bluuebunny/crossref_metadata_2025 huggingface dataset:
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

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

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
Experience-dependent plasticity mechanisms for neural rehabilitation in somatosensory cortex
Authors: Fox Kevin
Published: November 2008

Functional rehabilitation of the cortex following peripheral or central nervous system damage is likely to be improved by a combination of behavioural training and natural or therapeutically enhanced synaptic plasticity mechanisms. Experience-dependent plasticity studies in the somatosensory cortex have begun to reveal those synaptic plasticity mechanisms that are driven by sensory experience and might therefore be active during behavioural training. In this review the anatomical pathways, synaptic plasticity mechanisms and structural plasticity substrates involved in cortical plasticity are explored, focusing on work in the somatosensory cortex and the barrel cortex in particular.
Genetic variation and recent population history of the tropical garAtractosteus tropicusGill (Pisces: Lepisosteidae)
Authors: Barrientos‐Villalobos J. , Espinosa de los Monteros A.
Published: November 2008

The tropical garAtractosteus tropicusbelongs to one of the few extant lineages of early bony fishes. The genetic variation detected both within and among 11 natural populations ofA. tropicusin Mesoamerica along with the implications for their recent history are presented. Sequences from cytochromeb(307 bp) and cytochrome oxidase subunit II (607 bp) were used as data sources. Apparently, the populations of this fish have decreased in size because of anthropogenic pressures, such as habitat degradation and destruction. The observed values for nucleotide diversity (0·0016 ± 0·0018) and haplotype diversity (0·477 ± 0·302) suggest low levels of genetic variation. Nonetheless, most of the populations studied are currently in a period of genetic stasis. Recent isolation by distance, reduced gene flow and translocation were inferred as the processes maintaining this stasis. Phylogenetic analyses showed reciprocal monophyly between the haplotypes from Guatemala and the other populations. This, together with the observed genetic variation, suggests that the Guatemalan haplotypes might represent a new species. The haplotypes, other than those from Guatemala, exhibited a geographic pattern consistent with two main reproductive populations, one from the Pacific and the other from the Gulf of Mexico–Caribbean slope of Mesoamerica. Pleistocene glacial and interglacial periods might be responsible for moulding the heterogeneity in the genetic structure observed during this study.
Contrasting patterns of morphological and neutral genetic divergence among geographically proximate populations of sockeye salmon Oncorhynchus nerka in Lake Aleknagik, Alaska
Authors: Lin J. , Ziegler E. , Quinn T. P. , Hauser L.
Published: November 2008

Levels of differentiation in morphological traits (age at maturity, body length at age, egg mass and body depth) and spawning time were examined in sockeye salmon Oncorhynchus nerka from three geographically proximate but physically distinct creeks in Lake Aleknagik, Alaska. Happy Creek fish had significantly greater values for most measured morphological traits, and Eagle Creek fish spawned significantly later than fish in the other creeks. Phenotypic differentiation between creeks, measured as PST, was then compared with microsatellite marker differentiation between creeks, measured as FST. No correlations were apparent between PST and FST values, and PST values were generally significantly larger than zero (PST= 0·0018–0·31) whereas FST values were not (FST=−0·0004 to 0·0016). The insignificant pair‐wise FST values between creek samples indicated that gene flow occurs between creeks, assuming the creek populations have reached migration–drift equilibrium. However, the strong homing behaviour of sockeye salmon precludes a scenario in which fish from the three creeks constitute a single population that segregates by body size. Rather, significant phenotypic differentiation suggests that strong divergent selection occurs on the phenotypic traits despite the homogenizing effects of gene flow.
Cytotaxonomy of Astyanax (Characiformes, Characidae) from the Upper Iguaçu River Basin: confirmation of the occurrence of distinct evolutionary units
Authors: Kantek D. L. Z. , Noleto R. B. , Maurutto F. A. M. , Bertollo L. A. C. , Moreira‐Filho O. , Cestari M. M.
Published: November 2008

Taxonomic studies of the genus Astyanax from the Iguaçu River (Brazil) indicate that they may be differentiated into 11 distinct species, some of which have not been formally described and named so for. This study focuses on three of these species, Astyanax sp. B, Astyanax sp. C and Astyanax sp. D from the Upper Iguaçu River Basin. Comparative cytogenetic analyses of C‐banding, Ag‐NORs (silver nitrate stained nucleolar organizer region) and 18S and 5S rDNA corroborate that they are distinct species. A diploid number of 50 chromosomes and similar karyotypic formulae were observed in the three taxa, with the exception of Astyanax sp. D that differs in the number of submetacentric and subtelocentric chromosomes. However, the NOR silver‐staining pattern, the heterochromatic bands (C‐bands) and the mapping of the 18S and 5S rDNA sites in the chromosomes showed divergences between all three species under study, supporting the occurrence of distinct evolutionary units.
Phylogeography of the bigeye chub Hybopsis amblops (Teleostei: Cypriniformes): early Pleistocene diversification and post‐glacial range expansion
Authors: Berendzen P. B. , Gamble T. , Simons A. M.
Published: November 2008

The bigeye chub, Hybopsis amblops, is a member of the Central Highlands ichthyofauna of eastern North America. Phylogenetic analyses of the H. amblops species group based on a 1059 bp fragment of the mitochondrial DNA cytochrome b gene did not recover a monophyletic group. The inclusion of Hybopsis hypsinotus in the species complex is questionable. Within H. amblops, five strongly supported clades were identified; two clades containing haplotypes from the Ozark Highlands and three clades containing haplotypes from the Eastern Highlands and previously glaciated regions of the Ohio and Wabash River drainages. Estimates of the timing of divergence indicated that prior to the onset of glaciation, vicariant events separated populations east and west of the Mississippi River. East of the Mississippi River glacial cycles associated with the blocking and rerouting of the Teays River system caused populations to be pushed southward into refugia of the upper Ohio River. Following the most recent Wisconsinan glaciation, populations expanded northward into previously glaciated regions and southward into the Cumberland River drainage. In the Ozarks, west of the Mississippi River, isolation of clades appears to be maintained by the lack of stream capture events between the upper Arkansas and the White River systems and a barrier formed by the Arkansas River.
Establishment of a Chinese sturgeonAcipenser sinensistail‐fin cell line and its susceptibility to frog iridovirus
Authors: Zhou G. Z. , Gui L. , Li Z. Q. , Yuan X. P. , Zhang Q. Y.
Published: November 2008

Chinese sturgeonAcipenser sinensis, a cartilaginous ganoid, is a ‘living fossil’ on a deeply isolated evolutionary branch. A cell line was established from Chinese sturgeon tail‐fin tissue (CSTF) . These epithelial CSTF cells grew well in Dulbecco’s modified Eagle’s medium at 25° C. Karyotypic analysis revealed a normal diploid karyotype with 2n= 264 and large numbers of punctate chromosomes. A strain of frog iridoviruses [Rana gryliovirus (RGV)] was used to test the susceptibility of this cell line to infection. Infection was confirmed by cytopathic effect, immunofluorescence and electron‐microscope observations, which detected the viral antigens or particles in the cytoplasm of RGV‐infected cells. Molecular analysis further suggested thatc.550 bp DNA fragment could be cloned from the RGV‐infected CSTF cells’ DNA with major capsid protein gene polymerase chain reaction primers. Furthermore, after transfection with pEGFP vector DNA, the CSTF cell line produced significant fluorescent signals indicating its utility in exogenous studies.
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

Data 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

Understanding 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

Africa’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

A 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

The 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

The 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

Aim  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

We 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

Difficulties 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

Nocturnal 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

An 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

Neuroblastoma 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.
Approaches to the identification of susceptibility genes
Authors: COLLINS A.
Published: November 2008

Although previous studies have revealed a great deal about the genetic basis of susceptibility and resistance to parasite infection, there is now an opportunity to considerably enhance understanding through genome‐wide association mapping. The application of association mapping to complex inheritance has recently become achievable given reduced costs, sophisticated genotyping platforms and powerful statistical methods which build upon increased knowledge of the linkage disequilibrium structure of the human genome. Linkage mapping and related approaches remain useful for the localization of the rarer genetic variants and candidate region association studies can be a very cost‐effective route to progress. However, genome‐wide association offers the greatest promise, despite the challenges posed by phenotype complexity, ensuring genotype coverage/quality and robust statistical analysis. The available approaches for mapping genes underlying susceptibility are reviewed here, emphasizing their relative merits and drawbacks and highlighting specific software tools and resources that enable successful mapping.
Comparative analysis of leaf‐type ferredoxin‐NADP+ oxidoreductase isoforms in Arabidopsis thaliana
Authors: Lintala Minna , Allahverdiyeva Yagut , Kangasjärvi Saijaliisa , Lehtimäki Nina , Keränen Mika , Rintamäki Eevi , Aro Eva‐Mari , Mulo Paula
Published: November 2008

Physiological roles of the two distinct chloroplast‐targeted ferredoxin‐NADP+ oxidoreductase (FNR) isoforms in Arabidopsis thaliana were studied using T‐DNA insertion line fnr1 and RNAi line fnr2. In fnr2 FNR1 was present both as a thylakoid membrane‐bound form and as a soluble protein, whereas in fnr1 the FNR2 protein existed solely in soluble form in the stroma. The fnr2 plants resembled fnr1 in having downregulated photosynthetic properties, expressed as low chlorophyll content, low accumulation of photosynthetic thylakoid proteins and reduced carbon fixation rate when compared with wild type (WT). Under standard growth conditions the level of F0‘rise’ and the amplitude of the thermoluminescence afterglow (AG) band, shown to correlate with cyclic electron transfer (CET), were reduced in both fnr mutants. In contrast, when plants were grown under low temperatures, both fnr mutants showed an enhanced rate of CET when compared with the WT. These data exclude the possibility that distinct FNR isoforms feed electrons to specific CET pathways. Nevertheless, the fnr2 mutants had a distinct phenotype upon growth at low temperature. The fnr2 plants grown at low temperature were more tolerant against methyl viologen (MV)‐induced cell death than fnr1 and WT. The unique tolerance of fnr2 plants grown at low temperature to oxidative stress correlated with an increased level of reduced ascorbate and reactive oxygen species (ROS) scavenging enzymes, as well as with a scarcity in the accumulation of thylakoid membrane protein complexes, as compared with fnr1 and WT. These results emphasize a critical role for FNR2 in the redistribution of electrons to various reducing pathways, upon conditions that modify the photosynthetic capacity of the plant.
MTP1‐dependent Zn sequestration into shoot vacuoles suggests dual roles in Zn tolerance and accumulation in Zn‐hyperaccumulating plants
Authors: Gustin Jeffery L. , Loureiro Marcello E. , Kim Donggiun , Na Gunnam , Tikhonova Marina , Salt David E.
Published: November 2008

The integral membrane protein Thlaspi goesingense metal tolerance protein 1 (TgMTP1) has been suggested to play an important role in Zn hyperaccumulation in T. goesingense. Here, we show that the TgMTP1 protein is accumulated to high levels at the vacuolar membrane in shoot tissue of T. goesingense. TgMTP1 is likely to act in the transport of Zn into the vacuole, enhancing both Zn accumulation and tolerance. By specifically expressing TgMTP1 in Arabidopsis thaliana shoots, we show that TgMTP1, localized at the vacuolar membrane, can drive the enhanced shoot accumulation of Zn by initiating a systemic Zn deficiency response. The systematic response includes increased expression of Zn transporters (ZIP3, ZIP4, ZIP5 and ZIP9) in both shoot and root tissue. Furthermore, shoot‐specific accumulation of TgMTP1 at the vacuolar membrane also leads to increased resistance to Zn in A. thaliana, probably through enhanced Zn compartmentalization in the vacuole. Such evidence leads to the conclusion that the high levels of TgMTP1 at the vacuolar membrane in shoot tissue of the Zn hyperaccumulator T. goesingense play a role in both Zn tolerance and enhanced Zn uptake and accumulation, via the activation of a systemic Zn deficiency response.
Nitric oxide modulates ozone‐induced cell death, hormone biosynthesis and gene expression in Arabidopsis thaliana
Authors: Ahlfors Reetta , Brosché Mikael , Kollist Hannes , Kangasjärvi Jaakko
Published: November 2008

Nitric oxide (NO) is involved together with reactive oxygen species (ROS) in the activation of various stress responses in plants. We have used ozone (O3) as a tool to elicit ROS‐activated stress responses, and to activate cell death in plant leaves. Here, we have investigated the roles and interactions of ROS and NO in the induction and regulation of O3‐induced cell death. Treatment with O3 induced a rapid accumulation of NO, which started from guard cells, spread to adjacent epidermal cells and eventually moved to mesophyll cells. During the later time points, NO production coincided with the formation of hypersensitive response (HR)‐like lesions. The NO donor sodium nitroprusside (SNP) and O3 individually induced a large set of defence‐related genes; however, in a combined treatment SNP attenuated the O3 induction of salicylic acid (SA) biosynthesis and other defence‐related genes. Consistent with this, SNP treatment also decreased O3‐induced SA accumulation. The O3‐sensitive mutant rcd1 was found to be an NO overproducer; in contrast, Atnoa1/rif1 (Arabidopsis nitric oxide associated 1/resistant to inhibition by FSM1), a mutant with decreased production of NO, was also O3 sensitive. This, together with experiments combining O3 and the NO donor SNP suggested that NO can modify signalling, hormone biosynthesis and gene expression in plants during O3 exposure, and that a functional NO production is needed for a proper O3 response. In summary, NO is an important signalling molecule in the response to O3.
Reproduction of an early‐flowering Mediterranean mountain narrow endemic (Armeria caespitosa) in a contracting mountain island
Authors: García‐Camacho R. , Escudero A.
Published: November 2008

Reproduction at population lower edges is important for plant species persistence, especially in populations on contracting high‐mountain islands. In this context, the ability of plants to reproduce in different microhabitats seems to be important to guarantee seed production in stressful environments, such as Mediterranean high mountains. We hypothesised that the warmer and drier conditions at the lower edge would be deleterious for the reproduction of Armeria caespitosa, an early‐flowering plant. In addition, reproductive plasticity along this mountain gradient may also be microhabitat‐dependent. We studied factors affecting the reproductive success of A. caespitosa, an endemic of the Spanish Sistema Central. We considered a complex set of predictors, including phenology, plant size and environmental factors at different scales using generalised estimating equations and generalised linear models. Microhabitat, together with the position in the altitudinal gradient and inter‐annual variability affected the reproduction of A. caespitosa. In addition, individuals with longer flowering periods (duration of flowering) had significantly lower fruit set and a higher number of unviable seeds; delayed flowering peaks favoured the production of both viable and unviable fruits. Microhabitat variability over an altitudinal range is relevant for the reproduction of A. caespitosa, and is more important at the lower edge of the altitudinal range, where the species faces the most adverse conditions. In addition, the ability to reproduce in different microhabitats might increase the chances of the species to cope with environmental uncertainties under on‐going climate warming. Finally, reproduction of this early‐flowering plant is constrained by summer drought, which might shape its reproductive phenology.
Folliculogenesis and Morphometry of Oocyte and Follicle Growth in the Feline Ovary
Authors: Reynaud K , Gicquel C , Thoumire S , Chebrout M , Ficheux C , Bestandji M , Chastant‐Maillard S
Published: November 2008

Contents

This study was designed to describe, both quantitatively (morphometry) and qualitatively (histological differentiation), follicle and oocyte growth in the feline ovary. The ovaries of 43 cats were collected and processed for histology. The diameters of 832 follicle/oocyte pairs were measured, with and without zona pellucida (ZP), and a special emphasis was placed on the study of early folliculogenesis. Primordial, primary, secondary, pre‐antral and early antral follicles were measured at 44.3, 86.2, 126.0, 155.6 and 223.8 μm in diameter respectively. A biphasic pattern of follicle and oocyte growth was observed. Before antrum formation, follicle (x) and oocyte (y) size were positively and linearly correlated (y = 0.500x + 20.01, r2 = 0.89). Antrum formation occurred when the follicle reached 160–200 μm in diameter (when oocyte was at 102 μm). After antrum formation, a decoupling was observed, a minimal increase in oocyte size contrasting with a significant follicle development (y = 0.001x + 114.39, r2 = 0.01). The pre‐ovulatory follicle diameter was approximately 3500 μm and the maximal oocyte diameter was 115 μm. The ZP, absent in primordial and primary follicles, appeared at the secondary stage and reached almost 6 μm at the pre‐ovulatory stage. These results suggest that (i) in feline ovary, follicle and oocyte growth pattern is similar to that observed in other mammals; (ii) the antrum forms in 160–200 μm follicles, which represents 5% of the pre‐ovulatory diameter and (iii) the oocyte had achieved more than 90% of its maximal growth at the stage of antrum formation.
Technical Aspects of Laparoscopic Ovarian Autograft in Ewes After Cryopreservation by Slow‐Cooling Protocol
Authors: Massardier J , Courbiere B , Lornage J , Mazoyer C , Poirel MT , Martinot S , Franck M , Salle B
Published: November 2008

Contents

Iatrogenic ovarian failure and infertility are long term‐term side effects of anticancerous gonadotoxic treatments in children or women of reproductive year. Ovarian cortex cryopreservation can be a solution to preserve immature germinal cells before gonadotoxic treatment, for later transplantation. The aim of our study was to prove the efficiency of a laparoscopic technique for orthotopic graft after a slow‐freezing/thawing protocol, and to evaluate the effect of ovarian cryopreservation and autograft on the primordial follicle survival rate. Experimental surgical study was performed on 6‐ to 12‐month‐old ewes. The study was approved by the ethic committee of the Lyon‐veterinary‐school. The left ovary was removed by laparoscopy and cut in half, and medulla was excised. In group 1 (n = 6), autograft was performed immediately on the right ovary, and in group 2 (n = 6), graft was performed after a slow‐freezing/thawing protocol. The second hemi‐ovary served as an ungrafted control fragment. A polypropylene/polyglactin mesh was included between graft and base to separate the two structures, to help histological analysis. The mean graft performance time was 71 ± 8 min in the first group and 57 ± 10 min in the second. Freezing did not affect the number of primordial follicles. In the ungraft control fragments, the global anomaly rate (cytoplasm plus nuclear anomaly) increased after freezing (p < 0.05). Others results did not reach signification. Pelvic adhesion occurred only once. The post‐graft primordial follicle survival rate was 5.1 ± 2.8% in the non‐frozen group vs. 6.3 ± 2.3% after freezing/thawing. Kruskal–Wallis and Wilkoxon non‐parametric tests were used for statistical analysis. Laparoscopy seems to be a well‐adapted technique for ovarian tissue orthotopic autograft. The main follicle loss occurs before graft revascularization. Our orthotopic graft’s procedure has to be improved to obtain a better graft’s neovascularization, and to have a better long‐term post‐graft primordial follicle survival rate.
INERTIA OR INACTION? BLOOD PRESSURE MANAGEMENT AND CARDIOVASCULAR RISK IN DIABETES‡
Authors: Owen AJ , Retegan C , Rockell M , Jennings G , Reid CM
Published: November 2008

Diabetes is a significant risk factor for cardiovascular disease (CVD), but the presence of comorbidities, such as hypertension, markedly increases CVD risk. The aim of the present study was to determine the effectiveness of hypertension management in patients with diabetes.

The cvTRAC Study was a cross‐sectional study of CVD risk factors in primary care practices across Australia. General medical practitioners enrolled patients they considered to be at increased risk of CVD and reported on cardiovascular disease history, CVD risk factor levels and current therapy.

In all, 9857 men and 8332 women with diabetes participated in the study, with > ;85% having at least two CVD risk factors in addition to diabetes and 68% having a history of hypertension. Lost therapeutic benefit in diabetes patients with hypertension was seen in those who were failing to meet targets on antihypertensive drug therapy (therapeutic inertia: > ;73% of the hypertensive cohort), with a smaller proportion accounted for by those who met prescribing guidelines but were not being treated pharmacologically (treatment gap: 5.4% of the hypertensive cohort). Lack of compliance with lifestyle guidelines was estimated to account for over 8% of those not meeting blood pressure targets. Age (odds ratio (OR) 0.983, 95% confidence interval (CI) 0.980–0.986; P < 0.001), compliance with physical activity guidelines (OR 1.219, 95% CI 1.088–1.366; P = 0.001) and compliance with dietary guidelines (OR 1.298, 95% CI 1.188–1.420; P < 0.001) were independent predictors of target blood pressure attainment in the diabetic population.

Deficiencies in pharmacological and lifestyle‐related therapeutic strategies contribute to suboptimal hypertension management in diabetes. Therapeutic inertia is a greater contributor to lost therapeutic benefit than treatment gap in this population.
POSTOPERATIVE ANALGESIA INDUCED BY INTRATHECAL NEOSTIGMINE OR BETHANECHOL IN RATS
Authors: Prado WA , Dias TB
Published: November 2008

Cholinergic agonists and acetylcholinesterase inhibitors, such as neostigmine, produce a muscarinic receptor‐mediated antinociception in several animal species that depends on activation of spinal cholinergic neurons. However, neostigmine causes antinociception in sheep only in the early, and not late, postoperative period.

In the present study, a model of postoperative pain was used to determine the antinociceptive effects of bethanechol (a muscarinic agonist) and neostigmine administered intrathecally 2, 24 or 48 h after a plantar incision in a rat hind paw. Changes in the threshold to punctate mechanical stimuli were evaluated using an automated electronic von Frey apparatus.

Mechanical hyperalgesia was obtained following plantar incision, the effect being stronger during the immediate (2 h) than the late post‐surgical period. Bethanechol (15–90 µg/5 µL) or neostigmine (1–3 µg/5 µL) reduced incision‐induced mechanical hyperalgesia, the effects of both drugs being more intense during the immediate (2 h) than the late post‐surgical period.

The ED50for bethanechol injected at 2, 24 and 48 h was 5.6, 51.9 and 82.5 µg/5 µL, respectively. The corresponding ED50for neostigmine was 1.62, 3.02 and 3.8 µg/5 µL, respectively.

The decline in the antinociceptive potency of neostigmine with postoperative time is interpreted as resulting from a reduction in pain‐induced activation of acetylcholine‐releasing descending pathways. However, the similar behaviour of bethanechol in the same model points to an additional mechanism involving intrinsic changes in spinal muscarinic receptors.