bluuebunny/crossref_metadata_2025 huggingface dataset:
The Other Side of Agency
Authors: Reader Soran
Published: November 2007

In our philosophical tradition and our wider culture, we tend to think of persons as agents. This agential conception is flattering, but in this paper I will argue that it conceals a more complex truth about what persons are. In 1. I set the issues in context. In 2. I critically explore four features commonly presented as fundamental to personhood in versions of the agential conception: action, capability, choice and independence. In 3. I argue that each of these agential features presupposes a non-agential feature: agency presupposes patiency, capability presupposes incapability, choice presupposes necessity and independence presupposes dependency. In 4. I argue that such non-agential features, as well as being implicit within the agential conception, are as apt to be constitutive of personhood as agential features, and in 5. I conclude.
Moment‐tensor inversion of LP events recorded on Etna in 2004 using constraints obtained from wave simulation tests
Authors: Lokmer Ivan , Bean Christopher J. , Saccorotti Gilberto , Patanè Domenico
Published: November 2007

The persistent occurrence of long period (LP) events at Mt Etna became apparent with the installation of the first fixed broad‐band seismic network in late 2003. Repeating similar LP events from Nov. ‘03 to Sept. ‘04 indicate a non‐destructive source process. We perform moment tensor (MT) inversions on a stacked high S/N ratio representative LP signal, conducting a grid search for the source geometry and L2‐inversion for the source time function. Results indicate a NNW‐SSE oriented resonating sub‐vertical crack as the most probable source. This result is consistent with deformation and GPS observations. Crucial to this result are constraints imposed by detailed 3D full waveform numerical simulations in a heterogeneous tomographic model with topography, and in particular a detailed assessment of the influence of very near surface velocity structure on LP signals. Pulsating gas injection is hypothesised as the most likely LP trigger.
Observation of slow charge redistribution preceding excited-state proton transfer
Authors: Spry D. B. , Fayer M. D.
Published: November 2007

The photoacid 8-hydroxy-N,N,N′,N′,N′,N′-hexamethylpyrene-1,3,6-trisulfonamide (HPTA) and related compounds are used to investigate the steps involved in excited-state deprotonation in polar solvents using pump-probe spectroscopy and time correlated single photon counting fluorescence spectroscopy. The dynamics show a clear two-step process leading to excited-state proton transfer. The first step after electronic excitation is charge redistribution occurring on a tens of picoseconds time scale followed by proton transfer on a nanosecond time scale. The three states observed in the experiments (initial excited state, charge redistributed state, and proton transfer state) are recognized by distinct features in the time dependence of the pump-probe spectrum and fluorescence spectra. In the charge redistributed state, charge density has transferred from the hydroxyl oxygen to the pyrene ring, but the OH sigma bond is still intact. The experiments indicate that the charge redistribution step is controlled by a specific hydrogen bond donation from HPTA to the accepting base molecule. The second step is the full deprotonation of the photoacid. The full deprotonation is clearly marked by the growth of stimulated emission spectral band in the pump-probe spectrum that is identical to the fluorescence spectrum of the anion.
Wave packet driven dissociation and concerted elimination in CH2I2
Authors: Geißler Dominik , Pearson Brett J. , Weinacht Thomas
Published: November 2007

We follow the evolution of a vibrational wave packet in a highly excited state of the halogenated methane CH2I2. We observe how the wave packet modulates both dissociation and concerted elimination to form CH2I+ and I2+, respectively. We present a simple and intuitive interpretation of the molecular dynamics leading to the formation of the products.
Liouville theorems for Dirac-harmonic maps
Authors: Chen Q. , Jost J. , Wang G.
Published: November 2007

We prove Liouville theorems for Dirac-harmonic maps from the Euclidean space Rn, the hyperbolic space Hn, and a Riemannian manifold Sn (n⩾3) with the Schwarzschild metric to any Riemannian manifold N.
Observation of tilting activities in translated field reversed configuration plasma using computer tomography at two different cross sections
Authors: Yoshimura Satoru , Sugimoto Satoshi , Okada Shigefumi
Published: November 2007

Tilting activities of field reversed configuration (FRC) plasma were observed in translation experiments using computer tomography (CT) at two different cross sections in the FRC injection experiment (FIX) machine [S. Okada et al., Nucl. Fusion 47, 677 (2007)]. In these experiments, two sets of CT devices were installed at the upstream and downstream sides of the confinement chamber of the FIX. Each CT device was composed of three arrays of detectors sensitive to the near-infrared radiation. The peak of the reconstructed emission profile at one side was displaced from the center of the cross section of the chamber. On the other hand, the reconstructed profile at the other side was located around the center. This result suggests that the FRC plasma was tilting in the axial direction. The occurrence of the observed tilting activities had almost no effect on the lifetime of the FRC plasma.
Gate-tunable Ruderman-Kittel-Kasuya-Yosida interaction mediated by low-dimensional electrons with Rashba spin-orbit coupling
Authors: Lyu Pin , Liu Ning-Ning , Zhang Chao
Published: November 2007

The gate-controllable Ruderman-Kittel-Kasuya-Yosida (RKKY) magnetic interaction between the magnetic impurities embedded in one- and two-dimensional electron gas in the presence of Rashba spin-orbit coupling was analyzed theoretically. By using the eigenfunctions of the single-particle Rashba Hamiltonian as the basis of second quantization, we derived the RKKY interaction by fully taking into account the spin-orbit interaction. The dependence of the RKKY magnetic interaction on the Rashba spin-orbit coupling strength was obtained numerically. Our results clearly indicate that the RKKY interaction can be significantly modified by an applied voltage via the Rashba spin-orbit coupling.
Characterization of hydrogenated amorphous germanium compounds obtained by x-ray chemical vapor deposition of germane: Effect of the irradiation dose on optical parameters and structural order
Authors: Arrais Aldo , Benzi Paola , Bottizzo Elena , Demaria Chiara
Published: November 2007

Hydrogenated nonstoichiometric germanium materials have been produced by x-ray activated-chemical vapor deposition from germane. The reactions pattern leading to the solid products has been investigated. The dose effect on the composition, the local bonding configuration, and structural characteristics of the deposited solids has been studied using infrared absorption and Raman spectroscopy and has been discussed. Optical parameters have been also determined from ultraviolet-visible spectrophotometry data. The results show that the solids are formed by a random bound network of germanium and hydrogen atoms with a-Ge zones dispersed in the matrix. The Raman results and optical parameters indicate that the structural order, both short-range and intermediate-range, decreases with increasing irradiation time. This behavior suggests that the solid is involved in the reactions leading to the final product and indicates that the formation of amorphous germanium zones is stimulated by postdeposition irradiation, which induces compositional and structural modifications.
High electron mobility GaN grown under N-rich conditions by plasma-assisted molecular beam epitaxy
Authors: Koblmüller G. , Wu F. , Mates T. , Speck J. S. , Fernández-Garrido S. , Calleja E.
Published: November 2007

An alternative approach is presented for the plasma-assisted molecular beam epitaxy of high-quality GaN. Under N-rich growth conditions, an unexpected layer-by-layer growth mode was found for a wide range of growth temperatures in the GaN thermal decomposition regime (>750°C). Consequently, superior surface morphologies with roughness of less than 1nm (rms) have been achieved. For lightly Si-doped GaN films, room-temperature electron mobilities exceeding 1100cm2∕Vs were measured, surpassing the commonly insulating nature of GaN grown under N-rich conditions at low temperature.
Lattice thermal conductivity of nanoporous Si: Molecular dynamics study
Authors: Lee J.-H. , Grossman J. C. , Reed J. , Galli G.
Published: November 2007

Lattice thermal conductivity κl of Si with nanometer-sized pores along the [001] direction is calculated as a function of pore diameter (dp) and pore spacing (ds) by employing a molecular dynamics approach. Our results show that κl across pores is smaller than the bulk value by over two orders of magnitude at room temperature, and that it decreases (increases) as a function of dp (ds) for fixed ds (dp). This behavior is shown to originate from the reduction in the channels for phonon transport and the increased phonon scattering at the pore surfaces.
Markovian quasifree states on canonical anticommutation relation algebras
Authors: Pitrik József
Published: November 2007

The characterization of quasifree product states on CAR algebras is given. We also prove that the quasifree states on CAR algebra which saturate the strong additivity of von Neumann entropy with equality are product states.
Enhancement in open circuit voltage through a cascade-type energy band structure
Authors: Sista Srinivas , Yao Yan , Yang Yang , Tang Ming Lee , Bao Zhenan
Published: November 2007

In this paper, we report a method to increase the open-circuit voltage (VOC) of an organic solar cell by inserting an interfacial layer between the donor and acceptor layers to form a cascade-type energy band structure. We demonstrate its feasibility using a recently reported asymmetric pentacene derivative, tetraceno[2,3-b]thiophene (TT) as a donor material, C60 as an acceptor material, and copper phthalocyanine (CuPc) as the sandwich layer. The VOC was increased from 0.3V for the device with no CuPc sandwich layer to 0.56V for 13nm thick CuPc layer. The power conversion efficiency (PCE) of the device with 13nm CuPc layer was 1.53% and the fill factor (FF) was 0.64, in comparison to TT∕C60 device which had a PCE of 0.78% and a FF of 0.52.
Dielectrophoretic discrimination of bovine red blood cell starvation age by buffer selection and membrane cross-linking
Authors: Gordon Jason E. , Gagnon Zachary , Chang Hsueh-Chia
Published: November 2007

We report an interesting buffer electric relaxation time tuning technique, coupled with a glutaraldehyde cross-linking cell fixation reaction, which allows for sensitive dielectrophoretic analysis and discrimination of bovine red blood cell (bRBC) starvation age. The buffer composition is selected such that two easily accessible dielectrophoretic crossover frequencies (cof) exist. Low concentration glutaraldehyde fixation was observed to produce a threefold decrease in the higher cof with a comparable increase in the lower cof also witnessed. More importantly, increased glutaraldehyde fixation concentration significantly increased the higher cof by a factor found to be sensitive to the bRBC starvation age.
Allograft rejection mediated by memory T cells is resistant to regulation
Authors: Yang Jaeseok , Brook Matthew O. , Carvalho-Gaspar Manuela , Zhang Jidong , Ramon Hilda E. , Sayegh Mohamed H. , Wood Kathryn J. , Turka Laurence A. , Jones Nick D.
Published: November 2007

Alloreactive memory T cells may be refractory to many of the tolerance-inducing strategies that are effective against naive T cells and thus present a significant barrier to long-term allograft survival. Because CD4+CD25+regulatory T cells (Tregs) are critical elements of many approaches to successful induction/maintenance of transplantation tolerance, we used MHC class I and II alloreactive TCR-transgenic models to explore the ability of antigen-specific Tregs to control antigen-specific memory T cell responses. Upon coadoptive transfer into RAG-1−/−mice, we found that Tregs effectively suppressed the ability of naive T cells to reject skin grafts, but neither antigen-unprimed nor antigen-primed Tregs suppressed rejection by memory T cells. Interestingly, different mechanisms appeared to be active in the ability of Tregs to control naive T cell-mediated graft rejection in the class II versus class I alloreactive models. In the former case, we observed decreased early expansion of effector cells in lymphoid tissue. In contrast, in the class I model, an effect of Tregs on early proliferation and expansion was not observed. However, at a late time point, significant differences in cell numbers were seen, suggesting effects on responding T cell survival. Overall, these data indicate that the relative resistance of both CD4+and CD8+alloreactive memory T cells to regulation may mediate resistance to tolerance induction seen in hosts with preexisting alloantigen-specific immunity and further indicate the multiplicity of mechanisms by which Tregs may control alloimmune responsesin vivo.
Histamine is stored in mast cells of most evolutionarily advanced fish and regulates the fish inflammatory response
Authors: Mulero Iván , Sepulcre M. Pilar , Meseguer José , García-Ayala Alfonsa , Mulero Victoriano
Published: November 2007

Mast cells are important as initiators and effectors of innate immunity and regulate the adaptive immune responses. They have been described in all classes of vertebrates and seem to be morphologically and functionally similar. However, early studies had shown that fish and amphibian mast cells were devoid of histamine. In this study, we take a fresh look at the evolution of histamine and find that the mast cells of fish belonging to the Perciformes order, the largest and most evolutionarily advanced order of teleosts, are armed with histamine. More importantly, histamine is biologically active in these fish where it is able to regulate the inflammatory response by acting on professional phagocytes. In addition, the actions of histamine in these immune cells seem to be mediated through the engagement of H1and H2receptors, which, together with the H3receptor, are well conserved in bony fish. We propose that the storage of histamine in vertebrate mast cells and its use as an inflammatory messenger was established in primitive reptiles (Lepidosauria) ≈276 million years ago. This same feature seems to have developed independently in Perciform fish much more recently in the Lower Eocene, between 55 and 45 million years ago, a short period during which the great majority of Percomorph families appeared.
Matrix metalloproteinase 7 controls pancreatic acinar cell transdifferentiation by activating the Notch signaling pathway
Authors: Sawey Eric T. , Johnson Johnny A. , Crawford Howard C.
Published: November 2007

Acinar-to-ductal metaplasia in the pancreas is associated with an increased risk for tumorigenesis. Molecular dissection of this process
in vitro
has shown that primary acinar cells, in response to EGF receptor ligands, can transdifferentiate into duct-like epithelia, passing through a nestin-positive intermediate, in a Notch pathway-dependent manner. Here, we show that
in vitro
acinar transdifferentiation depends on matrix metalloproteinase 7 (MMP-7), a proteinase expressed in most metaplastic epithelia
in vivo
. MMP-7 was found to be required for Notch activation, which leads to dedifferentiation of acinar cells to the nestin-positive transitional cell. Besides being necessary for acinar transdifferentiation, it was found that MMP-7 activity was sufficient to induce the process, indicating that molecular signals capable of initiating MMP-7 expression also have the potential to induce formation of metaplastic epithelia in the pancreas.
Protein–protein interaction inhibition (2P2I) combining high throughput and virtual screening: Application to the HIV-1 Nef protein
Authors: Betzi Stéphane , Restouin Audrey , Opi Sandrine , Arold Stefan T. , Parrot Isabelle , Guerlesquin Françoise , Morelli Xavier , Collette Yves
Published: November 2007

Protein–protein recognition is the cornerstone of multiple cellular and pathological functions. Therefore, protein–protein interaction inhibition (2P2I) is endowed with great therapeutic potential despite the initial belief that 2P2I was refractory to small-molecule intervention. Improved knowledge of complex molecular binding surfaces has recently stimulated renewed interest for 2P2I, especially after identification of “hot spots” and first inhibitory compounds. However, the combination of target complexity and lack of starting compound has thwarted experimental results and created intellectual barriers. Here we combined virtual and experimental screening when no previously known inhibitors can be used as starting point in a structure-based research program that targets an SH3 binding surface of the HIV type I Nef protein. High-throughput docking and application of a pharmacophoric filter on one hand and search for analogy on the other hand identified drug-like compounds that were further confirmed to bind Nef in the micromolar range (isothermal titration calorimetry), to target the Nef SH3 binding surface (NMR experiments), and to efficiently compete for Nef–SH3 interactions (cell-based assay, GST pull-down). Initial identification of these compounds by virtual screening was validated by screening of the very same library of compounds in the cell-based assay, demonstrating that a significant enrichment factor was attained by the
in silico
screening. To our knowledge, our results identify the first set of drug-like compounds that functionally target the HIV-1 Nef SH3 binding surface and provide the basis for a powerful discovery process that should help to speed up 2P2I strategies and open avenues for new class of antiviral molecules.
The blinking spotlight of attention
Authors: VanRullen Rufin , Carlson Thomas , Cavanagh Patrick
Published: November 2007

Increasing evidence suggests that attention can concurrently select multiple locations; yet it is not clear whether this ability relies on continuous allocation of attention to the different targets (a “parallel” strategy) or whether attention switches rapidly between the targets (a periodic “sampling” strategy). Here, we propose a method to distinguish between these two alternatives. The human psychometric function for detection of a single target as a function of its duration can be used to predict the corresponding function for two or more attended targets. Importantly, the predicted curves differ, depending on whether a parallel or sampling strategy is assumed. For a challenging detection task, we found that human performance was best reflected by a sampling model, indicating that multiple items of interest were processed in series at a rate of approximately seven items per second. Surprisingly, the data suggested that attention operated in this periodic regime, even when it was focused on a single target. That is, attention might rely on an intrinsically periodic process.
Yeast gain-of-function mutations reveal structure–function relationships conserved among different subfamilies of transient receptor potential channels
Authors: Su Zhenwei , Zhou Xinliang , Haynes W. John , Loukin Stephen H. , Anishkin Andriy , Saimi Yoshiro , Kung Ching
Published: November 2007

Transient receptor potential (TRP) channels found in animals, protists, and fungi are primary chemo-, thermo-, or mechanosensors. Current research emphasizes the characteristics of individual channels in each animal TRP subfamily but not the mechanisms common across subfamilies. A forward genetic screen of the TrpY1, the yeast TRP channel, recovered gain-of-function (GOF) mutations with phenotype
in vivo
and
in vitro
. Single-channel patch-clamp analyses of these GOF-mutant channels show prominent aberrations in open probability and channel kinetics. These mutations revealed functionally important aromatic amino acid residues in four locations: at the intracellular end of the fifth transmembrane helix (TM5), at both ends of TM6, and at the immediate extension of TM6. These aromatics have counterparts in most TRP subfamilies. The one in TM5 (F380L) aligns precisely with an exceptional
Drosophila
mutant allele (F550I) that causes constitutive activity in the canonical TRP channel, resulting in rapid and severe retinal degeneration beyond mere loss of phototaxis. Thus, this phenylalanine maintains the balance of various functional states (conformations) of a channel for insect phototransduction as well as one for fungal mechanotransduction. This residue is among a small cluster of phenylalanines found in all known subfamilies of TRP channels. This unique case illustrates that GOF mutations can reveal structure–function principles that can be generalized across different TRP subfamilies. It appears that the conserved aromatics in the four locations have conserved functions in most TRP channels. The possible mechanistic roles of these aromatics and the further use of yeast genetics to dissect TRP channels are discussed.
Structural differentiation of skeletal muscle fibers in the absence of innervation in humans
Authors: Boncompagni Simona , Kern Helmut , Rossini Katia , Hofer Christian , Mayr Winfried , Carraro Ugo , Protasi Feliciano
Published: November 2007

The relative importance of muscle activity versus neurotrophic factors in the maintenance of muscle differentiation has been greatly debated. Muscle biopsies from spinal cord injury patients, who were trained with an innovative protocol of functional electrical stimulation (FES) for prolonged periods (2.4–9.3 years), offered the unique opportunity of studying the structural recovery of denervated fibers from severe atrophy under the sole influence of muscle activity. FES stimulation induced surprising recovery of muscle structure, mass, and force even in patients whose muscles had been denervated for prolonged periods before the beginning of FES training (up to 2 years) and had almost completely lost muscle-specific internal organization. Ninety percent (or more) of the fibers analyzed by electron microscopy showed a striking recovery of the ultrastructural organization of myofibrils and Ca
2+
-handling membrane systems. This functional/structural restoration follows a pattern that mimics some aspects of normal muscle differentiation. Most importantly, the recovery occurs in the complete absence of motor and sensory innervation and of nerve-derived trophic factors, that is, solely under the influence of muscle activity induced by electrical stimulation.
An assessment of the uses of homologous interactions
Authors: Saeed Ramazan , Deane Charlotte
Published: November 2007

Motivation: Protein–protein interactions have proved to be a valuable starting point for understanding the inner workings of the cell. Computational methodologies have been built which both predict interactions and use interaction datasets in order to predict other protein features. Such methods require gold standard positive (GSP) and negative (GSN) interaction sets. Here we examine and demonstrate the usefulness of homologous interactions in predicting good quality positive and negative interaction datasets.

Results: We generate GSP interaction sets as subsets from experimental data using only interaction and sequence information. We can therefore produce sets for several species (many of which at present have no identified GSPs). Comprehensive error rate testing demonstrates the power of the method. We also show how the use of our datasets significantly improves the predictive power of algorithms for interaction prediction and function prediction.

Furthermore, we generate GSN interaction sets for yeast and examine the use of homology along with other protein properties such as localization, expression and function. Using a novel method to assess the accuracy of a negative interaction set, we find that the best single selector for negative interactions is a lack of co-function. However, an integrated method using all the characteristics shows significant improvement over any current method for identifying GSN interactions. The nature of homologous interactions is also examined and we demonstrate that interologs are found more commonly within species than across species.

Conclusion: GSP sets built using our homologous verification method are demonstrably better than standard sets in terms of predictive ability. We can build such GSP sets for several species. When generating GSNs we show a combination of protein features and lack of homologous interactions gives the highest quality interaction sets.

Availability: GSP and GSN datasets for all the studied species can be downloaded from http://www.stats.ox.ac.uk/~deane/HPIV

Contact:  saeed@stats.ox.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
X-ray colour imaging
Authors: Cernik R.J , Khor K.H , Hansson C
Published: November 2007

A prototype X-ray colour imaging system has been assembled using the principle of tomographic energy-dispersive diffraction imaging (TEDDI). The new system has been tested using samples of nylon-6, aluminium powder and deer antler bone. Non-destructive three-dimensional images of the test objects have been reconstructed on a 300 μm scale with an associated diffraction pattern at each voxel. In addition, the lattice parameters of the polycrystalline material present in the sampled voxels have been determined using full pattern refinement methods. The use of multiple diffracted parallel colour X-ray beams has allowed simultaneous spatially resolved data collection across a plane of the sample. This has simplified the sample scan motion and has improved data collection times by a factor scaling with the number of detector pixels. The TEDDI method is currently limited to thin samples (approx. 1–2 mm) with light atoms owing to the very low detection efficiency of the silicon detector at X-ray energies above 25 keV. We describe how these difficulties can be removed by using semiconductor detectors made from heavier atomic material.
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs
Authors: Barrera Leah O. , Li Zirong , Smith Andrew D. , Arden Karen C. , Cavenee Webster K. , Zhang Michael Q. , Green Roland D. , Ren Bing
Published: November 2007

By integrating genome-wide maps of RNA polymerase II (Polr2a) binding with gene expression data and H3ac and H3K4me3 profiles, we characterized promoters with enriched activity in mouse embryonic stem cells (mES) as well as adult brain, heart, kidney, and liver. We identified ∼24,000 promoters across these samples, including 16,976 annotated mRNA 5′ ends and 5153 additional sites validating cap-analysis of gene expression (CAGE) 5′ end data. We showed that promoters with CpG islands are typically non-tissue specific, with the majority associated with Polr2a and the active chromatin modifications in nearly all the tissues examined. By contrast, the promoters without CpG islands are generally associated with Polr2a and the active chromatin marks in a tissue-dependent way. We defined 4396 tissue-specific promoters by adapting a quantitative index of tissue-specificity based on Polr2a occupancy. While there is a general correspondence between Polr2a occupancy and active chromatin modifications at the tissue-specific promoters, a subset of them appear to be persistently marked by active chromatin modifications in the absence of detectable Polr2a binding, highlighting the complexity of the functional relationship between chromatin modification and gene expression. Our results provide a resource for exploring promoter Polr2a binding and epigenetic states across pluripotent and differentiated cell types in mammals.
Characterization of an exosite binding inhibitor of matrix metalloproteinase 13
Authors: Gooljarsingh Lata T. , Lakdawala Ami , Coppo Frank , Luo Lusong , Fields Gregg B. , Tummino Peter J. , Gontarek Richard R.
Published: November 2007

Matrix metalloproteinase 13 (MMP13) is a key enzyme implicated in the degradation of the extracellular matrix in osteoarthritis. Clinical administration of broad spectrum MMP inhibitors such as marimastat has been implicated in severe musculo‐skeletal side effects. Consequently, research has been focused on designing inhibitors that selectively inhibit MMP13, thereby circumventing musculo‐skeletal toxicities. A series of pyrimidine dicarboxamides were recently shown to be highly selective inhibitors of MMP13 with a novel binding mode. We have applied a molecular ruler to this exosite by dual inhibition studies involving a potent dicarboxamide in the presence of two metal chelators of different sizes. A larger hydroxamate mimic overlaps and antagonizes binding of the dicarboxamide to the exosite whereas the much smaller acetohydroxamate synergizes with the dicarboxamide. These studies elucidate the steric requirement for compounds that fit exclusively into the active site, a mandate for generating highly selective MMP13 inhibitors.
The yeast Ski complex is a hetero‐tetramer
Authors: Synowsky Silvia A. , Heck Albert J.R.
Published: November 2007

The yeast Ski complex assists the exosome in the degradation of mRNA. The Ski complex consists of three components; Ski2, Ski3, and Ski8, believed to be present in a 1:1:1 stoichiometry. Measuring the mass of intact isolated endogenously expressed Ski complexes by native mass spectrometry we unambiguously demonstrate that the Ski complex has a hetero‐tetrameric stoichiometry consisting of one copy of Ski2 and Ski3 and two copies of Ski8. To validate the stoichiometry of the Ski complex, we performed tandem mass spectrometry. In these experiments one Ski8 subunit was ejected concomitant with the formation of a Ski2/Ski3/Ski8 fragment, confirming the proposed stoichiometry. To probe the topology of the Ski complex we disrupted the complex and mass analyzed the thus formed subcomplexes, detecting Ski8–Ski8, Ski2–Ski3, Ski8–Ski2, and Ski8–Ski8–Ski2. Combining all data we construct an improved structural model of the Ski complex.
Cross‐linking of sites involved with alcohol action between transmembrane segments 1 and 3 of the glycine receptor following activation
Authors: Lobo Ingrid A. , Harris R. Adron , Trudell James R.
Published: November 2007

J. Neurochem.(2008)104,1649–1662.

The glycine receptor is a member of the Cys‐loop, ligand‐gated ion channel family and is responsible for inhibition in the CNS. We examined the orientation of amino acids I229 in transmembrane 1 (TM1) and A288 in TM3, which are both critical for alcohol and volatile anesthetic action. We mutated these two amino acids to cysteines either singly or in double mutants and expressed the receptors inXenopus laevisoocytes. We tested whether disulfide bonds could form between A288C in TM3 paired with M227C, Y228C, I229C, or S231C in TM1. Application of cross‐linking (mercuric chloride) or oxidizing (iodine) agents had no significant effect on the glycine response of wild‐type receptors or the single mutants. In contrast, the glycine response of the I229C/A288C double mutant was diminished after application of either mercuric chloride or iodine only in the presence of glycine, indicating that channel gating causes I229C and A288C to fluctuate to be within 6 Å apart and form a disulfide bond. Molecular modeling was used to thread the glycine receptor sequence onto a nicotinic acetylcholine receptor template, further demonstrating that I229 and A288 are near‐neighbors that can cross‐link and providing evidence that these residues contribute to a single binding cavity.
Stand selection by birds in Scots pinewoods in Scotland: the need for more old‐growth pinewood
Authors: SUMMERS RON W.
Published: November 2007

A study at Abernethy Forest, Scotland, examined stand selection by some of the birds of conservation concern that inhabit pinewoods. Abernethy Forest was ideally suited for the study because all four main stand types of forest development (stand initiation, stem exclusion, understorey reinitiation and old‐growth) were represented. Capercaillies Tetrao urogallus(both males and females) and crossbills Loxiaspp. preferred old‐growth pinewood in winter, and Redstarts Phoenicurus phoenicurusand Tree Pipits Anthus trivialispreferred old‐growth in summer. Great Spotted Woodpecker Dendrocopos major selected snags in old‐growth to excavate nest and roost sites. In winter, Crested Tits Parus cristatus had a weak selection for old‐growth stands and Bullfinches Pyrrhula pyrrhulapreferred stands at initiation. Possible reasons for these preferences are put forward. Although the area of conifer woodland in Scotland is 888 000 ha, it largely comprises North American species destined to be cut before reaching old‐growth. Old‐growth pinewood in Scotland is largely confined to the fragments of ancient native pinewood, amounting to only 16 000 ha. To conserve some pinewood birds of conservation concern, a mechanism to allow more Scots Pine Pinus sylvestris woods to reach and remain in an old‐growth state needs to be pursued.
Influences of restock age and habitat patchiness on Tree Pipits Anthus trivialis breeding in Breckland pine plantations
Authors: BURTON NIALL H.K.
Published: November 2007

The British Tree Pipit Anthus trivialis population has shown a marked decline in recent decades, together with a range contraction that has been most apparent in central and southeast England. In East Anglia, the species is now largely restricted to heathland and, in particular, the conifer plantations established on light soils in these areas. Here I evaluate how Tree Pipits are influenced by the age of pine restock and the patchiness of habitat in Thetford Forest in the Breckland area of Norfolk and Suffolk, eastern England. Both the probability of occurrence and the densities of territory‐holding Tree Pipits varied according to the age of coupes of restock – densities peaking in restock 1–6 years old – and were also significantly higher in coupes (a stand comprising one or more forest subcompartments planted in the same year, usually with the same tree crop) in the largest, most central forest block than in smaller, isolated blocks peripheral to this. Within coupes, the distribution and thus densities of Tree Pipits were limited by the availability of songposts. Few songflights finished on the ground or in flight and displaying birds only perched on restock once trees were at least 3 years old (0.8 m high) – thus, territories were only established away from bordering or retained mature trees once restock had reached this age. Pairing success was reduced among males with territories of less than 1 ha, as found in the highest densities in restock, but was unrelated to the proportion of songflights that individuals finished on perches. Thus, although the availability of songposts limited the distribution of the species, it did not appear to affect individual breeding success. The study highlights the importance of pine plantations for the species in lowland England, but also the benefits of large blocks of habitat and targeted forest management, for instance, the retention of mature trees in coupes of restock for Pipits to use as songposts.
Habitat change and woodland birds in Britain: implications for management and future research
Authors: FULLER R. J. , SMITH K. W. , GRICE P. V. , CURRIE F. A. , QUINE C. P.
Published: November 2007

There is increasing evidence that changes in habitat structure in the form of reduced understorey and loss of open habitats, both probably a result of increases in shading and deer browsing, may be responsible for causing recent changes in the composition of breeding bird communities in many lowland British woods and forests. In contrast, management of upland coniferous forests may prevent the attainment of mature and old‐growth structures which would benefit community development in these new ecosystems. We suggest that the key challenge for woodland conservation policy is to create larger areas of both young‐growth and old‐growth habitat. These objectives need not necessarily conflict with each other, or with other multipurpose forestry objectives, provided that they inform strategic plans and are targeted at appropriate locations and scales. In the lowlands, the current large stock of middle‐aged, often unmanaged and species‐poor woodland provides an opportunity to restore or create new woodland habitats of high biodiversity value. The development of woodfuel markets may effectively increase the amount of young‐growth but it is unclear exactly what habitat structures might be created. In the uplands, allowing more natural development of native woodland in mosaics with other habitats may provide opportunities for both old‐ and young‐growth species. For the foreseeable future, deer impacts will continue to be widespread and probably increasingly severe in many areas. In view of the uncertainty about the implications of climate change for woodland ecosystems, a strong case can be made for attempting to buffer valued wildlife communities against damaging effects by creating and maintaining high structural diversity at a range of scales and increasing the area of woodland.
Myocardial Fiber Diameter as a Good Indicator of Outcome in Batista's Operation
Authors: Higuchi Maria de Lourdes , Moreira Luiz Felipe , Silvestre Julia Maria , Gutierrez Paulo Sampaio , Savalli Carine , Stolf Noedir , Bellotti Giovanni , Ramires José Antonio , Jatene Adib
Published: November 2007

Abstract Background: Despite the initial promissory results of partial left ventriculectomy, or Batista's operation, the postoperative mortality associated with the procedure has been too high. We described a histopathologic study performed to identify histological parameters that could help to determine outcomes of patients undergoing this procedure.

Methods and Results: Myocardial fiber diameter, myocardial fibrosis, thickness of the compact wall, and number of cells presenting from the endocardium to epicardium were analyzed in 32 patients with idiopathic dilated cardiomyopathy who underwent Batista's operation. Data were grouped by patients who died ≤ 6 months and patients who survived for > 6 months after the surgical procedure. Additional analyses were performed to compare results according the causes of death and to test the application of these results to biopsy.

Results: Myocardial fiber diameter was the only index that could distinguish the two groups. Myocardial fiber diameter < 22 μm distinguished the group of patients who survived the 6‐month postoperative period from patients who died during that time with sensitivity of 85.7 and specificity of 72.2. The subendocardial region of the compact wall and the trabecular portion of the wall exhibited comparable results.

Conclusion: Our results indicate that the myocardial fiber diameter of samples from the trabecular or subendocardial compact wall regions may help predict the outcome of left ventriculectomy. Samples from the trabecular or subendocardial compact wall regions were used for analysis. Further prospective studies involving left ventricular endomyocardial biopsies are necessary to confirm if the use of myocardial fiber diameter in the selection of patients for surgery improves the index of success of Batista's operation. Other factors that are involved remain unclear.
Total Arterial Myocardial Revascularization Using New Composite Graft Techniques for Internal Mammary and/or Radial Arteries Conduits
Authors: Bonacchi Massimo , Prifti Edvin , Frati Giacomo , Leacche Marzia , Salica Andrea , Giunti Gabriele , Proietti Piero , Furci Barbara , Miraldi Fabio
Published: November 2007

Abstract Background: Total arterial myocardial revascularization (TAMR) is feasible because of the excellent long‐term patency of the arterial conduits. We present five new surgical configurations for TAMR. Methods: Between December 1998 and July 1999,34 patients with triple vessel disease underwent TAMR. All patients were in CCS 111 or IV. Sketelonized internal mammary arteries (IMAs) were used. The surgical techniques for TAMR consisted of Y or T composite grafts constructed between the in situ RlMA and free LIMA graft or radial artery (RA) conduit in three different configurations. Other techniques uses included a T graft constructed between the RA conduit and free LIMA graft in two configurations. Twenty‐six (76%) patients underwent contrast‐enhanced TTE color Doppler before and a after adenosine provocative test, and seven (20%) patients had postoperative coronary angiography. Results: Overall, 144 anastomoses (average number per patient, 4.2) were completed. One (2.9%) patient undergoing an inverted T graft technique died on postoperative day 2. Another patient (2.9%) undergoing the right Y graft technique using IMAs and RA suffered pe‐rioperative AM1 due to RA conduit vasospasm. Contrast‐enhanced TTE color Doppler before and after the adenosine provocative test and at 1 week postoperation revealed a coronary flow reserve (CFR) of 2.1 ± 0.2 in the LIMA stem, and in the RlMA stem, a CFR of 2.3 ± 0.3 (P < 0.007). In one patient undergoing the right Y graft technique using IMAs, we found only anomalous flow dynamic parameters of RIMA, suggesting a partial graft closure. The angio‐graphic examination revealed a free LIMA graft closure. At 6 ± 2.4 months after operation 33 patients were alive and free of angina. The IMAs stem evaluation by TTE color Doppler at follow‐up revealed a 2.45 ± 0.1 mm LIMA diameter and 2.6 ± 0.2 mm RlMA diameter, which was more than early postoperative data of P < 0.001 and P < 0.007, respectively. Conclusion: These data indicate that TAMR in young patients perhaps offers a better postoperative outcome and perhaps should be part of the surgical armamentarium. These techniques apply the “nontouch” principle and should be taken into consideration in patients with a heavily calcified aorta. Contrast‐enhanced TTE color Doppler is a safe, accurate, and noninvasive test, which allows assessment of IMA patency and CFR evaluation. The flow reserve of the IMAs seems to be adequate for multiple coronary anastomoses.
Carotid Disease Is a Risk Factor for Stroke in Coronary Bypass Operations
Authors: Birincio˘lu Cemal Levent , Bayazit Murat , Ulus A. Tulga , Bardakçi Hagmet , Küçüker Şeref Alp , Taşdemir O˘uz
Published: November 2007

Abstract The purpose of this study was to investigate the risk of perioperative major cere‐brovascular events (MCVEs) in patients undergoing coronary artery bypass grafting (CABG) and to develop preventive therapy. After excluding the patients with marked ascending aortic atheromas and those with combined intracardiac procedures such as valve replacement and aneurysmectomy, 722 consecutive patients who had carotid artery duplex scanning (CADS) and CABG were studied. The results of the study showed the correlation of advanced age, smoking, previous major cerebrovascular event (MCVE), and severe coronary artery disease with high grade carotid artery stenosis of 80–99% (p < 0.05). A total of 13 patients had perioperative MCVE and an analysis of risk factors showed that the MCVE correlated with carotid stenosis of > 60% and reduced cardiac output requiring inotropic support (p < 0.01). Prophylactic carotid endarterectomy (CEA) in patients with 80% to 99% carotid stenosis notably decreased the incidence of MCVE (p < 0.01). and the use of the “pump off” technique instead of standard cardiopulmonary bypass decreased MCVE (p = 0.0561. On the basis of these data, prophylactic carotid endarterectomy is effective in averting perioperative MCVE in subjects with carotid stenosis of 80% to 99%. and for those with 6096 to 7996 carotid stenosis, the pump off technique decreases MCVE.
Mating with sperm‐depleted males does not increase female mating frequency in the parasitoid Lariophagus distinguendus
Authors: Steiner Sven , Henrich Nina , Ruther Joachim
Published: November 2007

Sexual conflicts due to divergent male and female interests in reproduction are common in parasitic Hymenoptera. The majority of parasitoid females are monandrous, whereas males are able to mate repeatedly. Thus, accepting only a single mate might be costly when females mate with a sperm‐depleted male, which may not transfer a sufficient amount of sperm. In the present study, we investigated the reproductive performance in the parasitoid Lariophagus distinguendus Först. (Hymenoptera: Pteromalidae) and studied whether mating with experimentally sperm‐depleted males increases the tendency of females to remate. Males were able to mate with up to 17 females offered in rapid succession within a 10‐h test period. The resulting female offspring, as an indirect measure of sperm transfer, remained constant during the first six matings and then decreased successively with increasing number of copulations by the males. Experimentally sperm‐depleted males continued to mate even if they transferred only small amounts or no sperm at all. Unlike males, the majority of females mated only once during a 192‐h test period. A second copulation was observed only in a few cases (maximum 16%). The frequency of remating was not influenced by the mating status of the first male the females had copulated with, suggesting that these events are not controlled by sperm deficiency of the females. Furthermore, we investigated male courtship behaviour towards mated females. Male courtship intensity towards mated females decreased with increasing time. However, females that had mated with an experimentally sperm‐depleted male did not elicit stronger or longer‐lasting behavioural responses in courting males than those that had mated with a virgin male. As the observed behaviours in L. distinguendus are known to be elicited by a courtship pheromone, these results suggest that females no longer invest in pheromone biosynthesis after mating (as indicated by ceasing behavioural responses of courting males), irrespective of whether they have received a sufficient amount of sperm or not. We discuss the results with respect to a possible mating strategy of sperm‐depleted males.
The integrated productivity of a Macrocystis integrifolia plant
Authors: Druehl Louis D.
Published: November 2007

The relative contributions of various plant parts to the integrated productivity of Macrocystis integrifolia Bory were determined by extrapolating the net photosynthetic capacity of each part, as observed in vitro, to its proportional contribution to the biomass of a M. integrifolia kelp bed. The nongrowing plant parts (primarily mature and senescing blades) which represented 66% of the total plant biomass were responsible for 58% of the plant's net productivity. This productivity was assumed, in part, to support growing portions of the plant and, in part, to be stored as reserves for the initiation of late-winter growth. Within the three classes of blades studied (growing, mature, and senescing), which constituted 79% of the total plant biomass, there were no significant differences in photosynthetic pigment concentrations or in net photosynthetic rates. Dark respiration rates were significantly different between these three classes of blades: the older the blade, the lower the respiratory rate. Macrocystis integrifolia optimized its productivity by reducing the respiratory demands of the fully grown tissue, and by having all blades contribute to the net photosynthate pool. These adaptations vary from those of the deeper-water Macrocystis pyrifera (L.) C. Ag., which has been shown by others not to have differential respiratory rates and to have net productivity generally restricted to the shallow-water canopy.
Technique for observation of mycorrhizal development under 0monoxenic conditions
Authors: Yang Chin S. , Wilcox Hugh E.
Published: November 2007

A culture system designed to study root growth and mycorrhizal formation is described. This technique allows shoots of seedlings to grow in the air while roots of the seedlings are growing in an aseptic condition where their growth and differentiation, fungal colonization, mantle formation, and mycorrhizal association can be observed. Packing vermiculite and ground peat moss into the tubes stabilized the pH. This technique has been successful with two pine species and three mycorrhizal fungi.