bluuebunny/crossref_metadata_2025 huggingface dataset:
Association between sequence variants at 17q12 and 17q24.3 and prostate cancer risk in European and African Americans
Authors: Sun Jielin , Purcell Lina , Gao Zhengrong , Isaacs Sarah D. , Wiley Kathleen E. , Hsu Fang‐Chi , Liu Wennuan , Duggan David , Carpten John D. , Grönberg Henrik , Xu Jianfeng , Chang Bao‐Li , Partin Alan W. , Walsh Patrick C. , Isaacs William B. , Zheng S. Lilly
Published: March 2008

Background

Three SNPs at 17q12 and four SNPs at 17q24.3 were recently identified to be associated with prostate cancer risk using a genome‐wide association study.

Methods

We evaluated these 7 SNPs in two hospital‐based case–control study populations, including European Americans (EA; 1,563 cases and 576 controls) and African Americans (AA; 364 cases and 353 controls).

Results

Each of the reported risk alleles of these seven SNPs were more common in cases than in controls among EA and AA. The differences were highly significant in EA (P = 10−4) and marginally significant in AA (P = 0.04) for SNPs at 17q12. In contrast, the differences were not statistically significant in EA or AA for SNPs at 17q24.3, but were marginally significant for two SNPs (P = 0.04–0.06) when EA and AA subjects were combined. Similar results were obtained when genotype and haplotype frequencies between cases and controls were analyzed. These risk variants were not associated with more aggressive prostate cancer or other clinical variables such as TNM stage, pre‐operative PSA, or age at diagnosis.

Conclusions

Results from our study provide the first confirmation of these 17q SNPs as novel prostate cancer susceptibility loci in EA and the first indication that these two loci may also play roles in prostate cancer risk among AA. Prostate 68: 691–697, 2008. © 2008 Wiley‐Liss, Inc.
Fast protein tertiary structure retrieval based on global surface shape similarity
Authors: Sael Lee , Li Bin , La David , Fang Yi , Ramani Karthik , Rustamov Raif , Kihara Daisuke
Published: March 2008

Characterization and identification of similar tertiary structure of proteins provides rich information for investigating function and evolution. The importance of structure similarity searches is increasing as structure databases continue to expand, partly due to the structural genomics projects. A crucial drawback of conventional protein structure comparison methods, which compare structures by their main‐chain orientation or the spatial arrangement of secondary structure, is that a database search is too slow to be done in real‐time. Here we introduce a global surface shape representation by three‐dimensional (3D) Zernike descriptors, which represent a protein structure compactly as a series expansion of 3D functions. With this simplified representation, the search speed against a few thousand structures takes less than a minute. To investigate the agreement between surface representation defined by 3D Zernike descriptor and conventional main‐chain based representation, a benchmark was performed against a protein classification generated by the combinatorial extension algorithm. Despite the different representation, 3D Zernike descriptor retrieved proteins of the same conformation defined by combinatorial extension in 89.6% of the cases within the top five closest structures. The real‐time protein structure search by 3D Zernike descriptor will open up new possibility of large‐scale global and local protein surface shape comparison. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Dendritic‐targeting GABA neurons in monkey prefrontal cortex: Comparison of somatostatin‐ and calretinin‐immunoreactive axon terminals
Authors: Melchitzky Darlene S. , Lewis David A.
Published: March 2008

Different subclasses of γ‐aminobutyric acid (GABA) cortical neurons can be distinguished by their content of neuropeptides such as somatostatin (SST), or calcium‐binding proteins such as calretinin (CR). SST, but not CR, neurons have been reported to be altered in the prefrontal cortex (PFC) of subjects with schizophrenia. Understanding the functional significance of the SST neuron disturbances in schizophrenia requires knowledge of the specialized synaptic circuitry of these neurons relative to that of CR neurons. Consequently, we used immuno‐electron microscopy to examine the synaptic type and postsynaptic targets of SST‐immunoreactive (IR) axon terminals in monkey PFC and compared these findings with similar data for CR‐IR axon terminals. SST‐IR axon terminals formed exclusively symmetric synapses and contacted only dendritic shafts (86%) and dendritic spines (14%), whereas CR‐IR terminals also formed synapses with cell bodies. The postsynaptic targets of SST‐IR axon terminals also differed across layers with synapses onto dendritic spines more frequent in the superficial (20%) than in the deep (8%) layers. Dual‐label immunoelectron microscopy revealed that CR‐IR axon terminals targeted GABA‐IR dendritic shafts with a greater frequency (60%) than did SST‐IR axon terminals (21.5%). Conversely, SST‐IR axon terminals contacted unlabeled dendritic shafts, presumably belonging to pyramidal neurons, more frequently than did CR‐IR axon terminals (57% vs. 19%, respectively). This specialized synaptic circuitry of SST neurons in the primate PFC suggests that the alterations of these neurons in schizophrenia is likely to have distinct functional consequences. Synapse 62:456–465, 2008. © 2008 Wiley‐Liss, Inc.
Altered synaptic synchrony in motor nerve terminals lacking P/Q‐calcium channels
Authors: Depetris Rafael S. , Nudler Silvana I. , Uchitel Osvaldo D. , Urbano Francisco J.
Published: March 2008

The variance in synaptic delays among endplate potentials events (referred here as jitter) was measured to study the contribution of voltage dependent calcium channels to transmission synchronicity in neuromuscular synapses from wild type and α‐1A knockout mice (i.e., lacking P/Q type calcium channels). Knockout synapses presented higher jitter values than wild type ones under a wide range of extracellular calcium concentration ([Ca2+]o) values. Accordingly, wild type synapses showed less synchronic neurotransmitter release when P/Q type calcium channels were partially blocked as well as under lower [Ca2+]o. In the knockout synapses, N‐type calcium channels mediated neurotransmitter release in a more temporally precise way than the R‐type ones. Our results suggest that the type of calcium channels mediating transmitter release influenced the degree of synaptic synchrony. Thus, these results provide insight on the mechanisms underlying several pathologies associated with P/Q type calcium channels. Synapse 62:466–471, 2008. © 2008 Wiley‐Liss, Inc.
Introduction to Asepsis: A Programmed Unit in Fundamentals of Nursing
Authors: Hadley Frances M.
Published: March 2008

Introduction to Asepsis: A Programmed Unit In Fundamentals Of Nursing, by Marie M. Seedor, Bureau of Publications, Teachers College, Columbia University, 1963, 275 pages. Price $3.50.
Endothelin (ET)‐1 and ET‐3 promote expression ofc‐fosandc‐junin human choriocarcinoma via ETBreceptor‐mediated Gi‐ and Gq‐pathways and MAP kinase activation
Authors: Rauh A , Windischhofer W , Kovacevic A , DeVaney T , Huber E , Semlitsch M , Leis H‐J , Sattler W , Malle E
Published: March 2008

Background and purpose:Endothelins (ETs) and their G protein‐coupled receptors exert key physiological functions during normal and aberrant placental development. Trophoblast cells mediate the contact between the embryo and the mother, by establishing a transient organ, the placenta. Choriocarcinoma cells display many of the biochemical and morphological characteristics ofin uteroinvasive trophoblast cells and may therefore be used as a suitable model to study epithelial tumour progression of foetal‐derived cells.

Experimental approach:The present study aimed at investigating ET receptor‐mediated activation of the mitogen‐activated protein kinase (MAPK) pathway in human choriocarcinoma.

Key results:Both JAR and Jeg‐3 choriocarcinoma cell lines expressedET receptor subtype B(ETB) but notETAreceptor transcripts. ETBreceptor engagement by ET‐1 and ET‐3 resulted in a similar time‐ and concentration‐dependent phosphorylation of p42/44 MAPK, also known as extracellular regulated kinase 1/2. Using specific pharmacological antagonists/inhibitors, we showed that ET‐1/‐3‐mediated signal transduction by the ETBreceptor is transmitted via Gi‐ and Gq‐dependent pathways through activation of the Src (Gi) and protein kinase C (Gq) axis that converge at Ras/Raf, leading to downstream activation of p42/44. On a functional level, ETBengagement and subsequent phosphorylation of p42/44 resulted in enhanced transcription of the immediate early response genesc‐fosandc‐jun, a process commonly assumed to be mediated by the ETAreceptor, and increased cell growth and relative cell area.

Conclusions and implications:As human choriocarcinoma cells secrete ETs, pharmacological antagonism of ETs and/or ETBreceptor‐mediated signal transduction could represent a likely target therapy for choriocarcinoma.
Effect of excess electron and one water molecule on relative stability of the canonical and zwitterionic tautomers of glycine
Authors: Haranczyk Maciej , Gutowski Maciej
Published: March 2008

The anionic and neutral complexes of glycine with water were studied at at the coupled cluster level of theory with single, double, and perturbative triple excitations. The most stable neutral complex has a relatively small dipole moment (1.74D) and does not bind an electron. Other neutral complexes involve a polar conformer of canonical glycine and support dipole-bound anionic states. The most stable anion is characterized by an electron vertical detachment energy of 1576cm−1, in excellent agreement with the experimental result of 1573cm−1. The (Gly⋅H2O)− complex supports local minima, in which the zwitterionic glycine is stabilized by one water and one excess electron. They are, however, neither thermodynamically nor kinetically stable with respect to the dipole-bound states based on the canonical tautomers of glycine. The electron correlation contributions to excess electron binding energies are important, in particular, for nonzwitterionic complexes. Our results indicate that the condensation energies for Gly(0,−)+H2O→(Gly⋅H2O)(0,−) are larger than the adiabatic electron affinity of Gly⋅H2O. The above results imply that collisions of Gly− with H2O might effectively remove Gly− from the ion distribution. This might explain why formation of Gly− and (Gly⋅H2O)− is very sensitive to source conditions. We analyzed shifts in stretching mode frequencies that develop upon formation of intra- and intermolecular hydrogen bonds and an excess electron attachment. The position of the main peak and a vibrational structure in the photoelectron spectroscopy spectrum of (Gly⋅H2O)− are well reproduced by our theoretical results.
The role of entanglements on the stability of microphase separated diblock copolymers in shear flow
Authors: Kindt P. , Briels W. J.
Published: March 2008

Various possible orientations of lamellar structures of diblock copolymers under shear are investigated with respect to their stability. A Brownian dynamics model is put forward in which each diblock is modeled as a dumbbell. The blobs in each dumbbell are held together by a finite extendable nonlinear elastic (FENE) potential and interact with all surrounding blobs by soft dissipative particle dynamics (DPD) potentials. In addition to this, the blobs have the possibility to entangle with each other. The corresponding interactions lead to large viscosities, which, however, quickly diminish with increasing shear rate. This fact turns out to be crucial for the stabilization of structures with the lamellae parallel to the velocity-vorticity plane. As a second result it is found that asymmetry in the entanglement interactions stimulates the actual reorientation into this state.
Field emission properties of carbon nanotube pillar arrays
Authors: Killian Jessica L. , Zuckerman Nathaniel B. , Niemann Darrell L. , Ribaya Bryan P. , Rahman Mahmud , Espinosa Robert , Meyyappan M. , Nguyen Cattien V.
Published: March 2008

Carbon nanotube pillar arrays (CPAs) for cold field emission applications were grown directly on polished 70∕30at.% NiCr alloy surfaces patterned by photolithography. A carbon nanotube (CNT) pillar is a localized, vertically aligned, and well-ordered group of multiwalled CNTs resulting from van der Waals forces within high-density CNT growth. The edge effect, in which the applied electric field is enhanced along the edge of each pillar, is primarily responsible for the excellent emission properties of CPAs. We achieved efficient emission with turn-on fields as low as 0.9V∕μm and stable current densities as high as 10mA∕cm2 at an applied macroscopic field of 5.7V∕μm. We investigated the effects of pillar aspect ratio, density, and spacing on CPA field emission and quantified the edge effect with respect to pillar aspect ratio through modeling. We also investigated the field emission stability and found substantial improvement with CPAs compared to continuous and patterned CNT films.
A method for high-resolution x-ray imaging of intermodal cargo containers for fissionable materials
Authors: Quiter B. J. , Prussin S. G. , Pohl B. , Hall J. , Trebes J. , Stone G. , Descalle M.-A.
Published: March 2008

The sensitivity for identification of high-Z objects in elemental form in the massive cargos of intermodal containers with continuous bremsstrahlung radiation depends critically on discriminating the weak signal from uncollided photons from the very intense flux of scattered radiations that penetrate the cargo. We propose that this might be accomplished by rejection of detected events with E⩽2–3MeV that contain the majority of multiply scattered photons along with a correction for single-scattered photons at higher energies. Monte Carlo simulations of radiographs with a 9MeV bremsstrahlung spectrum demonstrate that rejection of detected events with E⩽3MeV removes the majority of signals from scattered photons emerging through cargos with Z⩽30 and areal densities of at least 145gcm−2. With analytical estimates of the single-scattered intensity at higher energies, accurate estimates of linear attenuation coefficients for shielded and unshielded uranium spheres with masses as small as 0.08kg are found. The estimated maximum dose is generally so low that reasonable order tomography of interesting portions of a container should be possible.
Conductance of a tunnel point contact of noble metals in the presence of a single defect
Authors: Avotina Ye. S. , Kolesnichenko Yu. A. , Roobol S. B. , van Ruitenbeek J. M.
Published: March 2008

In a previous paper [Ye. S. Avotina et al., Phys. Rev. B 74, 085411 (2006)], the effect of Fermi surface anisotropy on the conductance of a tunnel point contact with a single point-like defect situated in its vicinity was investigated theoretically. The oscillatory dependence of the conductance on the distance between the contact and the defect was found for a general Fermi surface geometry. In the present paper the method developed in the cited work is applied to the calculation of the conductance of noble metal contacts. An original algorithm, which enables the computation of the conductance for any parametrically specified Fermi surface, is proposed. On this basis a pattern of the conductance oscillations, which can be observed by the method of scanning tunneling microscopy, is obtained for different orientations of the surface for the noble metals.
An experimental investigation and a simple model of a valveless pump
Authors: Bringley Thomas T. , Childress Stephen , Vandenberghe Nicolas , Zhang Jun
Published: March 2008

We construct a valveless pump consisting of a section of elastic tube and a section of rigid tube connected in a closed loop and filled with water. By periodically squeezing the elastic tube at an asymmetric location, a persistent flow around the tubes is created. This effect, called the Liebau phenomenon or valveless pumping, has been known for some time but is still not completely understood. We study the flow rates for various squeezing locations, frequencies, and elastic tube rigidities. To understand valveless pumping, we formulate a simple model that can be described by ordinary differential equations. The time series of flow velocities generated by the model are qualitatively and quantitatively similar to those seen in the experiment. The model provides a physical explanation of valveless pumping, and it allows us to identify the essential pumping mechanisms.
Supersymmetric associated vector coherent states and generalized Landau levels arising from two-dimensional supersymmetry
Authors: Ali S. Twareque , Bagarello F.
Published: March 2008

We describe a method for constructing vector coherent states for quantum supersymmetric partner Hamiltonians. The method is then applied to such partner Hamiltonians arising from a generalization of the fractional quantum Hall effect. Explicit examples are worked out.
Far-infrared reflectivity as a probe of point defects in Zn- and Cd-doped HgTe
Authors: Cebulski J. , Sheregii E. M. , Polit J. , Marcelli A. , Piccinini M. , Kisiel A. , Kucherenko I. V. , Triboulet R.
Published: March 2008

We present a nondestructive method for quantitative determination of the vacancy concentration in the lattice of Hg-based semiconductor alloys with tetrahedral structure. The method is based on the identification of additional vibrational modes (AVMs) induced by lattice deformations in the far-infrared (FIR) reflectivity spectrum. Although the method is restricted by sensitivity limitations, recent FIR experimental data carried out on HgZnTe and HgCdTe samples containing Hg vacancies confirmed the presence of AVMs induced by Hg vacancies in as-grown crystals.
Effects of patterned, stressed SiN overlayers on Si solid phase epitaxy
Authors: Saenger K. L. , Fogel K. E. , Ott J. A. , de Souza J. P. , Murray C. E.
Published: March 2008

Striking nonuniformities are observed in the solid phase epitaxy (SPE) of blanket amorphized Si layers recrystallized in the presence of stress distributions induced by a patterned SiN overlayer. Measurements conducted for a range of SiN feature sizes and intrinsic stress values allowed us to isolate the effects of stress on the crystallization front. It is concluded that SiN-induced variations in SPE rates arise both from line-edge stresses, which scale with feature stress and increase SPE rates where the hydrostatic stress is compressive, and a SiN body effect, which suppresses SPE rates under the SiN features, independent of SiN stress state.
Shape-engineered epitaxial InGaAs quantum rods for laser applications
Authors: Li L. H. , Ridha P. , Patriarche G. , Chauvin N. , Fiore A.
Published: March 2008

We apply artificial shape engineering of epitaxial semiconductor nanostructures to demonstrate InGaAs quantum rods (QRs), nanocandles, and quantum dots-in-rods on a GaAs substrate. The evolution of the QRs from a zero-dimensional to one-dimensional confinement is evidenced by systematically measuring the photoluminescence and photoluminescence decay as a function of the rod length. Lasers based on a three-stack QR active region are demonstrated at room temperature, validating the applicability of the QRs in the real devices.
Hedgehog signaling overrides p53-mediated tumor suppression by activating Mdm2
Authors: Abe Yoshinori , Oda-Sato Eri , Tobiume Kei , Kawauchi Keiko , Taya Yoichi , Okamoto Koji , Oren Moshe , Tanaka Nobuyuki
Published: March 2008

The hedgehog (Hh) signaling pathway regulates the development of many organs in mammals, and activation of this pathway is widely observed in human cancers. Although it is known that Hh signaling activates the expression of genes involved in cell growth, the precise role of the Hh pathway in cancer development is still unclear. Here, we show that constitutively activated mutants of Smoothened (Smo), a transducer of the Hh signaling pathway, inhibit the accumulation of the tumor suppressor protein p53. This inhibition was also observed in the presence of Hh ligand or with the overexpression of the transcription factors Gli1 and Gli2, downstream effectors of Smo, indicating that this inhibition is specific for the Hh pathway. We also report that Smo mutants augment p53 binding to the E3 ubiquitin-protein ligase Mdm2 and promote p53 ubiquitination. Furthermore, Hh signaling induced the phosphorylation of human Mdm2 protein on serines 166 and 186, which are activating phosphorylation sites of Mdm2. Smo mutants enhanced the proliferation of mouse embryonic fibroblasts (MEFs) while inducing a DNA-damage response. Moreover, Smo partially inhibited p53-dependent apoptosis and cell growth inhibition in oncogene-expressing MEFs. We also found that accumulation of p53 is inhibited by Hh signaling in several human cancer cell lines. Therefore, the Hh pathway may be a powerful accelerator of oncogenesis by activating cell proliferation and inhibiting the p53-mediated anti-cancer barrier induced by oncogenic stress.
The Drosophila CD2AP/CIN85 orthologue Cindr regulates junctions and cytoskeleton dynamics during tissue patterning
Authors: Johnson Ruth I. , Seppa Midori J. , Cagan Ross L.
Published: March 2008

Developing tissues require cells to undergo intricate processes to shift into appropriate niches. This requires a functional connection between adhesion-mediating events at the cell surface and a cytoskeletal reorganization to permit directed movement. A small number of proteins are proposed to link these processes. Here, we identify one candidate, Cindr, the sole Drosophila melanogaster member of the CD2AP/CIN85 family (this family has been previously implicated in a variety of processes). Using D. melanogaster retina, we demonstrate that Cindr links cell surface junctions (E-cadherin) and adhesion (Roughest) with multiple components of the actin cytoskeleton. Reducing cindr activity leads to defects in local cell movement and, consequently, tissue patterning and cell death. Cindr activity is required for normal localization of Drosophila E-cadherin and Roughest, and we show additional physical and functional links to multiple components of the actin cytoskeleton, including the actin-capping proteins capping protein alpha and capping protein beta. Together, these data demonstrate that Cindr is involved in dynamic cell rearrangement in an emerging epithelium.
WASP family members and formin proteins coordinate regulation of cell protrusions in carcinoma cells
Authors: Sarmiento Corina , Wang Weigang , Dovas Athanassios , Yamaguchi Hideki , Sidani Mazen , El-Sibai Mirvat , DesMarais Vera , Holman Holly A. , Kitchen Susan , Backer Jonathan M. , Alberts Art , Condeelis John
Published: March 2008

We examined the role of the actin nucleation promoters neural Wiskott-Aldrich syndrome protein (N-WASP) and WAVE2 in cell protrusion in response to epidermal growth factor (EGF), a key regulator in carcinoma cell invasion. We found that WAVE2 knockdown (KD) suppresses lamellipod formation and increases filopod formation, whereas N-WASP KD has no effect. However, simultaneous KD of both proteins results in the formation of large jagged protrusions with lamellar properties and increased filopod formation. This suggests that another actin nucleation activity is at work in carcinoma cells in response to EGF. A mammalian Diaphanous–related formin, mDia1, localizes at the jagged protrusions in double KD cells. Constitutively active mDia1 recapitulated the phenotype, whereas inhibition of mDia1 blocked the formation of these protrusions. Increased RhoA activity, which stimulates mDia1 nucleation, was observed in the N-WASP/WAVE2 KD cells and was shown to be required for the N-WASP/WAVE2 KD phenotype. These data show that coordinate regulation between the WASP family and mDia proteins controls the balance between lamellar and lamellipodial protrusion activity.
Collagen I–mediated up-regulation of N-cadherin requires cooperative signals from integrins and discoidin domain receptor 1
Authors: Shintani Yasushi , Fukumoto Yuri , Chaika Nina , Svoboda Robert , Wheelock Margaret J. , Johnson Keith R.
Published: March 2008

Tumor cells undergo epithelial-to-mesenchymal transition (EMT) to convert from a benign to a malignant phenotype. Our recent focus has been signaling pathways that promote EMT in response to collagen. We have shown that human pancreatic cancer cells respond to collagen by up-regulating N-cadherin, which promotes tumor growth, invasion, and metastasis. Initial characterization showed that knocking down c-Jun NH2-terminal kinase prevented N-cadherin up-regulation and limited tumor growth and invasion in a mouse model for pancreatic cancer. The current study was designed to understand the pathway from collagen to N-cadherin up-regulation. Initiation of the signal requires two collagen receptors, α2β1 integrin and discoidin domain receptor (DDR) 1. Each receptor propagates signals through separate pathways that converge to up-regulate N-cadherin. Focal adhesion kinase (FAK)–related protein tyrosine kinase (Pyk2) is downstream of DDR1, whereas FAK is downstream of α2β1 integrin. Both receptor complexes rely on the p130 Crk-associated substrate scaffold. Interestingly, Rap1, but not Rho family guanosine triphosphatases, is required for the response to collagen I.
Amino Acid Substitutions in Homologs of the STAY-GREEN Protein Are Responsible for thegreen-fleshandchlorophyll retainerMutations of Tomato and Pepper
Authors: Barry Cornelius S. , McQuinn Ryan P. , Chung Mi-Young , Besuden Anna , Giovannoni James J.
Published: March 2008

Color changes often accompany the onset of ripening, leading to brightly colored fruits that serve as attractants to seed-dispersing organisms. In many fruits, including tomato (Solanum lycopersicum) and pepper (Capsicum annuum), there is a sharp decrease in chlorophyll content and a concomitant increase in the synthesis of carotenoids as a result of the conversion of chloroplasts into chromoplasts. The green-flesh (gf) and chlorophyll retainer (cl) mutations of tomato and pepper, respectively, are inhibited in their ability to degrade chlorophyll during ripening, leading to the production of ripe fruits characterized by both chlorophyll and carotenoid accumulation and are thus brown in color. Using a positional cloning approach, we have identified a point mutation at the gf locus that causes an amino acid substitution in an invariant residue of a tomato homolog of the STAY-GREEN (SGR) protein of rice (Oryza sativa). Similarly, the cl mutation also carries an amino acid substitution at an invariant residue in a pepper homolog of SGR. Both GF and CL expression are highly induced at the onset of fruit ripening, coincident with the ripening-associated decline in chlorophyll. Phylogenetic analysis indicates that there are two distinct groups of SGR proteins in plants. The SGR subfamily is required for chlorophyll degradation and operates through an unknown mechanism. A second subfamily, which we have termed SGR-like, has an as-yet undefined function.
Diversity and functions of leaf‐decaying fungi in human‐altered streams
Authors: LECERF ANTOINE , CHAUVET ERIC
Published: March 2008

1. Stream conditions have been evaluated using leaf breakdown, and aquatic hyphomycetes are a diverse group of fungal decomposers which contribute to this process.

2. In field surveys of three pairs of impact‐control stream sites we assessed the effect of eutrophication, mine pollution and modification of riparian vegetation on alder leaf breakdown rate in coarse and fine mesh bags and on mycelial biomass, spore production and species diversity of leaf‐colonizing fungi.

3. In addition, we gathered published information on the response of leaf‐colonizing fungi to these three types of perturbations. We conducted a meta‐analysis of 23 published papers to look for consistent patterns across studies and to determine the relevance of four fungal‐based metrics (microbial breakdown rate, maximum spore production, maximum mycelial biomass and total species richness) to detect stream impairment.

4. In our field surveys, leaf breakdown rates in coarse mesh bags were lower at impact than at paired control sites regardless of perturbation type. A similar trend was observed for leaf breakdown rates in fine mesh bags. Mycelial biomass and spore production were higher in the eutrophied stream than in the control stream. Spore production was depressed in the mine polluted stream, while it was slightly enhanced in the stream affected by forestry. Fungal diversity tended to be lower at impact than at paired control sites, though the mean and cumulative species richness values were often inconsistent.

5. Results of the meta‐analysis confirmed that mine pollution reduces fungal diversity and performance. Eutrophication was not found to affect microbial breakdown rate, maximum spore production and maximum mycelial biomass in a predictable manner because both positive and negative effects were reported in the literature. However, fungal species richness was consistently reduced in eutrophied streams. Modification of riparian vegetation had at most a small stimulating effect on maximum spore production. Among the four fungal‐based metrics included in the meta‐analysis, maximum spore production emerged as the most sensitive indicator of human impact on streams.

6. Taken together, our findings indicate that human activities can affect the diversity and functions of aquatic hyphomycetes in streams. We also show that leaf breakdown rate and simple fungal‐based metrics, such as spore production, are relevant to assess stream condition.
Conserved residues of the C‐terminal p16 domain of primase are involved in modulating the activity of the bacterial primosome
Authors: Chintakayala Kiran , Larson Marilynn A. , Griep Mark A. , Hinrichs Steven H. , Soultanas Panos
Published: March 2008

The bacterial primosome comprises the replicative homo‐hexameric ring helicase DnaB and the primase DnaG. It is an integral component of the replisome as it unwinds the parental DNA duplex to allow progression of the replication fork, synthesizes the initiation primers at the replication origin, oriC, and the primers required for Okazaki fragment synthesis during lagging strand replication. The interaction between the two component proteins is mediated by a distinct C‐terminal domain (p16) of the primase. Both proteins mutually regulate each other's activities and a putative network of conserved residues has been proposed to mediate these effects. We have targeted 10 residues from this network. To investigate the functional contributions of these residues to the primase, ATPase and helicase activities of the primosome, we have used site‐directed mutagenesis and in vitro functional assays. Five of these residues (E464, H494, R495, Y548 and R555) exhibited some functional significance while the remaining five (E483, R484, E506, D512 and E530) exhibited no effects. E464 participates in functional modulation of the primase activity, whereas H494, R495 and R555 participate in allosteric functional modulation of the ATPase and/or helicase activities. Y548 contributes directly to the structural interaction with DnaB.
Quambalaria species associated with plantation and native eucalypts in Australia
Authors: Pegg G. S. , O'Dwyer C. , Carnegie A. J. , Burgess T. I. , Wingfield M. J. , Drenth A.
Published: March 2008

This study aimed to determine which species of Quambalaria are associated with shoot blight symptoms on Corymbia spp. An additional aim was to determine the presence and impact of quambalaria shoot blight on Eucalyptus species used in plantation development in subtropical and tropical regions of eastern Australia. Surveys identified three Quambalaria spp. –Q. pitereka, Q. eucalypti and Q. cyanescens– from native and plantation eucalypts, as well as amenity plantings, including the first confirmed report of Q. eucalypti from Eucalyptus plantations in Australia. Symptom descriptions and morphological studies were coupled with phylogenetic studies using ITS rDNA sequence data. Quambalaria pitereka was the causal agent of blight symptoms on species and hybrids in the Corymbia complex. Quambalaria eucalypti was identified from Eucalyptus species and a single Corymbia hybrid. Quambalaria cyanescens was detected from native and plantation Corymbia spp.
Effects of geological complexities on coseismic displacement: hints from 2D numerical modelling
Authors: Megna A. , Barba S. , Santini S. , Dragoni M.
Published: March 2008

By means of a 2D finite‐element procedure, we tested how heterogeneities at the scale of seismogenic fault affect the displacement. We defined one or more slip distributions for two typical normal‐faulting earthquakes in the Central Apennines, computed the displacement occurred within different structures including lateral heterogeneities, and compared the different displacement profiles to isolate the effect of the crustal structure. To understand at what magnitude the heterogeneities affect the observation significantly, we compared the predicted coseismic displacement with GPS and DInSAR data for the Colfiorito 1997 earthquake. We find that heterogeneities significantly affect the observable horizontal coseismic displacement for the larger magnitudes, whereas for smaller quakes, they affect horizontal displacement close to the fault trace only.
Assessment of Selected Quality Parameters of Epididymal Cat (Felis catus s. domestica, L. 1758) Sperm Using Flow Cytometry Method and Computer Assisted Sperm Analyser
Authors: Siemieniuch MJ , Woclawek‐Potocka I
Published: March 2008

Contents

The improvement of biotechnical methods connected with fast and precise semen quality assessment and its utilization in assisted reproductive techniques is an urgent necessity in felids. The aim of this study was to evaluate some quality parameters (i.e. the viability and share of cells with intact plasma membrane) of epididymal sperm of cats using the flow cytometry method and computer‐assisted sperm analysis (CASA) examination. The material consisted of epididymal spermatozoa flushed from 22 pairs of epididymes after routine neutering procedures obtained from domestic cats aged between 8 and 36 months. The epididymes were cut and incubated with an extender without egg yolk. The samples were assessed for sperm viability (Live/Dead Sperm Viability Kit®), percentage of subtle membrane changes (Apoptosis Detection Kit®) and motility using FACScalibur flow cytometer and assisted sperm analyser htm ivos version 12.2. The flow cytometry method revealed 71.3% and 84.4% of live sperm using Live/Dead Sperm Viability Kit and Apoptosis Detection Kit respectively. The population of early‐apoptotic and late‐apoptotic sperm were 0.8% and 1.1% respectively. The CASA examination found 51.5% of motile sperm. However, the motility examination under light microscope revealed 69.5% of motile sperm. The data revealed an indistinctive per cent of apoptotic cells and 18.9% and 15.6% of dead cells using Live/Dead Sperm Viability Kit and Apoptosis Detection Kit, respectively, which indicate that the sperm obtained after flushing the epididymis possess potential properties for further assisted reproduction techniques.
The Role of Platelet‐activating Factor in the Mammalian Female Reproductive Tract
Authors: Tiemann U
Published: March 2008

Contents

Platelet‐activating factor (PAF) is a potent lipid mediator produced by various cell types of mammals and is involved in an inflammatory‐like process with increased vascular permeability. Platelet‐activating factor exerts its actions through the activation of specific PAF receptors (PAF‐R) found in cells and tissues of the female reproductive tract. The aim of this article was summarized briefly in the current research on the role of PAF in female reproductive functions. Platelet‐activating factor has been implicated in processes of ovulation, implantation and parturition because of its angiogenic and growth factor properties. This factor is influenced by ovarian steroid hormones in bringing about changes in the uterus and is a candidate molecule for initial embryo–maternal dialogue. Tissue concentrations of PAF are regulated by the equilibrium between biosynthesis and degradation by PAF‐acetylhydrolase (PAF‐AH). Antagonists of PAF interfere with ovulation and implantation. Platelet‐activating factor, its receptor, and PAF‐AH activity play an important role in the maintenance of pregnancy.
ASSESSMENT OF LAPAROSCOPIC PSYCHOMOTOR SKILLS IN INTERNS USING THE MIST VIRTUAL REALITY SIMULATOR: A PREREQUISITE FOR THOSE CONSIDERING SURGICAL TRAINING?
Authors: Cope Daron H. , Fenton‐Lee Douglas
Published: March 2008

Selection for surgical training in Australia is currently based on assessment of a structured curriculum vitae, referral reports from selected clinicians and an interview. The formal assessment of laparoscopic psychomotor skill and ability to attain skills is not currently a prerequisite for selection. The aim of this study was to assess the innate psychomotor skills of interns and also to compare interns with an interest in pursuing a surgical career to interns with those with no interest in pursuing a surgical career. Twenty‐two interns were given the opportunity to carry out tasks on the Minimal Invasive Surgical Trainer, Virtual Reality (Mentice, Gothenburg, Sweden) Simulator. The candidates were required to complete six tasks, repeated six times each. Scores for each task were calculated objectively by the simulator software. Demographic data were similar between the two groups. Although some candidates who were interested in pursuing a surgical career performed poorly on the simulator, there was no significant difference when comparing the two groups. The Minimal Invasive Surgical Trainer, Virtual Reality (Mentice) Simulator provides an objective and comparable assessment of laparoscopic psychomotor skills. We can conclude that interns have varying inherent ability as judged by the simulator and this does not seem to have an influence on their career selection. There was no significant difference in the scores between the two groups. Interns with and without inherent abilities have aspirations to pursue surgical careers and their aptitude does not seem to influence this decision. Surgical colleges could use psychomotor ability assessments to recruit candidates to pursue a career in surgery. Trainees needing closer monitoring and additional training could be identified early and guided to achieve competency.
MINOR PAPILLA SPHINCTEROTOMY FOR PANCREATITIS DUE TO PANCREAS DIVISUM
Authors: Kwan Vu , Loh Sze M. , Walsh Patrick R. , Williams Stephen J. , Bourke Michael J.
Published: March 2008

Background:  Pancreas divisum (PD) is the commonest congenital pancreatic abnormality and is implicated as a cause of acute recurrent pancreatitis (ARP). We report our experience in minor papilla sphincterotomy (MPS) for this condition. Studies published at present have not examined MPS as the primary treatment method in a homogenous (i.e. only those with ARP) patient group.

Methods:  Patients with PD and ARP were identified from an endoscopic database. Treatment protocol consisted of minor papilla guidewire cannulation and sphincterotomy with either sphincterotome over the wire or needle knife over pancreatic stent. A 5‐Fr stent was placed for 1 week. Adjunctive therapy was carried out as required. Follow‐up data was collected by interview with the patient and referring doctors and review of the medical record.

Results:  Twenty‐one patients underwent MPS for PD and ARP (median age = 33 years, range 9–77 years, men = 14). Median number of procedures to achieve cannulation and MPS was 1 (range 1–3). Complications encountered were pancreatitis (n = 2) and pain (n = 3). MPS restenosis occurred in 2. Adjuvant therapy was required in 14: stricture dilatation (n = 9), stone extraction (n = 7) and extracorporeal shock‐wave lithotripsy (n = 6). Complete stone clearance was achieved in 7/7. Median follow up was 38 months (range 4–67 months). Median total number of pancreatitis episodes and hospitalizations pre‐MPS were 4 and 2, respectively (range 1–20 and 0–5, respectively). Post‐MPS these were reduced to 0 and 0, respectively (range 0–8 and 0–4; P = 0.0007 and P = 0.0003), with complete abolition of episodes in 13 patients.

Conclusion:  MPS in association with other endoscopic therapies imparts a significant clinical benefit to patients with ARP and PD. Complete clinical resolution occurs in the majority. Treatment is safe, and the response is durable.
DESMOPLASTIC MELANOMA: THE ROLE OF RADIOTHERAPY IN IMPROVING LOCAL CONTROL
Authors: Foote Matthew C. , Burmeister Bryan , Burmeister Elizabeth , Bayley Gerard , Smithers B Mark
Published: March 2008

Background:  Desmoplastic melanoma (DM) is a rare subtype of cutaneous malignant melanoma reported to have a high local recurrence rate with surgical excision alone. The incidence of regional and distant metastasis is considered to be lower than traditional cutaneous melanoma, warranting more aggressive treatment of local disease. We conducted a retrospective analysis of patients with DM treated through the Princess Alexandra Hospital Melanoma Clinic to address the role of radiotherapy in the local control of this tumour.

Methods:  A review of a clinical database identified 24 patients between January 1997 and March 2006 with histopathologically confirmed DM who had received surgical excision as initial treatment followed by postoperative radiotherapy. All histopathology reports and radiotherapy treatment plans were reviewed. The primary outcome measure was 3‐year in‐field relapse‐free survival.

Results:  There were 24 patients with 22 having a DM in the head and neck region. The median tumour thickness was 5.2 mm. The histopathological margin was less than 10 mm in 17 (71%) of patients. The 3‐year in‐field relapse‐free survival was 91% (95% confidence interval 68.1–97.6%), the 3‐year relapse‐free survival was 86% (95% confidence interval 63.2–95.4%) with a 3‐year overall survival of 83% (95% confidence interval 54.9–94.3%).

Conclusion:  In a selected series of patients with DM with a high risk of local recurrence, adjuvant radiotherapy may have been effective in reducing the rate of local recurrence after surgical resection. A randomized trial is currently being developed to confirm this possible benefit.
NEW STANDARDS AND CRITERIA FOR ACCREDITATION OF HOSPITALS AND POSTS FOR SURGICAL TRAINING
Authors: Collins John P.
Published: March 2008

Accreditation of hospitals, other health‐care facilities and the surgical posts involved is an important part of ensuring that trainees are working in an environment where their teaching and learning equip them with the competencies necessary to fulfil the many roles expected of a surgeon. To undertake this accreditation, clear processes and objective measurements are required. Recent external reviews of the College showed the necessity for improvement of its existing accreditation methodology. New processes, standards, criteria, factors to be assessed for each criterion and the minimum requirements for each factor have been developed in a uniform framework for the nine surgical specialties. Each criterion relates to the overall objectives of the educational programmes, and the factors to be assessed are explicit, objective and measurable and should be achievable. Consensus was eventually achieved across the nine specialties. Protected time for teaching and learning and safe working conditions including safe hours were considered by the hospitals to have important consequences for service delivery as well as industrial ramifications for surgeons’ and trainees’ contracts and required extensive dialogue for a successful resolution. The accreditation process has a potentially significant effect on the availability of surgical services. Publicly available information about the process and requirements, consistency in their application and inclusion in the accreditation team of a hospital representative and surgeon from another region helps to ensure confidence and impartiality.
NOVEL METHOD FOR ASSESSMENT AND SELECTION OF TRAINEES FOR HIGHER SURGICAL TRAINING IN GENERAL SURGERY
Authors: Gallagher Anthony G. , Neary Paul , Gillen Peter , Lane Brian , Whelan Anthony , Tanner William A , Traynor Oscar
Published: March 2008

The aim of the study was to select surgeons for a higher surgical training in general surgery programme at the Royal College of Surgeons in Ireland (RCSI) using an objective, transparent and fair assessment programme. Thirty‐two individuals applied for higher surgical training in general surgery in Ireland in 2006. Sixteen applicants were short‐listed for interview and further assessment. All applicants were required to report on their education performance at undergraduate level and their postgraduate professional development. Applicants were scored on their training record during basic surgical training, structures references, clinical experience, approved technical skills courses, validated logbook and consolidation sheet. Assessments of their research and academic surgery included, the award of a higher degree by thesis, and other surgically relevant degree’s or diplomas that had been obtained through part‐time studies and were awarded by educational establishments recognized by RCSI or the Irish Medical Council. Short‐listed applicants completed validated objective assessment simulations of surgical skills, an interview and assessment of their suitability for a career in surgery. The nine individuals who were selected for higher surgical training in general surgery consistently scored higher than those candidates who were not, in post‐graduate development (P < 0.001), surgical skills (P < 0.002), interview scores (P < 0.007) and suitability for a career in surgery (P < 0.002). All performance assessment elements except undergraduate education showed high internal reliability α = 0.89 and good statistical power (range 0.95–0.99). The statistical power of undergraduate education was 0.7. The objective assessment programme introduced by RCSI for selection of candidates for the programme in higher surgical training in general surgery reliably and consistently distinguished between candidates. Candidates selected for further training consistently outperformed those who were not in good concordance between measures. This common selection process for higher surgical training is now being rolled out for selection into higher surgical training across all surgical specialties in Ireland.
VIDEOCONFERENCING SURGICAL TUTORIALS: BRIDGING THE GAP
Authors: Holland Andrew J. A. , Soundappan Soundappan V. S. , Oldmeadow Wendy
Published: March 2008

The expansion in medical student numbers has been associated with a move to increase the amount of time students spend in rural and remote locations. Providing an equivalent educational experience for students in surgical subspecialties in this setting is a logistical challenge. We sought to address this issue by providing synchronous tutorials in paediatric surgery using videoconferencing (VC) at two rural sites with the tutor located at a metropolitan paediatric clinical school. Between March 2005 and July 2006, 43 graduate students in the University of Sydney Medical Program were assigned to receive the paediatric component of the course at one of two sites within the School of Rural Health. During this 9‐week rotation, students were involved in two or three surgical tutorials by videoconference. Students were then invited to complete a confidential, anonymous 20‐point structured evaluation using a Likert scale. Valid responses were received from 40 students, a response rate of 93%. There were 21 females (52%), with 21 students based in Dubbo and 19 in Orange. Students agreed or strongly agreed that VC surgical tutorials were useful, the content well covered and student involvement encouraged (mean scores 4.7, 4.5 and 4.5; standard deviation 0.56, 0.72 and 0.72, respectively). Overall, the majority of students strongly agreed that participation in VC of surgical tutorials was valuable (mean 4.68, standard deviation 0.57). VC surgical tutorials were highly valued by graduate medical students as an educational method. Our data suggest that tutorials can be successfully provided at remote sites using VC.