bluuebunny/crossref_metadata_2025 huggingface dataset:
A unique carbon with a high specific surface area produced by the carbonization of agar in the presence of graphene
Authors: Xie Tingting , Lv Wei , Wei Wei , Li Zhengjie , Li Baohua , Kang Feiyu , Yang Quan-Hong
Published: September 2013

A unique carbon with a large external surface and high rate performance is prepared by carbonization of agar in the presence of graphene.
Communication: Synperiplanar to antiperiplanar conformation changes as underlying the mechanism of Debye process in supercooled ibuprofen
Authors: Adrjanowicz K. , Kaminski K. , Dulski M. , Wlodarczyk P. , Bartkowiak G. , Popenda L. , Jurga S. , Kujawski J. , Kruk J. , Bernard M. K. , Paluch M.
Published: September 2013

In this Communication, we present experimental studies that put new insight into the puzzling nature of the Debye relaxation found in the supercooled liquid state of racemic ibuprofen. The appearance of D-relaxation in the loss spectra of non-hydrogen bonding methylated derivate of ibuprofen has proven that Debye relaxation is related solely with conformational changes of the carboxyl group, termed in this paper as synperiplanar-antiperiplanar. Our studies indicate that the presence of hydrogen bonding capabilities is not here the necessary condition to observe Debye process, however, their occurrence might strongly influence α- and D-relaxations dynamics. Interestingly, the activation energy of the D-process in ibuprofen methyl ester on approaching Tg was found to be perfectly consistent with that reported for ibuprofen by Affouard and Correia [J. Phys. Chem. B 114, 11397–11402 (2010)] (∼39 kJ/mol). Finally, IR measurements suggest that the equilibrium between conformers concentration depends on time and temperature, which might explain why the appearance of D-relaxation in supercooled ibuprofen depends on thermal history of the sample.
A compact 10 kW, 476 MHz solid state radio frequency amplifier for pre-buncher cavity of free electron laser injector linear accelerator
Authors: Mohania Praveen , Mahawar Ashish , Shrivastava Purushottam , Gupta P. D.
Published: September 2013

A 10 kW, 476 MHz, 0.1% duty cycle solid state RF amplifier system for driving sub-harmonic, pre-buncher cavity of IR-FEL injector LINAC, has been developed at RRCAT. The 10 kW power is achieved by combining output of eight 1400 W amplifier modules using 8-way planar corporate combiner. The solid state amplifier modules have been developed using 50 V RF LDMOS transistors which although meant for push-pull operation are being used in single ended configuration with matching circuit developed on a thin (25 mils), high dielectric constant (9.7), low loss microwave laminate with an aim to have a compact structure. Ease of fabrication, modularity, small size, and low cost are the important features of this design which could be used as a template for low duty cycle medium to high pulsed power UHF amplifier system.
Experimental study on macroscopic contact line behaviors during bubble formation on submerged orifice and comparison with numerical simulations
Authors: Chen Yuming , Liu Shuangfeng , Kulenovic Rudi , Mertz Rainer
Published: September 2013

The formation of bubbles on an orifice plate involves a moving contact line, especially in case of poor wetting conditions. The dynamics of the moving contact line and contact angle have a significant impact on the bubble departure size. This work presents visualization and numerical simulations on gas bubble formation on submerged orifices of different wettabilities and diameters. The transient bubble shape (image), departure diameter, contact line diameter, apparent contact angle, neck diameter, and neck height are obtained under various conditions. Under certain wetting and flow conditions, the relationship between moving contact line and apparent contact angle can be relatively well defined. However, this relationship cannot be generalized for other conditions. Two kinds of contact line models have been re-evaluated against experiments, one is a contact line velocity dependent model (Model-A) and the other is a stick-slip model (Model-B). Numerical simulations were performed using Model-B and the results show good agreement with the experiments. The bubble formation data provided are useful for supporting and verifying the numerical simulations.
Elastic, superconducting, and thermodynamic properties of the cubic metallic phase of AlH3 via first-principles calculations
Authors: Wei Yong-Kai , Ge Ni-Na , Ji Guang-Fu , Chen Xiang-Rong , Cai Ling-Cang , Zhou Su-Qin , Wei Dong-Qing
Published: September 2013

The lattice dynamic, elastic, superconducting, and thermodynamic properties of the high-pressure cubic metallic phase AlH3 are studied within density function theory. The calculated elastic modulus and phonon dispersion curves at various pressures indicate that the cubic phase is both mechanically and dynamically stable above 73 GPa. The superconducting transition temperature was calculated using Allen-Dynes modification of the McMillan formula based on the Bardeen-Cooper-Schrieffer theory. It is found that Tc approaches a linear decrease in the low pressure range at the rate dTC/dP≈−0.22 K/GPa but gradually decreases exponentially at higher pressure, and then it becomes 0 K upon further compression. The calculations indicate that Tc is about 2.042 K at 110 GPa, in agreement with experimental results. The soft phonon modes, especially the lowest acoustic mode, contribute almost 79% to the total electron-phonon coupling parameter sλ for cubic AlH3 at 73 GPa. However, they disappear gradually with increasing pressure, showing a responsibility for the variation of Tc. The thermodynamic properties of cubic AlH3, such as the dependence of thermal expansion coefficient αV on pressure and temperature, the specific heat capacity CP, as well as the electronic specific heat coefficient Cel, were also investigated by the quasi-harmonic approximation theory.
Formation and propagation of meter-scale laser filaments in water
Authors: Helle M. H. , Jones T. G. , Peñano J. R. , Kaganovich D. , Ting A.
Published: September 2013

We report the demonstration, characterization, and modeling of meter-scale underwater optical filaments using a nanosecond pulsed laser. We observed single filament formation for P/PCRIT = 1–5, where PCRIT ∼ 1 MW in water. We employed a variable distance water tube to characterize laser pulse evolution and filament formation. Filaments with uniform radius 50 ± 10 μm persisted for 55 cm (>35 Rayleigh lengths). Significant forward Stimulated Raman Scattering (up to 60%) was observed and characterized. Simulation results for propagation distances and radii were in agreement with experiment, and predict a structured plasma with peak density of 1.5 × 1018 cm−3.
Comparison of the structural and chemical composition of two unique micro/nanostructures produced by femtosecond laser interactions on nickel
Authors: Zuhlke Craig A. , Anderson Troy P. , Alexander Dennis R.
Published: September 2013

The structural and chemical composition of two unique microstructures formed on nickel, with nanoscale features, produced using femtosecond laser surface processing (FLSP) techniques is reported in this paper. These two surface morphologies, termed mounds and nanoparticle-covered pyramids, are part of a larger class of self-organized micro/nanostructured surfaces formed using FLSP. Cross-sections of the structures produced using focused ion beam milling techniques were analyzed with a transmission electron microscope. Both morphologies have a solid core with a layer of nanoparticles on the surface. Energy dispersive X-ray spectroscopy by scanning transmission electron microscopy studies reveal that the nanoparticles are a nickel oxide, while the core material is pure nickel.
Enhanced 4f-3d interaction by Ti-doping on the magnetic properties of perovskite SmFe1−xTixO3
Authors: Zhao Huazhi , Cao Shixun , Huang Ruoxiang , Ren Wei , Yuan Shujuan , Kang Baojuan , Lu Bo , Zhang Jincang
Published: September 2013

We report the Ti-doping effects on the total magnetization of perovskite SmFe1−xTixO3 samples with x = 0, 0.1, 0.2, and 0.3. X-ray diffraction and Raman spectroscopy studies indicate that with the increase of Ti doping concentration, the lattice parameter b decreases and the oxygen octahedron is compressed along b axis. Such lattice distortion is also reflected by the changes of antisymmetric stretching mode and symmetric stretching mode of the oxygen octahedron through Raman spectra measurement. An enhancement of the interaction between Sm-4f and Fe-3d electrons is observed due to Ti-doping. This strong interplay between Sm-4f and Fe-3d electrons weakens the total magnetization and considerably suppresses the weak ferromagnetism of Fe sublattice starting from 260 K.
Ultrahigh-Q, largely deformed microcavities coupled by a free-space laser beam
Authors: Shao Linbo , Wang Li , Xiong Wenjie , Jiang Xue-Feng , Yang Qi-Fan , Xiao Yun-Feng
Published: September 2013

We experimentally report the fabrication of deformed silica microtoroids with only one-axial symmetry and very large deformation reaching 18%. The largely deformed microcavities are demonstrated to support ultrahigh-Q resonant modes exceeding 6 × 107, though much more chaos emerges compared with slightly deformed microcavities. The chaotic behavior of rays is beneficial to enhance dynamical tunneling to high-Q whispering-gallery modes, and therefore allows efficient coupling by a free-space laser beam. The largely deformed microcavities hold great potential in applied photonics and fundamental studies.
Noise sources and competition between stimulated Brillouin and Raman scattering: A one-dimensional steady-state approach
Authors: Gong Tao , Li Zhichao , Zhao Bin , Hu Guang-yue , Zheng Jian
Published: September 2013

A 1D steady-state model is developed to deal with stimulated scattering processes. The volume and boundary noise sources for scattered light are discussed in detail. Our results indicate that the boundary noise sources may play a significant role in estimating the reflectivity of stimulated Brillouin scattering (SBS) and stimulated Raman scattering (SRS). With the capability of our model to deal with broadband scattered light, we find that pump depletion could be the main reason to the anti-correlation between SBS and SRS versus electron density observed in experiments. A simple method is proposed to phenomenologically include the effect of nonlinear saturation mechanisms in our model and reasonable results are obtained.
In-situ localized carbon nanotube growth inside partially sealed enclosures
Authors: van de Burgt Y. , Champion A. , Bellouard Y.
Published: September 2013

Carbon nanotube assemblies can be used for specific applications such as sensors and filters. We present a method and proof-of-concept to directly grow vertically-aligned carbon nanotube structures within sealed enclosures by means of a feedback-controlled laser-assisted chemical vapor deposition technique. The process is compatible with a variety of micro-fabrication processes and bypasses the need for post-process packaging. Our experiments raise interesting observations related to the gas diffusion dynamics in micro-scale and sub-micron enclosures.
Low temperature ac electrical study of Pr0.5−xLaxCa0.5MnO3 (x = 0.0–0.4) ceramics by employing impedance spectroscopy
Authors: Javid Iqbal M. , Nadeem M. , Hassan M. M.
Published: September 2013

Polycrystalline Pr0.5−xLaxCa0.5MnO3 (x = 0.0–0.40) ceramics are synthesized by conventional solid state reaction method, and phase purity is confirmed by employing X-ray diffraction. Temperature dependent ac impedance spectroscopic measurements enable us to determine an increasing trend in resistance values of these samples with the decrease in temperatures. However, a decreasing trend in resistance values with increase in the La-doping at Pr-site is observed. A metal to insulator transition (MIT) is reported for x ≥ 0.2, which is shifted to higher temperature values with further increase of x doping. Two equivalent circuit models, i.e., (ReQe)(RgbQgb) and (ReQe)(RgbQgb)(RgQg) are employed to explain the impedance data with and without MIT, respectively. Mott variable range hopping model is found to be an appropriate model for defining the conduction mechanism of charge carriers in the semiconducting region. The decrease in the impedance with x doping is explained in terms of increase in the localization length obtained from the fitting of Rgb. Using tanδ results, thermally activated relaxation behavior is discussed for x = 0.0 and 0.1; whereas for x = 0.2, a temperature independent relaxation behavior is conferred due to the change in the hopping process of charge carriers.
Metamaterial based embedded acoustic filters for structural applications
Authors: Zhu Hongfei , Semperlotti Fabio
Published: September 2013

We investigate the use of acoustic metamaterials to design structural materials with frequency selective characteristics. By exploiting the properties of acoustic metamaterials, we tailor the propagation characteristics of the host structure to effectively filter the constitutive harmonics of an incoming broadband excitation. The design approach exploits the characteristics of acoustic waveguides coupled by cavity modes. By properly designing the cavity we can tune the corresponding resonant mode and, therefore, coupling the waveguide at a prescribed frequency. This structural design can open new directions to develop broadband passive vibrations and noise control systems fully integrated in structural components.
Spatial dynamics of the Argentine sandperch, Pseudopercis semifasciata (Pinguipedidae), in temperate rocky reefs from northern Patagonia, Argentina
Authors: Venerus Leonardo A. , Irigoyen Alejo J. , Galván David E. , Parma Ana M.
Published: September 2013

The choice of appropriate conservation strategies for reef fishes depends on their mobility, degree of site fidelity and residence times. Here we report the results of a small-scale mark–recapture and resighting study conducted to investigate the spatial dynamics of the Argentine sandperch, Pseudopercis semifasciata. This is the flagship species of the rocky-reef fish assemblage from northern Patagonia, which has been the target of uncontrolled fishing since the early 1950s. About 19% of the fish tagged were recaptured up to four years after tagging. In total, 180 of 218 recaptured fish stayed in the reef of tagging. Thirty-six of 57 recaptures made at known locations within popular fishing areas of San José Gulf, densely covered by patchy reefs, occurred within 100 m of the tagging site, up to 793 days after tagging. Six fish were recovered more than 1 km from where they were tagged. Smaller fish were more prone to relocate, and were recovered farther from the tagging site. Fish stayed in the reefs for periods longer than a year; larger males remained longer in the same reefs. Our results indicate that relatively small reserves (in the order of a few kilometres) could be effective at protecting P. semifasciata populations within the northern Patagonian gulfs.
Resource partitioning and habitat-specific dietary plasticity of two estuarine sparid fishes increase food-web complexity
Authors: Sheaves Marcus , Sheaves Janine , Stegemann Krista , Molony Brett
Published: September 2013

The diets of the co-occurring sparid fishes Acanthopagrus australis and A. pacificus were investigated to assess dietary overlap and resource partitioning, the extent of spatial variation and implications for the complexity of trophic interactions in tropical estuaries. Both species consumed a wide variety of prey, including bivalves, gastropods, crustaceans and polychaetes. There were clear differences in diet among sites separated by less than a kilometre. Site-specific substrata determined prey type, so diets at sites within a sandy bay were comprised largely of benthic infauna, whereas those at mangrove-lined sites contained substantial amounts of mangrove-associated prey. Although there was general dietary overlap between the two species, their diets differed substantially at any one site when viewed at a fine taxonomic resolution. A. pacificus displayed a very region- and site-specific diet, apparently feeding in different, and spatially separate, food chains at these different locations. Its main prey varied markedly among sites, seemingly because of habitat differences. By feeding in different food chains (and potentially different food webs) at different points in space and time, species such as A. pacificus have the potential both to link food webs operating in a variety of habitats and to add substantially to the complexity of tropical estuarine food webs.
Do food quantity and quality affect food webs in streams polluted by acid mine drainage?
Authors: Hogsden Kristy L. , Winterbourn Michael J. , Harding Jon S.
Published: September 2013

Food influences the structure of consumer communities; however, in polluted streams food resources may be severely reduced and act as an additional stressor. We examined the quantity and quality of basal resources and prey items for invertebrate consumers in 12 streams along an acid mine drainage (AMD) gradient (pH range: 2.7–7.1) and characterised their diets using stable isotope and gut content analyses. Algal and detrital resource quantity (biomass) and quality (C : N ratio) did not differ significantly along the gradient, except algal C : N, which was lower in highly stressed and circumneutral streams. Furthermore, availability, size and diversity of animal prey decreased significantly with increasing stress. Most primary consumers were generalist feeders, but algae became increasingly common in their diets as pH increased. Predators were opportunistic and consumed prey that reflected locally abundant taxa. Generally, these were small-bodied chironomids in highly stressed streams and larger-bodied prey (mayflies, caddisflies, stoneflies) in moderately stressed and circumneutral streams. Our results indicated that acidity and metal toxicity were the primary stressors of communities in streams affected by AMD and that food quantity was unlikely to be limiting for primary consumers. However, food availability may be an additional stressor affecting predators in streams receiving AMD.
Impact of long-term wheat production management practices on soil acidity, phosphorus and some micronutrients in a semi-arid Plinthosol
Authors: Loke P. F. , Kotzé E. , Du Preez C. C.
Published: September 2013

Farmers continuously remove crop residues for use as building materials, fuel and animal feed or bedding as well as to avoid difficulties during tillage operations. Therefore, demonstrations of the benefits of recycling crop residues are necessary. The aim with this study was to evaluate the influence of different wheat production management practices on acidity and some essential nutrients from a long-term trial on a Plinthosol in semi-arid South Africa. The trial was set up in 1979, and since then two methods of straw management (unburned and burned), three methods of tillage (no-tillage, stubble mulch, and plough), two methods of weed control (chemical and mechanical), and three levels of nitrogen (N) fertiliser (20, 40 and 60 kg ha–1) have been applied. Soil samples were collected in June 2010 at depths of 0–50, 50–100, 100–150, 150–250, 250–350 and 350–450 mm from plots that received 40 kg N ha–1 and were analysed for pH, phosphorus (P), copper (Cu), iron (Fe), manganese (Mn) and zinc (Zn).
Results obtained showed that straw burning resulted in higher P and Mn but lower Cu than no-burning. No-tillage, and to some extent stubble mulch, suppressed soil acidification and increased P and Zn compared with ploughing, especially in the surface layers where crop residues accumulate. In contrast, mouldboard ploughing and stubble mulch increased Cu more than no-tillage, possibly due to the strong affinity of organic matter for Cu. Tillage effects on Mn were inconsistent and difficult to explain. Chemical weeding also improved P, probably because of the pesticide application, but resulted in lower pH and Cu values compared with mechanical weeding. Treatment combinations also had an influence on P and, to a lesser extent, on soil pH and Cu, which might be due to the higher organic matter present in no-tilled soils. Irrespective of straw management or weed-control methods, no-tillage resulted in higher P than did ploughing and stubble mulch. Nutrient concentrations and pH values were sufficient for wheat growth under all treatments. However, although the nutrients were highest under straw burning, no-tillage and, to some extent, stubble mulch, wheat yield was higher with unburned straw and mouldboard ploughing. Therefore, an integrated approach from various disciplines is recommended to identify and rectify yield-limiting factors under conservation tillage systems.
Short- and mid-term tillage-induced soil CO2 efflux on irrigated permanent- and conventional-bed planting systems with controlled traffic in southern Spain
Authors: Cid Patricio , Pérez-Priego Oscar , Orgaz Francisco , Gómez-Macpherson Helena
Published: September 2013

Use of permanent beds combined with controlled traffic (PB) has been proposed as an alternative planting system for reducing soil erosion and compaction while increasing soil organic carbon (SOC) in irrigated, annual-crop based systems in Mediterranean conditions. The objective of this study was to characterise, in space (beds and furrows with and without traffic) and time (hours, days, and weeks), soil CO2 efflux in PB compared with conventionally tilled bed planting (CB) and with a variant of PB in which subsoiling was performed in trafficked furrows (DPB). The three treatments were combined with controlled traffic. Tillage resulted in abrupt CO2 effluxes that lowered rapidly within hours. However, in CB, soil CO2 effluxes increased again significantly 12 days after tillage compared with PB or DPB. These differences were due to higher emissions from beds than from furrows where the soil had been compacted during the harrowing that formed the beds. In DPB, CO2 effluxes increased in furrows with traffic after subsoiling and the effect was maintained during the study despite subsequent traffic. Soil CO2 efflux increased with soil temperature (measured concomitantly) except after soil tillage. Tillage reduced SOC in both CB and DPB compared with PB.
Ionizing irradiation-induced radical stress stalls live meiotic chromosome movements by altering the actin cytoskeleton
Authors: Illner Doris , Scherthan Harry
Published: September 2013

Significance

Sexual reproduction depends on breaking, pairing, and repairing the parental chromosomes by homologous recombination. Homologs are separated in the meiosis I division whose prophase sees extraordinary chromosome mobility in the presence of physiological dsDNA breaks (DSBs). Ionizing radiation (IR) induces unscheduled DSBs and radicals. The G2 and meiotic prophase of yeast is particularly resistant to IR with efficient cell killing requiring doses of up to 1,000 Gy. This investigation discloses that low-dose X irradiation stalls meiotic chromosome mobility via IR-induced oxidative damage to the actin cytoskeleton, while IR-induced DSBs persist in the presence of antioxidants. Altogether, the data disclose a unique low-dose radiation response in yeast that may protect IR-damaged meiotic chromosomes from unwanted interactions.
Public goods dilemma in asexual ant societies
Authors: Dobata Shigeto , Tsuji Kazuki
Published: September 2013

Significance

This study reports experimental evidence for the “public goods dilemma” between cooperators and cheaters in an asexual ant society, in which cheating is always more rewarding for individuals but cooperation at the cost of individual fitness leads to better performance of groups. Although this dilemma provides the basic principle of social evolution, its experimental demonstration with underlying genetics and fitness evaluation for both cooperators and cheaters still lacks in societies other than microbial ones. By showing the striking evolutionary convergence between microbial societies and insect societies in fitness consequences and in phenotypic plasticity of cooperators against cheaters, our result suggests that a wide range of scales of cooperative systems could be understood in a unified manner.
Bacterial cytological profiling rapidly identifies the cellular pathways targeted by antibacterial molecules
Authors: Nonejuie Poochit , Burkart Michael , Pogliano Kit , Pogliano Joe
Published: September 2013

Significance

Some bacteria have evolved resistance to nearly every known class of antibiotic, creating an urgent need for new ones that work by different mechanisms. However, there has been no simple way to determine how new antibiotics work. We have developed a unique method that provides a shortcut for understanding how antibiotics kill bacteria. This method can be used to sift through compounds to rapidly identify and characterize antibiotics that work against multidrug-resistant pathogens.
Entropic factors provide unusual reactivity and selectivity in epoxide-opening reactions promoted by water
Authors: Byers Jeffery A. , Jamison Timothy F.
Published: September 2013

Significance

Mechanistic studies of a water-promoted cyclization reaction reveal that an unusual, multifaceted interaction between the organic substrate and water causes an otherwise disfavored chemical reaction. The combination of several factors leads to the unusual selectivity and highlights the beneficial features of water as a solvent in organic chemistry. Of particular importance is organization of the substrate, which is facilitated by synergistic interactions between the surprisingly simple organic substrate and water. In addition to providing insight into these important interactions, the results may be relevant to the biosynthetic origins of the ladder polyether natural products. These natural products are potent neurotoxins and are the active constituents of harmful algae blooms commonly referred to as “red tide.”
TRA-1 ChIP-seq reveals regulators of sexual differentiation and multilevel feedback in nematode sex determination
Authors: Berkseth Matt , Ikegami Kohta , Arur Swathi , Lieb Jason D. , Zarkower David
Published: September 2013

Significance

Sex-determining genes have been identified in many animals, but how they impose sex specificity on development is poorly understood. We ask how the nematode sex-determining transcription factor Transformer 1 (TRA-1) regulates sex by identifying where in the genome TRA-1 binds and which nearby genes may be affected by this binding. We find that TRA-1 promotes female development primarily by preventing the expression of genes involved in male development. Among the genes repressed by TRA-1 are a number that control the timing of developmental events and also several that function upstream of TRA-1 in the global sex-determination pathway. The suite of TRA-1 targets presented here provides a resource to continue uncovering the basis of sex-specific development.
Vintages of theSāqī-nāma: Fermenting and Blending the Cupbearer's Song in the Sixteenth Century
Authors: Losensky Paul
Published: September 2013

Drawing on a rich tradition of anacreontic poetry and taking inspiration from works by Nizāmī and Hāfiz, thesāqī-nāmaor “cupbearer's song” emerged as an independent genre in the early sixteenth century and flourished throughout the Persian literary world for the next 250 years. Looking back on the development of the genre, the early seventeenth-century literary historians ‘Abd al-Nabī Qazvīnī and Awhadī Balyānī give contrasting accounts of its formation, but both agree on the significance of the work of Hakīm Partuvī Shīrāzī (d. 928/1520–21). An examination of hissāqī-nāma, together with two other early representatives of the genre by Sidqī Astarābādī (d. 952/1545) and Sharaf Jahān Qazvīnī (d. 968/1561), shows how closely this new genre was tied to the politics and ideology of the new Safavid state and reveals profound structural similarities to the preeminent panegyric genre of the Islamicate world, theqasīda. But once the basic components of thesāqī-nāmāwere distilled and taken up by poets outside this socio-political environment, the genre proved to be as protean as the wine symbolism at its core. Cupbearer songs from the end of the century, particularly those of Muhammad Sūfī Māzandarānī (d. 1035/1625–26) and Sanjar Kāshānī (d. 1021/1612), show how the basic elements of the genre could be reconfigured to serve a variety of more personal interests.
Use of autocorrelation scanning in DNA copy number analysis
Authors: Zhang Liangcai , Zhang Li
Published: September 2013

Motivation: Data quality is a critical issue in the analyses of DNA copy number alterations obtained from microarrays. It is commonly assumed that copy number alteration data can be modeled as piecewise constant and the measurement errors of different probes are independent. However, these assumptions do not always hold in practice. In some published datasets, we find that measurement errors are highly correlated between probes that interrogate nearby genomic loci, and the piecewise-constant model does not fit the data well. The correlated errors cause problems in downstream analysis, leading to a large number of DNA segments falsely identified as having copy number gains and losses.

Method: We developed a simple tool, called autocorrelation scanning profile, to assess the dependence of measurement error between neighboring probes.

Results: Autocorrelation scanning profile can be used to check data quality and refine the analysis of DNA copy number data, which we demonstrate in some typical datasets.

Contact:  lzhangli@mdanderson.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Integrated profiling of three dimensional cell culture models and 3D microscopy
Authors: Bilgin Cemal Cagatay , Kim Sun , Leung Elle , Chang Hang , Parvin Bahram
Published: September 2013

Motivation: Our goal is to develop a screening platform for quantitative profiling of colony organizations in 3D cell culture models. The 3D cell culture models, which are also imaged in 3D, are functional assays that mimic the in vivo characteristics of the tissue architecture more faithfully than the 2D cultures. However, they also introduce significant computational challenges, with the main barriers being the effects of growth conditions, fixations and inherent complexities in segmentation that need to be resolved in the 3D volume.

Results: A segmentation strategy has been developed to delineate each nucleus in a colony that overcomes (i) the effects of growth conditions, (ii) variations in chromatin distribution and (iii) ambiguities formed by perceptual boundaries from adjacent nuclei. The strategy uses a cascade of geometric filters that are insensitive to spatial non-uniformity and partitions a clump of nuclei based on the grouping of points of maximum curvature at the interface of two neighboring nuclei. These points of maximum curvature are clustered together based on their coplanarity and proximity to define dissecting planes that separate the touching nuclei. The proposed curvature-based partitioning method is validated with both synthetic and real data, and is shown to have a superior performance against previous techniques. Validation and sensitivity analysis are coupled with the experimental design that includes a non-transformed cell line and three tumorigenic cell lines, which covers a wide range of phenotypic diversity in breast cancer. Colony profiling, derived from nuclear segmentation, reveals distinct indices for the morphogenesis of each cell line.

Availability: All software are developed in ITK/VTK and are available at https://vision.lbl.gov/Software/3DMorphometry.

Contact:  b_parvin@lbl.gov or hchang@lbl.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bridging the gap between transcriptome and proteome measurements identifies post-translationally regulated genes
Authors: Gunawardana Yawwani , Niranjan Mahesan
Published: September 2013

Motivation: Despite much dynamical cellular behaviour being achieved by accurate regulation of protein concentrations, messenger RNA abundances, measured by microarray technology, and more recently by deep sequencing techniques, are widely used as proxies for protein measurements. Although for some species and under some conditions, there is good correlation between transcriptome and proteome level measurements, such correlation is by no means universal due to post-transcriptional and post-translational regulation, both of which are highly prevalent in cells. Here, we seek to develop a data-driven machine learning approach to bridging the gap between these two levels of high-throughput omic measurements on Saccharomyces cerevisiae and deploy the model in a novel way to uncover mRNA-protein pairs that are candidates for post-translational regulation.

Results: The application of feature selection by sparsity inducing regression (l1 norm regularization) leads to a stable set of features: i.e. mRNA, ribosomal occupancy, ribosome density, tRNA adaptation index and codon bias while achieving a feature reduction from 37 to 5. A linear predictor used with these features is capable of predicting protein concentrations fairly accurately (). Proteins whose concentration cannot be predicted accurately, taken as outliers with respect to the predictor, are shown to have annotation evidence of post-translational modification, significantly more than random subsets of similar size . In a data mining sense, this work also shows a wider point that outliers with respect to a learning method can carry meaningful information about a problem domain.

Contact:  mn@ecs.soton.ac.uk
The puzzling radio source in the cool core cluster A2626
Authors: Gitti M.
Published: September 2013

We report on new Very Large Array (VLA) radio observations performed at 1.4 and 4.8 GHz with unprecedented sensitivity and angular resolution (∼1 arcsec) of the cool core cluster A2626, which is known to possess a radio mini-halo at its centre. The most unusual features of A2626 are two elongated radio features detected in previous observations to the north and south, having morphologies not common to the typical jet-lobe structures in cool cores. In our new sensitive images the two elongated features appears clearly as bright radio arcs, and we discover the presence of a new arc to the west. These radio arcs are not detected at 4.8 GHz, implying a steep (α > 1) spectrum, and their origin is puzzling. After subtracting the flux density contributed by these discrete features from the total flux measured at low resolution, we estimate a residual 18.0 ± 1.8 mJy flux density of diffuse radio emission at 1.4 GHz. We therefore confirm the detection of diffuse radio emission, which appears distinct from the discrete radio arcs embedded in it. Although its radio power is lower (1.4 × 1023 W Hz−1) than previously known, the diffuse emission may still be classified as a radio mini-halo.
Treating Thin Stillage and Condensed Distillers Solubles with Phytase for Production of Low‐Phytate Coproducts
Authors: Liu Keshun
Published: September 2013

Fuel ethanol production from grains is mainly based on dry‐grind processing, during which phytate is concentrated about threefold in distillers dried grains with solubles (DDGS), a major coproduct. To reduce phytate in DDGS, Natuphos and Ronozyme industrial phytase preparations were used to treat commercially made thin stillage (TS). Changes in phosphorous (P) profile were monitored, and effects of reaction temperature, time, and enzyme concentration were investigated. Results showed that at a temperature ≤60°C for Natuphos phytase (≤70°C for Ronozyme phytase) and a concentration ≤4.8 FTU/mL of TS for Natuphos phytase (≤48 FYT/mL for Ronozyme phytase), a complete phytate hydrolysis (phytate P decreased to 0) could be achieved within 5–60 min of enzymatic treatment. Reduction in phytate P was generally accompanied by increase in inorganic P, whereas total P remained relatively unchanged. When condensed distillers solubles (CDS), the concentrated form of TS, was used as the substrate, phytate hydrolysis by each of the two enzyme preparations was as effective as on TS. Because a previous study from the author's laboratory showed that all types of P are mostly concentrated in TS and CDS but much less in distillers wet grains, phytase treatments of TS and CDS described in the present study can be an effective means in producing low‐phytate DDGS.
The Tomato Kinome and the Tomato Kinase Library ORFeome: Novel Resources for the Study of Kinases and Signal Transduction in Tomato and Solanaceae Species
Authors: Singh Dharmendra K. , Calviño Mauricio , Brauer Elizabeth K. , Fernandez-Pozo Noe , Strickler Susan , Yalamanchili Roopa , Suzuki Hideyuki , Aoki Koh , Shibata Daisuke , Stratmann Johannes W. , Popescu George V. , Mueller Lukas A. , Popescu Sorina C.
Published: September 2013

Protein kinase–driven phosphorylation constitutes the core of cellular signaling. Kinase components of signal transduction pathways are often targeted for inactivation by pathogens. The study of kinases and immune signal transduction in the model crop tomato (Solanum lycopersicum) would benefit from the availability of community-wide resources for large scale and systems-level experimentation. Here, we defined the tomato kinome and performed a comprehensive comparative analysis of the tomato kinome and 15 other plant species. We constructed a tomato kinase library (TOKN 1.0) of over 300 full-length open reading frames (ORF) cloned into a recombination-based vector. We developed a high-throughput pipeline to isolate and transform tomato protoplasts. A subset of the TOKN 1.0 library kinases were expressed in planta, were purified, and were used to generate a functional tomato protein microarray. All resources created were utilized to test known and novel associations between tomato kinases and Pseudomonas syringae DC3000 effectors in a large-scale format. Bsk7 was identified as a component of the plant immune response and a candidate effector target. These resources will enable comprehensive investigations of signaling pathways and host-pathogen interactions in tomato and other Solanaceae spp.
Spatiotemporal Characterization of Sclerotinia Crown Rot Epidemics in Pyrethrum
Authors: Scott Jason B. , Gent David H. , Pethybridge Sarah J. , Hay Frank S.
Published: September 2013

Sclerotinia crown rot, caused by Sclerotinia minor and S. sclerotiorum, is a disease of pyrethrum in Australia that may cause substantial decline in plant density. The spatiotemporal characteristics of the disease were quantified in 14 fields during three growing seasons. Fitting the binary power law to disease incidence provided slope (b = 1.063) and intercept (ln(Ap) = 0.669) estimates significantly (P ≤ 0.0001) greater than 1 and 0, respectively, indicating spatial aggregation at the sampling unit scale that was dependent upon disease incidence. Covariate analyses indicated that application of fungicides did not significantly influence these estimates. Spatial autocorrelation and spatial analysis by distance indices indicated that spatial aggregation above the sampling unit scale was limited to 20 and 17% of transects analyzed, respectively. The range of significant aggregation was limited primarily to neighboring sampling units only. Simple temporal disease models failed to adequately describe disease progress, due to a decline in disease incidence in spring. The relationships between disease incidence at the scales of individual plants within quadrats and quadrats within a field was modeled using four predictors of sample size. The choice of the specific incidence–incidence relationship influenced the classification of disease incidence as greater than or less than 2% of plants, a provisional commercial threshold for fungicide application. Together, these studies indicated that epidemics of Sclerotinia crown rot were dominated by small-scale aggregation of disease. Larger scale patterns of diseased plants, when present, were associated with severe disease outbreaks. The spatial and temporal analyses were suggestive of disease epidemics being associated with localized primary inoculum and other factors that favor disease development at a small scale.
Characterization of Resistance to Pratylenchus thornei (Nematoda) in Wheat (Triticum aestivum): Attraction, Penetration, Motility, and Reproduction
Authors: Linsell Katherine Joanne , Riley Ian Timothy , Davies Kerrie Ann , Oldach Klaus Herbert
Published: September 2013

Lines from a cross between two wheat (Triticum aestivum) cultivars with contrasting resistance phenotypes to Pratylenchus thornei (Nematoda) were investigated to determine the stage at which resistance occurs. Host resistance was examined at nematode attraction to and penetration of roots and nematode motility, maturation, and reproduction within roots. There was no significant difference in the rate at which P. thornei was attracted toward or penetrated resistant or susceptible roots. However, suppression of migration, juvenile maturation, and reproduction in and near resistant roots was evident, suggesting that resistance acts post penetration. No preferential root penetration zone was observed in contrast to other studies. The inhibitory compounds from resistant wheat plants appeared to be constitutively expressed and water soluble because nematode migration was suppressed in roots and root exudates of unchallenged seedlings. The effects of these compounds were reversible and affected P. thornei but not P. neglectus. Apart from migration, nematode multiplication was greatly inhibited by resistance because only a few juveniles (10%) developed past stage three in roots of resistant compared with susceptible plants. Earlier in the life cycle, egg deposition and hatch of P. thornei were also significantly reduced in resistant roots and root exudates, suggesting the presence of hatching inhibitors.
Perioperative Auto-titrated Continuous Positive Airway Pressure Treatment in Surgical Patients with Obstructive Sleep Apnea
Authors: Liao Pu , Luo Quanwei , Elsaid Hisham , Kang Weimin , Shapiro Colin M. , Chung Frances
Published: September 2013

Background:

Obstructive sleep apnea (OSA) may worsen postoperatively. The objective of this randomized open-label trial is to determine whether perioperative auto-titrated continuous positive airway pressure (APAP) treatment decreases postoperative apnea hypopnea index (AHI) and improves oxygenation in patients with moderate and severe OSA.

Methods:

The consented patients with AHI of more than 15 events/h on preoperative polysomnography were randomized into the APAP or control group (receiving routine care). The APAP patients received APAP for 2 or 3 preoperative, and 5 postoperative nights. All patients were monitored with oximetry for 7 to 8 nights (N) and underwent polysomnography on postoperative N3. The primary outcome was AHI on the postoperative N3.

Results:

One hundred seventy-seven OSA patients undergoing orthopedic and other surgeries were enrolled (APAP: 87 and control: 90). There was no difference between the two groups in baseline data. One hundred six patients (APAP: 40 and control: 66) did polysomnography on postoperative N3, and 100 patients (APAP: 39 and control: 61) completed the study. The compliance rate of APAP was 45%. The APAP usage was 2.4–4.6 h/night. In the APAP group, AHI decreased from preoperative baseline: 30.1 (22.1, 42.5) events/h (median [25th, 75th percentile]) to 3.0 (1.0, 12.5) events/h on postoperative N3 (P < 0.001), whereas, in the control group, AHI increased from 30.4 (23.2, 41.9) events/h to 31.9 (13.5, 50.2) events/h, P = 0.302. No significant change occurred in the central apnea index.

Conclusions:

The trial showed the feasibility of perioperative APAP for OSA patients. Perioperative APAP treatment significantly reduced postoperative AHI and improved oxygen saturation in the patients with moderate and severe OSA.
Epidural Injections for Spinal Pain
Authors: Bicket Mark C. , Gupta Anita , Brown Charlie H. , Cohen Steven P.
Published: September 2013

Background:

Epidural steroid injection is the most frequently performed pain procedure. This study of epidural steroid “control” injections aimed to determine whether epidural nonsteroid injections constitute a treatment or true placebo in comparison with nonepidural injections for back and neck pain treatment.

Methods:

This systematic review with direct and indirect meta-analyses used PubMed and EMBASE searches from inception through October 2012 without language restrictions. Study selection included randomized controlled trials with a treatment group receiving epidural injections of corticosteroids or another analgesic and study control groups receiving either an epidural injection devoid of treatment drug or a nonepidural injection. Two reviewers independently extracted data including short-term (up to 12 weeks) pain scores and pain outcomes. All reviewers evaluated studies for eligibility and quality.

Results:

A total of 3,641 patients from 43 studies were included in this systematic review and meta-analysis. Indirect comparisons suggested epidural nonsteroid were more likely than nonepidural injections to achieve positive outcomes (risk ratio, 2.17; 95% CI, 1.87–2.53) and provide greater pain score reduction (mean difference, −0.15; 95% CI, −0.55 to 0.25). In the very limited direct comparisons, no significant differences were noted between epidural nonsteroid and nonepidural injections for either outcome (risk ratio [95% CI], 1.05 [0.88–1.25]; mean difference [95% CI], 0.22 [−0.50 to 0.94]).

Conclusion:

Epidural nonsteroid injections may provide improved benefit compared with nonepidural injections on some measures, though few, low-quality studies directly compared controlled treatments, and only short-term outcomes (≤12 weeks) were examined.
Risk Stratification Tools for Predicting Morbidity and Mortality in Adult Patients Undergoing Major Surgery
Authors: Moonesinghe Suneetha Ramani , Mythen Michael G. , Das Priya , Rowan Kathryn M. , Grocott Michael P. W.
Published: September 2013

Risk stratification is essential for both clinical risk prediction and comparative audit. There are a variety of risk stratification tools available for use in major noncardiac surgery, but their discrimination and calibration have not previously been systematically reviewed in heterogeneous patient cohorts.

Embase, MEDLINE, and Web of Science were searched for studies published between January 1, 1980 and August 6, 2011 in adult patients undergoing major noncardiac, nonneurological surgery. Twenty-seven studies evaluating 34 risk stratification tools were identified which met inclusion criteria. The Portsmouth-Physiology and Operative Severity Score for the enUmeration of Mortality and the Surgical Risk Scale were demonstrated to be the most consistently accurate tools that have been validated in multiple studies; however, both have limitations. Future work should focus on further evaluation of these and other parsimonious risk predictors, including validation in international cohorts. There is also a need for studies examining the impact that the use of these tools has on clinical decision making and patient outcome.