bluuebunny/crossref_metadata_2025 huggingface dataset:
Visual Data Mining of Multimedia Data for Social and Behavioral Studies
Authors: Yu Chen , Zhong Yiwen , Smith Thomas , Park Ikhyun , Huang Weixia
Published: February 2009

With advances in computing techniques, a large amount of high-resolution high-quality multimedia data (video and audio, and so on) has been collected in research laboratories in various scientific disciplines, particularly in cognitive and behavioral studies. How to automatically and effectively discover new knowledge from rich multimedia data poses a compelling challenge because most state-of-the-art data mining techniques can only search and extract pre-defined patterns or knowledge from complex heterogeneous data. In light of this challenge, we propose a hybrid approach that allows scientists to use data mining as a first pass, and then forms a closed loop of visual analysis of current results followed by more data mining work inspired by visualization, the results of which can be in turn visualized and lead to the next round of visual exploration and analysis. In this way, new insights and hypotheses gleaned from the raw data and the current level of analysis can contribute to further analysis. As a first step toward this goal, we implement a visualization system with three critical components: (1) a smooth interface between visualization and data mining; (2) a flexible tool to explore and query temporal data derived from raw multimedia data; and (3) a seamless interface between raw multimedia data and derived data. We have developed various ways to visualize both temporal correlations and statistics of multiple derived variables as well as conditional and high-order statistics. Our visualization tool allows users to explore, compare and analyze multi-stream derived variables and simultaneously switch to access raw multimedia data.
The Transfiguration of Existence and Sovereign Life: Sloterdijk and Nietzsche on Posthuman and Superhuman Futures
Authors: Ansell-Pearson Keith
Published: February 2009

This essay provides a close reading of Sloterdijk's book Thinker on Stage: Nietzsche's Materialism (1989, University of Minnesota Press, Minneapolis, MN). Sloterdijk's book is itself a discussion of Nietzsche's book The Birth of Tragedy, and the account offered here is a critical appreciation of both texts, focusing on the question of individual and collective existence. The essay looks at the question of the future of the human, raising the question of the superhuman alongside that of the posthuman. In doing so, it brings in other texts from Sloterdijk—especially “Rules for the human zoo”—and offers an account of Nietzsche's work on these themes as a whole. The essay criticises some aspects of Sloterdijk's appropriation, but more positively makes the case for retrieving the uniqueness of Nietzsche's answers. Human existence cannot be corrected, but it can be transfigured.
Being-with as Making Worlds: The ‘Second Coming’ of Peter Sloterdijk
Authors: Elden Stuart , Mendieta Eduardo
Published: February 2009

This introductory essay provides a background to the writings of Peter Sloterdijk. It begins with a discussion of writings translated into English in the late 1980s—the Critique of Cynical Reason and Thinker on Stage—but then shows how Sloterdijk's work has developed and changed over the last two decades. Particular attention is paid to his writings on Europe and politics; the three-volume book Sphären [Spheres]; and his most recent writings on globalisation. The suggestion is that with the extensive forthcoming programme of translations and renewed interest in his work the scene is set for an effective ‘second coming’ of Sloterdijk. This theme issue of Society and Space contributes to that work of translation and interpretation.
Bubbles, Globes, Wrappings, and Plektopoi: Minimal Notes to Rethink Metaphysics from the Standpoint of the Social Sciences
Authors: Nogueira Luis Castro
Published: February 2009

This essay aims to offer a critical development of some of the implications that the ideas of Peter Sloterdijk give rise to, in order to explore and rethink the microclimatic and self-immunological dimensions of the old metaphysical schools in particular and of metaphysics in general. Nevertheless, in order to achieve this task it is necessary to free Sloterdijk's thought from certain phantasms that beset and undermine the most promising of his categories. The first part of the paper consists of an exposition of some of the basic ideas regarding bubbles and globes (thus, following the first two volumes of the trilogy Sphären); and contends that it is not possible to pass from the first ( Blasen/bubbles) to the second ( Globen/globes) without losing the most critical and subversive elements concerning the task of rethinking the social sciences in their micro-anthropological dimensions. In the second part, against the account of Western metaphysics espoused by Sloterdijk but taking on board some of his most suggestive insights, a radically different materialist perspective is put to the test. Finally, the third part offers a summary of our differences.
Cohabitating in the Globalised World: Peter Sloterdijk's Global Foams and Bruno Latour's Cosmopolitics
Authors: Morin Marie-Eve
Published: February 2009

This paper seeks to present a comprehensive and systematic picture of Peter Sloterdijk's ambitious and provocative theory of globalisation. In the Sphären (Spheres) trilogy, Sloterdijk provides both a spatialised ontology of human existence and a historical thesis concerning the radical shifts in human conceptions of the space or sphere they inhabit. Essentially, Sloterdijk argues that global interconnectedness and increasing population and communication density have brought about a situation in which every human action is limited and inhibited by the proximity of others—a situation he describes using the metaphor of foam. In this context, are not all possibilities for constructive political action stifled from the very outset? I will argue that Bruno Latour's concept of cosmopolitics furnishes us with resources to respond to this collapse of political space.
Air Conditioning Spaceship Earth: Peter Sloterdijk's Ethico-Aesthetic Paradigm
Authors: van Tuinen Sjoerd
Published: February 2009

This paper explores the convergence of anthropology and ecology in the recent work of Peter Sloterdijk. Firstly, it is argued that Sloterdijk proposes an important new interpretation of Heideggerian Gelassenheit for which I propose the English word ‘relief. The concept of relief rests on the substitution of ontological difference by what I propose to call ‘natal’ or ‘natural’ difference. Secondly, I will develop the significance of these concepts in relation to complexity theory and cybernetics, focusing on a key subject in the Sphären trilogy—insulation—and on a key subject in Sloterdijk's essays on Heidegger—homeotechnics. Thirdly, it will be shown how the concepts of relief and natal difference can be further developed into an ethico-aesthetic paradigm for experimentation with new technologies, based on a reinterpretation of the Gestell as total work of art. Finally, by relating Sloterdijk's work to that of Michel Serres, it will be demonstrated why, for Sloterdijk, this paradigm finds its exemplary modal in the spaceship.
Airquakes
Authors: Sloterdijk Peter
Published: February 2009

In this excerpt from the introduction to volume three of Sphären ( Spheres), subtitled Schäume ( foam), Sloterdijk argues that what makes the 20th century uniquely singular and creative is its invention of what he calls here atmosterrorism, the assault not on the body of the enemy, but on his or her environment. This terrorism of the atmosphere is to be understood as a human-made form of quake that turns the enemy's environment into a weapon against them. Living organisms, among them humans, simply cannot not breathe, and it is this double negative that is at the heart of atmoterrorism. Weaving a fascinating narrative that links the development of insecticides and pesticides to the first use of poisonous gas during World War I, to the development of the gas chamber as the tool of supreme punishment in the United States, to the eventual convergence of putative humane killing and disinfection and delousing into the mobile and stationary gas chambers of extermination used in the Nazi concentration camps. Terrorism, argues Sloterdijk, reveals the essence of war, the will to exterminate the enemy, with the difference that the former expands the extermination of the enemy to the very world that enables the enemy to exist. In the 20th century, atmoterrorism leads to the exterminism of total war.
Geometry in the Colossal: The Project of Metaphysical Globalization
Authors: Sloterdijk Peter
Published: February 2009

“Geometry in the colossal” ( Geometrie in Ungeheurem) appears as pages 47–72 of the second volume of Peter Sloterdijk's Sphären—the volume is entitled Globen, ‘Globes’. The excerpt is a beginning of the history of the idea of the sphere or the globe. As claimed by Heidegger in the epigraph, the conquest of the world as picture is the fundamental event of modernity. The historical question that arises, then, is that of the rise of the globe as the fundamental picture of the world. Sloterdijk begins with remarks on what he calls a “treatise on the metaphysics of roundness”, Nicholas of Cusa's De Ludo Globi, set in a discussion concerning the movement of the notion of the globe from the Greek to the Roman world. The second half of the excerpt is devoted to a more focused analysis of the composition, history, and significance of the Farnese Atlas. In this work we see the world portrayed as a “poetic - scientific bastard heaven, a product of geometry as much as of mythology”, borne upon the shoulders of a titan - philosopher - athlete, images at once ancient and modern. The conquest of the world as picture thus transforms Atlas's punishment into a symbol of the greatest earthly power.
Rules for the Human Zoo: A Response to the Letter on Humanism
Authors: Sloterdijk Peter
Published: February 2009

Rules for the Human Zoo, also known as the Elmauer Rede, originally appeared in 1999 in the newspaper Die Zeit and was subsequently published by Suhrkamp in 2001. In this response to Heidegger's Letter on Humanism, Sloterdijk poses the basic question about the purpose of politics, governance, and civic solidarity. On the one hand, since Plato, politics has been conceived in part as concerned with the necessity of ‘taming’ humans into being good citizens. Sloterdijk thus follows Nietzsche and Heidegger in portraying humanism as one side in a “constant battle … between bestializing and taming tendencies”. It is in the Hobbesian state of nature that humans are ‘wolves’ to each other; but who turns the wolves into friendly, loyal dogs? Humanism has claimed, according to Sloterdijk, that it is “reading the right books” which “calms the inner beast”. It is the great books, the “thick letters” from one great thinker to another, that provide the “model presented by the wise”, which enables “the care of man by man”. At the present, Sloterdijk argues, we appear to have been abandoned by the wise. It is no longer the humanist but the archivist who bothers to look up the old, thick letters. Humanism thus gives way to archivism.
Ultraviolet radiation stimulated activity of extracellular carbonic anhydrase in the marine diatom Skeletonema costatum
Authors: Wu Hongyan , Gao Kunshan
Published: February 2009

Previous studies have shown that reduced levels of solar UV radiation (280–400 nm) can enhance photosynthetic carbon fixation of marine phytoplankton, but the mechanisms are not known. The supply of CO2 for photosynthesis is facilitated by extracellular (periplasmic) carbonic anhydrase (CAe) in most marine phytoplankton species. The present study showed that the CAe activity of Skeletonema costatum (Greville) Cleve was stimulated when treated with UV-A (320–395 nm) or UV-A + UV-B (295–320 nm) in addition to visible radiation. The presence of UV-A and UV-B enhanced the activity by 28% and 24%, respectively, at a low irradiance (PAR 161, UV-A 28, UV-B 0.9 W m−2) and by 21% and 19%, respectively, at a high irradiance (PAR 328, UV-A 58, UV-B 1.9 W m−2) level after exposure for 1 h. Ultraviolet radiation stimulated CAe activity contributed up to 6% of the photosynthetic carbon fixation as a result of the enhanced supply of CO2, as revealed using the CAe inhibitor (acetazolamide). As a result, there was less inhibition of photosynthetic carbon fixation compared with the apparent quantum yield of PSII. The UV radiation stimulated CAe activity coincided with the enhanced redox activity at the plasma membrane in the presence of UV-A and/or UV-B. The present study showed that UV radiation can enhance CAe activity, which plays an important role in counteracting UV inhibition of photosynthesis.
Using a mathematical model to evaluate the trophic and non-trophic determinants of axis development in grapevine
Authors: Pallas Benoît , Christophe Angélique , Cournède Paul-Henry , Lecoeur Jérémie
Published: February 2009

The grapevine (Vitis vinifera L.) shoot is a complex modular branching system, with one primary axis and many secondary axes organised into a repetitive structure of three successive phytomers (P0-P1-P2). P1-P2 phytomers bear one tendril or cluster, whereas P0 phytomers bear no tendrils or clusters. Axis development displays a high variability, due, partly, to trophic competition. The aim of this study was to estimate changes in trophic competition within the shoot, and to relate plasticity in axis development to changes in trophic competition. ‘Grenache N.’ and ‘Syrah’ cultivars were grown with two contrasting levels of cluster load. Organogenesis and organ mass were measured during shoot development. Changes in trophic competition were estimated, using the solver functions of the GreenLab model. Internodes and clusters were strong sinks. They affected the shoot development to the same extent, but the internodes showed an earlier effect. The cessation of development of the secondary axis was affected by trophic competition, but the primary axis continued to develop, regardless of trophic competition. Secondary axes differed in sensitivity to trophic competition as a function of two criteria: their type and their size. The most highly developed axes were less affected than the smaller axes, and secondary axes arising from a P0 phytomer were also less affected than secondary axes arising from a P1 or P2 phytomer.
Arabidopsis phospholipase Dδ as an initiator of cytoskeleton-mediated signalling to fundamental cellular processes
Authors: Ho Angela Y. Y. , Day David A. , Brown Melissa H. , Marc Jan
Published: February 2009

Phospholipase D (PLD), in combination with the cytoskeleton, plays a key role in plant signal transduction. One isotype of the multigene Arabidopsis PLD family, AtPLDδ, has been implicated in binding microtubules, although the molecular details of the mechanism and identities of potential interaction partners are unclear. We constructed a GFP-AtPLDδ reporter gene, stably transformed it into an Arabidopsis suspension cell line, and used epitope-tagged affinity pull-down assays to isolate a complex of co-purifying proteins. Mass spectrometry analysis of the complex revealed a set of proteins including β-tubulin, actin 7, HSP70, clathrin heavy chain, ATP synthase subunits, and a band 7–4/flotillin homologue. Sequence alignments with defined tubulin- and actin-binding regions from human HsPLD2 revealed highly homologous regions in all 12 AtPLD isotypes, suggesting direct interactions of AtPLDδ with tubulin and actin, while interactions with the remaining partners are likely to be mediated by the cytoskeleton. We propose that AtPLDδ acts through a complex of cytoskeletal and partner proteins to modulate fundamental cellular processes such as cytoskeletal rearrangements, vesicular trafficking, assembly of Golgi apparatus, mitosis and cytokinesis.
Invited Review: Cryo-scanning electron microscopy (CSEM) in the advancement of functional plant biology. Morphological and anatomical applications
Authors: McCully Margaret E. , Canny Martin J. , Huang Cheng X.
Published: February 2009

Cryo-scanning electron microscopy (CSEM) is reviewed by exploring how the images obtained have changed paradigms of plant functions and interactions with their environment. Its power to arrest and stabilise plant parts in milliseconds, and to preserve them at full hydration for examination at micrometre resolution has changed many views of plant function. For example, it provides the only feasible way of accurately measuring stomatal aperture during active transpiration, and volume and shape changes in guard cells, or examining the contents of laticifers. It has revealed that many xylem conduits contain gas, not liquid, during the day, and that they can be refilled with sap and resume water transport. It has elucidated the management of ice to prevent cell damage in frost tolerant plants and has revealed for the first time inherent biological and physical features of root/soil interactions in the field. CSEM is increasingly used to reveal complementary structural information in studies of metabolism, fungal infection and symbiosis, molecular and genetic analysis.
Culling experiments demonstrate size-class specific biomass increases with mortality
Authors: Schröder A. , Persson L. , de Roos A. M.
Published: February 2009

Size-selective mortality inevitably leads to a decrease in population density and exerts a direct negative effect on targeted size classes. But density and population size structure are also shaped by food-dependent processes, such as individual growth, maturation, and reproduction. Mortality relaxes competition and thereby alters the dynamic interplay among these processes. As shown by the recently developed size-structured theory, which can account for food-dependent individual performance, this altered interplay can lead to overcompensatory responses in size class–specific biomass, with increasing mortality. We experimentally tested this theory by subjecting laboratory fish populations to a range of size-selective mortality rates. Overall, the results were in agreement with theoretical predictions. Biomass of the juvenile size class increased above control levels at intermediate adult mortality rates and thereafter declined at high mortality rates. Juvenile biomass also increased when juveniles themselves were subjected to intermediate mortality rates. Biomass in other size classes decreased with mortality. Such biomass overcompensation can have wide-ranging implications for communities and food webs, including a high sensitivity of top predators to irreversible catastrophic collapses, the establishment of alternative stable community states, and the promotion of coexistence and biodiversity.
c-kit expression identifies cardiovascular precursors in the neonatal heart
Authors: Tallini Yvonne N. , Greene Kai Su , Craven Michael , Spealman Alyson , Breitbach Martin , Smith James , Fisher Patricia J. , Steffey Michele , Hesse Michael , Doran Robert M. , Woods Ashley , Singh Babu , Yen Andrew , Fleischmann Bernd K. , Kotlikoff Michael I.
Published: February 2009

Directed differentiation of embryonic stem cells indicates that mesodermal lineages in the mammalian heart (cardiac, endothelial, and smooth muscle cells) develop from a common, multipotent cardiovascular precursor. To isolate and characterize the lineage potential of a resident pool of cardiovascular progenitor cells (CPcs), we developed BAC transgenic mice in which enhanced green fluorescent protein (EGFP) is placed under control of the c-kit locus (c-kit
BAC
-EGFP mice). Discrete c-kit-EGFP
+
cells were observed at different stages of differentiation in embryonic hearts, increasing in number to a maximum at about postnatal day (PN) 2; thereafter, EGFP
+
cells declined and were rarely observed in the adult heart. EGFP
+
cells purified from PN 0–5 hearts were nestin
+
and expanded in culture; 67% of cells were fluorescent after 9 days. Purified cells differentiated into endothelial, cardiac, and smooth muscle cells, and differentiation could be directed by specific growth factors. CPc-derived cardiac myocytes displayed rhythmic beating and action potentials characteristic of multiple cardiac cell types, similar to ES cell-derived cardiomyocytes. Single-cell dilution studies confirmed the potential of individual CPcs to form all 3 cardiovascular lineages. In adult hearts, cryoablation resulted in c-kit-EGFP
+
expression, peaking 7 days postcryolesion. Expression occurred in endothelial and smooth muscle cells in the revascularizing infarct, and in terminally differentiated cardiomyocytes in the border zone surrounding the infarct. Thus, c-kit expression marks CPc in the neonatal heart that are capable of directed differentiation in vitro; however, c-kit expression in cardiomyocytes in the adult heart after injury does not identify cardiac myogenesis.
Genome, transcriptome, and secretome analysis of wood decay fungus
Postia placenta
supports unique mechanisms of lignocellulose conversion
Authors: Martinez Diego , Challacombe Jean , Morgenstern Ingo , Hibbett David , Schmoll Monika , Kubicek Christian P. , Ferreira Patricia , Ruiz-Duenas Francisco J. , Martinez Angel T. , Kersten Phil , Hammel Kenneth E. , Vanden Wymelenberg Amber , Gaskell Jill , Lindquist Erika , Sabat Grzegorz , Splinter BonDurant Sandra , Larrondo Luis F. , Canessa Paulo , Vicuna Rafael , Yadav Jagjit , Doddapaneni Harshavardhan , Subramanian Venkataramanan , Pisabarro Antonio G. , Lavín José L. , Oguiza José A. , Master Emma , Henrissat Bernard , Coutinho Pedro M. , Harris Paul , Magnuson Jon Karl , Baker Scott E. , Bruno Kenneth , Kenealy William , Hoegger Patrik J. , Kües Ursula , Ramaiya Preethi , Lucas Susan , Salamov Asaf , Shapiro Harris , Tu Hank , Chee Christine L. , Misra Monica , Xie Gary , Teter Sarah , Yaver Debbie , James Tim , Mokrejs Martin , Pospisek Martin , Grigoriev Igor V. , Brettin Thomas , Rokhsar Dan , Berka Randy , Cullen Dan
Published: February 2009

Brown-rot fungi such as
Postia placenta
are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the
P. placenta
genome, transcriptome, and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When
P. placenta
was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative β-1–4 endoglucanase were expressed at high levels relative to glucose-grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Also up-regulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H
2
O
2
. These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H
2
O
2
react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The
P. placenta
genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons with the closely related white-rot fungus
Phanerochaete chrysosporium
support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost.
Efficient gene therapy-based method for the delivery of therapeutics to primate cortex
Authors: Kells Adrian P. , Hadaczek Piotr , Yin Dali , Bringas John , Varenika Vanja , Forsayeth John , Bankiewicz Krystof S.
Published: February 2009

Transduction of the primate cortex with adeno-associated virus (AAV)-based gene therapy vectors has been challenging, because of the large size of the cortex. We report that a single infusion of AAV2 vector into thalamus results in widespread expression of transgene in the cortex through transduction of widely dispersed thalamocortical projections. This finding has important implications for the treatment of certain genetic and neurodegenerative diseases.
Glutamatergic regulation of serine racemase via reversal of PIP2 inhibition
Authors: Mustafa Asif K. , Rossum Damian B. van , Patterson Randen L. , Maag David , Ehmsen Jeffrey T. , Gazi Sadia K. , Chakraborty Anutosh , Barrow Roxanne K. , Amzel L. Mario , Snyder Solomon H.
Published: February 2009

D-serine is a physiologic coagonist with glutamate at NMDA-subtype glutamate receptors. As D-serine is localized in glia, synaptically released glutamate presumably stimulates the glia to form and release D-serine, enabling glutamate/D-serine cotransmission. We show that serine racemase (SR), which generates D-serine from L-serine, is physiologically inhibited by phosphatidylinositol (4,5)-bisphosphate (PIP2) presence in membranes where SR is localized. Activation of metabotropic glutamate receptors (mGluR5) on glia leads to phospholipase C-mediated degradation of PIP2, relieving SR inhibition. Thus mutants of SR that cannot bind PIP2 lose their membrane localizations and display a 4-fold enhancement of catalytic activity. Moreover, mGluR5 activation of SR activity is abolished by inhibiting phospholipase C.
Discovery of a functional protein complex of netrin-4, laminin γ1 chain, and integrin α6β1 in mouse neural stem cells
Authors: Staquicini Fernanda I. , Dias-Neto Emmanuel , Li Jianxue , Snyder Evan Y. , Sidman Richard L. , Pasqualini Renata , Arap Wadih
Published: February 2009

Molecular and cellular interactions coordinating the origin and fate of neural stem cells (NSCs) in the adult brain are far from being understood. We present a protein complex that controls proliferation and migration of adult NSCs destined for the mouse olfactory bulb (OB). Combinatorial selection based on phage display technology revealed a previously unrecognized complex between the soluble protein netrin-4 and laminin γ1 subunit that in turn activates an α6β1 integrin-mediated signaling pathway in NSCs. Differentiation of NSCs is accompanied by a decrease in netrin-4 receptors, indicating that netrin-4 participates in the continual propagation of this stem cell population. Notably, the stem cells themselves do not synthesize netrin-4. Further, we show that netrin-4 is produced by selected GFAP-positive astrocytes positioned close to newborn neurons migrating in the anterior part of the rostral migratory stream (RMS) and within the OB. Our findings present a unique molecular mechanism mediating astrocytic/neuronal crosstalk that regulates ongoing neurogenesis in the adult olfactory system.
Growth of graphene on Ir(111)
Authors: Coraux Johann , T N'Diaye Alpha , Engler Martin , Busse Carsten , Wall Dirk , Buckanie Niemma , Meyer zu Heringdorf Frank-J , van Gastel Raoul , Poelsema Bene , Michely Thomas
Published: February 2009

Catalytic decomposition of hydrocarbons on transition metals attracts a renewed interest as a route toward high-quality graphene prepared in a reproducible manner. Here we employ two growth methods for graphene on Ir(111), namely room temperature adsorption and thermal decomposition at 870–1470 K (temperature programmed growth (TPG)) as well as direct exposure of the hot substrate at 870–1320 K (chemical vapor deposition (CVD)). The temperature- and exposure-dependent growth of graphene is investigated in detail by scanning tunneling microscopy. TPG is found to yield compact graphene islands bounded by C zigzag edges. The island size may be tuned from a few to a couple of tens of nanometers through Smoluchowski ripening. In the CVD growth, the carbon in ethene molecules arriving on the Ir surface is found to convert with probability near unity to graphene. The temperature-dependent nucleation, interaction with steps and coalescence of graphene islands are analyzed and a consistent model for CVD growth is developed.
Clustering of C-Terminal Stromal Domains of Tha4 Homo-oligomers during Translocation by the Tat Protein Transport System
Authors: Dabney-Smith Carole , Cline Kenneth
Published: February 2009

The chloroplast Twin arginine translocation (Tat) pathway uses three membrane proteins and the proton gradient to transport folded proteins across sealed membranes. Precursor proteins bind to the cpTatC-Hcf106 receptor complex, triggering Tha4 assembly and protein translocation. Tha4 is required only for the translocation step and is thought to be the protein-conducting component. The organization of Tha4 oligomers was examined by substituting pairs of cysteine residues into Tha4 and inducing disulfide cross-links under varying stages of protein translocation. Tha4 formed tetramers via its transmembrane domain in unstimulated membranes and octamers in membranes stimulated by precursor and the proton gradient. Tha4 formed larger oligomers of at least 16 protomers via its carboxy tail, but such C-tail clustering only occurred in stimulated membranes. Mutational studies showed that transmembrane domain directed octamers as well as C-tail clusters require Tha4's transmembrane glutamate residue and its amphipathic helix, both of which are necessary for Tha4 function. A novel double cross-linking strategy demonstrated that both transmembrane domain directed- and C-tail directed oligomerization occur in the translocase. These results support a model in which Tha4 oligomers dock with a precursor–receptor complex and undergo a conformational switch that results in activation for protein transport. This possibly involves accretion of additional Tha4 into a larger transport-active homo-oligomer.
qvality: non-parametric estimation of q-values and posterior error probabilities
Authors: Käll Lukas , Storey John D. , Noble William Stafford
Published: February 2009

Summary: Qvality is a C++ program for estimating two types of standard statistical confidence measures: the q-value, which is an analog of the p-value that incorporates multiple testing correction, and the posterior error probability (PEP, also known as the local false discovery rate), which corresponds to the probability that a given observation is drawn from the null distribution. In computing q-values, qvality employs a standard bootstrap procedure to estimate the prior probability of a score being from the null distribution; for PEP estimation, qvality relies upon non-parametric logistic regression. Relative to other tools for estimating statistical confidence measures, qvality is unique in its ability to estimate both types of scores directly from a null distribution, without requiring the user to calculate p-values.

Availability: A web server, C++ source code and binaries are available under MIT license at http://noble.gs.washington.edu/proj/qvality

Contact:  lukas.kall@cbr.su.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
Radié: visualizing taxon properties and parsimonious mappings using a radial phylogenetic tree
Authors: Whalley Jacqueline , Brooks Stephen , Beiko Robert G.
Published: February 2009

Summary: A phenotypic character has a convex mapping to a given phylogenetic tree if each character state can be assigned a single point of origin in the tree. However, phenomena such as convergent evolution and lateral genetic transfer can lead to intermingling of character states and a consequent non-convex mapping. The phylogenetic heterogeneity of different characters can identify subsets of states that are non-randomly associated or which may have been transferred from one lineage to another. We have developed Radié, an interactive 3D Java application for mapping character states to the leaves and internal edges of a radial phylogenetic tree. In Radié each state of a given character is associated with a unique color, and internal edges with many descendant character states can be represented in a number of different ways to illustrate the diversity within each group.

Availability: Radié is freely available for download at http://kiwi.cs.dal.ca/~beiko/software-and-data/radie; source code is available upon request from the authors.

Contact:  beiko@cs.dal.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods
Authors: Bengtsson Henrik , Ray Amrita , Spellman Paul , Speed Terence P.
Published: February 2009

Motivation: The rapid expansion of whole-genome copy number (CN) studies brings a demand for increased precision and resolution of CN estimates. Recent studies have obtained CN estimates from more than one platform for the same set of samples, and it is natural to want to combine the different estimates in order to meet this demand. Estimates from different platforms show different degrees of attenuation of the true CN changes. Similar differences can be observed in CNs from the same platform run in different labs, or in the same lab, with different analytical methods. This is the reason why it is not straightforward to combine CN estimates from different sources (platforms, labs and analysis methods).

Results: We propose a single-sample multi source normalization that brings full-resolution CN estimates to the same scale across sources. The normalized CNs are such that for any underlying CN level, their mean level is the same regardless of the source, which make them better suited for being combined across sources, e.g. existing segmentation methods may be used to identify aberrant regions. We use microarray-based CN estimates from ‘The Cancer Genome Atlas’ (TCGA) project to illustrate and validate the method. We show that the normalized and combined data better separate two CN states at a given resolution. We conclude that it is possible to combine CNs from multiple sources such that the resolution becomes effectively larger, and when multiple platforms are combined, they also enhance the genome coverage by complementing each other in different regions.

Availability: A bounded-memory implementation is available in aroma.cn.

Contact:  hb@stat.berkeley.edu
CoCAS: a ChIP-on-chip analysis suite
Authors: Benoukraf Touati , Cauchy Pierre , Fenouil Romain , Jeanniard Adrien , Koch Frederic , Jaeger Sébastien , Thieffry Denis , Imbert Jean , Andrau Jean-Christophe , Spicuglia Salvatore , Ferrier Pierre
Published: February 2009

Motivation: High-density tiling microarrays are increasingly used in combination with ChIP assays to study transcriptional regulation. To ease the analysis of the large amounts of data generated by this approach, we have developed ChIP-on-chip Analysis Suite (CoCAS), a standalone software suite which implements optimized ChIP-on-chip data normalization, improved peak detection, as well as quality control reports. Our software allows dye swap, replicate correlation and connects easily with genome browsers and other peak detection algorithms. CoCAS can readily be used on the latest generation of Agilent high-density arrays. Also, the implemented peak detection methods are suitable for other datasets, including ChIP-Seq output.

Availability: The software is available for download along with a sample dataset at http://www.ciml.univ-mrs.fr/software/ferrier.htm.

Contact:  ferrier@ciml.univ-mrs.fr; andrau@ciml.univ-mrs.fr; spicuglia@ciml.univ-mrs.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Pensions and Providence: Dutch Employers and the Creation of Funded Pension Schemes
Authors: Nijhof Erik
Published: February 2009

From an international perspective, the Dutch system of old age provisions stands out for its wide coverage, fixed benefits, and an overall actuarial soundness that seem to make this system more shock proof to demographic shifts and economic adversities than those in other “Western” countries. Its actual foundation is a compulsory old age insurance for all citizens, enforced by law and implemented by the state; this insurance is supplemented by fully funded pension schemes for workers and employees, operating under legal control; and finally there is a variety of additional and noncompulsory pension benefits and individual insurance arrangements. The main impetus to the genesis of this system came from employers who, with different agendas, created various pension funds; eventually it was the state, which set a decisive example with a funded pension fund for its civil servants. This became the standard to all corporate pension schemes and provoked innovations like branch funds. These initiatives were supported and regulated by legislation that made these arrangements compulsory and guaranteed their juridical independence and actuarial soundness. Only after this legally promoted maturation of private funds, the state set out to create public arrangements on a “pay-as-you-go” basis for all citizens. This delicate interplay between private and public pension arrangements is highly characteristic of the Dutch variety of capitalism in a broader context. In the polarity between liberal and coordinated market economies, as developed by Soskice and Hall, the Dutch system of old age provisions has played a prominent role in ranking this country more firmly into the latter category. However, within this range of countries the Dutch system of old age provisions is also a bit atypical: private corporate and branch arrangements were encouraged and at the same time embedded in a legal framework. The role of the state was also remarkable: a supervisor of the private funds, a collector and distributor in a universal insurance system, and an employer with an exemplary pension scheme.
Inhibition of platelet activation in rats with severe congestive heart failure by a novel endothelial nitric oxide synthase transcription enhancer
Authors: Schäfer Andreas , Fraccarollo Daniela , Widder Julian , Eigenthaler Martin , Ertl Georg , Bauersachs Johann
Published: February 2009

Aims

Increased risk of thrombo‐embolic events in congestive heart failure (CHF) has been attributed to a hypercoagulable state including vascular endothelial dysfunction and reduced bioavailability of nitric oxide (NO) as well as platelet activation. We investigated whether treatment with a novel endothelial NO synthase (eNOS)‐transcription enhancer positively modulates systemic NO bioavailability and reduces platelet activation in rats with CHF.

Methods and results

After experimental myocardial infarction, male Wistar rats were treated with either placebo or the eNOS‐transcription enhancer, AVE9488 (25 ppm/day) for 10 weeks. In rats with severe CHF (left ventricular end‐diastolic pressure >15 mmHg), platelet vasodilator‐stimulated phosphoprotein (VASP)‐phosphorylation reflecting the integrity of the NO/cGMP pathway was significantly reduced (mean immunofluorescence at Ser157: Sham, 61.4 ± 9.1; CHF‐Placebo, 37.4 ± 4.9; P < 0.05; Ser239: Sham, 18.1 ± 2.5; CHF‐Placebo, 13.2 ± 0.6; P < 0.05). Platelet surface expression of P‐selectin and glycoprotein 53 were increased in CHF rats compared with sham‐operated animals. Chronic treatment with AVE9488 significantly enhanced platelet VASP‐phosphorylation in CHF rats (Ser157: 70.4 ± 16.2; Ser239: 19.3 ± 1.8). In parallel, platelet surface expression of P‐selectin and glycoprotein 53 was reduced in the treatment group.

Conclusion

Platelet activation was evident in CHF rats. Therapy with the eNOS‐transcription enhancer, AVE9488, reduced platelet activation in parallel to normalization of platelet NO bioavailability.
Acute biopsy‐proven lymphocytic myocarditis mimicking Takotsubo cardiomyopathy
Authors: Caforio Alida L.P. , Tona Francesco , Vinci Annalisa , Calabrese Fiorella , Ramondo Angelo , Cacciavillani Luisa , Corbetti Francesco , Leoni Loira , Thiene Gaetano , Iliceto Sabino , Angelini Annalisa
Published: February 2009

Endomyocardial biopsy (EMB), the diagnostic gold standard for myocarditis, has not been systematically performed in the reported case series of Takotsubo cardiomyopathy, although proposed Mayo Criteria specify exclusion of myocarditis. Moreover, there is no specific recommendation for infarct‐like acute myocarditis in the recently published guidelines on the role of EMB. Here we present a thoroughly documented case fulfilling both the proposed Mayo criteria for Takotsubo cardiomyopathy and the World Health Organization criteria for active, virus‐negative, immune‐mediated myocarditis. Since myocarditis can mimic acute myocardial infarction with normal coronary arteries, EMB should be performed to rule out myocarditis in patients presenting with LV apical ballooning syndrome (or Takotsubo cardiomyopathy).
Estimating tail-beat frequency using split-beam echosounders
Authors: Handegard Nils Olav , Pedersen Geir , Brix Ole
Published: February 2009

Handegard, N. O., Pedersen, G., and Brix, O. 2009. Estimating tail-beat frequency using split-beam echosounders. – ICES Journal of Marine Science, 66: 1252–1258. Data from a standard split-beam echosounder are used to estimate tail-beat frequency within a dense herring (Clupea harengus L.) layer. The data were collected by lowering a horizontally projecting 38 kHz split-beam transducer into a herring layer at 245-m depth. Individual targets were concatenated into tracks, and a fast Fourier transform was used to estimate the periodogram of the backscattering strengths along each track. A simple model, assumed accurate under certain conditions, was used to relate the periodogram to tail-beat frequency. The requisite conditions are discussed. Examples of accurate tail-beat estimates from single high-quality tracks, which are consistent with statistics on all tracks in the test dataset, are presented. In addition, the cross periodogram between closely spaced individuals was calculated on selected tracks to estimate the relative phase between the adjacent tracks within the school. Finally, the potential use of this method to resolve schooling behaviour, improve target-strength estimates, and even estimate fish condition, is discussed.
Political Science, Biometric Theory, and Twin Studies: A Methodological Introduction
Authors: Medland Sarah E. , Hatemi Peter K.
Published: February 2009

As political scientists begin to incorporate biological influences as explanatory factors in political behavior, the need to present a methodological road map for utilizing biometric genetic theory and twin data is apparent. The classical twin design (CTD) remains the most popular design for initial examinations of the source of variance among social and political behaviors, and a vast majority of advanced variance components models as well as some molecular analyses are extensions of the CTD. Thus, it is appropriate to begin a series of works with the CTD and its most common variants. The CTD has strong roots in biometrical genetic theory and provides estimates of the correlations between observed traits of monozygotic and dizygotic twins in terms of underlying genetic and environmental influences. The majority of these analyses utilize SEMs of observed covariances for both twin types to assess the relative importance of these “latent” factors.
Introduction to the Special Issue: The Statistical Analysis of Political Text
Authors: Monroe Burt L. , Schrodt Philip A.
Published: February 2009

Text is arguably the most pervasive—and certainly the most persistent—artifact of political behavior. Extensive collections of texts with clearly recognizable political—as distinct from religious—content go back as far as 2500 BCE in the case of Mesopotamia and 1300 BCE for China, and 2400-year-old political discussions dating back to the likes of Plato, Aristotle, and Thucydides are common fare even in the introductory study of political thought. Political tracts were among the earliest productions following the introduction of low-cost printing in Europe—fueling more than a few revolutions and social upheavals—and continuous printed records of legislative debates, such as the British parliament's Hansard and precursors tracing to 1802, cover centuries of political discussion.
Minimally Invasive Technique for Iliac Revascularization after Large-Bore Sheath Traumatic Avulsion
Authors: Brinster Derek R.
Published: February 2009

Percutaneous treatments of cardiac valvular and thoracic aortic diseases are rapidly progressing. To maintain an indispensable part of their treatment, cardiothoracic surgeons must evolve to be able to handle all complications related to the use of percutaneous devices. One of the most common complications is vascular access disruption. Presented here is a method for a combined surgical and endovascular treatment for minimally invasive repair of an iliac artery avulsion.
Off-Pump Atrial Septal Defect Closure Using the Universal Cardiac Introducer®
Authors: Guiraudon Gerard M. , Jones Douglas L. , Bainbridge Daniel , Moore John T. , Wedlake Chris , Linte Cristian , Wiles Andrew , Peters Terry M.
Published: February 2009

Objective

Optimal atrial septal defect (ASD) closure should combine off-pump techniques with the effectiveness and versatility of open-heart techniques. We report our experience with off-pump ASD closure using the Universal Cardiac Introducer (UCI) in a porcine model. The goal was to create an ASD over the fossa ovale (FO) and position a patch over the ASD under ultrasound (US) imaging and augmented virtual reality guidance.

Methods

An US probe (tracked with a magnetic tracking system) was positioned into the esophagus (transesophageal echocardiographic probe) for real-time image-guidance. The right atrium (RA) of six pigs was exposed via a right lateral thoracotomy or medial sternotomy. The UCI was attached to the RA wall. A punching tool was introduced via the UCI, navigated and positioned, under US guidance, to create an ASD into the FO. A patch with its holder and a stapling device were introduced into the RA via the UCI. The patch was positioned on the ASD. Occlusion of the ASD was determined using US and Doppler imaging.

Results

The FO membrane was excised successfully in all animals. US image-guidance provided excellent visualization. The patch was positioned in all cases with complete occlusion of the ASD. The stapling device proved too bulky, impeding circumferential positioning.

Conclusions

Using the UCI, ASD closure was safe and feasible. US imaging, combined with virtual and augmented reality provided accurate navigating and positioning. This study also provided valuable information on the future design of anchoring devices for intracardiac procedures.
Thoracoscopic Lobectomy with Chest Wall Resection after Neoadjuvant Therapy
Authors: Yendamuri Sai , Nwogu Chukwumere E. , Demmy Todd L.
Published: February 2009

Chest wall involvement from lung malignancy presents technical challenges for a minimally invasive surgical approach. Recently, new thoracoscopic rib cutting instrumentation has been developed and may offer a safe and efficient resection. Compared with thoracotomy, thoracoscopic lung and chest wall resection may potentially lower the morbidity associated with chest wall resection by thoracotomy. We present a case of thoracoscopic lobectomy with an en bloc chest wall resection.