bluuebunny/crossref_metadata_2025 huggingface dataset:
From pedagogically relevant corpora to authentic language learning contents
Authors: BRAUN SABINE
Published: May 2005

The potential of corpora for language learning and teaching has been widely acknowledged and their ready
availability on the Web has facilitated access for a broad range of users, including language teachers and learners. However,
the integration of corpora into general language learning and teaching practice has so far been disappointing. In this paper,
I will argue that the shape of many existing corpora, designed with linguistic research goals in mind, clashes with pedagogic
requirements for corpus design and use. Hence, a ‘pedagogic mediation
of corpora’ is required (cf. Widdowson, 2003). I will also show that the realisation of this requirement touches on
both the development of appropriate corpora and the ways in which they are exploited by learners and teachers. I will use a
small English Interview Corpus (ELISA) to outline possible solutions for a pedagogic mediation. The major aspect of this is the
combination of two approaches to the analysis and exploitation of a pedagogically relevant corpus: a corpus-based and a
discourse-based approach.
Computer corpora and the language classroom: on the potential and limitations of computer corpora in language teaching
Authors: KALTENBÖCK GUNTHER , MEHLMAUER-LARCHER BARBARA
Published: May 2005

With computer corpora firmly established as research tools in linguistics, their application for language teaching
purposes is also increasingly advocated to the extent that corpus-based language teaching has even been praised as the new revolution
in language teaching (cf. Sinclair, 2004b). This article takes a more critical view and examines some of the potential as well as
the limitations of computer corpora in the language classroom, providing practical examples from the British Component of the
International Corpus of English. It is argued that only a balanced view, which takes into account both the strengths and weaknesses of
computer corpora for language teaching, can ensure their successful integration into the language classroom. The discussion first
focuses on the limitations of corpus data, which are identified as
‘externalized’, as opposed to ‘internalized’ language, lacking contextual, as opposed to co-textual,
information. On the other hand, computer corpora provide access to information not easily available from other sources, viz.
information on frequency of occurrence in various text types, and co-occurrence patterns, e.g. collocation, colligation, semantic
prosody). This information, however, also has to be seen in the light of the more general questions of how representative corpus
results are and to what extent they are generalisable. The article concludes with a discussion of pedagogical implications of the use
of computer corpora, especially with regard to their application as tools for exploratory/discovery learning and as means for promoting
learner autonomy.
Learner interaction using email: the effects of task modification
Authors: KNIGHT PAUL
Published: May 2005

This paper outlines the findings of a research project studying the effects of task modification on learner
interaction when using email. Taking as its starting point interactionalist theories of SLA, it argues that if those interactional
features characteristic of negotiation of meaning which have been identified as promoting SLA are to be preserved when tasks are
transferred from a face-to-face spoken environment to a computer-mediated written asynchronous environment, then modifications to
the tasks need to be made.
FOZO, HIMU, and the rest of the mantle zoo
Authors: Stracke Andreas , Hofmann Albrecht W. , Hart Stan R.
Published: May 2005

The parameter μ describes the 238U/204Pb ratio of an Earth reservoir. Mantle domains labeled HIMU (high μ) originally defined reservoirs with highly radiogenic Pb isotope ratios observed in basalts from a select number of ocean islands, St. Helena in the Atlantic Ocean and the Cook‐Austral islands in the South Pacific Ocean. While some authors use the term HIMU in this original sense, others refer to HIMU as a widespread component in many mid‐ocean ridge and ocean island basalt (MORB and OIB) sources. Here we show that highly radiogenic Pb isotope signatures in MORB and OIB originate from two different sources. In addition to the classical HIMU component observed at St. Helena and the South Pacific (named HIMU in the following), we define a component with slightly less radiogenic Pb but significantly more radiogenic Sr isotope signatures. This component lies at the extension of the (Atlantic and Pacific) MORB array in a Sr‐Pb isotope ratio diagram and is argued to be a ubiquitous component in MORB and many OIB sources. The inferred role of this component in the mantle and its inferred genetic origin closely resemble those originally suggested for a mantle component termed FOZO by Hart and coworkers. By redefining the composition, the origin, and the role of FOZO in the mantle, we establish a simple conceptual framework that explains the isotopic variability in both MORB and OIB with the lowest number of components. OIB are grouped into HIMU‐type OIB and basalts from islands that diverge from the MORB‐FOZO array toward various isotopically “enriched” compositions (EM). The apparent ubiquity of FOZO in the mantle and the calculated isotopic evolution of compositionally diverse MORB suggest that normal mantle melting and continuous subduction and aging of that crust during recycling through the mantle are the dominant causes of the MORB‐FOZO array. In contrast to FOZO, HIMU‐type OIB are quite rare, and if an origin by recycling of oceanic crust is also postulated, the production of HIMU sources has to be a special and rare combination of age and composition of subduction‐modified recycled oceanic crust.
Growth of molten zone as a mechanism of slip weakening of simulated faults in gabbro during frictional melting
Authors: Hirose Takehiro , Shimamoto Toshihiko
Published: May 2005

To understand how frictional melting affects fault instability, we performed a series of high‐velocity friction experiments on gabbro at slip rates of 0.85–1.49 m s−1, at normal stresses of 1.2–2.4 MPa and with displacements up to 124 m. Experiments have revealed two stages of slip weakening; one following the initial slip and the other immediately after the second peak friction. The first weakening is associated with flash heating, and the second weakening is due to the formation and growth of a molten layer along a simulated fault. The two stages of weakening are separated by a marked strengthening regime in which melt patches grow into a thin, continuous molten layer at the second peak friction. The frictional coefficient decays exponentially from 0.8–1.1 to 0.6 during the second weakening. The host rocks are separated completely by a molten layer during this weakening so that the shear resistance is determined by the gross viscosity and shear strain rate of the molten layer. Melt viscosity increases notably soon after a molten layer forms. However, a fault weakens despite the increase in melt viscosity, and the second weakening is caused by the growth of molten layer resulting in the reduction in shear strain rate of the molten layer. Very thin melt cannot be squeezed out easily from a fault zone so that the rate of melting would be the most critical factor in controlling the slip‐weakening distance. Effect of frictional melting on fault motion can be predicted by solving a Stefan problem dealing with moving host rock/molten zone boundaries.
Development and evaluation of an urban parameterization scheme in the Penn State/NCAR Mesoscale Model (MM5)
Authors: Dandou A. , Tombrou M. , Akylas E. , Soulakellis N. , Bossioli E.
Published: May 2005

In the present study, the Penn State/NCAR Mesoscale Model (MM5) was modified by considering recent advances in the urban boundary layer. In particular, the modifications were carried out in two directions: (1) With respect to the thermal properties of an urban surface the surface energy balance was modified by taking into account the anthropogenic heat released in urban areas and the urban heat storage term to account for urban/building mass effects, including hysteresis; and (2) the surface stress and fluxes of heat and momentum were modified following recent advances in the atmospheric boundary layer over rough surfaces under unstable conditions. The whole process was supplemented by detailed information on land use cover, derived from satellite image analysis. The modifications were applied to the high‐resolution nonlocal medium‐range forecast planetary boundary layer parameterization scheme, based on work by Troen and Mahrt (1986). The improvements seen with the modified model, after comparison with available measurements of temperature and fluxes, refer to (1) the strengthening of the nocturnal urban heat island; (2) the changes in the temperature, which proved to be favorable through the whole diurnal cycle, resulting in decreasing the temperature amplitude wave; (3) the decrease of turbulence and fluxes during the daytime; and (4) the diffusion coefficient and potential temperature profiles that are reduced during daytime and are increased at the lower levels during the night and thus affect accordingly the mixing height.
Atmospheric modeling of high‐ and low‐frequency methane observations: Importance of interannually varying transport
Authors: Chen Yu‐Han , Prinn Ronald G.
Published: May 2005

We compare modeled and observed atmospheric methane (CH4) between 1996 and 2001, focusing on the role of interannually varying (IAV) transport. The comparison uses observations taken at 13 high‐frequency (∼hourly) in situ and 6 low‐frequency (∼weekly) flask measurement sites. To simulate atmospheric methane, we use the global 3‐D chemical transport model (MATCH) driven by NCEP reanalyzed winds at T62 resolution (∼1.8° × 1.8°). For the simulation, both methane surface emissions and atmospheric sink (OH destruction) are prescribed as annually repeating fields; thus, atmospheric transport is the only IAV component in the simulation. MATCH generally reproduces the amplitude and phase of the observed methane seasonal cycles. At the high‐frequency sites, the model also captures much of the observed CH4 variability due to transient synoptic events, which are sometimes related to global transport events. For example, the North Atlantic Oscillation (NAO) and El Niño are shown to influence year‐to‐year methane observations at Mace Head (Ireland) and Cape Matatula (Samoa), respectively. Simulations of individual flask measurements are generally more difficult to interpret at certain sites, partially due to observational undersampling in areas of high methane variability. A model‐observational comparison of methane monthly means at seven coincident in situ and flask locations shows a better comparison at the in situ sites. Additional simulations conducted at coarser MATCH resolution (T42, ∼2.8° × 2.8°) showed differences from the T62 simulation at sites near strong emissions. This study highlights the importance of using consistent observed meteorology to simulate atmospheric methane, especially when comparing to high‐frequency observations.
Dynamic river channels suggest a long‐lived Noachian crater lake on Mars
Authors: Bhattacharya Janok P. , Payenberg Tobias H. D. , Lang Simon C. , Bourke Mary
Published: May 2005

Recent images of the Noachian‐age Holden Northeast Crater show spectacular meandering channels that form a complex 150 meter thick lacustrine river delta deposit confined to the northwest margin of the crater. We identify 11 major avulsion events in the topmost layer and suggest an avulsion frequency of a few hundred years. The meandering nature of the channels and numerous avulsions is incompatible with deposition on an alluvial fan and clearly reflects a complex history of multiple sustained flows. Assuming an average sedimentation rate of 1mm/year, we suggest that Holden NE Crater contained a lake that persisted for at least 150,000 years. Our analysis is incompatible with this feature being the result of a major bolide impact that would have released a catastrophic flood by groundwater sapping and supports the hypothesis that early Mars was both warmer and wetter during the Noachian.
Separation of melting and environmental signals in an ice core with seasonal melt
Authors: Moore John C. , Grinsted Aslak , Kekonen Teija , Pohjola Veijo
Published: May 2005

We examine the impact of melt water percolation on the soluble ion chemical record from the Lomonosovfonna ice core. Principle component analysis shows that melting produces only simple changes between bubbly and clear ice facies, due to elution of ions. The data can be naturally split into four groups: pre‐industrial, immediately before, and after the end of the Little Ice Age, and anthropogenic impact eras. The 2nd, 3rd and 4th principle components for these periods all differ significantly, reflecting complex changes in environmental conditions. Thus the core preserves a rich record of environmental history, and simple one of melting. We construct a model of percolation effects to reconstruct “pristine” ice chemical composition, finding that even with melt percentages as high as 80%, there is little disturbance to the chemical stratigraphy. This suggests that ionic records from Arctic ice cap cores are nearly as reliable as those from Greenland or Antarctica.
Differential Profile of Nix Upregulation and Translocation during Hypoxia/Ischaemia in Vivo Versus in Vitro
Authors: Birse-Archbold Jui-Lee A , Kerr Lorraine E , Jones Paul A , McCulloch James , Sharkey John
Published: May 2005

Nix, a hypoxia-sensitive member of the Bcl-2 family, is upregulated at the mRNA level during hypoxia through induction of a hypoxia-inducible factor-1α (HIF-1α) response element in its promoter sequence. However, the mechanism(s) regulating Nix protein activation remain unclear. The present studies examine Nix protein expression and subcellular distribution in response to hypoxic stimuli in vivo and in culture and to two disparate apoptotic stimuli in vitro. Upregulation and translocation of Nix (by day 5) in hypoxic/serum-deprived CHO-K1 cells, was preceded by Bax activation (by day 4) and caspase-3 processing (by day 2), suggesting that initiation of cell death in vitro is a Nix-independent event. In contrast, an early Nix response (upregulation and translocation to the mitochondria) was observed after 6 h of middle cerebral artery occlusion in the rat. Nix translocation was observed in the ipsilateral cortex and striatum before other histological (infarct development, neuronal loss, apoptotic body formation) or biochemical (Bax activation or caspase-3 cleavage) markers of damage were detected. While fundamental differences between hypoxia/ischaemia in culture and in vivo likely explain the different temporal profiles of Nix, Bax, and caspase-3 activation observed, these studies show that like Bax, mitochondrial accumulation is a common event during Nix activation. These are the first studies to show upregulation and translocation of Nix in the ischaemic brain and suggest Nix to be a novel therapeutic target in ischaemic research. Moreover, Nix upregulation in staurosporine-treated SH-SY5Y cells and dexamethasone-treated A1.1 cells supports a more generalized role for Nix in apoptotic cell death.
Cortical Fluoro-Jade Staining and Blunted Adrenomedullary Response to Hypoglycemia after Noncoma Hypoglycemia in Rats
Authors: Tkacs Nancy C , Pan Yanhua , Raghupathi Ramesh , Dunn-Meynell Ambrose A , Levin Barry E
Published: May 2005

Intensive insulin therapy in patients with type 1 diabetes mellitus reduces long-term complications; however, intensive therapy is also associated with a three-fold increase in hypoglycemic episodes. The present study in conscious rats characterizes the physiologic and neuropathologic consequences of a single episode of moderate hypoglycemia. In this model, intravenous insulin is used to reduce plasma glucose to 30 to 35 mg/dL for 75mins. This single hypoglycemic insult acutely induces hypoglycemia-associated autonomic failure (HAAF), with epinephrine responses to hypoglycemia reduced more than 36% from control. Neuropathology after this insult includes the appearance of dying cells, assessed with the marker Fluoro-jade B (FJ). After hypoglycemic insult, FJ+ cells were consistently seen in subdivisions of the medial prefrontal cortex, the orbital cortex, and the piriform cortex. There was a significant correlation between depth of hypoglycemia and number of FJ+ cells, suggesting that there is a critical threshold below which vulnerable cells begin to die. These data suggest that there is a population of cells that are vulnerable to moderate levels of hypoglycemia commonly experienced by patients with insulin-treated diabetes. These cells, which may be neurons, are primarily found in cortical regions implicated in visceral perception and autonomic control, raising the possibility that their loss contributes to clinically reported deficits in autonomic and perceptual responses to hypoglycemia.
The Epstein–Glaser approach to perturbative quantum field theory: graphs and Hopf algebras
Authors: Lange Alexander
Published: May 2005

The paper aims at investigating perturbative quantum field theory in the approach of Epstein and Glaser (EG) and, in particular, its formulation in the language of graphs and Hopf algebras (HAs). Various HAs are encountered, each one associated with a special combination of physical concepts such as normalization, localization, pseudounitarity, causal regularization, and renormalization. The algebraic structures, representing the perturbative expansion of the S-matrix, are imposed on operator-valued distributions equipped with appropriate graph indices. Translation invariance ensures the algebras to be analytically well defined and graded total symmetry allows to formulate bialgebras. The algebraic results are given embedded in the corresponding physical framework, covering the two EG versions by Fredenhagen and Scharf that differ with respect to the concrete recursive implementation of causality. Besides, the ultraviolet divergences occurring in Feynman’s representation are mathematically reasoned. As a final result, the change of the renormalization scheme in the context of EG is modeled via a HA and interpreted as the EG analog of Kreimer’s HA.
Compact radio-frequency power supply for ion and particle guides and traps
Authors: Cermak Ivo
Published: May 2005

In this article, we present a modern compact rf or ac power generator that uses a resonant driving scheme without the necessity for any matching device. The developed unit also does not need any expensive high voltage power supply for generating output voltages in the range of some 100V typically required for the function of trapping devices. The high efficiency of the generator allows long-term operation at output powers of around 50W without any performance losses. The frequency range of the device is determined by the output transformer. It can be varied from the megahertz range down to some kilohertz by replacing the output transformer and several capacitors in the control part of the generator. Thus, our device can be used for supplying traps operating with ions as well as with charged nano- or microparticles.
Pseudorotation motion in tetrahydrofuran: An ab initio study
Authors: Rayón Víctor M. , Sordo Jose A.
Published: May 2005

The use of different models based on experimental information about the observed level splitings, rotational constants, and far-infrared transition frequencies leads to different predictions on the equilibrium geometry for tetrahydrofuran. High-level ab initio calculations [coupled cluster singles, doubles (triples)/complete basis set (second order Moller–Plesset triple, quadrupole, quintuple)+zero-point energy(anharmonic)] suggest that the equilibrium conformation of tetrahydrofuran is an envelope Cs structure. The theoretical geometrical parameters might be helpful to plan further microwave spectroscopic studies in order to get a physical interpretation of the measurements.
Techniques for combinatorial molecular beam epitaxy
Authors: Tsui Frank , He Liang
Published: May 2005

Basic considerations for implementing combinatorial approach to molecular beam epitaxy (MBE) are discussed, focusing on the key issues relevant to conventional MBE synthesis using solid sources and characterization. The primary objective for implementing combinatorial approach is to make MBE do more, more able to carry out controlled and systematic work in large parameter space, without sacrificing any existing capabilities of conventional MBE. Methods for accomplishing this by integrating current instrumentation technology are described.
Current loop generated from a generalized impedance converter: A new sensor signal conditioning circuit
Authors: Muñoz Diego Ramírez , Berga Silvia Casans , Escrivá Càndid Reig
Published: May 2005

A sensor signal conditioning circuit using a generalized impedance converter (GIC) is presented. The circuit is dc polarized and able to feed a constant current to one or more sensors. GIC input impedance is kept high to maintain the load current of its input reference voltage very low. Experimental results show the feasibility of the dc modified GIC as an electronic conditioning circuit for two resistive temperature detectors (RTD-Pt100) sharing the same current loop.
Megapixel ion imaging with standard video
Authors: Li Wen , Chambreau Steven D. , Lahankar Sridhar A. , Suits Arthur G.
Published: May 2005

We present an ion imaging approach employing a real-time ion counting method with standard video. This method employs a center-of-mass calculation of each ion spot (more than 3×3pixels spread) prior to integration. The results of this algorithm are subpixel precision position data of the corresponding ion spots. These addresses are then converted to the final image with user selected resolution, which can be up to ten times higher than the standard video camera resolution (640×480). This method removes the limiting factor imposed by the resolution of standard video cameras and does so at very low cost. The technique is used in conjunction with dc slice imaging, replacing the local maximum searching algorithm developed by Houston and co-workers [B. Y. Chang, R. C. Hoetzlein, J. A. Mueller, J. D. Geiser, and P. L. Houston, Rev. Sci. Instrum. 69, 1665 (1998)]. The performance is demonstrated using HBr and DBr photodissociation at 193nm with 3+1 resonance enhanced multiphoton ionization detection of hydrogen and deuterium atom products. The measured velocity resolution for DBr dissociation is 0.50% (δv∕v), mainly limited in this case by the bandwidth of the photolysis laser. Issues affecting slice imaging resolution and performance are also discussed.
Versatile portable fluorometer for time-resolved luminescence analysis
Authors: Chen Guoying
Published: May 2005

A robust, filter-based portable fluorometer was designed, prototyped, and tested for time-resolved luminescence (TRL) analysis. Its flexible optical design allows interchangeable configurations to support three measurement modes: liquid-phase TRL using a sample cuvette, solid-matrix TRL using a sorbent strip, and evanescent-field TRL using a quartz-rod waveguide. A xenon flashlamp is used as the light source and a photomultiplier tube (PMT) as the photodetector. A gating technique was implemented to overcome PMT saturation by the intense xenon lamp flash, therefore higher gains can be set to measure weak luminescence signals. The TRL signal is digitized at a 4μs time resolution and a 12bit amplitude resolution. Individual flashes were monitored by a photodiode and its current was integrated to compensate for source light fluctuation. Using tetracycline as a model analyte, a 0.025ppb limit of detection (LOD) with a typical 2% relative standard deviation, and a 3 orders of magnitude (0.5–300ppb) linear dynamic range (r2=0.9996) were achieved.
Environment of hafnium and silicon in Hf-based dielectric films: An atomistic study by x-ray absorption spectroscopy and x-ray diffraction
Authors: Morais J. , Miotti L. , Bastos K. P. , Teixeira S. R. , Baumvol I. J. R. , Rotondaro A. L. P. , Chambers J. J. , Visokay M. R. , Colombo L. , Alves M. C. Martins
Published: May 2005

The atomic structure of HfSiO and HfSiON was investigated before and after thermal annealing using x-ray diffraction and x-ray absorption spectroscopy. In HfSiO, the Hf atoms are arranged in a monoclinic HfO2 structure with Hf as second nearest neighbors, while Si is in a SiO2 environment. Thermal annealing induces crystallization of HfSiO with subtle changes in Hf–Hf distances. In the case of HfSiON, a stable structure is observed around the Hf atoms, which remains unaffected after annealing. Nitrogen is present in the first coordination shell of the Hf atoms, with Si in a SiON environment.
Spin photovoltaic effect in quantum wires with Rashba interaction
Authors: Pershin Yuriy V. , Piermarocchi Carlo
Published: May 2005

We propose a mechanism for spin-polarized photocurrent generation in quantum wires. The effect is due to the combined effect of Rashba spin-orbit interaction, external magnetic field, and microwave radiation. The time-independent interactions in the wire give rise to a spectrum asymmetry in k space. The microwave radiation induces transitions between spin-splitted subbands, and, due to the peculiar energy dispersion relation, charge and spin currents are generated at zero-bias voltage. We demonstrate that the generation of pure spin currents is possible under an appropriate choice of external control parameters.
Cathodic arcs: Fractal voltage and cohesive energy rule
Authors: Anders André , Oks Efim M. , Yushkov Georgy Yu.
Published: May 2005

The noise of the burning voltage of cathodic arcs in vacuum was analyzed for a range of cathode materials (C, Mg, Ti, V, Ni, Cu, Zr, Nb, Ag, Hf, Ta, W, Pt, Bi, and Si). Cathodic arcs were generated in a coaxial plasma source, and the voltage noise was measured with a broadband measuring system. Each measurement was analyzed by fast Fourier transform, revealing a power spectrum ∼1∕f2 for all cathode materials over several orders of magnitude of frequency f (brown noise). The absence of any characteristic time down to possible cutoffs at high frequencies supports a fractal model of cathode spots. The amplitude of colored noise scaled approximately linearly with the cathode’s cohesive energy, which is another manifestation of the cohesive energy rule.
Nonideal effects on electron-atom bremsstrahlung in partially ionized hydrogen plasmas
Authors: Jung Young-Dae
Published: May 2005

The nonideal collective and plasma screening effects on nonrelativistic electron-atom bremsstrahlung process are investigated in partially ionized hydrogen plasmas. The effective pseudopotential model taking into account the screening and collective effects is applied to describe the interaction potential in nonideal plasmas. The electron-atom bremsstrahlung radiation cross section is obtained as a function of the nonideality plasma parameter, Debye length, projectile energy, and radiation photon energy. The results show that the collective and screening effects reduce the electron-atom bremsstrahlung radiation cross section in nonideal plasmas, especially, for the soft radiation region. It is also found that the atomic correlation effect suppresses the bremsstrahlung radiation cross section and is decreased with the increase in the nonideality plasma parameter.
Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations
Authors: Hamilton Grant , Stoneking Mark , Excoffier Laurent
Published: May 2005

Human social organization can deeply affect levels of genetic diversity. This fact implies that genetic information can be used to study social structures, which is the basis of ethnogenetics. Recently, methods have been developed to extract this information from genetic data gathered from subdivided populations that have gone through recent spatial expansions, which is typical of most human populations. Here, we perform a Bayesian analysis of mitochondrial and Y chromosome diversity in three matrilocal and three patrilocal groups from northern Thailand to infer the number of males and females arriving in these populations each generation and to estimate the age of their range expansion. We find that the number of male immigrants is 8 times smaller in patrilocal populations than in matrilocal populations, whereas women move 2.5 times more in patrilocal populations than in matrilocal populations. In addition to providing genetic quantification of sex-specific dispersal rates in human populations, we show that although men and women are exchanged at a similar rate between matrilocal populations, there are far fewer men than women moving into patrilocal populations. This finding is compatible with the hypothesis that men are strictly controlling male immigration and promoting female immigration in patrilocal populations and that immigration is much less regulated in matrilocal populations.
An ancestral oomycete locus contains late blight avirulence gene
Avr3a
, encoding a protein that is recognized in the host cytoplasm
Authors: Armstrong Miles R. , Whisson Stephen C. , Pritchard Leighton , Bos Jorunn I. B. , Venter Eduard , Avrova Anna O. , Rehmany Anne P. , Böhme Ulrike , Brooks Karen , Cherevach Inna , Hamlin Nancy , White Brian , Fraser Audrey , Lord Angela , Quail Michael A. , Churcher Carol , Hall Neil , Berriman Matthew , Huang Sanwen , Kamoun Sophien , Beynon Jim L. , Birch Paul R. J.
Published: May 2005

The oomycete
Phytophthora infestans
causes late blight, the potato disease that precipitated the Irish famines in 1846 and 1847. It represents a reemerging threat to potato production and is one of >70 species that are arguably the most devastating pathogens of dicotyledonous plants. Nevertheless, little is known about the molecular bases of pathogenicity in these algae-like organisms or of avirulence molecules that are perceived by host defenses. Disease resistance alleles, products of which recognize corresponding avirulence molecules in the pathogen, have been introgressed into the cultivated potato from a wild species,
Solanum demissum
, and
R1
and
R3a
have been identified. We used association genetics to identify
Avr3a
and show that it encodes a protein that is recognized in the host cytoplasm, where it triggers
R3a
-dependent cell death.
Avr3a
resides in a region of the
P. infestans
genome that is colinear with the locus containing avirulence gene

ATR1
NdWsB

in
Hyaloperonospora parasitica
, an oomycete pathogen of
Arabidopsis
. Remarkably, distances between conserved genes in these avirulence loci were often similar, despite intervening genomic variation. We suggest that
Avr3a
has undergone gene duplication and that an allele evading recognition by
R3a
arose under positive selection.
Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps
Authors: Coifman R. R. , Lafon S. , Lee A. B. , Maggioni M. , Nadler B. , Warner F. , Zucker S. W.
Published: May 2005

We provide a framework for structural multiscale geometric organization of graphs and subsets of

\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
\begin{equation*}{\mathbb{R}}^{n}\end{equation*}\end{document}

. We use diffusion semigroups to generate multiscale geometries in order to organize and represent complex structures. We show that appropriately selected eigenfunctions or scaling functions of Markov matrices, which describe local transitions, lead to macroscopic descriptions at different scales. The process of iterating or diffusing the Markov matrix is seen as a generalization of some aspects of the Newtonian paradigm, in which local infinitesimal transitions of a system lead to global macroscopic descriptions by integration. We provide a unified view of ideas from data analysis, machine learning, and numerical analysis.
Geometric diffusions as a tool for harmonic analysis and structure definition of data: Multiscale methods
Authors: Coifman R. R. , Lafon S. , Lee A. B. , Maggioni M. , Nadler B. , Warner F. , Zucker S. W.
Published: May 2005

In the companion article, a framework for structural multiscale geometric organization of subsets of

\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
\begin{equation*}{\mathbb{R}}^{n}\end{equation*}\end{document}

and of graphs was introduced. Here, diffusion semigroups are used to generate multiscale analyses in order to organize and represent complex structures. We emphasize the multiscale nature of these problems and build scaling functions of Markov matrices (describing local transitions) that lead to macroscopic descriptions at different scales. The process of iterating or diffusing the Markov matrix is seen as a generalization of some aspects of the Newtonian paradigm, in which local infinitesimal transitions of a system lead to global macroscopic descriptions by integration. This article deals with the construction of fast-order
N
algorithms for data representation and for homogenization of heterogeneous structures.
A single amino acid converts a repressor to an activator of flowering
Authors: Hanzawa Yoshie , Money Tracy , Bradley Desmond
Published: May 2005

Homologous proteins occurring through gene duplication may give rise to novel functions through mutations affecting protein sequence or expression. Comparison of such homologues allows insight into how morphological traits evolve. However, it is often unclear which changes are key to determining new functions. To address these ideas, we have studied a system where two homologues have evolved clear and opposite functions in controlling a major developmental switch. In plants, flowering is a major developmental transition that is critical to reproductive success.Arabidopsisphosphatidylethanolamine-binding protein homologuesTERMINAL FLOWER 1(TFL1) andFLOWERING LOCUS T(FT) are key controllers of flowering, determining when and where flowers are made, but as opposing functions: TFL1 is a repressor, FT is an activator. We have uncovered a striking molecular basis for how these homologous proteins have diverged. Although <60% identical, we have shown that swapping a single amino acid is sufficient to convert TFL1 to FT function and vice versa. Therefore, these key residues may have strongly contributed to the selection of these important functions over plant evolution. Further, our results suggest that TFL1 and FT are highly conserved in biochemical function and that they act as repressors or activators of flowering through discrimination of structurally related interactors by a single residue.
Male genital size reflects a tradeoff between attracting mates and avoiding predators in two live-bearing fish species
Authors: Langerhans R. Brian , Layman Craig A. , DeWitt Thomas J.
Published: May 2005

Male genitalia may experience more rapid, divergent evolution than any other animal character, but why? Research during the past several decades has culminated in the view that genital diversification primarily results from postmating sexual selection (e.g., sperm competition or cryptic female choice). However, the potential roles of premating sexual selection (e.g., mate choice) and natural selection have received little attention. We examined the possible importance of these mechanisms by investigating divergence in male genitalia among populations differing in predator regime for two species of live-bearing fish (
Gambusia affinis
in Texas and
Gambusia hubbsi
in The Bahamas). When controlled for body size, males exhibited a larger gonopodium (sperm-transfer organ) in predator-free environments than in predatory environments, a trend that persisted across space (multiple populations), time (multiple years), and species. By conducting laboratory experiments with
G. affinis
, we found that premating sexual selection seems to favor larger male genitalia (females exhibited mating preference for males having larger gonopodia), but natural selection in the presence of predatory fishes seems to favor reduced genital size (larger gonopodium size was associated with reduced burst-swimming performance, an important antipredator behavior). Although postmating sexual selection is widely presumed to be the most important mechanism driving genital diversification, these findings suggest that alternative mechanisms, particularly for organisms that cannot retract their genitalia, may also prove important.
Prion and water: Tight and dynamical hydration sites have a key role in structural stability
Authors: De Simone Alfonso , Dodson Guy G. , Verma Chandra S. , Zagari Adriana , Fraternali Franca
Published: May 2005

The propensity to form fibril in disease-related proteins is a widely studied phenomenon, but its correlation, if any, with structural characteristics of the associated proteins is not clearly understood. However, the observation has been made that some proteins that readily form amyloid have a significant number of backbone H bonds that are exposed to solvent molecules, suggesting that these regions have a propensity toward protein interaction and aggregation [Fernandez, A. & Scheraga, H. A. (2003)
Proc. Natl. Acad. Sci. USA
100, 113–118]. High-resolution x-ray structures of the sheep and human C-terminal prion protein have provided a useful description of surface and partially buried waters. By molecular dynamics simulations, we investigated the structural role of these water molecules. The solvent dynamical behavior on the protein surface reveals significant features about the stability and the potential interactions of the prion protein. The protein presents regions of tightly bound conserved waters that are necessary to hold in place local elements of the fold, as well as regions where the local water is in fast exchange with bulk water. These results are evidenced by a map of the spatial distribution entropy of the solvent around the protein. The particular behavior of the solvent around these regions may be crucial in the folding stability and in terms of aggregation loci.
Demasking biological oscillators: Properties and principles of entrainment exemplified by the
Neurospora
circadian clock
Authors: Roenneberg Till , Dragovic Zdravko , Merrow Martha
Published: May 2005

Oscillations are found throughout the physical and biological worlds. Their interactions can result in a systematic process of synchronization called entrainment, which is distinct from a simple stimulus-response pattern. Oscillators respond to stimuli at some times in their cycle and may not respond at others. Oscillators can also be driven if the stimulus is strong (or if the oscillator is weak); i.e., they restart their cycle every time they receive a stimulus. Stimuli can also directly affect rhythms without entraining the underlying oscillator (masking): Drivenness and masking are often difficult to distinguish. Here we use the circadian biological clock to explore properties of entrainment. We confirm previous results showing that the residual circadian system in
Neurospora
can be entrained in a mutant of the clock gene
frequency
(

frq
9

, a strain deficient in producing a functional FRQ protein). This finding has implications for understanding the evolution of circadian programs. By comparing data sets from independent studies, we develop a template for analyzing, modeling, and dissecting the interactions of entrained and masked components. These insights can be applied to oscillators of all periodicities.
CDX1 is an important molecular mediator of Barrett's metaplasia
Authors: Wong N. A. C. S. , Wilding J. , Bartlett S. , Liu Y. , Warren B. F. , Piris J. , Maynard N. , Marshall R. , Bodmer W. F.
Published: May 2005

The molecular pathogenesis of Barrett's metaplasia (BM) of the esophagus is poorly understood. The change to an intestinal phenotype occurs on a background of esophagitis due to refluxing acid and bile. CDX1, an important regulator of normal intestinal development, was studied as a potential key molecule in the pathogenesis of BM. CDX1 mRNA and protein were universally expressed in all samples of BM tested but not in normal esophageal squamous or gastric body epithelia. This tissue-specific expression was attributable to the methylation status of the
CDX1
promoter. Conjugated bile salts and the inflammatory cytokines TNF-α and IL-1β were all found to increase CDX1 mRNA expression
in vitro
. These effects were primarily mediated by NF-κB signaling but only occurred when the
CDX1
promoter was unmethylated or partially methylated. The data suggest that CDX1 is a key molecule linking etiological agents of BM to the development of an intestinal phenotype. Although the initial trigger for
CDX1
promoter demethylation is not yet identified, it seems likely that demethylation of its promoter may be the key to the induction and maintenance of CDX1 expression and so of the BM phenotype.
Inhibition of amyloid precursor protein processing by β-secretase through site-directed antibodies
Authors: Arbel Michal , Yacoby Iftach , Solomon Beka
Published: May 2005

Amyloid-β peptide (AβP) that accumulates in the Alzheimer's diseased brain is derived from proteolytic processing of the amyloid precursor protein (APP) by means of β- and γ-secretases. The β-secretase APP cleaving enzyme (BACE), which generates the N terminus of AβP, has become a target of intense research aimed at blocking the enzyme activity, thus reducing AβP and, subsequently, plaque formation. The search for specific inhibitors of β-secretase activity as a possible treatment for Alzheimer's disease intensified with the discovery that BACE may be involved in processing other non-APP substrates. The presence of the APP–BACE complex in early endosomes highlights the cell surface as a potential therapeutic target, suggesting that interference in APP–BACE interaction at the cell surface may affect amyloid-β production. We present here a unique approach to inhibit AβP production by means of antibodies against the β-secretase cleavage site of APP. These antibodies were found to bind human APP overexpressed by CHO cells, and the formed immunocomplex was visualized in the early endosomes. Indeed, blocking of the β-secretase site by these antibodies interfered with BACE activity and inhibited both intracellular and extracellular AβP formation in these cells.
A study of the effect of exposure in the reticulo-rumen of the cow on the strength of cotton, grass, hay and straw
Authors: Evans E. W. , Burnett J. , Bines J. A.
Published: May 2005

1. Changes in strength of cotton, Italian ryegrass leaf, hay stem and barley-straw stem on immersion in the contents of the reticulo-rumen, at two sites in the rumen and at one site in the reticulum, for periods of up to 56 h were measured using a cow on a hay diet. Specimens of the fibrous materials were immersed in the rumen digesta in such a way that they were not damaged by agitation or by rumination.

2. Load-to-fracture and elongation were measured on a machine using a constant-speed cross-head at a strain of about 10−3/s. The ratio strength:density (breaking load/mass per unit length) was determined.

3. Leaf of Italian ryegrass and stem of hay and of barley straw had strengths of about 37, 150 and 210 MN/m2. They lost strength at different rates when immersed in the rumen digesta, the times to half strength being in the ratio grass: hay: straw = 1:1.9:3.8. The similarity of this ratio to that for total time for eating and ruminating as given by Balch (1969), namely 1:2.0:3.5, for similar materials was noted.
Ruminal bioshynthesis of aromatic amino acids from arylacetic acids, glucose, shikimic acid and phenol
Authors: Kristensen S.
Published: May 2005

1. Ruminal metabolism of labelled phenylacetic acid, 4-hydroxyphenylacetic acid, indole-3-acetic acid, glucose, shikimic acid, phenol, and serine was studied in vitro by short-term incubation with special reference to incorporation rates into aromatic amino acids.

2. Earlier reports on reductive carboxylation of phenylacetic acid and indole-3-acetic acid in the rumen were confirmed and the formation of tyrosine from 4-hydroxyphenylacetic acid was demonstrated for the first time.

3. The amount of phenylalanine synthesized from phenylacetic acid was estimated to be 2 mg/1 rumen contents per 24 h, whereas the amount synthesized from glucose might be eight times as great, depending on diet.

4. Shikimic acid was a poor precursor of the aromatic amino acids, presumably owing to its slow entry into rumen bacteria.

5. A slow conversion of phenol into tyrosine was observed.
Vitamin B12absorption in megaloblastic anaemia
Authors: Senewiratne B. , Hettiarachchi J. , Senewiratne Kamalini
Published: May 2005

1. The response to cyanocobalamin and folic acid therapy was studied in forty-seven subjects with severe nutritional megaloblastic anaemia; twenty-five were vitamin B12deficient and, of these, ten were also folic acid deficient.

2. In twenty-four of the subjects, absorption of orally administered cyanocobalamin was normal, and there was a haematological response to small doses of orally administered cyanocobalamin, indicating adequate absorption. In one subject there was impaired cyanocobalamin absorption although free gastric hydrochloric acid was present.

3. The findings indicate that the absorptive function of the small intestine was unimpaired, with one exception, although there was a possible defect in nucleoprotein synthesis associated with a lack of vitamin B12and folic acid. Addisonian pernicious anaemia was not found in any of the subjects.
Jejunal absorption rates of glucose, glycine and glycylglycine in Zambian African adults with malnutrition
Authors: Cook G. C.
Published: May 2005

1. Absorption rates of glucose (from a 200 mM solution), glycine (from a 100 mM solution), and glycylglycine (from a 50 mM solution) have been estimated in six Zambian African adults with clinical evidence of malnutrition. A double-lumen tube technique was used to determine absorption rates from a 300 mm section of jejunum in vivo.

2. Two of the subjects had ileal tuberculosis and Kaposi's sarcoma respectively. A third probably had abdominal tuberculosis. Three of them had pellagra. Mean serum albumin concentration was 24 (14–43) g/l. Absorption rates have been compared with those in Zambian Africans (control subjects), previously studied, who had no clinical evidence of malnutrition, systemic infection or of gastrointestinal disease.

3. Mean glucose, glycine and glycylglycine absorption rates in the malnourished subjects were not significantly different from those in the control subjects. Mean net water absorption rate from the glucose solution was similar in the malnourished subjects and controls; during the glycine and glycylglycine perfusions the mean net absorption rate was, however, significantly lower in the malnourished subjects (P < 0.01 and P < 0.05 respectively); mean net water transfer during the glycine perfusions was towards the jejunal lumen in the malnourished subjects. One subject with pellagra had an abnormal excretion of D-xylose after a 25 g oral load; all other tests were normal.

4. It seems probable that malnutrition must be very severe, with jejunal mucosal abnormalities, before absorption rates of glucose, glycine and glycylglycine are significantly altered. The present study does not support the view that subclinical malnutrition is important in producing malabsorption of dietary components in Zambian African subjects. Systemic bacterial infections, and raised serum γ-globulin and immunoglobulin IgG concentrations have previously been associated with an impairment of glucose absorption rate in Zambian African subjects; those factors seem much more likely than subclinical malnutrition to be relevant, in the context of absorption, in the pathogenesis of overt malnutrition.