bluuebunny/crossref_metadata_2025_split huggingface dataset:
New developments in understanding the role of salicylic acid in plant defence.
Authors: Molinari S. 
Published: October 2007

Abstract

Salicylic acid (SA) is currently considered as a key molecule in activating plant defence against various insects and pathogenic invaders. Its role in determining the so-called systemic acquired resistance (SAR), that confers long-lasting protection against a broad spectrum of pathogens, has definitely been established. The activation of an SA-dependent signalling pathway is also associated with more specific plant defences, such as those determined by gene-for-gene recognition of the pathogen by plants carrying resistance genes (
R
-genes). A recent further impulse in the investigation of the role of SA, both in local defences and SAR, has come either from genetic screens of
Arabidopsis
or from SA-degrading transgenic plants that express the bacterial salicylate hydroxylase gene (
NahG
). Genetic screens of
Arabidopsis
and the recently developed microarray technology allowed us to identify several genes involved in SA synthesis and signalling. However, the biochemical mechanisms by which SA can exert its many functions are not clear yet and the scope of this review is to report on such mechanisms. SA signalling is indicated here as a complex network operating through gene expressions and biochemical pathways which are finely regulated by SA concentration. According to its level in plants, SA may operate as a beneficial anti-inflammatory compound or as a cell killer. New developments in understanding the role of SA in plant defence are reported from studies on root response to soil pests, such as root-knot nematodes. The role of SA in diseases of roots has been reviewed here for the first time, as most of our knowledge on this matter is based on studies carried out on leaves.
Ozone impacts on forests.
Authors: Paoletti E. 
Published: October 2007

Abstract

Ozone is the air pollutant of major concern for forests, and is also recognized as a significant greenhouse gas. Current background O
3
levels in the Northern Hemisphere have increased around 2-4.5 times since pre-industrial times. Although many questions remain, we now know a great deal about how O
3
affects forests at the cell/leaf level (by inducing a cascade of biochemical, physiological and morphological responses) and at the tree/canopy level (by affecting allocation and carbon strength, reproduction, hydrology and the response to co-occurring stressors). The most significant O
3
impact is on the regulatory capacity of resource allocation rather than on productivity. However, forest ecosystems are much complex. Gas exchange measurements carried out at steady state suggest that O
3
reduces stomatal conductance and thus increases protection from drought and additional O
3
. Ozone, however, may impair stomatal control and predispose trees to drought stress under dynamic conditions, as those in forests. Ozone-induced increases in sap-flow have been shown to result in stem growth losses, depletion of soil moisture in the rooting zone and reduced streamflow, with implications for all the forest hydrological processes. In addition, species-specific and individual-specific responses to O
3
affect forest competition and biodiversity. There is a need to scale from the cell and leaf level up to the ecosystem and regional level, and to develop a biologically significant and usable standard to protect forests from O
3
. Further work is needed for understanding the cause/effect-based relationships between O
3
and other stresses at the stand and ecosystem level. Modelling may provide new insights into O
3
impacts on forests, even though scalar and conceptual uncertainties still limit the current understanding of basic physiological mechanisms.
Feature construction from synergic pairs to improve microarray-based classification
Authors: Hanczar Blaise , Zucker Jean-Daniel , Henegar Corneliu , Saitta Lorenza 
Published: October 2007

AbstractMotivation: Microarray experiments that allow simultaneous expression profiling of thousands of genes in various conditions (tissues, cells or time) generate data whose analysis raises difficult problems. In particular, there is a vast disproportion between the number of attributes (tens of thousands) and the number of examples (several tens). Dimension reduction is therefore a key step before applying classification approaches. Many methods have been proposed to this purpose, but only a few of them considered a direct quantification of transcriptional interactions. We describe and experimentally validate a new dimension reduction and feature construction method, which assesses interactions between expression profiles to improve microarray-based classification accuracy.Results: Our approach relies on a mutual information measure that exposes some elementary constituents of the information contained in a pair of gene expression profiles. We show that their analysis implies a term that represents the information of the interaction between the two genes. The principle of our method, called FeatKNN, is to exploit the information provided by highly synergic gene pairs to improve classification accuracy. First, a heuristic search selects the most informative gene pairs. Then, for each selected pair, a new feature, representing the classification margin of a KNN classifier in the gene pairs space, is constructed. We show experimentally that the interactional information has a degree of significance comparable to that of the gene expression profiles considered separately. Our method has been tested with different classifiers and yielded significant improvements in accuracy on several public microarray databases. Moreover, a synthetic assessment of the biological significance of the concept of synergic gene pairs suggested its ability to uncover relevant mechanisms underlying interactions among various cellular processes.Contact: hanczar_blaise@yahoo.frSupplementary information: Complementary results can be found on the companion website at http://featknn.nutriomique.org
Naïve Bayes for microRNA target predictions—machine learning for microRNA targets
Authors: Yousef Malik , Jung Segun , Kossenkov Andrew V. , Showe Louise C. , Showe Michael K. 
Published: October 2007

AbstractMotivation: Most computational methodologies for miRNA:mRNA target gene prediction use the seed segment of the miRNA and require cross-species sequence conservation in this region of the mRNA target. Methods that do not rely on conservation generate numbers of predictions, which are too large to validate. We describe a target prediction method (NBmiRTar) that does not require sequence conservation, using instead, machine learning by a naïve Bayes classifier. It generates a model from sequence and miRNA:mRNA duplex information from validated targets and artificially generated negative examples. Both the ‘seed’ and ‘out-seed’ segments of the miRNA:mRNA duplex are used for target identification.Results: The application of machine-learning techniques to the features we have used is a useful and general approach for microRNA target gene prediction. Our technique produces fewer false positive predictions and fewer target candidates to be tested. It exhibits higher sensitivity and specificity than algorithms that rely on conserved genomic regions to decrease false positive predictions.Availability: The NBmiRTar program is available at http://wotan.wistar.upenn.edu/NBmiRTar/Contact: yousef@wistar.orgSupplementary information: http://wotan.wistar.upenn.edu/NBmiRTar/
Radiation sensitivity and genomic instability in the hematopoietic system: Frequencies of micronucleated reticulocytes in whole‐body X‐irradiated BALB/c and C57BL/6 mice
Authors: Hamasaki Kanya , Imai Kazue , Hayashi Tomonori , Nakachi Kei , Kusunoki Yoichiro 
Published: October 2007

Using flow cytometry, we quantified the number of micronucleated reticulocytes in peripheral blood of whole‐body X‐irradiated mice in order to evaluate the radiation sensitivity and the induced genomic instability of the hematopoietic system. An acute effect of radiation dose as small as 0.1 Gy was detectable 2 days after irradiation, and the radiation dose effect was significantly greater in BALB/c mice than in C57BL/6 mice, that is, 3.0‐ and 2.3‐fold increases in frequencies of micronuclei were noted in the two groups of mice, respectively. Even 1 year after irradiation, mice irradiated with 2.5 Gy of X‐rays showed significantly increased frequencies of micronucleated reticulocytes, that is, 1.6‐ and 1.3‐fold increases in BALB/c and C57BL/6 mice, respectively. However, this delayed effect was not apparent when the same mice were analyzed for T‐cell receptor mutant frequencies in splenocytes. A significant mouse strain difference in the delayed radiation effect on micronucleated reticulocyte frequencies was noted as well. The results indicate that delayed genomic effects of irradiation on the murine hematopoietic system can persist in vivo for prolonged periods, and that there are mouse strain differences in sensitivity to radiation‐induced genomic instability. (Cancer Sci 2007; 98: 1840–1844)
How the 1977 World Health Organization report on alcohol‐related disabilities came to be written: a provisional analysis
Authors: Edwards Griffith 
Published: October 2007

ABSTRACTBackground  In 1977 the World Health Organization (WHO) published a report entitled ‘Alcohol‐Related Disabilities’. The crucial contribution of this report was to differentiate between alcohol dependence, on one hand, and alcohol‐related disabilities (or problems) on the other hand. Essentially, it offered a bi‐axial mapping of the field of concern.Aims  This paper seeks to identify the multiple influences which shaped the evolution of this report.Methods  Use is made of unpublished archival material and recall of personal involvement, together with relevant published material.Results  Three major influences made it possible to move beyond the confines of previous WHO thinking on alcohol: the multi‐disciplinary nature of the input; the internationality of the enterprise; and the expectations set that the concepts developed should speak to the practical world.Conclusions  The arena of drug and alcohol policy has, for more than a century, been rich in its reports. This case study, although limited in its immediate content, points to the need for further analysis of the history of such reports.
Early access and use of housing: care leavers and other young people in difficulty
Authors: Simon Antonia 
Published: October 2007

ABSTRACTThis paper presents findings from a study of how care leavers access and use housing services, and what they said had helped them to do so. The sample comprised 80 care leavers, and, for comparison, a group of 59 young people (termed ‘in difficulty’) who met certain criteria of disadvantage. Care leavers were found to have fewer crisis transitions and less experience of homelessness, together with a much higher level of autonomy and support in their first accommodation, relative to other young people in difficulty. Several factors are identified that, from the care leavers' point of view, contributed to their better access and use of housing services, including having family and friends to turn to, and leaving care teams that negotiated on their behalf with housing services. The paper concludes that care leavers had more positive housing experiences than other young people in difficulty, helped by the improved preparation for independence and ongoing support available to them from leaving care teams.
RNA–DNA ratio of herring and sand lance larvae from Port Moller, Alaska: Comparison with prey concentration and temperature
Authors: McGURK M. D. , WARBURTON H. D. , GALBRAITH M. , KUSSER W. C. 
Published: October 2007

ABSTRACTA key assumption of hypotheses that link the production of prey for larval fish with year‐class strength of fish is that larval growth and condition is food‐limited. We tested this assumption by comparing whole‐body RNA‐DNA ratios of individual Pacific herring, Clupea pallasi, larvae and Pacific sand lance, Ammodytes hex‐apterus, larvae from Port Moller, a subarctic Alaskan estuary, with prey concentration and temperature. RNA‐DNA ratios were correlated with larval length, but not with prey concentration or temperature. Ratios were not significantly different between a warm, well‐mixed station with low prey concentrations and a colder, stratified station with higher prey concentrations. Using RNA‐DNA ratios, we classified as starving 11 to 23% of first‐feeding (< 13 mm long) herring larvae and 45% of first‐feeding (< 7 mm long) sand lance larvae. However, starvation could not have been caused by low concentrations of prey because micro‐zooplankton prey concentrations were high enough (16 to 84 prey L_l) to support relatively high rates of growth. Therefore, starving larvae were either abnormal or they were stIII learning to forage. We conclude that the magnitude of starvation among first‐feeding herring and sand lance larvae, and, therefore, the total contribution of starvation to year‐class strength, is dependent not only on prey concentration, but on the proportion of a population of larvae that can feed effectively.
Effects of pre‐existing submersed vegetation and propagule pressure on the invasion success of Hydrilla verticillata
Authors: Chadwell Todd B. , Engelhardt Katharina A. M. 
Published: October 2007

Summary

With biological invasions causing widespread problems in ecosystems, methods to curb the colonization success of invasive species are needed. The effective management of invasive species will require an integrated approach that restores community structure and ecosystem processes while controlling propagule pressure of non‐native species.
We tested the hypotheses that restoring native vegetation and minimizing propagule pressure of invasive species slows the establishment of an invader. In field and greenhouse experiments, we evaluated (i) the effects of a native submersed aquatic plant species, Vallisneria americana, on the colonization success of a non‐native species, Hydrilla verticillata; and (ii) the effects of H. verticillata propagule density on its colonization success.
Results from the greenhouse experiment showed that V. americana decreased H. verticillata colonization through nutrient draw‐down in the water column of closed mesocosms, although data from the field experiment, located in a tidal freshwater region of Chesapeake Bay that is open to nutrient fluxes, suggested that V. americana did not negatively impact H. verticillata colonization. However, H. verticillata colonization was greater in a treatment of plastic V. americana look‐alikes, suggesting that the canopy of V. americana can physically capture H. verticillata fragments. Thus pre‐emption effects may be less clear in the field experiment because of complex interactions between competitive and facilitative effects in combination with continuous nutrient inputs from tides and rivers that do not allow nutrient draw‐down to levels experienced in the greenhouse.
Greenhouse and field tests differed in the timing, duration and density of propagule inputs. However, irrespective of these differences, propagule pressure of the invader affected colonization success except in situations when the native species could draw‐down nutrients in closed greenhouse mesocosms. In that case, no propagules were able to colonize.
Synthesis and applications. We have shown that reducing propagule pressure through targeted management should be considered to slow the spread of invasive species. This, in combination with restoration of native species, may be the best defence against non‐native species invasion. Thus a combined strategy of targeted control and promotion of native plant growth is likely to be the most sustainable and cost‐effective form of invasive species management.
Atlantic reef fish biogeography and evolution
Authors: Floeter S. R. , Rocha L. A. , Robertson D. R. , Joyeux J. C. , Smith‐Vaniz W. F. , Wirtz P. , Edwards A. J. , Barreiros J. P. , Ferreira C. E. L. , Gasparini J. L. , Brito A. , Falcón J. M. , Bowen B. W. , Bernardi G. 
Published: October 2007

AbstractAim  To understand why and when areas of endemism (provinces) of the tropical Atlantic Ocean were formed, how they relate to each other, and what processes have contributed to faunal enrichment.Location  Atlantic Ocean.Methods  The distributions of 2605 species of reef fishes were compiled for 25 areas of the Atlantic and southern Africa. Maximum‐parsimony and distance analyses were employed to investigate biogeographical relationships among those areas. A collection of 26 phylogenies of various Atlantic reef fish taxa was used to assess patterns of origin and diversification relative to evolutionary scenarios based on spatio‐temporal sequences of species splitting produced by geological and palaeoceanographic events. We present data on faunal (species and genera) richness, endemism patterns, diversity buildup (i.e. speciation processes), and evaluate the operation of the main biogeographical barriers and/or filters.Results  Phylogenetic (proportion of sister species) and distributional (number of shared species) patterns are generally concordant with recognized biogeographical provinces in the Atlantic. The highly uneven distribution of species in certain genera appears to be related to their origin, with highest species richness in areas with the greatest phylogenetic depth. Diversity buildup in Atlantic reef fishes involved (1) diversification within each province, (2) isolation as a result of biogeographical barriers, and (3) stochastic accretion by means of dispersal between provinces. The timing of divergence events is not concordant among taxonomic groups. The three soft (non‐terrestrial) inter‐regional barriers (mid‐Atlantic, Amazon, and Benguela) clearly act as ‘filters’ by restricting dispersal but at the same time allowing occasional crossings that apparently lead to the establishment of new populations and species. Fluctuations in the effectiveness of the filters, combined with ecological differences among provinces, apparently provide a mechanism for much of the recent diversification of reef fishes in the Atlantic.Main conclusions  Our data set indicates that both historical events (e.g. Tethys closure) and relatively recent dispersal (with or without further speciation) have had a strong influence on Atlantic tropical marine biodiversity and have contributed to the biogeographical patterns we observe today; however, examples of the latter process outnumber those of the former.
Island biogeography of bats in Baja California, Mexico: patterns of bat species richness in a near‐shore archipelago
Authors: Frick Winifred F. , Hayes John P. , Heady III Paul A. 
Published: October 2007

AbstractAim We studied the relationship between the size and isolation of islands and bat species richness in a near‐shore archipelago to determine whether communities of vagile mammals conform to predictions of island biogeography theory. We compared patterns of species richness in two subarchipelagos to determine whether areaper seor differences in habitat diversity explain variations in bat species richness.Location Islands in the Gulf of California and adjacent coastal habitats on the Baja California peninsula in northwest Mexico.Methods Presence–absence surveys for bats were conducted on 32 islands in the Gulf of California using acoustic and mist‐net surveys. We sampled for bats in coastal habitats of four regions of the Baja peninsula to characterize the source pool of potential colonizing species. We fitted a semi‐log model of species richness and multiple linear regression and used Akaike information criterion model selection to assess the possible influence of log10area, isolation, and island group (two subarchipelagos) on the species richness of bats. We compared the species richness of bats on islands with greater vegetation densities in the southern gulf (n = 20) with that on drier islands with less vegetation in the northern gulf (n = 12) to investigate the relationship between habitat diversity and the species richness of bats.Results Twelve species of bats were detected on islands in the Gulf of California, and 15 species were detected in coastal habitats on the Baja peninsula. Bat species richness was related to both area and isolation of islands, and was higher in the southern subarchipelago, which has denser vegetation. Log10area was positively related to bat species richness, which increased by one species for every 5.4‐fold increase in island area. On average, richness declined by one species per 6.25 km increase in isolation from the Baja peninsula.Main conclusions Our results demonstrate that patterns of bat species richness in a near‐shore archipelago are consistent with patterns predicted by the equilibrium theory of island biogeography. Despite their vagility, bats may be more sensitive to moderate levels of isolation than previously expected in near‐shore archipelagos. Differences in vegetation and habitat xericity appear to be associated with richness of bat communities in this desert ecosystem. Although observed patterns of species richness were consistent with those predicted by the equilibrium theory, similar relationships between species richness and size and isolation of islands may arise from patch‐use decision making by individuals (optimal foraging strategies).
Group intervention to improve quality of life in haemodialysis patients
Authors: Lii Yueh‐Ching , Tsay Shiow‐Luan , Wang Tsae‐Jyy 
Published: October 2007

Aim and objective. The purpose of this study was to investigate the effects of group intervention on depression, self‐efficacy and quality of life in haemodialysis patients.Background. Chronic renal failure and haemodialysis treatment is a long‐term process; patients need to have an appropriate adaptive strategy to confront the stress stemming from the disease and subsequent haemodialysis treatment. The application of group intervention for haemodialysis patients has been limited.Design. This study applied an experimental design methodology. Patients were selected at two haemodialysis units of major medical centres in northern Taiwan.Methods. Out of 60 original patients randomly assigned into experimental or control groups, 48 completed the study. Twenty patients in the experimental group received group psychosocial intervention. The therapy ran for two hours per week for two months. Twenty‐eight patients in the comparison group received routine unit care and a self‐care booklet. Instruments included the Strategies Used by People to Promote Health, the Beck Depression Inventory and the Short Form‐36. Data were collected at pretest and one month following the therapy.Results. The findings demonstrated that self‐care self‐efficacy, depression and quality of life significantly improved statistically for patients in the therapy group, compared with patients in the comparison group.Conclusions. The study indicated that group psychosocial intervention significantly reduced depression, improved self‐care self‐efficacy and quality of life in haemodialysis patients.Relevance to clinical practice. The present study was conducted with a group of outpatients, did not require expensive resources and was not time intensive, making it a viable therapy, clinically suitable for haemodialysis patients.