bluuebunny/crossref_metadata_2025 huggingface dataset:
Superconducting nanowire single photon detector on diamond
Authors: Atikian Haig A. , Eftekharian Amin , Jafari Salim A. , Burek Michael J. , Choy Jennifer T. , Hamed Majedi A. , Lončar Marko
Published: March 2014

Superconducting nanowire single photon detectors are fabricated directly on diamond substrates and their optical and electrical properties are characterized. Dark count performance and photon count rates are measured at varying temperatures for 1310 nm and 632 nm photons. A multi-step diamond surface polishing procedure is reported, involving iterative reactive ion etching and mechanical polishing to create a suitable diamond surface for the deposition and patterning of thin film superconducting layers. Using this approach, diamond substrates with less than 300 pm Root Mean Square surface roughness are obtained.
Low-lying excited states in armchair polyacene within Pariser-Parr-Pople model: A density matrix renormalization group study
Authors: Das Mousumi
Published: April 2014

We studied the nature of the ground state and low-lying excited states of armchair polyacene oligomers (Polyphenanthrene) within long-range Pariser-Parr-Pople model Hamiltonian with up to 14 monomers using symmetrized density matrix renormalization group technique. The ground state of all armchair polyacenes studied is found to be singlet. The results show that lowest singlet dipole allowed excited state has higher energy for armchair polyacenes as compared to linear fused polyacenes. Moreover, unlike linear fused polyacenes, the lowest singlet excited state of these oligomers is always found to lie below the lowest dipole forbidden two-photon state indicating that these armchair polyacene oligomers strongly fluoresce. The calculations of low-lying excitations on singly and triply electron doped armchair polyacene oligomers show a low energy band with strong transition dipole moment that coupled to charge conductivity. This implies armchair polyacene posses novel field-effect transistor properties.
Induced lattice strain in epitaxial Fe-based superconducting films on CaF2 substrates: A comparative study of the microstructures of SmFeAs(O,F), Ba(Fe,Co)2As2, and FeTe0.5Se0.5
Authors: Ichinose Ataru , Tsukada Ichiro , Nabeshima Fuyuki , Imai Yoshinori , Maeda Atsutaka , Kurth Fritz , Holzapfel Bernhard , Iida Kazumasa , Ueda Shinya , Naito Michio
Published: March 2014

The microstructures of SmFeAs(O,F), Ba(Fe,Co)2As2, and FeTe0.5Se0.5 prepared on CaF2 substrates were investigated using transmission electron microscopy. The SmFeAs(O,F)/CaF2 interface is steep, without a disordered layer. By contrast, a chemical reaction occurs at the interface in the cases of Ba(Fe,Co)2As2 and FeTe0.5Se0.5. The reaction layers are located on opposite sides of the interface for Ba(Fe,Co)2As2 and FeTe0.5Se0.5. We found that the lattice distortion of the three superconducting films on the CaF2 substrates enhances the TC values compared with films prepared on oxide substrates. The origin of this lattice deformation varies depending on the superconducting material.
Reading data stored in the state of metastable defects in silicon using band-band photoluminescence: Proof of concept and physical limits to the data storage density
Authors: Rougieux F. E. , Macdonald D.
Published: March 2014

The state of bistable defects in crystalline silicon such as iron-boron pairs or the boron-oxygen defect can be changed at room temperature. In this letter, we experimentally demonstrate that the chemical state of a group of defects can be changed to represent a bit of information. The state can then be read without direct contact via the intensity of the emitted band-band photoluminescence signal of the group of defects, via their impact on the carrier lifetime. The theoretical limit of the information density is then computed. The information density is shown to be low for two-dimensional storage but significant for three-dimensional data storage. Finally, we compute the maximum storage capacity as a function of the lower limit of the photoluminescence detector sensitivity.
Hypersonic phonon propagation in one-dimensional surface phononic crystal
Authors: Graczykowski B. , Sledzinska M. , Kehagias N. , Alzina F. , Reparaz J. S. , Sotomayor Torres C. M.
Published: March 2014

Hypersonic, thermally activated surface acoustic waves propagating in the surface of crystalline silicon patterned with periodic stripes were studied by Brillouin light scattering. Two characteristic directions (normal and parallel to the stripes) of surface acoustic waves propagation were examined exhibiting a distinctive propagation behavior. The measured phononic band structure exhibits diverse features, such as zone folding, band gap opening, and hybridization to local resonance for waves propagating normal to the stripes, and a variety of dispersive modes propagating along the stripes. Experimental results were supported by theoretical calculations performed using finite element method.
Improved bias-temperature instability characteristics in SiC metal-oxide-semiconductor devices with aluminum oxynitride dielectrics
Authors: Chanthaphan Atthawut , Hosoi Takuji , Nakano Yuki , Nakamura Takashi , Shimura Takayoshi , Watanabe Heiji
Published: March 2014

Significant improvement of bias-temperature instability characteristics in SiC-based metal-oxide-semiconductor (MOS) devices was demonstrated with high-permittivity aluminum oxynitride (AlON) dielectrics deposited on thin thermal oxides. AlON/SiO2 stacked dielectrics were found to be beneficial not only for reducing gate leakage current but also for suppressing diffusion of positively charged ions, leading to stable SiC-MOS characteristics even under strong electric fields and high temperatures. Unlike the prompt electric-field-induced ion migration in thermally grown and sputter-deposited SiO2 dielectrics, the ion drift for the stacked gate dielectrics was confined within the thin SiO2 underlayers owing to low ion diffusivity in AlON layers. Impacts of mobile ions on interface properties of SiC-MOS devices and effects of intentional ion trapping within the AlON layers were also systematically investigated.
Manganese ion-assisted assembly of superparamagnetic graphene oxide microbowls
Authors: Tian Zhengshan , Xu Chunxiang , Li Jitao , Zhu Gangyi , Xu Xiaoyong , Dai Jun , Shi Zengliang , Lin Yi
Published: March 2014

A facile manganese ion Mn(II)-assisted assembly has been designed to fabricate microbowls by using graphene oxide nanosheets as basic building blocks, which were exfoliated ultrasonically from the oxidized soot powders in deionized water. From the morphology evolution observations of transmission electron microscope and scanning electron microscope, a coordinating-tiling-collapsing manner is proposed to interpret the assembly mechanism based on attractive Van der Waals forces, π-π stacking, and capillary action. It is interesting to note that the as-prepared microbowls present a room temperature superparamagnetic behavior.
Large enhanced dielectric permittivity in polyaniline passivated core-shell nano magnetic iron oxide by plasma polymerization
Authors: Joy Lija K. , Sooraj V. , Sajeev U. S. , Nair Swapna S. , Narayanan T. N. , Sethulakshmi N. , Ajayan P. M. , Anantharaman M. R.
Published: March 2014

Commercial samples of Magnetite with size ranging from 25–30 nm were coated with polyaniline by using radio frequency plasma polymerization to achieve a core shell structure of magnetic nanoparticle (core)–Polyaniline (shell). High resolution transmission electron microscopy images confirm the core shell architecture of polyaniline coated iron oxide. The dielectric properties of the material were studied before and after plasma treatment. The polymer coated magnetite particles exhibited a large dielectric permittivity with respect to uncoated samples. The dielectric behavior was modeled using a Maxwell–Wagner capacitor model. A plausible mechanism for the enhancement of dielectric permittivity is proposed.
Structural, magnetic, and magnetodielectric studies of metamagnetic DyFe0.5Cr0.5O3
Authors: Nair Vidhya G. , Pal L. , Subramanian V. , Santhosh P. N.
Published: March 2014

We present here the detailed structural, magnetic, and magnetodielectric properties of polycrystalline DyFe0.5Cr0.5O3. Rietveld refinement reveals that DyFe0.5Cr0.5O3 crystallizes in an orthorhombic structure, with Pnma space group, having a disordered arrangement of Fe and Cr ions. An anomaly observed around 250 K in the temperature dependence of magnetization indicates an onset of magnetic ordering. The field dependent magnetization of DyFe0.5Cr0.5O3 at 13 K, 120 K, and 240 K has a small loop indicating weak ferromagnetic nature and the corresponding curve at 5 K indicates a metamagnetic behavior. The small loop and the unsaturated magnetization even for a high applied magnetic field of 7 T indicate a canted antiferromagnetic structure, the canting can be explained due to Dzyaloshinsky–Moriya antisymmetric exchange interaction. The temperature dependence of the dielectric permittivity shows a transition around 500 K. An anomaly in the temperature dependence of magnetization (supported by differential scanning calorimetry) corresponding to this dielectric transition suggests the possibility of magnetodielectric effect in DyFe0.5Cr0.5O3.
Experimental verification of effects of barrier dopings on the internal electric fields and the band structure in InGaN/GaN light emitting diodes
Authors: Song Jung-Hoon , Kim Tae-Soo , Park Ki-Nam , Lee Jin-Gyu , Hong Soon-Ku , Cho Sung-Royng , Lee Seogwoo , Whan Cho Meoung
Published: March 2014

We experimentally clarify the effects of barrier dopings on the polarization induced electric fields and the band structure in InGaN/GaN blue light emitting diodes. Both effects were independently verified by using electric field modulated reflectance and capacitance-voltage measurement. It is shown that the Si barrier doping does reduce the polarization induced electric field in the quantum wells. But the benefit of Si-doping is nullified by modification of the band structure and depletion process. With increased number of doped barriers, smaller number of quantum wells remains in the depletion region at the onset of the diffusion process, which can reduce the effective active volume and enhance the electron overflow.
A prototype micro-thermoelectric power generator for micro-electromechanical systems
Authors: Yadav Shambhoo , Sharma Pooja , Yamasani Prathima , Minaev S. , Kumar Sudarshan
Published: March 2014

A prototype micro-thermoelectric power generator (micro-TEG) system based on micro-combustion concept has been developed and presented here. The system consists of Bismuth-Telluride based thermoelectric modules mounted on a 0.5 cm3 volume microcombustor. The hot combustion gases from the microcombustor are allowed to flow in reverse direction through a heating cup to maximize the heat transfer from hot combustion products to thermoelectric modules. The system delivers a maximum power of 2.35 W with a fuel (propane) flow rate of 3.98 g/h. Maximum power is achieved at a voltage of 4.34 V, current 0.54 A with a maximum conversion efficiency of 4.58%. The system generates electric power with an improvement of over 83% in energy conversion efficiency over existing micro-TEG systems.
Seasonal variation in urinary and salivary reproductive hormone levels in Amazonian manatees (Trichechus inunguis)
Authors: Amaral Rodrigo S. , Rosas Fernando C. W. , da Silva Vera M. F. , Graham Laura H. , Viau Priscila , Nichi Marcilio , Oliveira Claudio A.
Published: April 2014

The Amazonian manatee (Trichechus inunguis) is a threatened aquatic mammal endemic to the Amazon basin. The aim of this study was to evaluate the urinary and salivary reproductive hormone levels of captive Amazonian manatees collected during two seasons of the year. Salivary samples from four males and urinary and salivary samples from three females were collected during two seasons (March–June and September–November) over two consecutive years. Salivary testosterone in males was measured by radioimmunoassay and reproductive hormones in females (salivary progesterone and oestradiol and urinary progestogens, oestrogens and luteinising hormone) were measured by enzyme immunoassay. The data were analysed in a 2×2 factorial design, where the factors were year and season. There was no effect of year or season for salivary testosterone. All female hormones showed a seasonal effect (higher hormone levels during March–June than September–November) or an interaction between year and season (P < 0.05). These results strongly indicate the existence of reproductive seasonality in Amazonian manatees; however, apparently only females exhibit reproductive quiescence during the non-breeding season. Further long-term studies are necessary to elucidate which environmental parameters are related to reproductive seasonality in T. inunguis and how this species responds physiologically to those stimuli.
Strain-specific parallel evolution drives short-term diversification during
Pseudomonas aeruginosa
biofilm formation
Authors: McElroy Kerensa E. , Hui Janice G. K. , Woo Jerry K. K. , Luk Alison W. S. , Webb Jeremy S. , Kjelleberg Staffan , Rice Scott A. , Thomas Torsten
Published: March 2014

Significance

Within-population genetic diversity is an essential evolutionary prerequisite for processes ranging from antibiotic resistance to niche adaptation, but its generation is poorly understood, with most studies focusing on fixed substitutions at the end point of long-term evolution. Using deep sequencing, we analyzed short-term, within-population genetic diversification occurring during biofilm formation of the model bacterium
Pseudomonas aeruginosa
. We discovered extensive parallel evolution between biological replicates at the level of pathways, genes, and even individual nucleotides. Short-term diversification featured positive selection of relatively few nonsynonymous mutations, with the majority of the genome being conserved by negative selection. This result is broadly consistent with observations of long-term evolution and suggests diversifying selection may underlie genetic diversification of
Pseudomonas aeruginosa
biofilms.
Language universals at birth
Authors: Gómez David Maximiliano , Berent Iris , Benavides-Varela Silvia , Bion Ricardo A. H. , Cattarossi Luigi , Nespor Marina , Mehler Jacques
Published: April 2014

Significance

It is well known that across languages, certain structures are preferred to others. For example, syllables likeblifare preferred to syllables likebdifandlbif. But whether such regularities reflect strictly historical processes, production pressures, or universal linguistic principles is a matter of much debate. To address this question, we examined whether some precursors of these preferences are already present early in life. The brain responses of newborns show that, despite having little to no linguistic experience, they reacted to syllables likeblif, bdif,andlbifin a manner consistent with adults’ patterns of preferences. We conjecture that this early—possibly universal—bias helps shaping language acquisition.
Trait-mediated assembly processes predict successional changes in community diversity of tropical forests
Authors: Lasky Jesse R. , Uriarte María , Boukili Vanessa K. , Chazdon Robin L.
Published: April 2014

Significance

The assembly of ecological communities results from multiple mechanisms acting concurrently. Disentangling their relative importance represents a major challenge. Our study quantifies the relative importance of four trait-mediated mechanisms and associated changes in functional diversity over succession. We leverage the rapid community assembly in tropical successional forests and the rich information in functional trait data and spatially explicit long-term tree demographic data. Trait correlations with average species survival rates were the most important processes affecting survival and linked to a decrease in wood trait diversity during succession. Simultaneously, evidence for stabilizing niche differences associated with leaf traits was reflected in increasing leaf functional diversity. Our results suggest mechanisms by which individual performance affects successional change in community-wide diversity.
Neural representations of ethologically relevant hand/mouth synergies in the human precentral gyrus
Authors: Desmurget Michel , Richard Nathalie , Harquel Sylvain , Baraduc Pierre , Szathmari Alexandru , Mottolese Carmine , Sirigu Angela
Published: April 2014

Significance

The motor repertoire of infants is narrow. Yet newborns can accurately bring their hands toward their mouth for self-feeding, thumb-sucking, or perioral exploration, thus showing fine coordinated movement synergies between the hand and mouth. Here, we show that these gestures of high ethological value are selectively encoded in the human brain and represented as integrated primitives within the precentral gyrus, a key region for sensorimotor processing. These findings have major implications for our understanding of the organization and phylogenesis of motor functions in primates.
Compound facial expressions of emotion
Authors: Du Shichuan , Tao Yong , Martinez Aleix M.
Published: April 2014

Significance

Though people regularly recognize many distinct emotions, for the most part, research studies have been limited to six basic categories—happiness, surprise, sadness, anger, fear, and disgust; the reason for this is grounded in the assumption that only these six categories are differentially represented by our cognitive and social systems. The results reported herein propound otherwise, suggesting that a larger number of categories is used by humans.
Deoxygenation of the Baltic Sea during the last century
Authors: Carstensen Jacob , Andersen Jesper H. , Gustafsson Bo G. , Conley Daniel J.
Published: April 2014

Significance

Oxygen-deficient waters are expanding globally in response to warming and coastal eutrophication. Coastal ecosystems provide valuable services to humans, but these services are severely reduced with decreasing oxygen conditions. In the Baltic Sea, oxygen-deficient waters have expanded from 5,000 to over 60,000 km
2
with large decadal fluctuations over the last century, reducing the potential fish yield and favoring noxious algal blooms. This increase is due to the imbalance between oxygen supply from physical processes and oxygen demand from consumption of organic material, enhanced by nutrient inputs and temperature increases. Further nutrient reductions will be necessary to restore a healthier Baltic Sea and counteract effects from warming.
Bypass of the pre-60S ribosomal quality control as a pathway to oncogenesis
Authors: Sulima Sergey O. , Patchett Stephanie , Advani Vivek M. , De Keersmaecker Kim , Johnson Arlen W. , Dinman Jonathan D.
Published: April 2014

Significance

Ribosomopathies are paradoxical: They first appear as diseases caused by too few cells but later present as diseases caused by too many. Here, we show that the presence of too few cells is caused by a quality control system that eliminates mutant ribosomes before they are allowed to translate mRNAs. Genetic suppression of this quality control system increases the amount of ribosomes available to cells. However, this 60S subunit deficiency results in release of defective ribosomes into the translationally active pool. A genetic model is presented describing how these types of defects may result in cancer, resolving the ribosomopathy paradox.
Grammatical Variation and Change in Jersey English
Authors: Rosen Anna
Published: March 2014

Situated at the crossroads of dialectology, sociolinguistics and contact linguistics, this volume provides a first comprehensive description of the morphosyntactic inventory of the variety of English spoken on Jersey, the largest of the Channel Islands. Based on a specially compiled corpus of spoken material containing both present-day sociolinguistic and archive data, it thereby reveals an intricate network of variation and change in this language-shift variety. The study adopts a cross-varietal approach for its analyses, which enables a first more systematic comparison between the Englishes spoken on Jersey, on its sister island Guernsey and beyond. In addition, it discusses the implications of identity aspects for language use in Jersey. The book will therefore be of major interest to any researcher or student working in the areas of language variation and change, language contact or dialectology and to those interested in sociolinguistic methodology and the relationships between language and identity.
EAT-2, a SAP-like adaptor, controls NK cell activation through phospholipase Cγ, Ca++, and Erk, leading to granule polarization
Authors: Pérez-Quintero Luis-Alberto , Roncagalli Romain , Guo Huaijian , Latour Sylvain , Davidson Dominique , Veillette André
Published: April 2014

Ewing’s sarcoma-associated transcript 2 (EAT-2) is an Src homology 2 domain-containing intracellular adaptor related to signaling lymphocytic activation molecule (SLAM)–associated protein (SAP), the X-linked lymphoproliferative gene product. Both EAT-2 and SAP are expressed in natural killer (NK) cells, and their combined expression is essential for NK cells to kill abnormal hematopoietic cells. SAP mediates this function by coupling SLAM family receptors to the protein tyrosine kinase Fyn and the exchange factor Vav, thereby promoting conjugate formation between NK cells and target cells. We used a variety of genetic, biochemical, and imaging approaches to define the molecular and cellular mechanisms by which EAT-2 controls NK cell activation. We found that EAT-2 mediates its effects in NK cells by linking SLAM family receptors to phospholipase Cγ, calcium fluxes, and Erk kinase. These signals are triggered by one or two tyrosines located in the carboxyl-terminal tail of EAT-2 but not found in SAP. Unlike SAP, EAT-2 does not enhance conjugate formation. Rather, it accelerates polarization and exocytosis of cytotoxic granules toward hematopoietic target cells. Hence, EAT-2 promotes NK cell activation by molecular and cellular mechanisms distinct from those of SAP. These findings explain the cooperative and essential function of these two adaptors in NK cell activation.
Author‐initiated repurposing of reviews: the Streamline Reviews initiative at Virology
Authors: EMERMAN Michael
Published: March 2014

The Elsevier journal Virology has started a trial program of author‐initiated repurposing of reviews from papers previously rejected from high‐impact journals. The program, called Streamline Reviews, is described and compared to other recent initiatives in portable reviews.
Trash journals in China
Authors: Lin SONGQING , Zhan LIJUAN
Published: March 2014

Over the last two decades, China has seen an enormous rise in the number of scientific journals, second only to the USA. However, their overall academic level has not been high as expected. In fact the frequent occurrence of ‘trash’ journals has been a very negative development. In this regard, we will define trash journals and analyze their characteristics. In addition, we explore how such journals come into existence and look at their relationship with ‘legal’ journals. The development of trash journals is directly associated with market demand and profit, and a flawed academic evaluation system. We advocate action by government departments to purge academia of trash journals and give examples of how this could be done.
Book reviews
Authors: CLARK Cindy
Published: March 2014

Expert Internet Searching, 4th edition Phil Bradley London, Facet Publishing, 2013, 282pp. ISBN: 978‐1‐85604‐605‐3, £49.95, pbk
Book reviews
Authors: SOUDER Lawrence
Published: March 2014

Learn to Write Badly: How to Succeed in the Social Sciences Michael Billig Cambridge, Cambridge University Press, 2013, 240pp. ISBN 978‐1‐107‐67698‐5, £14.99, $20.37 pbk (also hbk, ebook)
Bicentennial of the Great Poncelet Theorem (1813–2013): Current advances
Authors: Dragović Vladimir , Radnović Milena
Published: April 2014

We present very recent results related to the Poncelet Theorem on the occasion of its bicentennial. We are telling the story of one of the most beautiful theorems of geometry, recalling for general mathematical audiences the dramatic historic circumstances which led to its discovery, a glimpse of its intrinsic appeal, and the importance of its relationship to dynamics of billiards within confocal conics. We focus on the three main issues: A) The case of pseudo-Euclidean spaces, for which we present a recent notion of relativistic quadrics and apply it to the description of periodic trajectories of billiards within quadrics. B) The relationship between so-called billiard algebra and the foundations of modern discrete differential geometry which leads to double-reflection nets. C) We present a new class of dynamical systems—pseudo-integrable billiards generated by a boundary composed of several arcs of confocal conics having nonconvex angles. The dynamics of such billiards have several extraordinary properties, which are related to interval exchange transformations and which generate families of flows that are minimal but not uniquely ergodic. This type of dynamics provides a novel type of Poncelet porisms—the local ones.
Kähler-Einstein metrics on Fano manifolds. III: Limits as cone angle approaches \boldmath2𝜋 and completion of the main proof
Authors: Chen Xiuxiong , Donaldson Simon , Sun Song
Published: March 2014

This is the third and final article in a series which prove the fact that a K-stable Fano manifold admits a Kähler-Einstein metric. In this paper we consider the Gromov-Hausdorff limits of metrics with cone singularities in the case when the limiting cone angle approaches 2

π
\pi

. We also put all our technical results together to complete the proof of the main theorem.
flowFit: a Bioconductor package to estimate proliferation in cell-tracking dye studies
Authors: Rambaldi Davide , Pece Salvatore , Di Fiore Pier Paolo
Published: March 2014

Summary: Herein we introduce flowFit, a Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The software, distributed as an R Bioconductor library, is based on a mathematical model that takes into account the height of each peak, the size and position of the parental population (labeled but not proliferating) and the estimated distance between the brightness of a cell and the brightness of its daughter (in which the dye is assumed to undergo a 2-fold dilution). Although the algorithm does not make any inference on cell types, rates of cell divisions or rates of cell death, it deconvolutes the actual collected data into a set of peaks, whereby each peak corresponds to a subpopulation of cells that have divided N times. We validated flowFit by retrospective analysis of published proliferation-tracking experiments and demonstrated that the algorithm predicts the same percentage of cells/generation either in samples with discernible peaks (in which the peaks are visible in the collected raw data) or in samples with non-discernible peaks (in which the peaks are fused together). To the best of our knowledge, flowFit represents the first open-source algorithm in its category and might be applied to numerous areas of cell biology in which quantitative deconvolution of tracking dye-based experiments is desired, including stem cell research.

Availability and implementation:  http://www.bioconductor.org/packages/devel/bioc/html/flowFit.html

(Bioconductor software page). http://www.bioconductor.org/packages/2.13/bioc/vignettes/flowFit/inst/doc/HowTo-flowFit.pdf (package vignette). http://rpubs.com/tucano/flowFit (online tutorial).

Contact:  pierpaolo.difiore@ifom.eu or davide.rambaldi@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Census 2: isobaric labeling data analysis
Authors: Park Sung Kyu Robin , Aslanian Aaron , McClatchy Daniel B. , Han Xuemei , Shah Harshil , Singh Meha , Rauniyar Navin , Moresco James J. , Pinto Antonio F.M. , Diedrich Jolene K. , Delahunty Claire , Yates John R.
Published: March 2014

Motivation: We introduce Census 2, an update of a mass spectrometry data analysis tool for peptide/protein quantification. New features for analysis of isobaric labeling, such as Tandem Mass Tag (TMT) or Isobaric Tags for Relative and Absolute Quantification (iTRAQ), have been added in this version, including a reporter ion impurity correction, a reporter ion intensity threshold filter and an option for weighted normalization to correct mixing errors. TMT/iTRAQ analysis can be performed on experiments using HCD (High Energy Collision Dissociation) only, CID (Collision Induced Dissociation)/HCD (High Energy Collision Dissociation) dual scans or HCD triple-stage mass spectrometry data. To improve measurement accuracy, we implemented weighted normalization, multiple tandem spectral approach, impurity correction and dynamic intensity threshold features.

Availability and implementation: Census 2 supports multiple input file formats including MS1/MS2, DTASelect, mzXML and pepXML. It requires JAVA version 6 or later to run. Free download of Census 2 for academic users is available at http://fields.scripps.edu/census/index.php .

Contact:  jyates@scripps.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies
Authors: Thangakani A. Mary , Kumar Sandeep , Nagarajan R. , Velmurugan D. , Gromiha M. Michael
Published: March 2014

Motivation: Distinguishing between amyloid fibril-forming and amorphous β-aggregating aggregation-prone regions (APRs) in proteins and peptides is crucial for designing novel biomaterials and improved aggregation inhibitors for biotechnological and therapeutic purposes.

Results: Adjacent and alternate position residue pairs in hexapeptides show distinct preferences for occurrence in amyloid fibrils and amorphous β-aggregates. These observations were converted into energy potentials that were, in turn, machine learned. The resulting tool, called Generalized Aggregation Proneness (GAP), could successfully distinguish between amyloid fibril-forming and amorphous β-aggregating hexapeptides with almost 100 percent accuracies in validation tests performed using non-redundant datasets.

Conclusion: Accuracies of the predictions made by GAP are significantly improved compared with other methods capable of predicting either general β-aggregation or amyloid fibril-forming APRs. This work demonstrates that amino acid side chains play important roles in determining the morphological fate of β-mediated aggregates formed by short peptides.

Availability and implementation:  http://www.iitm.ac.in/bioinfo/GAP/ .

Contact:  gromiha@iitm.ac.in

Supplementary information:  Supplementary data are available at Bioinformatics online.
Krill, climate, and contrasting future scenarios for Arctic and Antarctic fisheries
Authors: McBride Margaret M. , Dalpadado Padmini , Drinkwater Kenneth F. , Godø Olav Rune , Hobday Alistair J. , Hollowed Anne B. , Kristiansen Trond , Murphy Eugene J. , Ressler Patrick H. , Subbey Sam , Hofmann Eileen E. , Loeng Harald
Published: March 2014

Arctic and Antarctic marine systems have in common high latitudes, large seasonal changes in light levels, cold air and sea temperatures, and sea ice. In other ways, however, they are strikingly different, including their: age, extent, geological structure, ice stability, and foodweb structure. Both regions contain very rapidly warming areas and climate impacts have been reported, as have dramatic future projections. However, the combined effects of a changing climate on oceanographic processes and foodweb dynamics are likely to influence their future fisheries in very different ways. Differences in the life-history strategies of the key zooplankton species (Antarctic krill in the Southern Ocean and Calanus copepods in the Arctic) will likely affect future productivity of fishery species and fisheries. To explore future scenarios for each region, this paper: (i) considers differing characteristics (including geographic, physical, and biological) that define polar marine ecosystems and reviews known and projected impacts of climate change on key zooplankton species that may impact fished species; (ii) summarizes existing fishery resources; (iii) synthesizes this information to generate future scenarios for fisheries; and (iv) considers the implications for future fisheries management. Published studies suggest that if an increase in open water during summer in Arctic and Subarctic seas results in increased primary and secondary production, biomass may increase for some important commercial fish stocks and new mixes of species may become targeted. In contrast, published studies suggest that in the Southern Ocean the potential for existing species to adapt is mixed and that the potential for the invasion of large and highly productive pelagic finfish species appears low. Thus, future Southern Ocean fisheries may largely be dependent on existing species. It is clear from this review that new management approaches will be needed that account for the changing dynamics in these regions under climate change.
Bycatch and discards: from improved knowledge to mitigation programmes
Authors: Rochet Marie-Joëlle , Catchpole Tom , Cadrin Steve
Published: April 2014

Discarding is considered by many as an important problem in world fisheries. In many regions, data collection onboard commercial vessels has intensified, and the understanding of both human and ecological drivers of discards is improving quickly. Discarding patterns vary widely across regions, fisheries, gears, and species. Fishers' responses to regulations and markets explain these complex patterns, on top of resource availability partly driven by environmental fluctuations. This expanded knowledge base provides an appropriate basis for discussing the discard mitigation measures proposed in various settings. In September 2012, a theme session was convened at the ICES Annual Science Conference in Bergen, Norway, to discuss these issues. This themed set of articles includes several of the studies presented at the theme session. Owing to the wide diversity of drivers and reasons for discarding, no single management measure or even framework is expected to address the issue. Rather, discard mitigation measures need to be tailored to each particular fishery, or even species within a fishery, and the effectiveness of solutions is greatest when they are used in combination with other approaches. Bottom-up approaches to bycatch and discard management, which involve incentive-based solutions to bycatch problems, were agreed to be the most promising.
Ghosts of fisheries-induced depletions: do they haunt us still?
Authors: Hutchings Jeffrey A. , Kuparinen Anna
Published: March 2014

The depletion of several North Atlantic gadoids in the 1980s and 1990s stimulated an unprecedented amount of research on the recovery of marine fish. Some of this work addressed long-standing questions of teleost population dynamics: (i) Does per capita population growth rate (r) always increase as abundance declines? (ii) Do teleost fish possess greater intrinsic recovery abilities (as reflected by rmax) than terrestrial vertebrates? (iii) Does the magnitude of population reduction influence the probability of recovery? (iv) If fish evolve in response to fishing, changing average fitness and thus rmax, are the population-dynamic consequences likely to be negative, positive, or neutral? Challenging some long-standing perceptions and beliefs, recent meta-analyses and empirically based model simulations on marine teleost fish support theoretically based postulates that: (i) rmax does not differ from that of terrestrial mammals; (ii) high fecundity has no influence on recovery potential; (iii) Allee effects can be manifest in some depleted populations; (iv) the greater the magnitude of population reduction, the greater the uncertainty of recovery; and (v) the consequences of fisheries-induced evolution for recovery need not always be negative. An emerging imperative of the work examined here is the need to more fully embrace and comprehensively examine the links that exist between fitness and per capita population growth, given that what happens at the level of the individual will have consequences for how populations respond to natural and anthropogenic environment change.
From supernovae to neutron stars
Authors: Suwa Yudai
Published: March 2014

Gravitational collapse, bounce, and explosion of an iron core of an 11.2 M⊙ star are simulated by two-dimensional neutrino-radiation hydrodynamic code. The explosion is driven by the neutrino heating aided by multi-dimensional hydrodynamic effects such as convection. Following the explosion phase, we continue the simulation focusing on the thermal evolution of the protoneutron star up to ∼ 70 s when the crust of the neutron star is formed, using one-dimensional simulation. We find that the crust forms at a high-density region (ρ ∼ 1014 g cm−3) and it proceeds from inside to outside. This is the first self-consistent simulation that successfully follows from the collapse phase to the protoneutron star cooling phase based on multi-dimensional hydrodynamic simulation.
Finitistic Arithmetic and Classical Logic†
Authors: Ganea Mihai
Published: March 2014

It can be argued that only the equational theories of some sub-elementary function algebras are finitistic or intuitive according to a certain interpretation of Hilbert's conception of intuition. The purpose of this paper is to investigate the relation of those restricted forms of equational reasoning to classical quantifier logic in arithmetic. The conclusion reached is that Edward Nelson's ‘predicative arithmetic’ program, which makes essential use of classical quantifier logic, cannot be justified finitistically and thus requires a different philosophical foundation, possibly as a restricted form of logicism.
Hymenobacter kanuolensis sp. nov., a novel radiation-resistant bacterium
Authors: Su Shiyou , Chen Ming , Teng Chao , Jiang Shijie , Zhang Chen , Lin Min , Zhang Wei
Published: March 2014

A Gram-reaction-negative, rod-shaped, non-motile, red-pigmented, radiation-resistant, aerobic bacterium designated T-3T was isolated from a soil sample from the Qinghai–Tibet Plateau in Tibet, China, after exposure to 10 kGy gamma radiation. Phylogenetic analysis based on 16S rRNA sequences indicated that this isolate represented a novel member of the genus

Hymenobacter

. Sequence identities of the 16S rRNA gene of strain T-3T with the type strains of species of the genus

Hymenobacter

with validly published names range from 89 % to 97 %, and the most closely related species is

Hymenobacter psychrotolerans

Tibet-IIU11T (97 %). The DNA–DNA relatedness between strain T-3T and

H. psychrotolerans

is 59.10 %. The major fatty acids of strain T-3T were iso-C15 : 0 (27.66 %), summed feature 4 (iso-C17 : 1I and/or anteiso-C17 : 1B, 15.84 %), anteiso-C15 : 0 (14.08 %) and summed feature 3 (C16 : 1ω7c and/orC16 : 1ω6c, 12.38 %). The major menaquinone of strain T-3T was MK-7. Phosphatidylethanolamine (PE) was predominant in the polar lipid profile. The G+C content of the DNA of strain T-3T was 69.17 mol%. On the basis of the results of the polyphasic characterization presented in this study, it is concluded that strain T-3T represents a novel species of the genus

Hymenobacter

, for which the name Hymenobacter kanuolensis is proposed. The type strain is T-3T ( = ACCC 05760T = KCTC 32407T).
Wickerhamiella kiyanii f.a., sp. nov. and Wickerhamiella fructicola f.a., sp. nov., two yeasts isolated from native plants of Atlantic rainforest in Brazil
Authors: Dayo-Owoyemi Ifeloju , Rosa Carlos Augusto , Rodrigues André , Pagnocca Fernando Carlos
Published: March 2014

Two novel species, Wickerhamiella kiyanii f.a., sp. nov. (type strain FB1-1DASPT = CBS 12905T = CBMAI 1613T) and Wickerhamiella fructicola f.a., sp. nov. (type strain H10YT = CBS 12902T = CBMAI 1614T) are proposed in the Wickerhamiella clade (Saccharomycetes, Saccharomycetales) to accommodate three strains isolated from flowers and fruits typical of the Brazilian Atlantic rainforest. The novel status of these yeast species was established by sequence divergence observed in the D1/D2 domains of the LSU rRNA gene from the most closely related, described species as well as by phylogenetic analysis. Wickerhamiella kiyanii sp. nov. differs from its nearest phylogenetic neighbours W. pagnoccae CBS 12178T, Candida jalapaonensis CBS 10935T and Candida drosophilae CBS 8459T by 2.2–4.2 % in the D1/D2 sequences. By contrast, a sequence divergence of 13.2–13.8 % was observed between W. fructicola sp. nov. and its closest, described phylogenetic relative Candida kazoui JCM 12558T and Candida hasegawae JCM 12559T. Taxonomic descriptions of the two novel species are given.
Pseudozyma brasiliensis sp. nov., a xylanolytic, ustilaginomycetous yeast species isolated from an insect pest of sugarcane roots
Authors: Oliveira Juliana Velasco de Castro , Borges Thuanny A. , Corrêa dos Santos Renato Augusto , Freitas Larissa F. D. , Rosa Carlos Augusto , Goldman Gustavo Henrique , Riaño-Pachón Diego Mauricio
Published: March 2014

A novel ustilaginomycetous yeast isolated from the intestinal tract of an insect pest of sugarcane roots in Ribeirão Preto, São Paulo State, Brazil, represents a novel species of the genus Pseudozyma based on molecular analyses of the D1/D2 rDNA large subunit and the internal transcribed spacer (ITS1+ITS2) regions. The name Pseudozyma brasiliensis sp. nov. is proposed for this species, with GHG001T ( = CBS 13268T = UFMG-CM-Y307T) as the type strain. P. brasiliensis sp. nov. is a sister species of Pseudozyma vetiver, originally isolated from leaves of vetiver grass and sugarcane in Thailand. P. brasiliensis sp. nov. is able to grow well with xylan as the sole carbon source and produces high levels of an endo-1,4-xylanase that has a higher specific activity in comparison with other eukaryotic xylanases. This enzyme has a variety of industrial applications, indicating the great biotechnological potential of P. brasiliensis.
Association between HACEK bacteraemia and endocarditis
Authors: Sen Yew Haur , Chambers Stephen T. , Roberts Sally A. , Holland David J. , Julian Kylie A. , Raymond Nigel J. , Beardsley Justin , Read Kerry M. , Murdoch David R.
Published: March 2014

We retrospectively examined medical records of 87 patients with bacteraemia caused by members of the HACEK group (Haemophilus parainfluenzae, Aggregatibacter actinomycetemcomitans, Aggregatibacter aphrophilus, Aggregatibacter paraphrophilus, Cardiobacterium spp., Eikenella corrodens and Kingella spp.) to determine whether endocarditis was present, as defined by the Duke criteria. The overall positive predictive value (PPV) of HACEK bacteraemia for endocarditis was 60 %. The PPV varied with different HACEK species from 0 % (E. corrodens) to 100 % (A. actinomycetemcomitans).
Mutagenesis of the hydrocarbon monooxygenase indicates a metal centre in subunit-C, and not subunit-B, is essential for copper-containing membrane monooxygenase activity
Authors: Liew Elissa F. , Tong Daochen , Coleman Nicholas V. , Holmes Andrew J.
Published: March 2014

The hydrocarbon monooxygenase (HMO) of Mycobacterium NBB4 is a member of the copper-containing membrane monooxygenase (CuMMO) superfamily, which also contains particulate methane monooxygenases (pMMOs) and ammonia monooxygenases (AMOs). CuMMOs have broad applications due to their ability to catalyse the oxidation of difficult substrates of environmental and industrial relevance. Most of our understanding of CuMMO biochemistry is based on pMMOs and AMOs as models. All three available structures are from pMMOs. These share two metal sites: a dicopper centre coordinated by histidine residues in subunit-B and a ‘variable-metal’ site coordinated by carboxylate and histidine residues from subunit-C. The exact nature and role of these sites is strongly debated. Significant barriers to progress have been the physiologically specialized nature of methanotrophs and autotrophic ammonia-oxidizers, lack of a recombinant expression system for either enzyme and difficulty in purification of active protein. In this study we use the newly developed HMO model system to perform site-directed mutagenesis on the predicted metal-binding residues in the HmoB and HmoC of NBB4 HMO. All mutations of predicted HmoC metal centre ligands abolished enzyme activity. Mutation of a predicted copper-binding residue of HmoB (B-H155V) reduced activity by 81 %. Mutation of a site that shows conservation within physiologically defined subgroups of CuMMOs was shown to reduce relative HMO activity towards larger alkanes. The study demonstrates that the modelled dicopper site of subunit-B is not sufficient for HMO activity and that a metal centre predicted to be coordinated by residues in subunit-C is essential for activity.
The Scramble Conversion Tool
Authors: Bonfield James K
Published: March 2014

Motivation

The reference CRAM file format implementation is in Java. We present “Scramble”: a new C implementation of SAM, BAM and CRAM file I/O.

Results

The C API for CRAM is 1.5–1.7x slower than BAM at decoding, but 1.8–2.6x faster at encoding. We see file size savings of 40–50%.

Availability

Source code is available fromhttp://sourceforge.net/projects/staden/files/io_lib/
Whole-Mount X-Gal Staining of Mouse Tissues
Authors: Gierut Jessica J. , Jacks Tyler E. , Haigis Kevin M.
Published: April 2014

Although the development of improved mouse models, including conditional deletions, marks an exciting time in mouse genetics, it is important to characterize and validate these models. Cre reporter strains allow researchers to assess the recombinase expression profile and function in individual Cre mouse lines. These strains are engineered to express a reporter gene (usually LacZ) following the removal of a floxed STOP cassette, thus marking cell lineages that can be targeted with a given Cre line. This protocol provides a detailed method for the histochemical detection of β-galactosidase activity in Cre mouse strains.
Systematic Structural Characterization of Metabolites in Arabidopsis via Candidate Substrate-Product Pair Networks
Authors: Morreel Kris , Saeys Yvan , Dima Oana , Lu Fachuang , Van de Peer Yves , Vanholme Ruben , Ralph John , Vanholme Bartel , Boerjan Wout
Published: April 2014

Plant metabolomics is increasingly used for pathway discovery and to elucidate gene function. However, the main bottleneck is the identification of the detected compounds. This is more pronounced for secondary metabolites as many of their pathways are still underexplored. Here, an algorithm is presented in which liquid chromatography–mass spectrometry profiles are searched for pairs of peaks that have mass and retention time differences corresponding with those of substrates and products from well-known enzymatic reactions. Concatenating the latter peak pairs, called candidate substrate-product pairs (CSPP), into a network displays tentative (bio)synthetic routes. Starting from known peaks, propagating the network along these routes allows the characterization of adjacent peaks leading to their structure prediction. As a proof-of-principle, this high-throughput cheminformatics procedure was applied to the Arabidopsis thaliana leaf metabolome where it allowed the characterization of the structures of 60% of the profiled compounds. Moreover, based on searches in the Chemical Abstract Service database, the algorithm led to the characterization of 61 compounds that had never been described in plants before. The CSPP-based annotation was confirmed by independent MSn experiments. In addition to being high throughput, this method allows the annotation of low-abundance compounds that are otherwise not amenable to isolation and purification. This method will greatly advance the value of metabolomics in systems biology.