bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome
Authors: Wang Xiangfeng , Yu Zhihui , Yang Xiaozeng , Deng Xing-Wang , Li Lei
Published: March 2009

The unprecedented complexity of the transcriptomic data obtained in recent years creates opportunities for new genomic studies aimed at interpolating regulatory code of gene expression and tracing genome evolution. We report here the identification and characterization of a set of 851 intergenic loci that represent transcribed gene fragments (TGFs) ectopically duplicated from 1030 non-transposable element (non-TE) donor genes in the rice genome. We analyzed the genomic context of the TGFs and donor genes. We show that the TGFs have adopted transcriptional orientation and pattern independent of the donor genes. We further show that TGFs have undergone relaxed purifying selection, consistent with their being pseudogenized. We found that the donor genes, which are biased toward certain molecular functions, exhibit an accelerated evolution rate comparing to the genome average. Our results demonstrated a large number of actively TGFs in the rice genome and shed light on the origin, mode of action and function of the TGFs.

Contact:  114jn@virginia.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Increased expression of CD208 (DC‐LAMP) in epidermal keratinocytes of psoriatic lesions
Authors: HIGAKI Megumu , HIGAKI Yuko , KAWASHIMA Makoto
Published: March 2009

Psoriasis is a chronic inflammatory skin disease characterized by epidermal hyperproliferation and infiltration of inflammatory leukocytes. The aim of this study was to clarify the role of innate immunity involving dendritic cells (DC) and keratinocytes in psoriasis. We immunohistochemically examined the expression of DC markers such as CD1a, CD83, CD207 (Langerin), CD208 (DC‐LAMP) and CD209 (DC‐SIGN) in psoriatic skin and γ‐interferon (IFN‐γ)/12‐O‐tetradecanoylphorbol‐13‐acetate (TPA)‐stimulated keratinocytes in vitro. CD208 was strongly expressed in basal and suprabasal layer keratinocytes in addition to DC in the perivascular lesions of the psoriatic dermis. Furthermore, the enhanced expression of CD208 in the perinuclear lesions of IFN‐γ‐/TPA‐stimulated keratinocytes was observed in vitro. Because a defect of the granular layer in psoriatic lesions has been recognized, increased expression of lysosome‐related CD208 in the basal and suprabasal keratinocytes of psoriatic lesions might represent aberrant epidermal differentiation. Additionally, these CD208‐positive keratinocytes possessing putative antigen‐processing activity might play a key role as antigen‐presenting cells in psoriatic skin.
Cornoid lamellae associated with follicular infundibulum and acrosyringium in porokeratosis
Authors: MINAMI‐HORI Masako , ISHIDA‐YAMAMOTO Akemi , IIZUKA Hajime
Published: March 2009

Skin lesions of porokeratosis consist of an atrophic center bordered by a peripheral grooved keratotic ridge that corresponds histopathologically to the cornoid lamella. Originally porokeratosis was named based on the assumption that the columns of parakeratosis emerge from the ostia of eccrine ducts. Despite this, it is generally accepted that the cornoid lamellae are rarely related to the acrosyringium. We recently encountered two cases of porokeratosis, where the cornoid lamellae were related to the follicular infundibulums. Therefore, we analyzed the location of the cornoid lamellae in 86 lesions of porokeratosis from 73 patients from our archives. We found that many cornoid lamellae are also detected at follicular infundibulum and acrosyringium. The existence of so many cornoid lamellae at follicular infundibulum and acrosyringium inside the plaques cannot be explained by pure coincidence and may be more than fortuitous.
Case of regional lymphomatoid papulosis confined to the periorbital areas
Authors: KIM Yeon Jin , RHO Yong Kwan , YOO Kwang Ho , KIM Ji Young , SEO Seong Jun , HONG Chang Kwun , MOON Nam Ju , SONG Kye Yong
Published: March 2009

A localized form of lymphomatoid papulosis (LyP) has been described very rarely. A 38‐year‐old Korean man presented with a single bean‐sized, non‐tender, erythematous nodule confined to periorbital areas with three recurrences over a 2‐year duration. With findings of biopsy, immunohistochemical staining and T‐cell receptor gene rearrangement, LyP was diagnosed. We report a case of CD30 (Ki‐1)‐positive LyP which developed recurrently and was confined to the periorbital areas.
Case of congenital esophageal stricture by ganglioneuroma and acro‐flexural hyperpigmentation: A coincidence?
Authors: KIM Beom Joon , CHOI Jung Won , YEON Je Ho , SHIN Choong Ho , PARK Kwi Won , CHO Kwang Hyun , KWON Oh Sang
Published: March 2009

Congenital hyperpigmentation in the acro‐genital area and simultaneous occurrence of ganglioneuroma in the esophagus have yet to be reported. Herein, we report a 4‐month‐old girl presenting with feeding difficulty by esophageal ganglioneuroma and symmetrically distributed brown pigmented patches on the lips, axillae, dorsa of fingers and toes, and genital area. Although the esophageal stricture was resolved by surgical removal of ganglioneuroma, her skin manifestations remained for over 2 years.
Merkel cell carcinoma of the inguinal lymph node with an unknown primary site
Authors: KIM Eun Jung , KIM Hei Sung , KIM Hyung Ok , JUNG Chan Kwon , KO Yoon‐Ho , KIM Taeg Hyun , PARK Young Min
Published: March 2009

Merkel cell carcinoma (MCC) is an uncommon and aggressive primary neuroendocrine malignancy of the skin. Frequent local recurrences and disseminations to regional lymph nodes and distant organs are characteristic. MCC within the lymph nodes in the absence of a primary site is rare and has only been reported sporadically. We report a case of MCC presenting as a painless mass in the left inguinal area for 5 months in a 57‐year‐old man. The histopathology of the excised lesion revealed a poorly differentiated basophilic small cell tumor. The tumor cells were positive for cytokeratin 20 and CD56, negative for cytokeratin 7, thyroid transcription factor‐1 and CDX‐2. These immunohistochemical findings were consistent with the diagnosis of a metastatic MCC. Despite extensive clinical and radiological investigation, we failed to identify the origin of the tumor. Our case may represent a lymph node metastasis from an occult or regressed skin primary, but we cannot preclude the possibility of a primary nodal tumor.
Psychopathological changes and quality of life in hepatitis C virus‐infected, opioid‐dependent patients during maintenance therapy
Authors: Schäfer Arne , Wittchen Hans‐Ulrich , Backmund Markus , Soyka Michael , Gölz Jörg , Siegert Jens , Schäfer Martin , Tretter Felix , Kraus Michael R.
Published: March 2009

Aims  To examine among maintenance patients (methadone or buprenorphine) with and without hepatitis C virus (HCV) infection (i) the frequency of psychopathological symptoms at baseline and 1‐year follow‐up; (ii) the association between antiviral interferon (IFN) treatment and psychopathological symptoms; and (iii) to explore whether IFN therapy has an effect on 1‐year outcome of maintenance treatment.

Design  Naturalistic prospective longitudinal cohort design.

Setting  A total of 223 substitution centres in Germany.

Participants  A nationally representative sample of 2414 maintenance patients, namely 800 without and 1614 with HCV infection, of whom 122 received IFN therapy.

Measures  HCV infection (HCV+/HCV‐), IFN (IFN+/IFN‐) treatment status and clinical measures. Diagnostic status and severity (rated by clinician), psychopathology (BSI—Brief Symptom Inventory) and quality of life (EQ‐5D—EuroQol Group questionnaire).

Findings  HCV+ patients revealed indications for a moderately increased psychopathological burden and poorer quality of life at baseline and follow‐up compared to HCV‐ patients. HCV+ patients showed a marked deterioration over time only in the BSI subscale somatization (P = 0.002), and the frequency of sleep disorders almost doubled over time (12.8% at baseline; 24.1% at follow‐up; P < 0.01). IFN treatment, received by 10% of HCV+ patients, did not impair efficacy or tolerability of maintenance therapy and was associated overall with neither increased psychopathological burden nor reduced quality of life.

Conclusions  Findings suggest no increased risk among HCV+ patients on maintenance therapy for depressive or other psychopathological syndromes. In our patient sample, IFN treatment was not associated with increased psychopathological burden, reduced quality of life or poorer tolerability and efficacy of maintenance treatment.
Weakening of one more alcohol control pillar: a review of the effects of the alcohol tax cuts in Finland in 2004
Authors: Mäkelä Pia , Österberg Esa
Published: March 2009

Aims  To review the consequences of the changes in Finnish alcohol policy in 2004, when quotas for travellers' tax‐free imports of alcoholic beverages from other European Union (EU) countries were abolished, Estonia joined the EU and excise duties on alcoholic beverages were reduced in Finland by one‐third, on average.

Design  A review of published research and routinely available data.

Setting  Finland.

Measurements  Prices of alcoholic beverages, recorded and unrecorded alcohol consumption, data on criminality and other police statistics, alcohol‐related deaths and hospitalizations, service use.

Findings  Alcohol consumption increased 10% in 2004, clearly more than in the early 2000s. With few exceptions, alcohol‐related harms increased. Alcohol‐induced liver disease deaths increased the most, by 46% in 2004–06 compared to 2001–03, which indicates a strong effect on pre‐2004 heavy drinkers. Consumption and harms increased most among middle‐aged and older segments of the population, and harms in the worst‐off parts of the population in particular.

Conclusions  Alcohol taxation and alcohol prices affect consumption and related harms, and heavy drinkers are responsive to price. In Finland in 2004, the worst‐off parts of the population paid the highest price in terms of health for cuts in alcohol prices. The removal of travellers' import quotas, which was an inherent part of creating the single European market, had serious public health consequences in Finland.
Safety and tolerability of omalizumab
Authors: Corren J. , Casale T. B. , Lanier B. , Buhl R. , Holgate S. , Jimenez P.
Published: March 2009

Background
Omalizumab (Xolair®) is a recombinant humanized monoclonal anti‐IgE antibody with proven efficacy in patients with moderate‐to‐severe and severe persistent allergic (IgE‐mediated) asthma.

Objective
To review clinical study data to assess the safety profile of omalizumab.

Methods
We analysed the safety of omalizumab using data from completed clinical studies (up to 1 year) involving more than 7500 patients with asthma, rhinitis or related conditions and up to 4 years in one study of patients with severe allergic asthma, as well as post‐marketing safety data. Analysis focuses on the risk of immune‐system effects, hypersensitivity reactions, malignant neoplasia, parasitic infections and thrombocytopenia.

Results
Omalizumab exhibited a good safety and tolerability profile that was maintained up to 4 years in one study. The incidence of anaphylaxis was 0.14% in omalizumab‐treated patients and 0.07% in control patients. No omalizumab‐treated patient developed measurable anti‐omalizumab antibodies. Post‐marketing, based on estimated exposure of 57 300 patients (June 2003–December 2006), the frequency of anaphylaxis attributed to omalizumab use was estimated to be at least 0.2% of patients. Current clinical trial data do not support an increased risk of malignant neoplasia or thrombocytopenia with omalizumab.

Conclusion
Data indicate that the proven efficacy of add‐on omalizumab in patients with moderate‐to‐severe or severe allergic asthma is accompanied by a favourable safety and tolerability profile.
Improved analysis and modelling of soil diffuse reflectance spectra using wavelets
Authors: Viscarra Rossel R. A. , Lark R. M.
Published: March 2009

Diffuse reflectance spectroscopy using visible (vis), near‐infrared (NIR) and mid‐infrared (mid‐IR) energy can be a powerful tool to assess and monitor soil quality and function. Mathematical pre‐processing techniques and multivariate calibrations are commonly used to develop spectroscopic models to predict soil properties. These models contain many predictor variables that are collinear and redundant by nature. Partial least squares regression (PLSR) is often used for their analysis. Wavelets can be used to smooth signals and to reduce large data sets to parsimonious representations for more efficient data storage, computation and transmission. Our aim was to investigate their potential for the analyses of soil diffuse reflectance spectra. Specifically we wished to: (i) show how wavelets can be used to represent the multi‐scale nature of soil diffuse reflectance spectra, (ii) produce parsimonious representations of the spectra using selected wavelet coefficients and (iii) improve the regression analysis for prediction of soil organic carbon (SOC) and clay content. We decomposed soil vis‐NIR and mid‐IR spectra using the discrete wavelet transform (DWT) using a Daubechies’s wavelet with two vanishing moments. A multiresolution analysis (MRA) revealed their multi‐scale nature. The MRA identified local features in the spectra that contain information on soil composition. We illustrated a technique for the selection of wavelet coefficients, which were used to produce parsimonious multivariate calibrations for SOC and clay content. Both vis‐NIR and mid‐IR data were reduced to less than 7% of their original size. The selected coefficients were also back‐transformed. Multivariate calibrations were performed by PLSR, multiple linear regression (MLR) and MLR with quadratic polynomials (MLR‐QP) using the spectra, all wavelet coefficients, the selected coefficients and their back transformations. Calibrations by MLR‐QP using the selected wavelet coefficients produced the best predictions of SOC and clay content. MLR‐QP accounted for any nonlinearity in the data. Transforming soil spectra into the wavelet domain and producing a smaller representation of the data improved the efficiency of the calibrations. The models were computed with reduced, parsimonious data sets using simpler regressions.
Invertebrate grazing during the regenerative phase affects the ultimate structure of macrophyte communities
Authors: ELGER ARNAUD , WILLBY NIGEL J. , CABELLO‐MARTINEZ MÓNICA
Published: March 2009

1. Although the biomass of freshwater macrophytes consumed by invertebrate herbivores (excluding crayfish) is usually low, there is growing evidence that invertebrates do exert a structuring effect on macrophyte communities. To explain this, we postulated that the effect of invertebrates may be concentrated on macrophytes during their regenerative phase.

2. We tested this hypothesis by means of a mesocosm‐based experiment, in which we investigated the effects of different densities of pond snails [Lymnaea stagnalis (L.)] on macrophytes regenerating from the natural sediment propagule bank.

3. After 2 months, a diverse macrophyte community had established in the absence of snails, mainly from sexual propagules. Under moderate snail grazing (4 individuals m−2), the ultimate biomass of macrophytes was similar, but its species composition differed dramatically. Only a few unpalatable taxa, such as Ceratophyllum demersum and Nymphaeaceae, persisted. Moreover, the relative success of macrophytes regenerating from vegetative rather than sexual propagules improved. Under higher snail grazing (20 m−2), all macrophytes disappeared before the end of the experiment.

4. These results confirm that snails at natural densities can have a strong effect on the ultimate structure of macrophyte communities by selectively consuming some species at a juvenile stage. Therefore, the regenerative phase can be seen as a window of opportunity for invertebrate grazers, which can have a qualitative effect on communities that is disproportionate to the biomass consumed.
Does mobility explain variation in colonisation and population recovery among stream fishes?
Authors: ALBANESE BRETT , ANGERMEIER PAUL L. , PETERSON JAMES T.
Published: March 2009

1. Colonisation and population recovery are crucial to species persistence in environmentally variable ecosystems, but are poorly understood processes. After documenting movement rates for several species of stream fish, we predicted that this variable would influence colonisation rates more strongly than local abundance, per cent occupancy, body size and taxonomic family. We also predicted that populations of species with higher movement rates would recover more rapidly than species with lower movement rates and that assemblage structure would change accordingly.

2. To test these predictions, we removed fishes from a headwater and a mainstem creek in southwest Virginia and monitored colonisation over a 2‐year period. Using an information–theoretic approach, we evaluated the relative plausibility of 15 alternative models containing different combinations of our predictor variables. Our best‐supported model contained movement rate and abundance and was 41 times more likely to account for observed patterns in colonisation rates than the next‐best model. Movement rate and abundance were both positively related to colonisation rates and explained 88% of the variation in colonisation rates among species.

3. Population recovery, measured as the per cent of initial abundance restored, was also positively associated with movement rate. One species recovered within 3 months, most recovered within 2 years, but two species still had not recovered after 2 years. Despite high variation in recovery, the removal had only a slight impact on assemblage structure because species that were abundant in pre‐removal samples were also abundant in post‐removal samples.

4. The significance of interspecific variation in colonisation and recovery rates has been underappreciated because of the widely documented recovery of stream fish assemblages following fish kills and small‐scale experimental defaunations. Our results indicate that recovery of the overall assemblage does not imply recovery of each component species. Populations of species that are rare and less mobile will recover more slowly and will be more vulnerable to extinction in systems where chemical spills, hydrological alteration, extreme droughts and other impacts are frequent.
Interpreting temporal variation in omnivore foraging ecology via stable isotope modelling
Authors: Kurle Carolyn M.
Published: March 2009

The use of stable carbon (C) and nitrogen (N) isotopes (δ15N and δ13C, respectively) to delineate trophic patterns in wild animals is common in ecology. Their utility as a tool for interpreting temporal change in diet due to seasonality, migration, climate change or species invasion depends upon an understanding of the rates at which stable isotopes incorporate from diet into animal tissues. To best determine the foraging habits of invasive rats on island ecosystems and to illuminate the interpretation of wild omnivore diets in general, I investigated isotope incorporation rates of C and N in fur, liver, kidney, muscle, serum and red blood cells (RBC) from captive rats raised on a diet with low δ15N and δ13C values and switched to a diet with higher δ15N and δ13C values.

I used the reaction progress variable method (RPVM), a linear fitting procedure, to estimate whether a single or multiple compartment model best described isotope turnover in each tissue. Small sample Akaike Information criterion (AICc) model comparison analysis indicated that 1 compartment nonlinear models best described isotope incorporation rates for liver, RBC, muscle, and fur, whereas 2 compartment nonlinear models were best for serum and kidney.

I compared isotope incorporation rates using the RPVM versus nonlinear models. There were no differences in estimated isotope retention times between the model types for serum and kidney (except for N turnover in kidney from females). Isotope incorporation took longer when estimated using the nonlinear models for RBC, muscle, and fur, but was shorter for liver tissue.

There were no statistical differences between sexes in the isotope incorporation rates. I also found that N and C isotope incorporation rates were decoupled for liver, with C incorporating into liver tissue faster than N.

The data demonstrate the utility of analysing isotope ratios of multiple tissues from a single animal when estimating temporal variation in mammalian foraging ecology.
Evidence for the involvement of an alternate rodent host in the dynamics of introduced plague in prairie dogs
Authors: Stapp Paul , Salkeld Daniel J. , Franklin Heather A. , Kraft John P. , Tripp Daniel W. , Antolin Michael F. , Gage Kenneth L.
Published: March 2009

The introduction of plague to North America is a significant threat to colonies of prairie dogs (Cynomys ludovicianus), a species of conservation concern in the Great Plains. Other small rodents are exposed to the causative agent,Yersinia pestis, during or after epizootics; yet, its effect on these rodents is not known, and their role in transmitting and maintaining plague in the absence of prairie dogs remains unclear.

We live‐trapped small rodents and collected their fleas on 11 colonies before, during and after plague epizootics in Colorado, USA, from 2004 to 2006. Molecular genetic (polymerase chain reaction) assays were used to identifyY. pestisin fleas.

Abundance of northern grasshopper mice (Onychomys leucogaster) was low on sites following epizootics in 2004, and declined markedly following plague onset on other colonies in 2005. These changes coincided with exposure of grasshopper mice to plague, and with periods when mice became infested with large numbers of prairie dog fleas (Oropsylla hirsuta), including some that were infected withY. pestis. Additionally, severalPleochaetis exilis, fleas restricted to grasshopper mice and never found on prairie dogs on our site, were polymerase chain reaction‐positive forY. pestis, indicating that grasshopper mice can infect their own fleas. No changes in abundance of other rodent species could be attributed to plague, and no other rodents hostedO. hirsutaduring epizootics, or harbouredY. pestis‐infected fleas.

In spring 2004, grasshopper mice were most numerous in colonies that suffered plague the following year, and the pattern of colony extinctions over a 12‐year period mirrored patterns of grasshopper mouse abundance in our study area, suggesting that colonies with high densities of grasshopper mice may be more susceptible to outbreaks. We speculate that grasshopper mice help spreadY. pestisduring epizootics through their ability to survive infection, harbour prairie dog fleas and, during their wide‐ranging movements, transport infected fleas among burrows, which functionally connects prairie dog coteries that would otherwise be socially distinct.
Landscape barriers reduce gene flow in an invasive carnivore: geographical and local genetic structure of American mink in Scotland
Authors: ZALEWSKI ANDRZEJ , PIERTNEY STUART B. , ZALEWSKA HANNA , LAMBIN XAVIER
Published: March 2009

To be effective, management programmes geared towards halting or reversing the spread of invasive species must focus on defined and defensible areas. This requires knowledge of the dispersal of non‐native species targeted for control to better understand invasion and recolonisation scenarios. We investigated the genetic structure of invasive American mink (Neovison vison) in Scotland, and incorporated landscape genetic approaches to examine resultant patterns in relation to geographical features that may influence dispersal. Populations of mink sampled from 10 sites in two regions (Argyll and Northeast Scotland) show a distinct genetic structure. First, the majority of pairwise population comparisons yielded FST values that were significantly greater than zero. Second, amova revealed that most of the genetic variance was attributable to differences among regions. Assignment tests placed 89 or more of individuals into their sampled region. Bayesian clustering methods grouped samples into two clusters according to their region of origin. Wombling approach identified the Cairngorms Mountains as a major impediment to gene flow between the regions. Mantel pairwise correlations between genetic and geographical distances estimated as least‐cost distance assuming a linear increase in the cost of movement with increasing elevation were higher than Euclidean distances or distance along waterways. Spatial autocorrelation analyses revealed stronger spatial structuring for females than for males. These results suggest that gene flow by American mink is restricted by landscape features (mountain ranges) and that eradication attempt should in the first instance break down the connectivity between management units separated by mountains.
Influence of life‐history variation on the genetic structure of two sympatric salamander taxa
Authors: STEELE C. A. , BAUMSTEIGER J. , STORFER ANDREW
Published: March 2009

Life‐history characteristics are an important determinant of a species’ dispersal abilities. We predict that variation in life history can influence population‐level genetic patterns. To test this prediction, we estimate population‐level genetic structure for two sympatric species of stream‐breeding salamander. The Cope's giant salamander (Dicamptodon copei) rarely metamorphoses into a terrestrial adult, thereby limiting overland dispersal and potentially gene flow. In contrast, the Pacific giant salamander (D. tenebrosus) commonly metamorphoses, which is expected to facilitate overland dispersal and gene flow. Three sets of analyses based on microsatellite data support these hypotheses, showing that D. tenebrosus displays minimal population‐level genetic structuring and no pattern of isolation by distance, whereas D. copei displays a high degree of population‐level genetic structure and significant isolation by distance. Specifically, nearly all pairwise FST values were significantly different from 0 between populations of D. copei, with fewer than half the pairwise FST values significant from 0 in D. tenebrosus. Additionally, Structure analyses indicated eight genetic clusters for D. copei but only one genetic cluster for D. tenebrosus. Finally, Mantel tests showed significant correlations between stream and overland distance with genetic distance for D. copei but no significant correlations of either landscape feature for D. tenebrosus at the scale of the study. These results provide a case study of the link between life‐history variation and population genetic patterns while controlling for phylogeny and environmental variation.
Polygyny can increase rather than decrease genetic diversity contributed by males relative to females: evidence from red deer
Authors: PÉREZ‐GONZÁLEZ J. , MATEOS C. , CARRANZA J.
Published: March 2009

Polygyny is expected to erode genetic variability by reducing the diversity of genetic contribution of males to the next generation, although empirical evidence shows that genetic variability in polygynous populations is not lost as rapidly as expected. We used microsatellite markers to study the genetic variability transmitted by mothers and fathers to offspring during a reproductive season in wild populations of a polygynous mammal, the red deer. Contrary to expectations, we found that males contributed more genetic diversity than females. Also, we compared study populations with different degrees of polygyny to find that polygyny was not related to a decrease in genetic diversity contributed by males. On the contrary, when population genetic diversity was relatively low, polygyny associated with higher genetic diversity of paternal lineage. Our results show that sexual selection, by favouring heterozygote individuals, may compensate the potential reduction of effective population size caused by polygyny, thus contributing to explain why genetic diversity is not depleted in polygynous systems.
End‐signature of deep‐marine basin‐fill, as a structurally confined low‐gradient clastic system: the Middle Eocene Guaso system, South‐central Spanish Pyrenees
Authors: SUTCLIFFE CLARE , PICKERING KEVIN T.
Published: March 2009

The ca 300 m thick Guaso system is the youngest part of the ca 4 km thick deep‐marine fill of the Middle Eocene Ainsa basin, Spanish Pyrenees. It is overlain by 150 to 200 m of fine‐grained slope, prodelta and deltaic sediments. The ca 25 discrete deep‐marine sandbodies within the Ainsa basin accumulated over ca 10 Myr, making eustasy the most likely control for coarse sand deposition (probably the ca 400 kyr Milankovitch mode). The first‐order control on basin‐scale accommodation, however, was tectonically‐driven subsidence. Previously, the Guaso sandbodies were interpreted as linked to deep erosional, canyon‐like features, but here it is argued that they are laterally extensive sandbodies, built by lateral‐switching of 3 to 10 m deep erosional channels, and confined only by basin structure during deposition. The Guaso system represents the end of deep‐marine deposition in a structurally‐confined, delta‐fed, low‐gradient clastic system. The critical end‐signature of deep‐marine deposition was a phase of differential tectonic uplift above the underlying (Boltaña) thrust creating a narrower and shallower basin morphology, thus allowing sedimentation to create a low‐gradient clastic system. Then, the next eustatic sea‐level fall was insufficient to permit the cutting of canyons or deeply‐incised slope channels, as had been the case earlier when the topographic relief between shelf and basin was at least several hundred metres greater. Such low‐gradient clastic systems may characterize the end‐signature for the infill of other shallowing‐up deep‐marine basins where a tectonic driver on subsidence is removed and/or differential uplift/subsidence leads to reduced sea floor gradients, leaving eustasy and sediment flux as the principal control on sediment supply.
Fine‐scale relief related to Late Holocene channel shifting within the floor of the upper Redondo Fan, offshore Southern California
Authors: NORMARK WILLIAM R. , PAULL CHARLES K. , CARESS DAVID W. , USSLER III WILLIAM , SLITER RAY
Published: March 2009

Erosional and depositional bedforms have been imaged at outcrop scale in the upper Redondo Fan, in the San Pedro Basin of offshore Southern California in ≥600 m water depths, using an Autonomous Underwater Vehicle developed by the Monterey Bay Aquarium Research Institute. The Autonomous Underwater Vehicle is equipped with multibeam and chirp sub‐bottom sonars. Sampling and photographic images using the Monterey Bay Aquarium Research Institute Remotely Operated Vehicle Tiburon provide groundtruth for the Autonomous Underwater Vehicle survey. The 0·3 m vertical and 1·5 m lateral bathymetric resolution and 0·1 m sub‐bottom profile resolution provide unprecedented detail of bedform morphology and structure. Multiple channels within the Redondo Fan have been active at different times during the Late Holocene (0 to 3000 yr bp). The currently active channel extending from Redondo Canyon makes an abrupt 90° turn at the canyon mouth before resuming a south‐easterly course along the east side of the Redondo Fan. This channel is floored by sand and characterized by small steps generally <1 m in relief, spaced 10 to 80 m in the down‐channel direction. A broader channel complex lies along the western side of the fan valley that was last active more than 850 years ago. Two distinct trains of large scours, with widths ranging from tens to a few hundred metres and depths of 20 m, occur on the floor of the western channel complex, which has a thin mud drape. If observed in cross‐section only, these large scours would probably be misidentified as the thalweg of an active channel.
Complete genomic sequence of a novel HLA‐B allele, B*4456N
Authors: Tijssen H. J. , Driessen S. W. , Van Houwelingen K. P. , Allebes W. A. , Joosten I.
Published: March 2009

A novel allele, HLA‐B*4456N, was identified upon cloning and sequencing of genomic DNA.
Budding dispersal and the sex ratio
Authors: Gardner A. , Arce A. , Alpedrinha J.
Published: March 2009

There is much interest in understanding how population demography impacts upon social evolution. Here, we consider the impact of rate and pattern of dispersal upon a classic social evolutionary trait – the sex ratio. We recover existing analytical results for individual dispersal, and we extend these to allow for budding dispersal. In particular, while a cancelling of relatedness and kin competition effects means that the sex ratio is unaffected by the rate of individual dispersal, we find that a decoupling of relatedness and kin competition means that budding dispersal favours increasingly female‐biased sex ratios. More generally, our analysis illustrates the relative ease with which biological problems involving class structure can be solved using a kin selection approach to social evolution theory.
Risk Assessment and Withdrawal Behavior by Two Species of Aposematic Poison Frogs, Dendrobates auratus and Oophaga pumilio, on Forest Trails
Authors: Cooper Jr William E. , Caldwell Janalee P. , Vitt Laurie J.
Published: March 2009

Many chemically defended prey advertize toxicity to predators by aposematic coloration. When aposematic prey are approached, they often move slowly or not at all, allowing predators to evaluate their unprofitability. Poison frogs (Dendrobatidae) are toxic, aposematically colored, forage openly and diurnally, and are much easier to capture than many palatable frogs. Although protected against diverse predators, they are sometimes attacked and are subjected to injury by large animals without predatory intent. We predicted that they have limited escape behavior, but retain ability to assess and respond to risk. When we approached Dendrobates auratus and Oophaga pumilio on forest trails, both species hopped by the shortest route to the nearer forest edge and stopped there. When approached, D. auratus moved after shorter latency at an angle closer to perpendicular to the forest edge, were more likely to leave the trail, and left the trail sooner with fewer changes in direction after moving a shorter distance than when not approached. In agreement with predictions of optimal escape theory based on risk, flight initiation distance by D. auratus was greater when approached directly than indirectly and rapidly than slowly, and was greater when frogs were in the open than partially concealed. Frogs neither attempted rapid escape nor entered refuges. Both species hopped leisurely and remained visible after stopping. They exhibit the diminished escape behavior of aposematic prey, yet retain the capacity to assess risk and adjust behavior accordingly. Their behavior demonstrates continued need for escape behavior by highly toxic aposematic prey.
Mate Attraction in a Burrowing Wolf‐Spider (Araneae, Lycosidae) is not Olfactory Mediated
Authors: Fernández‐Montraveta Carmen , Cuadrado Mariano
Published: March 2009

Spiders are mostly solitary living animals, and males actively search for females by using chemical cues. Compared with the overwhelming evidence demonstrating the role of spider contact sex‐pheromones, support for the role of olfactory sex‐pheromones in spider communication is scarce. In Lycosa tarantula (L., 1758), a Mediterranean burrowing wolf spider inhabiting dry and open habitats and dependent on chemical cues for mate searching, we investigated the role of olfactory sex‐pheromones in mate attraction. We conducted both laboratory and field experiments, using multiple experimental approaches (two‐choice olfactometer in the laboratory and pit‐fall traps and two‐choice open arenas in the field) and controlling for male sexual arousal. Our results support the hypothesis that mate attraction in this species is not olfactory‐mediated. In the two‐choice olfactometer, males did not orient preferentially to the side where the stimulus was concealed. Stimuli did not influence response latency or the relative time spent in the experimental side of the olfactometer. In the field, the effectiveness of experimental pit‐fall traps baited with potential olfactory sex‐pheromones did not differ from that of control traps. In the two‐choice open arenas, males did not show any clear preference for the experimental half containing the potential olfactory sex‐pheromone, nor did they show any sexual response. These results demonstrate that olfactory‐mediated cues are not important during mate attraction in this species, and enforce the idea that habitat preferences and life style might explain the relative role of contact and olfactory‐mediated chemical cues during spider mate searching.
Social Networks and the Formation and Maintenance of River Otter Groups
Authors: Hansen Heidi , McDonald David B. , Groves Pamela , Maier Julie A. K. , Ben‐David Merav
Published: March 2009

Many studies have evaluated why male mammals form social groups; few however have investigated how these groups are formed and maintained. We observed behavioral interactions of 15 male river otters (Lontra canadensis) captured in Prince William Sound (PWS), Alaska, and held in captivity for 10 mo. Because the otters were captured in various areas and differed in age and relatedness, we were able to test how kinship and age influenced social interactions. We also explored how kinship, age and social interactions in captivity related to geographic spacing after the otters were released back in PWS. In 284 h of observations, the otters exhibited more positive than negative interactions. Social network models indicated that in the early stage of captivity, there were more links among individuals than in the late stage. In the late‐stage period, older animals that had higher testosterone levels exhibited increased social distance and lower information centrality (a network connectivity metric). Social distance was not related to genetic distance, nor did it relate directly to age, although both social distance and age were correlated with post‐release geographic distance. Thus, the formation of male groups in coastal river otters is largely influenced by familiarity and past experience, rather than kinship. The maintenance of groups, especially during the mating season, is a function of reproductive status and age, with older animals withdrawing from the social network during that time. What other phenotypic characters may contribute to the formation and maintenance of river otter groups merit future exploration.
Immunohistochemical detection of advanced glycation end products in human bladder with specific monoclonal antibody
Authors: Matsumoto Kenshi , Fujiwara Yukio , Nagai Ryoji , Yoshida Masaki
Published: March 2009

Objective:  To investigate the accumulation of advanced glycation end products (AGE) in human bladder.

Methods:  Human bladder specimens were obtained from nine patients during radical cystectomy. Frozen sections were immunohistochemically analyzed by three different monoclonal anti‐AGE antibodies such as anti‐Nε‐(carboxymethyl)lysine (CML), anti‐imidazolone and anti‐pentosidine antibodies. Bladder sections were stained with these antibodies by indirect immunoperoxidase methods. Double immunohistochemical staining with one of the anti‐AGE antibodies or an anti‐human macrophage antibody was also carried out.

Results:  We demonstrated that CML and pentosidine were accumulated in human bladder extracellularly as well as intracellularly, whereas any accumulation of imidazolone was not observed. Double immunohistochemical staining indicated that AGE‐accumulated cells in human bladder were derived from macrophages.

Conclusions:  The present study demonstrated that AGE‐structures such as CML and pentosidine are accumulated extracellularly in human bladder, and were endocytosed by tissue macrophages.
Tethyan relicts on continental coastlines of the northwestern Pacific Ocean and Australasia: molecular phylogeny and fossil record of batillariid gastropods (Caenogastropoda, Cerithioidea)
Authors: Ozawa Tomowo , Köhler Frank , Reid David G. , Glaubrecht Matthias
Published: March 2009

The Batillariidae are a family of cerithioidean gastropods consisting of 14 living species, classified in six to eight genera. They are abundant on sandy mudflats and sometimes on rocky shores, on continental margins in the warm‐temperate to tropical regions of the northwestern Pacific Ocean, Australasia and the Americas. Using samples from all 14 nominal batillariid species, we present a molecular phylogenetic hypothesis constructed from two genes, mitochondrial 16S rRNA and nuclear 28S rRNA, with taxa from four marine cerithioidean families as outgroups (Cerithiidae, Modulidae, Planaxidae, Potamididae). The Batillariidae as traditionally conceived are not monophyletic, because the Neotropical ‘batillariids’Lampanella and Rhinocoryne are sister to the Planaxidae. The monophyletic Batillariidae sensu stricto are restricted to the northwestern Pacific and Australasia; we suggest a revised generic classification consistent with our phylogenetic hypothesis and recognize the four genera Batillaria, Pyrazus, Velacumantus and Zeacumantus. We propose a definition of the family using shell characters, as a basis for a review of the extensive fossil record. Batillariids appeared in the Late Cretaceous or Palaeocene, and the extinct genera Pyrazopsis, Vicinocerithium and Granulolabium became diverse in the Tethyan realm before the group disappeared from Europe at the end of the Miocene. The Batillariidae s. s. reached Australia and New Zealand by the Late Oligocene, and the genera Pyrazus, Velacumantus and Zeacumantus still survive in this refugium of Tethyan fauna. Two lineages, Batillaria and the extinct Tateiwaia, migrated north to China and Japan in the Early Miocene, to establish the present disjunct distribution of this relictual group in southern Australasia and the Oriental region.
A Structural Model of Australia as a Small Open Economy
Authors: Nimark Kristoffer P.
Published: March 2009

This paper sets up and estimates a structural model of Australia as a small open economy using Bayesian techniques. Unlike other recent studies, the paper shows that a small micro‐founded model can capture the open economy dimensions quite well. Specifically, the model attributes a substantial fraction of the volatility of domestic output and inflation to foreign disturbances, close to what is suggested by unrestricted VAR studies. The paper also investigates the effects of various exogenous shocks on the Australian economy.
The Influences of Institution Attended and Field of Study on Graduates' Starting Salaries
Authors: Birch Elisa Rose , Li Ian , Miller Paul W.
Published: March 2009

This paper examines the determinants of Australian university graduates' starting salaries, with an emphasis on the institution attended and field of study. It is shown that there is little difference between the starting salaries of students who attended Group of Eight universities and those who attended other universities. There are modest differences in starting salaries across fields of study. However, these differences are considerably less than those associated with the type of employment obtained. These results suggest it is what you do in the labour market, rather than where or what you have studied, that is the main determinant of labour market outcomes.
In the Wake of Mantzikert: The First Crusade and the Alexian Reconquest of Western Anatolia
Authors: ROCHE JASON T.
Published: March 2009

The main aims of this article are threefold. It initially seeks to address two popular misconceptions frequently found in crusade histories and general histories of the Byzantine empire concerning the Turkish invasion and settlement of western Anatolia after the battle of Mantzikert in 1071. The article maintains that blurring the distinctions between the Seljuk Turks of Ransūm and the tribes of pastoral nomads or rather transhumants who came to be known as Türkmens or Turcomans is incorrect. The oft‐repeated assumption that the Seljuk Turks of Baghdad oversaw the Turkish conquest of Anatolia is addressed when tracing the unstructured nature of the Turkish migration and the subsequent lack of unity amongst the invaders. After providing the context of the Turkish settlement in western Anatolia, the article throws new light on the relative ease with which the armies of the First Crusade traversed the Anatolian plateau and Byzantine forces compelled the speedy capitulation of Turkish towns and territories along the western coastal plains and river valleys of Anatolia in 1097 and 1098 respectively.
Cough Headache: A Study of 83 Consecutive Patients
Authors: Chen P-K , Fuh J-L , Wang S-J
Published: March 2009

To delineate the differences in clinical characteristics and evaluate the outcome between primary and secondary cough headache, 83 consecutive patients (59M/ 24F, mean age 61.5 ± 17.7 years) with cough headache (1.2%) out of 7100 patients in a headache clinic were studied. All of them received brain imaging studies. Most did not have relevant brain lesions ( n = 74, 89.2%, primary group) except for nine patients (10.8%, the secondary group). Most of the intracranial lesions were located in the posterior fossa ( n = 6, 67%), including only two patients with Chiari malformation. The primary group had a higher response rate to indomethacin than the secondary group (72.7% vs. 37.5 %, P = 0.046). Mild to moderate headache intensity and age onset < 50 years predicted a favourable response. At a mean follow-up of 51.4 months, 83.9% of patients with primary cough headache completely remitted. Inconsistent with the proposed International Classification of Headache Disorders, 2nd edn criteria, 10.8% of patients with primary cough headache had headache duration of > 30 min. Clinical features, neurological examinations and drug response could not safely differentiate primary from secondary cough headache. Neuroimaging studies are required in each patient.
Keloids treated with postoperative Iridium 192* brachytherapy: a retrospective study
Authors: Arnault JP , Peiffert D , Latarche C , Chassagne JF , Barbaud A , Schmutz JL
Published: March 2009

Background  Post‐excisional brachytherapy with Iridium 192 is a treatment of keloids scars (KS). Its indications and its parameters are not subject to any consensus.

Objective  We wanted to assess the effectiveness and satisfaction of patients treated in our centre.

Patients and Methods  This was a retrospective study conducted from November 2006 to November 2007. Patients with clinically and histologically proven KS treated between 1990 and 2005, were convened in consultation between September and October 2007. Clinical data and parameters of the brachytherapy have been collected.

Results  Eighty‐seven patients (138 KS) were treated. Eighty‐two KS (46 patients) met the criteria for inclusion. Thirty‐two patients (55 KS) have been seen in consultation. The average time between the onset of KS and treatment was 63.5 months. The brachytherapy has begun after a maximum of 7 hours posterior to surgery for all KS. The average dose was 17.9 Gy calculated at 5 mm. We observed 23.6% of recurrence after treatment. Seventy‐nine per cent of itching and 87.5% of pain have totally disappeared. The phototypes 5 and 6 had an increased risk of reccurence.

Discussion  This is the most important series of KS treated with Post‐excisional brachytherapy presented so far. The technique is efficient in preventing keloid reccurence and in treating the functional signs, but at the expense of an unaesthetic result, of wich patient must be warned about. A follow‐up of at least two years after treatment is recommended.

Conflicts of interest

None declared