bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature-time transformation diagram for Pb(Zr,Ti)O3 thin films
Authors: Varghese Ronnie , Williams Matthew , Gupta Shashaank , Priya Shashank
Published: July 2011

In this paper, we describe an analytical model to define the temperature-time- transformation (TTT) diagram of sol-gel deposited Pb(Zr,Ti)O3 thin films on platinized silicon substrates. Texture evolution in film occurred as the pyrolysis and thermal annealing conditions were varied. We demonstrate that the developed model can quantitatively predict the outcome of thermal treatment conditions in terms of texture evolution. Multinomial and multivariate regression techniques were utilized to create the predictor models for TTT data. Further, it was found that multinomial regression can provide better fit as compared to standard regression and multivariate regression. We have generalized this approach so that it can be applied to other thin film deposition techniques and bulk ceramics.
A new technique for the characterization of chaff elements
Authors: Scholfield David , Myat Maung , Dauby Jason , Fesler Jonathon , Bright Jonathan
Published: July 2011

A new technique for the experimental characterization of electromagnetic chaff based on Inverse Synthetic Aperture Radar is presented. This technique allows for the characterization of as few as one filament of chaff in a controlled anechoic environment allowing for stability and repeatability of experimental results. This approach allows for a deeper understanding of the fundamental phenomena of electromagnetic scattering from chaff through an incremental analysis approach. Chaff analysis can now begin with a single element and progress through the build-up of particles into pseudo-cloud structures. This controlled incremental approach is supported by an identical incremental modeling and validation process. Additionally, this technique has the potential to produce considerable savings in financial and schedule cost and provides a stable and repeatable experiment to aid model valuation.
Improved carrier concentration control in Zn-doped Ca5Al2Sb6
Authors: Zevalkink Alex , Toberer Eric S. , Bleith Tim , Flage-Larsen Espen , Snyder G. Jeffrey
Published: July 2011

Ca5Al2Sb6 is an inexpensive, Earth-abundant compound that exhibits promising thermoelectric efficiency at temperatures suitable for waste heat recovery. Inspired by our previous study of p-type Ca5−xNaxAl2Sb6, this work investigates doping with Zn2+ on the Al3+ site (Ca5Al2−xZnxSb6). We find Zn to be an effective p-type dopant, in contrast to the low solubility limit and poor doping efficiency of Na. Seebeck coefficient measurements indicate that the hole band mass is unaffected by the dopant type in the high-zT temperature range. Band structure and density of states calculations are employed in order to understand the carrier concentration-dependent effective mass. Ca5Al2−xZnxSb6 has a low lattice thermal conductivity that approaches the predicted minimum value at high temperature (1000 K) due to the complex crystal structure and high mass contrast.
Ternary mixed crystal effect on electron mobility in a strained wurtzite AlN/GaN/AlN quantum well with an InxGa1−xN nanogroove
Authors: Qu Y. , Ban S. L.
Published: July 2011

Based on the dielectric continuum phonon model, uniaxial model and force balance equation, the influence of an InxGa1−xN nanogroove inserted in a strained wurtzite AlN/GaN/AlN quantum well on electron mobility is studied. The results show that the optical phonon modes will be changed by the introduction of InGaN/GaN interfaces and the In component. It can be also found that the electron wave function will shift to the InGaN layer as long as the conductor band energy at GaN/InGaN interface gets lower than that at the AlN/GaN interface. Electron mobility first increases and then decreases as x increases, whereas the mobility is always greater than the case without an InGaN nanogroove when electrons mainly distribute in the GaN layer. Once most of the electrons transfers to the InGaN nanogroove, electron mobility drops sharply and then increases with the increase of x.
Origin of shape anisotropy effects in solution-phase synthesized FePt nanomagnets
Authors: Ferrer D. A. , Guchhait S. , Liu H. , Ferdousi F. , Corbet C. , Xu H. , Doczy M. , Bourianoff G. , Mathew L. , Rao R. , Saha S. , Ramon M. , Ganguly S. , Markert J. T. , Banerjee S. K.
Published: July 2011

Controlling the morphology of inorganic nanocrystals is important because many of their electronic attributes are highly sensitive to shape and aspect ratio. FePt nanocrystals have potential as advanced magnetic materials for ultrahigh-density memory. This is due to their high shape and/or magnetocrystalline anisotropy, which allows bits as small as 3 nm to be thermally stable over typical data storage periods of 10 years. Herein, nanocrystals were simply fabricated by simultaneous reduction of platinum acetylacetonate and thermal decomposition of iron pentacarbonyl in properly chosen conditions of solvent/surfactant proportions and temperature for rational design of their shape and magnetic properties. This work has combined magnetometry measurements and micromagnetic simulations to illustrate the role of the external shape on the rotation of the magnetization vector for colloidal assemblies.
Radial space-charge-limited electron flow in semi-insulating GaN:Fe
Authors: Mareš Jiří J. , Hubík Pavel , Krištofik Jozef , Prušáková Lucie , Uxa Štěpán , Paskova Tanya , Evans Keith
Published: July 2011

Semi-insulating iron-doped gallium nitride (GaN:Fe), a promising material for microwave electronics and optoelectronics, is characterized by means of current-voltage curves measured under non-equilibrium charge carrier injection conditions. To increase the electric field and enable local characterization of GaN:Fe, measurements are performed using a two-electrode configuration including a point contact with a diameter of 30 μm and large-area alloyed counter contact. Experimental evidence for various radial flow regimes corresponding to the universal 3/2 and quadratic power laws and to the so-called trap-filled-limit is presented. Furthermore, it is shown that the space-charge-limited current injected from the point contact may serve as a probe to measure both local and average scale density of electrically active traps, i.e., parameters that are necessary for GaN:Fe to be applied and optimized.
Vacuum electron heating by surface plasma wave
Authors: Kumar Pawan , Tripathi V. K.
Published: July 2011

Vacuum heating of electrons by a large amplitude surface plasma wave (SPW) over a metal surface due to the Brunel effect is studied. The surface plasma wave has large normal component of electric vector. The normal field pulls the electrons away from the plasma during the half cycle. Each electron sees, besides the E⊥ of the surface plasma wave, a static space charge field. As the electron returns back to the interface, it possesses kinetic energy that is deposited into the plasma, leading to plasma heating.
Enhancing light harvesting in organic solar cells with pyramidal rear reflectors
Authors: Cao Weiran , Myers Jason D. , Zheng Ying , Hammond William T. , Wrzesniewski Edward , Xue Jiangeng
Published: July 2011

We report enhanced light absorption in semi-transparent organic solar cells by using pyramidal rear reflectors to induce light trapping in the photoactive layer. Pyramidal rear reflectors with a base angle of 30° were molded from a transparent polymer on planar substrates. Compared with a planar rear reflector, the pyramidal structure leads to a more than 2.5 times longer path length in the active layer for the incident light. Experimental demonstration showed an 11%–75% enhancement in the photocurrent and overall efficiency of the solar cells, depending on the device size and active layer thickness.
Large-scale, nonsubtractive patterning of transparent conducting oxides by ion bombardment
Authors: Sosa Norma E. , Chen Christopher , Liu Jun , Marks Tobin J. , Hersam Mark C.
Published: July 2011

While significant progress has been achieved in the fabrication and performance of transparent electronic devices, substantially less research effort has been devoted to transparent interconnects, despite their critical importance for transparent integrated circuitry. Here, we exploit the crystal disorder induced by Ar+ ion bombardment to achieve efficient fabrication of electrically conductive patterns on indium oxide surfaces. The resulting ion-induced patterns are characterized by conductive atomic force microscopy, secondary ion mass spectrometry, and four-point charge transport measurements. Massively parallel patterning is demonstrated over square centimeter areas with a patterned electrical conductivity of ∼104 S cm−1.
Optical characterization of CdSe quantum dots with metal chalcogenide ligands in solutions and solids
Authors: Zhang Y. Q. , Cao X. A.
Published: July 2011

The exchange of the original organic ligands of colloidal CdSe core and CdSe/CdS/ZnS core/multishell quantum dots (QDs) with inorganic metal chalcogenide ligands (SnS44−) resulted in carrier delocalization in solutions and enhanced inter-QD electronic coupling in solids, as inferred from peak redshift and broadening of the absorption and photoluminescence (PL) spectra. The SnS4-capped QDs retained strong excitonic absorption but suffered significant PL quenching. Mild thermal treatment below 350 °C transformed the SnS4 ligands into a more conductive phase, leading to stronger coupling yet complete PL quenching. These findings suggest that QD solids with metal chalcogenide ligands may have high quantum yields of photocurrent generation and can be used as functional blocks in thin-film solar cells for efficient solar energy conversion.
Laser writing of the electronic activity of N- and H-atoms in GaAs
Authors: Balakrishnan N. , Patanè A. , Makarovsky O. , Polimeni A. , Capizzi M. , Martelli F. , Rubini S.
Published: July 2011

We use a focussed laser beam to control the electronic activity of N- and H-atoms in a dilute nitride Ga(AsN)/GaAs quantum well. Our approach yields submicron resolution in the spatial manipulation of the electronic properties and can provide an alternative method to masking techniques for H-defect engineering and in-plane patterning of the band gap energy.
Temperature dependence of nonequilibrium transport time of electrons in bulk GaAs investigated by time-domain terahertz spectroscopy
Authors: Zhu Y. M. , Chen L. , Peng Y. , Yuan M. H. , Wen Y. , Zhuang S. L.
Published: July 2011

By using free space terahertz electro-optic sampling technique, the terahertz (THz) waveforms emitted from intrinsic bulk GaAs photoexcited by femtosecond laser pulses under strong bias electric fields at various temperatures were recorded. We clearly observe the velocity of electrons exhibits a pounced overshoot behavior. The nonequiliburm transport time of electrons, τɛ, has been obtained from the THz waveforms. From the temperature dependence of τɛ, we find that τɛ is governed by the polar scattering process of electrons in Γ valley via longitudinal opticalphonon emissions.
High density multi-level recording for archival data preservation
Authors: Holzner F. , Paul Ph. , Drechsler U. , Despont M. , Knoll A. W. , Duerig U.
Published: July 2011

Archival data storage is predominantly based on magnetic tape technology. An alternative probe based multi-level recording scheme is proposed which specifically addresses the issue of long term data preservation. In a first step, the data are written as topographic relief in an organic resist. To achieve long term preservation, the relief structure is transferred in a Si based inorganic carrier by means of reactive ion etching. Thereby, the data are preserved as written in stone. Using 3-level logic, a storage density of 99 Gb/in2 is demonstrated and read-back of the data is accomplished with an error rate of 10−3 based on threshold detection. Exploiting etch anisotropy in layered substrates, logic levels can be physically separated from one another in different layers which enhances tamper resistance and also provides a means for heterogeneous storage concepts.
Surface-related two-photon absorption and refraction of CdSe quantum dots
Authors: Zhu B. H. , Zhang H. C. , Zhang J. Y. , Cui Y. P. , Zhou Z. Q.
Published: July 2011

Colloidal CdSe quantum dots (QDs), whose surface traps are controlled with the purification process, are measured with a Z-scan technique using an 80 femtosecond pulse duration laser source. Their two-photon absorption coefficient and refractive index are decreased more than one order of magnitude with the increase of the density of surface traps, indicating that the surface states are involved in the two-photon process.
Extraordinary magnetoresistance in shunted chemical vapor deposition grown graphene devices
Authors: Friedman Adam L. , Robinson Jeremy T. , Perkins F. Keith , Campbell Paul M.
Published: July 2011

We report gate tunable linear magnetoresistances (MRs) of ∼600% at 12 T in metal-shunted devices fabricated on chemical vapor deposition (CVD) grown graphene. The effect occurs due to decreasing conduction through the shunt as the magnetic field increases (known as the extraordinary magnetoresistance effect) and yields an MR that is at least an order-of-magnitude higher than in un-shunted graphene devices.
Asymmetric cancer cell division regulated by AKT
Authors: Dey-Guha Ipsita , Wolfer Anita , Yeh Albert C. , G. Albeck John , Darp Revati , Leon Eduardo , Wulfkuhle Julia , Petricoin Emanuel F. , Wittner Ben S. , Ramaswamy Sridhar
Published: July 2011

Human tumors often contain slowly proliferating cancer cells that resist treatment, but we do not know precisely how these cells arise. We show that rapidly proliferating cancer cells can divide asymmetrically to produce slowly proliferating “G0-like” progeny that are enriched following chemotherapy in breast cancer patients. Asymmetric cancer cell division results from asymmetric suppression of AKT/PKB kinase signaling in one daughter cell during telophase of mitosis. Moreover, inhibition of AKT signaling with small-molecule drugs can induce asymmetric cancer cell division and the production of slow proliferators. Cancer cells therefore appear to continuously flux between symmetric and asymmetric division depending on the precise state of their AKT signaling network. This model may have significant implications for understanding how tumors grow, evade treatment, and recur.
Graphene field-effect transistors
Authors: Reddy Dharmendar , Register Leonard F , Carpenter Gary D , Banerjee Sanjay K
Published: July 2011

Owing in part to scaling challenges for metal oxide semiconductor field-effect transistors (MOSFETs) and complementary metal oxide semiconductor (CMOS) logic, the semiconductor industry is placing an increased emphasis on emerging materials and devices that may provide improved MOSFET performance beyond the 22 nm node, or provide novel functionality for, e.g. ‘beyond CMOS’ devices. Graphene, with its novel and electron–hole symmetric band structure and its high carrier mobilities and thermal velocities, is one such material that has garnered a great deal of interest for both purposes. Single and few layer carbon sheets have been fabricated by a variety of techniques including mechanical exfoliation and chemical vapour deposition, and field-effect transistors have been demonstrated with room-temperature mobilities as high as 10 000 cm2 V−1 s−1. But graphene is a gapless semiconductor and gate control of current is challenging, off-state leakage currents are high, and current does not readily saturate with drain voltage. However, various ways to overcome, adapt to, or even embrace this property are now being considered for device applications. In this work we explore through illustrative examples the potential of and challenges to graphene use for conventional and novel device applications.
Microscopic dipole–exchange theory for planar nanostriped magnonic crystals
Authors: Nguyen Hoa T , Cottam M G
Published: July 2011

Microscopic (or Hamiltonian-based) calculations are reported for the collective spin-wave bands and gaps in one-dimensional magnonic crystals consisting of a periodic array of ferromagnetic stripes separated by nonmagnetic spacers. This is achieved by generalizing a previous approach for the dipole–exchange spin waves in individual (or non-interacting) stripes and small finite arrays of nanoelements to cases where there is an effectively infinite periodic array of striped elements. This involves introducing a Bloch wavenumber associated with the periodicity property and reformulating the microscopic dipole–dipole and exchange sums for a periodic structure to include the inter-stripe and intra-stripe contributions. The theory gives good agreement when compared with Brillouin light scattering data for Permalloy magnonic structures. Applications of the microscopic theory are also made to cases where the applied magnetic field has a component transverse to the easy axis of the stripes, favouring the formation of edge modes.
Time-resolved spectroscopy of exciton states in single crystals and single crystalline films of YAlO3 and YAlO3 : Ce
Authors: Babin V , Gorbenko V , Kondakova I , Kärner T , Laguta V V , Nikl M , Zazubovich S , Zorenko Yu
Published: July 2011

Luminescence characteristics of single crystals (SC) and single crystalline films (SCF) of YAlO3 and YAlO3 : Ce are studied at 4.2–300 K under photoexcitation in the 4–20 eV energy range. The origin and structure of the intrinsic and impurity defects responsible for various exciton-related emission and excitation bands are identified. The ≈5.6 eV emission of YAlO3 SCF is ascribed to the self-trapped excitons. In YAlO3 SC, the dominating 5.63 eV and 4.12 eV emissions are ascribed to the excitons localized at the isolated antisite defect
and at the
defect associated with the nearest-neighbouring oxygen vacancy, respectively. The thermally stimulated release of the electrons, trapped at these defects, takes place around 200 K and 280 K, respectively. The presence of
-related defects and isolated oxygen vacancies (AlO5 units) in YAlO3 SC is confirmed by NMR measurements. The formation energies of various
-related defects are calculated within the density functional theory. The influence of various intrinsic and impurity defects on the luminescence characteristics of Ce3+ centres is clarified.
An all-metal route to broadband low-loss electromagnetic cloaks
Authors: Wang Jiafu , Qu Shaobo , Xu Zhuo , Ma Hua , Wang Xinhua , Zhou Hang , Lu Lei , Xia Song
Published: July 2011

Narrow bandwidth significantly limits the development of electromagnetic cloaks. Here, we demonstrated both numerically and experimentally a new route to broadband low-loss electromagnetic cloak. The cloak is all-metallic and non-resonant, avoiding both the narrow bandwidth and high loss problems. To verify the proposed cloak, a sample operating at X-band was fabricated and tested. Both the simulation and experiment results convincingly confirm the broadband property of such cloaks.
Trapped particle stability for the kinetic stabilizer
Authors: Berk H.L. , Pratt J.
Published: July 2011

A kinetically stabilized axially symmetric tandem mirror (KSTM) uses the momentum flux of low-energy, unconfined particles that sample only the outer end-regions of the mirror plugs, where large favourable field-line curvature exists. The window of operation is determined for achieving magnetohydrodynamic (MHD) stability with tolerable energy drain from the kinetic stabilizer. Then MHD stable systems are analysed for stability of the trapped particle mode. This mode is characterized by the detachment of the central-cell plasma from the kinetic-stabilizer region without inducing field-line bending. Stability of the trapped particle mode is sensitive to the electron connection between the stabilizer and the end plug. It is found that the stability condition for the trapped particle mode is more constraining than the stability condition for the MHD mode, and it is challenging to satisfy the required power constraint. Furthermore, a severe power drain may arise from the necessary connection of low-energy electrons in the kinetic stabilizer to the central region.
Fine-tuning of the Msn2/4–mediated yeast stress responses as revealed by systematic deletion of Msn2/4 partners
Authors: Sadeh Amit , Movshovich Natalia , Volokh Misha , Gheber Larisa , Aharoni Amir
Published: July 2011

The Msn2 and Msn4 transcription factors play major roles in the yeast general stress response by mediating the transcription of hundreds of genes. Despite extensive information on Msn2/4–mediated gene expression profiles, much less is known regarding the network of proteins that regulate its activity. Here we describe a systematic approach designed to examine the roles of 35 Msn2/4 partners in regulating Msn2/4 transcriptional activity in the face of four different environmental conditions. Our analysis indicates that single deletions of 26 Msn2/4 partners significantly affect Msn2/4 transcription activity under four different conditions. The low functional redundancy of the Msn2 regulatory network indicates that Msn2/4 activity is finely tuned by many of Msn2/4 partners to provide an optimized stress response through differential activation, nuclear localization, degradation, and chromatin remodeling. Our specific analysis of Msn2 activity showed that a relatively large number of partners act to suppress Msn2 activity under nonstress conditions through independent mechanisms, including cytoplasmic retention, proteosome-mediated Msn2 degradation, and chromatin remodeling. Such negative regulation is crucial to minimize the cost of uncontrolled stress response gene expression and ensures a high growth rate in the absence of stress.
Neuroprotective role of PrPCagainst kainate-induced epileptic seizures and cell death depends on the modulation of JNK3 activation by GluR6/7–PSD-95 binding
Authors: Carulla Patricia , Bribián Ana , Rangel Alejandra , Gavín Rosalina , Ferrer Isidro , Caelles Carme , del Río José Antonio , Llorens Franc
Published: July 2011

Cellular prion protein (PrPC) is a glycosyl-phosphatidylinositol–anchored glycoprotein. When mutated or misfolded, the pathogenic form (PrPSC) induces transmissible spongiform encephalopathies. In contrast, PrPChas a number of physiological functions in several neural processes. Several lines of evidence implicate PrPCin synaptic transmission and neuroprotection since its absence results in an increase in neuronal excitability and enhanced excitotoxicity in vitro and in vivo. Furthermore, PrPChas been implicated in the inhibition of N-methyl-d-aspartic acid (NMDA)–mediated neurotransmission, and prion protein gene (Prnp) knockout mice show enhanced neuronal death in response to NMDA and kainate (KA). In this study, we demonstrate that neurotoxicity induced by KA in Prnp knockout mice depends on the c-Jun N-terminal kinase 3 (JNK3) pathway since Prnpo/oJnk3o/omice were not affected by KA. Pharmacological blockage of JNK3 activity impaired PrPC-dependent neurotoxicity. Furthermore, our results indicate that JNK3 activation depends on the interaction of PrPCwith postsynaptic density 95 protein (PSD-95) and glutamate receptor 6/7 (GluR6/7). Indeed, GluR6–PSD-95 interaction after KA injections was favored by the absence of PrPC. Finally, neurotoxicity in Prnp knockout mice was reversed by an AMPA/KA inhibitor (6,7-dinitroquinoxaline-2,3-dione) and the GluR6 antagonist NS-102. We conclude that the protection afforded by PrPCagainst KA is due to its ability to modulate GluR6/7-mediated neurotransmission and hence JNK3 activation.
A Grid-enabled web portal for NMR structure refinement with AMBER
Authors: Bertini Ivano , Case David A. , Ferella Lucio , Giachetti Andrea , Rosato Antonio
Published: July 2011

Motivation: The typical workflow for NMR structure determination involves collecting thousands of conformational restraints, calculating a bundle of 20–40 conformers in agreement with them and refining the energetics of these conformers. The structure calculation step employs simulated annealing based on molecular dynamics (MD) simulations with very simplified force fields. The value of refining the calculated conformers using restrained MD (rMD) simulations with state-of-art force fields is documented. This refinement however presents various subtleties, from the proper formatting of conformational restraints to the definition of suitable protocols.

Results: We describe a web interface to set up and run calculations with the AMBER package, which we called AMPS-NMR (AMBER-based Portal Server for NMR structures). The interface allows the refinement of NMR structures through rMD. Some predefined protocols are provided for this purpose, which can be personalized; it is also possible to create an entirely new protocol. AMPS-NMR can handle various restraint types. Standard rMD refinement in explicit water of the structures of three different proteins are shown as examples. AMPS-NMR additionally includes a workspace for the user to store different calculations. As an ancillary service, a web interface to AnteChamber is available, enabling the calculation of force field parameters for organic molecules such as ligands in protein–ligand adducts.

Availability and Implementation: AMPS-NMR is embedded within the NMR services of the WeNMR project and is available at http://py-enmr.cerm.unifi.it/access/index/amps-nmr; its use requires registration with a digital certificate.

Contact:  ivanobertini@cerm.unifi.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments
Authors: Semegni J. Y. , Wamalwa M. , Gaujoux R. , Harkins G. W. , Gray A. , Martin D. P.
Published: July 2011

Summary:Many natural nucleic acid sequences have evolutionarily conserved secondary structures with diverse biological functions. A reliable computational tool for identifying such structures would be very useful in guiding experimental analyses of their biological functions. NASP (Nucleic Acid Structure Predictor) is a program that takes into account thermodynamic stability, Boltzmann base pair probabilities, alignment uncertainty, covarying sites and evolutionary conservation to identify biologically relevant secondary structures within multiple sequence alignments. Unique to NASP is the consideration of all this information together with a recursive permutation-based approach to progressively identify and list the most conserved probable secondary structures that are likely to have the greatest biological relevance. By focusing on identifying only evolutionarily conserved structures, NASP forgoes the prediction of complete nucleotide folds but outperforms various other secondary structure prediction methods in its ability to selectively identify actual base pairings.

Availability: Downloable and web-based versions of NASP are freely available at http://web.cbio.uct.ac.za/~yves/nasp_portal.php

Contact:  yves@cbio.uct.ac.za

Supplementary information:  Supplementary data are available at Bioinformatics online.
Sufficient statistics and expectation maximization algorithms in phylogenetic tree models
Authors: Kiryu Hisanori
Published: July 2011

Motivation: Measuring evolutionary conservation is a routine step in the identification of functional elements in genome sequences. Although a number of studies have proposed methods that use the continuous time Markov models (CTMMs) to find evolutionarily constrained elements, their probabilistic structures have been less frequently investigated.

Results: In this article, we investigate a sufficient statistic for CTMMs. The statistic is composed of the fractional duration of nucleotide characters over evolutionary time, Fd, and the number of substitutions occurring in phylogenetic trees, Ns. We first derive basic properties of the sufficient statistic. Then, we derive an expectation maximization (EM) algorithm for estimating the parameters of a phylogenetic model, which iteratively computes the expectation values of the sufficient statistic. We show that the EM algorithm exhibits much faster convergence than other optimization methods that use numerical gradient descent algorithms. Finally, we investigate the genome-wide distribution of fractional duration time Fd which, unlike the number of substitutions Ns, has rarely been investigated. We show that Fd has evolutionary information that is distinct from that in Ns, which may be useful for detecting novel types of evolutionary constraints existing in the human genome.

Availability: The C++ source code of the ‘Fdur’ software is available at http://www.ncrna.org/software/fdur/

Contact:  kiryu-h@k.u-tokyo.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Epipelagic fish distributions in relation to thermal fronts in a coastal upwelling system using high-resolution remote-sensing techniques
Authors: Reese Douglas C. , O'Malley Robert T. , Brodeur Richard D. , Churnside James H.
Published: July 2011

Reese, D. C., O'Malley, R. T., Brodeur, R. D., and Churnside, J. H. 2011. Epipelagic fish distributions in relation to thermal fronts in a coastal upwelling system using high-resolution remote-sensing techniques. – ICES Journal of Marine Science, 68: 1865–1874. Coastal upwelling systems are characterized by substantial spatial and temporal variability with respect to surface conditions, with fauna patchily distributed and high abundances in localized areas. Examining habitat associations on finer spatial scales than previous studies have been able to achieve would advance the understanding of important marine coastal ecosystems. This study evaluates the spatial and temporal relationships of single fish and fish schools with sea surface temperature (SST) fronts in the northern California Current upwelling system, using lidar (light detection and ranging) from an aircraft to sample surface waters over the continental shelf. High-resolution data were collected on the distribution of surface nekton and SST, then the locations of fish were analysed with respect to their proximity to SST fronts using GIS spatial analyses. Both fish schools and solitary fish were located significantly closer to fronts than would be expected by chance. The association of fish to fronts varied with the progression of the upwelling season such that fish associated less with fronts under stronger upwelling conditions. The relationships observed indicate the importance of thermal features to fish as a habitat component in a variable upwelling environment and have implications for management and conservation.
The ups and downs of working with industry to collect fishery-dependent data: the Irish experience
Authors: Lordan Colm , Ó Cuaig Macdara , Graham Norman , Rihan Dominic
Published: July 2011

Lordan, C., Ó Cuaig, M., Graham, N., and Rihan, D. 2011. The ups and downs of working with industry to collect fishery-dependent data: the Irish experience. – ICES Journal of Marine Science, 68: 1670–1678. Working with the fishing industry to collect fishery-dependent data for scientific and advisory purposes is essential in most countries, but despite the many advantages of working with fishers, it is not without challenges. The objectives and the ups and downs of 16 recent projects in Ireland are described, and four case studies are discussed in detail. Some common themes that characterize both successful and unsuccessful experiences are identified. One critical aspect is industry's sometimes unrealistic time-horizons and expectations when engaging in scientific data collection. Detailed communication of objectives, procedures, results, and relevance not only to industry representatives, but also to vessel owners and crew, is required throughout the life cycle of a project. For some projects, there is a clear need to include incentives in the design, but for others this is less critical. The critical needs for ongoing quality control and assurance, validation of data, and appropriate project design are discussed, along with the link between successful management systems and participatory research. Finally, comment is provided on how the expected reforms of the EU's Common Fisheries Policy will place new demands on joint research.
Dehydroepiandrosterone and ageing
Authors: Arlt Wiebke
Published: July 2011

Dehydroepiandrosterone (DHEA) is the crucial precursor of human sex steroid synthesis and thus mediates the majority of its effects indirectly, following downstream conversion to sex steroids and other steroids of potentially distinct activity. No specific receptor for DHEA or its sulfate ester DHEAS has been identified yet. However, there is evidence of specific binding sites for DHEA on immune and vascular cells and for direct interaction with cell signaling cascades, which may facilitate direct effects of DHEA.

DHEA is mainly secreted by the adrenal zona reticularis and, together with cortisol and aldosterone, represents one of three major steroids produced by the adrenal glands. However, in contrast to cortisol and aldosterone, circulating concentrations of DHEA and its sulfate ester DHEAS show a physiological decline with ageing.

Seminal studies in patients with adrenal insufficiency, who suffer from pronounced DHEA deficiency, have illustrated the physiological significance of DHEA (1–4) (Chaper 5.9) and its role as an efficient vehicle for female androgen replacement. Importantly, studies in systemic lupus erythematosus have started to define a role for DHEA as an immune modulatory drug. By contrast, the few randomized controlled trials on DHEA supplementation in healthy elderly adults have yielded largely disappointing results. However, irrespective of the very scarce evidence, DHEA is perceived by the lay public as a ‘fountain of youth’ hormone, based merely on the observation of declining serum levels with ongoing ageing. This has led to widespread, uncontrolled use, further facilitated by its inappropriate classification as a ‘food supplement’ by the US Food and Drug Administration.

Two issues are important to consider when assessing the scientific literature on the potential clinical effects of DHEA. Firstly, the capability of the adrenal gland to produce DHEA is only observed in some but not all mammals, and thus represents a recent evolutionary development. Most importantly, the adrenal glands of rodents do not express CYP17 and therefore cannot synthesize DHEA. Therefore, the potential for transferring results of rodent experiments to the human situation is limited. To date, many reports on DHEA effects, in particular with regard to protection against cancer, heart disease, diabetes, and obesity (5) are based on the administration of grossly supraphysiologic DHEA doses in rodent models. The second problem in the scientific DHEA literature is the multitude of studies based on associations rather than mechanistic insights, which often results in oversimplification of perceived causalities. This is exemplified by the multitude of studies demonstrating various effects of DHEA on longevity, which then is used by many to claim a general antiageing effect. In this chapter, a closer look at the available current evidence with regard to the role of DHEA in ageing humans is provided.
Bone disease in older people
Authors: Prince R. L.
Published: July 2011

Bone disease is a common problem in the elderly, and its clinical manifestation are a major preventable public health problem. The disorders of the skeleton have been classified in a variety of ways, an approach which tends to restrict understanding of the clinical problem in a particular patient. Frequently, several separate disorders coexist, each contributing to impairment of bone form or function, and each requiring a separate intervention.

The major categories of disorder are osteoporosis, too little bone within the bone, osteomalacia, impaired mineralization of bone matrix, and infiltration of bone with cancer cells. Each represents a distinct pathological processes that results in abnormal bone structure and function, which may present as bone pain and/or fracture.
Hormones and the kidney
Authors: Park Jong Chan , Hirschberg Raimund
Published: July 2011

As producers of hormones the kidneys are an endocrine organ. Hormones that are produced in the kidneys include 1,25-dihydroxyvitamin D3, renin and angiotensin, and erythropoietin. The kidney also contributes to the circulating pool of growth factors such as insulin-like growth factor-1 (IGF-1). Moreover, the kidneys participate in the regulation of hormonal action by eliminating hormones from the circulation, primarily polypeptide hormones. Renal elimination contributes significantly to the degradation of many peptide hormones and, to a lesser extent, catecholamines and some steroid hormones (Box 10.2.1.1). Hence, in advanced renal failure the half-lives and serum levels of these hormones are altered. In addition, the kidneys are target organs for hormones. The nephron is a major or exclusive receptor-bearing site for some hormones, and several other hormones are important in the regulation of aspects of renal function (Box 10.2.1.2). Certain abnormalities in the levels and activities of some of these latter hormones play significant roles in chronic renal failure and the progression of renal disease, and inhibitory therapeutic interventions are important treatment strategies in some renal diseases.
Hypercalcaemia
Authors: Levi Ronen , Silver Justin
Published: July 2011

Ionized calcium is essential for several physiological functions, including neuromuscular activation, endocrine and exocrine secretions, integrity of cellular bilayers, plasma coagulation, immune functions and bone metabolism. Extracellular fluid (ECF) calcium is uniquely controlled by its own calcium-sensing receptor, regulating the secretion of parathyroid hormone (PTH), synthesis of 1,25-dihydroxyvitamin D, and the renal reabsorption of filtered calcium (see Chapter 4.1). With the advent of the autoanalyser and routine determination of serum calcium levels, recognition of hypercalcaemia has become common. However, the clinical spectrum of hypercalcaemia varies from a laboratory-detected, asymptomatic mineral disorder to a life-threatening state.
Rickets and osteomalacia (acquired and heritable forms) and skeletal dysplasias
Authors: Whyte Michael P. , Liberman Uri A.
Published: July 2011

Mineralization of newly formed organic matrix of bone is a complex and highly ordered process. The requirements include adequate extracellular concentrations of calcium (Ca 2+) and phosphorous, as inorganic phosphate (Pi), and normal function of bone-forming cells. Disturbances in either requirement can lead to a stereotypic response of impaired skeletal mineralization (1).

Rickets describes the clinical consequences of diminished mineralization of matrix throughout a growing skeleton. Infants, children, and adolescents can be affected. Osteomalacia results from the same disturbance after growth plates fuse. However, neither term denotes a specific disease. Each is a generic label for the signs and symptoms that follow perturbations that disrupt the orderly deposition of hydroxyapatite crystals into skeletal tissue. Nevertheless, in nearly all patients, there are low extracellular levels of Ca 2+ and/or Pi. Often, diminished stores or impaired bioactivation of vitamin D are involved and cause hypocalcaemia, secondary hyperparathyroidism, and hypophosphataemia (1). Occasionally, it is kidney tubule dysfunction that results directly in urinary Pi wasting and leads to hypophosphataemia, sometimes associated with impaired bioactivation of vitamin D. Rarely, disturbances involving chondrocytes and osteoblasts, defective bone matrix, or other disruptions interfere with Ca 2+ and Pi deposition into the skeleton. The number of conditions that cause rickets and osteomalacia is considerable – some are acquired and some are inherited.
Adrenal incidentaloma
Authors: Terzolo Massimo
Published: July 2011

Adrenal incidentaloma is an adrenal mass that is discovered serendipitously with a radiological examination performed for indications unrelated to adrenal disease (1). The incidental discovery of an adrenal mass has become an increasingly common problem, because of the widespread use of ultrasonography, CT, and MRI in clinical practice (2, 3). These techniques have greatly improved their power of resolution over recent years, thereby increasing the possibility of detection of tiny adrenal lumps.

Several factors hinder a clear characterization of the phenomenon ‘adrenal incidentaloma’, which may be considered as a byproduct of technology applied to medical practice. Adrenal incidentaloma is not a single pathological entity and the likelihood of any specific diagnosis depends both on the circumstances of discovery and the applied definition of incidentaloma. Unfortunately, published reports are inconsistent in applying inclusion and exclusion criteria for these various factors, making the results difficult to interpret. A further issue is the lack of specific clinical features of the patients carrying an adrenal incidentaloma.
Adrenocortical cancer
Authors: Libè Rossella , Groussin Lionel , Bertagna Xavier , Bertherat Jérôme
Published: July 2011

Adrenocortical cancer (ACC) is among the most aggressive endocrine tumours with an overall very poor prognosis. Morbidity and mortality can be secondary to steroid hormone excess and/or tumour growth and metastases. This potentially poor outcome justifies the importance of considering malignancy in the man-agement of an adrenal mass. The diagnosis of malignancy in a patient with an adrenal tumour relies on careful investigations of clinical, biological, and imaging features before surgery and path-ological examination after tumour removal. Appropriate man-agement and follow-up by an expert multidisciplinary team is important to improve prognosis and to progress in these rare neoplasms.
Phaeochromocytomas, paragangliomas, and neuroblastoma
Authors: Mackenzie Isla S. , Brown Morris J.
Published: July 2011

Phaeochromocytomas are rare neuroendocrine tumours of neural crest origin, which often produce excess catecholamines (1). Although usually arising from the chromaffin cells of the adrenal medulla, phaeochromocytomas may also arise at other sites of sympathetic or parasympathetic chromaffin tissue anywhere from the base of the skull to the pelvis. Extra-adrenal phaeochromocytomas are called paragangliomas. Some patients with phaeochromocytoma or paraganglioma present with the classical triad of symptoms of headaches, palpitations, and sweating but many others present with less specific features such as hypertension or with an unidentified mass lesion.

Owing to the rarity of the condition and the relatively nonspecific symptoms with which it often presents, it is not unusual for several years to pass from symptom onset until the diagnosis of phaeochromocytoma is made. However, the consequences of not finding a phaeochromocytoma can be severe and may even result in death. In fact, in one study, around 50% of cases of phaeochromocytoma found at post mortem were unsuspected during life. Interestingly, a former US President, Dwight Eisenhower, was found to have a 1.5 cm adrenal phaeochromocytoma at post mortem, which was undiagnosed during life despite a history of severe hypertension and headaches (2). Patients with untreated phaeochromocytoma are at risk of the cardiovascular consequences of catecholamine surges, including hypertensive emergencies, intracerebral haemorrhage, and acute heart failure. Approximately 10% of phaeochromocytomas are malignant and some represent part of familial syndromes. The genetic basis of many phaeochromocytomas is becoming increasingly apparent as more mutations are found.
Glucocorticoid resistance—a defect of the glucocorticoid receptor
Authors: van Rossum Elisabeth F. C. , Lamberts Steven W. J.
Published: July 2011

The first case of glucocorticoid resistance was reported in 1976 by Vingerhoeds et al. (1). The patient was suffering from hypercortisolism with none of the tissue effects of Cushing’s disease. Further evaluation revealed that the ligand-binding affinity of the glucocorticoid receptor (GR) was diminished. His son and nephew were mildly affected and their GR also showed a reduced hormone affinity, although this was to a lesser extent. Later, the GR gene of the index patient was sequenced and showed a homozygous mutation at position 2054, yielding a valine for aspartic acid substitution at amino acid residue 641 (2). The other two family members appeared to be heterozygous carriers of the same mutation, which can explain their milder clinical picture. Since then, other patients with mutations in the GR gene leading to the syndrome of generalized glucocorticoid resistance have been described (Table 5.8.1) (18).

Familial glucocorticoid resistance is a rare disease, characterized by reduced cortisol action at the tissue level, which is compensated for by elevation of ACTH levels, resulting in an increase of adrenal steroids (glucocorticoids, androgens, mineralocorticoids) (18). It is rather unfamiliar and may confuse clinicians, since the signs and symptoms can be nonspecific. This syndrome has an autosomal recessive or dominant mode of inheritance.
Familial glucocorticoid deficiency
Authors: Hughes Claire , Metherell Louise , Clark Adrian J.L.
Published: July 2011

Familial glucocorticoid deficiency (FGD), also known as isolated glucocorticoid deficiency or hereditary unresponsiveness to ACTH, is a rare, genetically heterogeneous autosomal recessive disorder. It is characterized by resistance of the adrenal cortex to ACTH, resulting in adrenal failure with isolated glucocorticoid deficiency. Mineralocorticoid production by the adrenal gland remains near normal.

Patients with FGD usually present in early childhood with symptoms relating to cortisol deficiency, including hypoglycaemia, jaundice, recurrent infection, and failure to thrive. Patients are hyperpigmented due to grossly elevated ACTH levels.

FGD was first described in 1959 by Shepard et al. who reported two sisters as having Addison’s disease without hypoaldosteronism (1). Subsequently, a number of patients were reported with an inherited form of adrenal insufficiency also without hypoaldosteronism (2–5). In contrast to Addison’s disease (see Chapter 5.9), FGD is a genetic disorder resulting from mutations in genes encoding essential proteins involved in the early response to ACTH.
Congenital adrenal hyperplasia
Authors: Krone Nils
Published: July 2011

Congenital adrenal hyperplasia (CAH) represents a group of autosomal recessive disorders of steroidogenesis caused by defects in steroidogenic enzymes involved in glucocorticoid synthesis or in enzymes providing cofactors to steroidogenic enzymes (1, 2). Congenital lipoid adrenal hyperplasia (CLAH) caused by steroidogenic acute regulatory protein (StAR) deficiency is distinct in origin and presentation from the conventional variants of CAH, with the unique feature of lipid accumulation subsequently leading to destruction of adrenal function. This chapter will also mention aldosterone synthase deficiency, which is the only defect in adrenal steroidogenesis causing deficient mineralocorticoid biosynthesis without affecting glucocorticoid biosynthesis. The disorder cannot strictly be considered a CAH variant as it does not result in increased ACTH drive and thus not in adrenal hyperplasia.

Novel forms of CAH have emerged during recent years. These include P450 oxidoreductase deficiency (ORD), P450 side-chain cleavage (CYP11A1) deficiency, the nonclassic form of CLAH (StAR deficiency), and apparent cortisone reductase deficiency. All forms of congenital adrenal hyperplasia resemble a disease continuum spanning from mild nonclassic presentations to classic onset with severe signs and symptoms.