially reduce the number of nuisance parameters in our statistical model.
Results: The proposed model is more parsimonious, which leads to efficient computation under an empirical Bayes estimation procedure. We consider two real examples and simulate data using our method. Desired low classification error rates are obtained even when a large number of genes are pre-selected for class prediction.
Availability: Supplemental materials including technical details are available at “http://odin.mdacc.tmc.edu/~yuanj/papers/sup.pdf”. An R program for computation is available upon request by email to Yuan Ji (yuanji@mdanderson.org)
Contact: yuanji@mdanderson.org
Extracting relations between promoter sequences and their strengths from microarray data
Authors: Kiryu Hisanori , Oshima Taku , Asai Kiyoshi 
Published: October 2004

AbstractMotivation: The relations between the promoter sequences and their strengths were extensively studied in the 1980s. Although these studies uncovered strong sequence-strength correlations, the cost of their elaborate experimental methods have been too high to be applied to a large number of promoters. On the contrary, a recent increase in the microarray data allows us to compare thousands of gene expressions with their DNA sequences.Results: We studied the relations between the promoter sequences and their strengths using the Escherichia coli microarray data. We modeled those relations using a simple weight matrix, which was optimized with a novel support vector regression method. It was observed that several non-consensus bases in the ‘−35’ and ‘−10’ regions of promoter sequences act positively on the promoter strength and that certain consensus bases have a minor effect on the strength. We analyzed outliers for which the observed gene expressions deviate from the promoter strength predictions, and identified several genes with enhanced expressions due to multiple promoters and genes under strong regulation by transcription factors. Our method is applicable to other procaryotes for which both the promoter sequences and the microarray data are available.Contact: hisano-k@is.aist-nara.ac.jp
Finding regulatory modules through large-scale gene-expression data analysis
Authors: Kloster M. , Tang C. , Wingreen N.S. 
Published: October 2004

AbstractMotivation: The use of gene microchips has enabled a rapid accumulation of gene-expression data. One of the major challenges of analyzing this data is the diversity, in both size and signal strength, of the various modules in the gene regulatory networks of organisms.Results: Based on the iterative signature algorithm [Bergmann,S., Ihmels,J. and Barkai,N. (2002) Phys. Rev. E67, 031902], we present an algorithm—the progressive iterative signature algorithm (PISA)—that, by sequentially eliminating modules, allows unsupervised identification of both large and small regulatory modules. We applied PISA to a large set of yeast gene-expression data, and, using the Gene Ontology database as a reference, found that the algorithm is much better able to identify regulatory modules than methods based on high-throughput transcription-factor binding experiments or on comparative genomics.Contact: tang@nec-labs.com
Evolutionary optimization with data collocation for reverse engineering of biological networks
Authors: Tsai Kuan-Yao , Wang Feng-Sheng 
Published: October 2004

Abstract
Motivation: Modern experimental biology is moving away from analyses of single elements to whole-organism measurements. Such measured time-course data contain a wealth of information about the structure and dynamic of the pathway or network. The dynamic modeling of the whole systems is formulated as a reverse problem that requires a well-suited mathematical model and a very efficient computational method to identify the model structure and parameters. Numerical integration for differential equations and finding global parameter values are still two major challenges in this field of the parameter estimation of nonlinear dynamic biological systems.
Results: We compare three techniques of parameter estimation for nonlinear dynamic biological systems. In the proposed scheme, the modified collocation method is applied to convert the differential equations to the system of algebraic equations. The observed time-course data are then substituted into the algebraic system equations to decouple system interactions in order to obtain the approximate model profiles. Hybrid differential evolution (HDE) with population size of five is able to find a global solution. The method is not only suited for parameter estimation but also can be applied for structure identification. The solution obtained by HDE is then used as the starting point for a local search method to yield the refined estimates.
Availability: The algorithm, implemented by Compaq Visual Fortran Professional Edition 6.6, and the supplements are available at http://www.che.ccu.edu.tw/~bioproc/index-english.html/. IMSL Math/Library is a commercial library included in Compaq Visual Fortran Professional Edition.
Contact: chmfsw@ccu.edu.tw
Genetic algorithm optimization for pre-processing and variable selection of spectroscopic data
Authors: Jarvis Roger M. , Goodacre Royston 
Published: October 2004

AbstractMotivation: The major difficulties relating to mathematical modelling of spectroscopic data are inconsistencies in spectral reproducibility and the black box nature of the modelling techniques. For the analysis of biological samples the first problem is due to biological, experimental and machine variability which can lead to sample size differences and unavoidable baseline shifts. Consequently, there is often a requirement for mathematical correction(s) to be made to the raw data if the best possible model is to be formed. The second problem prevents interpretation of the results since the variables that most contribute to the analysis are not easily revealed; as a result, the opportunity to obtain new knowledge from such data is lost.Methods: We used genetic algorithms (GAs) to select spectral pre-processing steps for Fourier transform infrared (FT-IR) spectroscopic data. We demonstrate a novel approach for the selection of important discriminatory variables by GA from FT-IR spectra for multi-class identification by discriminant function analysis (DFA).Results: The GA selects sensible pre-processing steps from a total of ∼1010 possible mathematical transformations. Application of these algorithms results in a 16% reduction in the model error when compared against the raw data model. GA-DFA recovers six variables from the full set of 882 spectral variables against which a satisfactory DFA model can be formed; thus inferences can be made as to the biochemical differences that are reflected by these spectral bands.Availability: Supplementary information, datasets and scripts are available from the corresponding author.Contact: roy.goodacre@manchester.ac.uk
Predicting protein localization in budding Yeast
Authors: Chou Kuo-Chen , Cai Yu-Dong 
Published: October 2004

Abstract
Motivation: Most of the existing methods in predicting protein subcellular location were used to deal with the cases limited within the scope from two to five localizations, and only a few of them can be effectively extended to cover the cases of 12–14 localizations. This is because the more the locations involved are, the poorer the success rate would be. Besides, some proteins may occur in several different subcellular locations, i.e. bear the feature of ‘multiplex locations’. So far there is no method that can be used to effectively treat the difficult multiplex location problem. The present study was initiated in an attempt to address (1) how to efficiently identify the localization of a query protein among many possible subcellular locations, and (2) how to deal with the case of multiplex locations.
Results: By hybridizing gene ontology, functional domain and pseudo amino acid composition approaches, a new method has been developed that can be used to predict subcellular localization of proteins with multiplex location feature. A global analysis of the proteins in budding yeast classified into 22 locations was performed by jack-knife cross-validation with the new method. The overall success identification rate thus obtained is 70%. In contrast to this, the corresponding rates obtained by some other existing methods were only 13–14%, indicating that the new method is very powerful and promising. Furthermore, predictions were made for the four proteins whose localizations could not be determined by experiments, as well as for the 236 proteins whose localizations in budding yeast were ambiguous according to experimental observations. However, according to our predicted results, many of these ‘ambiguous proteins’ were found to have the same score and ranking for several different subcellular locations, implying that they may simultaneously exist, or move around, in these locations. This finding is intriguing because it reflects the dynamic feature of these proteins in a cell that may be associated with some special biological functions.
Contact: kchou@san.rr.com
Supplementary information: www.pami.sjtu.edu.cn/kcchou
Normalization of two-channel microarray experiments: a semiparametric approach
Authors: Eckel J. E. , Gennings C. , Therneau T. M. , Burgoon L. D. , Boverhof D. R. , Zacharewski T. R. 
Published: October 2004

Abstract
Motivation: An important underlying assumption of any experiment is that the experimental subjects are similar across levels of the treatment variable, so that changes in the response variable can be attributed to exposure to the treatment under study. This assumption is often not valid in the analysis of a microarray experiment due to systematic biases in the measured expression levels related to experimental factors such as spot location (often referred to as a print-tip effect), arrays, dyes, and various interactions of these effects. Thus, normalization is a critical initial step in the analysis of a microarray experiment, where the objective is to balance the individual signal intensity levels across the experimental factors, while maintaining the effect due to the treatment under investigation.
Results: Various normalization strategies have been developed including log-median centering, analysis of variance modeling, and local regression smoothing methods for removing linear and/or intensity-dependent systematic effects in two-channel microarray experiments. We describe a method that incorporates many of these into a single strategy, referred to as two-channel fastlo, and is derived from a normalization procedure that was developed for single-channel arrays. The proposed normalization procedure is applied to a two-channel dose–response experiment.
Availability: The SAS macro for two-channel fastlo is available from the authors upon request and the data used to test the methods is publicly available at http://www.bch.msu.edu/~zacharet/publications/supplementary/ee_dr
Contact: eckel@mayo.edu
Theoretical and practical advances in genome halving
Authors: Yin Peng , Hartemink Alexander J. 
Published: October 2004

Abstract
Motivation: Duplication of an organism's entire genome is a rare but spectacular event, enabling the rapid emergence of multiple new gene functions. Over time, the parallel linkage of duplicated genes across chromosomes may be disrupted by reciprocal translocations, while the intra-chromosomal order of genes may be shuffled by inversions and transpositions. Some duplicate genes may evolve unrecognizably or be deleted. As a consequence, the only detectable signature of an ancient duplication event in a modern genome may be the presence of various chromosomal segments containing parallel paralogous genes, with each segment appearing exactly twice in the genome. The problem of reconstructing the linkage structure of an ancestral genome before duplication is known as genome halving with unordered chromosomes.
Results: In this paper, we derive a new upper bound on the genome halving distance that is tighter than the best known, and a new lower bound that is almost always tighter than the best known. We also define the notion of genome halving diameter, and obtain both upper and lower bounds for it. Our tighter bounds on genome halving distance yield a new algorithm for reconstructing an ancestral duplicated genome. We create a software package GenomeHalving based on this new algorithm and test it on the yeast genome, identifying a sequence of translocations for halving the yeast genome that is shorter than previously conjectured possible.
Availability: GenomeHalving is available upon email request.
Contact: py@cs.duke.edu; amink@cs.duke.edu
Identifying differentially expressed genes from microarray experiments via statistic synthesis
Authors: Yang Yee Hwa , Xiao Yuanyuan , Segal Mark R. 
Published: October 2004

AbstractMotivation: A common objective of microarray experiments is the detection of differential gene expression between samples obtained under different conditions. The task of identifying differentially expressed genes consists of two aspects: ranking and selection. Numerous statistics have been proposed to rank genes in order of evidence for differential expression. However, no one statistic is universally optimal and there is seldom any basis or guidance that can direct toward a particular statistic of choice.Results: Our new approach, which addresses both ranking and selection of differentially expressed genes, integrates differing statistics via a distance synthesis scheme. Using a set of (Affymetrix) spike-in datasets, in which differentially expressed genes are known, we demonstrate that our method compares favorably with the best individual statistics, while achieving robustness properties lacked by the individual statistics. We further evaluate performance on one other microarray study.Availability: The approach is implemented in an R package called DEDS, which is available for download from the Bioconductor website (http://www.bioconductor.org/).Contact: mark@biostat.ucsf.edu
PERIZONIUM AND INITIAL VALVE FORMATION IN THE DIATOM NAVICULA CUSPIDATA (BACILLARIOPHYCEAE)1
Authors: Cohn Stanley A. , Spurck Timothy P. , Pickett‐Heaps Jeremy D. , Edgar Lesley A. 
Published: October 2004

ABSTRACTThis paper describes the perizonium and initial valve formation in Navicula cuspidata Kütz., based on light microscope (LM) and scanning electron microscope (SEM) observations. The perizonium consists of concentric over‐lapping bands, laid down sequentially at the tips of the expanding biconical auxospore during its elongation. The central perizonial band has fimbriate edges and is considerably more rigid than the more distal bands. During auxospore elongation and the band secretion, the chloroplasts continuously oscillate between the two ends of the cell; this oscillation ceases once the elongation is complete. The initial valves, formed within the perizonium, are molded into the basically biconical shape of the perizonium except for a central flattening of each valve face. In contrast to the raphes in gametangial and vegetative valves which are surrounded by a smooth axial area, the raphes in initial valves lie within a raised ridge running along the apical axis of the valve. The regular pattern of apically oriented ridges on the outer surface of vegetative valves is also lacking on initial valves. Comparison of pore–pore spacing within striae of gametangial valves, initial values and post‐initial valves (first division and vegetative cells) reveals that the pore–pore distance within striae is conserved at all sexual stages. However, the distance between striae is considerably larger in initial valves than in gametangial and post‐initial valves. Vegetative interstriae spacing as well as the planar morphology of the valve face is regained at the first division of the initial cell. This suggests that the spacing between striae is dependent on the sexual stage of the cell during valve formation (i.e. not directly dependent on the cell size) and can be altered independently of the pore–pore spacing.
COMPARATIVE ANALYSES OF THE DINOFLAGELLATE FLAGELLAR APPARATUS. I. WOLOSZYNSKIA SP.1
Authors: Roberts Keith R. , Timpano Peter 
Published: October 2004

ABSTRACTThe three‐dimensional structure of the flagellar apparatus in Woloszynskia sp. was determined. This recently discovered dinoflagellate possesses two basal bodies that are offset from one another and lie at an angle of approximately 110°. The transverse basal body is associated with a striated fibrous root assemblage that consists of two differently staining fibrous portions with identical striation periodicity. Unlike the transverse striated fibrous roots reported in other dinoflagellates, this assemblage extends to the cell's right beyond the proximal end of the transverse basal body. The striated fibrous root complex is attached to the anterior end of the longitudinal microtubular root by a broad striated fibrous connective. The longitudinal basal body is also associated with the longitudinal microtubular root. The flagellar opening of each emerging axoneme is surrounded by a striated collar. The striated collars are linked to one another by a striated fibrous, striated collar connective. The variations and similarities of the flagellar apparatus and the ventral ridge/striated collar connective in Woloszynskia sp. are compared to similar components in other dinoflagellates.
EFFECTS OF TEMPERATURE, NITROGEN SUPPLY, AND TISSUE NITROGEN ON AMMONIUM UPTAKE RATES OF THE CHLOROPHYTE SEAWEEDS ULVA CURVATA AND CODIUM DECORTICATUM1
Authors: Duke Clifford S. , Litaker Wayne , Ramus J. 
Published: October 2004

ABSTRACTNitrogen uptake rates of Ulva curvata (Kütz.) de Toni (Ulvales) and Codium decorticatum (Woodw.) Howe (Caulerpales) grown under several N addition regimes were determined by perturbation and continuous mode techniques, and as N demand, by the product of growth rate and tissue N. Uptake rates are reported as the slope of rate vs. concentration curves in each case. N uptake rates of U. curvata were inversely correlated with tissue N and affected only slightly by temperature. There was no correlation of N uptake rate with tissue N in C. decorticatum. N uptake rates of C. decorticatum were affected by temperature but to a lesser degree than were growth rates. Neither N addition per se nor light affected N uptake capacity of either species. The proximal mechanism for seaweeds accumulation of N at low light and temperatures may be that N uptake is less limited by light and temperature than is growth. This in turn may partially compensate for the effects of reduced light and temperature on growth by increasing pigment and enzyme levels. Perturbation uptake rates were higher than continuous mode or N demand rates in Ulva but not in Codium. N uptake rates of Ulva were higher than those of Codium, but N storage capacities were lower. These two observations suggest that Ulva experiences a fundamentally more variable N supply than does Codium. This is consistent with the clarification of Ulva as an ephemeral form and of Codium as persistent. A seaweed's functional form therefore appears to influence the spectrum of resource variability available to it as well as its ability to persist in the environment.
MANTONIELLAIN ANTARCTIC WATERS INCLUDING THE DESCRIPTION OFM. ANTARCTICASP. NOV. (PRASINOPHYCEAE)1
Authors: Marchant Harvey J. , Buck Kurt R. , Garrison David L. , Thomsen Helge A. 
Published: October 2004

ABSTRACTWe report the finding of two species ofMantoniellafrom the Weddell Sen and Prydz Bay, Antarctica. As well asM. squamata,a cosmopolitan species, we describeM. antarcticasp. nov., the second species in this genus.M. antarcticais covered with two distinctive types of discoid scales. The flagella bear only the smaller of the scale types whereas the cell body has both types, the larger overlying the smaller.
THE WAVELENGTH DEPENDENCE OF MASSIVE CAROTENE SYNTHESIS IN DUNALIELLA BARDAWIL (CHLOROPHYCEAE)1
Authors: Ben‐Amotz Ami , Avron Mordhay 
Published: October 2004

ABSTRACT Dunaliella bardawil Ben‐Amotz & Avron accumulates high concentrations of β‐carotene when grown under high light intensity. The β‐carotene is composed mainly of 9‐cis and all‐trans β‐carotene. Accumulation of β‐carotene and an increase in the ratio of the 9‐cis to the all‐trans isomer are strongly dependent on the light intensity under which the algae are cultivated but are independent of light quality within the photosynthetically active radiation range. Cells grown under continuous red (>645 nm) or white light of 500 W·m−2 reach a value of about 32 pg β‐carotene·cell−1 and a ratio of 9‐cis to all‐trans β‐carotene of around 2, whereas cells grown under low red or white light intensity of 25 W·m−2 contain about 3 pg·cell−1 and a ratio of isomers of around 0.3.