bluuebunny/crossref_metadata_2025_split huggingface dataset:
Top‐down or Bottom‐up Effects by Fish: Issues of Concern in Biomanipulation of Lakes
Authors: Horppila Jukka , Peltonen Heikki , Malinen Tommi , Luokkanen Eira , Kairesalo Timo 
Published: June 2003

AbstractA large‐scale biomanipulation trial was carried out on Lake Vesijärvi in Finland during 1989–1993. Following the mass removal of coarse fish the biomass of cyanobacteria collapsed from 1.4 g/m−3 to below 0.4 g/m−3, while total phosphorus concentration declined from 45 μg/L to 30 μg/L. No relevant changes in zooplankton communities were observed. The results suggest that the success of food web manipulation as a tool for lake restoration is not necessarily dependent on the grazing rate of zooplankton. The effects of reduced fish‐mediated internal loading and recycling of nutrients are in many cases stronger than those of reduced planktivory. Alternative stable states of water quality may also exist in lakes not covered by macrophytes, owing to the changes in the behavior of fish stocks. Year‐to‐year variation in the littoral zone may cause large oscillations in lake ecosystems—for example, through the recruitment of fish. In addition, the nutrients translocated by fish from the littoral zone may affect the nutrient dynamics of the pelagial plankton community. In terms of phytoplankton species composition and the ratio of phosphorus to chlorophyll a, the water quality in Lake Vesijärvi has improved in a stepwise fashion within the last 10 years. This is probably due to the fact that the five‐year mass removal of fish in Enonselkä fulfilled the requirement of sustained management of fish stocks in order to maintain nonequilibrial conditions between alternate stable states. The prediction of the water quality development is obscured, however, by spatial and temporal within‐lake variation, which sets high requirements for sampling programs.
Seed Inputs to Microsite Patch Recovery on Two Tropandean Landslides in Ecuador
Authors: Myster Randall W. , Sarmiento Fausto O. 
Published: June 2003

AbstractTo understand landslide regeneration and provide information necessary for restoration, we sampled seed rain, seed pool, and plant cover on two Ecuadorian landslides. We trapped 1304 seeds and found that, while most seeds were in the family Asteraceae, there was substantial variation in seed rain among plant families. Four hundred and seventy‐five seedlings emerged from soil samples, including nonvascular and vascular families; again, species in Asteraceae dominated, with species in Piperaceae also very common. Plant cover, consisting of members of four fern families and 20 vascular plant families—with species in Asteraceae, Melastomataceae and Poaceae most common—was scored as a percentage of the total plot area. Principal components analysis (PCA) showed that, for all three of these plant life stages (seed rain, seed‐propagule pool, plant cover), spatial variation was dominated by differences between the two landslides rather than within‐landslide plot differences. PCA also showed that plots separated best on axes defined by the families Cecropiaceae, Urticaceae, Melastomataceae, Papilionaceae, Asteraceae, and Araceae with clumping of families in PCA space suggesting common successional strategies. Another multivariate technique, canonical correspondence analysis (CCA), showed that the combined seed rain and seed pool data could predict the percent cover of the family Verbenaceae and that the current plant cover families could predict Asteraceae seeds and seedlings. Finally, we use our past and present landslide data, along with multivariate modeling results, to suggest strategies for successful landslide restoration.
Migraine in Twins Raised Together and Apart
Authors: Ziegler Dewey K. , Hur Yoon‐Mi , Bouchard Thomas J. , Hassanein Ruth S. , Barter Ruth 
Published: June 2003

History of headache and migraine diagnosed by structured interview utilizing International Headache Society criteria was obtained in two samples of female twin pairs—154 raised together and 43 raised apart since infancy. Zygosity was determined by standard methods. Probandwise concordance rates were determined. Assuming that liability to migraine has a multifactorial etiology involving a number of genetic and environmental risk factors acting additively, tetrachoric correlations in the four groups of twins (monozygotic raised together, monozygotic raised apart, dizygotic raised together, and dizygotic raised apart) were then calculated. The genetic and environmental influences in the liability to migraine were estimated using biometrical model‐fitting methods.Tetrachoric correlations for migraine were consistently higher in monozygotic than in dizygotic twins, for both reared together and reared apart samples, with a heritability estimate of 52%. Model fitting also suggested that approximately 50% of the variance in liability to migraine was attributable to genetic factors with nonshared environmental factors and measurement errors responsible for the remaining variance.
Anticephalgic Photoprotective Premeditated Mask. A Report of a Successful Double‐Blind Placebo‐Controlled Study of a New Treatment for Headaches With Associated Frontalis Pain and Photophobia
Authors: Hyson Morton I. 
Published: June 2003

This study was performed to determine the efficacy of an anticephalgic photoprotective premedicated mask in the treatment of migraine and/or tension‐type headaches. There were 54 patients. They were given masks and numbered bottles of topical medication containing either salicin or placebo. The patients were instructed to apply the medication to their frontalis region in the event they should suffer a headache, apply a photoprotective mask, and lie down. Furthermore, they were instructed to take their usual oral or parenteral medications, if required, for relief of the headache. They subsequently filled out forms rating the degree of relief which they attributed to the topical medications and the masks using a 0 to 10 scale. They were also simply asked if this form of treatment helped or not.Seven of the 20 patients receiving placebo stated the medication and mask helped. The placebo group rated the treatment an average of 4.31 on a 0 to 10 scale. Twenty‐eight of 34 patients receiving salicin stated it was effective. The salicin group rated it 7.42 on a 0 to 10 scale (P<0.001). The majority of the salicin patients stated the duration of their headaches was significantly reduced, as was their need for analgesic and/or narcotic medications.This study demonstrates a significant difference between placebo and salicin in association with the photoprotective mask in treating migraines and/or tension‐type headaches with associated frontalis pain and photophobia.
Prevalence of Frequent Headache in a Population Sample
Authors: Scher Ann I. , Stewart Walter F. , Liberman Joshua , Lipton Richard B. 
Published: June 2003

Purpose.—Patients with daily or near‐daily headaches are commonly seen in neurology practices and in headache subspecialty centers, but there is little information on the prevalence of this condition in the general population. We present the first US‐based study describing the prevalence and characteristics of frequent headache in the general population.Methods.—In Baltimore County, Maryland, 13 343 individuals 18 to 65 years of age were selected by random‐digit dialing and interviewed by telephone about their headaches. Subjects reporting 180 or more headaches per year were classified as having frequent headache. Three mutually exclusive subtypes of frequent headache were identified: frequent headache with migrainous features, chronic tension‐type headache, and unclassified frequent headache.Results.—The overall prevalence of frequent headache was 4.1% (5.0% female, 2.8% male; 1.8:1 female to male ratio). Frequent headache was 33% more common in Caucasians (4.4%) than in African Americans (3.3%). In both males and females, prevalence was highest in the lowest educational category. Among frequent headache sufferers, more than half (52% female, 56% male) met criteria for chronic tension‐type headache, almost one third (33% female, 25% male) met criteria for frequent headache with migrainous features, and the remainder (15% female, 19% male) were unclassified. Overall, 30% of female and 25% of male frequent headache sufferers met International Headache Society (IHS) criteria for migraine (with or without aura).Conclusions.—Frequent headache is common in the general population and is more prevalent in Caucasians and in those with less than a high school education. Chronic tension‐type headache is more common than frequent headache with migrainous features, though the latter is more disabling. Although more common in females than males, the female preponderance of frequent headache is less marked than in migraine. The sex ratio varies by frequent headache subtype.
Comparison of Butorphanol Nasal Spray and Fiorinal With Codeine in the Treatment of Migraine
Authors: Goldstein Jerome , Gawel Marek J. , Winner Paul , Diamond Seymour , Reich Linda , Davidson Wendy J. , Sussman Neil M. 
Published: June 2003

Butorphanol tartrate is a synthetic mixed agonist‐antagonist opioid analgesic. Its transnasal dosage form, which may be self‐administered when the use of an opioid analgesic is appropriate, was previously shown to provide rapid relief of migraine pain. In this double‐blind, parallel‐group, outpatient study, we compared butorphanol nasal spray 1 mg followed in 1 hour by an optional second 1‐mg dose with the orally administered analgesic, Fiorinal with Codeine (one capsule containing butalbital 50 mg, caffeine 40 mg, aspirin 325 mg, and codeine phosphate 30 mg). Patients (N=321) were assigned by randomization to one of two treatment groups (butorphanol or Fiorinal with Codeine) and instructed to self‐administer medication when migraine pain reached an intensity of moderate or severe and to record study‐related events in a diary for 24 hours posttreatment. Efficacy analyses were performed on data from 275 patients who took study medication and returned a patient diary; 136 in the butorphanol group and 139 in the Fiorinal with Codeine group.During the first 2 hours after treatment, butorphanol was more effective than Fiorinal with Codeine in treating migraine pain as measured by pain intensity difference scores, percentage of responders (pain decreased to mild or none), percentage of pain‐free patients, and degree of pain relief, with a more rapid time to onset of 15 minutes. A similar percentage of patients in the two groups used rescue medication during the first 4 hours, after which more butorphanol‐treated than Fiorinal with Codeine‐treated patients used rescue medication. Butorphanol patients had more side effects, less improvement in digestive symptoms, and less improvement in functional ability than Fiorinal with Codeine patients.
Development of Chronic Daily Headache: A Clinical Study
Authors: Spierings Egilius L.H. , Schroevers Maya , Honkoop Peter C. , Sorbi Marjolijn 
Published: June 2003

We studied the development of chronic daily headache in 258 headache practice patients, 50 men and 208 women. Chronic daily headache was defined as headaches occurring at least 5 days per week for at least 1 year.Twenty‐two percent of the patients had daily headaches from the onset, and 78% initially experienced intermittent headaches. Of the patients with initially intermittent headaches, 19% experienced an abrupt transition into daily headaches and 81% a gradual one. The distribution of the age of daily headache onset was the same in the patients with daily headaches from the onset and in those with initially intermittent headaches but with abrupt transition into daily headaches. The distribution of the circumstances of daily headache onset was also the same in the groups. The most common circumstance of abrupt onset of daily headaches was head, neck, or back injury, in 61% caused by a motor vehicle accident. In the patients with initially intermittent headaches but with gradual transition into daily headaches, the transition took an average of 10.7 years.
The prevalences of overweight and obesity in children aged 4 to 12 years in Gibraltar
Authors: Kirk Sara FL , McLeod Melanie 
Published: June 2003

AbstractObjective:To determine the prevalences of overweight and obesity in children aged 4 to 12 years, using the standard definitions proposed by the International Obesity Taskforce.Design:Population prevalence cross-sectional survey involving measurement of height and weight. Data collection took place in 1998.Setting:Schools in Gibraltar.Subjects:In total 2994 children, aged 4–12 years, attending these schools (1540 boys, 1454 girls).Results:Prevalence of overweight in boys was 19.7%, while obesity prevalence was 10.8%. For the girls, overweight prevalence was 21.4%, while obesity prevalence was 10.6%. There were no significant differences in the proportions of overweight or obesity between boys and girls.Conclusions:This was the first time that the prevalences of overweight and obesity have been estimated in children from Gibraltar. These data provide further information on prevalence rates of overweight and obesity, using defined cut-offs for comparison with data from other countries.
Impact of ready-to-eat breakfast cereal (RTEBC) consumption on adequacy of micronutrient intakes and compliance with dietary recommendations in Irish adults
Authors: Galvin MA , Kiely M , Flynn A 
Published: June 2003

AbstractObjective:To describe the consumption of ready-to-eat-breakfast cereals (RTEBCs) in Irish adults and its impact on adequacy and safety of micronutrient intakes and compliance with dietary recommendations.Design:Analysis for this paper used data from the North/South Ireland Food Consumption Survey that estimated habitual food intake using a 7-day food diary in a representative sample of adults aged 18–64 years (n=1379; 662 men, 717 women).Results:Despite the small quantity consumed (mean 28.6gday-1or 4.7% of total energy intake), RTEBCs made an important contribution to the mean daily intake of carbohydrate (8.1%), starch (10.8%), dietary fibre (9.8%) and non-starch polysaccharides (NSP) (10.8%) in consumers. Increased consumption was associated with a more fibre-dense diet and with greater compliance with dietary recommendations for fat, carbohydrate and NSP. Fortified RTEBCs contributed significantly to mean daily intakes of iron (18%), thiamin (14%), riboflavin (17%), niacin (15%), vitamin B6(13%), total folate (18%) and vitamin D (10%) and most of the contribution was from micronutrients added to RTEBCs. Increased consumption of fortified RTEBCs was associated with an increased nutrient density for a number of micronutrients and with a lower prevalence of dietary inadequacy of calcium, iron, riboflavin and folate, particularly in women. However, it was not associated with intakes in excess of the Tolerable Upper Intake Level for any micronutrient.Conclusions:The consumption of RTEBCs is associated with improved compliance with dietary recommendations for fat, carbohydrate and fibre, with a more micronutrient-dense diet and a reduced risk of dietary inadequacy for calcium, iron, riboflavin and folate, without increasing the risk of excessive intakes of micronutrients.
Statistical adjustment of signal censoring in gene expression experiments
Authors: Wit Ernst , McClure John 
Published: June 2003

Abstract
Motivation: Numerical output of spotted microarrays displays censoring of pixel intensities at some software dependent threshold. This reduces the quality of gene expression data, because it seriously violates the linearity of expression with respect to signal intensity. Statistical methods based on typically available spot summaries together with some parametric assumptions can suggest ways to correct for this defect
Results: A maximum likelihood approach is suggested together with a sensible approximation to the joint density of the mean, median and variance—which are typically available to the biological end-user. The method ‘corrects’ the gene expression values for pixel censoring. A by-product of our approach is a comparison between several two-parameter models for pixel intensity values. It suggests that pixels separated by one or two other pixels can be considered independent draws from a Lognormal or a Gamma distribution
Availability: The R/S-Plus code is available at http://www.stats.gla.ac.uk/~microarray/software
Contact: ernst@stats.gla.ac.uk
* To whom correspondence should be addressed.
K-ary clustering with optimal leaf ordering
for gene expression data
Authors: Bar-Joseph Ziv , Demaine Erik D. , Gifford David K. , Srebro Nathan , Hamel Angèle M. , Jaakkola Tommi S. 
Published: June 2003

Abstract
Motivation: A major challenge in gene expression analysis is effective data organization and visualization. One of the most popular tools for this task is hierarchical clustering. Hierarchical clustering allows a user to view relationships in scales ranging from single genes to large sets of genes, while at the same time providing a global view of the expression data. However, hierarchical clustering is very sensitive to noise, it usually lacks of a method to actually identify distinct clusters, and produces a large number of possible leaf orderings of the hierarchical clustering tree. In this paper we propose a new hierarchical clustering algorithm which reduces susceptibility to noise, permits up to k siblings to be directly related, and provides a single optimal order for the resulting tree
Results: We present an algorithm that efficiently constructs a k-ary tree, where each node can have up to k children, and then optimally orders the leaves of that tree. By combining k clusters at each step our algorithm becomes more robust against noise and missing values. By optimally ordering the leaves of the resulting tree we maintain the pairwise relationships that appear in the original method, without sacrificing the robustness.
Our k-ary construction algorithm runs in O(n3) regardless of k and our ordering algorithm runs in O(4kn3). We present several examples that show that our k-ary clustering algorithm achieves results that are superior to the binary tree results in both global presentation and cluster identification
Availability: We have implemented the above algorithms in C++ on the Linux operating system. Source code is available upon request from zivbj@mit.edu
Contact: zivbj@mit.edu
* To whom correspondence should be addressed.
Learning rule-based models of biological process from
gene expression time profiles using Gene Ontology
Authors: Hvidsten Torgeir R. , Lægreid Astrid , Komorowski Jan 
Published: June 2003

Abstract
Motivation: Microarray technology enables large-scale inference of the participation of genes in biological process from similar expression profiles. Our aim is to induce classificatory models from expression data and biological knowledge that can automatically associate genes with novel hypotheses of biological process
Results: We report a systematic supervised learning approach to predicting biological process from time series of gene expression data and biological knowledge. Biological knowledge is expressed using gene ontology and this knowledge is associated with discriminatory expression-based features to form minimal decision rules. The resulting rule model is first evaluated on genes coding for proteins with known biological process roles using cross validation. Then it is used to generate hypotheses for genes for which no knowledge of participation in biological process could be found. The theoretical foundation for the methodology based on rough sets is outlined in the paper, and its practical application demonstrated on a data set previously published by Cho et al. (Nat. Genet., 27, 48–54, 2001)
Availability: The Rosetta system is available at http://www.idi.ntnu.no/~aleks/rosetta
Contact: Jan.Komorowski@lcb.uu.se
Supplementary Information: http://www.lcb.uu.se/~hvidsten/bioinf_cho/
* To whom correspondence should be addressed.
Novel clustering algorithm for microarray expression data in a truncated SVD space
Authors: Horn David , Axel Inon 
Published: June 2003

Abstract
Motivation: This paper introduces the application of a novel clustering method to microarray expression data. Its first stage involves compression of dimensions that can be achieved by applying SVD to the gene–sample matrix in microarray problems. Thus the data (samples or genes) can be represented by vectors in a truncated space of low dimensionality, 4 and 5 in the examples studied here. We find it preferable to project all vectors onto the unit sphere before applying a clustering algorithm. The clustering algorithm used here is the quantum clustering method that has one free scale parameter. Although the method is not hierarchical, it can be modified to allow hierarchy in terms of this scale parameter
Results: We apply our method to three data sets. The results are very promising. On cancer cell data we obtain a dendrogram that reflects correct groupings of cells. In an AML/ALL data set we obtain very good clustering of samples into four classes of the data. Finally, in clustering of genes in yeast cell cycle data we obtain four groups in a problem that is estimated to contain five families
Availability: Software is available as Matlab programs at http://neuron.tau.ac.il/~horn/QC.htm
Contact: horn@post.tau.ac.il
* To whom correspondence should be addressed.
Gene interaction in DNA microarray data is
decomposed by information geometric measure
Authors: Nakahara Hiroyuki , Nishimura Shin-ichi , Inoue Masato , Hori Gen , Amari Shun-ichi 
Published: June 2003

Abstract
Motivation: Given the vast amount of gene expression data, it is essential to develop a simple and reliable method of investigating the fine structure of gene interaction. We show how an information geometric measure achieves this
Results: We introduce an information geometric measure of binary random vectors and show how this measure reveals the fine structure of gene interaction. In particular, we propose an iterative procedure by using this measure (called IPIG). The procedure finds higher-order dependencies which may underlie the interaction between two genes of interest. To demonstrate the method, we investigate the interaction between the two genes of interest in the data from human acute lymphoblastic leukemia cells. The method successfully discovered biologically known findings and also selected other genes as hidden causes that constitute the interaction
Availability: Softwares are currently not available but are possibly made available in future at http://www.mns.brain.riken.go.jp/~nakahara/DNA_pub.html where all the related information is also linked.
Contact: hiro@brain.riken.go.jp
* To whom correspondence should be addressed.
Classification of multiple cancer types by multicategory
support vector machines using gene expression data
Authors: Lee Yoonkyung , Lee Cheol-Koo 
Published: June 2003

Abstract
Motivation: High-density DNA microarray measures the activities of several thousand genes simultaneously and the gene expression profiles have been used for the cancer classification recently. This new approach promises to give better therapeutic measurements to cancer patients by diagnosing cancer types with improved accuracy. The Support Vector Machine (SVM) is one of the classification methods successfully applied to the cancer diagnosis problems. However, its optimal extension to more than two classes was not obvious, which might impose limitations in its application to multiple tumor types. We briefly introduce the Multicategory SVM, which is a recently proposed extension of the binary SVM, and apply it to multiclass cancer diagnosis problems
Results: Its applicability is demonstrated on the leukemia data (Golub et al., 1999) and the small round blue cell tumors of childhood data (Khan et al., 2001). Comparable classification accuracy shown in the applications and its flexibility render the MSVM a viable alternative to other classification methods
Supplementary Information: http://www.stat.ohio-state.edu/~yklee/msvm.html
Contact: yklee@stat.ohio-state.edu
* To whom correspondence should be addressed.