bluuebunny/crossref_metadata_2025 huggingface dataset:
Design of underwater superoleophobic TiO2 coatings with additional photo-induced self-cleaning properties by one-step route bio-inspired from fish scales
Authors: Wang Hao , Guo Zhiguang
Published: May 2014

Self-cleaning properties inspired by the structures and functions of some creatures are of great interest since the late 20th century. In this paper, TiO2 coatings with hierarchical rutile TiO2 flowers on fluorine-doped tin oxide substrate are fabricated through a simple one-step hydrothermal method. The flower-like coatings exhibit superhydrophilicity in air and superoleophobicity underwater with a contact angle as high as 157°, presenting good underwater self-cleaning performance. In addition, when contaminated by oleic acid, the as-prepared TiO2 coatings also exhibit excellent photocatalytic capability under ultraviolet irradiation, which demonstrated self-cleaning properties in a different way. This self-cleaning film provides a good strategy for some industrial and ocean applications.
Large scale two-dimensional arrays of magnesium diboride superconducting quantum interference devices
Authors: Cybart Shane A. , Wong T. J. , Cho E. Y. , Beeman J. W. , Yung C. S. , Moeckly B. H. , Dynes R. C.
Published: May 2014

Magnetic field sensors based on two-dimensional arrays of superconducting quantum interference devices were constructed from magnesium diboride thin films. Each array contained over 30 000 Josephson junctions fabricated by ion damage of 30 nm weak links through an implant mask defined by nano-lithography. Current-biased devices exhibited very large voltage modulation as a function of magnetic field, with amplitudes as high as 8 mV.
Continuously-tuned tunneling behaviors of ferroelectric tunnel junctions based on BaTiO3/La0.67Sr0.33MnO3 heterostructure
Authors: Ou Xin , Xu Bo , Gong Changjie , Lan Xuexin , Yin Qiaonan , Xia Yidong , Yin Jiang , Liu Zhiguo
Published: May 2014

In this work, we fabricate BaTiO3/La0.67Sr0.33MnO3 (BTO/LSMO) ferroelectric tunnel junction on (001) SrTiO3 substrate by pulsed laser deposition method. Combining piezoresponse force and conductive-tip atomic force microscopy, we demonstrate robust and reproducible polarization-controlled tunneling behaviors with the resulting tunneling electroresistance value reaching about 102 in ultrathin BTO films (∼1.2 nm) at room temperature. Moreover, local poling areas with different conductivity are finally achieved by controlling the relative proportion of upward and downward domains, and different poling areas exhibit stable transport properties.
Optical nonlinear dynamics in ZnS from femtosecond laser pulses
Authors: Wu Yu-E , Ren Mengxin , Wang Zhenhua , Li Wenhua , Wu Qiang , Yi Sanming , Zhang Xinzheng , Xu Jingjun
Published: May 2014

A wavelength swapping nondegenerate pump-probe technique to measure the magnitudes of the nonlinear optical dynamics as well as the relaxation time of electrons in high energy levels is presented using a ZnS single crystal wafer as an example. By pumping the sample with 800 nm femtosecond pulses and probing at 400 nm, nondegenerate two-photon absorption (N-2PA) happens exclusively, and the measured curves only show instantaneous features without relaxation tails. The N-2PA coefficient was derived explicitly as 7.52 cm/GW. Additionally, when the wavelengths of the pump and probe beams are swapped, extra information about the relaxation time of the hot electrons excited in the conduction band is obtained. The combined results above are helpful for evaluating the characteristics of an optical switches based on ZnS or other materials with respect to its nonlinear optical dynamic aspect.
Anomalous diffusion of Ga and As from semi-insulating GaAs substrate into MOCVD grown ZnO films as a function of annealing temperature and its effect on charge compensation
Authors: Biswas Pranab , Halder Nripendra N. , Kundu Souvik , Banerji P. , Shripathi T. , Gupta M.
Published: May 2014

The diffusion behavior of arsenic (As) and gallium (Ga) atoms from semi-insulating GaAs (SI-GaAs) into ZnO films upon post-growth annealing vis-à-vis the resulting charge compensation was investigated with the help of x-ray photoelectron spectroscopy (XPS) and secondary ion mass spectroscopy. The films, annealed at 600 ºC and 700 ºC showed p-type conductivity with a hole concentration of 1.1 × 1018 cm−3 and 2.8 × 1019 cm−3 respectively, whereas those annealed at 800 ºC showed n-type conductivity with a carrier concentration of 6.5 × 1016 cm−3. It is observed that at lower temperatures, large fraction of As atoms diffused from the SI-GaAs substrates into ZnO and formed acceptor related complex, (AsZn–2VZn), by substituting Zn atoms (AsZn) and thereby creating two zinc vacancies (VZn). Thus as-grown ZnO which was supposed to be n-type due to nonstoichiometric nature showed p-type behavior. On further increasing the annealing temperature to 800 ºC, Ga atoms diffused more than As atoms and substitute Zn atoms thereby forming shallow donor complex, GaZn. Electrons from donor levels then compensate the p-type carriers and the material reverts back to n-type. Thus the conversion of carrier type took place due to charge compensation between the donors and acceptors in ZnO and this compensation is the possible origin of anomalous conduction in wide band gap materials.
Injected-charge-driven increase in electro-optic effect of KTN crystals
Authors: Toyoda Seiji , Imai Tadayuki , Miyazu Jun , Okabe Yuichi , Ueno Masahiro , Kobayashi Junya
Published: May 2014

We report a significant increase in the electro-optic (EO) effect of KTaxNb1-xO3 (KTN) crystals that we achieved by injecting carriers into them. The dielectric constant of KTN was increased approximately twofold by carrier injection. The EO beam scanning performance was effectively improved by the increase in the EO effect resulting from the increased dielectric constant. The estimated densities of the trapped electrons were as small as 5.8 × 1020m-3. The very small quantity of injected electrons greatly affected the dielectric constant and EO effect of the KTN crystals.
Field-induced domain wall motion of amorphous [CoSiB/Pt]N multilayers with perpendicular anisotropy
Authors: Choi Y. H. , Lee K. J. , Yoon J. B. , Cho J. H. , You C.-Y. , Kim T. W. , Jung M. H.
Published: May 2014

Amorphous CoSiB/Pt multilayer is a perpendicular magnetic anisotropy material to achieve high squareness, low coercivity, strong anisotropy, and smooth domain wall (DW) motion, because of the smoother interface compared with crystalline multilayers. For [CoSiB(6 Å)/Pt (14 Å)]N multilayers with N = 3, 6, and 9, we studied the field-induced DW dynamics. The effective anisotropy constant K1eff is 1.5 × 106 erg/cm3 for all the N values, and the linear increment of coercive field Hc with N gives constant exchange coupling J. By analyzing the field dependence of DW images at room temperature, a clear creep motion with the exponent μ = 1/4 could be observed. Even though the pinning field Hdep slightly increases with N, the pinning potential energy Uc is constant (=35 kBT) for all the N values. These results imply that the amorphous [CoSiB/Pt]N multilayers are inherently homogeneous compared to crystalline multilayers. For N ≤ 6, the pinning site density ρpin is less than 1000/μm2, which is about 1 pinning site per the typical device junction size of 30 × 30 nm2. Also, the exchange stiffness constant Aex is obtained to be 0.48 × 10−6 erg/cm, and the domain wall width is expected to be smaller than 5.5 nm. These results may be applicable for spin-transfer-torque magnetic random access memory and DW logic device applications.
Temperature insensitive refractive index sensor based on single-mode micro-fiber Sagnac loop interferometer
Authors: Chunyang Han , Hui Ding , Xianli Li , Shaofei Dong
Published: May 2014

A single-mode micro-fiber Sagnac loop interferometer (SMSLI) based on single-mode micro-fiber with a diameter of wavelength scale is demonstrated theoretically and experimentally. The influence of structure parameters in SMSLI on its transmission spectra has been investigated by both experimental and theoretical analysis. The sensor responses to the ambient refractive index (RI) and temperature are also investigated experimentally. Experimental results show that the proposed sensor exhibits quite high sensitivity to the ambient RI, which is found to be ∼12 500 nm/RIU. In addition, the sensitivity of SMSLI to ambient temperature is also demonstrated to be only ∼3 pm/ °C by experiments.
AlGaN/GaN heterostructure prepared on a Si (110) substrate via pulsed sputtering
Authors: Watanabe T. , Ohta J. , Kondo T. , Ohashi M. , Ueno K. , Kobayashi A. , Fujioka H.
Published: May 2014

GaN films were grown on Si (110) substrates using a low-temperature growth technique based on pulsed sputtering. Reduction of the growth temperature suppressed the strain in the GaN films, leading to an increase in the critical thickness for crack formation. In addition, an AlGaN/GaN heterostructure with a flat heterointerface was prepared using this technique. Furthermore, the existence of a two dimensional electron gas at the heterointerface with a mobility of 1360 cm2/Vs and a sheet carrier density of 1.3 × 1013 cm−2 was confirmed. Finally, the use of the AlGaN/GaN heterostructure in a high electron mobility transistor was demonstrated. These results indicate that low-temperature growth via pulsed sputtering is quite promising for the fabrication of GaN-based electronic devices.
Influence of defect thickness on the angular dependence of coercivity in rare-earth permanent magnets
Authors: Bance S. , Oezelt H. , Schrefl T. , Ciuta G. , Dempsey N. M. , Givord D. , Winklhofer M. , Hrkac G. , Zimanyi G. , Gutfleisch O. , Woodcock T. G. , Shoji T. , Yano M. , Kato A. , Manabe A.
Published: May 2014

The coercive field and angular dependence of the coercive field of single-grain Nd2Fe14B permanent magnets are computed using finite element micromagnetics. It is shown that the thickness of surface defects plays a critical role in determining the reversal process. For small defect thicknesses reversal is heavily driven by nucleation, whereas with increasing defect thickness domain wall de-pinning becomes more important. This change results in an observable shift between two well-known behavioral models. A similar trend is observed in experimental measurements of bulk samples, where an Nd-Cu infiltration process has been used to enhance coercivity by modifying the grain boundaries. When account is taken of the imperfect grain alignment of real magnets, the single-grain computed results appears to closely match experimental behaviour.
Enhancing light out-coupling of organic light-emitting devices using indium tin oxide-free low-index transparent electrodes
Authors: Huang Yi-Hsiang , Lu Chun-Yang , Tsai Shang-Ta , Tsai Yu-Tang , Chen Chien-Yu , Tsai Wei-Lung , Lin Chun-Yu , Chang Hong-Wei , Lee Wei-Kai , Jiao Min , Wu Chung-Chih
Published: May 2014

With its increasing and sufficient conductivity, the conducting polymer poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) has been capable of replacing the widely used but less cost-effective indium tin oxides (ITOs) as alternative transparent electrodes for organic light-emitting devices (OLEDs). Intriguingly, PEDOT:PSS also possesses an optical refractive index significantly lower than those of ITO and typical organic layers in OLEDs and well matching those of typical OLED substrates. Optical simulation reveals that by replacing ITO with such a low-index transparent electrode, the guided modes trapped within the organic/ITO layers in conventional OLEDs can be substantially suppressed, leading to more light coupled into the substrate than the conventional ITO device. By applying light out-coupling structures onto outer surfaces of substrates to effectively extract radiation into substrates, OLEDs using such low-index transparent electrodes achieve enhanced optical out-coupling and external quantum efficiencies in comparison with conventional OLEDs using ITO.
Manganese oxidation and reduction in soils: effects of temperature, water potential, pH and their interactions
Authors: Sparrow L. A. , Uren N. C.
Published: May 2014

Manganese (Mn) toxicity is a potential limitation to plant growth on acidic and poorly drained soils. Five laboratory experiments using such soils were conducted to examine the influence of soil temperature, pH and water potential on the redox reactions of Mn and the potential for Mn toxicity. The microbial inhibitor sodium azide was used in some experiments to assess the role of microorganisms in these reactions. The reduction of Mn oxides (MnOx) during waterlogging was faster at 20°C and 30°C than at 10°C or 4°C. Sodium azide slowed the reduction of Mn oxides at 20°C and 30°C during waterlogging but had little effect at 4°C and 10°C, suggesting that microbial MnOx reduction during waterlogging was minimal at the lower temperatures. Re-oxidation of Mn2+ in soil drained after severe waterlogging was only observed in soil not treated with sodium azide, indicating that even when very high concentrations of Mn2+ were present, Mn2+ oxidation was still microbial. Prior liming of aerobic soil established lower starting concentrations of water-soluble plus exchangeable (WS+E) Mn2+ and slowed the reduction of Mn oxides during subsequent waterlogging. After drainage, rapid re-oxidation of Mn2+ was observed in all lime treatments but was fastest at the two highest lime rates. In the fourth and fifth experiments, interactions between temperature and water potential were observed. When waterlogged soils were drained to –5 and –10 kPa, re-oxidation of Mn2+ occurred at both 10°C and 20°C. At –1 kPa, there was no net change in WS+E Mn2+ at 10°C, whereas at 20°C, the concentration of WS+E Mn2+ increased, possibly due to the lower concentration of O2 in the soil water at the higher temperature. In the fifth experiment, at 4°C and 10°C there was little or no effect on Mn reactions of varying water potential from –1 to –1500 kPa, but at 20°C and especially at 30°C, both Mn2+ oxidation and Mn oxide reduction were slowed at –1500 kPa compared with the higher water potentials. Overall, the experiments show that a delicate balance between the microbial oxidation of Mn2+ and the reduction of Mn oxides can exist, and that it can be shifted by small changes in soil water potential along with changes in temperature and pH.
Stability and storage of soil organic carbon in a heavy-textured Karst soil from south-eastern Australia
Authors: Hobley Eleanor , Willgoose Garry R. , Frisia Silvia , Jacobsen Geraldine
Published: May 2014

Both aggregation and mineral association have been previously found to enhance soil organic carbon (SOC) storage (the amount of organic C retained in a soil), and stability (the length of time organic C is retained in a soil). These mechanisms are therefore attractive targets for soil C sequestration. In this study, we investigate and compare SOC storage and stability of SOC associated with fine minerals and stored within aggregates using a combination of particle-size fractionation, elemental analysis and radiocarbon dating. In this heavy-textured, highly aggregated soil, SOC was found to be preferentially associated with fine minerals throughout the soil profile. By contrast, the oldest SOC was located in the coarsest, most highly aggregated fraction. In the topsoil, radiocarbon ages of the aggregate-associated SOC indicate retention times in the order of centuries. Below the topsoil, retention times of aggregate-SOC are in the order of millennia. Throughout the soil profile, radiocarbon dates indicate an enhanced stability in the order of centuries compared with the fine mineral fraction. Despite this, the radiocarbon ages of the mineral-associated SOC were in the order of centuries to millennia in the subsoil (30–100 cm), indicating that mineral-association is also an effective stabilisation mechanism in this subsoil. Our results indicate that enhanced SOC storage does not equate to enhanced SOC stability, which is an important consideration for sequestration schemes targeting both the amount and longevity of soil carbon.
Solution conditions determine the relative importance of nucleation and growth processes in α-synuclein aggregation
Authors: Buell Alexander K. , Galvagnion Céline , Gaspar Ricardo , Sparr Emma , Vendruscolo Michele , Knowles Tuomas P. J. , Linse Sara , Dobson Christopher M.
Published: May 2014

Significance

The deposition of α-synuclein as insoluble amyloid fibrils and the spreading of such species in the brain are two hallmarks of Parkinson disease. It is therefore of great importance to understand in detail the process of aggregation of this protein. We show by a series of in vitro measurements that amyloid fibrils of α-synuclein can grow under a wide range of solution conditions but that they can multiply rapidly only under a much more select set of solution conditions, mimicking those in endosomes and other organelles. The quantitative characterization of α-synuclein aggregation described here provides new insights into the microscopic mechanisms underlying α-synuclein aggregation in the context of Parkinson disease.
DNMT3a epigenetic program regulates the HIF-2α oxygen-sensing pathway and the cellular response to hypoxia
Authors: Lachance Gabriel , Uniacke James , Audas Timothy E. , Holterman Chet E. , Franovic Aleksandra , Payette Josianne , Lee Stephen
Published: May 2014

Significance

DNA methyltransferase 3a (DNMT3a) mediates the de novo methylation of DNA to regulate gene expression and maintain cellular homeostasis. Mutations in
DNMT3a
in primary tumors suggest that the DNMT3a epigenetic program is modified during early tumorigenesis. We show that a major consequence of DNMT3a defects is the epigenetic deregulation and unscheduled activation of the
EPAS1
(hypoxia-inducible factor 2α) gene that facilitates growth and viability under conditions of low oxygen availability. This represents a critical step during tumorigenesis, because cancer cells must adapt to hypoxia during the formation of the earliest multicellular foci. The data identify the DNMT3a epigenetic program as a gatekeeper of the hypoxic cancer cell phenotype.
Configuración de la metafunción ideacional en la conversación coloquial
Authors: Ferrari Maria Carolina , Granato Luisa
Published: May 2014

Este artículo presenta los resultados de una investigación cualitativa, exploratoria en la que se analizó la conversación coloquial de estudiantes universitarios argentinos que hablan la variedad de español de la provincia de Buenos Aires. El objetivo de este estudio es determinar cómo los hablantes representan ciertos aspectos del mundo en el discurso, es decir, cómo se configuran los significados ideacionales; particularmente, la influencia que los diminutivos tienen en el plano ideacional. El trabajo se inscribe dentro de la perspectiva de la Lingüística Sistémico-Funcional, iniciada por Halliday (1978, 1985, 1994; Halliday y Mathiessen 2004) y Halliday y Hasan (1980, 1985) y desarrollada por discípulos de Halliday en la Escuela de Sydney. El análisis muestra que los diminutivos son un rasgo importante de la conversación coloquial y que, a pesar de que dichas expresiones tienen un fuerte componente interpersonal, inciden en la representación de los significados ideacionales. En este plano, los diminutivos pueden indicar una relación de similitud, expresar solidaridad o afectividad, y acentuar o atenuar ciertos rasgos de los participantes.
The Indian Diaspora and policy formulation in Kenya
Authors: Kiamba Anita
Published: May 2014

The relations between the East African region and India predate a shared colonial experiences. The close cooperation enjoyed by India and the East African states is further enhanced by the presence of Indian Diaspora, which coincides with the globalisation of economic activities and the pursuit of development. The presence of the Diaspora has been a catalyst for industrial growth and investment in the region, more particularly in Kenya. Indeed, economic growth has been attributed to, among other factors, the Diaspora. This in turn has placed the Diaspora in the path towards attracting and shaping patterns of trade, investment and economic growth. The role of the Diaspora in trade, investment and economic growth has remained perceptible from colonialism to date. Given the predominant influence of the Diaspora in investment, an account of the Diaspora in articulating policy in other sectors such as politics is slightly evident. The article identifies this concern given that the Diaspora has a stake in the economy and also has the potential to enhance comprehensive relations between Kenya and India.

The article begins by providing a brief overview of the Diaspora in Kenya and identifies notable individuals who have shaped policies across politics and economics. It argues that the Indian Diaspora have been somewhat inconspicuous in the enunciation of policies due to the inclination of the Diaspora to maintain an indiscernible ‘political’ identity, which in this context is largely based on post-colonial experiences. The article argues that in order to promote the role of the Diaspora in policy formulation, there is a need to acknowledge that political processes are important avenues through which economic processes of investment, trade and development are achieved. Consequently, a more comprehensive approach is required. The article is as a result of perceptions and expectations on the Diaspora in policy formulation and articulation. It juxtaposes various watershed moments to query the imperceptible ‘political’ identity of the Diaspora. International events such as India’s pre-colonial trade with East Africa, the role of the Diaspora in struggle for independence, particularly, in Kenya and South Africa, the establishment of the Non-Aligned Movement and attendant principles of Bon Voisagne or Panscheel and South–South cooperation reflect India’s connection with and importance to developing countries. In retrospect though, developing countries like Kenya continue to put emphasis on economic and industrial development, subsequently pursuing and attracting trade and investment from developing and developed countries. Given the importance attached to the Indian Diaspora since independence as instrumental vehicles in industrial development, the article considers the role of the Diaspora in a more comprehensive formulation of policy. The conclusion identifies how India and Kenya can mutually enhance the role of the Diaspora amid a variety of interests.
A framework for installable external tools in Skyline
Authors: Broudy Daniel , Killeen Trevor , Choi Meena , Shulman Nicholas , Mani Deepak R. , Abbatiello Susan E. , Mani Deepak , Ahmad Rushdy , Sahu Alexandria K. , Schilling Birgit , Tamura Kaipo , Boss Yuval , Sharma Vagisha , Gibson Bradford W. , Carr Steven A. , Vitek Olga , MacCoss Michael J. , MacLean Brendan
Published: May 2014

Summary: Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. The Skyline document model contains extensive mass spectrometry data from targeted proteomics experiments performed using selected reaction monitoring, parallel reaction monitoring and data-independent and data-dependent acquisition methods. Researchers have developed software tools that perform statistical analysis of the experimental data contained within Skyline documents. The new external tools framework allows researchers to integrate their tools into Skyline without modifying the Skyline codebase. Installed tools provide point-and-click access to downstream statistical analysis of data processed in Skyline. The framework also specifies a uniform interface to format tools for installation into Skyline. Tool developers can now easily share their tools with proteomics researchers using Skyline.

Availability and implementation: Skyline is available as a single-click self-updating web installation at http://skyline.maccosslab.org. This Web site also provides access to installable external tools and documentation.

Contact:  brendanx@u.washington.edu

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Ceiba: scalable visualization of phylogenies and 2D/3D image collections
Authors: Sanderson Michael J.
Published: May 2014

Summary: Phylogenetic trees with hundreds of thousands of leaves are now being inferred from sequence data, posing significant challenges for visualization and exploratory analysis. Image data supplying valuable context for species in trees (and cues for exploring them) are becoming increasingly available in biodiversity databases and elsewhere but have rarely been built into tree visualization software in a scalable way. Ceiba lets the user explore large trees and inspect image collection arrays (sets of ‘homologous’ images) comprising mixtures of 2D and 3D image objects. Ceiba exploits recent improvements in graphics hardware, OpenGL toolkits and many standard high-performance computer graphics strategies, such as texture compression, level of detail control, culling, animations and image caching. Its tree layouts can be tuned by user-provided phylogenetic definitions of subtrees. The code has been extensively tested on phylogenies of up to 55 000 leaves and images.

Availability and implementation: A manual, datasets, source code (distributed under GPL) and binaries for OS X are available at http://sourceforge.net/projects/ceiba.

Contact:  sanderm@email.arizona.edu

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Efficient RNA isoform identification and quantification from RNA-Seq data with network flows
Authors: Bernard Elsa , Jacob Laurent , Mairal Julien , Vert Jean-Philippe
Published: May 2014

Motivation: Several state-of-the-art methods for isoform identification and quantification are based on ℓ1-regularized regression, such as the Lasso. However, explicitly listing the—possibly exponentially—large set of candidate transcripts is intractable for genes with many exons. For this reason, existing approaches using the ℓ1-penalty are either restricted to genes with few exons or only run the regression algorithm on a small set of preselected isoforms.

Results: We introduce a new technique called FlipFlop, which can efficiently tackle the sparse estimation problem on the full set of candidate isoforms by using network flow optimization. Our technique removes the need of a preselection step, leading to better isoform identification while keeping a low computational cost. Experiments with synthetic and real RNA-Seq data confirm that our approach is more accurate than alternative methods and one of the fastest available.

Availability and implementation: Source code is freely available as an R package from the Bioconductor Web site (http://www.bioconductor.org/), and more information is available at http://cbio.ensmp.fr/flipflop.

Contact:  Jean-Philippe.Vert@mines.org

Supplementary information:  Supplementary Data are available at Bioinformatics online.
lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs
Authors: Park Charny , Yu Namhee , Choi Ikjung , Kim Wankyu , Lee Sanghyuk
Published: May 2014

Motivation: A number of long non-coding RNAs (lncRNAs) have been identified by deep sequencing methods, but their molecular and cellular functions are known only for a limited number of lncRNAs. Current databases on lncRNAs are mostly for cataloging purpose without providing in-depth information required to infer functions. A comprehensive resource on lncRNA function is an immediate need.

Results: We present a database for functional investigation of lncRNAs that encompasses annotation, sequence analysis, gene expression, protein binding and phylogenetic conservation. We have compiled lncRNAs for six species (human, mouse, zebrafish, fruit fly, worm and yeast) from ENSEMBL, HGNC, MGI and lncRNAdb. Each lncRNA was analyzed for coding potential and phylogenetic conservation in different lineages. Gene expression data of 208 RNA-Seq studies (4995 samples), collected from GEO, ENCODE, modENCODE and TCGA databases, were used to provide expression profiles in various tissues, diseases and developmental stages. Importantly, we analyzed RNA-Seq data to identify coexpressed mRNAs that would provide ample insights on lncRNA functions. The resulting gene list can be subject to enrichment analysis such as Gene Ontology or KEGG pathways. Furthermore, we compiled protein–lncRNA interactions by collecting and analyzing publicly available CLIP-seq or PAR-CLIP sequencing data. Finally, we explored evolutionarily conserved lncRNAs with correlated expression between human and six other organisms to identify functional lncRNAs. The whole contents are provided in a user-friendly web interface.

Availability and implementation: lncRNAtor is available at http://lncrnator.ewha.ac.kr/.

Contact:  sanghyuk@ewha.ac.kr

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Successful Aging and Its Discontents: A Systematic Review of the Social Gerontology Literature
Authors: Martinson Marty , Berridge Clara
Published: May 2014

Purpose of the Study:

The purpose of this study was to analyze the range of critiques of successful aging models and the suggestions for improvement as expressed in the social gerontology literature.

Design and Methods:

We conducted a systematic literature review using the following criteria: journal articles retrieved in the Abstracts in Social Gerontology, published 1987–2013, successful aging/ageing in the title or text (n = 453), a critique of successful aging models as a key component of the article. Sixty-seven articles met the criteria. Qualitative methods were used to identify key themes and inductively configure meanings across the range of critiques.

Results:

The critiques and remedies fell into 4 categories. The Add and Stir group suggested a multidimensional expansion of successful aging criteria and offered an array of additions. The Missing Voices group advocated for adding older adults’ subjective meanings of successful aging to established objective measures. The Hard Hitting Critiques group called for more just and inclusive frameworks that embrace diversity, avoid stigma and discrimination, and intervene at structural contexts of aging. The New Frames and Names group presented alternative ideal models often grounded in Eastern philosophies.

Implications:

The vast array of criteria that gerontologists collectively offered to expand Rowe and Kahn’s original successful model is symptomatic of the problem that a normative model is by definition exclusionary. Greater reflexivity about gerontology’s use of “successful aging” and other normative models is needed.
Does a strong particle accelerator arise very close to the light cylinder in a pulsar magnetosphere?
Authors: Hirotani K.
Published: May 2014

We examine if an efficient particle acceleration takes place by a magnetic-field-aligned electric field near the light cylinder in a rotating neutron star magnetosphere. Constructing the electric current density with the actual motion of collisionless plasmas, we express the rotationally induced Goldreich–Julian charge density as a function of position. It is demonstrated that the ‘light cylinder gap’, which emits very high energy photons via curvature process by virtue of a strong magnetic-field-aligned electric field very close to the light cylinder, will not arise in an actual pulsar magnetosphere.
Corticosteroid Effects on Sputum Culture in Pulmonary Tuberculosis: A Meta-Regression Analysis
Authors: Wallis Robert S.
Published: May 2014

Objectives.  There is increasing interest in the potential role of adjunctive anti-inflammatory therapy to accelerate tuberculosis (TB) treatment. Sputum culture conversion is an important biomarker predictor of durable TB cure.

Methods.  This study used meta-regression analysis to examine the relationship between corticosteroid dose and sputum culture conversion, using published data from controlled clinical trials including 1806 corticosteroid-treated TB patients.

Results.  Linear models with 2 or 3 variables, including corticosteroid dose and the proportion of culture positive control subjects, predicted therapeutic benefit of corticosteroids at 1 and 2 months. The 3-variable model predicted that 134 mg of prednisolone per day, given together with standard 4-drug TB chemotherapy, would reduce the proportion of positive culture at 2 months from 15% to 2%. The estimate accounts for a 50% reduction in steroid exposure due to rifampin. A proportion of 2% of subjects with positive cultures at 2 months has been proposed as a target for new 4-month TB regimens.

Conclusions.  These positive findings must be tempered by recognition that the metabolic and cardiovascular risks of corticosteroids administered at this dose for this duration are unlikely to be acceptable when examined from a patient-level benefit-risk perspective. In future research studies to shorten TB treatment, biologic anti-inflammatory therapies with similar therapeutic effects but superior safety profiles should be considered.
Higher Human T-Lymphotropic Virus Type 1 Subtype C Proviral Loads Are Associated With Bronchiectasis in Indigenous Australians: Results of a Case-Control Study
Authors: Einsiedel Lloyd , Cassar Olivier , Goeman Emma , Spelman Tim , Au Virginia , Hatami Saba , Joseph Sheela , Gessain Antoine
Published: May 2014

Background.  We previously suggested that infection with the human T-lymphotropic virus type 1 (HTLV-1) subtype C is associated with bronchiectasis among Indigenous Australians. Bronchiectasis might therefore result from an HTLV-1-mediated inflammatory process that is typically associated with a high HTLV-1 proviral load (PVL). Human T-lymphotropic virus type 1 PVL have not been reported for Indigenous Australians.

Methods.  Thirty-six Indigenous adults admitted with bronchiectasis from June 1, 2008, to December 31, 2009 were prospectively recruited and matched by age, sex, and ethno-geographic origin to 36 controls. Case notes and chest high-resolution computed tomographs were reviewed, and pulmonary injury scores were calculated. A PVL assay for the HTLV-1c subtype that infects Indigenous Australians was developed and applied to this study. Clinical, radiological, and virological parameters were compared between groups and according to HTLV-1 serostatus.

Results.  Human T-lymphotropic virus type 1 infection was the main predictor of bronchiectasis in a multivariable model (adjusted risk ratio [aRR], 1.84; 95% confidence interval [CI], 1.19–2.84; P = .006). Moreover, the median HTLV-1c PVL (interquartile range) for cases was >100-fold that of controls (cases, 0.319 [0.007, 0.749]; controls, 0.003 [0.000, 0.051] per 100 peripheral blood lymphocytes; P = .007), and HTLV-1c PVL were closely correlated with radiologically determined pulmonary injury scores (Spearman's rho = 0.7457; P = .0000). Other predictors of bronchiectasis were positive Strongyloides serology (aRR, 1.69; 95% CI, 1.13–2.53) and childhood skin infections (aRR, 1.62; 95% CI, 1.07–2.44). Bronchiectasis was the major predictor of death (aRR, 2.71; 95% CI, 1.36–5.39; P = .004).

Conclusions.  These data strongly support an etiological association between HTLV-1 infection and bronchiectasis in a socially disadvantaged population at risk of recurrent lower respiratory tract infections.
Bacteremia with Aerococcus sanguinicola: Case Series with Characterization of Virulence Properties
Authors: Senneby Erik , Eriksson Birger , Fagerholm Erik , Rasmussen Magnus
Published: May 2014

Background.  Since Aerococcus sanguinicola was designated as a species in 2001, only a few cases of bacteremia have been reported. The aim with this study was to describe the clinical presentation of A sanguinicola bacteremia and to determine the antibiotic susceptibility and the capacity of the bacteria to form biofilm and to induce platelet aggregation.

Methods.  Isolates of A sanguinicola from blood cultures were retrospectively identified from 2 clinical microbiology laboratories for 2006 to 2012. Species identity was confirmed through sequencing of the 16S rRNA gene. The medical charts of patients were reviewed. The minimum inhibitory concentration (MIC) for relevant antibiotics was determined. Biofilm formation was measured as the amount of crystal violet absorbed. Platelet aggregation was determined by aggregometry.

Results.  Eleven cases of A sanguinicola bacteremia were identified. All patients were male and the median age was 82 years (range 67–93). Nine patients fulfilled criteria for severe sepsis, and 2 patients died at hospital. Two patients were diagnosed with infective endocarditis. Most patients had underlying urinary tract diseases or an indwelling urinary tract catheter. Five patients suffered from dementia. None of the patients was treated with immunosuppressive medications. The MIC values of the isolates were in line with previous reports, with low MICs for penicillin, cefotaxime, and vancomycin. All 11 isolates produced biofilms but not all could induce platelet aggregation.

Conclusions.  A sanguinicola can cause severe infections in elderly men with urinary tract abnormalities and the bacteria possess potential virulence mechanisms.
Candida Pneumonia in Intensive Care Unit?
Authors: Schnabel Ronny M. , Linssen Catharina F. , Guion Nele , van Mook Walther N. , Bergmans Dennis C.
Published: May 2014

It has been questioned if Candida pneumonia exists as a clinical entity. Only histopathology can establish the definite diagnosis. Less invasive diagnostic strategies lack specificity and have been insufficiently validated. Scarcity of this pathomechanism and nonspecific clinical presentation make validation and the development of a clinical algorithm difficult. In the present study, we analyze whether Candida pneumonia exists in our critical care population. We used a bronchoalveolar lavage (BAL) specimen database that we have built in a structural diagnostic approach to ventilator-associated pneumonia for more than a decade consisting of 832 samples. Microbiological data were linked to clinical information and available autopsy data. We searched for critically ill patients with respiratory failure with no other microbiological or clinical explanation than exclusive presence of Candida species in BAL fluid. Five cases could be identified with Candida as the likely cause of pneumonia.
International Trade Puzzles: A Solution Linking Production and Preferences
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Authors: Caron Justin , Fally Thibault , Markusen James R.
Published: May 2014

International trade literature tends to focus heavily on the production side of general equilibrium, leaving us with a number of empirical puzzles. There is, for example, considerably less world trade than predicted by Heckscher-Ohlin-Vanek (HOV) models. Trade among rich countries is higher and trade between rich and poor countries lower than suggested by HOV and other supply-driven theories, and trade-to-GDP ratios are higher in rich countries. Our approach focuses on the relationship between characteristics of goods and services in production and characteristics of preferences. In particular, we find a strong and significant positive correlation of more than 45% between a good’s skilled-labor intensity and its income elasticity, even when accounting for trade costs and cross-country price differences. Exploring the implications of this correlation for empirical trade puzzles, we find that it can reduce HOV’s overprediction of the variance of the net factor content of trade relative to that in the data by about 60%. Since rich countries are relatively skilled-labor abundant, they are relatively specialized in consuming the same goods and services that they are specialized in producing, and so trade more with one another than with poor countries. We also find a positive sector-level correlation between income elasticity and a sector’s tradability, which helps explain the higher trade-to-GDP ratios in high-income relative to low-income countries.
First Report of Southern Blight of Swiss Chard (Beta vulgaris subsp. cicla) Caused by Sclerotium rolfsii in California
Authors: Koike S. T.
Published: May 2014

In June 2013, a commercial organic planting of Swiss chard (Beta vulgaris subsp. cicla) in Monterey County, CA, showed symptoms of a soilborne disease. Early symptoms consisted of delayed and stunted growth, with wilting of foliage during the warmer times of the day. Initially, a light brown discoloration developed on stems at the soil line. As disease progressed, a dark brown necrosis extended up the main stem and down along the upper portion of the taproot. In advanced cases, the plants collapsed and died. Extensive white cottony mycelium and numerous brown, spherical sclerotia, approximately 1 mm in diameter, developed externally on the lower stem, crown, and adhering adjacent soil. For this particular planting, approximately 10% of the 0.4 ha was lost. Sequentially planted sets of chard placed in other parts of the farm were unaffected. Isolations from necrotic plant tissues, sclerotia, and white mycelium all resulted in recovery of the same white fungus that in culture produced identical sclerotia but no other reproductive structures. Based on white mycelium, sclerotia morphology, and the presence of clamp connections at hyphal septa, the fungus was identified as Sclerotium rolfsii (1). Pathogenicity was tested by growing isolates on potato dextrose agar, drying the resulting sclerotia for 48 h, then burying 5 to 8 sclerotia adjacent to the crowns of healthy Swiss chard plants grown in pots. Three isolates were tested using 24 plants per isolate. Six control plants were inoculated with sterilized sand. All plants were incubated in a greenhouse at 22 to 25°C. After 8 days, inoculated plants began to wilt. By 14 days after inoculation, 100% of the inoculated plants showed symptoms identical to those observed in the field. One half of the plants were used for re-isolations, from which S. rolfsii was recovered from all necrotic crown and stem tissues. The other half of the plants were maintained in the greenhouse; these plants later supported the development of sclerotia. Sand-inoculated control plants did not develop any disease symptoms. The experiment was repeated and the results were the same. To our knowledge, this is the first report of southern blight of Swiss chard in California. Southern blight has not previously been found in this cooler, western part of the county adjacent to the Pacific Ocean; southern blight has been documented on other crops such as pepper, tomato, and chives (3) in the warmer eastern and southern parts of Monterey County. S. rolfsii has been reported on Swiss chard in Louisiana, South Carolina, and Cuba (2).

References: (1) K. H. Domsch et al. Compendium of Soil Fungi, 2nd edition. IHW-Verlag, Eching, Germany, 2007. (2) D. F. Farr and A. Y. Rossman. Fungal Databases. Syst. Mycol. Microbiol. Lab. Online publication, ARS, USDA. Retrieved July 26, 2013. (3) S. T. Koike et al. Plant Dis. 78:208, 1994.
Using Volume Index and Lateral Hepatic Angle to Differentiate Biliary Atresia From TPN‐Associated Cholestasis
Authors: Peng Steven Shinn‐Forng , Hsu Wen‐Ming , Chen Huey‐Ling , Mo Yuan‐Heng
Published: May 2014

Objectives:

Differential diagnosis between biliary atresia (BA) and total parenteral nutrition–associated cholestasis (TPN‐AC) and early treatment for cholestatic infants are challenges for evaluating neonatal or infantile cholestasis. The aim of our retrospective study was to apply noninvasive indices of magnetic resonance images to differentiate BA from TPN‐AC.

Methods:

A total of 44 patients diagnosed as having BA (n = 30) or TPN‐AC (n = 14) were included in the present retrospective study and underwent abdominal magnetic resonance imaging to evaluate the possibility of BA. The left lateral hepatic angle was determined from the coronal image of the left portal vein and portal vein of segment II. Adjusted volume indices of the right hepatic lobe (AVIR) and left lateral segment (AVILL) were calculated as the product of 3 diameters (centimeters) divided by each patient's body weight.

Results:

The left lateral hepatic angles of patients with BA (74° ± 21°) were significantly larger than for patients with TPN‐AC (33° ± 9°) and controls (36° ± 5°, P < 0.05). AVILL of the BA (0.037 ± 0.012 cm3/g) and TPN‐AC groups (0.042 ± 0.030 cm3/g) were not significantly different (P = 0.61) but were significantly larger than for controls (0.020 ± 0.011 cm3/g) (P < 0.05). The right hepatic lobe to left lateral hepatic segment ratio (RLR) of patients with BA was significantly (P < 0.05) smaller (1.61 ± 0.58) than for patients with TPN‐AC (3.08 ± 2.43) and controls (2.98 ± 0.92). Patients with BA could have relative sparing and selective enlargement of the left lateral liver with a resultant lobar difference and blunt left lateral hepatic angle.

Conclusions:

Noninvasive indices of lobar difference and left lateral hepatic angle help differentiate patients with BA from those with TPN‐AC.
Thermomicrobium carboxidum sp. nov., and Thermorudis peleae gen. nov., sp. nov., carbon monoxide-oxidizing bacteria isolated from geothermally heated biofilms
Authors: King C. E. , King G. M.
Published: May 2014

Two thermophilic, Gram-stain-positive, rod-shaped, non-spore-forming bacteria (strains KI3T and KI4T) were isolated from geothermally heated biofilms growing on a tumulus in the Kilauea Iki pit crater on the flank of Kilauea Volcano (Hawai‘i, USA). Strain KI3T grew over an examined temperature range of 50–70 °C (no growth at 80 °C) and a pH range of 6.0–9.0, with optimum growth at 70 °C and pH 7.0. Strain KI4T grew at temperatures of 55–70 °C and a pH range of 5.8–8.0, with optimum growth at 65 °C and pH 6.7–7.1. The DNA G+C contents of strains KI3T and KI4T were 66.0 and 60.7 mol%, respectively. The major fatty acid for both strains was 12-methyl C18 : 0. Polar lipids in strain KI3T were dominated by glycolipids and phosphatidylinositol, while phosphatidylinositol and phosphoglycolipids dominated in strain KI4T. Strain KI3T oxidized carbon monoxide [6.7±0.8 nmol CO h−1 (mg protein)−1], but strain KI4T did not. 16S rRNA gene sequence analyses determined that the strains belong to the class

Thermomicrobia

, and that strains KI3T and KI4T are related most closely to

Thermomicrobium roseum

DSM 5159T (96.5 and 91.1 % similarity, respectively). 16S rRNA gene sequence similarity between strain KI3T and strain KI4T was 91.4 %. Phenotypic features and phylogenetic analyses supported the affiliation of strain KI3T to the genus

Thermomicrobium

, while results of chemotaxonomic, physiological and biochemical assays differentiated strains KI3T and KI4T from

Thermomicrobium roseum

. Strain KI3T ( = DSM 27067T = ATCC BAA-2535T) is thus considered to be the type strain of a novel species, for which the name

Thermomicrobium

carboxidum sp. nov. is proposed. Additionally, the characterization and phylogenetic position of strain KI4T showed that it represents a novel species of a new genus, for which the name Thermorudis peleae gen. nov., sp. nov. is proposed. The type strain of Thermorudis peleae is KI4T ( = DSM 27169T = ATCC BAA-2536T).