bluuebunny/crossref_metadata_2025 huggingface dataset:
Gyrokinetic particle simulation of drift-compressional modes in dipole geometry
Authors: Porazik Peter , Lin Zhihong
Published: July 2011

Gyrokinetic particle simulation of low frequency compressional modes has been developed using flux coordinates in the global magnetic dipole geometry. The compressional component is formulated in a scalar form of the parallel magnetic perturbation, and the gyro-averaging is performed explicitly in the configuration space. A reduced gyrokinetic model, in which the compressional perturbations are decoupled from the shear Alfvén and electrostatic perturbations, has been implemented. Linear simulation results have been verified using a numerical Nyquist analysis of the dispersion relation in the slab limit. Global simulations of unstable drift-compressional modes in the dipole geometry with kinetic ions find that finite Larmor radius (FLR) effects reduce the linear growth rate significantly but change little the real frequency. Global eigenmode structures show that the modes are even along the equilibrium magnetic field and broadened by the FLR effects in the radial direction. Radial propagation away from the region of excitation is observed.
Quantum kinetic theory of the filamentation instability
Authors: Bret A. , Haas F.
Published: July 2011

The quantum electromagnetic dielectric tensor for a multi-species plasma is re-derived from the gauge-invariant Wigner-Maxwell system and presented under a form very similar to the classical one. The resulting expression is then applied to a quantum kinetic theory of the electromagnetic filamentation instability. Comparison is made with the quantum fluid theory including a Bohm pressure term and with the cold classical plasma result. A number of analytical expressions are derived for the cutoff wave vector, the largest growth rate, and the most unstable wave vector.
Concentration polarization and second-kind electrokinetic instability at an ion-selective surface admitting normal flow
Authors: Khair Aditya S.
Published: July 2011

The passage of ionic current across a charge-selective surface has been studied for over a century and is relevant to well-established processes such as electrodialysis, electrodeposition, and electrochromatography. Recent years have witnessed a resurgence of interest in this subject, motivated by experiments demonstrating charge-selective transport of ions and solutes in nanofluidic devices. In this paper, we revisit and build upon the prototypical problem of one-dimensional ion transport across a flat ideally ion-selective surface, by examining the influence of imposed fluid flows on concentration polarization, over-limiting current, and second-kind (non-equilibrium) electro-osmotic instability at the surface. Specifically, we consider a simple model system of a cation-selective surface or membrane that admits a uniform fluid flow across itself. The membrane resides against a binary symmetric electrolyte, whose concentration is uniform in a “well-mixed” region at a prescribed distance from the membrane. A potential difference across the system drives an ionic current, leading to concentration polarization in the “unstirred layer” between the membrane and well-mixed bulk. The concentration polarization profile reflects a balance between advection of ions with the imposed “normal flow” and diffusion. The relative importance of these effects is parameterized by a Pećlet number Pe; notably, Pe is a signed quantity as the flow can be imposed toward or away from the membrane. An asymptotic analysis in the thin-Debye-layer limit reveals a significant impact of normal flow on concentration polarization and the advection-diffusion limiting current across the membrane. In particular, there exists a nonlinear concentration profile in the unstirred layer for non-zero Pe, in contrast to the familiar linear (diffusive) concentration polarization at Pe = 0. Next, we use matched asymptotic expansions to explore the structure of the unstirred layer at over-limiting currents, wherein a non-equilibrium space-charge layer develops near the membrane surface. A key step in this process is the derivation of a “generalized master equation” for the electric field across the unstirred layer. Finally, we examine the instability of the quiescent concentration polarization resulting from second-kind electro-osmotic slip in the space-charge layer. A linear stability analysis shows that normal flow can either enhance or retard the instability, depending on the flow direction.
Dynamics of dust-free cavities behind fast projectiles in a dusty plasma under microgravity conditions
Authors: Caliebe D. , Arp O. , Piel A.
Published: July 2011

The penetration of a dusty plasma by fast charged projectiles is studied under microgravity conditions. The mass and charge of the projectiles are larger than those of the target particles. A projectile generates a dust-free cavity in its wake, whose shape strongly depends on the projectile velocity. The faster the projectile the more elongated becomes the cavity while its cross-section decreases. The opening time of the cavity is found independent of the projectile velocity. For supersonic projectiles, the dynamics of the cavity can be decomposed into an initial impulse and a subsequent elastic response that can be modeled by a damped harmonic oscillator.
The effects of patch-potentials on the gravity probe B gyroscopes
Authors: Buchman S. , Turneaure J. P.
Published: July 2011

Gravity probe B (GP-B) was designed to measure the geodetic and frame dragging precessions of gyroscopes in the near field of the Earth using a drag-free satellite in a 642 km polar orbit. Four electrostatically suspended cryogenic gyroscopes were designed to measure the precession of the local inertial frame of reference with a disturbance drift of about 0.1 marc sec/yr–0.2 marc sec/yr. A number of unexpected gyro disturbance effects were observed during the mission: spin-speed and polhode damping, misalignment and roll-polhode resonance torques, forces acting on the gyroscopes, and anomalies in the measurement of the gyro potentials. We show that all these effects except possibly polhode damping can be accounted for by electrostatic patch potentials on both the gyro rotors and the gyro housing suspension and ground-plane electrodes. We express the rotor and housing patch potentials as expansions in spherical harmonics Yl,m(θ,ϕ). Our analysis demonstrates that these disturbance effects are approximated by a power spectrum for the coefficients of the spherical harmonics of the form $V_0^2 /l^r$V02/lr with V0 ≈ 100 mV and r ≈ 1.7.
Spectroscopic analysis of Eu3+ in single-crystal hexagonal phase AlN
Authors: Gruber John B. , Vetter Ulrich , Taniguchi Takashi , Burdick Gary W. , Hofsäss Hans , Chandra Sreerenjini , Sardar Dhiraj K.
Published: July 2011

A detailed spectroscopic analysis of the crystal-field splitting of the energy levels of Eu3+(4f6) in single crystals of hexagonal phase aluminum nitride is reported based on assignments made to the high-resolution cathodoluminescence spectra observed between 500 nm and 750 nm obtained at 11 K and room temperature. Single crystals doped with trivalent europium were grown by high pressure, high temperature technology, and the crystal structure was confirmed by x ray diffraction methods to be the hexagonal phase. The Eu3+ ions substitute for Al3+ ions in sites of C3v symmetry during crystal growth. More than 97% of the observed spectra are attributed to Eu3+ in the majority site. The spectra are identified as transitions from the excited 5D0 and 5D1multiplets of Eu3+ to the ground-state multiplets 7F0, 7F1, 7F2, 7F3,7F4, 7F5, and 7F6 split by the crystal field into energy (Stark) levels. A parameterized Hamiltonian defined to operate within the 4f6 electronic configuration of Eu3+ was used to model the experimental Stark levels and their symmetry assignments or irreducible representations (irreps). The crystal-field parameters were determined through use of a Monte Carlo method in which the six Bqk were given random starting values and optimized using standard least-squares fitting between calculated and experimental levels. The final fitting, which involved 20 Stark levels and their irreps from 5D1, 5D0, and 7F0–4, resulted in a rms deviation of 6.7 cm−1. The predicted splitting of the 7F5 and 7F6 multiplets was used to assign the experimental splitting for these manifolds since the spectra involved are weak and broad, precluding detailed Stark-level assignments.
Axisymmetric turbulent statistics of long slender circular cylinders
Authors: Jordan Stephen A.
Published: July 2011

The experimental evidence leads us to believe that long slender circular cylinders have similar axisymmetric turbulent statistics along most of their axial length. The respective boundary layer reaches a maximum thickness (δ) with no further downstream net growth. Despite their small radius (a), these long cylinders still own high radius-based Reynolds numbers (Rea) as well as transverse curvatures (δ/a). The influence of these flow conditions (and others) on the turbulent statistics is still chiefly unknown. The present effort begins an investigation that targets axial similarity (or homogeneity) of the long thin cylinder statistics. The database is a collection of previous experimental measurements and observations as well as the present computational results by the large-eddy simulation methodology. Interestingly, this investigation shows that reaching axial homogeneity is reliant essentially on Rea with lesser influence by the transverse curvature. But the Rea value depends on the turbulent statistic of interest. Likewise, this same result was found for spotting the radial location of the respective statistical peak. Axial homogeneity starts near the cylinder wall then migrates outward radially with increasing Rea until full saturation through the turbulent intermediate layer.
Novel pattern forming states for Marangoni convection in volatile binary liquids
Authors: Zhang Jie , Oron Alexander , Behringer Robert P.
Published: July 2011

We describe experiments on Marangoni convection in thin evaporating liquid films. The films are binary mixtures of ethanol and water exposed to the ambient room air during all experimental runs. These experiments exhibit a variety of different, often novel, patterns, depending on the concentration (weight fraction) c of ethanol. Among these are mobile circular convective patterns, which have not been previously observed, to our knowledge. The convective patterns evolve due to the evaporation of both the solvent and the solute, and their size increases substantially with the initial concentration c. The patterns reported here differ from those found in binary mixtures of NaCl and water, where only water evaporates.
Role of loop entropy in the force induced melting of DNA hairpin
Authors: Mishra Garima , Giri Debaprasad , Li M. S. , Kumar Sanjay
Published: July 2011

Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction based on the lattice model. Probability analysis of the extreme bases of the stem revealed that at high temperature, the hairpin to coil transition is entropy dominated and the loop contributes significantly in its opening. However, at low temperature, the transition is force driven and the hairpin opens from the stem side. It is shown that the elastic energy plays a crucial role at high force. As a result, the force-temperature diagram differs significantly with the theoretical prediction.
Post-complementary metal-oxide-semiconductor vertical and molecular transistors: A platform for molecular electronics
Authors: Mentovich Elad D. , Richter Shachar
Published: July 2011

We demonstrate two types of post-complementary vertical-metal-insulator tunneling transistor in which a self-assembled monolayer is coupled to the channel of one of them. It is found that the properties of the molecular device are better than those of similar transistors in which these molecules are absent. The molecular transistor exhibits higher currents than the non-molecular device and shows negligible leakage currents, with clear features which are attributed to the properties of the molecules.
Superconducting quantum interference devices with submicron Nb/HfTi/Nb junctions for investigation of small magnetic particles
Authors: Nagel J. , Kieler O. F. , Weimann T. , Wölbing R. , Kohlmann J. , Zorin A. B. , Kleiner R. , Koelle D. , Kemmler M.
Published: July 2011

We investigated, at temperature 4.2 K, electric transport, flux noise, and resulting spin sensitivity of miniaturized Nb direct current superconducting quantum interference devices (SQUIDs) based on submicron Josephson junctions with HfTi barriers. The SQUIDs are either of the magnetometer-type or gradiometric in layout. In the white noise regime, for the best magnetometer we obtain a flux noise SΦ1/2=250nΦ0/Hz1/2, corresponding to a spin sensitivity Sμ1/2≥29μB/Hz1/2. For the gradiometer we find SΦ1/2=300nΦ0/Hz1/2 and Sμ1/2≥44μB/Hz1/2. The devices can still be optimized with respect to flux noise and coupling between a magnetic particle and the SQUID, leaving room for further improvement towards single spin resolution.
Sb-rich Si-Sb-Te phase change material for multilevel data storage: The degree of disorder in the crystalline state
Authors: Zhou Xilin , Wu Liangcai , Song Zhitang , Rao Feng , Cheng Yan , Peng Cheng , Yao Dongning , Song Sannian , Liu Bo , Feng Songlin , Chen Bomy
Published: July 2011

The phase change memory with monolayer chalcogenide film (Si18Sb52Te30) is investigated for the feasibility of multilevel data storage. During the annealing of the film, a relatively stable intermediate resistance can be obtained at an appropriate heating rate. The transmission electron microscopy in situ analysis reveals a conversion of crystallization mechanism from nucleation to crystal growth, which leads a continuous reduction in the degree of disorder. It is indicated from the electrical properties of the devices that the fall edge of the voltage pulse is the critical factor that determines a reliable triple-level resistance state of the phase change memory cell.
High-temperature ultraviolet detection based on InGaN Schottky photodiodes
Authors: Sang Liwen , Liao Meiyong , Koide Yasuo , Sumiya Masatomo
Published: July 2011

A thermally stable metal-insulator-semiconductor (MIS) Schottky-type photodiode with high performance based on the InGaN film is demonstrated at high temperatures up to 523 K. The reverse leakage current remains at a low level (10−7−10−8 A), while the UV responsivity is as high as 5.6 A/W at −3 V under 523 K, without observing the persistent photoconductivity. The discrimination ratio between ultraviolet (378 nm) and visible light (600 nm) is maintained to be more than 105. The temperature-dependent current-voltage characteristics of the MIS diode were analyzed. The photocurrent gain at reverse biases was interpreted in term of thermionic-field emission (TFE) and field-emission tunneling mechanism from room-temperature to 463 K, while TFE becomes the dominant mechanism at high temperatures.
Electronic states and spin-orbit splitting of lanthanum dimer
Authors: Liu Yang , Wu Lu , Zhang Chang-Hua , Krasnokutski Serge A. , Yang Dong-Sheng
Published: July 2011

Lanthanum dimer (La2) was studied by mass-analyzed threshold ionization (MATI) spectroscopy and a series of multi-configuration ab initio calculations. The MATI spectrum exhibits three band systems originating from ionization of the neutral ground electronic state, and each system shows vibrational frequencies of the neutral molecule and singly charged cation. The three ionization processes are La2+ (a2∑g+) ← La2 (X1∑g+), La2+ (b2Π3/2, u) ← La2 (X1∑g+), and La2+ (b2Π1/2, u) ← La2 (X1∑g+), with the ionization energies of 39 046, 40 314, and 40 864 cm−1, respectively. The vibrational frequency of the X1Σg+ state is 207 cm−1, and those of the a2Σg+, b2Π3/2, u and b2Π1/2, u are 235.7, 242.2, and 240 cm−1. While X1Σg+ is the ground state of the neutral molecule, a2Σg+ and b2Πu are calculated to be the excited states of the cation. The spin-orbit splitting in the b2Πu ion is 550 cm−1. An X4Σg− state of La2+ was predicted by theory, but not observed by the experiment. The determination of a singlet ground state of La2 shows that lanthanum behaves differently from scandium and yttrium.
Mutation in the type IB bone morphogenetic protein receptor
alk6b
impairs germ-cell differentiation and causes germ-cell tumors in zebrafish
Authors: Neumann Joanie C. , Chandler Garvin L. , Damoulis Vanessa A. , Fustino Nicholas J. , Lillard Katherine , Looijenga Leendert , Margraf Linda , Rakheja Dinesh , Amatruda James F.
Published: July 2011

Germ-cell tumors (GCTs), which arise from pluripotent embryonic germ cells, exhibit a wide range of histologic differentiation states with varying clinical behaviors. Although testicular GCT is the most common cancer of young men, the genes controlling the development and differentiation of GCTs remain largely unknown. Through a forward genetic screen, we previously identified a zebrafish mutant line,
tgct
, which develops spontaneous GCTs consisting of undifferentiated germ cells [Neumann JC, et al. (2009)
Zebrafish
6:319–327]. Using positional cloning we have identified an inactivating mutation in
alk6b
, a type IB bone morphogenetic protein (BMP) receptor, as the cause of the zebrafish GCT phenotype. Alk6b is expressed in spermatogonia and early oocytes, and
alk6b
mutant gonads display impaired BMP signal transduction, altered expression of BMP target genes, and abnormal germ-cell differentiation. We find a similar absence of BMP signaling in undifferentiated human GCTs, such as seminomas and embryonal carcinoma, but not in normal testis or in differentiated GCTs. These results indicate a germ-cell–autonomous role for BMP signal transduction in germ-cell differentiation, and highlight the importance of the BMP pathway in human GCTs.
The pivotal twin histidines and aromatic triad of the
Escherichia coli
ammonium channel AmtB can be replaced
Authors: Hall Jason A. , Kustu Sydney
Published: July 2011

In
Escherichia coli
, each subunit of the trimeric channel protein AmtB carries a hydrophobic pore for transport of NH
4
+
across the cytoplasmic membrane. Positioned along this substrate conduction pathway are two conserved elements—a pair of hydrogen-bonded histidines (H168/H318) located within the pore itself and a set of aromatic residues (F107/W148/F215) at its periplasmic entrance—thought to be critical to AmtB function. Using site-directed mutagenesis and suppressor genetics, we examined the requirement for these elements in NH
4
+
transport. This analysis shows that AmtB can accommodate, by either direct substitution or suppressor generation, acidic residues at one or both positions of the H168/H318 twin-histidine site while retaining near wild-type activity. Similarly, study of the F107/W148/F215 triad indicates that good-to-excellent AmtB function is preserved upon individual and simultaneous replacement of these aromatic amino acids with aliphatic residues. Our findings lead us to conclude that these elements and their component parts are not required for AmtB function, but instead serve to optimize its performance.
The weight of history: structures, patterns and legacies of secondary education in the British Isles, c.1200–c.1980
Authors: Richardson William
Published: July 2011

This article serves as context for the other papers in this special issue, all of which deal with developments in UK secondary education since c.1980. The paper comprises a review of selected impulses and imperatives that saw the substantial legacy of medieval and humanist schooling
in Britain re-shaped, during the period c.1830–c.1980, into the outline of today's landscape of secondary schooling. Three parallel themes are examined: the influence of universities and examinations in framing the secondary curriculum; the role of ideas about ability in shaping the
growth of secondary education; and the place of practical/technical education in the secondary school years. By tracing these themes, an account of the changing patterns of institutional provision across the British Isles is provided that, by 1980, had led to a thriving independent sector
of schools for a small minority coexisting alongside the massive enterprise of broadly comprehensive, state-funded secondary education in which significant tensions remained between separate 'grammar' and 'upper-elementary' traditions. Conclusions are drawn as to significant aspects of this
historic inheritance acting on developments in secondary education in the contemporary era.
Joining the big society: am I bothered?
Authors: Hayward Geoff , Williams Richard
Published: July 2011

This contribution takes the form of a reflective essay informed by 15 years of working and undertaking research with young people at risk of social exclusion and non-participation in the post-compulsory education and training system in the UK. In particular, it draws upon our experience
of working with young people, youth workers and other adults in the 'Engaging Youth Enquiry' undertaken as part of the Nuffield 14–19 Review. This research challenges two key policy assumptions: raising aspirations will lead to increased educational engagement and attainment and thereby
reduced social exclusion; and that an alternative more 'vocational' curriculum will improve young people's life chances. The work indicates a clear need to pay much greater attention to opportunity structures in thinking through policy interventions to support young people's transitions to
the labour market.
Teachers and teaching in upper secondary education: a comparison of systems in place across secondary and FE sectors
Authors: Rogers Lynne
Published: July 2011

The training of teachers in upper secondary education varies considerably dependent on whether training is undertaken as a secondary school teacher or as a teacher within the Further Education (FE) system. Indeed, until the late 1990s, the training of teachers in FE had been the focus
of little regulation by Government. Differences also occur across the UK with different pathways in place in the home countries. Regardless of the pathway taken to teaching in upper secondary education there are concerns that the teaching in schools and FE is still not good enough. The Coalition
Government has proposed many reforms to the training of teachers in schools and a consultation exercise has been undertaken on the training of teachers in the FE sector. This article will review current approaches to the training of teachers in the home countries of the UK. Attention will
be given to the proposed reforms in order to consider how these might contribute to raising the standard of teacher training and hence the quality of teaching in schools and FE.
Hypoxia-inducible factor-1α mRNA: a new target for destabilization by tristetraprolin in endothelial cells
Authors: Chamboredon Sandrine , Ciais Delphine , Desroches-Castan Agnès , Savi Pierre , Bono Françoise , Feige Jean-Jacques , Cherradi Nadia
Published: July 2011

Endothelial cells (ECs) are the primary sensors of variations in blood oxygen concentrations. They use the hypoxia-sensitive stabilization of the hypoxia-inducible factor-1α (HIF-1α) transcription factor to engage specific transcriptional programs in response to oxygen changes. The regulation of HIF-1α expression is well documented at the protein level, but much less is known about the control of its mRNA stability. Using small interfering RNA knockdown experiments, reporter gene analyses, ribonucleoprotein immunoprecipitations, and mRNA half-life determinations, we report a new regulatory mechanism of HIF-1α expression in ECs. We demonstrate that 1) sustained hypoxia progressively decreases HIF-1α mRNA while HIF-1α protein levels rapidly peak after 3 h and then slowly decay; 2) silencing the mRNA-destabilizing protein tristetraprolin (TTP) in ECs reverses hypoxia-induced down-regulation of HIF-1α mRNA; 3) the decrease in the half-life of Luciferase-HIF-1α-3′UTR reporter transcript that is observed after prolonged hypoxia is mediated by TTP; 4) TTP binds specifically to HIF-1α 3′UTR; and 5) the most distal AU-rich elements present in HIF-1α 3′UTR (composed of two hexamers) are sufficient for TTP-mediated repression. Finally, we bring evidence that silencing TTP expression enhances hypoxia-induced increase in HIF-1α protein levels with a concomitant increase in the levels of the carbonic anhydrase enzyme CA IX, thus suggesting that TTP physiologically controls the expression of a panel of HIF-1α target genes. Altogether, these data reveal a new role for TTP in the control of gene expression during the response of endothelial cell to hypoxia.
A novel organelle, the piNG-body, in the nuage ofDrosophilamale germ cells is associated with piRNA-mediated gene silencing
Authors: Kibanov Mikhail V. , Egorova Ksenia S. , Ryazansky Sergei S. , Sokolova Olesia A. , Kotov Alexei A. , Olenkina Oxana M. , Stolyarenko Anastasia D. , Gvozdev Vladimir A. , Olenina Ludmila V.
Published: July 2011

Proteins of the PIWI subfamily Aub and AGO3 associated with the germline-specific perinuclear granules (nuage) are involved in the silencing of retrotransposons and other selfish repetitive elements in the Drosophila genome. PIWI proteins and their 25- to 30-nt PIWI-interacting RNA (piRNAs) are considered as key participants of the piRNA pathway. Using immunostaining, we found a large, nuage-associated organelle in the testes, the piNG-body (piRNA nuage giant body), which was significantly more massive than an ordinary nuage granule. This body contains known ovarian nuage proteins, including Vasa, Aub, AGO3, Tud, Spn-E, Bel, Squ, and Cuff, as well as AGO1, the key component of the microRNA pathway. piNG-bodies emerge at the primary spermatocyte stage of spermatogenesis during the period of active transcription. Aub, Vasa, and Tud are located at the periphery of the piNG-body, whereas AGO3 is found in its core. Mutational analysis revealed that Vasa, Aub, and AGO3 were crucial for both the maintenance of the piNG-body structure and the silencing of selfish Stellate repeats. The piNG-body destruction caused by csul mutations that abolish specific posttranslational symmetrical arginine methylation of PIWI proteins is accompanied by strong derepression of Stellate genes known to be silenced via the piRNA pathway.
Zwint-1 is a novel Aurora B substrate required for the assembly of a dynein-binding platform on kinetochores
Authors: Kasuboski James M. , Bader Jason R. , Vaughan Patricia S. , Tauhata Sinji B. F. , Winding Michael , Morrissey Meghan A. , Joyce Michelle V. , Boggess William , Vos Larissa , Chan Gordon K. , Hinchcliffe Edward H. , Vaughan Kevin T.
Published: July 2011

Aurora B (AurB) is a mitotic kinase responsible for multiple aspects of mitotic progression, including assembly of the outer kinetochore. Cytoplasmic dynein is an abundant kinetochore protein whose recruitment to kinetochores requires phosphorylation. To assess whether AurB regulates recruitment of dynein to kinetochores, we inhibited AurB using ZM447439 or a kinase-dead AurB construct. Inhibition of AurB reduced accumulation of dynein at kinetochores substantially; however, this reflected a loss of dynein-associated proteins rather than a defect in dynein phosphorylation. We determined that AurB inhibition affected recruitment of the ROD, ZW10, zwilch (RZZ) complex to kinetochores but not zwint-1 or more-proximal kinetochore proteins. AurB phosphorylated zwint-1 but not ZW10 in vitro, and three novel phosphorylation sites were identified by tandem mass spectrometry analysis. Expression of a triple-Ala zwint-1 mutant blocked kinetochore assembly of RZZ-dependent proteins and induced defects in chromosome movement during prometaphase. Expression of a triple-Glu zwint-1 mutant rendered cells resistant to AurB inhibition during prometaphase. However, cells expressing the triple-Glu mutant failed to satisfy the spindle assembly checkpoint (SAC) at metaphase because poleward streaming of dynein/dynactin/RZZ was inhibited. These studies identify zwint-1 as a novel AurB substrate required for kinetochore assembly and for proper SAC silencing at metaphase.
What is the Future of Agricultural Economics Departments and the Agricultural and Applied Economics Association?
Authors: Perry Gregory M.
Published: July 2011

The downward trends in Agricultural and Applied Economics Association (AAEA) membership and faculty numbers nationwide have many departments wondering about the future of agricultural economics. The author examines trends in undergraduate and graduate enrollment, as well as trends in extension and experiment‐station funding, to suggest what the prospects are for future survival and growth. Although there exist challenges like shrinking faculty numbers, agricultural economics programs still have a strong undergraduate element and address important research issues. Consequently, agricultural economics should remain viable for many years to come.
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
Authors: Grant Gregory R. , Farkas Michael H. , Pizarro Angel D. , Lahens Nicholas F. , Schug Jonathan , Brunk Brian P. , Stoeckert Christian J. , Hogenesch John B. , Pierce Eric A.
Published: July 2011

Motivation: A critical task in high-throughput sequencing is aligning millions of short reads to a reference genome. Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing. A number of RNA-Seq algorithms are available, and claim to align reads with high accuracy and efficiency while detecting splice junctions. RNA-Seq data are discrete in nature; therefore, with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. The exercise to rigorously compare all viable published RNA-Seq algorithms has not been performed previously.

Results: We developed an RNA-Seq simulator that models the main impediments to RNA alignment, including alternative splicing, insertions, deletions, substitutions, sequencing errors and intron signal. We used this simulator to measure the accuracy and robustness of available algorithms at the base and junction levels. Additionally, we used reverse transcription–polymerase chain reaction (RT–PCR) and Sanger sequencing to validate the ability of the algorithms to detect novel transcript features such as novel exons and alternative splicing in RNA-Seq data from mouse retina. A pipeline based on BLAT was developed to explore the performance of established tools for this problem, and to compare it to the recently developed methods. This pipeline, the RNA-Seq Unified Mapper (RUM), performs comparably to the best current aligners and provides an advantageous combination of accuracy, speed and usability.

Availability: The RUM pipeline is distributed via the Amazon Cloud and for computing clusters using the Sun Grid Engine (http://cbil.upenn.edu/RUM).

Contact:  ggrant@pcbi.upenn.edu; epierce@mail.med.upenn.edu

Supplementary Information:The RNA-Seq sequence reads described in the article are deposited at GEO, accession GSE26248.
miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants
Authors: Yang Xiaozeng , Li Lei
Published: July 2011

Motivation: Ultra-deep sampling of small RNA libraries by next-generation sequencing has provided rich information on the microRNA (miRNA) transcriptome of various plant species. However, few computational tools have been developed to effectively deconvolute the complex information.

Results: We sought to employ the signature distribution of small RNA reads along the miRNA precursor as a model in plants to profile expression of known miRNA genes and to identify novel ones. A freely available package, miRDeep-P, was developed by modifying miRDeep, which is based on a probabilistic model of miRNA biogenesis in animals, with a plant-specific scoring system and filtering criteria. We have tested miRDeep-P on eight small RNA libraries derived from three plants. Our results demonstrate miRDeep-P as an effective and easy-to-use tool for characterizing the miRNA transcriptome in plants.

Availability:  http://faculty.virginia.edu/lilab/miRDP/

Contact:  ll4jn@virginia.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Fishery-dependent information and the ecosystem approach: what role can fishers and their knowledge play in developing countries?
Authors: Mathew Sebastian
Published: July 2011

Mathew, S. 2011. Fishery-dependent information and the ecosystem approach: what role can fishers and their knowledge play in developing countries? – ICES Journal of Marine Science, 68: 1805–1808. An ecosystem approach to fishery management is as much a mechanism to deal with the impact of fishing on targeted, associated, and dependent fish stocks, and on the habitat, as it is to deal with the impact of habitat degradation from natural and anthropogenic factors on fishing. In developing countries, often with little institutional capacity for generating timely and reliable information for managing fisheries, effective integration of the knowledge possessed by fishers and their communities regarding, for example, oceanographic, biological, economic, social, and cultural aspects can contribute to an ecosystem approach to fisheries. The challenge is to identify and validate such knowledge and to create policy and legal space to integrate it into management, also drawing upon good practice in industrialized countries. An attempt is made to identify such knowledge, to discuss its salient aspects, and to look at the conditions under which its practical value can be enhanced and integrated into formal fishery-management systems in developing countries.
Hemorrhagic Shock-induced Endothelial Cell Activation in a Spontaneous Breathing and a Mechanical Ventilation Hemorrhagic Shock Model Is Induced by a Proinflammatory Response and Not by Hypoxia
Authors: van Meurs Matijs , Wulfert Francis M. , Jongman Rianne M. , Schipper Martin , Houwertjes Martin C. , Vaneker Michiel , Scheffer Gert Jan , Teppema Luc J. , Aarts Leon P. H. J. , Heeringa Peter , Zijlstra Jan G. , Molema Grietje
Published: July 2011

Introduction

The interaction between neutrophils and activated endothelium is essential for the development of multiple organ dysfunction in patients with hemorrhagic shock (HS). Mechanical ventilation frequently is used in patients with HS. The authors sought to investigate the consequences of mechanical ventilation of mice subjected to HS on microvascular endothelial activation in the lung and kidney.

Methods

Anesthetized wild type C57BL/6 male mice were subjected to controlled hemorrhage; subgroups of mice were mechanically ventilated during the HS insult. To study the effect of acute hypoxia on the mice, the animals were housed in hypoxic cages. Gene expression levels was assessed by quantitative real-time polymerase chain reaction. Protein expression was assessed by immunohistochemistry and enzyme-linked immunosorbent assay.

Results

Ninety minutes after the shock induction, a vascular bed-specific, heterogeneous proinflammatory endothelial activation represented by E-selectin, vascular cell adhesion molecule 1, and intercellular adhesion molecule 1 expression was seen in kidney and lung. No differences in adhesion molecules between the spontaneously breathing and mechanically ventilated mice were found. Concentrations of the proinflammatory cytokines chemokine (C-X-C motif) ligand 1 (11.0-fold) and interleukin-6 (21.7-fold) were increased after 90 min of HS. Two hours of 6% oxygen did not induce the expression of E-selectin, vascular cell adhesion molecule 1, and intercellular adhesion molecule 1 in the kidneys and the lung.

Conclusions

Hemorrhagic shock leads to an early and reversible proinflammatory endothelial activation in kidney and lung. HS-induced endothelial activation is not changed by mechanical ventilation during the shock phase. Hypoxia alone does not lead to endothelial activation. The observed proinflammatory endothelial activation is mostly ischemia- or reperfusion-dependent and not related to hypoxia.
Sliding-induced non-uniform pre-tension governs robust and reversible adhesion: a revisit of adhesion mechanisms of geckos
Authors: Cheng Q. H. , Chen B. , Gao H. J. , Zhang Y. W.
Published: July 2011

Several mechanisms have been proposed in the literature to explain the robust attachment and rapid, controllable detachment of geckos' feet on vertical walls or ceilings, yet, it is still debatable, which one is ultimately responsible for geckos' extraordinary capabilities for robust and reversible adhesion. In this paper, we re-examine some of the key movements of geckos' spatula pads and seta hairs during attachment and detachment, and propose a sequence of simple mechanical steps that would lead to the extraordinary properties of geckos observed in experiments. The central subject under study here is a linear distribution of pre-tension along the spatula pad induced by its sliding motion with respect to a surface. The resulting pre-tension, together with a control of setae's pulling force and angle, not only allows for robust and strong attachment, but also enables rapid and controllable detachment. We perform computational modelling and simulations to validate the following key steps of geckos' adhesion: (i) creation of a linear distribution of pre-tension in spatula through sliding, (ii) operation of an instability envelope controlled by setae's pulling force and angle, (iii) triggering of an adhesion instability leading to partial decohesion along the interface, and (iv) complete detachment of spatula through post-instability peeling. The present work not only reveals novel insights into the adhesion mechanism of geckos, but also develops a powerful numerical simulation approach as well as additional guidelines for bioinspired materials and devices.
Characterization of IcmF of the type VI secretion system in an avian pathogenic Escherichia coli (APEC) strain
Authors: de Pace Fernanda , Boldrin de Paiva Jacqueline , Nakazato Gerson , Lancellotti Marcelo , Sircili Marcelo Palma , Guedes Stehling Eliana , Dias da Silveira Wanderley , Sperandio Vanessa
Published: July 2011

The intracellular multiplication factor (IcmF) protein is a component of the recently described type VI secretion system (T6SS). IcmF has been shown to be required for intra-macrophage replication and inhibition of phagosome–lysosome fusion inLegionella pneumophila. InVibrio choleraeit is involved in motility, adherence and conjugation. Given that we previously reported that two T6SS genes (hcpandclpV) contribute to the pathogenesis of a septicaemic strain (SEPT362) of avian pathogenicEscherichia coli(APEC), we investigated the function of IcmF in this strain. Further elucidation of the virulence mechanisms of APEC is important because this pathogen is responsible for financial losses in the poultry industry, and is closely related to human extraintestinal pathogenicE. coli(ExPEC) strains, representing a potential zoonotic risk, as well as serving as a reservoir of virulence genes. Here we show that an APECicmFmutant has decreased adherence to and invasion of epithelial cells, as well as decreased intra-macrophage survival. TheicmFmutant is also defective for biofilm formation on abiotic surfaces. Additionally, expression of the flagella operon is decreased in theicmFmutant, leading to decreased motility. The combination of these phenotypes culminates in this mutant being altered for infection in chicks. These results suggest that IcmF in APEC may play a role in disease, and potentially also in the epidemiological spread of this pathogen through enhancement of biofilm formation.
Three sympatrically occurring species of Metarhizium show plant rhizosphere specificity
Authors: Wyrebek Michael , Huber Cristina , Sasan Ramanpreet Kaur , Bidochka Michael J.
Published: July 2011

Here we tested the hypothesis that species of the soil-inhabiting insect-pathogenic fungusMetarhiziumare not randomly distributed in soils but show plant-rhizosphere-specific associations. We isolatedMetarhiziumfrom plant roots at two sites in Ontario, Canada, sequenced the 5′ EF-1α gene to discernMetarhiziumspecies, and developed an RFLP test for rapid species identification. Results indicated a non-random association of threeMetarhiziumspecies (Metarhizium robertsii,Metarhizium brunneumandMetarhizium guizhouense) with the rhizosphere of certain types of plant species (identified to species and categorized as grasses, wildflowers, shrubs and trees).M. robertsiiwas the only species that was found associated with grass roots, suggesting a possible exclusion ofM. brunneumandM. guizhouense. Supporting this,in vitroexperiments showed thatM. robertsiiconidia germinated significantly better inPanicum virgatum(switchgrass) root exudate than didM. brunneumorM. guizhouense.M. guizhouenseandM. brunneumonly associated with wildflower rhizosphere when co-occurring withM. robertsii. With the exception of these co-occurrences,M. guizhouensewas found to associate exclusively with the rhizosphere of tree species, predominantlyAcer saccharum(sugar maple), whileM. brunneumwas found to associate exclusively with the rhizosphere of shrubs and trees. These associations demonstrate that different species ofMetarhiziumassociate with specific plant types.
Associative retrieval processes in the human medial temporal lobe: Hippocampal retrieval success and CA1 mismatch detection
Authors: Chen Janice , Olsen Rosanna K. , Preston Alison R. , Glover Gary H. , Wagner Anthony D.
Published: July 2011

Hippocampal subfields CA3 and CA1 are hypothesized to differentially support the generation of associative predictions and the detection of associative mismatches, respectively. Using high-resolution functional MRI, we examined hippocampal subfield activation during associative retrieval and during subsequent comparisons of memory to matching or mismatching decision probes. Activity in the dentate gyrus/CA2/3, CA1, and other medial temporal lobe subregions tracked associative retrieval success, whereas activity in CA1 and the perirhinal cortex tracked the presence of associative mismatches. These data support the hypothesis that CA1 acts as a “comparator,” detecting when memory for the past and sensory input in the present diverge.
Germline alterations in the CDH1 gene in familial gastric cancer in the Japanese population
Authors: Yamada Hidetaka , Shinmura Kazuya , Ito Hiroaki , Kasami Masako , Sasaki Naomi , Shima Hideyuki , Ikeda Masami , Tao Hong , Goto Masanori , Ozawa Takachika , Tsuneyoshi Toshihiro , Tanioka Fumihiko , Sugimura Haruhiko
Published: July 2011

Germline point or small frameshift mutations of the CDH1 (E‐cadherin) gene are known to cause familial gastric cancer (FGC), but the frequency of CDH1 mutations is low in Japanese patients with FGC. Because recent studies have reported germline large genomic deletions of CDH1 in European and Canadian patients with FGC, in the present study we examined DNA samples from 13 Japanese patients with FGC to determine whether similar germline changes were present in CDH1 in this population. Using a sequencing analysis, a 1‐bp deletion (c.1212delC), leading to the production of a truncated protein (p.Asn405IlefsX12), was found in an FGC family; immunohistochemical analysis revealed the loss of CDH1 protein expression in the tumors in this family. Using a combination of multiplex ligation‐dependent probe amplification (MLPA) and RT‐PCR analyses, we also found a large genomic deletion (c.164‐?_387+?del), leading to the loss of exon 3 and the production of a truncated protein (p.Val55GlyfsX38), in another FGC family. The functional effects of the detected mutations were examined using a slow aggregation assay. Significant impairment of cell–cell adhesion was detected in CHO‐K1 cells expressing Ile405fsX12‐ and Gly55fsX38‐type CDH1 compared with cells expressing wild‐type CDH1. Our results suggest that the p.Asn405IlefsX12 and p.Val55GlyfsX38 mutations of the CDH1 gene contribute to carcinogenesis in patients with FGC. This is the first report of CDH1 germline truncating mutations in Japanese patients with FGC. Screening for large germline rearrangements should be included in CDH1 genetic testing for FGC. (Cancer Sci 2011; 102: 1782–1788)
Pregnancy in acromegaly: experience from two referral centers and systematic review of the literature
Authors: Cheng Sonia , Grasso Ludovica , Martinez‐Orozco Jose A. , Al‐Agha Rany , Pivonello Rosario , Colao Annamaria , Ezzat Shereen
Published: July 2011

Background  Acromegaly results from increased growth hormone and its target insulin‐like growth factor‐1, most commonly due to a pituitary tumour. As it is frequently accompanied by infertility, little is known about the course of this disease in pregnancy.

Objective  We describe 13 new pregnancies in acromegalic women and compare their outcomes in a systematic review of the literature.

Methods  We collected clinical, biochemical, imaging, and outcomes data during and following pregnancy and performed a systematic review for a total of 47 pregnancies. An extended analysis of 106 pregnancies was also performed.

Results  In 13 newly described cases, pregnancy was un‐complicated without need for additional surgical intervention. In these pregnancies, adjunctive medical therapy was required in three patients. This was in the form of somatostatin analogs (SA) (3/13) as well as pegvisomant in 1/13 to control symptomatic and biochemical progression. One 37‐year‐old female succeeded in having two separate pregnancies 2 years apart both without need for any form of medical therapy. Review of an additional 34 published reports allowed for an analysis of outcomes in 47 pregnancies. Adjunctive medical therapy during pregnancy was required in 15 of these cases where 12 received SA and an additional three received dopamine agonists. None of these patients developed endocrine or neurologic complications during pregnancy. In an extended analysis of 106 pregnancies, treatment during pregnancy appears to be associated with good disease control but increased risk of microsomic or macrosomic newborns depending on the medical agent used.

Conclusions  In 13 newly described pregnancies along with systematic review of an additional 34 cases indicate that pregnancy in treated acromegalic women can proceed without significant complications or teratogenicity. Medical treatment during pregnancy with DA or SA appears to be associated with altered neonatal weight. Nevertheless, gestation may have a beneficial impact on acromegaly control both during and following pregnancy.