bluuebunny/crossref_metadata_2025 huggingface dataset:
Recent network evolution increases the potential for large epidemics in the British cattle population
Authors: Robinson S.E , Everett M.G , Christley R.M
Published: February 2007

Following the foot and mouth disease epidemic in Great Britain (GB) in 2001, livestock movement bans were replaced with mandatory periods of standstill for livestock moving between premises. It was anticipated that these movement restrictions would limit each individual's contact networks, the extent of livestock movements and thus the spread of future disease outbreaks. However, the effect of behaviour changes on the global network in adapting to these restrictions is currently unknown. Here, we take a novel approach using GB cattle movement data to construct week-by-week contact networks between animal holdings (AH) to explore the evolution of the network since this policy was introduced, the first time network theory has been used for this purpose. We show that the number of AH moving cattle as part of the giant strong component (GSC), representing the region of maximal connectivity, has been increasing linearly over time. This is of epidemiological significance as the size of the GSC indicates the number of holdings potentially exposed to disease, thus giving a lower bound of maximum epidemic size. Therefore, despite restriction of cattle movements, emergent behaviour in this self-organizing system has potentially increased the size of infectious disease epidemics within the cattle industry.
Wake structure and wingbeat kinematics of a house-martinDelichon urbica
Authors: Rosén M , Spedding G.R , Hedenström A
Published: February 2007

The wingbeat kinematics and wake structure of a trained house martin in free, steady flight in a wind tunnel have been studied over a range of flight speeds, and compared and contrasted with similar measurements for a thrush nightingale and a pair of robins. The house martin has a higher aspect ratio (more slender) wing, and is a more obviously agile and aerobatic flyer, catching insects on the wing. The wingbeat is notable for the presence at higher flight speeds of a characteristic pause in the upstroke. The essential characteristics of the wing motions can be reconstructed with a simple two-frequency model derived from Fourier analysis. At slow speeds, the distribution of wake vorticity is more simple than for the other previously measured birds, and the upstroke does not contribute to weight support. The upstroke becomes gradually more significant as the flight speed increases, and although the vortex wake shows a signature of the pause phase, the global circulation measurements are otherwise in good agreement with surprisingly simple aerodynamic models, and with predictions across the different species, implying quite similar aerodynamic performance of the wing sections. The local Reynolds numbers of the wing sections are sufficiently low that the well-known instabilities of attached laminar flows over lifting surfaces, which are known to occur at two to three times this value, may not develop.
Two-phase equilibria in the anti-plane shear of an elastic solid with interfacial effects via global bifurcation
Authors: Healey Timothy J , Miller Ulrich
Published: February 2007

We consider a simplified model of a two-phase elastic solid with small interfacial energy in forced anti-plane shear. We propose a novel approach to finding meta-stable equilibria (local minima of the potential energy), based upon global bifurcation theory,a prioribounds and numerical path following. In particular, we treat the reciprocal of the capillarity coefficient as a continuation parameter, and we fully exploit the hidden symmetry of our elliptic boundary-value problem, both strategies of which are crucial for obtaining rigorous existence results and for performing reliable and efficient computation. We obtain branches of locally stable equilibria exhibiting phase nucleation (and anti-nucleation) and fine layering of mixtures.
Could Vikings have navigated under foggy and cloudy conditions by skylight polarization? On the atmospheric optical prerequisites of polarimetric Viking navigation under foggy and cloudy skies
Authors: Hegedüs Ramón , Åkesson Susanne , Wehner Rüdiger , Horváth Gábor
Published: February 2007

In sunshine, the Vikings navigated on the open sea using sundials. According to a widespread hypothesis, when the Sun was occluded by fog or clouds the Vikings might have navigated by skylight polarization detected with an enigmatic birefringent crystal (sunstone). There are two atmospheric optical prerequisites for this alleged polarimetric Viking navigation under foggy/cloudy skies: (1) the degree of linear polarization
p
of skylight should be high enough and (2) at a given Sun position, the pattern of the angle of polarization
α
of the foggy/cloudy sky should be similar to that of the clear sky. Until now, these prerequisites have not been investigated. Using full-sky imaging polarimetry, we measured the
p
- and
α
-patterns of Arctic foggy and cloudy skies when the Sun was invisible. These patterns were compared with the polarization patterns of clear Arctic skies. We show here that although prerequisite (2) is always fulfilled under both foggy and cloudy conditions, if the fog layer is illuminated by direct sunlight, prerequisite (1) is usually satisfied only for cloudy skies. In sunlit fog, the Vikings could have navigated by polarization only, if
p
of light from the foggy sky was sufficiently high.
Social recognition in wild fish populations
Authors: Ward Ashley J.W , Webster Michael M , Hart Paul J.B
Published: February 2007

The ability of animals to gather information about their social and physical environment is essential for their ecological function. Odour cues are an important component of this information gathering across taxa. Recent laboratory studies have revealed the importance of flexible chemical cues in facilitating social recognition of fishes. These cues are known to be mediated by recent habitat experience and fishes are attracted to individuals that smell like themselves. However, to be relevant to wild populations, where animals may move and forage freely, these cues would have to be temporally flexible and allow spatial resolution. Here, we present data from a study of social recognition in wild populations of three-spined sticklebacks (Gasterosteus aculeatus). Focal fish preferentially associated with conspecifics from the same habitat as themselves. These preferences were changed and updated following translocation of the focal fish to a different site. Further investigation revealed that association preferences changed after 3 h of exposure to different habitat cues. In addition to temporal flexibility, the cues also allowed a high degree of spatial resolution: fish taken from sites 200 m apart produced cues that were sufficiently different to enable the focal fish to discriminate and associate with fish captured near their own home site. The adaptive benefits of this social recognition mechanism remain unclear, though they may allow fish to orient within their social environment and gain current local information.
Evolution of the wave: aerodynamic and aposematic functions of butterfly wing motion
Authors: Srygley Robert B
Published: February 2007

Many unpalatable butterfly species use coloration to signal their distastefulness to birds, but motion cues may also be crucial to ward off predatory attacks. In previous research, captive passion-vine butterfliesHeliconiusmimetic in colour pattern were also mimetic in motion. Here, I investigate whether wing motion changes with the flight demands of different behaviours. If birds select for wing motion as a warning signal, aposematic butterflies should maintain wing motion independently of behavioural context. Members of one mimicry group (Heliconius cydnoandHeliconius sapho) beat their wings more slowly and their wing strokes were more asymmetric than their sister-species (Heliconius melpomeneandHeliconius erato, respectively), which were members of another mimicry group having a quick and steady wing motion. Within mimicry groups, wing beat frequency declined as its role in generating lift also declined in different behavioural contexts. In contrast, asymmetry of the stroke was not associated with wing beat frequency or behavioural context—strong indication that birds process and store the Fourier motion energy of butterfly wings. Although direct evidence that birds respond to subtle differences in butterfly wing motion is lacking, birds appear to generalize a motion pattern as much as they encounter members of a mimicry group in different behavioural contexts.
Lizards speed up visual displays in noisy motion habitats
Authors: Ord Terry J , Peters Richard A , Clucas Barbara , Stamps Judy A
Published: February 2007

Extensive research over the last few decades has revealed that many acoustically communicating animals compensate for the masking effect of background noise by changing the structure of their signals. Familiar examples include birds using acoustic properties that enhance the transmission of vocalizations in noisy habitats. Here, we show that the effects of background noise on communication signals are not limited to the acoustic modality, and that visual noise from windblown vegetation has an equally important influence on the production of dynamic visual displays. We found that two species of Puerto Rican lizard,Anolis cristatellusandA. gundlachi, increase the speed of body movements used in territorial signalling to apparently improve communication in visually ‘noisy’ environments of rapidly moving vegetation. This is the first evidence that animals change how they produce dynamic visual signals when communicating in noisy motion habitats. Taken together with previous work on acoustic communication, our results show that animals with very different sensory ecologies can face similar environmental constraints and adopt remarkably similar strategies to overcome these constraints.
Evolutionary response to size-selective mortality in an exploited fish population
Authors: Swain Douglas P , Sinclair Alan F , Mark Hanson J
Published: February 2007

Many collapsed fish populations have failed to recover after a decade or more with little fishing. This may reflect evolutionary change in response to the highly selective mortality imposed by fisheries. Recent experimental work has demonstrated a rapid genetic change in growth rate in response to size-selective harvesting of laboratory fish populations. Here, we use a 30-year time-series of back-calculated lengths-at-age to test for a genetic response to size-selective mortality in the wild in a heavily exploited population of Atlantic cod (Gadus morhua). Controlling for the effects of density- and temperature-dependent growth, the change in mean length of 4-year-old cod between offspring and their parental cohorts was positively correlated with the estimated selection differential experienced by the parental cohorts between this age and spawning. This result supports the hypothesis that there have been genetic changes in growth in this population in response to size-selective fishing. Such changes may account for the continued small size-at-age in this population despite good conditions for growth and little fishing for over a decade. This study highlights the need for management regimes that take into account the evolutionary consequences of fishing.
Phylogenetic history underlies elevational biodiversity patterns in tropical salamanders
Authors: Wiens John J , Parra-Olea Gabriela , García-París Mario , Wake David B
Published: February 2007

Elevational variation in species richness is ubiquitous and important for conservation, but remains poorly explained. Numerous studies have documented higher species richness at mid-elevations, but none have addressed the underlying evolutionary and biogeographic processes that ultimately explain this pattern (i.e. speciation, extinction and dispersal). Here, we address the evolutionary causes of the mid-elevational diversity hump in the most species-rich clade of salamanders, the tropical bolitoglossine plethodontids. We present a new phylogeny for the group based on DNA sequences from all 13 genera and 137 species. Using this phylogeny, we find no relationship between rates of diversification of clades and their elevational distribution, and no evidence for a rapid ‘species pump’ in tropical montane regions. Instead, we find a strong relationship between the number of species in each elevational zone and the estimated time when each elevational band was first colonized. Mid-elevation habitats were colonized early in the phylogenetic history of bolitoglossines, and given similar rates of diversification across elevations, more species have accumulated in the elevational zones that were inhabited the longest. This pattern may be widespread and suggests that mid-elevation habitats may not only harbour more species, but may also contain more phylogenetic diversity than other habitats within a region.
Dispersive and non-dispersive waves through plants: implications for arthropod vibratory communication
Authors: Casas Jérôme , Magal Christelle , Sueur Jérôme
Published: February 2007

Vibratory communication in arthropods is a widespread phenomenon. Arthropods living on plants have been reported to use only dispersive bending waves in the context of prey–predator, competition, social and sexual interactions. Differences in signal structure have also been postulated to work as species recognition mechanisms and speciation agents. Using two identical laser Doppler vibrometers and a wavelet analysis, we quantified the wave propagation modes in rush stems (Juncus effusus) over the whole range of frequencies used by arthropods. A non-dimensionalized analysis shows that mechanical waves propagate not only as dispersive bending waves, but also as non-dispersive waves. Our analysis implies that an arthropod can communicate through non-dispersive bending waves by either producing signals of high frequencies or by choosing large stems, two widely different options tapping into the physiological and the behavioural repertoires, respectively. Non-dispersive waves, unreported so far in insect vibratory communication in plants, present serious advantages over dispersive bending waves in terms of signal integrity and may well be much more widely used than anticipated, in particular for species recognition.
Experimental simulations about the effects of overexploitation and habitat fragmentation on populations facing environmental warming
Authors: Mora Camilo , Metzger Rebekka , Rollo Audrey , Myers Ransom A
Published: February 2007

Populations of many species are dramatically declining worldwide, but the causal mechanism remains debated among different human-related threats. Coping with this uncertainty is critical to several issues about the conservation and future of biodiversity, but remains challenging due to difficulties associated with the experimental manipulation and/or isolation of the effects of such threats under field conditions. Using controlled microcosm populations, we quantified the individual and combined effects of environmental warming, overexploitation and habitat fragmentation on population persistence. Individually, each of these threats produced similar and significant population declines, which were accelerated to different degrees depending upon particular interactions. The interaction between habitat fragmentation and harvesting generated an additive decline in population size. However, both of these threats reduced population resistance causing synergistic declines in populations also facing environmental warming. Declines in population size were up to 50 times faster when all threats acted together. These results indicate that species may be facing risks of extinction higher than those anticipated from single threat analyses and suggest that all threats should be mitigated simultaneously, if current biodiversity declines are to be reversed.
Carbon dioxide capture and geological storage
Authors: Holloway Sam
Published: February 2007

Carbon dioxide capture and geological storage is a technology that could be used to reduce carbon dioxide emissions to the atmosphere from large industrial installations such as fossil fuel-fired power stations by 80–90%. It involves the capture of carbon dioxide at a large industrial plant, its transport to a geological storage site and its long-term isolation in a geological storage reservoir. The technology has aroused considerable interest because it can help reduce emissions from fossil fuels which are likely to remain the dominant source of primary energy for decades to come. The main issues for the technology are cost and its implications for financing new or retrofitted plants, and the security of underground storage.
Wind energy
Authors: Leithead W.E
Published: February 2007

From its rebirth in the early 1980s, the rate of development of wind energy has been dramatic. Today, other than hydropower, it is the most important of the renewable sources of power. The UK Government and the EU Commission have adopted targets for renewable energy generation of 10 and 12% of consumption, respectively. Much of this, by necessity, must be met by wind energy. The US Department of Energy has set a goal of 6% of electricity supply from wind energy by 2020. For this potential to be fully realized, several aspects, related to public acceptance, and technical issues, related to the expected increase in penetration on the electricity network and the current drive towards larger wind turbines, need to be resolved. Nevertheless, these challenges will be met and wind energy will, very likely, become increasingly important over the next two decades. An overview of the technology is presented.
The path to fusion power
Authors: Llewellyn Smith Chris , Ward David
Published: February 2007

Fusion is potentially an environmentally responsible and intrinsically safe source of essentially limitless power. It should be possible to build viable fusion power stations, and it looks as if the cost of fusion power will be reasonable. But time is needed to further develop the technology and to test in power station conditions the materials that would be used in their construction. Assuming no major adverse surprises, an orderly fusion development programme could lead to a prototype fusion power station putting electricity into the grid within 30 years, with commercial fusion power following some 10 or more years later. In the second half of the century, fusion could therefore be an important part of the portfolio of measures that are needed to cope with rising demand for energy in an environmentally responsible manner. In this paper, we describe the basics of fusion, its potential attractions, the status of fusion R&D, the remaining challenges and how they will be tackled at the International Tokamak Experimental Reactor and the proposed International Fusion Materials Irradiation Facility, and the timetable for the subsequent commercialization of fusion power.
Nuclear energy: current situation and prospects to 2020
Authors: Ion Sue
Published: February 2007

For close to half a century nuclear fission has been providing reliable supplies of electricity to the UK, with virtually no emissions of carbon dioxide. Over that period, the UK nuclear industry has avoided the emission of over one and a half billion tonnes of CO
2
. Yet no nuclear plant has been built in the UK for over two decades even though many of the stations in our current fleet are now within a decade or so of the end of their lifetime. Without new plants being ordered soon, the UK's nuclear capacity will decline dramatically, from 23% today to 3% post-2020—just as considerations of supply security and climate change are becoming increasingly important. Elsewhere in the world, many countries such as China, India, Japan, South Korea, Finland and France are building new stations. Other countries such as the USA, South Africa, and some nations that currently do not have nuclear stations (such as Indonesia and Poland) are making preparations for future nuclear stations.

Globally capacity factors for nuclear plants are higher than they have ever been, averaging around 85% and with the best stations achieving well over 90%. Lifetime can be 60 years. That the economics of such stations compete well with other technologies is well founded and easily verifiable—especially in the face of rising fossil fuel prices and the pricing in of costs for CO
2
emissions—both of which stand to improve the economics of nuclear energy still further. Waste volumes arising from modern plants are just a fraction of those of some earlier stations, and the technologies are in place to deal with them safely and effectively.

Following recent reviews and international developments, there is growing confidence that internationally available competitive designs of nuclear plant will provide part of the solution to the UK's long-term energy needs.
Good enough tools for global warming policy making
Authors: Socolow R.H , Lam S.H
Published: February 2007

We present a simple analysis of the global warming problem caused by the emissions of CO
2
(a major greenhouse gas) into the atmosphere resulting from the burning of fossil fuels. We provide quantitative tools which enable policymakers and interested citizens to explore the following issues central to the global warming problem.

At what rate are we permitted to continue to emit CO
2
after the global average atmospheric concentration has ‘stabilized’ at some chosen target level? The answer here provides
the magnitude of the effort
, measured by the necessary total reduction of today's global (annual) emissions rate to achieve stabilization. We shall see that stabilized emissions rates for all interesting stabilized concentration levels are
much lower
than the current emissions rate, but these small finite values are very important.

Across how many years can we spread the total effort to reduce the annual CO
2
emissions rate from its current high value to the above-mentioned low and stabilized target value? The answer here provides
the time-scale of the total mitigation effort
for any chosen atmospheric concentration target level. We confirm the common understanding that targets below a doubling of the pre-industrial concentration create great pressure to produce action immediately, while targets above double the pre-industrial level can tolerate longer periods of inaction.

How much harder is the future mitigation effort, if we do not do our share of the job now? Is it a good idea to overshoot a stabilization target? The quantitative answers here provide
the penalty of procrastination
. For example, the mitigation task to avoid doubling the pre-industrial level is a problem that can be addressed gradually, over a period extending more than a century, if started immediately, but procrastination can turn the effort into a much more urgent task that extends over only a few decades. We also find that overshooting target levels is a bad idea.

The quality of public discourse on this subject could be much enhanced if ball-park quantitative answers to these questions were more widely known.
Photovoltaic and photoelectrochemical conversion of solar energy
Authors: Grätzel Michael
Published: February 2007

The Sun provides approximately 100 000 terawatts to the Earth which is about 10 000 times more than the present rate of the world's present energy consumption. Photovoltaic cells are being increasingly used to tap into this huge resource and will play a key role in future sustainable energy systems. So far, solid-state junction devices, usually made of silicon, crystalline or amorphous, and profiting from the experience and material availability resulting from the semiconductor industry, have dominated photovoltaic solar energy converters. These systems have by now attained a mature state serving a rapidly growing market, expected to rise to 300 GW by 2030. However, the cost of photovoltaic electricity production is still too high to be competitive with nuclear or fossil energy. Thin film photovoltaic cells made of CuInSe or CdTe are being increasingly employed along with amorphous silicon. The recently discovered cells based on mesoscopic inorganic or organic semiconductors commonly referred to as ‘bulk’ junctions due to their three-dimensional structure are very attractive alternatives which offer the prospect of very low cost fabrication. The prototype of this family of devices is the dye-sensitized solar cell (DSC), which accomplishes the optical absorption and the charge separation processes by the association of a sensitizer as light-absorbing material with a wide band gap semiconductor of mesoporous or nanocrystalline morphology. Research is booming also in the area of third generation photovoltaic cells where multi-junction devices and a recent breakthrough concerning multiple carrier generation in quantum dot absorbers offer promising perspectives.
Hydrogen energy
Authors: Edwards P.P , Kuznetsov V.L , David W.I.F
Published: February 2007

The problem of anthropogenically driven climate change and its inextricable link to our global society's present and future energy needs are arguably the greatest challenge facing our planet. Hydrogen is now widely regarded as one key element of a potential energy solution for the twenty-first century, capable of assisting in issues of environmental emissions, sustainability and energy security. Hydrogen has the potential to provide for energy in transportation, distributed heat and power generation and energy storage systems with little or no impact on the environment, both locally and globally. However, any transition from a carbon-based (fossil fuel) energy system to a hydrogen-based economy involves significant scientific, technological and socio-economic barriers. This brief report aims to outline the basis of the growing worldwide interest in hydrogen energy and examines some of the important issues relating to the future development of hydrogen as an energy vector.
Proliferation, neurogenesis and regeneration in the non-mammalian vertebrate brain
Authors: Kaslin Jan , Ganz Julia , Brand Michael
Published: February 2007

Post-embryonic neurogenesis is a fundamental feature of the vertebrate brain. However, the level of adult neurogenesis decreases significantly with phylogeny. In the first part of this review, a comparative analysis of adult neurogenesis and its putative roles in vertebrates are discussed. Adult neurogenesis in mammals is restricted to two telencephalic constitutively active zones. On the contrary, non-mammalian vertebrates display a considerable amount of adult neurogenesis in many brain regions. The phylogenetic differences in adult neurogenesis are poorly understood. However, a common feature of vertebrates (fish, amphibians and reptiles) that display a widespread adult neurogenesis is the substantial post-embryonic brain growth in contrast to birds and mammals. It is probable that the adult neurogenesis in fish, frogs and reptiles is related to the coordinated growth of sensory systems and corresponding sensory brain regions. Likewise, neurons are substantially added to the olfactory bulb in smell-oriented mammals in contrast to more visually oriented primates and songbirds, where much fewer neurons are added to the olfactory bulb. The second part of this review focuses on the differences in brain plasticity and regeneration in vertebrates. Interestingly, several recent studies show that neurogenesis is suppressed in the adult mammalian brain. In mammals, neurogenesis can be induced in the constitutively neurogenic brain regions as well as ectopically in response to injury, disease or experimental manipulations. Furthermore, multipotent progenitor cells can be isolated and differentiatedin vitrofrom several otherwise silent regions of the mammalian brain. This indicates that the potential to recruit or generate neurons in non-neurogenic brain areas is not completely lost in mammals. The level of adult neurogenesis in vertebrates correlates with the capacity to regenerate injury, for example fish and amphibians exhibit the most widespread adult neurogenesis and also the greatest capacity to regenerate central nervous system injuries. Studying these phenomena in non-mammalian vertebrates may greatly increase our understanding of the mechanisms underlying regeneration and adult neurogenesis. Understanding mechanisms that regulate endogenous proliferation and neurogenic permissiveness in the adult brain is of great significance in therapeutical approaches for brain injury and disease.
Myelin repair: the role of stem and precursor cells in multiple sclerosis
Authors: Chandran Siddharthan , Hunt David , Joannides Alexis , Zhao Chao , Compston Alastair , Franklin Robin J.M
Published: February 2007

Multiple sclerosis is the most common potential cause of neurological disability in young adults. The disease has two distinct clinical phases, each reflecting a dominant role for separate pathological processes: inflammation drives activity during the relapsing–remitting stage and axon degeneration represents the principal substrate of progressive disability. Recent advances in disease-modifying treatments target only the inflammatory process. They are ineffective in the progressive stage, leaving the science of disease progression unsolved. Here, the requirement is for strategies that promote remyelination and prevent axonal loss. Pathological and experimental studies suggest that these processes are tightly linked, and that remyelination or myelin repair will both restore structure and protect axons. This review considers the basic and clinical biology of remyelination and the potential contribution of stem and precursor cells to enhance and supplement spontaneous remyelination.
Identification of novel peptide hormones in the human proteome by hidden Markov model screening
Authors: Mirabeau Olivier , Perlas Emerald , Severini Cinzia , Audero Enrica , Gascuel Olivier , Possenti Roberta , Birney Ewan , Rosenthal Nadia , Gross Cornelius
Published: February 2007

Peptide hormones are small, processed, and secreted peptides that signal via membrane receptors and play critical roles in normal and pathological physiology. The search for novel peptide hormones has been hampered by their small size, low or restricted expression, and lack of sequence similarity. To overcome these difficulties, we developed a bioinformatics search tool based on the hidden Markov model formalism that uses several peptide hormone sequence features to estimate the likelihood that a protein contains a processed and secreted peptide of this class. Application of this tool to an alignment of mammalian proteomes ranked 90% of known peptide hormones among the top 300 proteins. An analysis of the top scoring hypothetical and poorly annotated human proteins identified two novel candidate peptide hormones. Biochemical analysis of the two candidates, which we called spexin and augurin, showed that both were localized to secretory granules in a transfected pancreatic cell line and were recovered from the cell supernatant. Spexin was expressed in the submucosal layer of the mouse esophagus and stomach, and a predicted peptide from the spexin precursor induced muscle contraction in a rat stomach explant assay. Augurin was specifically expressed in mouse endocrine tissues, including pituitary and adrenal gland, choroid plexus, and the atrio-ventricular node of the heart. Our findings demonstrate the utility of a bioinformatics approach to identify novel biologically active peptides. Peptide hormones and their receptors are important diagnostic and therapeutic targets, and our results suggest that spexin and augurin are novel peptide hormones likely to be involved in physiological homeostasis.
Improvement of whole-genome annotation of cereals through comparative analyses
Authors: Zhu Wei , Buell C. Robin
Published: February 2007

Rice is an important model species for the Poaceae and other monocotyledonous plants. With the availability of a near-complete, finished, and annotated rice genome, we performed genome level comparisons between rice and all plant species in which large genomic or transcriptomic data sets are available to determine the utility of cross-species sequence for structural and functional annotation of the rice genome. Through comparative analyses with four plant genome sequence data sets and transcript assemblies from 185 plant species, we were able to confirm and improve the structural annotation of the rice genome. Support for 38,109 (89.3%) of the total 42,653 nontransposable element-related genes in the rice genome in the form of a rice expressed sequence tag, full-length cDNA, or plant homolog from our comparative analyses could be found. Although the majority of the putative homologs were obtained from Poaceae species, putative homologs were identified in dicotyledonous angiosperms, gymnosperms, and other plants such as algae, moss, and fern. A set of rice genes (7669) lacking a putative homolog was identified which may be lineage-specific genes that evolved after speciation and have a role in species diversity. Improvements to the current rice gene structural annotation could be identified from our comparative alignments and we were able to identify 487 genes which were mostly likely missed in the current rice genome annotation and another 500 genes for structural annotation review. We were able to demonstrate the utility of cross-species comparative alignments in the identification of noncoding sequences and in confirmation of gene nesting in rice.
A meiotic linkage map of the silver fox, aligned and compared to the canine genome
Authors: Kukekova Anna V. , Trut Lyudmila N. , Oskina Irina N. , Johnson Jennifer L. , Temnykh Svetlana V. , Kharlamova Anastasiya V. , Shepeleva Darya V. , Gulievich Rimma G. , Shikhevich Svetlana G. , Graphodatsky Alexander S. , Aguirre Gustavo D. , Acland Gregory M.
Published: February 2007

A meiotic linkage map is essential for mapping traits of interest and is often the first step toward understanding a cryptic genome. Specific strains of silver fox (a variant of the red fox, Vulpes vulpes), which segregate behavioral and morphological phenotypes, create a need for such a map. One such strain, selected for docility, exhibits friendly dog-like responses to humans, in contrast to another strain selected for aggression. Development of a fox map is facilitated by the known cytogenetic homologies between the dog and fox, and by the availability of high resolution canine genome maps and sequence data. Furthermore, the high genomic sequence identity between dog and fox allows adaptation of canine microsatellites for genotyping and meiotic mapping in foxes. Using 320 such markers, we have constructed the first meiotic linkage map of the fox genome. The resulting sex-averaged map covers 16 fox autosomes and the X chromosome with an average inter-marker distance of 7.5 cM. The total map length corresponds to 1480.2 cM. From comparison of sex-averaged meiotic linkage maps of the fox and dog genomes, suppression of recombination in pericentromeric regions of the metacentric fox chromosomes was apparent, relative to the corresponding segments of acrocentric dog chromosomes. Alignment of the fox meiotic map against the 7.6x canine genome sequence revealed high conservation of marker order between homologous regions of the two species. The fox meiotic map provides a critical tool for genetic studies in foxes and identification of genetic loci and genes implicated in fox domestication.
The Impact of Cardiovascular Risk Factor Case Management on the Metabolic Syndrome in a Primary Prevention Population: Results From a Randomized Controlled Trial
Authors: O'Malley Patrick G. , Kowalczyk Courtney , Bindeman Jody , Taylor Allen J.
Published: February 2007

No study has examined the effect of case management on the development of the metabolic syndrome. The authors randomized 450 consenting, asymptomatic men and women to a 6‐month cardiovascular case management program or usual care. Participants were reassessed at 1 year for change in a composite measure of five factors that define the metabolic syndrome. Of the cohort (mean age 42 years; 79% male), 46% had at least one metabolic syndrome factor and 4.3% had the metabolic syndrome. At 1 year, there was greater improvement in motivation to change in the case management group (+0.58 vs. +0.06, 10‐point scale; p=0.001), lower incidence of the metabolic syndrome (1.5% vs. 4.5%; p=0.12), and lower prevalence (decrease of 0.8% vs. increase of 2.6%; p=0.04). A 6‐month case management program focused on cardiovascular risk factors had a modest effect on the prevalence of the metabolic syndrome in this primary prevention screening population after 1 year. Further study is needed to clarify the overall health impact of preventing the metabolic syndrome.
A Triglyceride/High‐Density Lipoprotein Ratio ≥3.5 Is Associated With an Increased Burden of Coronary Artery Disease on Cardiac Catheterization
Authors: Ostfeld Robert , Mookherjee Disha , Spinelli Michael , Holtzman Dvorah , Shoyeb Abu , Schaefer Michael , Doddamani Sanjay , Spevack Daniel , Du Yunling
Published: February 2007

An elevated triglyceride (TG)/high‐density lipoprotein (HDL) ratio has been described as a predictor of insulin resistance and cardiovascular events. We evaluated whether a TG/HDL ratio ≥3.5 was associated with the burden of coronary artery disease (CAD) on cardiac catheterization. A retrospective chart review of 156 consecutive adults presenting to the Montefiore Medical Center Emergency Department with symptoms of unstable angina and no known history of CAD who underwent cardiac catheterization as part of their index hospitalization was performed. TG and HDL data were available in 100 patients within 6 months prior to admission and no more than 24 hours after presentation. A priori, a burden of CAD score was developed. On multivariate analysis, a TG/HDL ratio ≥3.5 was associated with the burden of CAD (odds ratio, 2.87; 95% confidence interval, 1.03–7.96; p=0.04). Further study is warranted.
A Swedish alcohol ignition interlock programme for drink‐drivers: effects on hospital care utilization and sick leave
Authors: Bjerre Bo , Marques Paul , Selén Jan , Thorsson Ulf
Published: February 2007

Aims  This project evaluates health outcomes following an alcohol ignition interlock programme (AIIP) by assessing hospital care utilization and sick‐leave register data relative to controls with revoked licences, but with no comparable opportunity to participate in an AIIP.

Setting  In Sweden, driving while impaired (DWI) offenders can now select voluntarily a 2‐year AIIP in lieu of 12 months' licence revocation. The AIIP includes regular medical check‐ups designed to alter alcohol use.

Design  The study is a quasi‐experimental intent‐to‐treat design; accordingly, the intervention group includes 48% of the participants who were dismissed from the AIIP before completion.

Finding  The control group (865 individuals) showed increased hospital care and sick leave after licence revocation following the DWI. Among the 1266 people in the AIIP, however, significantly fewer needed hospital care relative to controls, and relative to their own care utilization before the DWI offence. This occurred whether care reflected all diagnosis or only alcohol‐related diagnosis. Also, sick‐leave data showed significantly fewer AIIP group individuals using sick leave relative to the control group, and relative to their own pre‐treatment period. These significant health benefits disappear in the post‐treatment period. However, among those who actually do complete the entire AIIP, sustained positive health effects are observed 3 and 4 years after the DWI offence.

Conclusions  Voluntary participation in an AIIP has favourable effects with less need for hospital care or sick leave. This is probably linked to reduced alcohol consumption during the programme and to the ability to continue driving.
Concurrent buprenorphine and benzodiazepines use and self‐reported opioid toxicity in opioid substitution treatment
Authors: Nielsen Suzanne , Dietze Paul , Lee Nicole , Dunlop Adrian , Taylor David
Published: February 2007

Aims  To examine concurrent buprenorphine and benzodiazepine consumption and to compare opioid toxicity symptoms induced by methadone and buprenorphine, examining factors associated with the reporting of these symptoms.

Design  Self‐report cross‐sectional survey.

Setting  Five needle syringe programmes and five opioid substitution treatment services in Melbourne, Australia.

Participants  A total of 250 people who had experience with methadone or buprenorphine. Eligibility criteria were current or previous methadone or buprenorphine use.

Measurements  Structured questionnaire covering: demographic characteristics; current treatment and drug use; concurrent use of buprenorphine and benzodiazepines, including route of administration and source of medications; and opioid toxicity symptoms reported in association with methadone and buprenorphine consumption.

Findings  Of those reporting buprenorphine use, two‐thirds reported concurrent benzodiazepine use, with a median dose reported of 30 mg diazepam equivalents. A greater number of opioid toxicity symptoms were reported in relation to methadone consumption compared with buprenorphine. Those reporting opioid toxicity with buprenorphine were more likely to report intravenous use compared with those reporting opioid toxicity with methadone.

Conclusions  The risk of opioid toxicity appeared greater with methadone compared with buprenorphine, despite high levels of benzodiazepine consumption and injection being reported in relation to buprenorphine use. The prevalence of buprenorphine injection and the normalization of methadone‐induced sedation are two findings that merit further investigation. Establishing recommendations as to the safest and most effective way to manage benzodiazepine‐using people in opioid substitution treatment is necessary for the optimization of treatment for opioid dependence in polydrug‐using individuals.
Prognostic indicators in carcinoma of the nasal vestibule
Authors: Jeannon J.‐P. , Riddle P.J. , Irish J. , O'Sullivan B. , Brown D.H. , Gullane P.
Published: February 2007

Objectives:  Squamous cell carcinoma of the nasal vestibule is rare variant of skin cancer. The TNM classification for skin cancer has been used, whereas, Wang has devised an independent staging system, which he stated was more accurate. The purpose of this study was to analyse the prognostic indicators for survival in a patients with nasal vestibule cancer from the Princess Margaret Hospital, Toronto.

Design:  A retrospective review of case notes from the Princess Margaret Hospital archives was performed.

Setting:  The Princess Margaret Hospital/Ontario Cancer Institute is the tertiary regional Head and Neck Oncology Centre for ON, Canada.

Participants:  All patients with nasal vestibule cancer (ICD10 C300) were included.

Main outcome measures:  Univariate and multivariate analyses were performed and Kaplan–Meier survival curves constructed.

Results:  Eighty‐four patients were identified. The mean age was 67, there was a male preponderance of 2 : 1. Primary radical radiation was used in 77% of patients. Age (P = 0.02), N stage (P = 0.0001) and Wang classification (P = 0.0001) were associated with prediction of overall survival using multivariate analysis. Grade, depth of invasion and N stage were associated with disease‐free survival outcome. A 5‐year overall survival rate of 58% and disease‐free survival of 52% was seen.

Conclusion:  Nasal vestibule cancer behaves in a more aggressive manner than any other skin cancers affecting the head and neck. The Wangs’ classification appears to be a better prognostic indicator for overall survival then the TNM classification for skin cancer.
The genetics of paragangliomas: a review
Authors: T.P.C. Martin , R.M. Irving , E.R. Maher
Published: February 2007

Keypoints

• Familial head and neck paragangliomas account for ≈10% of all head and neck paragangliomas.

• There are three known genes associated with genetic susceptibility to head and neck paragangliomas: succinate dehydrogenase complex subunit ‘D’, ‘B’ and ‘C’ (SDHD, SDHB and SDHC).

• The genes most frequently implicated: SDHD and SDHB, also predispose to phaeochromocytoma

• SDHD shows a complex inheritance pattern – tumours do not develop if the mutation is inherited from the mother.

• SDHB mutations are associated with malignant phaeochromocytoma

• Patients who present with a family history of paraganglioma or phaeochromocytoma, with multiple tumours, or early onset tumours (<50 years), should be referred for genetic investigation.
Predictive factors for recurrent laryngeal nerve palsy and hypoparathyroidism after thyroid surgery
Authors: Erbil Y. , Barbaros U. , İşsever H. , Borucu İ. , Salmaslıoğlu A. , Mete Ö. , Bozbora A. , Özarmağan S.
Published: February 2007

Objectives:  To evaluate the incidence and risk factors of recurrent laryngeal nerve palsy and hypoparathyroidism following thyroidectomy.

Design:  Retrospective case–control study.

Setting:  Tertiary clinic.

Participants:  From September 1990 to September 2005, 3250 consecutive patients who had a thyroidectomy for treatment of various thyroid diseases.

Main outcome measures:  The rates of nerve palsy and hypoparathyroidism were evaluated based on thyroid pathology, the choice of operative procedure, whether the nerve was identified, and the experience of the surgeon.

Results:  Overall, the rate of nerve palsy was 1.8% and that of hypoparathyroidism was 6.6%. On univariate analysis the rates of complications were siginificantly higher in the patients who had an extended thyroidectomy, identification of the recurrent laryngeal nerve during surgery, repeat surgery and patients older than 50 years of age. Complications were no commoner in operations performed by trainees under supervision than experienced surgeons. On multivariate analysis extended thyroidectomy had a 12 fold (95% CI 1.7, 92) increased risk of nerve palsy. Repeat surgery had a 3 fold (95% CI 2.1, 4.7) increased risk of postoperative hypoparathyroidism.

Conclusion:  Extentended thyroidectomy and repeat surgery had a significant effect on the incidence of recurrent laryngeal nerve palsy and postoperative hyperparathyroidism respectively following thyroid surgery.
Mechanisms of acid buffering and formation of secondary minerals in vitric Andosols
Authors: Herre A. , Lang F. , Siebe Ch. , Dohrmann R. , Kaupenjohann M.
Published: February 2007

Andosols in the vicinity of active volcanoes receive large inputs of SO2and HCl. We studied (i) the mechanisms of acid buffering, (ii) the effect of cation removal on the short‐term acid neutralization capacity and (iii) the consequences of acid buffering for secondary mineral formation in vitric Andosols around the Central American volcanoes Poás and Masaya. Two types of short‐term (24 hour) acidification experiments at pH 3 were conducted to simulate an open system in which leaching prevails (extraction with protonated cation exchange resin) and a closed system with no leaching (pHstattitration with cation accumulation). Long‐term buffering under field conditions (mean soil pH: 4.6) and its effect on secondary mineral formation were studied by analysis of samples from a transect of decreasing acid input by IR spectroscopy, microscopic methods and geochemical equilibrium modelling. In Poás samples the main short‐term buffering mechanisms at pH 3 are plagioclase dissolution and protonation of organic matter. Long‐term acid buffering under field conditions led to weathering of plagioclase crystals but did not result in protonated carboxyl groups. In Masaya samples mineral and/or glass dissolution are the dominant acid buffering mechanisms in laboratory experiments and under field conditions. For both sites, cation accumulation during pH 3 acidification experiments led to a decrease of the effective acid neutralization capacity. Due to different climatic conditions, Al is precipitated as basaluminite at Masaya while it seems to be susceptible to leaching at Poás. Acid buffering resulted in the formation of amorphous silica at both sites.