bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular theory for self assembling mixtures of patchy colloids and colloids with spherically symmetric attractions: The single patch case
Authors: Marshall Bennett D. , Chapman Walter G.
Published: September 2013

In this work we develop a new theory to model self assembling mixtures of single patch colloids and colloids with spherically symmetric attractions. In the development of the theory we restrict the interactions such that there are short ranged attractions between patchy and spherically symmetric colloids, but patchy colloids do not attract patchy colloids and spherically symmetric colloids do not attract spherically symmetric colloids. This results in the temperature, density, and composition dependent reversible self assembly of the mixture into colloidal star molecules. This type of mixture has been recently synthesized by grafting of complimentary single stranded DNA [L. Feng, R. Dreyfus, R. Sha, N. C. Seeman, and P. M. Chaikin, Adv. Mater. 25(20), 2779–2783 (2013)]10.1002/adma.201204864. As a quantitative test of the theory, we perform new monte carlo simulations to study the self assembly of these mixtures; theory and simulation are found to be in excellent agreement.
Role of sampling in evaluating classical time autocorrelation functions
Authors: Zimmermann Tomáš , Vaníček Jiří
Published: September 2013

We analyze how the choice of the sampling weight affects efficiency of the Monte Carlo evaluation of classical time autocorrelation functions. Assuming uncorrelated sampling or sampling with constant correlation length, we propose a sampling weight for which the number of trajectories needed for convergence is independent of the correlated quantity, dimensionality, dynamics, and phase-space density. By contrast, it is shown that the computational cost of the “standard” algorithm sampling from the phase-space density may scale exponentially with the number of degrees of freedom. Yet, for the stationary Gaussian distribution of harmonic systems and for the autocorrelation function of a linear function of phase-space coordinates, the computational cost of this standard algorithm is also independent of dimensionality.
Optical properties of Si-doped and Be-doped InAlAs lattice-matched to InP grown by molecular beam epitaxy
Authors: Lumb M. P. , Yakes M. K. , González M. , Tischler J. G. , Walters R. J.
Published: September 2013

In this paper, we determine the optical constants and carrier mobilities of Si-doped and Be-doped InAlAs lattice matched to InP. The samples were grown using molecular beam epitaxy and characterized using Hall measurements, variable angle spectroscopic ellipsometry, and room temperature photoluminescence spectroscopy. A Moss-Burstein shift in the fundamental absorption edge was observed in both Si-doped and Be-doped materials. We fitted a multiple-oscillator, critical point model to the dielectric function of the materials extracted using the spectroscopic ellipsometry. The tabulated input parameters of this model allow for accurate calculations of the dielectric function of doped InAlAs to be made, which is useful information for simulating a variety of InP-based optoelectronic devices.
Study of the structure dependent behavior of polyelectrolyte in water
Authors: Tucker Ashley K. , Stevens Mark J.
Published: September 2013

We examine the effect of pendant architecture on linear polyelectrolytes in solution using molecular dynamics simulations. A comparison is done between the standard bead-spring polyelectrolyte system and a system which has the charged beads pendant to neutral backbone beads. Recent simulations of ionomer melts have found significant differences in the structure between the two architectures, but we find the structure is not dramatically affected by the different geometry. In general, the backbone architecture is slightly more compact than the pendant architecture. The counterion condensation is typically larger for the backbone systems, which yields the more compact structures. Only when both the Bjerrum length is much larger than the spacing between charges and the spacing between pendants is twice the backbone bead spacing, is the peak in the monomer-counterion radial distribution function larger for the pendant architecture. The radius of gyration for the pendant remains larger than backbone architecture because of the extra excluded volume of the pendant.
Transport and magnetic properties of highly densified CoS2 ceramic
Authors: Hébert S. , Guilmeau E. , Berthebaud D. , Lebedev O. I. , Roddatis V. , Maignan A.
Published: September 2013

Dense ceramics of the itinerant ferromagnet CoS2 have been prepared by the spark plasma sintering technique. The structural study confirms a cubic unit-cell for CoS2 with a = 5.539(6)Å (SG=Pa3¯). Scanning and transmission electron microscopy reveal the existence of sulfur deficient regions of composition “Co2S3” with a structure compatible to that of CoS2 where 0.5 S atom are missing in one out of two successive layers along the b direction. The volume of these regions estimated to be less than 1% is explained by possible S losses from the surface during the sintering. The physical properties measurements show a high TC (122 K), large saturated magnetization (0.88 μB/f.u.), with a ∼100% magnetoresistance at 5 K in 9 T. Also, the value of the residual resistivity ratio, ρ300 K/ρ5 K = 45, between those of crystal and conventional ceramics, attest for both good compacity and grain connectivity. Interestingly, the Seebeck coefficient exhibits negative values reaching S = −47.5 μV K−1 at 675 K and below TC, S can be fitted by a diffusion model with a magnon term related to the ferromagnetism. A large power factor (S2/ρ) of 1 mW m−1 K−2 is obtained over a broad T range but the too high thermal conductivity (κ675 K ∼ 8.7 W K−1 m−1) is a limiting physical parameter to use CoS2 ceramics in thermoelectric devices.
Singular resonance in the high-frequency photoacoustic effect with multilayers
Authors: Hu Hanping , Xu Jun , Xia Xiang , Wu Shaobin , Liu Yanlong , Li Ang
Published: September 2013

A singular resonance is discovered in investigating the features of high-frequency photoacoustic (PA) effect with multilayers. Theoretical analysis of its formation is carried out and reveals that it is a result of interaction between the resonance of gas-heat and that of solid-heat, while they happen simultaneously and fight for vibrational energy at some higher frequencies. This finding presents a new gas-solid-heat coupling phenomenon with dual resonance and may be of significance for recognizing of high-frequency PA effect and characterizing of micro/nano films.
Laser-induced synthesis of metallic silver-gold nanoparticles encapsulated in carbon nanospheres for surface-enhanced Raman spectroscopy and toxins detection
Authors: Povolotskiy Alexey , Povolotckaia Anastasia , Petrov Yuriy , Manshina Alina , Tunik Sergey
Published: September 2013

Metallic silver-gold nanoparticles (1–5 nm) encapsulated into carbon nanospheres (20–30 nm) were synthesized via laser-induced chemical liquid phase deposition. The obtained carbon-silver-gold nanostructures were characterized by high specific surface area and demonstrated high sensitivity as a material for surface-enhanced Raman scattering and adsorption properties allowing analyte extraction from a dilute solution for quantitative monitoring of low concentration components.
Magnetic design evolution in perpendicular magnetic recording media as revealed by resonant small angle x-ray scattering
Authors: Wang Tianhan , Mehta Virat , Ikeda Yoshihiro , Do Hoa , Takano Kentaro , Florez Sylvia , Terris Bruce D. , Wu Benny , Graves Catherine , Shu Michael , Rick Ramon , Scherz Andreas , Stöhr Joachim , Hellwig Olav
Published: September 2013

We analyze the magnetic design for different generations of perpendicular magnetic recording (PMR) media using resonant soft x-ray small angle x-ray scattering. This technique allows us to simultaneously extract in a single experiment the key structural and magnetic parameters, i.e., lateral structural grain and magnetic cluster sizes as well as their distributions. We find that earlier PMR media generations relied on an initial reduction in the magnetic cluster size down to the grain level of the high anisotropy granular base layer, while very recent media designs introduce more exchange decoupling also within the softer laterally continuous cap layer. We highlight that this recent development allows optimizing magnetic cluster size and magnetic cluster size distribution within the composite media system for maximum achievable area density, while keeping the structural grain size roughly constant.
Love waves in two-dimensional phononic crystals with depth-dependent properties
Authors: Korotyaeva M. E. , Kutsenko A. A. , Shuvalov A. L. , Poncelet O.
Published: September 2013

We calculate subsonic spectra of the Love waves, i.e., of the shear horizontal waves in the coated substrate, using developed analytical approach. Coating or substrate or both are two-dimensional heterogeneous in the sagittal plane and uniform along the out-of-plane direction. Slow coating permits multiple subsonic dispersion branches which are folded due to lateral periodicity. It is observed that low-frequency branches may either cross or repulse each other, the latter giving rise to low-frequency band gaps inside the Brillouin zone. Such behavior is likelier when the periodic inclusion occurs within the coating close enough to its free surface.
Interstitial O2 distribution in amorphous SiO2 nanoparticles determined by Raman and photoluminescence spectroscopy
Authors: Agnello S. , Di Francesca D. , Alessi A. , Iovino G. , Cannas M. , Girard S. , Boukenter A. , Ouerdane Y.
Published: September 2013

The O2 content and emission properties in silica nanoparticles after thermal treatments in oxygen rich atmosphere have been investigated by Raman and photoluminescence measurements. The nanoparticles have different sizes with average diameter ranging from 7 up to 40 nm. It is found that O2 concentration in nanoparticles monotonically increases with nanoparticles size. This finding is independent on the measurement technique and evidences that oxygen molecules are not present in all the nanoparticles volume. This dependence is interpreted on the basis of a structural model for nanoparticles consisting of a core region able to host the oxygen molecules and a surface shell of fixed size and free from O2.
High carrier mobility and electrical stability under negative bias illumination stress of ZnO thin-film transistors with N2O plasma treated HfOx gate dielectrics
Authors: Chen Wei-Yu , Jeng Jiann-Shing , Chen Jen-Sue
Published: September 2013

ZnO thin-film transistors (TFTs) using high-k hafnium oxide (HfO)x as the gate dielectrics achieve a low operating voltage of below 1 V. A negative threshold voltage shift of devices was observed after the negative bias illumination stress (NBIS) from a 635 nm laser. Plasma treatment of the HfOx dielectric surface using different gases (i.e., N2O and O2) was used to improve the TFTs' electrical stability. By calculating the subthreshold swing and analyzing the oxygen chemical bonding states nearby the ZnO/HfOx interface by x-ray photoelectron spectroscopy, we found that the interface trapped state and oxygen vacancies existed in ZnO active layer caused this unstable performance. The stability of ZnO TFTs is improved with using N2O plasma-treated HfOx dielectric, as this eliminate the defect in the ZnO layer.
Deoxyribonucleic acid-ceramic hybrid dielectrics for potential application as gate insulators in organic field effect transistors
Authors: Ouchen Fahima , Venkat Narayanan , Joyce Donna M. , Singh Kristi M. , Smith Steven R. , Yaney Perry P. , Heckman Emily M. , Bartsch Carrie M. , Grote James G.
Published: September 2013

Hybrid films incorporating high dielectric constant k ceramics (BaTiO3 and TiO2) in deoxyribonucleic acid (DNA) were fabricated from highly stable dispersions of the ceramic nanoparticles in viscous, aqueous DNA solutions. Dielectric and electrical properties of the as-prepared nanocomposite films were investigated for potential use as gate insulators in organic field effect transistors. A k value as high as 14 was achieved with a 40 wt. % loading of ceramic nanoparticles in DNA. Electrical resistivities on the order of 1014 Ω cm with leakage current densities on the order of 10−9 A/cm2 were measured from current-voltage experiments under electric field biases up to 50 V/μm.
Spin transport in bimetallocene
Authors: Matsuura Y.
Published: September 2013

I present a theoretical study on the spin-transport behavior of bimetallocenes of cobalt or nickel, wherein electronic communication between the two metal centers can be efficiently performed via a fulvalene ligand. The transmission of electrons in the bimetallocene connected to two gold electrodes was calculated using a first-principles density functional method. Spin transport was estimated from the difference between the transmissions of the spin-up and spin-down states. Results revealed that bicobaltocene has a perfect spin-filtering effect because the supply of excess electrons to the electronic state of ferrocene causes a split in the energy levels of the spin-up and spin-down states. As surmised, it was found that spin polarization was caused by strong interactions between the two metal centers via the fulvalene ligand. Furthermore, bicobaltocene exhibited a negative differential resistance at a relatively low bias voltage.
Dynamics of positive probes in underdense, strongly magnetized, E×B drifting plasma: Particle-in-cell simulations
Authors: Heinrich Jonathon R. , Cooke David L.
Published: September 2013

Electron trapping, electron heating, space-charge wings, wake eddies, and current collection by a positive probe in E×B drifting plasma were studied in three-dimensional electromagnetic particle-in-cell simulations. In these simulations, electrons and ions were magnetized with respect to the probe and the plasma was underdense (ωpe<ωce). A large drift velocity (Mach 4.5 with respect to the ion acoustic speed) between the plasma and probe was created with background electric and magnetic fields. Four distinct regions developed in the presences of the positive probe: a quasi-trapped electron region, an electron-depletion wing, an ion-rich wing, and a wake region. We report on the observations of strong electron heating mechanisms, space-charge wings, ion cyclotron charge-density eddies in the wake, electron acceleration due to a magnetic presheath, and the current-voltage relationship.
Fabrication of p-type porous GaN on silicon and epitaxial GaN
Authors: Bilousov O. V. , Geaney H. , Carvajal J. J. , Zubialevich V. Z. , Parbrook P. J. , Giguère A. , Drouin D. , Díaz F. , Aguiló M. , O'Dwyer C.
Published: September 2013

Porous GaN layers are grown on silicon from gold or platinum catalyst seed layers, and self-catalyzed on epitaxial GaN films on sapphire. Using a Mg-based precursor, we demonstrate p-type doping of the porous GaN. Electrical measurements for p-type GaN on Si show Ohmic and Schottky behavior from gold and platinum seeded GaN, respectively. Ohmicity is attributed to the formation of a Ga2Au intermetallic. Porous p-type GaN was also achieved on epitaxial n-GaN on sapphire, and transport measurements confirm a p-n junction commensurate with a doping density of ∼1018 cm−3. Photoluminescence and cathodoluminescence confirm emission from Mg-acceptors in porous p-type GaN.
Modifying exciton optical properties in quantum dots with coherent phonons induced by ultrafast optical pulses
Authors: Gotoh Hideki , Sanada Haruki , Yamaguchi Hiroshi , Sogawa Tetsuomi
Published: September 2013

The distinctive effects of coherent phonons (groups of phase-matched phonons) on exciton states are reported by using single dot photoluminescence (PL) spectroscopy in semiconductor quantum dots (QDs). Coherent phonons that were induced with titanium thin metal films close to QDs by irradiating ultrafast optical pulses caused marked changes in the PL spectra including changes to the PL peak energies and PL intensities. Time-dependent reflectance measured with a pump-probe technique confirmed that coherent phonons were created at the surface of the QD sample. These results suggest that coherent phonons provide a good way to manipulate the optical properties of QDs.
High-power, high-brightness continuous-wave interband cascade lasers with tapered ridges
Authors: Bewley W. W. , Kim C. S. , Canedy C. L. , Merritt C. D. , Vurgaftman I. , Abell J. , Meyer J. R. , Kim M.
Published: September 2013

We report tapered-ridge mid-infrared (λ = 3.75 μm) interband cascade lasers emitting up to 403 mW of continuous wave output power at T = 25 °C, with beam quality characterized by M2 = 2.3. One index-guided tapered structure consisted of a single 4-mm-long section with ridge width varying linearly from 5 μm to 63 μm. Another device that combined a narrow ridge of uniform width with a tapered section produced slightly lower maximum output power and brightness.
Cryotolerance and global gene-expression patterns of Bos taurus indicus and Bos taurus taurus in vitro- and in vivo-produced blastocysts
Authors: Sudano Mateus J. , Caixeta Ester S. , Paschoal Daniela M. , Martins Alicio , Machado Rui , Buratini José , Landim-Alvarenga Fernanda D. C.
Published: September 2013

In a 2 × 2 factorial experimental design, embryo development, cryotolerance and global gene expression of Nellore (Bos taurus indicus) and Simmental (Bos taurus taurus) blastocysts produced in vitro (IVP) and in vivo (multiple ovulation derived embryo, MODE) were assessed. Blastocyst production was higher in Nellore than in Simmental (47.7 ± 2.0% vs 27.0 ± 2.0%) cows. The total numbers of ova or embryos recovered (5.5 ± 0.9 vs 3.7 ± 0.8) and transferable embryos (3.8 ± 1.0 vs 2.3 ± 0.8) per cow were not different between breeds. Simmental and MODE (34.6% and 38.5%, n = 75 and 70) blastocysts had higher survival rates after cryopreservation compared with Nellore and IVP (20.2% and 18.1%, n = 89 and 94) embryos, respectively. Differences between transcriptomes were addressed by principal-component analysis, which indicated that gene expression was affected by subspecies (158 genes), origin (532 genes) and interaction between both subspecies and origin (53 genes). Several functional processes and pathways relevant to lipid metabolism and embryo viability involving differentially expressed genes were identified. The lipid metabolism-related genes were upregulated in Simmental (AUH and ELOVL6) and IVP (ACSL3 and ACSL6) blastocysts. The expression profiles of genes related to mitochondrial metabolism (ATP5B), oxidative stress (GPX4), apoptosis (DAD1, DAP, PRDX2), heat shock (HSPA5), pregnancy (IFNT2, PAG2) and cell differentiation (KRT18) varied between experimental groups.
Uracil in duplex DNA is a substrate for the nucleotide incision repair pathway in human cells
Authors: Prorok Paulina , Alili Doria , Saint-Pierre Christine , Gasparutto Didier , Zharkov Dmitry O. , Ishchenko Alexander A. , Tudek Barbara , Saparbaev Murat K.
Published: September 2013

Significance

Hydrolytic deamination of cytosine to uracil generates a highly mutagenic DNA base lesion and is considered one of the major sources of spontaneous mutation in living organisms. We report that the major human apurinic/apyrimidinic (AP) endonuclease, APE1, is a deoxyuridine endonuclease and can remove uracil residues in the DNA glycosylase-independent nucleotide incision repair pathway. This new repair function of AP endonucleases is evolutionarily conserved in Archaea and humans, pointing to a possible evolutionary origin of the DNA repair mechanisms for spontaneous damage to DNA in a common ancestor to all living forms.
The phase transition for dyadic tilings
Authors: Angel Omer , Holroyd Alexander , Kozma Gady , Wästlund Johan , Winkler Peter
Published: September 2013

A dyadic tile of order

n
n

is any rectangle obtained from the unit square by

n
n

successive bisections by horizontal or vertical cuts. Let each dyadic tile of order

n
n

be available with probability

p
p

, independent of the others. We prove that for

p
p

sufficiently close to

1
1

, there exists a set of pairwise disjoint available tiles whose union is the unit square, with probability tending to

1
1

as

n
→
∞

n\to \infty

, as conjectured by Joel Spencer in 1999. In particular, we prove that if

p
=
7

/

8

p=7/8

, such a tiling exists with probability at least

1
−
(
3

/

4

)
n

1-(3/4)^n

. The proof involves a surprisingly delicate counting argument for sets of unavailable tiles that prevent tiling.
eSBMTools 1.0: enhanced native structure-based modeling tools
Authors: Lutz Benjamin , Sinner Claude , Heuermann Geertje , Verma Abhinav , Schug Alexander
Published: September 2013

Motivation: Molecular dynamics simulations provide detailed insights into the structure and function of biomolecular systems. Thus, they complement experimental measurements by giving access to experimentally inaccessible regimes. Among the different molecular dynamics techniques, native structure-based models (SBMs) are based on energy landscape theory and the principle of minimal frustration. Typically used in protein and RNA folding simulations, they coarse-grain the biomolecular system and/or simplify the Hamiltonian resulting in modest computational requirements while achieving high agreement with experimental data. eSBMTools streamlines running and evaluating SBM in a comprehensive package and offers high flexibility in adding experimental- or bioinformatics-derived restraints.

Results: We present a software package that allows setting up, modifying and evaluating SBM for both RNA and proteins. The implemented workflows include predicting protein complexes based on bioinformatics-derived inter-protein contact information, a standardized setup of protein folding simulations based on the common PDB format, calculating reaction coordinates and evaluating the simulation by free-energy calculations with weighted histogram analysis method or by phi-values. The modules interface with the molecular dynamics simulation program GROMACS. The package is open source and written in architecture-independent Python2.

Availability:  http://sourceforge.net/projects/esbmtools/

Contact:  alexander.schug@kit.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Accounting for epistatic interactions improves the functional analysis of protein structures
Authors: Wilkins Angela D. , Venner Eric , Marciano David C. , Erdin Serkan , Atri Benu , Lua Rhonald C. , Lichtarge Olivier
Published: September 2013

Motivation: The constraints under which sequence, structure and function coevolve are not fully understood. Bringing this mutual relationship to light can reveal the molecular basis of binding, catalysis and allostery, thereby identifying function and rationally guiding protein redesign. Underlying these relationships are the epistatic interactions that occur when the consequences of a mutation to a protein are determined by the genetic background in which it occurs. Based on prior data, we hypothesize that epistatic forces operate most strongly between residues nearby in the structure, resulting in smooth evolutionary importance across the structure.

Methods and Results: We find that when residue scores of evolutionary importance are distributed smoothly between nearby residues, functional site prediction accuracy improves. Accordingly, we designed a novel measure of evolutionary importance that focuses on the interaction between pairs of structurally neighboring residues. This measure that we term pair-interaction Evolutionary Trace yields greater functional site overlap and better structure-based proteome-wide functional predictions.

Conclusions: Our data show that the structural smoothness of evolutionary importance is a fundamental feature of the coevolution of sequence, structure and function. Mutations operate on individual residues, but selective pressure depends in part on the extent to which a mutation perturbs interactions with neighboring residues. In practice, this principle led us to redefine the importance of a residue in terms of the importance of its epistatic interactions with neighbors, yielding better annotation of functional residues, motivating experimental validation of a novel functional site in LexA and refining protein function prediction.

Contact:  lichtarge@bcm.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Precise inference of copy number alterations in tumor samples from SNP arrays
Authors: Chen Gary K. , Chang Xiao , Curtis Christina , Wang Kai
Published: September 2013

Motivation: The accurate detection of copy number alterations (CNAs) in human genomes is important for understanding susceptibility to cancer and mechanisms of tumor progression. CNA detection in tumors from single nucleotide polymorphism (SNP) genotyping arrays is a challenging problem due to phenomena such as aneuploidy, stromal contamination, genomic waves and intra-tumor heterogeneity, issues that leading methods do not optimally address.

Results: Here we introduce methods and software (PennCNV-tumor) for fast and accurate CNA detection using signal intensity data from SNP genotyping arrays. We estimate stromal contamination by applying a maximum likelihood approach over multiple discrete genomic intervals. By conditioning on signal intensity across the genome, our method accounts for both aneuploidy and genomic waves. Finally, our method uses a hidden Markov model to integrate multiple sources of information, including total and allele-specific signal intensity at each SNP, as well as physical maps to make posterior inferences of CNAs. Using real data from cancer cell-lines and patient tumors, we demonstrate substantial improvements in accuracy and computational efficiency compared with existing methods.

Availability: Source code, documentation and example datasets are freely available at http://sourceforge.net/projects/penncnv-2.

Contact:  gary.k.chen@usc.edu or kaichop@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data
Authors: Ashoor Haitham , Hérault Aurélie , Kamoun Aurélie , Radvanyi François , Bajic Vladimir B. , Barillot Emmanuel , Boeva Valentina
Published: September 2013

Motivation: Cancer cells are often characterized by epigenetic changes, which include aberrant histone modifications. In particular, local or regional epigenetic silencing is a common mechanism in cancer for silencing expression of tumor suppressor genes. Though several tools have been created to enable detection of histone marks in ChIP-seq data from normal samples, it is unclear whether these tools can be efficiently applied to ChIP-seq data generated from cancer samples. Indeed, cancer genomes are often characterized by frequent copy number alterations: gains and losses of large regions of chromosomal material. Copy number alterations may create a substantial statistical bias in the evaluation of histone mark signal enrichment and result in underdetection of the signal in the regions of loss and overdetection of the signal in the regions of gain.

Results: We present HMCan (Histone modifications in cancer), a tool specially designed to analyze histone modification ChIP-seq data produced from cancer genomes. HMCan corrects for the GC-content and copy number bias and then applies Hidden Markov Models to detect the signal from the corrected data. On simulated data, HMCan outperformed several commonly used tools developed to analyze histone modification data produced from genomes without copy number alterations. HMCan also showed superior results on a ChIP-seq dataset generated for the repressive histone mark H3K27me3 in a bladder cancer cell line. HMCan predictions matched well with experimental data (qPCR validated regions) and included, for example, the previously detected H3K27me3 mark in the promoter of the DLEC1 gene, missed by other tools we tested.

Availability: Source code and binaries can be downloaded at http://www.cbrc.kaust.edu.sa/hmcan/, implemented in C++.

Contact:  haitham.ashoor@kaust.edu.sa

Supplementary information:  Supplementary data are available at Bioinformatics online.
BioPig: a Hadoop-based analytic toolkit for large-scale sequence data
Authors: Nordberg Henrik , Bhatia Karan , Wang Kai , Wang Zhong
Published: September 2013

Motivation: The recent revolution in sequencing technologies has led to an exponential growth of sequence data. As a result, most of the current bioinformatics tools become obsolete as they fail to scale with data. To tackle this ‘data deluge’, here we introduce the BioPig sequence analysis toolkit as one of the solutions that scale to data and computation.

Results: We built BioPig on the Apache’s Hadoop MapReduce system and the Pig data flow language. Compared with traditional serial and MPI-based algorithms, BioPig has three major advantages: first, BioPig’s programmability greatly reduces development time for parallel bioinformatics applications; second, testing BioPig with up to 500 Gb sequences demonstrates that it scales automatically with size of data; and finally, BioPig can be ported without modification on many Hadoop infrastructures, as tested with Magellan system at National Energy Research Scientific Computing Center and the Amazon Elastic Compute Cloud. In summary, BioPig represents a novel program framework with the potential to greatly accelerate data-intensive bioinformatics analysis.

Availability and implementation: BioPig is released as open-source software under the BSD license at https://sites.google.com/a/lbl.gov/biopig/

Contact:  ZhongWang@lbl.gov
DEC-205-mediated antigen targeting to steady-state dendritic cells induces deletion of diabetogenic CD8+ T cells independently of PD-1 and PD-L1
Authors: Mukherjee Gayatri , Geliebter Ari , Babad Jeffrey , Santamaria Pere , Serreze David V. , Freeman Gordon J. , Tarbell Kristin V. , Sharpe Arlene , DiLorenzo Teresa P.
Published: September 2013

CD8+ T cells specific for islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP) have been implicated in type 1 diabetes in both humans and non-obese diabetic (NOD) mice, in which T cells specific for IGRP206–214 are highly prevalent. We sought to manipulate these pathogenic T cells by exploiting the ability of steady-state dendritic cells (DCs) to present antigens in a tolerogenic manner. The endocytic receptor DEC-205 was utilized to deliver an IGRP206–214 mimotope to DCs in NOD mice, and the impact of this delivery on a polyclonal population of endogenous islet-reactive cognate T cells was determined. Assessment of islet-infiltrating CD8+ T cells showed a decrease in the percentage, and the absolute number, of endogenous IGRP206–214-specific T cells when the mimotope was delivered to DCs, compared with delivery of a specificity control. Employing an adoptive transfer system, deletion of CD8+ T cells as a result of DEC-205-mediated antigen targeting was found to occur independently of programmed death-1 (PD-1) and its ligand (PD-L1), both often implicated in the regulation of peripheral T-cell tolerance. Given its promise for the manipulation of self-reactive polyclonal T cells demonstrated here, the distinctive characteristics of this antigen delivery system will be important to appreciate as its potential as an intervention for autoimmune diseases continues to be investigated.
Anesthesia Outside of the Operating Room
Authors: Urman Richard , Gross Wendy , Philip Beverly
Published: September 2013

This is a comprehensive, up-to-date resource that covers all aspects of anesthesia care in OOR settings, from financial considerations to anesthetic techniques to quality assurance. With increasing numbers of procedures such as cardiac catheterization and imaging taking place outside of the main OR, anesthesia providers as well as non-anesthesia members of the patient care team will find this resource critical to their understanding of the principles of anesthesia care in unique settings which may have limited physical resources. Topics include patient monitoring techniques, pre-procedure evaluation and post-procedure care, and procedural sedation performed by non-anesthesia providers.
Challenges of Anesthesia Outside of the Operating Room
Authors: Gross Wendy L. , Urman Richard D.
Published: September 2013

As health care bears the simultaneous burden of rapid technological development and increasing financial constraints, diagnostic and therapeutic interventions are performed more frequently outside of the operating room (OOOR) by a broadening spectrum of medical practitioners. The broadening scope and complexity of noninvasive procedures as well as the increasing acuity of patients undergoing them often make deeper sedation, general anesthesia (GA), and robust hemodynamic monitoring necessary and challenging. Anesthesiologists are more frequently called upon to provide care for sicker patients (American Society of Anesthesiologists (ASA) III/IV patients) undergoing novel, unfamiliar procedures in nontraditional locations. As technology advances, the number of procedure areas and the need for anesthesia services proliferates. As the OOOR cases continue to grow at an exponential rate, the landscape of anesthesiology is changing; new challenges and opportunities emerge.
Patient Monitoring
Authors: Galvagno Jr Samuel M. , Kodali Bhavani
Published: September 2013

The expertise and skill of the modern anesthesiologist is increasingly required when anesthesia is administered for procedures performed outside of the operating room (OOOR). The OOOR environment is fraught with challenges and often requires a great deal of flexibility without compromising patient care. In the practice of anesthesiology, physiological monitoring of patients is imperative and is recognized as a standard of care. Although definitive data are lacking, some studies have suggested that adverse events occurring in the OOOR environment have a higher severity of injury and may result from substandard care, including lack of adherence to minimum monitoring guidelines.1
,
2 This chapter will focus on the physics, physiology, limitations, and recommendations for standard physiological monitors that should be utilized in the OOOR environment. A special emphasis is placed on pulse oximetry and capnography.
Anesthesia in the Radiation Oncology Suite
Authors: Harris Eric A. , Candiotti Keith
Published: September 2013

Cancer continues to be a leading cause of death in the developed world, with physicians and scientists constantly devising new weapons to combat it. Chemotherapy, surgery, nutrition, and holistic medicine all have a place in the multimodal approach that can prolong longevity and ameliorate quality of life. As part of this armamentarium, radiation therapy (XRT) has proven to be a safe and effective technique for the management of various malignant (and occasionally nonmalignant) lesions. XRT can be used for both curative and palliative purposes; in the latter case, patients benefit from decreased pain, preserved organ function, and the maintenance of lumen patency in hollow organs.1 The medical team, led by a radiation oncologist, often includes a physicist, a dosimetrist, several radiation therapists (technologists), and the patient’s primary care physician.2 Anesthesiologists are increasingly being asked to join this team, as our services are recognized as a vital component for patient safety and comfort.
New Challenges for Anesthesiologists Outside of the Operating Room: The Cardiac Catheterization and Electrophysiology Laboratories
Authors: Gross Wendy L. , Faillace Robert T. , Shook Douglas C. , Daves Suanne M. , Savage Robert M.
Published: September 2013

Chapter 19 discusses invasive cardiology procedures performed in the cardiac catheterization laboratory (CCL), the electrophysiology laboratory (EPL), and the transesophageal echocardiography laboratory, and which have become the purview of anesthesiologists. Common CCL procedures include the following: diagnostic cardiac catheterizations, percutaneous coronary interventions, peripheral vascular diagnostic and therapeutic procedures, implantation of percutaneous left ventricular assist devices, placement of septal occlusion devices, and percutaneous valve repair or replacement procedures. Common EPL procedures consist of EP studies, atrial and ventricular radiofrequency (RF) ablation procedures, implantation and removal of pacing and cardioverter defibrillator devices, and electrical cardioversion. TEE procedures include trans-esophageal echocardiography (TEE) and combined TEE/direct current cardioversions (DCCV). All of these procedures may require the involvement of anesthesiologists if the patient has significant comorbidities or if the procedure requires that the patient be absolutely still and/or asleep.
Health promotion and health care for school-age children and young people
Authors: Hall David M.
              B. , Elliman David
Published: September 2013

Chapter 5 reviews the changing needs of health care for school-age children, a needs-based approach, the views of children and young people about their concerns and the service they want, starting school—preparation for school and reception into school, special medical needs of children in school, emotional and behavioural problems, bullying, the need for confidential advice and support, the National Healthy Schools Standard and other Government initiatives—health promotion in school, profiles, and prevention of unwanted pregnancy and support for young mothers.
Physical examination
Authors: Hall David M.
              B. , Elliman David
Published: September 2013

Chapter 7 covers the neonatal and 6–8 week examinations, the school entrant examination, and screening by physical examination for developmental dysplasia of the hip (DDH) (previously known as congenital dislocation of the hip), heart disease including hypertrophic cardiomyopathy (HCM), hypertension, asthma, and undescended testes and other genital abnormalities.
The universal programme
Authors: Hall David M.
              B. , Elliman David
Published: September 2013

Chapter 18 summarizes the justification for providing a universal preventive child health service for families, children, and young people, sets out the general principles which underpin such a programme, summarizes the objectives of a universal programme, describes the core programme of pre-school care and the need for a programme for school-age children and young people, and emphasizes the importance of adequate community resources to deal with problems detected and to undertake effective prevention and health promotion strategies.
Writing a research protocol
Authors: Peacock Janet
              L. , Kerry Sally
              M.
Published: September 2013

Chapter 3 discusses writing a research proposal, and covers the development cycle, the
title, primary and secondary aims, study design, sample sizes, statistical analysis,
ethical approval, and where it can go wrong.
Introduction to presenting statistical analyses
Authors: Peacock Janet
              L. , Kerry Sally
              M.
Published: September 2013

Chapter 5 discusses presenting statistical analyses, and covers numerical data, results
section, describing the results, assessing non-response bias, presenting results for
different media, drawing up subject profiles, graphs and tables, and categorical and
continuous data.
Introduction
Authors: Giles I.P. , Isenberg David A.
Published: September 2013

About 1 in 20 people develop an autoimmune disease, many of which involve the musculoskeletal system. Young women are particularly at risk, but the development at any age of symptoms such as unexplained fever, rash, polyarthritis, Raynaud’s phenomenon or mouth ulcers should encourage serological screening for autoimmune rheumatic or vasculitic disorder....
Ethics in paediatric research: principles and processes
Authors: Winter Edward
                M. , Cobb Mark
Published: September 2013

Chapter 1 outlines principles that underpin ethics approval and processes by which ethics approval can be sought and granted. While the former is important, emphasis will be placed on the latter because it is the practicalities that are particularly challenging, and a key intention of this chapter is to help researchers chart their way through the tortuous and convoluted pathways that characterize research governance. Out of necessity, the approach will tend to take a United Kingdom-centric perspective, but much of current practice is determined by European Union legislation, and similar procedures are in place elsewhere in the world.
Interpreting exercise performance data in relation to body size
Authors: Welsman Joanne
                R. , Armstrong Neil
Published: September 2013

The appropriate normalization of exercise performance data for differences in body size underpins the clarification of growth and maturational influences on physiological function. Therefore, scaling is an issue of fundamental importance for all paediatric exercise scientists. The selection and application of a scaling method appropriate for the data and research question being addressed is at least as important as ensuring that the methodology used to collect the data is valid, reliable, and appropriate for use with young people. Several scaling methods are available and some methods can be applied in different ways. Unfortunately, taken as a whole, the extant literature presents a confusing picture as to which of these techniques is preferable, how they should be applied, and the meaning of the results obtained. The aim of this chapter is to clarify these issues through a description of the techniques available for analysing both cross-sectional and longitudinal data sets, highlighting their statistical and theoretical derivations.
Maximal intensity exercise
Authors: Armstrong Neil , Welsman Joanne
                R. , Williams Craig
                A.
Published: September 2013

Chapter 5 discusses maximal intensity exercise, which is often associated with maximal or peak oxygen uptake (VO2·). However, this convention ignores the fact that, for short periods of time, anaerobic provision of adenosine triphosphate (ATP) can support exercise of much greater intensity than that at peak VO2· Th erefore, for the purpose of this chapter, maximal intensity exercise is defi ned as that which is performed ‘all-out’ and is sustained by an anaerobic ATP yield which exceeds that of oxidative metabolism.
Cardiovascular function
Authors: Warburton Darren
                E.R. , Nettlefold Lindsay , McGuire K.
                Ashlee , Bredin Shannon
                S.D.
Published: September 2013

The physiological adaptations to exercise training have been evaluated extensively in children and youth. In particular, considerable research has examined the changes in cardiovascular function that occur with aerobic exercise training. Various indicators of cardiovascular function have been assessed at rest and during exercise. Many of these measures have important implications from performance and health-related perspectives. Owing to the importance of oxygen (O2) transport for human performance and health, this chapter reviews comprehensively the varied non-invasive and invasive methods of assessing cardiac function including an in-depth evaluation of the limitations and strengths of each methodology. Specific reference is given to the applicability and ease of usage of each technology with young people. This chapter also deals extensively with the evaluation of cardiovascular regulation and vascular function owing to their role in optimal exercise performance and health.
Muscle strength
Authors: De Ste Croix Mark B.
                A.
Published: September 2013

Despite a relatively limited understanding of the factors associated with strength development, advances in equipment, and increased understanding of growth and maturation issues, have provided new insights into paediatric muscle strength development. Strength testing of children is performed routinely by researchers to monitor the determinants and development of strength throughout childhood, and also by physiotherapists to assess the degree of muscle disability and to diagnose the rate of recovery. It is important for strength test administrators to be equipped with knowledge of the normal age and sex-associated variations in strength and the factors attributable to that variation. Over time, the use of differing techniques to adjust for body size has changed our perspective of the historical concept of the age- and sex-associated differences in muscle strength. Likewise, the development of more sophisticated techniques to determine muscle size and body composition has allowed researchers to explore the factors associated with the development of strength during growth with a greater degree of validity.
Maximal intensity exercise
Authors: Williams Craig
                A.
Published: September 2013

Despite a surge of interest over the past 10 years in young people’s maximal intensity exercise, the growth and maturation of anaerobic performance is still poorly understood. This observation is interesting for a number of reasons. First, during the prepubertal years, children’s physical activity patterns are characterized by short duration but high intensity bouts of effort.5 Second, investigators are limited by the range of available methodologies, most of which are assessing external but indirect mechanical indices of maximal intensity so as to deduce metabolic changes. Third, there are few data available from females. Finally, due to the importance of maximal intensity efforts during team sports and the increasing emphasis on organized youth sport programmes, the differentiation between growth and maturation and training adaptations of maximal intensity performance need to be addressed. As a consequence of these four observations, important reliability and validity issues need to be resolved prior to paediatric exercise scientists determining which key factors influence maximal intensity exercise during childhood and adolescence. This chapter will therefore focus on the variables that have been most commonly measured and review the explanatory factors related to maximal intensity exercise during growth and maturation.
Aerobic fitness
Authors: Armstrong Neil , McManus Alison
                M. , Welsman Joanne
                R.
Published: September 2013

Peak V·O2 limits the child’s capacity to perform aerobic exercise but it does not describe fully all aspects of aerobic fitness. Exercise of the intensity and duration required to elicit peak V·O2 is rarely experienced by many young people.17,18 The vast majority ofhabitual physical activity is submaximal and of short duration and, under these circumstances, it is the transient kinetics of V·O2 which reflect the integrated response of the oxygen delivery system and the metabolic requirements of the exercising muscle.19–21 Furthermore, peak V·O2 is neither the best measure of a child’s ability to sustain submaximal aerobic exercise nor the most sensitive means to detect improvements in aerobic fitness after a training programme. Despite its origins in anaerobic metabolism, blood lactate accumulation is a valuable indicator of aerobic fitness and it can be used to monitor improvements in muscle oxidative capacity with exercise training in the absence of changes in peak V·O2.16,22 However, as V·O2 kinetics is comprehensively reviewed in Chapter 22 and blood lactate accumulation during exercise is analysed in Chapter 8, we will focus herein on aerobic fitness as described by peak V·O2.
Locomotor economy
Authors: Morgan Don
                W.
Published: September 2013

Chapter 21 presents and synthesizes research findings related to various aspects of locomotor economy during the childhood and adolescent years. Because the majority of research has been conducted on walking and running, the material presented in this chapter will focus exclusively on these modes of gait. It concludes by proposing future research directions to guide sport scientists, coaches, and clinicians in their quest to understand the factors responsible for efficient locomotion in children, improve the athletic performance of youngsters, and enhance the functional mobility and quality of life of physically challenged youth.