bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermodynamic model for growth mechanisms of multiwall carbon nanotubes
Authors: Kaatz F. H. , Siegal M. P. , Overmyer D. L. , Provencio P. P. , Tallant D. R.
Published: December 2006

Multiwall carbon nanotubes are grown via thermal chemical vapor deposition between temperatures of 630 and 830°C using acetylene in nitrogen as the carbon source. This process is modeled using classical thermodynamics to explain the total carbon deposition as a function of time and temperature. An activation energy of 1.60eV is inferred for nanotube growth after considering the carbon solubility term. Scanning electron microscopy shows growth with diameters increasing linearly with time. Transmission electron microscopy and Raman spectroscopy show multiwall nanotubes surrounded by a glassy-carbon sheath, which grows with increasing wall thickness as growth temperatures and times rise.
Synthesis of (K0.5Bi0.5)0.4Ba0.6TiO3 nanowires and ceramics by sol-gel–hydrothermal method
Authors: Hou Yudong , Hou Lei , Zhu Mankang , Yan Hui
Published: December 2006

( K 0.5 Bi 0.5 ) 0.4 Ba 0.6 Ti O 3 nanowires have been fabricated by a sol-gel–hydrothermal method at 200°C. X-ray diffraction result shows that the nanowires have a tetragonal perovskite structure. Transmission electron microscopy investigations exhibit that the as-prepared nanowires are single crystalline grains with diameters of about 40nm and lengths reaching up to 800nm. The (K0.5Bi0.5)0.4Ba0.6TiO3 ceramics with a relative density of 97% can be fabricated from the high quality nanowires even by a conventional sintering process, which showed that typical characteristics of relaxor ferroelectrics, the indicator of degree of diffuseness γ and Curie temperature TC (100kHz), were 1.65 and 220°C, respectively.
Room-temperature weak ferromagnetism of amorphous HfAlOx thin films deposited by pulsed laser deposition
Authors: Qiu X. Y. , Liu Q. M. , Gao F. , Lu L. Y. , Liu J.-M.
Published: December 2006

The room-temperature weak ferromagnetism of amorphous HfAlOx thin films deposited by pulsed laser deposition on various substrates in oxygen-defective ambient is demonstrated. The magnetization is independent of film thickness, but depends on substrates and deposition temperatures. A magnetic moment of ∼0.26μB per HfAlOx f.u. is recorded for HfAlOx films deposited under optimized conditions [deposited at 600°C on (001) sapphire in high vacuum]. It is argued that interfacial defects are one of the possible sources of the weak ferromagnetism.
Stress dependence of ferromagnetic resonance and magnetic anisotropy in a thin NiMnSb film on InP(001)
Authors: Botters Bernhard , Giesen Fabian , Podbielski Jan , Bach Peter , Schmidt Georg , Molenkamp Laurens W. , Grundler Dirk
Published: December 2006

The authors have investigated the effect of stress on the room-temperature magnetism of a 10nm thick Heusler-alloy film NiMnSb grown epitaxially on InP. Tensile stress, which the authors applied externally along the easy axis using a piezostack, is shown to reduce the coercivity and the anisotropy coefficient. Using broadband ferromagnetic resonance measurements, the authors find that a relative variation in the lattice constant as small as 0.08% changes the in-plane uniaxial anisotropy by 20%. This explains the significant variation of anisotropy with film thickness, which was recently reported for NiMnSb.
Giant electrocaloric effect in the thin film relaxor ferroelectric 0.9PbMg1∕3Nb2∕3O3–0.1PbTiO3 near room temperature
Authors: Mischenko A. S. , Zhang Q. , Whatmore R. W. , Scott J. F. , Mathur N. D.
Published: December 2006

The authors have recently observed a giant electrocaloric effect (12K in 25V) in 350nm sol-gel PbZr0.95Ti0.05O3 films near the ferroelectric Curie temperature of 242°C. Here the authors demonstrate a giant electrocaloric effect (5K in 25V) in 260nm sol-gel films of the relaxor ferroelectric 0.9PbMg1∕3Nb2∕3O3–0.1PbTiO3 near the Curie temperature of 60°C. This reduction in operating temperature widens the potential for applications in cooling systems.
Thermophysical and elastic properties of Cu50Zr50 and (Cu50Zr50)95Al5 bulk-metallic-glass-forming alloys
Authors: Fan G. J. , Freels M. , Choo H. , Liaw P. K. , Li J. J. Z. , Rhim Won-Kyu , Johnson W. L. , Yu P. , Wang W. H.
Published: December 2006

By employing a containerless high-temperature high-vacuum electrostatic levitation technique, the thermophysical properties, including the ratio between the specific heat capacity and the hemispherical total emissivity, the specific volume, and the viscosity, of Cu50Zr50 and (Cu50Zr50)95Al5 bulk-metallic-glass (BMG)-forming liquids have been measured. Compared with Cu50Zr50, the improved glass-forming ability of (Cu50Zr50)95Al5 can be attributed to its dense liquid structure and its high value of viscosity. Additionally, the relationship between the viscosity of various BMG forming liquids at the melting temperature and the elastic properties of the corresponding glasses at room temperature will be compared.
Robust detection of hydrogen using differential AlGaN∕GaN high electron mobility transistor sensing diodes
Authors: Wang Hung-Ta , Anderson T. J. , Ren F. , Li Changzhi , Low Zhen-Ning , Lin Jenshan , Gila B. P. , Pearton S. J. , Osinsky A. , Dabiran Amir
Published: December 2006

The use of AlGaN∕GaN high electron mobility transistor (HEMT) differential sensing diodes is shown to provide robust detection of 1% H2 in air at 25°C. The active device in the differential pair is coated with 10nm of Pt to enhance catalytic dissociation of molecular hydrogen, while the reference diode is coated with Ti∕Au. The active diode in the pair shows an increase in forward current of several milliamperes at a bias voltage of 2.5V when exposed to 1% H2 in air. The HEMT diodes show a response approximately twice that of GaN Schottky diodes, due to the presence of piezoelectric and spontaneous polarization in the heterostructure. The use of the differential pair removes false alarms due to ambient temperature variations.
Triphenylamine-functionalized rhenium (I) complex as a highly efficient yellow-green emitter in electrophosphorescent devices
Authors: Liu Chunbo , Li Jiang , Li Bin , Hong Ziruo , Zhao Feifei , Liu Shiyong , Li Wenlian
Published: December 2006

A complex (3-ethyl-2-(4′-triphenylamino)imidazo[4,5-f] 1,10-phenanthroline) Re(CO)3Br functionalized by a hole-transport group triphenylamine was used to fabricate organic light-emitting devices (OLEDs). A current efficiency up to 17.6cd∕A corresponding to a power efficiency of 9.2ml∕W and a peak brightness as high as 6500cd∕m2 were obtained. These results represent the best values reported for OLEDs based on rhenium complexes. Enhanced carrier injection capability of Re complex and efficient charge-trapping formation followed by triplet exciton confinement in the emissive layer make for the outstanding electrophosphorescent performances.
Vertical injection thin-film AlGaN∕AlGaN multiple-quantum-well deep ultraviolet light-emitting diodes
Authors: Zhou L. , Epler J. E. , Krames M. R. , Goetz W. , Gherasimova M. , Ren Z. , Han J. , Kneissl M. , Johnson N. M.
Published: December 2006

Vertically injected thin-film ultraviolet light-emitting diodes operating at 325 and 280nm are demonstrated. Low-temperature AlN interlayers allow crack-free growth of AlxGa1−xN with compositions up to x=0.53 on GaN-on-sapphire templates. The GaN layer allows laser-induced separation of the highly strained epi stack from the sapphire substrate with high yield. Cathode contacts are formed on nitrogen-face AlxGa1−xN (up to x=0.53) and allow vertical injection of current into the active region. Controlled roughening of the nitrogen-face AlxGa1−xN is also demonstrated through photoelectrochemical etching and results in >2.5× light extraction gain for 325 and 280nm devices.
Multiple intermediates in SNARE-induced membrane fusion
Authors: Yoon Tae-Young , Okumus Burak , Zhang Fan , Shin Yeon-Kyun , Ha Taekjip
Published: December 2006

Membrane fusion in eukaryotic cells is thought to be mediated by a highly conserved family of proteins called SNAREs (soluble
N
-ethyl maleimide sensitive-factor attachment protein receptors). The vesicle-associated v-SNARE engages with its partner t-SNAREs on the target membrane to form a coiled coil that bridges two membranes and facilitates fusion. As demonstrated by recent findings on the hemifusion state, identifying intermediates of membrane fusion can help unveil the underlying fusion mechanism. Observation of SNARE-driven fusion at the single-liposome level has the potential to dissect and characterize fusion intermediates most directly. Here, we report on the real-time observation of lipid-mixing dynamics in a single fusion event between a pair of SNARE-reconstituted liposomes. The assay reveals multiple intermediate states characterized by discrete values of FRET between membrane-bound fluorophores. Hemifusion, flickering of fusion pores, and kinetic transitions between intermediates, which would be very difficult to detect in ensemble assays, are now identified. The ability to monitor the time course of fusion events between two proteoliposomes should be useful for addressing many important issues in SNARE-mediated membrane fusion.
Calorie restriction up-regulates the plasma membrane redox system in brain cells and suppresses oxidative stress during aging
Authors: Hyun Dong-Hoon , Emerson Scott S. , Jo Dong-Gyu , Mattson Mark P. , de Cabo Rafael
Published: December 2006

The plasma membrane (PM) contains redox enzymes that provide electrons for energy metabolism and recycling of antioxidants such as coenzyme Q and α-tocopherol. Brain aging and neurodegenerative disorders involve impaired energy metabolism and oxidative damage, but the involvement of the PM redox system (PMRS) in these processes is unknown. Caloric restriction (CR), a manipulation that protects the brain against aging and disease, increased activities of PMRS enzymes (NADH-ascorbate free radical reductase, NADH-quinone oxidoreductase 1, NADH-ferrocyanide reductase, NADH-coenzyme Q10 reductase, and NADH-cytochrome
c
reductase) and antioxidant levels (α-tocopherol and coenzyme Q10) in brain PM during aging. Age-related increases in PM lipid peroxidation, protein carbonyls, and nitrotyrosine were attenuated by CR, levels of PMRS enzyme activities were higher, and markers of oxidative stress were lower in cultured neuronal cells treated with CR serum compared with those treated with ad libitum serum. These findings suggest important roles for the PMRS in protecting brain cells against age-related increases in oxidative and metabolic stress.
Evolutionary theory for modifiers of epistasis using a general symmetric model
Authors: Liberman Uri , Feldman Marcus W.
Published: December 2006

Genetic interactions in fitness are studied by using modifier theory. The effects on fitness of two linked genes are perturbed by alleles at a third linked locus that controls the extent of epistasis in fitness between the first two. This epistasis is determined by a symmetric interaction matrix, and it is shown that a modifier allele that increases epistasis will invade when the linkage between the other two genes is sufficiently tight and these genes are in linkage disequilibrium. With linkage equilibrium among the major loci, increased or decreased epistasis may evolve depending on the allele frequencies at these loci.
Segmentation and intensity estimation of microarray images using a gamma-t mixture model
Authors: Baek Jangsun , Son Young Sook , McLachlan Geoffrey J.
Published: December 2006

Motivation: We present a new approach to the analysis of images for complementary DNA microarray experiments. The image segmentation and intensity estimation are performed simultaneously by adopting a two-component mixture model. One component of this mixture corresponds to the distribution of the background intensity, while the other corresponds to the distribution of the foreground intensity. The intensity measurement is a bivariate vector consisting of red and green intensities. The background intensity component is modeled by the bivariate gamma distribution, whose marginal densities for the red and green intensities are independent three-parameter gamma distributions with different parameters. The foreground intensity component is taken to be the bivariate t distribution, with the constraint that the mean of the foreground is greater than that of the background for each of the two colors. The degrees of freedom of this t distribution are inferred from the data but they could be specified in advance to reduce the computation time. Also, the covariance matrix is not restricted to being diagonal and so it allows for nonzero correlation between R and G foreground intensities. This gamma-t mixture model is fitted by maximum likelihood via the EM algorithm. A final step is executed whereby nonparametric (kernel) smoothing is undertaken of the posterior probabilities of component membership.

The main advantages of this approach are: (1) it enjoys the well-known strengths of a mixture model, namely flexibility and adaptability to the data; (2) it considers the segmentation and intensity simultaneously and not separately as in commonly used existing software, and it also works with the red and green intensities in a bivariate framework as opposed to their separate estimation via univariate methods; (3) the use of the three-parameter gamma distribution for the background red and green intensities provides a much better fit than the normal (log normal) or t distributions; (4) the use of the bivariate t distribution for the foreground intensity provides a model that is less sensitive to extreme observations; (5) as a consequence of the aforementioned properties, it allows segmentation to be undertaken for a wide range of spot shapes, including doughnut, sickle shape and artifacts.

Results: We apply our method for gridding, segmentation and estimation to cDNA microarray real images and artificial data. Our method provides better segmentation results in spot shapes as well as intensity estimation than Spot and spotSegmentation R language softwares. It detected blank spots as well as bright artifact for the real data, and estimated spot intensities with high-accuracy for the synthetic data.

Availability: The algorithms were implemented in Matlab. The Matlab codes implementing both the gridding and segmentation/estimation are available upon request.

Contact:  jbaek@chonnam.ac.kr

Supplementary information: Supplementary material is available at Bioinformatics online.
Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies
Authors: Haarer Brian , Viggiano Susan , Hibbs Mathew A. , Troyanskaya Olga G. , Amberg David C.
Published: December 2006

Multigenic influences are major contributors to human genetic disorders. Since humans are highly polymorphic, there are a high number of possible detrimental, multiallelic gene pairs. The actin cytoskeleton of yeast was used to determine the potential for deleterious bigenic interactions; ∼4800 complex hemizygote strains were constructed between an actin-null allele and the nonessential gene deletion collection. We found 208 genes that have deleterious complex haploinsufficient (CHI) interactions with actin. This set is enriched for genes with gene ontology terms shared with actin, including several actin-binding protein genes, and nearly half of the CHI genes have defects in actin organization when deleted. Interactions were frequently seen with genes for multiple components of a complex or with genes involved in the same function. For example, many of the genes for the large ribosomal subunit (RPLs) were CHI with act1Δ and had actin organization defects when deleted. This was generally true of only one RPL paralog of apparently duplicate genes, suggesting functional specialization between ribosomal genes. In many cases, CHI interactions could be attributed to localized defects on the actin protein. Spatial congruence in these data suggest that the loss of binding to specific actin-binding proteins causes subsets of CHI interactions.
The role of the proteasomal ATPases and activator monoubiquitylation in regulating Gal4 binding to promoters
Authors: Ferdous Anwarul , Sikder Devanjan , Gillette Thomas , Nalley Kip , Kodadek Thomas , Johnston Stephen Albert
Published: December 2006

Recent studies have shown that the intersection between transcription and proteins involved in the ubiquitin–proteasome pathway encompasses both proteolytic and nonproteolytic functions. Examples of the latter type include evidence that monoubiquitylation of some transcriptional activators stimulates their activity. In addition, the proteasomal ATPases are recruited to many active promoters through binding to activators and play an important, nonproteolytic role in promoter escape and elongation. In this study, we report the discovery of a new nonproteolytic activity of the proteasome (specifically the proteasomal ATPases): the active destabilization of activator–promoter complexes. This reaction depends on the presence of an activation domain and ATP. Destabilization is inhibited in vitro and in vivo if the protein is monoubiquitylated or if ubiquitin is genetically fused to the activator. The fact that monoubiquitylated activator is resistant to the “stripping” activity of the proteasomal ATPases may explain, in part, why some activators require this modification in order to function efficiently.
Readiness for change and drug use outcomes after treatment
Authors: Gossop Michael , Stewart Duncan , Marsden John
Published: December 2006

Aims  The present study represents the first large‐scale test of the capacity to predict illicit drug treatment outcomes of an instrument [Stages of Change and Treatment Eagerness Scale (SOCRATES)] purporting to measure processes underlying stages of change. The main hypothesis was that ‘taking steps’ should be predictive of less frequent use of illicit opiates (heroin and non‐prescribed methadone) at follow‐up.

Design  The sample comprised 1075 people seeking treatment for drug abuse problems in 54 treatment agencies in England. The study uses a longitudinal, prospective cohort design. Structured interviews were conducted at treatment intake and at 1‐year follow‐up. Data were collected about illicit drug use (frequency of use of heroin, non‐prescribed methadone, cocaine and amphetamines, and non‐prescribed benzodiazepines) and other problems.

Findings  Results failed to support the hypothesis that taking steps should be associated with less frequent use of illicit opiates at follow‐up. No statistically significant associations of any kind were found between readiness for change measures and use of opiates or stimulants at follow‐up. A negative association was found between taking steps and benzodiazepine misuse. Readiness for change measures were correlated with heroin use and psychiatric symptom scores at treatment intake.

Conclusions  Readiness for change measures were not associated with illicit drug use outcomes. Of the 12 hypothesized relationships between readiness for change measures and outcomes, our results show only one ‘hit’ and 11 ‘misses’.
Excessive alcohol consumption is associated with reduced quality of life among methadone patients
Authors: Senbanjo Richard , Wolff Kim , Marshall Jane
Published: December 2006

Aim  To evaluate the impact of excessive alcohol consumption on the health‐related quality of life of patients receiving methadone treatment for opioid dependence.

Design  A cross‐sectional survey.

Participants  One hundred and ninety‐two patients attending out‐patient methadone clinics in the south‐east of England, United Kingdom.

Measurements  Quality of life (QoL) was assessed using the Medical Outcomes Study: General Health Survey, Short Form (SF‐12). Alcohol consumption was assessed using the Alcohol Use Disorders Identification Test (AUDIT).

Findings  Approximately one‐third of the sample (57/192) were AUDIT‐positive (score ≥ 8) and 20 of the 135 AUDIT‐negative patients reported past history of alcohol problems. AUDIT‐positive patients were less satisfied with their methadone dose than AUDIT‐negative patients (P = 0.002), despite having a higher dose. AUDIT‐positive patients reported more physical (P = 0.020) and psychological (P = 0.034) health problems and poorer QoL (P = 0.008) with an estimated effect size of 0.46. Lower QoL scores for AUDIT‐positive patients affected both ‘physical’ (P = 0.009) and ‘psychological’ (P = 0.012) health domains with poor role functioning (‘role limitation’ due to physical health, P < 0.001 and to emotional health, P = 0.009), social functioning (P = 0.015) and self‐perceived general health (P = 0.029).

Conclusion  Excessive alcohol consumption may be associated with a distinctive pattern of QoL impairment in methadone patients. In addition to advising methadone patients regarding their alcohol consumption, comprehensive care plans should seek to restore normal personal, family and social role functioning through the provision of appropriate health and social care.
Germination responses of the Rubia fruticosa Ait. seed dispersal system in different experimental seasons
Authors: Rodríguez A. , Nogales M. , Nieves C.
Published: December 2006

In this paper, we present results on germination patterns of the seed dispersal system of an endemic Macaronesian plant (Rubia fruticosa). Seeds from this plant are mainly dispersed by endemic lizards and native warblers; therefore, we included three different treatments: control seeds, seeds extracted from lizards and seeds found in warbler droppings. Seeds from the same pool of every treatment were germinated in two different seasons, one in autumn, coinciding with the arrival of the first rains, and another in spring, coinciding with the arrival of the dry season. A clear differential pattern of germination success was observed between the two seasons. Seeds planted in autumn achieved a higher percentage of germination than those sown in spring in all treatments. The great robustness of these results seems to indicate that germination timing is strongly selected in R. fruticosa and this evolutionary trend probably extends to other vascular plants growing in xeric coastal environments of the Macaronesian islands.
Novel methodology for assessment of prophylactic platelet transfusion therapy by measuring increased thrombus formation and thrombin generation
Authors: Cauwenberghs Sandra , Feijge Marion A. H. , Theunissen Evi , Heemskerk Johan W. M. , Van Pampus Elisabeth C. M. , Curvers Joyce
Published: December 2006

Currently, patients developing severe thrombocytopenia during chemotherapy treatment are prophylactically transfused with platelets. We developed two platelet function tests to report the improved haemostasis in the transfused patients, which were capable of detecting aberrant responsiveness of the platelets after transfusion. First, in a whole‐blood flow test, platelet adhesion and thrombus formation were determined under high‐shear flow conditions. Second, the procoagulant function of platelets was assayed in platelet‐rich plasma by measurement of thrombin generation. Experimental conditions were established, where flow‐induced adhesion and thrombin generation test parameters increased semi‐linearly with the platelet concentration, and informed on the activation properties of platelets. The transfusion effects were evaluated for 38 thrombocytopenic patients, who were transfused with platelets stored in plasma or in synthetic medium (platelet additive solution II). In most but not all patients, transfusion resulted in increased adhesion and thrombus formation, as well as in improved platelet‐dependent coagulation. Taken together, the increase in platelet count after transfusion explained 57% of the overall improvement in platelet function. In acute graft‐versus‐host disease, thrombus formation was normal, while platelet‐dependent coagulation was higher than expected. We conclude that assessment of flow‐induced adhesion and thrombin generation in acquired thrombocytopenia adequately determines the improved haemostatic activity by transfused platelets.
Case report of HbC/β0‐thalassemia from India
Authors: KUMAR S. , RANA M. , HANDOO A. , SAXENA R. , VERMA I. C. , BHARGAVA M. , SOOD S. K.
Published: December 2006

This 22‐year‐old women presented to the ante‐natal clinic of this hospital for prenatal screening for β‐thalassemia. Cation exchange high performance liquid chromatography (HPLC) using ‘Beta Thalassemia Short Program’ on Bio‐Rad ‘Variant’ system revealed HbC value of 81.6%. The CBC showed microcytic hypochromic anemia. The HPLC and CBC suggested the possibility of compound heterozygote state for HbC/β‐thalassemia. The alkali and acid electrophoresis findings were consistent with the above diagnosis. The DNA analysis confirmed compound heterozygote state for HbC/β0‐thalassemia (Fr 8/9 mutation). The studies on the parents showed that mother was a compound heterozygote for HbDPunjab and HbC while father had β‐thalassemia trait. To the best of our knowledge, this is the first confirmed report of HbC from India. The paper discusses the hematological findings in this subject and her mother (a compound heterozygote for HbDPunjab and HbC).
Seasonal flow variation allows ‘time‐sharing’ by disparate aquatic insect communities in montane desert streams
Authors: BOGAN MICHAEL T. , LYTLE DAVID A.
Published: December 2006

1. Flow variation can drive major abiotic changes in stream environments between seasons. Theoretically, disparate biotic communities could be maintained during different seasons at a single site if suitable refuges and colonist sources were available. Using isolated montane desert streams in south‐east Arizona as a model system, we hypothesised that two disparate aquatic insect faunas (montane temperate and neotropical) could be maintained at the same sites through strong seasonal variation in abiotic conditions.

2. We collected aquatic insects representing 59 families from seven streams during high‐flow (March–April) and low‐flow (June) sampling periods across two years. We assessed changes in aquatic insect community and functional feeding group composition by habitat (riffle, pool) and season (high flow, low flow).

3. Within sites, wetted stream area decreased by an average of 97% between high‐flow (predominately riffles) and low‐flow (predominately pools) seasons. Community composition likewise showed strong seasonal patterns; the montane temperate fauna was strongly associated with the high‐flow season while neotropical hemipterans and coleopterans were associated with the low‐flow season. Increased water temperature was significantly associated with this shift from temperate to neotropical assemblages.

4. Functional feeding group composition shifted dramatically by season. The proportion of predators increased from 24.5% (high flow) to 75.2% (low flow) while collector–filterers and shredders declined from 38.4% (high flow) to 1.7% (low flow).

5. We suggest that habitat ‘time‐sharing’ by disparate communities is facilitated via strong seasonal variation in temperature and flow and the presence of high elevation refuges or diapause stages for temperate montane taxa to survive the dry season.
Persistence and colonisation as measures of success in bog restoration for aquatic invertebrates: a question of detection
Authors: MAZEROLLE MARC J. , POULIN MONIQUE
Published: December 2006

1. van Duinen et al. (Freshwater Biol., 2006) raise an interesting point regarding Mazerolle et al.’s (Freshwater Biol., 2006, 51, p. 333) conclusion on the ability of invertebrates, especially sedentary species, to colonise newly created bogs pools. We wish to clarify that Mazerolle et al. (2006) targeted large arthropods and the absence of smaller sedentary species was purely a result of sampling design.

2. van Duinen et al. (2006) postulate that colonisation rates by bog specialists should be higher in Canada than in the Netherlands, given the extensive amount of intact peatlands in Canada. Here, we emphasise the importance of taking the regional context into account when assessing restoration success as our study site occurs in a landscape where most bog pools have been drained.

3. An evaluation of restoration efforts should focus on both sedentary and vagile invertebrates, to resolve the importance of persistence and colonisation. Such patterns are difficult to interpret, however, when sampling designs and analyses do not account for the probability of detection: an absence may be due to non‐detection or true absence. We strongly urge investigators to directly estimate detection probability in addition to the parameters of interest (e.g. presence, abundance) to provide the best information possible regarding restoration success.
Fire and ice: unravelling the climatic and volcanic history of James Ross Island, Antarctic Peninsula
Authors: Smellie John , Nelson Anna , Williams Mark
Published: December 2006

Back in the mid‐nineteenth century British explorer James Clark Ross took his ships, HMS Terror and HMS Erebus, farther south than anyone else had been. He now lends his name to James Ross Island, a part‐volcanic edifice that rises out of the sea off the north‐east tip of the Antarctic Peninsula. The island records a geological history dating back to the Cretaceous, though its great peaks are volcanic. The most recent rocks of the island record a monumental struggle between fire and ice, the volcanoes, and the ice sheets that cover them. The glacigenic sediments that are interspersed with the volcanic rocks contain rich fossil assemblages which suggest that at times, the climate was warmer, with the ice retreating. Their study may help us to delimit the patterns of climate change in the Antarctic Peninsula region as Earth's global climate warms.
Classification of colorectal cancer based on correlation of clinical, morphological and molecular features
Authors: Jass J R
Published: December 2006

Over the last 20 years it has become clear that colorectal cancer (CRC) evolves through multiple pathways. These pathways may be defined on the basis of two molecular features: (i) DNA microsatellite instability (MSI) status stratified as MSI‐high (MSI‐H), MSI‐low (MSI‐L) and MS stable (MSS), and (ii) CpG island methylator phenotype (CIMP) stratified as CIMP‐high, CIMP‐low and CIMP‐negative (CIMP‐neg). In this review the morphological correlates of five molecular subtypes are outlined: Type 1 (CIMP‐high/MSI‐H/BRAF mutation), Type 2 (CIMP‐high/MSI‐L or MSS/BRAF mutation), Type 3 (CIMP‐low/MSS or MSI‐L/KRAS mutation), Type 4 (CIMP‐neg/MSS) and Type 5 or Lynch syndrome (CIMP‐neg/MSI‐H). The molecular pathways are determined at an early evolutionary stage and are fully established within precancerous lesions. Serrated polyps are the precursors of Types 1 and 2 CRC, whereas Types 4 and 5 evolve through the adenoma–carcinoma sequence. Type 3 CRC may arise within either type of polyp. Types 1 and 4 are conceived as having few, if any, molecular overlaps with each other, whereas Types 2, 3 and 5 combine the molecular features of Types 1 and 4 in different ways. This approach to the classification of CRC should accelerate understanding of causation and will impact on clinical management in the areas of both prevention and treatment.
Molecular cloning and heterologous expression of an α‐adrenergic‐like octopamine receptor from the silkworm Bombyx mori
Authors: Ohtani A. , Arai Y. , Ozoe F. , Ohta H. , Narusuye K. , Huang J. , Enomoto K. , Kataoka H. , Hirota A. , Ozoe Y.
Published: December 2006

A cDNA encoding an octopamine (OA) receptor (BmOAR1) was isolated from the nerve tissue of silkworm (Bombyx mori) larvae. Comparison of amino acid sequences showed that BmOAR1 is highly identical to OA receptors isolated from Periplaneta americana (Pa oa1), Apis mellifera (AmOA1), and Drosophila melanogaster (OAMB or DmOA1A). BmOAR1 was stably expressed in HEK‐293 cells. OA above 1 µm led to an increase in intracellular cyclic AMP concentration ([cAMP]i). The synthetic OA‐receptor agonist demethylchlordimeform also elevated [cAMP]i to the same maximal level (≈ 5‐fold over the basal level) as that induced by OA. However, other biogenic amines, tyramine and dopamine, and chlordimeform were without effects. The [cAMP]i level raised by OA was lowered by antagonists; the rank order of antagonist activity was chlorpromazine > mianserin = yohimbine. Cyproheptadine and metoclopramide had little effect. OA above 100 nm induced a transient or sustained increase in intracellular Ca2+ concentration ([Ca2+]i), depending on the concentration of OA. Sequence homology and functional analysis data indicate that BmOAR1 is an α‐adrenergic‐like OA receptor of B. mori.
Cathepsin L function in insect moulting: molecular cloning and functional analysis in cotton bollworm, Helicoverpa armigera
Authors: Liu J. , Shi G.‐P. , Zhang W.‐Q. , Zhang G.‐R. , Xu W.‐H.
Published: December 2006

Moulting is an essential process of insect development but little is known about cysteine proteases in the process. Here, we detail a proteolytic activity profile from fifth larval instar to new pupae of the lepidopteran Helicoverpa armigera. At fifth to sixth instar moulting, the activities were significantly higher than those in non‐moulting stages, and were inhibited by the cysteine protease inhibitor, 2S, 3S‐trans‐epoxysuccinyl‐L‐leucylamido‐3‐methylbutane ethyl ester (E‐64), or by the cathepsin L‐selective inhibitor CLIK148. Further, a 1513 bp cathepsin L cDNA (Har‐CL) was isolated from the H. armigera larval cuticle and epidermis layer. Har‐CL gene expression, which is correlated closely with ecdysone, was higher during larval moulting. Injection of E‐64 or CLIK148 resulted in delayed fifth to sixth instar moulting, suggesting an essential role for cathepsin L in larval moulting.
GUEST EDITORIAL: Hello New Zealand
Authors: Trewick Steven A. , Paterson Adrian M. , Campbell Hamish J.
Published: December 2006

Islands of the Pacific Ocean have long fascinated evolutionists. Oceanic islands, generally the products of volcanic activity, provide natural experiments as biological populations are well delimited and the age of islands can be determined using radiometric dating. ‘Continental islands’, including New Caledonia and New Zealand, provide equally valuable opportunities for evolutionary study. For students of New Zealand biogeography, the peculiar composition of the biota coupled with a limited interpretation of geology has resulted in the widespread acceptance that the flora and fauna is primarily ancient and of vicariant Gondwanan origin. There is increasing evidence from molecular data that much of this biodiversity is the product of evolution following relatively recent colonization. Such data have prompted biologists to consider geological information on New Zealand in more detail. At the heart of the issue is the question of whether modern New Zealand has a terrestrial link through time with the continent Zealandia that split from Gondwanaland some 80 Ma. Zealandia, which includes New Caledonia, Lord Howe Island and several of the subantarctic islands, is now largely submerged, and New Zealand's present terrestrial existence is the product of tectonic activity initiated around 26 Ma. We argue that for the purposes of biogeographical interpretation, New Zealand can be treated as an oceanic island.
Consequences of herbivory by native ungulates for the reproduction of a savanna tree
Authors: GOHEEN JACOB R. , YOUNG TRUMAN P. , KEESING FELICIA , PALMER TODD M.
Published: December 2006

Herbivores may negatively impact plant populations by reducing the survival, growth and reproduction of individual plants.

In African savannas, browsing by large mammalian herbivores has been shown repeatedly to reduce adult survival and growth of members of the genusAcacia, the dominant trees in these systems. However, the potential costs of mammalian herbivory toAcaciareproduction are largely unexplored, and have never been investigated experimentally in African savannas.

Using a long‐term, large‐scale field experiment, we demonstrate that, in the absence of native herbivores, individual trees were twice as likely to reproduce, and those that reproduced produced a greater biomass of seeds. In addition, spine length (an indicator of past herbivory) was correlated with reduced reproduction ofAcacia drepanolobium, the dominant tree across large areas of East Africa. Browsing by native herbivores triggers the production of longer spines, an induced resistance, and spine length was significantly and negatively related both to the occurrence and magnitude of reproduction.

Induced resistance appeared to mitigate the negative effects of herbivory where large herbivores were present: trees with long spines reproduced at levels comparable to trees with similarly long spine lengths in the absence of browsers.

Large mammalian herbivores kill and suppress the growth of adultAcacia, and therefore often are regarded as critical in maintaining the co‐dominance of trees and grasses in African savannas. Our results provide the first experimental evidence that large mammalian herbivores can suppress reproduction inAcacia, thus highlighting an additional pathway through which these herbivores might impact population dynamics of this important and widespread genus.

In savanna systems, declining populations of large herbivores may trigger a series of complex demographic responses for trees, with potentially strong consequences for the structure and function of savannas.
Identifying mechanisms of competition in multi‐species communities
Authors: WEIGELT ALEXANDRA , SCHUMACHER JENS , WALTHER TIM , BARTELHEIMER MAIK , STEINLEIN TOM , BEYSCHLAG WOLFRAM
Published: December 2006

We tested the hypothesis that the competitive effect of multi‐species mixtures on a single target plant can be described as a simple additive function of the effects of single species.

In a controlled field competition experiment on sand, we used four common species of dry acidic grasslands (Hieracium pilosella,Jasione montana,Corynephorus canescensandFestuca ovina) to study the effects of both, single‐ and multi‐species neighbourhoods on the target speciesH. pilosella.

Target plant biomass points at a competitive ranking of neighbour species withF. ovinaas the strongest competitor followed byC. canescensandH. pilosella, whileJ. montanahas a lower effect on the target. The analysis of the competitive response gives no indication of competitive release or amplification with increasing number of neighbouring species.

Further analysis with yield‐density models reveals that the competition intensity of most multi‐species mixtures is well predicted by the effect of pairwise interactions. Hence, for the majority of species combinations, our results indicate additive effects of species competition.

Specific species combinations, however, significantly deviate from this result. For combinations ofC. canescenswith either one of the herbs, the models show a significantly better fit if a non‐additivity parameter is included. The important missing factor to describe target plant growth is species‐specific biomass of neighbouring plants and here root biomass is the most crucial determinant. The addition of each of these factors as non‐additive parameters significantly increases the predictive power of the model.

Our work adds to the increasing evidence that interactions in diverse plant communities are not simply a sum of their component species interactions. For a better understanding of the effect of competition on the structure and development of diverse plant communities, future studies need to consider both additive and non‐additive effects of competing species.
Human pregnancy‐associated malaria‐specific B cells target polymorphic, conformational epitopes in VAR2CSA
Authors: Barfod Lea , Bernasconi Nadia L. , Dahlbäck Madeleine , Jarrossay David , Andersen Pernille Haste , Salanti Ali , Ofori Michael F. , Turner Louise , Resende Mafalda , Nielsen Morten A. , Theander Thor G. , Sallusto Federica , Lanzavecchia Antonio , Hviid Lars
Published: December 2006

Pregnancy‐associated malaria (PAM) is caused by Plasmodium falciparum‐infected erythrocytes (IEs) that bind to chondroitin sulphate A (CSA) in the placenta by PAM‐associated clonally variant surface antigens (VSA). Pregnancy‐specific VSA (VSAPAM), which include the PfEMP1 variant VAR2CSA, are targets of IgG‐mediated protective immunity to PAM. Here, we report an investigation of the specificity of naturally acquired immunity to PAM, using eight human monoclonal IgG1 antibodies that react exclusively with intact CSA‐adhering IEs expressing VSAPAM. Four reacted in Western blotting with high‐molecular‐weight (> 200 kDa) proteins, while seven reacted with either the DBL3‐X or the DBL5‐ε domains of VAR2CSA expressed either as Baculovirus constructs or on the surface of transfected Jurkat cells. We used a panel of recombinant antigens representing DBL3‐X domains from P. falciparum field isolates to evaluate B‐cell epitope diversity among parasite isolates, and identified the binding site of one monoclonal antibody using a chimeric DBL3‐X construct. Our findings show that there is a high‐frequency memory response to VSAPAM, indicating that VAR2CSA is a primary target of naturally acquired PAM‐specific protective immunity, and demonstrate the value of human monoclonal antibodies and conformationally intact recombinant antigens in VSA characterization.
Phenotypic heterogeneity can enhance rare‐cell survival in ‘stress‐sensitive’ yeast populations
Authors: Bishop Amy L. , Rab Faiza A. , Sumner Edward R. , Avery Simon V.
Published: December 2006

Individual cells within isogenic microbial cultures exhibit phenotypic heterogeneity, an issue that is attracting intense interest. Heterogeneity could confer benefits, in generating variant subpopulations that may be better equipped to persist during perturbation. We tested this hypothesis by comparing the survival of wild‐type Saccharomyces cerevisiae with that of mutants which are considered stress‐sensitive but which, we demonstrate, also have increased heterogeneity. The mutants (e.g. vma3, ctr1, sod1) exhibited the anticipated sensitivities to intermediate doses of nickel, copper, alkaline pH, menadione or paraquat. However, enhanced heterogeneity meant that the resistances of individual mutant cells spanned a broad range, and at high stress occasional‐cell survival in most of these populations overtook that of the wild type. Green fluorescent protein (GFP) reporter studies showed that this heterogeneity‐dependent advantage was not related to perturbation of buffered gene expression. Deletion strain screens combined with other approaches revealed that vacuolar alkalinization resulting from loss of Vma‐dependent vacuolar H+‐ATPase activity was not the cause of vma mutants' net stress sensitivities. An alternative Vma‐dependent resistance mechanism was found to suppress an influence of variable vacuolar pH on the metal resistances of individual wild‐type cells. In addition to revealing new mechanisms of heterogeneity generation, the results demonstrate experimentally a benefit under adverse conditions that arises specifically from heterogeneity, and in populations conventionally considered to be disadvantaged.
The Aspergillus fumigatus metacaspases CasA and CasB facilitate growth under conditions of endoplasmic reticulum stress
Authors: Richie Daryl L. , Miley Michael D. , Bhabhra Ruchi , Robson Geoffrey D. , Rhodes Judith C. , Askew David S.
Published: December 2006

We have examined the contribution of metacaspases to the growth and stress response of the opportunistic human mould pathogen, Aspergillus fumigatus, based on increasing evidence implicating the yeast metacaspase Yca1p in apoptotic‐like programmed cell death. Single metacaspase‐deficient mutants were constructed by targeted disruption of each of the two metacaspase genes in A. fumigatus, casA and casB, and a metacaspase‐deficient mutant, ΔcasA/ΔcasB, was constructed by disrupting both genes. Stationary phase cultures of wild‐type A.  fumigatus were associated with the appearance of typical markers of apoptosis, including elevated proteolytic activity against caspase substrates, phosphatidylserine exposure on the outer leaflet of the membrane, and loss of viability. By contrast, phosphatidylserine exposure was not observed in stationary phase cultures of the ΔcasA/ΔcasB mutant, although caspase activity and viability was indistinguishable from wild type. The mutant retained wild‐type virulence and showed no difference in sensitivity to a range of pro‐apoptotic stimuli that have been reported to initiate yeast apoptosis. However, the ΔcasA/ΔcasB mutant showed a growth detriment in the presence of agents that disrupt endoplasmic reticulum homeostasis. These findings demonstrate that metacaspase activity in A. fumigatus contributes to the apoptotic‐like loss of membrane phospholipid asymmetry at stationary phase, and suggest that CasA and CasB have functions that support growth under conditions of endoplasmic reticulum stress.
The human anionic antimicrobial peptide dermcidin induces proteolytic defence mechanisms in staphylococci
Authors: Lai Yuping , Villaruz Amer E. , Li Min , Cha David J. , Sturdevant Daniel E. , Otto Michael
Published: December 2006

Antimicrobial peptides (AMPs) represent a key component of innate host defence against bacterial pathogens. Bacterial resistance mechanisms usually depend on the characteristic positive charge of AMPs. However, several human cell types also produce anionic AMPs, mechanisms of resistance to which are poorly understood. Here we demonstrate that the skin commensal and leading nosocomial pathogen Staphylococcus epidermidis senses and efficiently inactivates the anionic AMP dermcidin. Dermcidin induced differential expression of global regulatory systems, leading to increased expression of proteases with the capacity to degrade dermcidin, particularly S. epidermidis SepA. A similar induction of extracellular proteolytic activity was found in Staphylococcus aureus, suggesting a common regulatory mechanism in staphylococci. Notably, human cationic AMPs also led to the activation of global regulators, but inactivation of dermcidin by SepA was much more effective than of the tested cationic peptides. The ability to react to the unusual, anionic dermcidin with effective countermeasures likely contributes to the extraordinary success of staphylococci as colonizers and infective agents on human epithelia. Our study indicates that staphylococci can react to human AMPs by specific mechanisms of resistance and establishes a crucial role for staphylococcal proteases in the interaction with human innate host defence.
Sumatriptan is an agonist at 5‐HT1P receptors on myenteric neurones in the guinea‐pig gastric antrum
Authors: Tack J. , Berghe P. Vanden , Coulie B. , Janssens J.
Published: December 2006

Abstract  Sumatriptan, a 5‐hydroxytryptamine1D (5‐HT1D)‐receptor agonist used in the treatment in migraine, inhibits gastric motility via the enteric nervous system. As no studies have reported enteric neuronal 5‐HT1D receptors, we used conventional intracellular recordings to characterize the actions of sumatriptan on 145 guinea‐pig antral myenteric neurones. In 24 of 29 neurones with a 5‐HT1P receptor‐mediated depolarizing response to 5‐HT, application of sumatriptan caused a dose‐dependent depolarization, accompanied by increased membrane resistance and enhanced excitability. Depolarizing responses to sumatriptan occurred both in cholinergic and in nitrergic neurones. Sumatriptan did not mimic the 5‐HT3 receptor‐mediated fast‐depolarizing responses or 5‐HT1A receptor‐mediated inhibitory responses to 5‐HT. Sumatriptan had no effect on neurones not responding to 5‐HT. The depolarizing response to sumatriptan was inhibited by renzapride, but not by 5‐HT1−7 receptor antagonists. We conclude that sumatriptan behaves as an agonist at the 5‐HT1P receptor on myenteric neurones in the guinea‐pig gastric antrum. The actions of sumatriptan on gastric motility seem to be attributable to a direct action on enteric neurones.