bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clustering of time-course gene expression data
using a mixed-effects model with B-splines
Authors: Luan Yihui , Li Hongzhe 
Published: February 2003

Abstract
Motivation: Time-course gene expression data are often measured to study dynamic biological systems and gene regulatory networks. To account for time dependency of the gene expression measurements over time and the noisy nature of the microarray data, the mixed-effects model using B-splines was introduced. This paper further explores such mixed-effects model in analyzing the time-course gene expression data and in performing clustering of genes in a mixture model framework.
Results: After fitting the mixture model in the framework of the mixed-effects model using an EM algorithm, we obtained the smooth mean gene expression curve for each cluster. For each gene, we obtained the best linear unbiased smooth estimate of its gene expression trajectory over time, combining data from that gene and other genes in the same cluster. Simulated data indicate that the methods can effectively cluster noisy curves into clusters differing in either the shapes of the curves or the times to the peaks of the curves. We further demonstrate the proposed method by clustering the yeast genes based on their cell cycle gene expression data and the human genes based on the temporal transcriptional response of fibroblasts to serum. Clear periodic patterns and varying times to peaks are observed for different clusters of the cell-cycle regulated genes. Results of the analysis of the human fibroblasts data show seven distinct transcriptional response profiles with biological relevance.
Availability: Matlab programs are available on request from the authors.
Supplementary Information: http://dna/ucdavis.edu/~hli/bioinforsupp.pdf
Contact: hli@ucdavis.edu
* To whom correspondence should be addressed.
A multivariate approach applied to microarray data for
identification of genes with cell cycle-coupled transcription
Authors: Johansson Daniel , Lindgren Petter , Berglund Anders 
Published: February 2003

Abstract
We have analyzed microarray data using a modeling approach based on the multivariate statistical method partial least squares (PLS) regression to identify genes with periodic fluctuations in expression levels coupled to the cell cycle in the budding yeast, Saccharomyces cerevisiae. PLS has major advantages for analyzing microarray data since it can model data sets with large numbers of variables and with few observations.
A response model was derived describing the expression profile over time expected for periodically transcribed genes, and was used to identify budding yeast transcripts with similar profiles. PLS was then used to interpret the importance of the variables (genes) for the model, yielding a ranking list of how well the genes fitted the generated model. Application of an appropriate cutoff value, calculated from randomized data, allows the identification of genes whose expression appears to be synchronized with cell cycling. Our approach also provides information about the stage in the cell cycle where their transcription peaks.
Three synchronized yeast cell microarray data sets were analyzed, both separately and combined. Cell cycle-coupled periodicity was suggested for 455 of the 6,178 transcripts monitored in the combined data set, at a significance level of 0.5%. Among the candidates, 85% of the known periodic transcripts were included. Analysis of the three data sets separately yielded similar ranking lists, showing that the method is robust.
Contact: anders.berglund@chem.umu.se
Supplementary material: Available at: http://www.chem.umu.se/dep/orgchem/forskning/chemometrics/bioinformatic.stm
* To whom correspondence should be addressed.
† The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Prevention of injuries to children and adolescents
Authors: Rivara F P 
Published: February 2003

Objective:To outline an approach and agenda for research to prevent injuries to children and adolescents.Methods:Injuries to children and adolescents 18 years and younger in low, middle, and high income countries were investigated.Results:A new paradigm for considering injury control research is presented. Research studies are suggested for the areas of etiologic research, intervention research, and outcomes research.Conclusions:Injuries are an important cause of death and disability adjusted life years lost worldwide. Translation of existing research and rigorous randomized trials are needed to reduce the global burden of trauma.
The behaviour of purchasing smuggled cigarettes in Taiwan
Authors: Tsai Y-W , Sung H-Y , Yang C-L , Shih S-F 
Published: February 2003

Objective:Since market liberalisation in 1987, the Taiwan Tobacco and Wine Monopoly Bureau (TTWMB) annual statistics indicate that both the demand for imported cigarettes as well as the number of seized smuggled packs have increased with an average revenue loss of NT$4942 million over the past 15 years. The NT$10 average increase in cigarette prices after Taiwan entered the World Trade Organization (WTO) and the implementation of the Tobacco and Alcohol Tax Law in 2002 are forcing policy makers to examine smuggling even more closely. This study evaluates factors that affect an individual smoker’s decision to purchase smuggled cigarettes, particularly when faced with higher prices.Design:437 male smokers of imported cigarettes were drawn from a national interview survey on cigarette consumption, which the Division of Health Policy Research at the National Health Research Institutes conducted during the year 2000. Multiple logistic regression models were used to analyse the behaviour of purchasing smuggled cigarettes with respect to demographic factors, economic factors, smoking behaviour, and other variables.Results:Cigarette price was the driving factor most closely linked to the purchase of smuggled cigarettes—a 1% increase in cigarette price raised the likelihood of purchasing smuggled cigarettes at least 2.60 times (95% confidence interval (CI) 1.08 to 6.26). Smokers who spent more than NT$1000/month on cigarettes were twice as likely to purchase smuggled cigarettes as those who spent less than NT$1000 (odds ratio (OR) 2.34, 95% CI 1.48 to 3.70). Betel nut chewers were more likely to purchase smuggled cigarettes (OR 1.80, 95% CI 1.09 to 2.90). Smokers who opposed cigarette taxation policy were 1.69 times more likely to buy smuggled cigarettes. Personal income was not significantly associated with smuggled cigarettes purchases.Conclusions:This study evaluates what causes smokers to purchase smuggled cigarettes. We have determined that cigarette price is the most important factor and that betel nut vendors are the main suppliers. Our study provides policy makers with information that can help them develop effective strategies to curb cigarette smuggling after Taiwan’s recent cigarette tax reform, which has increased cigarette prices.
Increase in common cold symptoms and mouth ulcers following smoking cessation: Table 1
Authors: Ussher M , West R , Steptoe A , McEwen A 
Published: February 2003

Objective:To examine changes in reports of common cold symptoms and mouth ulcers following smoking cessation. It was hypothesised that reports of these symptoms would increase on stopping smoking.Design:Smokers were assessed one week before stopping smoking (baseline), then after one, two, and six weeks of smoking abstinence.Participants:174 smokers attending a seven week smoking cessation programme combining behavioural support with nicotine patches.Main outcome measures:Self reports of cold symptoms, mouth ulcers, and smoking abstinence (validated using expired carbon monoxide) were recorded on each measurement occasion.Results:Following one, two, and six weeks of smoking abstinence 73.0% (127/174), 57.5% (100/174), and 44.8% (78/174) of the participants, respectively, maintained continuous abstinence and provided reports of cold symptoms and mouth ulcers. For those abstinent from smoking for six weeks, relative to baseline, a significant increase in reports of the number of cold symptoms was observed following one and two weeks of smoking abstinence (p = 0.009 and p = 0.038, respectively) and an increase in reports of mouth ulcers after one and two weeks of abstinence (p = 0.004 and p = 0.008, respectively). Following one week of abstinence significant increases in reports of sore throat, coughing, deafness, and sneezing were observed (p = 0.049, p < 0.001, p< 0.039, and p < 0.003, respectively).Conclusions:This is the first study to systematically document significant increases in cold symptoms and mouth ulcers following smoking cessation. Smokers should be informed that they have an increased chance of experiencing these symptoms on stopping smoking. Being psychologically prepared for these effects may reduce their impact on the attempt to stop smoking.
Cross-cultural differences in the epidemiology of unexplained fatigue syndromes in primary care
Authors: Skapinakis Petros , Lewis Glyn , Mavreas Venetsanos 
Published: February 2003

BackgroundUnexplained fatigue has been extensively studied but most of the samples used were from Western countries.AimsTo present international data on the prevalence of unexplained fatigue and fatigue as a presenting complaint in primary care.MethodSecondary analysis of the World Health Organization study of psychological problems in general health care. A total of 5438 primary care attenders from 14 countries were assessed with the Composite International Diagnostic Interview.ResultsThe prevalence of unexplained fatigue of 1-month duration differed across centres, with a range between 2.26 (95% CI 1.17–4.33) and 15.05 (95% CI 10.85–20.49). Subjects from more-developed countries were more likely to report unexplained fatigue but less likely to present with fatigue to physicians compared with subjects from less developed countries.ConclusionsIn less-developed countries fatigue might be an indicator of unmet psychiatric need, but in more-developed countries it is probably a symbol of psychosocial distress.
Diffusion of H2O in Smectite Gels: Obstruction Effects of Bound H2O Layers
Authors: Nakashima Yoshito 
Published: February 2003

AbstractIn water-rich smectite gels, bound or less mobile H2O layers exist near negatively-charged clay platelets. These bound H2O layers are obstacles to the diffusion of unbound H2O molecules in the porespace, and therefore reduce the H2O self-diffusion coefficient, D, in the gel system as a whole. In this study, the self-diffusion coefficients of H2O molecules in water-rich gels of Na-rich smectites (montmorillonite, stevensite and hectorite) were measured by pulsed-gradient spin-echo proton nuclear magnetic resonance (NMR) to evaluate the effects of obstruction on D. The NMR results were interpreted using random-walk computer simulations which show that unbound H2O diffuses in the gels while avoiding randomly-placed obstacles (clay platelets sandwiched in immobilized bound H2O layers). A ratio (volume of the clay platelets and immobilized H2O layers)/(volume of clay platelets) was estimated for each water-rich gel. The results showed that the ratio was 8.92, 16.9, 3.32, 3.73 and 3.92 for Wyoming montmorillonite (⩽ 5.74 wt.% clay), Tsukinuno montmorillonite (⩽ 3.73 wt.% clay), synthetic stevensite (⩽ 8.97 wt.% clay), and two synthetic hectorite samples (⩽ 11.0 wt.% clay), respectively. The ratios suggest that the thickness of the immobilized H2O layers in the gels is 4.0, 8.0, 1.2, 1.4 and 1.5 nm, respectively, assuming that each clay particle in the gels consists of a single 1 nm-thick platelet. The present study confirmed that the obstruction effects of immobilized H2O layers near the clay surfaces are important in restricting the self-diffusion of unbound H2O in water-rich smectite gels.
Exchangeable Ion and Thermal Treatment Effects on Basal Spacings of Al-Hydroxy Pillared Montmorillonites
Authors: Reis Aluísio Sousa , Ardisson José Domingos 
Published: February 2003

AbstractAl-hydroxy intercalated clays (ALHICs) obtained from different parent clays were used to investigate the interactions between oligomers and clay surface layers.The thermal stability of ALHICs obtained from natural, Cs-, Ca-, Ba-, Fe-, Cu- or Ce-montmorillonites has been investigated by studying the relationship between basal spacing and calcination temperature. X-ray diffraction has shown that the basal spacing of ALHICs obtained from Cu-montmorillonite calcined at 550°C is 13.4 Å, different from basal spacings of ALHICs obtained from Fe-montmorillonite (16.0 Å) and other parent clays (16.7 Å). Thermograms for AlHICs obtained from natural, Fe- and Ce-montmorillonites displayed distinct steps at 225 and 650°C, attributed to the dehydration of Al13 oligomers, and the dehydroxylation of the surface layer, respectively. By contrast, thermograms of ALHICs obtained from Cu-montmorillonite displayed one step between 250 and 700°C for both dehydration and dehydroxylation. Mössbauer parameters showed that Fe3+ octahedra in octahedral sheets are distorted in pillared interlayered clay (PILC) obtained from Cu-montmorillonite and undistorted in that obtained from Fe-montmorillonite. The difference in thermal stability for the various ALHICs is attributed to the retention of some of the original cations after intercalation with Al13 oligomers, which induces several interactions between the oligomers and the clay surface layers.
Preparation and Characterization of Ti-Pillared Clays Using Ti Alkoxides. Influence of the Synthesis Parameters
Authors: Valverde José Luis , Sánchez Paula , Dorado Fernando , Asencio Isaac , Romero Amaya 
Published: February 2003

AbstractTitanium was introduced into the clay structure by cation exchange with polymeric Ti cations which were formed by partial hydrolysis of Ti alkoxide in HCl. X-ray diffraction, N2 adsorption-desorption, chemical analysis, thermogravimetric analysis, differential thermal analysis, temperature-programmed desorption of ammonia and temperature-programmed reduction were used to characterize the resulting Ti-pillared clays (Ti-PILCs). Titanium methoxide allows the synthesis of a solid with a large basal spacing (26 Å), a large surface area (360 m2/g), a significant amount of micropore surface area (90%), and notable acidity. Moreover, Ti-PILCs obtained from methoxide were found to be thermally stable up to 500°C. A correlation between the increase in acidity and the increases in both microporosity and Ti content was observed. The surface area, the micropore volume, the acidity and the d001 peak intensity all increased upon increasing the amount of Ti added to the preparation (up to ∼15 mmoles of Ti/g clay). The use of an aqueous suspension of 0.13 wt.% of clay yielded the best structural and textural properties in terms of subsequent use of the clay as a catalyst.
Loss of K-Bearing Clay Minerals in Flood-Irrigated, Rice-Growing Soils in Jiangxi Province, China
Authors: Li Zhongpei , Velde B. , Li Decheng 
Published: February 2003

AbstractThe loss of K-bearing clay minerals has been observed over an 80 y cultivation period in Chinese rice paddies despite the use of NKP fertilizers. Clay mineral determinations were made in flood-irrigated paddies cultivated for 3, 10, 15, 30 and 80 y in clayey (45 wt.%), red soils derived from red Quaternary sediments. Three clay minerals are initially present in these soils: illite-mica, magnesian chlorite and an interstratified mica-aluminous chlorite mineral. This last phase was identified using computer simulations. The K-bearing phases (discrete mica and illite as well as interstratified mica layers) are to a large extent lost while the Fe content decreases in the soil as a whole and increases in the chlorite. The mica component in the mixed-layer mineral decreases also. These changes in clay mineralogy and relative abundance suggest a loss of potassic minerals and an increase in the formation of less siliceous, more ferro-magnesian chlorite. These changes occur over 30 y or less, a rather rapid, irreversible transformation of soil clay minerals. Such loss of potassic minerals renders the cultivation more dependent on fertilizer amendment.
Does the cognitive interview help children to resist the effects of suggestive questioning?
Authors: Milne Rebecca , Bull Ray 
Published: February 2003

Purpose. The first set of aims of the present study concerned event recall and examined; (1) whether the cognitive interview (CI) would enhance event recall when used with children, (2) which category(ies) of event recall might be affected, and (3) where in the interview any CI effect emanates from. The second set of aims concerned suggestibility issues and set out to determine whether (1) the CI increased the resistance of children to suggestive questions, and (2) whether scripts had a role in susceptibility to suggestion.Methods. Eighty‐four 8‐10‐year‐old children were shown a video recording of a magic show. A day later they were interviewed individually using either the CI or a structured interview. A pre‐set list of suggestive questions was also given to the children either before or after being interviewed.Results. Those children interviewed using the CI recalled significantly more correct details pertaining to persons and actions, with no increase in the reporting of erroneous information. These effects were found to emanate from the questioning phase of the CI. In addition, those children interviewed with the CI were more resistant to subsequently asked suggestive questions, especially misleading script‐consistent questions.Conclusions. The CI has been found to be a reliable interviewing technique which not only enhances recall but helps to inoculate children against the effects of misleading questions.
Personality traits, personality disorders and sensational interests in mentally disordered offenders
Authors: Egan Vincent , Austin Elizabeth , Elliot Debbie , Patel Darshana , Charlesworth Phillip 
Published: February 2003

Purpose. Sensational interests (e.g. an interest in the occult or the methods of violence) in mentally disordered offenders are claimed to signify greater risk of psychopathology, but evidence to support this view is slight.Methods. The relationships between self‐reported DSM‐IV personality disorder (PD), general personality traits and sensational interests were examined in 155 of 167 consecutively referred offenders to a forensic psychology service. The subscales of the PD and personality trait measures were reduced to the four basic PD/trait dimensions (asocial, antisocial, anxious and anankastic) using confirmatory factor analysis.Results. Those high on the ‘antisocial’ factor (which was primarily defined by low Agreeableness, low Conscientiousness, and substantial elements of Paranoid, Antisocial and Borderline PD) were more interested in ‘violent‐occult’ and militaristic topics.Conclusions. The aspects of the antisocial factor primarily associated with an interest in sensational and potentially violent topics cover a wide range of putative disorders. However, the factors reflecting asocial, anxious or anankastic disorders do not show a reliable association with measures of sensational interests. These results suggest that the personality dimensions reflecting an interest in ‘sensational’ topics in mentally disordered offenders are relatively specific.
Measuring the real impact of accredited offending behaviour programmes
Authors: Friendship Caroline , Falshaw Louise , Beech Anthony R. 
Published: February 2003

Purpose. This paper describes an integrated model for the evaluation of offending behaviour programmes in order to assess their real impact.Arguments. To date there has been an over‐reliance on reconviction data as the sole measure of treatment efficacy. Reconviction has a fundamental role to play but cannot be considered in isolation from other empirically related treatment and re‐settlement factors. A rigorous reconviction study requires an adequate comparison group but few papers describe with transparency how this has been achieved. There is also the assumption that participation in treatment renders an individual offender as treated. A treated profile is contingent upon the treatment climate, the quality of programme delivery and how the individual responds to treatment. The influence of life‐style or dynamic risk factors must also be acknowledged in terms of their effect on reconviction.Conclusions. It is recommended that researchers use an integrated approach to the evaluation of accredited offending behaviour programmes. In order to establish a broad balance of treatment outcomes, a shift away from reconviction rates is needed. This paper presents an integrated model for the evaluation of offending behaviour programmes.
Two new species of Mycobilimbia from Spain
Authors: Sarrión Francisco José , Aragón Gregorio , Hafellner Josef , Rico Victor J. , Burgaz Ana Rosa 
Published: February 2003

AbstractTwo new species of Mycobilimbia are described from Spain. Mycobilimbia olwacea has a minutely squamulose and olivaceous thalli and dark reddish brown apothecia, colourless inside; it has been found at middle to high altitudes (from 900 to 1750 m), growing on humid tree bases of Pinus nigra and lignum of Quercus pyrenaica. Mycobilimbia parvilobulosa is closely related to M. berengeriana, but differs markedly by its squamulose thalli, with crenate to subdigitiform margins, dark reddish brown excipulum and colourless epithecium. It grows on moss-covered old trunks of fagaceous trees. The new taxa are compared with M. berengeriana, M. hypnorum and M. sanguineoatra and their main distinguishing characters are tabulated.
First trimester sonographic diagnosis of holoprosencephaly
Authors: Tongsong T. , Wanapirak C. , Chanprapaph P. , Siriangkul S. 
Published: February 2003

AbstractObjective: To describe our experience with sonographic diagnosis of fetal holoprosencephaly in first trimester. Subjects: A total of three fetuses with early prenatal diagnosis of holoprosencephaly were sonographically evaluated and followed up. Results: The study revealed that all showed monoventricular cavity, fused thalami, no falx and cavum septum pellucidum. All of them were correctly diagnosed sonographically in the first trimester. Extracranial anomalies had also been identified in all three fetuses and all of them had facial abnormalities. Cytogenetic studies were successfully carried out in only one case. No polyhydramnios was demonstrated in all cases. Conclusion: This small series indicates that holoprosencephaly can be diagnosed in the first trimester. The most valuable clue to the diagnosis is the demonstration of the single ventricle.
Preoperative ultrasound assessment of adnexal masses in premenopausal women
Authors: Milad M.P. , Cohen L. 
Published: February 2003

AbstractObjectives: This study was undertaken to determine the accuracy of preoperative transvaginal ultrasound in predicting ovarian histopathology in premenopausal women. Methods: A retrospective cohort study was performed from reproductive‐age women that underwent removal of an ovarian cyst between May 1990 and April 1998. Results: Of the 120 consecutive patients identified, 19 did not meet inclusion criteria. Pathologic diagnosis confirmed endometriomas (n=55), mature teratoma (n=25), serous cystadenoma (n=18), persistent corpus luteum (n=7) and other (n=5). The primary preoperative transvaginal ultrasound impression was accurate in most cases (endometrioma: 85%, mature teratoma: 86%, serous cystadenoma: 80%). Conclusion: Endometriomas and mature cystic teratomas can be predicted with a moderate degree of accuracy by preoperative ultrasound.