bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are Dumbbell Brightest Cluster Members Signposts to Galaxy Cluster Activity?
Authors: Pimbblet K. A. 
Published: November 2008

AbstractWe assemble a sample of galaxy clusters whose brightest members are dumbbell galaxies and compare them with a control sample in order to investigate if they are the result of recent mergers. We show that the dumbbell sample is no more likely than other clusters to exhibit subclustering. However, they are much more likely to have at least one dumbbell component possessing a significant peculiar velocity with respect to the parent cluster than a non-dumbbell brightest cluster member. We interpret this in the context of seeing the clusters at various stages of post-merger relaxation.
LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data
Authors: Sartor Maureen A. , Leikauf George D. , Medvedovic Mario 
Published: November 2008

Abstract
Motivation: The elucidation of biological pathways enriched with differentially expressed genes has become an integral part of the analysis and interpretation of microarray data. Several statistical methods are commonly used in this context, but the question of the optimal approach has still not been resolved.
Results: We present a logistic regression-based method (LRpath) for identifying predefined sets of biologically related genes enriched with (or depleted of) differentially expressed transcripts in microarray experiments. We functionally relate the odds of gene set membership with the significance of differential expression, and calculate adjusted P-values as a measure of statistical significance. The new approach is compared with Fisher's exact test and other relevant methods in a simulation study and in the analysis of two breast cancer datasets. Overall results were concordant between the simulation study and the experimental data analysis, and provide useful information to investigators seeking to choose the appropriate method. LRpath displayed robust behavior and improved statistical power compared with tested alternatives. It is applicable in experiments involving two or more sample types, and accepts significance statistics of the investigator's choice as input.
Availability: An R function implementing LRpath can be downloaded from http://eh3.uc.edu/lrpath.
Contact: mario.medvedovic@uc.edu
Supplementary information: Supplementary data are available at Bioinformatics online and at http://eh3.uc.edu/lrpath.
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB
Authors: Rayner Tim F. , Rezwan Faisal Ibne , Lukk Margus , Bradley Xiangqun Zheng , Farne Anna , Holloway Ele , Malone James , Williams Eleanor , Parkinson Helen 
Published: November 2008

Abstract
Summary: The MAGE-TAB format for microarray data representation and exchange has been proposed by the microarray community to replace the more complex MAGE-ML format. We present a suite of tools to support MAGE-TAB generation and validation, conversion between existing formats for data exchange, visualization of the experiment designs encoded by MAGE-TAB documents and the mining of such documents for semantic content.
Availability: Software is available from http://tab2mage.sourceforge.net/
Contact: tfrayner@gmail.com
Differences in clinical manifestations of influenza‐associated encephalopathy by age
Authors: Wada Tomoaki , Morishima Tsuneo , Okumura Akihisa , Tashiro Masato , Hosoya Mitsuaki , Shiomi Masashi , Okuno Yoshinobu 
Published: November 2008

ABSTRACTData from patients in Japan was analyzed to examine the age distribution and differences by age in the clinical manifestations of influenza‐associated encephalopathy. Between 1998 and 2002, 472 cases of influenza‐associated encephalopathy in patients aged 15 years or younger were reported to the Collaborative Study Group on Influenza‐Associated Encephalopathy. These cases were divided into two groups by age: 0–5 and 6–15 years. The differences between the groups were estimated based on the data for those aged 0–5 years, and the odds ratios and 95% confidence intervals calculated. Distribution was inversely correlated with age, with a peak at 1–2 years old. In comparison with patients aged 0–5, those aged 6–15 years had a significantly greater incidence of type B infection, lower frequency of convulsions, higher frequency of loss of consciousness and altered consciousness as the initial neurological symptom, lower serum transaminase levels, lower frequency of low‐density area for brain CT upon admission, and lower incidence of sequelae. Our analysis indicates that the clinical course, laboratory data, and brain imaging findings of influenza‐associated encephalopathy exhibits patterns that vary with age.
Golden monkey ranging in relation to spatial and temporal variation in food availability
Authors: Twinomugisha Dennis , Chapman Colin A. 
Published: November 2008

AbstractUnderstanding the determinants of a species’ range use aids in understanding their ecological requirements, which in turn facilitates designing effective conservation strategies. The ranging behaviour of golden monkeys (Cercopithecus mitis kandti) in Mgahinga Gorilla National Park, Uganda was studied from January 2003 to February 2004 to establish habitat preferences. In each 0.25 ha grid cell in the group’s home range we quantified the basal area of food trees (n = 12,133 trees), measured bamboo (Arundinaria alpina) stems (n = 103,548), and estimated vine and shrub coverage. The evaluation of habitat preferences was facilitated by the fact that only five plant species, plus invertebrates (7.5%) constituted 96.4% of the group’s foraging effort; this included bamboo (59.9%), Maesa lanceolata (18.7%), Hypericum revolutum (6.8%), Galiniera saxifraga (2.1%) and Ilex mitis (1.4%). Phenology data were collected for all five food tree species, three vines, and two shrubs. Range use generally followed food tree basal area distribution and not the distribution of bamboo, with the abundance of M. lanceolata being more closely associated with home range use than any other food plant. Bamboo was ubiquitous in distribution and a vital year‐round resource for golden monkeys, which they combined with other food items to meet their nutritional requirements. Illegal bamboo or tree extraction both pose a serious threat to the conservation of the golden monkey, but activities that affect food tree abundance will likely have the most influence on monkey persistence.
Urban ecological footprints in Africa
Authors: Clancy Joy S. 
Published: November 2008

AbstractAfrica’s rate of urbanization is the highest in the world. This is relevant to ecologists working in Africa because urban growth is strongly associated with habitat destruction, and also creates new fields of study. The ecological footprint concept is used to illustrate how urban settlements in Africa impact on rural ecosystems. At an aggregate level, African countries have the lowest ecological footprints in the world. However, there is little available data for individual cities, so evidence is fragmented making concerted policy initiatives difficult. Wood fuel continues to be a major source of energy for urban households and there is a long running debate as to what extent providing wood fuel for urban use damages forest ecosystems. Growing evidence contests the assertion that urban wood fuel markets are responsible for forest degradation. Although there are other options available, the social consequences of switching energy sources need to be taken into account. Outright bans, for example on charcoal, would lead to a loss of livelihoods in rural and urban households, and may not solve deforestation as well as increasing fossil fuel use would increase the ecological footprint.
Smoking‐related changes in the background lung of specimens resected for lung cancer: a semiquantitative study with correlation to postoperative course
Authors: Kawabata Y , Hoshi E , Murai K , Ikeya T , Takahashi N , Saitou Y , Kurashima K , Ubukata M , Takayanagi N , Sugita H , Kanauchi S , Colby T V 
Published: November 2008

Aims: To assess the pathological findings in lobectomy specimens, to correlate them with smoking history and postoperative course and to compare the findings with those in smoking‐related interstitial lung disease.Methods and results: Patients who had undergone lobectomy for lung cancer were reviewed. Subjects included 230 non‐smokers and 587 smokers, of whom 572 had a known smoking index (SI). They were classified into mild, moderate and heavy smokers. Centrilobular emphysema (CLE), respiratory bronchiolitis, airspace enlargement with fibrosis (AEF), the presence of foci resembling usual interstitial pneumonia pattern (UIP/P) and the rate of postoperative respiratory failure were assessed. The incidence of AEF was 6.5% in mild smokers, and 17.7% in moderate smokers (P < 0.01) with lower lobe predominance. There were significant correlations (P < 0.01) between AEF and CLE and AEF and UIP/P. The rate of respiratory failure after lobectomy was 6%, and 10% in patients having UIP/P with or without AEF, but was not seen in patients with AEF alone (P < 0.01).Conclusions: AEF is an important smoking‐related change in the lung that appears to correlate with the smoking history, and its distinction from UIP/P may be important.
Effects of pH, cinnamaldehyde and heat‐treatment time on spore viability of Alicyclobacillus acidoterrestris
Authors: Bevilacqua Antonio , Sinigaglia Milena , Corbo Maria Rosaria 
Published: November 2008

SummaryA three variables–five levels central composite design was used to study the effects of pH (3.5, 4.0, 4.5, 5.0 and 5.5), cinnamaldehyde (0, 40, 80, 120 and 160 ppm) and heating temperature (80, 84, 88, 92 and 96 °C) on the spores of Alicyclobacillus acidoterrestris in malt extract broth (MEB). The heat shock resulted in a slight decrease of spore number from 3.2 to 2.5 log CFU mL−1 and occurred at 80–85 °C depending on the pH of the medium. Otherwise, cinnamaldehyde acted as an additional hurdle within the storage time; the critical amounts to be used were included in the range 41.35–44.42 ppm of cinnamaldehyde and were related positively to the pH, i.e. the critical amount of active compound decreased with the decreasing of the pH.
Oxidative stability of brined anchovies (Engraulis encrasicholus) with plant extracts
Authors: Turhan Sadettin , Sagir Inci , Temiz Hasan 
Published: November 2008

SummaryThe effect of brining with plant extracts on the oxidative stability of anchovies was investigated during storage. The brining process was done in 15 g 100 mL−1 of sodium chloride solution with water, and with myrtle, rosemary and nettle extracts. Brined anchovies were stored at 4 ± 1 °C for 28 days. Brining with plant extracts slowed down the lipid oxidation of anchovies. The highest antioxidant effect was observed in brined anchovies with rosemary and myrtle extracts during storage as indicated by peroxide value (POV), thiobarbituric acid reactive substance and oxidative rancidity (OR) scores. Furthermore, OR scores in brined anchovies were well correlated with thiobarbituric acid reactive substance (r2 = 0.66, P < 0.01) and POV (r2 = 0.87; P < 0.01). The fatty acid profiles were similar among the brined anchovies with plant extracts. These results suggest that brining with rosemary, myrtle and to a lesser extent, nettle extracts prevents development of oxidation in lipids of anchovies during storage.
Headspace‐based techniques to identify the principal volatile compounds in red grape cultivars
Authors: González‐Mas M. Carmen , García‐Riaño Luisa M. , Alfaro Cristina , Rambla José L. , Padilla Ana I. , Gutierrez Abelardo 
Published: November 2008

SummaryThe control of the raw material has a great influence on the final quality of wine. Nowadays, wineries have practically not incorporated an effective quality control of grape juice on their production process. Although wine aroma has been widely analysed, grape juice aroma for wine‐making has been poorly studied. In this study, two headspace‐based technique methodologies have been proposed to characterise the aroma of grape juice: static headspace (SHS) and headspace solid phase microextraction (HS‐SPME). Both techniques were applied on the samples from three maturation stages of two red grape cultivars: Tempranillo and Bobal, ranked first in Spanish and in Valencian Community cultivars, respectively. This study identifies the principal volatile compounds of grape juice: C6 compounds, especially alcohols and aldehydes, using both techniques. It was confirmed that SHS and HS‐SPME techniques could be incorporated into the process of the grape quality control in wineries as a result of its operational simplicity, low cost and reduced ecological impact compared with other conventional organic solvent‐based techniques.
Long‐distance colonization of the Western Mediterranean by Cistus ladanifer (Cistaceae) despite the absence of special dispersal mechanisms
Authors: Guzmán Beatriz , Vargas Pablo 
Published: November 2008

AbstractAim  There are few biogeographical and evolutionary studies that address plant colonization and lineage origins in the Mediterranean. Cistus serves as an excellent model with which to study diaspore dispersal and distribution patterns of plants exhibiting no special long‐distance dispersal mechanisms. Here we analyse the pattern of genetic variation and divergence times to infer whether the African–European disjunction of C. ladanifer L. is the result of long‐distance dispersal or of vicariance events.Location  Principally the Western Mediterranean region, with a focus on the Strait of Gibraltar.Methods  We used DNA sequence phylogenetic approaches, based on plastid (rbcL/trnK‐matK) and nuclear (ITS) sequence data sets, and the penalized likelihood method, to date the diversification of the 21 species of Cistus. Phylogenetic relationships and phylogeographical patterns in 47 populations of C. ladanifer were also analysed using two plastid DNA regions (trnS‐trnG, trnK‐matK). These sequence data were analysed using maximum parsimony, Bayesian inference and statistical parsimony.Results  Dating estimates indicated divergence dates of the C. ladanifer lineage in the Pleistocene. Eight nucleotide‐substitution haplotypes distributed on the European (four haplotypes) and African (five haplotypes) sides of the Strait of Gibraltar were revealed from C. ladanifer sequences. Both the haplotype network and the phylogenetic analyses depicted two main Cistus lineages distributed in both Europe and North Africa. An Iberian haplotype forms part of the North African lineage, and another haplotype distributed on both continents is related to the European lineage. Haplotype relationships with respect to outgroup sequences supported the hypothesis that the centre of genetic diversity is in northern Africa.Main conclusions  Based on lineage divergence‐time estimates and disassociation between geographical and lineage haplotype distributions, we inferred at least two intercontinental colonization events of C. ladanifer post‐dating the opening of the Strait of Gibraltar (c. 5 Ma). This result supports a hypothesis of long‐distance dispersal rather than a hypothesis of vicariance. We argue that, despite limited dispersal abilities, preference for disturbed habitats was integral to historical colonization after the advent of the Mediterranean climate (c. 3.2 Ma), when Cistus species diverged and became established as a dominant element in the Mediterranean scrub.
Effects of long working hours and the night shift on severe sleepiness among workers with 12‐hour shift systems for 5 to 7 consecutive days in the automobile factories of Korea
Authors: SON MIA , KONG JEONG‐OK , KOH SANG‐BAEK , KIM JAEYOUNG , HÄRMÄ MIKKO 
Published: November 2008

SummaryWe investigated the effects of 12‐hour shift work for five to seven consecutive days and overtime on the prevalence of severe sleepiness in the automobile industry in Korea. [Correction added after online publication 28 Nov: Opening sentence of the summary has been rephrased for better clarity.] A total of 288 randomly selected male workers from two automobile factories were selected and investigated using questionnaires and sleep‐wake diaries in South Korea. The prevalence of severe sleepiness at work [i.e. Karolinska Sleepiness Scale (KSS) score of 7 or higher] was modeled using marginal logistic regression and included theoretical risk factors related to working hours and potential confounding factors related to socio‐economic status, work demands, and health behaviors. Factors related to working hours increased the risk for severe sleepiness at the end of the shift in the following order: the night shift [odds ratio (OR): 4.7; 95% confidence interval (CI): 3.6–6.0)], daily overtime (OR: 2.2; 95% CI: 1.7–2.9), weekly overtime (OR: 1.6; 95% CI: 1.0–2.6), and night overtime (OR: 1.6; 95% CI: 0.8–3.0). Long working hours and shift work had a significant interactive effect for severe sleepiness at work. Night shift workers who worked for 12 h or more a day were exposed to a risk of severe sleepiness that was 7.5 times greater than day shift workers who worked less than 11 h. Night shifts and long working hours were the main risk factors for severe sleepiness among automobile factory workers in Korea. Night shifts and long working hours have a high degree of interactive effects resulting in severe sleepiness at work, which highlight the need for immediate measures to address these characteristics among South Korean labor force patterns.
Cold extremities and difficulties initiating sleep: evidence of co‐morbidity from a random sample of a Swiss urban population
Authors: KRÄUCHI KURT , GASIO PAOLA FONTANA , VOLLENWEIDER STEPHANIE , VON ARB MARIELLA , DUBLER BARBARA , ORGÜL SELIM , FLAMMER JOSEF , STUTZ ELISABETH ZEMP 
Published: November 2008

SummaryDifficulties initiating sleep (DIS) can frequently occur in psychiatric disorders but also in the general population. The primary vasospastic syndrome is a functional disorder of vascular regulation in otherwise healthy subjects complaining of thermal discomfort from cold extremities (TDCE). Laboratory studies have shown a close relationship between long sleep onset latency and increased distal vasoconstriction in healthy young subjects. Considering these findings, the aims of the Basel Survey were to assess the prevalence rates for DIS and TDCE and to determine whether both symptoms can be associated in the general population. In a random population sample of Basel‐Stadt, 2800 subjects (age: 20–40 years) were requested to complete a questionnaire on sleep behavior and TDCE (response rate: 72.3% in women, n = 1001; 60.0% in men, n = 809). Values of DIS and TDCE were based on questionnaire‐derived scores. In addition, TDCE was externally validated in a separate group of subjects (n = 256) by finger skin temperature measurements—high TDCE values were significantly associated with low finger skin temperature. A total of 31.1% of women and 6.9% of men complain of TDCE. In contrast, prevalence rates of DIS were only slightly higher in women in comparison to men (9.3% versus 6.7%, P < 0.1). Irrespective of gender, each seventh subject complaining of TDCE had concomitant DIS and the relative risk in these subjects was approximately doubled. Therefore, a thermophysiological approach to DIS may be relevant for its differential diagnosis and its treatment.
Interaction of chronic sleep restriction and circadian system in humans
Authors: ROGERS NAOMI L. , DINGES DAVID F. 
Published: November 2008

SummaryNocturnal sleep restriction and compensation with daytime naps is common in today’s society. In a between‐participants design, we examined the effects of chronic (10 nights) sleep restriction on 24 h plasma melatonin profiles in humans. Following a baseline period with 8.2 h time in bed (TIB) for sleep, participants were randomized to a control (8.2 h TIB) or sleep‐restriction condition (4.2 h TIB), with and without diurnal naps. Sleep restriction was achieved via delaying bedtime and advancing wake time by 2 h each relative to the baseline sleep period. Participants were maintained in a controlled, time isolated laboratory environment throughout the protocol, with light levels below 40 lx at all times. Twenty‐four hour plasma melatonin profiles were assessed at baseline and at the end of the sleep‐restriction period, with subjects maintained in a constant posture protocol. Compared with the baseline assessment and the 8.2 h TIB control group, a significant phase delay in melatonin onset (1.2 ± 0.9 h) occurred in all sleep‐restriction (4.2 h TIB) groups (P < 0.05). There was no evidence of a phase advance or shortening of the period of melatonin secretion associated with the advanced waking time. These results suggest that nocturnal light and dark exposure may be more potent in effecting circadian phase shifts than exposure to morning light, at least in conditions of controlled, dim lighting in the laboratory.
Sleep position alters arousal processes maximally at the high‐risk age for sudden infant death syndrome
Authors: RICHARDSON HEIDI LOUISE , WALKER ADRIAN MARK , HORNE ROSEMARY SYLVIA CLAIRE 
Published: November 2008

SummaryAn impaired ability to arouse from sleep may play an important role in the pathogenesis of sudden infant death syndrome (SIDS). This study aimed to investigate the effects of prone sleeping on the nature of both induced and spontaneous arousal responses in infants. Thirteen healthy term infants were studied longitudinally at 2–4 weeks, 2–3 months and 5–6 months postnatal age. A pulsatile jet of air to the nostrils was used to induce arousal from both active sleep and quiet sleep in both prone and supine positions. For each stimulus, arousals were classified as sub‐cortical activations and cortical arousals, scored using physiological and electroencephalogram changes and expressed as a percentage of the total number of arousals. Spontaneous arousals were similarly analysed. Increased proportions of cortical arousals, hence decreased proportions of sub‐cortical activations, were observed in the prone position at 2–3 months. This distinct peak in the proportion of cortical arousals occurred regardless of sleep state and regardless of whether the arousal occurred spontaneously or was induced by air‐jet stimulation. The nature of arousal responses in healthy term infants is altered in the prone sleeping position at 2–3 months after birth, the age where SIDS incidence is highest. We postulate that a greater propensity for cortical arousal may be a protective mechanism to promote complete arousal in a vulnerable sleeping position and/or a vulnerable period of maturation. Inadequate or incomplete cortical arousals may explain the increased risk of SIDS associated with the prone position at this age.
The epidemiology of neuroblastoma: a review
Authors: Heck Julia E. , Ritz Beate , Hung Rayjean J. , Hashibe Mia , Boffetta Paolo 
Published: November 2008

SummaryNeuroblastoma is the most common tumour in children less than 1 year of age. The goal of this review was to summarise the existing epidemiological research on risk factors for neuroblastoma.A comprehensive search of the literature was undertaken using PubMed for epidemiological studies on neuroblastoma risk factors. We ascertained 47 articles which examined the risk factors. Ten studies employed population‐based case‐control designs; six were hospital‐based case‐control studies; two were cohort studies; and five employed ecological designs. Studies ranged in size from 42 to 538 cases. Three studies showed evidence of an increased risk of disease with use of alcohol during pregnancy (OR range 1.1, 12.0). Protective effects were seen with maternal vitamin intake during pregnancy (OR range 0.5, 0.7) in two studies, while risk of disease increased with maternal intake of diuretics (OR range 1.2, 5.8) in three studies. Three studies reported a decrease in risk for children with a history of allergic disease prior to neuroblastoma diagnosis (OR range 0.2, 0.4). The rarity of neuroblastoma makes this disease particularly challenging to study epidemiologically. We review the methodological limitations of prior research and make suggestions for further areas of study.