bluuebunny/crossref_metadata_2025 huggingface dataset:
Transfer RNA in the hybrid P/E state: Correlating molecular dynamics simulations with cryo-EM data
Authors: Li Wen , Frank Joachim
Published: October 2007

Transfer RNA (tRNA) transiently occupies the hybrid P/E state (P/E-tRNA) when mRNA–tRNA are translocated in the ribosome. In this study, we characterize the structure of P/E-tRNA and its interactions with the ribosome by correlating the results from molecular dynamics simulations on free tRNA with the cryo-EM map of P/E-tRNA. In our approach, we show that the cryo-EM map may be interpreted as a conformational average. Along the molecular dynamics trajectories (44 ns, 18 ns, and 18 ns), some of the snapshots prove to be quite close to the observed density. In a representative structure, the CCA (3′) arm is uniquely twisted, and the anticodon stem loop is kinked at the junctions to both the anticodon loop and the D stem. In addition, the map shows that the P/E-tRNA is no longer bound to helix H69 of 23S rRNA and is flexible, and the conformations of helices H68 and h44 of 16S rRNA differ from those in the x-ray structure. Thus, our study presents structural and dynamic information on the P/E-tRNA and characterizes its interactions with the translocating ribosome.
Biological control of citrus insect pests in Turkey.
Authors: Erkıliıç¸ L. Erkıliıç¸ L. , Demirbaș H.
Published: October 2007

The usage and acceptability of biological control methods are set to increase in agriculture in the future because of food safety and pesticide residue issues. Biological control implementation in Turkey started with control of cottony cushion scale
Icerya purchasi
(Homoptera: Margarodidae) through the introduction and release of
Rodolia cardinalis
(Coleoptera: Coccinellidae) in citrus plantations. Currently, the key pests of citrus, i.e. citrus mealybug (
Planococcus citri
(Homoptera: Pseudococcidae)), citrus rust mite (Phyllocoptruta oleivora (Acarina: Eriophyidae)) and California red scale (
Aonidiella aurantii
(Homoptera: Diaspididae)), can be suppressed by biological control, a specific acaricide and summer oil applications, respectively. As a main pest, the citrus mealybug infested area is approximately 100 000 ha in total on the East and West Mediterranean coasts of Turkey. Until now, biological control for citrus mealybug has been implemented on only 3000 ha (3.5%) of the citrus growing area. However, the small-scale nature of biological control applications in relation to the size of infested area is set to change as public awareness will lead to an increase in the area over which biological control is implemented in the future.
Bt corn and impact on mycotoxins.
Authors: Wu F.
Published: October 2007

This review summarizes the literature linking Bt [
Bacillus thuringiensis
] corn and the reduction of the mycotoxins fumonisin, aflatoxin, deoxynivalenol (DON) and zearalenone. Mycotoxins in field corn cause hundreds of millions of dollars in economic losses annually in the USA, and substantially greater losses in other regions of the world. Most of the losses are from aflatoxin contamination, while significant but smaller losses are due to
Fusarium
mycotoxins, fumonisins and DON. The insecticidal proteins in genetically modified hybrid Bt corn (
Zea mays
spp.) reduce insect damage from certain Lepidopteran larvae, which in turn can reduce infection of the grain by mycotoxigenic fungi. Where such insect damage is a major factor in mycotoxin contamination, Bt corn can lower mycotoxin levels. Since such damage is not always the most important factor, experimental results have been mixed, especially with aflatoxin levels. Bt corn appears to have a greater impact on the
Fusarium
mycotoxins than on aflatoxin levels. Studies on economic impacts of Bt corn's mycotoxin reduction are briefly summarized. The benefits in developing countries from mycotoxin reduction could be more significant, particularly in regions where unprocessed corn is a staple in the human diet.
Passive immunity in poultry coccidiosis.
Authors: Cozma V. , Titilincu A.
Published: October 2007

Coccidiosis is a protozoosis causing important economic losses in poultry industry throughout the world, either due to mortality or to weight losses. The species belonging to the
Eimeria
genus are host-specific, and the resulting immunity is species-specific. The immune response to coccidiosis is primarily cellularly mediated and secondarily humorally mediated, by means of antibodies. Within the cellular immune response, the CD4
+
and CD8
+
cells, and the cytokines they secrete, play an important role. Nevertheless, it seems that in the first days of life, chicks are protected against infection by maternal antibodies, transferred via egg yolk. This type of immune protection is well known in the case of the Gumboro disease. Research over the past 16 years has shown that the immunoglobulin Y (IgY) transferred via the egg yolk to the chicks prevents the appearance of clinical coccidiosis in chicks. The production of specific antibodies in breeders can be stimulated through infections or immunization. It has also been demonstrated that the maternal antibodies that appear as a result of an infection with
Eimeria
spp. (
Eimeria maxima
) offer the chicks partial protection against infection with another species (
Eimeria tenella
), owing to the fact that some eimerian proteins seem to be common to more species.
Growing plants in space.
Authors: Musgrave M. E.
Published: October 2007

Plants have been a part of the space programme for nearly half a century. Incremental improvements in our understanding of the spaceflight environment have led to the development of specialized hardware that enables plants to grow in space. For spacecraft travelling in low earth orbit, free-fall results in a weightless environment, which brings with it a host of horticultural challenges. A particulate matrix is used to facilitate water and nutrient delivery in the rootzone while optimizing gas exchange. Compact, short-lived plants have been developed for use in the spaceflight setting, and these adapt to the relatively low light (300 µmol/m
2
/s) and high carbon dioxide provided by the power- and space-limited flight hardware. Operationally, seeds can be stored dry in space for many years without damage. Seeds must be properly oriented when set to germinate so that the emerging plant will be able to reach light and orient its axis through phototropism. Growth form changes in the absence of gravity include loss of drooping (including wilting) and altered branching angles, both of which influence plant architecture and light interception. Seed production is challenged by lack of convective air movement in microgravity so it is important to provide active ventilation for the plants. Directional air movement may easily blow pollen, seeds or abscised plant parts out of the hardware and must be worked around to ensure adequate pollination and seed collection. Considerable work remains to understand how microgravity changes the plant's role as food and how fractional g-levels, as on the moon and Mars, will affect plant performance.
Impacts on forestry of changing energy sources.
Authors: Sedjo R. A.
Published: October 2007

Global reliance on the use of fossil fuels has increased dramatically over the past century but we are now at a crossroads. Questions have been raised about the long-term availability of the energy resource supply, as shown by the Hubbard Curve for petroleum. (Hirsch RL. The Shape of World Oil Peaking: Learning from Experience. Available from: URL: http://www.netl.doe.gov/energy-analyses/pubs/Peak_Shape_Study.pdf (accessed 15 May 2007).). Major petroleum-producing regions in the Middle East, parts of Africa and South America, as well as Russia are plagued by political and security concerns. As a result, the rising petroleum price is often associated with a rising security 'risk' premium. Global warming and the role of carbon dioxide (CO
2
) emissions, which are tied directly to fossil fuel usage, further exacerbate an already overwhelmingly complex problem. Concerns about the future availability of traditional energy sources and their usability have given rise to the exploration and preliminary development of a number of alternative energy sources. Renewables provide opportunities, but perhaps largely for niche markets. For example, although solar energy often appears attractive, it continues to be relatively expensive (Borenstein S. Valuing the Time-varying Electricity Production of Solar Photovoltaic Cells. Center for the Study of Energy Markets Working Paper No. 142. University of California Energy Institute; 2005.) and best suited for specialized situations off the grid. Also, while wind and hydropower can be important energy sources, they also have serious limitations and locational constraints. One renewable energy source that offers significant advantages is biomass because it is renewable and is viewed as free from net 'greenhouse gas' (GHG) emissions, primarily CO
2
emissions. Although biomass energy does release CO
2
into the atmosphere, the general approach is to treat the biological system as a closed loop where emissions are viewed as subsequently sequestered in replacement biological growth. This system gives rise to the interpretation that there are no direct net CO
2
emissions associated with biomass as an energy feedstock, and consequently, no penalties are likely to be assessed. Widespread biomass use for energy would have land use implications, particularly on the condition of forests, both in the USA and especially in the developing world. This paper focuses on the possible uses of biological materials and biomass to produce bioenergy, the technologies that would be needed, and the possible impacts of alternative energy and bioenergy sources on forests and forestry.
Complexes pondérés sur les compactifications de Baily-Borel: Le cas des variétés de Siegel
Authors: Morel Sophie
Published: October 2007

In this work, we calculate the trace of a Hecke correspondance composed with a power of the Frobenius endomorphism on the fibre of the intersection complexes of the Baily-Borel compactification of a Siegel modular variety. Our main tool is Pink’s theorem about the restriction to the strata of the Baily-Borel compactification of the direct image of a local system on the Shimura variety. To use this theorem, we give a new construction of the intermediate extension of a pure perverse sheaf as a weight truncation of the full direct image. More generally, we are able to define analogs in positive characteristic of the weighted cohomology complexes introduced by Goresky, Harder and MacPherson.
The strange duality conjecture for generic curves
Authors: Belkale Prakash
Published: October 2007

Let

X
X

be a smooth connected projective algebraic curve of genus

g
≥
1

g\geq 1

. The strange duality conjecture connects non-abelian theta functions of rank

r
r

and level

k
k

and those of rank

k
k

and level

r
r

on

X
X

(for

S
U
(
r
)

SU(r)

and

U
⁡
(
k
)

\operatorname {U}(k)

, respectively). In this paper we prove this conjecture for

X
X

generic in the moduli space of curves of genus

g
g

.
Euclidean distortion and the sparsest cut
Authors: Arora Sanjeev , Lee James , Naor Assaf
Published: October 2007

We prove that everynn-point metric space of negative type (and, in particular, everynn-point subset ofL1L_1) embeds into a Euclidean space with distortionO(log⁡n⋅log⁡log⁡n)O(\sqrt {\log n} \cdot \log \log n), a result which is tight up to the iterated logarithm factor. As a consequence, we obtain the best known polynomial-time approximation algorithm for the Sparsest Cut problem with general demands. If the demand is supported on a subset of sizekk, we achieve an approximation ratio ofO(log⁡k⋅log⁡log⁡k)O(\sqrt {\log k}\cdot \log \log k).
Parabolic transfer for real groups
Authors: Arthur James
Published: October 2007

We shall establish an identity between distributions on different real reductive groups. The distributions arise from the trace formula. They represent the main archimedean terms in both the invariant and stable forms of the trace formula. The identity will be an essential part of the comparison of these formulas. As such, it is expected to lead to reciprocity laws among automorphic representations on different groups. Our techniques are analytic. We shall show that the difference of the two sides of the proposed identity is the solution of a homogeous boundary value problem. More precisely, we shall show that it satisfies a system of linear differential equations, that it obeys certain boundary conditions around the singular set, and that it is asymptotic to zero. We shall then show that any such solution vanishes.
Successful anti-cancer drug targets able to pass FDA review demonstrate the identifiable signature distinct from the signatures of random genes and initially proposed targets
Authors: Mayburd Anatoly L. , Golovchikova Inna , Mulshine James L.
Published: October 2007

Motivation: New efforts to guide and prioritize the selection of cancer drug targets are urgently needed, as is evident by the slow development of novel anti-cancer agents and the narrow therapeutic index of existing drugs. Given these limitations, the current study was conducted to explore the classification features defining the therapeutic success that can result from targeting a particular gene.

Results: Classification was based on extracting features specific to known successful anti-cancer targets and combining them in a linear classifier, resulting in calculation of an enrichment score for each gene. Extended description, the search tool used in this study, enriched existing drug target candidates by up to 10-fold at an ∼50% recall rate, covering ∼24 000 genes or ∼80% of genome. More importantly, the target category with high attrition rate was classified from target category with low attrition rate, allowing to refine the drug development portfolios. Biological relevance of the parameters comprising the enrichment score was explored. Enrichment in cancer-specific effects was independently demonstrated by literature analysis. Imposing these enrichment scores on existing structural, pathway and phenotype-based procedures for prospective target selection may enhance the efficiency and accuracy of target identification and accelerate drug design.

Availability: The software used in this work is available upon request.

Contact:  amayburd@cpaglobal.com, James_L_Mulshine@rush.edu

Supplementary information: Supplementary data are available at www.mayburd.com; http://www.rush.edu/rumc/page-1120170920643.html
Computation of the Kirkendall velocity and displacement fields in a one-dimensional binary diffusion couple with a moving interface
Authors: Boettinger W.J , Guyer J.E , Campbell C.E , McFadden G.B
Published: October 2007

The moving interface problem in a one-dimensional binary α/β diffusion couple is studied using sharp and diffuse interface (Cahn–Hilliard) approaches. With both methods, we calculate the solute field and the Kirkendall marker velocity and displacement fields. In the sharp interface treatment, the velocity field is generally discontinuous at the interphase boundary, but can be integrated to obtain a displacement field that is continuous everywhere. The diffuse interface approach avoids this discontinuity, simplifies the integration and yet gives the same qualitative behaviour. Special features observed experimentally and reported in the literature are also studied with the two methods: (i) multiple Kirkendall planes, where markers placed on the initial compositional discontinuity of the diffusion couple bifurcate into two locations, and (ii) a Kirkendall plane that coincides with the interphase interface. These situations occur with special values of the interdiffusion coefficients and starting couple compositions. The details of the deformation in these special situations are given using both methods and are discussed in terms of the stress-free strain rate associated with the Kirkendall effect.
Understanding height-structured competition in forests: is there anR*for light?
Authors: P. Adams Thomas , W. Purves Drew , W. Pacala Stephen
Published: October 2007

Tree species differ from one another in, and display trade-offs among, a wide range of attributes, including canopy and understorey growth and mortality rates, fecundity, height and crown allometry, and crown transmissivity. But how does this variation affect the outcome of interspecific competition and hence community structure? We derive criteria for the outcome of competition among tree species competing for light, given their allometric and life-history parameters. These criteria are defined in terms of a new simple whole life-cycle measure of performance, which provides a simple way to organize and understand the many ways in which species differ. The general case, in which all parameters can differ between species, can produce coexistence, founder control or competitive exclusion: thus, competition for light need not be hierarchical as implied byR*theory. The special case in which species differ only in crown transmissivity produces neutral dynamics. The special case in which species differ in all parameters except crown transmissivity gives hierarchical competition, where the equivalent ofR*is, the height at which trees enter the canopy in an equilibrium monoculture.
A supertree of Temnospondyli: cladogenetic patterns in the most species-rich group of early tetrapods
Authors: Ruta Marcello , Pisani Davide , Lloyd Graeme T , Benton Michael J
Published: October 2007

As the most diverse group of early tetrapods, temnospondyls provide a unique opportunity to investigate cladogenetic patterns among basal limbed vertebrates. We present five species-level supertrees for temnospondyls, built using a variety of methods. The standard MRP majority rule consensus including minority components shows slightly greater resolution than other supertrees, and its shape matches well several currently accepted hypotheses of higher-level phylogeny for temnospondyls as a whole. Also, its node support is higher than those of other supertrees (except the combined standard plus Purvis MRP supertree). We explore the distribution of significant as well as informative changes (shifts) in branch splitting employing the standard MRP supertree as a reference, and discuss the temporal distribution of changes in time-sliced, pruned trees derived from this supertree. Also, we analyse those shifts that are most relevant to the end-Permian mass extinction. For the Palaeozoic, shifts occur almost invariably along branches that connect major Palaeozoic groups. By contrast, shifts in the Mesozoic occur predominantly within major groups. Numerous shifts bracket narrowly the end-Permian extinction, indicating not only rapid recovery and extensive diversification of temnospondyls over a short time period after the extinction event (possibly less than half a million years), but also the role of intense cladogenesis in the late part of the Permian (although this was counteracted by numerous ‘background’ extinctions).
The relationship between caudal differential pressure and activity of Atlantic cod: a potential method to predict oxygen consumption of free‐swimming fish
Authors: Steinhausen M. F. , Steffensen J. F. , Andersen N. G.
Published: October 2007

This study reports the first results on telemetry of caudal differential pressure during spontaneous swimming activity in cod Gadus morhua and demonstrates that tail‐beat pressure may be used as a predictor of activity and swimming costs of free‐swimming cod. Tail‐beat pressure was monitored using a differential pressure sensor on the caudal peduncle of cod and spontaneous swimming activity was quantified using a customized video‐computer tracking programme. Tail‐beat pressure was found to correlate with (1) swimming speed (U) and oxygen consumption during forced swimming and (2) mean U during spontaneous activity. Based on the relationship between and the integrated pressure performed by the tail during forced swimming, it should be possible to predict during spontaneous activity. To gain precise measures of activity and thus predictions of for free‐swimming fish, however, individual calibrations are necessary.
Social facilitation of learning in mixed‐species schools of common carp Cyprinus carpio L. and Nile tilapia Oreochromis niloticus (L.)
Authors: Karplus I. , Zion B. , Rosenfeld L. , Grinshpun Y. , Slosman T. , Goshen Z. , Barki A.
Published: October 2007

The process of learning to associate a visual cue with food was studied in groups of common carp Cyprinus carpio and Nile tilapia Oreochromis niloticus by means of a classical conditioning paradigm. In the first phase of the study, fishes were conditioned in either single‐species or mixed‐species groups to associate a blinking blue light with food. In the second phase, group composition was altered so that only single species were reconditioned, composed of individuals previously paired with the same or the other species. In the first phase, in the single‐species groups, Nile tilapia rapidly formed an association between the visual cue and food, whereas common carp failed to do so. In mixed‐species groups, both Nile tilapia and common carp associated a visual cue with food. In the second phase of the study, Nile tilapia retained that ability irrespective of whether they had previously been trained in single‐species or mixed‐species groups, common carp previously trained with Nile tilapia, were not repelled by the blinking blue light and gradually approached it from a distance, whereas common carp previously trained in homogenous groups continued to be repelled by the blinking light. Fish arrivals and departures from the feeding zones as well as fish position in the testing apparatus were analysed and contrasted in single‐species and mixed‐species groups outside the training sessions, revealing mutual impacts of one species on the other in mixed‐species groups. The findings of this study demonstrated interspecific social facilitation of learning to associate a visual cue with food.
Comparison of spatial variation in otolith chemistry of two fish species and relationships with water chemistry and otolith growth
Authors: Hamer P. A. , Jenkins G. P.
Published: October 2007

Spatial variation in the chemistry (Mg, Mn, Sr and Ba) of recently deposited otolith material (last 20–30 days of life) was compared between two demersal fish species; snapper Pagrus auratus (Sparidae) and sand flathead Platycephalus bassensis (Platycephalidae), that were collected simultaneously at 12 sites across three bays in Victoria, south‐eastern Australia. Otolith chemistry was also compared with ambient water chemistry and among three sampling positions adjacent to the proximal otolith margin. For both species, variation in otolith chemistry among bays was significant for Ba, Mn and Sr; however, differences among bays were only similar between species for Ba and Mn. Only Ba showed significant variation at the site level. Across the 12 sites, mean otolith Ba levels were significantly positively correlated between species. Further, although incorporation rates differed, mean ambient Ba levels for both species were positively correlated with ambient Ba levels. Spatial variation in multi‐element otolith chemistry was also broadly similar between species and with multi‐element water chemistry. Partition coefficients clearly indicated species‐specific incorporation of elements into otoliths. Mg and Mn were consistently higher in snapper than sand flathead otoliths (mean ±s.d., Mg snapper 22·1 ± 3·8 and sand flathead 9·9 ± 1·5 μg g−1, Mn snapper 4·4 ± 2·6 and sand flathead 0·5 ± 0·3 μg g−1), Sr was generally higher in sand flathead otoliths (sand flathead 1570 ± 235 and snapper 1346 ± 104 μg g−1) and Ba was generally higher in snapper otoliths (snapper 12·1 ± 12·8 and sand flathead 1·8 ± 1·4 μg g−1). For both species, Mg and Mn were higher in the faster accreting regions of the otolith margin, Sr was lower in the slower accreting region and Ba showed negligible variation among the three sampling regions. This pattern was consistent with the higher Mg and Mn, and generally lower Sr observed in the faster accreting snapper otoliths. It is hypothesized that the differences between species in the incorporation of these elements may be at least partly related to differences in metabolic and otolith accretion rate. Although rates of elemental incorporation into otoliths appear species specific, for elements such as Ba where incorporation appears consistently related to ambient concentrations, spatial variation in otolith chemistry should show similarity among co‐occurring species.
Identification and characterization of a novel splice variant of gonadotropin α subunit in the common carp Cyprinus carpio
Authors: Wang Y. , Hu W. , Liu W.‐y. , Wang Y.‐p. , Zhu Z.‐y.
Published: October 2007

In this study, an alternative splicing transcript GtH‐α291 was identified by RT‐PCR, which is 291 nt and exists not only in the pituitary but also in the ovary in common carp Cyprinus carpio. The analysis of GtH‐α291 amino acid sequence by the SignalP server predicted that the ‘missing segment’ might characterize as a signal peptide. In the secretion experiment, GtH‐α357 subunit could be secreted out of HeLa cells while GtH‐α291 could not, which confirmed the prediction. Co‐immunoprecipitation assay proved that GtH‐α291 subunit is able to interact with both FSH‐β and LH‐β as GtH‐α357 does. This is the first report concerning an alternative splicing transcript of a GtH α subunit. Further studies are necessary to elucidate the specific role of this variant in the regulation of gonadal development and sexual maturation.
Sulphur, thiols, and disulphides in the fish epidermis, with remarks on keratinization
Authors: Meyer W. , Seegers U. , Stelzer R.
Published: October 2007

Energy dispersive x‐ray (EDX) analysis and qualitative and quantitative histochemistry were applied to study the distribution and contents of sulphur, thiols and disulphides in the epidermis of the river lamprey Lampetra fluviatilis, the lesser spotted dogfish Scyliorhinus canicula and the brown trout Salmo trutta fario. Thiols generally reacted weakly throughout the entire epidermis, whereas disulphide reactions were more distinct and differentiated. In the river lamprey, the concentrations of ‐S‐S‐ groups clearly increased in the developing mucous cells from the stratum basale to the stratum superficiale; skein cells and granular cells reacted negatively to weakly. In the lesser spotted dogfish, amounts of disulphides appeared at moderate concentrations, and only goblet cells displayed a strong reaction. In the brown trout, filament cells showed low concentrations or weak reactions of disulphides, goblet cells and the most outer superficial cells stained strongly. Sulphur distribution and contents generally supported the histochemical observations in normal epidermis cells (absolute sulphur contents: 41–59 mM), only the brown trout showed high amounts of sulphur in the stratum basale (81 mM). The findings corroborate the view that there is an inverse correlation between keratinization and mucous secretion in normal fish epidermis. The sometimes distinct contents of disulphides in the outer mucous layer indicate that this system could endure higher mechanical stress than predictable from its large amounts of neutral glycoproteins.
Abnormal hermaphroditism in the multispine skate Bathyraja multispinis (Chondrichthyes, Rajidae)
Authors: Scenna L. B. , Díazde Astarloa J. M. , Cousseau M. B.
Published: October 2007

A hermaphroditic individual of the multispine skate, Bathyraja multispinis, caught on the Argentinean continental shelf, is described. This is the first record of hermaphroditism in the genus Bathyraja and one of the very few hermaphroditic specimens reported in the Rajidae.
Occurrence of Pleuroscopus pseudodorsalis Barnard, 1927 (Uranoscopidae) near Rio Grande Plateau, western South Atlantic
Authors: Mincarone M. M. , Bernardes R. A. , Peppes F. V.
Published: October 2007

The first record of the uranoscopid Pleuroscopus pseudodorsalis from the western South Atlantic, near Rio Grande Plateau, is based on the unusual collection of a specimen by pelagic longline. The species was previously known only off southern Africa and Australasia.
Concomitant activation of AKT with extracellular‐regulated kinase 1/2 occurs independently of PTEN or PIK3CA mutations in endometrial cancer and may be associated with favorable prognosiss
Authors: Mori Noriko , Kyo Satoru , Sakaguchi Junko , Mizumoto Yasunari , Ohno Satoshi , Maida Yoshiko , Hashimoto Manabu , Takakura Masahiro , Inoue Masaki
Published: October 2007

Deregulated signaling via the phosphatidylinositol 3‐kinase (PI3K) pathway is common in many types of cancer, but its clinicopathological significance in endometrial cancer remains unclear. In the present study, we examined the status of the PI3K signaling pathway, especially in relation to PTEN and PIK3CA status, in endometrioid‐type endometrial cancer. The immunohistochemical analysis revealed a high level of phosphorylated (p)‐AKT expression, which is a hallmark of activated PI3K signaling, in approximately 60% of endometrial cancers. There was no correlation between p‐AKT expression and clinicopathological characteristics, such as International Federation of Gynecology and Obstetrics stage, tumor grade, and myometrial invasion. Unexpectedly, a high level of p‐AKT expression occurred independently of the presence of PTEN or PIK3CA mutations. Furthermore, p‐AKT expression did not correlate with the expression of potential downstream targets, including p‐mTOR and p‐FOXO1/3a. In turn, p‐AKT expression was strongly associated with extracellular‐regulated kinase 1/2 expression (P = 0.0031), which is representative of the activated RAS–MAP kinase pathway. Kaplan–Meier analysis suggested that low p‐AKT expression was associated with low rates of relapse‐free survival, although the difference was not statistically significant, indicating that AKT activation does not confer worse prognosis. The present study demonstrates the presence of complex signaling pathways that might mask the conventional tumorigenic PTEN–PI3K–AKT–mTOR pathway, and strongly suggests a close association between the extracellular‐regulated kinase and PI3K pathways in this tumor type. (Cancer Sci 2007; 98: 1881–1888)
Community pharmacies and the provision of opioid substitution services for drug misusers: changes in activity and attitudes of community pharmacists across England 1995–2005
Authors: Sheridan Janie , Manning Victoria , Ridge Gayle , Mayet Soraya , Strang John
Published: October 2007

Aims  In England, the role of community pharmacy in service provision to drug misusers was studied in 1995. Extensive involvement was identified, and considerable underused capacity was noted. This study explores these and potential new roles 10 years on.

Design  Cross‐sectional national study. Postal survey (three mailshots), plus a fourth telephone follow‐up using a structured questionnaire based on the 1995 questionnaire.

Setting  Community pharmacies in England.

Measurements  Involvement in opioid substitution therapy services (e.g. methadone, buprenorphine) and related activities. Attitudes towards service provision and novel services.

Findings  A 95% response rate was obtained. This was higher than in 1995, due largely to the use of a telephone follow‐up. There had been an increase in the proportion providing substitution therapy dispensing services from 51% to 63% and in the average current case‐load (from 5.9 to 9.2); and consequently a large increase in the numbers being treated (approximately × 1.9). Similarly, supervised consumption of methadone and buprenorphine was being provided more widely (increasing from 0 to 59% of all responding pharmacists). Attitudes towards existing roles were more positive than in 1995, and providers tended to be more positive than non‐providers. For newer roles (e.g. supervise medications for comorbidity; provide hepatitis B vaccination), there was support from around one‐quarter of respondents.

Conclusion  Community pharmacy continues to play an important role in delivering treatment, including prescribing services, to drug misusers. There still appears to be untapped capacity, and moderate support for newer roles.
From microscopic minerals to global climate change?
Authors: Brown David J. , Lee Martin
Published: October 2007

The study of minerals is often focused on their crystallographic properties, chemistry and economic importance, and so their breakdown, or ‘weathering’. by physical, chemical and biological processes is less well understood. However, mineral weathering is of considerable environmental significance. The interaction of minerals with water and microbes, such as algae and bacteria, controls soil fertility, the transportation of pollutants through the ground, and ultimately the removal of CO2 from the atmosphere over geological timescales. Therefore, minerals are a key factor in moderating global climate change. This article introduces conventional and new techniques that are being used by geologists to investigate these processes.
Phylogeny and historical biogeography of the cave‐adapted shrimp genus Typhlatya (Atyidae) in the Caribbean Sea and western Atlantic
Authors: Hunter Rebecca L. , Webb Michael Scott , Iliffe Thomas M. , Bremer Jaime R. Alvarado
Published: October 2007

Aim  To infer phylogenetic relationships among five species of the cave‐adapted shrimp genus Typhlatya in order to test competing hypotheses of dispersal and colonization of the disjunct cave localities occupied by these five species.

Location  Typhlatya species are found in caves and anchialine ponds across the northern margin of the Caribbean Sea, along the Mediterranean and Adriatic coasts and on oceanic islands in the Atlantic and eastern Pacific oceans. This study focuses on five species, one from Bermuda, one from the Caicos Islands and three from the Yucatan Peninsula of Mexico.

Methods  Partial sequences (c. 1400 bp) from the mitochondrial cytochrome b, 16S rDNA and COI genes were obtained from representative samples of the five species. Phylogenetic inference was carried out with maximum parsimony and maximum likelihood analyses. Parsimony networks were constructed for the Bermudian species Typhlatya iliffei and one Yucatan species Typhlatya mitchelli, to determine the degree of connectivity among populations inhabiting different cave systems.

Results  All three land masses were recovered as monophyletic. The two insular marine species from Bermuda and the Caicos Islands formed a clade, while the three continental freshwater species from the Yucatan Peninsula formed another. Within both Bermuda and the Yucatan, shared haplotypes were found in different cave systems, suggesting recent or ongoing gene flow among populations in both locales.

Main conclusions  The two insular marine Typhlatya species originated from an ancestral marine population, possibly already cave‐adapted, that is suggested to have colonized the Caicos Islands and subsequently dispersed to Bermuda via the Gulf Stream. Divergence estimates suggest that colonization occurred before the formation of present‐day anchialine cave habitat, which did not form on either island until the late Pliocene to early Pleistocene. Divergence estimates also indicate that the Yucatan freshwater species split before the formation of freshwater cave habitat in the Yucatan. These species could have inhabited crevicular marine habitats before the late Pliocene/early Pleistocene in the Yucatan or elsewhere in the Caribbean, and subsequently migrated to freshwater caves once they formed.
Environmental setting of human migrations in the circum‐Pacific region
Authors: Pope Kevin O. , Terrell John E.
Published: October 2007

Aim  To assess the genetic and archaeological evidence for the migration of modern humans out of Africa to the circum‐Pacific region and compare the migration patterns with Late Pleistocene and Holocene changes in sea level and climate.

Location  Southern and eastern Asia, Australia, and Oceania.

Methods  Review of the literature and detailed compilations of data on early human settlements, sea level, and climate change.

Results  The expansion of modern humans out of Africa, following a coastal route into southern Asia, was initially thwarted by a series of large and abrupt environmental changes. A period of relatively stable climate and sea level from c. 45,000 yr bp to 40,000 yr bp supported a rapid coastal expansion of modern humans throughout much of Southeast Asia, enabling them to reach the coasts of northeast Russia and Japan by 38,000–37,000 yr bp. Further northwards, migrations were delayed by cold northern climates, which began to deteriorate rapidly after 33,000 yr bp. Human migrations along the coast of the Bering Sea into the New World appear to have occurred much later, c. 14,000 yr bp, probably by people from central Asia who were better adapted to cold northern climates. Cold, dry climates and rapidly changing sea levels leading into and out of the Last Glacial Maximum inhibited coastal settlement, and many of the sites occupied prior to 33,000 yr bp were abandoned. After 16,000 yr bp, the sea‐level rise slowed enough to permit coastal ecosystems to develop and coasts to be re‐colonized, but abrupt changes in climate and sea level inhibited this development until after 12,000 yr bp. Between 12,000 yr bp and 7000 yr bp there was a dramatic increase in reef and estuary/lagoon ecosystems, concurrent with a major expansion of coastal settlements. This early Holocene increase in coastal environments and the concomitant expansion of human coastal‐resource exploitation were followed by corresponding declines in both phenomena in the mid‐Holocene, c. 6000–4000 yr bp. This decline in coastal resources is linked to the drop in sea level throughout the Pacific, which may have caused the widespread population dislocations that ultimately led to the human expansion throughout Oceania.

Main conclusions  Climate and sea‐level changes played a central role in the peopling of the circum‐Pacific region.
A controlled trial of an educational programme for people with Parkinson's disease
Authors: Lindskov Susanne , Westergren Albert , Hagell Peter
Published: October 2007

Aims and objective.  To evaluate patient‐reported health outcomes of a multidisciplinary group educational programme for people with Parkinson's disease (PD), delivered as part of routine clinical practice.

Background.  Studies suggest that educational programmes for people with PD have potential to improve patients’ perceived health and well‐being. However, controlled trials of multidisciplinary group educational programmes are lacking.

Design.  Naturalistic non‐randomized controlled trial.

Methods.  Following ethical approval and informed consent, 48 people with PD (58% men; mean age, 69·3) received the intervention and 48 (52% men; mean age, 72) were allocated to a delayed intervention control group. The intervention was a six‐week (two hours per week) multidisciplinary group educational programme. Patient‐reported health outcomes were assessed by the 12‐item short‐form health survey (SF‐12) at baseline and one month postintervention.

Results.  Changes in SF‐12 scores at follow‐up did not differ between the groups and there were no within‐group differences over time. Daily dopaminergic medication increased in the control group but not in the intervention group.

Conclusions.  Slightly, but significantly, increased drug requirement in the control group may in part have masked deterioration in perceived health. However, failure to demonstrate improved patient‐reported health may relate to the intervention design, response shift (i.e. change in how people perceive their health), and/or quality and choice of outcome measures. Further studies that take these aspects into consideration are needed to determine the potential for patient education interventions in PD.

Relevance to clinical practice.  Nurses and other healthcare professionals need to document the effects of patient educational programmes and to be aware of the importance of intervention design and challenges associated with evaluating programme outcomes. Otherwise, there is a risk that benefits cannot be demonstrated and that decision makers will not invest resources in interventions that actually are beneficial for chronically ill people.
Genetic structure in a tropical lek‐breeding bird, the blue manakin (Chiroxiphia caudata) in the Brazilian Atlantic Forest
Authors: FRANCISCO MERCIVAL R. , GIBBS H. LISLE , GALETTI MAURO , LUNARDI VITOR O. , JUNIOR PEDRO M. GALETTI
Published: October 2007

Determining the genetic structure of tropical bird populations is important for assessing potential genetic effects of future habitat fragmentation and for testing hypotheses about evolutionary mechanisms promoting diversification. Here we used 10 microsatellite DNA loci to describe levels of genetic differentiation for five populations of the lek‐mating blue manakin (Chiroxiphia caudata), sampled along a 414‐km transect within the largest remaining continuous tract of the highly endangered Atlantic Forest habitat in southeast Brazil. We found small but significant levels of differentiation between most populations.FSTvalues varied from 0.0 to 0.023 (overallFST = 0.012) that conformed to a strong isolation by distance relationship, suggesting that observed levels of differentiation are a result of migration–drift equilibrium.Nemvalues estimated using a coalescent‐based method were small (≤ 2 migrants per generation) and close to the minimum level required to maintain genetic similarity between populations. An implication of these results is that if future habitat fragmentation reduces dispersal between populations to even a small extent, then individual populations may undergo a loss of genetic diversity due to an increase in the relative importance of drift, since inbreeding effective population sizes are relatively small (Ne~1000). Our findings also demonstrate that population structuring can occur in a tropical bird in continuous habitat in the absence of geographical barriers possibly due to behavioural features of the species.
Comparative phylogeography and speciation of dung beetles from the Australian Wet Tropics rainforest
Authors: BELL KAREN L. , MORITZ CRAIG , MOUSSALLI ADNAN , YEATES DAVID K.
Published: October 2007

In tropical rainforests, insects show especially high species richness and local endemism of species relative to vertebrates. One possible cause is that insects respond to historical fluctuations of rainforests on a smaller spatial scale than do vertebrates. To evaluate this hypothesis, we combine environmental niche models and mitochondrial DNA phylogeography for two pairs of sister species of the dung beetle genus Temnoplectron (T. aeneopiceum–T. subvolitans and T. politulum–T. reyi) from the rainforests of northeastern Australia, where climate‐driven rainforest fluctuations in the Quaternary have strongly influenced genetic and species diversity of vertebrates. Within both species pairs, the bioclimatic niche was conserved, but the T. aeneopiceum–T. subvolitans species pair had the narrower environmental range, and thus more restricted potential distribution. Coalescent analyses indicated Late Pliocene or Early Pleistocene divergences for both species pairs, and earlier speciation in (T. aeneopiceum–T. subvolitans) than in (T. politulum–T. reyi). Phylogeographic structure in (T. aeneopiceum–T. subvolitans) was more pronounced than in (T. politulum–T. reyi), with significant isolation‐by‐distance in the former species‐pair only. Nested clade and coalescence analyses indicated local range expansions for the T. aeneopiceum–subvolitans species pair and range‐wide expansion for both T. politulum and T. reyi. We suggest that stronger phylogeographic structure and earlier divergence in (T. aeneopiceum–T. subvolitans) than in (T. politulum–T. reyi) reflects a stronger influence of environmental barriers to gene flow under the present climate and greater sensitivity to warmer and drier periods of the Quaternary. The two species pairs evidently responded to Quaternary rainforest fluctuations at spatial scales similar to those seen within low‐vagility species of vertebrate. Despite this similarity of scale, these insect lineages are reproductively isolated at parapatric boundaries, whereas analogous lineages of vertebrates often are not. We suggest that rapid evolution of genitalia may facilitate geographic speciation in rainforest beetles.
Rangewide phylogeography in the greater horseshoe bat inferred from microsatellites: implications for population history, taxonomy and conservation
Authors: ROSSITER STEPHEN J. , BENDA PETR , DIETZ CHRISTIAN , ZHANG SHUYI , JONES GARETH
Published: October 2007

The distribution of genetic variability across a species’ range can provide valuable insights into colonization history. To assess the relative importance of European and Asian refugia in shaping current levels of genetic variation in the greater horseshoe bats, we applied a microsatellite‐based approach to data collected from 56 localities ranging from the UK to Japan. A decline in allelic richness from west Asia to the UK and analyses of FST both imply a northwestward colonization across Europe. However, sharp discontinuities in gene frequencies within Europe and between the Balkans and west Asia (Syria/Russia) are consistent with suture zones following expansion from multiple refugia, and a lack of recent gene flow from Asia Minor. Together, these results suggest European populations originated from west Asia in the ancient past, and experienced a more recent range expansion since the Last Glacial Maximum. Current populations in central Europe appear to originate from the Balkans and those from west Europe from either Iberia and/or Italy. Comparisons of RST and FST suggest that stepwise mutation has contributed to differentiation between island and continental populations (France/UK and China/Japan) and also among distant samples. However, pairwise RST values between distant populations appear to be unreliable, probably due to size homoplasy. Our findings also highlight two priorities for conservation. First, stronger genetic subdivision within the UK than across 4000 km of continental Eurasia is most likely the result of population fragmentation and highlights the need to maintain gene flow in this species. Second, deep splits within China and between Europe and China are indicative of cryptic taxonomic divisions which need further investigation.