bluuebunny/crossref_metadata_2025 huggingface dataset:
Heating Microscopy and its Applications
Authors: Venturelli Chiara
Published: January 2011

Heating microscopes were commercially introduced 60 years ago, and they immediately gained an important role in material science and engineering thanks to their wide field of application. Nowadays, these instruments are used in both industry and research in many sectors: traditional and advanced ceramic industries, the glass industry, power plants, the metallurgical sector, and, generally, in all fields where the melting behavior of materials has to be determined. Heating microscopy techniques can be successfully applied to the direct characterization of glazes, glasses, frits, ashes, mold powders for continuous casting, coals, slags, etc.—during a heat treatment.
Young rift kinematics in the Tadjoura rift, western Gulf of Aden, Republic of Djibouti
Authors: Daoud Mohamed A. , Le Gall Bernard , Maury René C. , Rolet Joël , Huchon Philippe , Guillou Hervé
Published: January 2011

The Tadjoura rift forms the westernmost edge of the westerly propagating Sheba ridge, between Arabia and Somalia, as it enters into the Afar depression. From structural and remote sensing data sets, the Tadjoura rift is interpreted as an asymmetrical south facing half‐graben, about 40 km wide, dominated by a large boundary fault zone to the north. It is partially filled up by the 1–3 Myr old Gulf Basalts which onlapped the older Somali Basalts along its shallower southern flexural margin. The major and trace element analysis of 78 young onshore lavas allows us to distinguish and map four distinct basaltic types, namely the Gulf, Somali, Goumarre, and Hayyabley Basalts. These results, together with radiometric age data, lead us to propose a revised volcano‐stratigraphic sketch of the two exposed Tadjoura rift margins and to discriminate and date several distinct fault networks of this oblique rift. Morphological and statistical analyses of onshore extensional fault populations show marked changes in structural styles along‐strike, in a direction parallel to the rift axis. These major fault disturbances are assigned to the arrest of axial fault tip propagation against preexisting discontinuities in the NS‐oriented Arta transverse zone. According to our model, the sinistral jump of rifting into the Asal‐Ghoubbet rift segment results from structural inheritance, in contrast with the en échelon or transform mechanism of propagation that prevailed along the entire length of the Gulf of Aden extensional system.
Integrating microbial community data with ecological theory
Authors: Allison Steven
Published: January 2011

Background/Question/Methods

Molecular and bioinformatics techniques are revealing the rich diversity of microbial communities. These approaches generate valuable data that ecologists could use to develop and test theories that apply to a large fraction of living organisms. However, the complexity of microbial community data is a challenge to achieving this integration. A fundamental question in microbial ecology is how to aggregate microbial communities so that their taxa may be represented in theoretical models. Recently, models based on microbial traits have been developed to tackle this question. Such models may represent microbial taxa as functional groups or stochastic assemblages with a distribution of trait values. Here, I define these two model types and show how they can be used to make predictions about the function of complex microbial communities. I focus on organic matter decomposition and nutrient mineralization because this function is typically driven by complex microbial communities.

Results/Conclusions

When applying ecological theory to predict rates of organic matter turnover, complex communities can be aggregated based on relevant traits, such as the ability to produce extracellular enzymes. Ecological and evolutionary theories provide a framework for predicting the distribution of these traits across time and space. For example, theories on ecological succession may predict the temporal progression of enzyme traits that occur in association with a decomposing substrate. Dispersal parameters from island biogeography theory may determine the movement of enzyme traits across the microbial landscape. Evolutionary theory can be used to predict the appearance and loss of enzyme traits due to selective pressures in microbial ecosystems. All of these theories then determine the abundance of particular functional groups, or the means and variances of trait distributions that directly affect ecological function. Functional group models may be useful in simple systems, but stochastic models based on distributions may be more relevant for complex communities with a diversity of continuous traits and many unidentified members.*The audio track for talks in this symposium may be obtained at the following web address:**https://sites.google.com/site/esa2010symposium13audiocontent/esa2010-symposium13-audio-content*
Development of Integrative Bioinformatics Applications using Cloud Computing resources and Knowledge Organization Systems (KOS).
Authors: Almeida Jonas , Deus Helena , Maass Wolfgang
Published: January 2011

Use of semantic web abstractions, in particular of domain neural Knowledge Organization Systems (KOS), to manage distributed, cloud based, integrative bioinformatics infrastructure. This presentation derives from recent publication:Almeida JS, Deus HF, Maass W. (2010) S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics. 2010 Jul 20;11(1):387. [PMID 20646315].These PowerPoint slides were presented at Semantic Web Applications and Tools for Life Sciences December 10th, 2010, Berlin, Germany (http://www.swat4ls.org/2010/progr.php), keynote 9-10 am.
High-pressure x-ray diffraction studies on the structure of liquid silicate using a Paris–Edinburgh type large volume press
Authors: Yamada Akihiro , Wang Yanbin , Inoue Toru , Yang Wenge , Park Changyong , Yu Tony , Shen Guoyin
Published: January 2011

An experimental setup for high-pressure liquid structure studies with synchrotron x-ray diffraction using the Paris–Edinburgh press has been installed at station 16-BM-B (HPCAT) of the Advanced Photon Source, Argonne National Laboratory. By collecting energy-dispersive data with a synchrotron white beam at various 2θ angles, the present device allows us to obtain the structure factor, S(Q), over a wide range of Q ( = 4πsinθ/λ) owing to the excellent angular accessibility up to 37° in 2θ and high energy photons well beyond 100 keV. We have successfully collected XRD data on silicate (albite, NaAlSi3O8) liquids with Q up to ∼22 Å−1 and pressure up to 5.3 GPa and temperature 1873 K, and obtained the radial distribution function, G(r), with a reasonable resolution. The T–O bond length (where T = Al, Si), which is a fundamental measure of local structure for aluminous silicate consisting of SiOn and AlOn polyhedra (tetrahedra at 1 atm condition), was found to be slightly shortened to 1.626 Å compared to that of glass at 1 atm. The T–O–T bound angle, which is the linkage of the above polyhedra, is the most responsible for densification. The T–O–T peak in G(r) splits into two peaks, suggesting a differentiation of the bond angle at high-pressure. The present technical development demonstrates that the Paris–Edinburgh press is suitable for studies of silicate liquids under high-pressure conditions.
Dipolar interactions in arrays of ferromagnetic nanowires: A micromagnetic study
Authors: Zighem Fatih , Maurer Thomas , Ott Frédéric , Chaboussant Grégory
Published: January 2011

We explore the behavior of periodic arrays of magnetic nanowires by micromagnetic simulations using the NMAG modeling package. A large number of modeling studies on such arrays of nanowires have been performed using finite size models. We show that these finite size micromagnetic descriptions can only be used in specific situations. We perform a systematic study of more or less dense one- and two-dimensional arrays of nanowires using either finite size or infinite size models and we show that finite size models fail to capture some of the features of real infinite systems. We show that the mean field model scaled to the system porosity is valid. This work can be used as a basis to the extension of micromagnetic calculations of the magnetization dynamics in arrays of nanowires.
Interface state energy distribution and Pb defects at Si(110)/SiO2 interfaces: Comparison to (111) and (100) silicon orientations
Authors: Thoan N. H. , Keunen K. , Afanas’ev V. V. , Stesmans A.
Published: January 2011

Traps at the (110)Si/SiO2 interface are investigated by combining electrical methods with electron spin resonance (ESR) measurements, and the results are compared to the well studied (100) and (111)Si/SiO2 interfaces. At all three Si crystal faces, the interface trap density Dit as function of energy E in the Si band gap exhibits two peaks at about 0.25 and 0.85 eV above the Si valence band, found to be well correlated with Pb(0) centers (Si3≡Si• defects). By comparing capacitance-voltage (CV) curves at 300 and 77 K of both n- and p-type samples, the Pb(0) defects are confirmed to be amphoteric. Effective passivation of interface traps by H2 annealing suggests that Pb0 defects are responsible for most of interface traps observed in (110)Si/SiO2. The truly amphoteric behavior, implying that one Pb0 defect delivers two interface trap levels, was observed for the (100) and (111)Si faces but not for the (110) face. The estimated interface trap density Nit at the (110)Si/SiO2 interface oxidized at 930 °C is (6.7±0.5)×1012, while the Pb0 density as determined by ESR is about (6±1)×1012 cm−2. Lowering of the oxidation temperature leads to further reduction in the electrically active Pb0 centers fraction at the (110)Si/SiO2 interface.
Ultrafast optical multidimensional spectroscopy without interferometry
Authors: Davis J. A. , Calhoun T. R. , Nugent K. A. , Quiney H. M.
Published: January 2011

We present here the details of a phase retrieval technique that provides access to multidimensional modalities that are not currently available using existing interferometric techniques. The development of multidimensional optical spectroscopy has facilitated significant insights into electronic processes in physics, chemistry, and biology. The versatility and number of available techniques are, however, significantly limited by the requirement that the detection be interferometric. Many of these techniques are closely related to the vast range of multidimensional NMR spectroscopies, which revolutionized analytical chemistry more than 30 years ago. We focus here on the specific case of two-color multidimensional spectroscopy (analogous to heteronuclear NMR) and discuss the details of an iterative algorithm that recovers the relative phase relationships required to perform the Fourier transformation and find the unique solution for the 2D spectrum. A detailed guide is provided that describes the practical implementation of such algorithms. The effectiveness and accuracy of the phase retrieval process are assessed for simulated one- and two-color experiments. It is also compared with one-color experimental data for which the target phase information has been obtained independently by interferometry. In all the cases, the present algorithm yields results that compare well with the solutions obtained by other means. There are, however, some limitations and potential pitfalls that are identified and discussed. We conclude with a discussion of the potential applications and further advances that may be possible by adopting iterative phase retrieval algorithms of the type discussed here.
Microstructure, optical, and scintillation characteristics of Pr3+ doped Lu3Al5O12 optical ceramics
Authors: Shi Yun , Nikl Martin , Feng Xiqi , Mares Jiri A. , Shen Yiqiang , Beitlerova A. , Kucerkova R. , Pan Yubai , Liu Qian
Published: January 2011

0.5, 1.0, and 5.0 at. % Pr3+ doped Lu3Al5O12 (Pr:LuAG) optical ceramics are fabricated and compared with Bi4Ge3O12 (BGO) and Pr:LuAG single crystals as for their optical, luminescence and scintillation properties. Radio-luminescence intensity of the fast UV emission based on 5d1→4f Pr3+ transition reaches up to 20 times of that of BGO single crystal reference scintillator. Photoelectron yield of the best performing 0.5 at. % Pr:LuAG ceramic sample is about 1002 phels/MeV, about 30% lower than that of BGO reference sample and about 65% lower than that of Pr:LuAG single crystal. The trapping phenomena at grain boundaries and/or structural defects are proposed as the main cause of degradation of the scintillation response of the Pr:LuAG optical ceramics.
The detection of terahertz waves by semimetallic and by semiconducting materials
Authors: Gouider F. , Nachtwei G. , Brüne C. , Buhmann H. , Vasilyev Yu. B. , Salman M. , Könemann J. , Buckle P. D.
Published: January 2011

We present a survey of photoresponse (PR) measurements of various devices containing quantum wells (QWs) of HgTe of various widths dQW and of InSb. By varying dQW for HgTe, the material properties of the QW material change from semiconducting to semimetallic as dQW is increased above a value of about 6nm. We have studied the PR of devices made from CdxHg1−xTe/HgTe/CdxHg1−xTe wafers with values of the QW width in the range of 6 nm≤dQW≤21 nm. Only for samples with semimetallic HgTe QWs, a measurable PR could be detected. However, our investigations of samples made from AlxIn1−xSb/InSb/AlxIn1−xSb wafers gave evidence that a measurable PR also can appear from devices with a semiconducting QW. Both cyclotron-resonant (CR) and nonresonant (bolometric, BO) interaction mechanisms can contribute to the PR signal. Whereas the CR contribution is dominant in AlxIn1−xSb/InSb/AlxIn1−xSb samples, in CdxHg1−xTe/HgTe/CdxHg1−xTe samples the behavior is more complex. In a sample with dQW=8 nm, the PR is clearly dominated by the BO contribution. In the PR of another sample of dQW=12 nm, both contributions (BO and CR) are present. The sample of dQW=21 nm shows a PR with not clearly separable BO and CR contributions.
Strong stress-enhanced diffusion in amorphous lithium alloy nanowire electrodes
Authors: Gao Y. F. , Zhou M.
Published: January 2011

Diffusion-induced stress (DIS) development and stress-enhanced diffusion (SED) in amorphous lithium alloy nanowire battery electrodes are investigated using a finite deformation model, accounting for full two-way coupling between diffusion and stress evolution. Analytical solutions are derived using a perturbation method. The analyses reveal significant contributions to the driving force for diffusion by stress gradient, an effect much stronger than those seen in cathode lattices but so far has been neglected for alloy-based anodes. The contribution of stress to diffusion is small at low lithium concentrations, this lack of SED leads to significantly higher DIS levels in early stages of a charging cycle. As lithium concentration increases, SED becomes more pronounced, leading to lower DIS levels. The long-term DIS level in the material scales with charging rate, nanowire radius, and the mobility of Li ions as modulated by the effect of stress. The solutions obtained provide guidance for lowering stresses during charging. In particular, lower charging rates should be used during the initial stages of charging cycles.
Intrinsic ambient ferromagnetism in ZnO:Co induced by Eu codoping
Authors: Assadi M. H. N. , Zhang Y. B. , Photongkam P. , Li S.
Published: January 2011

We manipulate the interaction of Co’s 3d and Eu’s 4f electrons to design and fabricate ZnO:Co+Eu, which possesses intrinsic ferromagnetism at ambient temperature. The results show that the Eu ions tend to neighboring Co ions in order to eliminate the lattice distortion caused by the larger Eu ions via strain coupling. It was also revealed that the preference of parallel spin alignment between Eu and Co ions results in ferromagnetism. The theoretical analyses and our experimental results evidenced that the induced ferromagnetism in the Eu and Co codoped ZnO is intrinsic at ambient temperature.
Metallic clusters in nonstoichiometric gallium oxide films
Authors: Petitmangin Aline , Hébert Christian , Perrière Jacques , Gallas Bruno , Binet Laurent , Barboux Philippe , Vermaut Philippe
Published: January 2011

Oxygen deficient gallium oxide films have been grown by pulsed-laser deposition. Depending on the growth conditions (oxygen pressure and laser power density), amorphous and insulating or partially crystalline and conducting gallium oxide films can be obtained. For very large oxygen deficiencies (Ga2O2.3), the oxide is not stable, and a phase separation leads to metallic Ga nanoparticles embedded in a stoichiometric Ga2O3 matrix. The resistivity measurements evidence the melting and freezing of Ga metallic nanoparticles in addition to their superconducting transition at low temperature. Due to small size both transitions are shifted as compared to the bulk properties.
Spatially resolved argon microplasma diagnostics by diode laser absorption
Authors: Miura Naoto , Hopwood Jeffrey
Published: January 2011

Microplasmas were diagnosed by spatially resolved diode laser absorption using the Ar 801.4 nm transition (1s5-2p8). A 900 MHz microstrip split ring resonator was used to excite the microplasma which was operated between 100–760 Torr (13–101 kPa). The gas temperatures and the Ar 1s5 line-integrated densities were obtained from the atomic absorption lineshape. Spatially resolved data were obtained by focusing the laser to a 30 μm spot and translating the laser path through the plasma with an xyz microdrive. At 1 atm, the microplasma has a warm core (850 K) that spans 0.2 mm and a steep gradient to room temperature at the edge of the discharge. At lower pressure, the gas temperature decreases and the spatial profiles become more diffuse.
Influence of surface roughness of aluminum-doped zinc oxide buffer layers on the performance of inverted organic solar cells
Authors: Cho Sung-Woo , Kim Young Tae , Shim Won Hyun , Park Sun-Young , Kim Kwang-Dae , Seo Hyun Ook , Dey Nilay Kumar , Lim Jae-Hong , Jeong Yongsoo , Lee Kyu Hwan , Kim Young Dok , Lim Dong Chan
Published: January 2011

Aluminum-doped zinc oxide (AZO) films (70 nm thick) with dissimilar surface roughness were created on indium tin oxide coated glass and were used as electrodes for inverted organic solar cells. The photovoltaic performance of the devices depended strongly on the surface roughness of the AZO films. Increases in the surface root-mean-square roughness of AZO films from 2.5 to 10.9 nm enhanced power conversion efficiency from 0.5% to 1.4% due to increased contact area between electrode and active layer.
Proposal for a topological plasmon spin rectifier
Authors: Appelbaum Ian , Drew H. D. , Fuhrer M. S.
Published: January 2011

We propose a device in which the spin-polarized ac plasmon mode in the surface state of a topological insulator nanostructure induces a static spin accumulation in a resonant, normal metal structure coupled to it. Using a finite-difference time-domain model, we simulate this spin-pump mechanism with drift, diffusion, relaxation, and precession in a magnetic field. This optically driven system can serve as a dc “spin battery” for spintronic devices.
Enhanced intermixing in Ge nanoprisms on groove-patterned Si(1 1 10) substrates
Authors: Chen G. , Vastola G. , Zhang J. J. , Sanduijav B. , Springholz G. , Jantsch W. , Schäffler F.
Published: January 2011

The morphological and compositional evolution of {105}-bounded SiGe nanoripples on groove-patterned Si(1 1 10) substrates is reported for varying groove widths. Enhanced Si-Ge intermixing between the nanoripples and the groove sidewalls is interpreted as the driving force for the observed increase of the ripple volume with decreasing groove width and for the reduction of the total number of ripples. Finite element simulations reveal that the enhanced intermixing arises from the minimization of the total energy density of the ripples. Our experiments and modeling suggest a direct route for controlling the composition of the nanoripples.
Social performance reveals unexpected vocal competency in young songbirds
Authors: Kojima Satoshi , Doupe Allison J.
Published: January 2011

Vocal ontogeny in songbirds provides a good model for understanding how complex motor behavior, including speech, is learned. For birdsong, as for other motor learning, it has generally been assumed that a subject's motor output at any point during learning represents what the subject has learned to produce by that time. Here, we show, however, that juvenile zebra finches partway through song learning, singing immature song, are capable of producing song with much more mature properties, depending on the behavioral context. In these birds, we were able to elicit courtship (female-directed) song, which young birds normally sing infrequently, and to compare it with the alone or “undirected” song (Undir) predominantly produced during learning as well as with the same bird's subsequent adult song. We found that the juvenile courtship song was much less variable than the immature Undir and as stereotyped as the adult song produced after a further month of practice. More strikingly, the juvenile courtship song was also acoustically much more similar than Undir to the adult song. This finding demonstrates that the Undir that juvenile birds usually produce underestimates the extent of learning and that song structure is learned faster than previously thought. Moreover, the rapid improvement in song quality in response to external social cues supports the idea that courtship singing is a state of motor “performance,” in which the bird selects the best variants of the song learned during singing alone, and suggests that such performance states can reveal unappreciated progression of learning.
Irradiation induces bone injury by damaging bone marrow microenvironment for stem cells
Authors: Cao Xu , Wu Xiangwei , Frassica Deborah , Yu Bing , Pang Lijuan , Xian Lingling , Wan Mei , Lei Weiqi , Armour Michael , Tryggestad Erik , Wong John , Wen Chun Yi , Lu William Weijia , Frassica Frank J.
Published: January 2011

Radiation therapy can result in bone injury with the development of fractures and often can lead to delayed and nonunion of bone. There is no prevention or treatment for irradiation-induced bone injury. We irradiated the distal half of the mouse left femur to study the mechanism of irradiation-induced bone injury and found that no mesenchymal stem cells (MSCs) were detected in irradiated distal femora or nonirradiated proximal femora. The MSCs in the circulation doubled at 1 week and increased fourfold after 4 wk of irradiation. The number of MSCs in the proximal femur quickly recovered, but no recovery was observed in the distal femur. The levels of free radicals were increased threefold at 1 wk and remained at this high level for 4 wk in distal femora, whereas the levels were increased at 1 wk and returned to the basal level at 4 wk in nonirradiated proximal femur. Free radicals diffuse ipsilaterally to the proximal femur through bone medullary canal. The blood vessels in the distal femora were destroyed in angiographic images, but not in the proximal femora. The osteoclasts and osteoblasts were decreased in the distal femora after irradiation, but no changes were observed in the proximal femora. The total bone volumes were not affected in proximal and distal femora. Our data indicate that irradiation produces free radicals that adversely affect the survival of MSCs in both distal and proximal femora. Irradiation injury to the vasculatures and the microenvironment affect the niches for stem cells during the recovery period.
Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus
Authors: Chen Dong-Hua , Baker Matthew L. , Hryc Corey F. , DiMaio Frank , Jakana Joanita , Wu Weimin , Dougherty Matthew , Haase-Pettingell Cameron , Schmid Michael F. , Jiang Wen , Baker David , King Jonathan A. , Chiu Wah
Published: January 2011

Formation of many dsDNA viruses begins with the assembly of a procapsid, containing scaffolding proteins and a multisubunit portal but lacking DNA, which matures into an infectious virion. This process, conserved among dsDNA viruses such as herpes viruses and bacteriophages, is key to forming infectious virions. Bacteriophage P22 has served as a model system for this study in the past several decades. However, how capsid assembly is initiated, where and how scaffolding proteins bind to coat proteins in the procapsid, and the conformational changes upon capsid maturation still remain elusive. Here, we report Cα backbone models for the P22 procapsid and infectious virion derived from electron cryomicroscopy density maps determined at 3.8- and 4.0-Å resolution, respectively, and the first procapsid structure at subnanometer resolution without imposing symmetry. The procapsid structures show the scaffolding protein interacting electrostatically with the N terminus (N arm) of the coat protein through its C-terminal helix-loop-helix motif, as well as unexpected interactions between 10 scaffolding proteins and the 12-fold portal located at a unique vertex. These suggest a critical role for the scaffolding proteins both in initiating the capsid assembly at the portal vertex and propagating its growth on a
T
 = 7 icosahedral lattice. Comparison of the procapsid and the virion backbone models reveals coordinated and complex conformational changes. These structural observations allow us to propose a more detailed molecular mechanism for the scaffolding-mediated capsid assembly initiation including portal incorporation, release of scaffolding proteins upon DNA packaging, and maturation into infectious virions.
Reactive oxygen species are indispensable in ovulation
Authors: Shkolnik Ketty , Tadmor Ari , Ben-Dor Shifra , Nevo Nava , Galiani Dalia , Dekel Nava
Published: January 2011

Ovulation is stimulated by the preovulatory surge of the pituitary luteinizing hormone (LH). Because the ovulatory response is commonly identified with inflammation, we explored the involvement of reactive oxygen species (ROS) in this process. Our experiments show that administration of broad-range scavengers of oxidative species into the ovarian bursa of mice, hormonally induced to ovulate, significantly reduced the rate of ovulation. LH-induced cumulus mucification/expansion, a necessary requirement for ovulation, was prevented by antioxidants both in vivo and in an ex vivo system of isolated intact ovarian follicles. Along this line, H
2
O
2
fully mimicked the effect of LH, bringing about an extensive mucification/expansion of the follicle-enclosed cumulus–oocyte complexes. Impaired progesterone production was observed in isolated follicles incubated with LH in the presence of the antioxidant agents. Furthermore, LH-stimulated up-regulation of genes, the expression of which is crucial for ovulation, was substantially attenuated upon ROS ablation. This system was also used for demonstrating the role of ROS in phosphorylation and activation of the EGF receptor as well as its downstream effector, p42/44 MAPK. Together, our results provide evidence that ovarian production of ROS is an essential preovulatory signaling event, most probably transiently triggered by LH.
The scholar, historian, and public advocate: the contributions of Paul Robert Magocsi to our understanding of Ukraine and Central Europe
Authors: Arel Dominique
Published: January 2011

In a recent reflective essay written on his dual role as a scholar and public advocate, Paul Robert Magocsi with self-deprecation described himself as a loser on the margins. The sentiment of loss came with his emotional attachment to the wrong baseball team (the Dodgers rather than the Yankees) (“The Scholar as Nation-Builder”). What is clear, however, is that Magocsi is no loser in academia. My esteemed colleagues in this symposium are echoing what has become incontrovertible: Magocsi is a towering figure in Ukrainian Studies.
Skew categories, smash product categories and quasi-Koszul categories
Authors: Zhao Deke
Published: January 2011

Let

A

\mathscr {A}

be a small additive Krull-Schmidt locally radical finite category over a field

K
K

and let

G
G

be a finite group. We show that if

A

\mathscr {A}

is a free

G
G

-category (resp.

G
G

-graded category), then

A

\mathscr {A}

is quasi-Koszul if and only if the skew (resp. smash product) category

G
∗

A

G*\mathscr {A}

(resp.

A

#
G

\mathscr {A}\#G

) is.
Minimizing the discrete logarithmic energy on the sphere: The role of random polynomials
Authors: Armentano Diego , Beltrán Carlos , Shub Michael
Published: January 2011

We prove that points in the sphere associated with roots of random polynomials via the stereographic projection are surprisingly well-suited with respect to the minimal logarithmic energy on the sphere. That is, roots of random polynomials provide a fairly good approximation to elliptic Fekete points.
R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines
Authors: Huang B. Emma , George Andrew W.
Published: January 2011

Summary: Multiparent crosses of recombinant inbred lines provide opportunity to map markers and quantitative trait loci (QTL) with much greater resolution than is possible in biparental crosses. Realizing the full potential of these crosses requires computational tools capable of handling the increased statistical complexity of the analyses. R/mpMap provides a flexible and extensible environment, which interfaces easily with other packages to satisfy this demand. Functions in the package encompass simulation, marker map construction, haplotype reconstruction and QTL mapping. We demonstrate the easy-to-use features of mpMap through a simulated data example.

Availability:  www.cmis.csiro.au/mpMap.

Contact:  emma.huang@csiro.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Robust linear regression methods in association studies
Authors: Lourenço V. M. , Pires A. M. , Kirst M.
Published: January 2011

Motivation: It is well known that data deficiencies, such as coding/rounding errors, outliers or missing values, may lead to misleading results for many statistical methods. Robust statistical methods are designed to accommodate certain types of those deficiencies, allowing for reliable results under various conditions. We analyze the case of statistical tests to detect associations between genomic individual variations (SNP) and quantitative traits when deviations from the normality assumption are observed. We consider the classical analysis of variance tests for the parameters of the appropriate linear model and a robust version of those tests based on M-regression. We then compare their empirical power and level using simulated data with several degrees of contamination.

Results: Data normality is nothing but a mathematical convenience. In practice, experiments usually yield data with non-conforming observations. In the presence of this type of data, classical least squares statistical methods perform poorly, giving biased estimates, raising the number of spurious associations and often failing to detect true ones. We show through a simulation study and a real data example, that the robust methodology can be more powerful and thus more adequate for association studies than the classical approach.

Availability: The code of the robustified version of function lmekin() from the R package kinship is provided as Supplementary Material.

Contact:  vmml@fct.unl.pt

Supplementary Information:  Supplementary data are available at Bioinformatics online.
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
Authors: Marçais Guillaume , Kingsford Carl
Published: January 2011

Motivation: Counting the number of occurrences of every k-mer (substring of length k) in a long string is a central subproblem in many applications, including genome assembly, error correction of sequencing reads, fast multiple sequence alignment and repeat detection. Recently, the deep sequence coverage generated by next-generation sequencing technologies has caused the amount of sequence to be processed during a genome project to grow rapidly, and has rendered current k-mer counting tools too slow and memory intensive. At the same time, large multicore computers have become commonplace in research facilities allowing for a new parallel computational paradigm.

Results: We propose a new k-mer counting algorithm and associated implementation, called Jellyfish, which is fast and memory efficient. It is based on a multithreaded, lock-free hash table optimized for counting k-mers up to 31 bases in length. Due to their flexibility, suffix arrays have been the data structure of choice for solving many string problems. For the task of k-mer counting, important in many biological applications, Jellyfish offers a much faster and more memory-efficient solution.

Availability: The Jellyfish software is written in C++ and is GPL licensed. It is available for download at http://www.cbcb.umd.edu/software/jellyfish.

Contact:  gmarcais@umd.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
A Degree-Day Model for the Latent Period of Stagonospora nodorum Blotch in Winter Wheat
Authors: Zearfoss A. D. , Cowger C. , Ojiambo P. S.
Published: January 2011

Stagonospora nodorum blotch (SNB), which is caused by Stagonospora nodorum, occurs frequently in the southeastern United States, and severe epidemics can lead to substantial yield losses. To develop a model for the progress of SNB based on the effects of temperature on the latent period of the pathogen, batches of two winter wheat cultivars, AGS 2000 and USG 3209, were inoculated with S. nodorum at weekly intervals for 16 weeks. After 72 h of incubation, inoculated plants were exposed to outdoor conditions where temperatures ranged from –6.6 to 35.8°C, with a mean batch temperature ranging from 9.7 to 24.7°C. Latent period, expressed as time from inoculation until the first visible lesions with pycnidia, ranged from 13 to 34 days. The relationship between the inverse of the latent period and mean temperature was best described by a linear model, and the estimated thermal time required for the completion of the latent period was 384.6 degree-days. A shifted cumulative gamma distribution model with a base temperature of 0.5°C significantly (P < 0.0001) described the relationship between increasing number of lesions with pycnidia and accumulated thermal time. When latent period was defined as time to 50% of the maximum number of lesions with pycnidia (L50), the model estimated L50 as 336 and 326 degree-days above 0.5°C for AGS 2000 and USG 3209, respectively. The relationship between 1/L50 and mean temperature was also best described using a linear model (r2 = 0.93, P < 0.001). This study provides data that link disease progress with wheat growth, which facilitates accurate identification of thresholds for timing of fungicide applications.
First Report of Flavescence Dorée-Related Phytoplasma Affecting Grapevines in Croatia
Authors: Šeruga Musić M. , Škorić D. , Haluška I. , Križanac I. , Plavec J. , Mikec I.
Published: January 2011

Flavescence dorée (FD) and Bois noir (BN) phytoplasmas are principal grapevine yellows (GY) agents in the wider Euro-Mediterranean Region. While BN phytoplasma belongs to the ribosomal subgroup 16SrXII-A, the FD agents belong either to the ribosomal subgroups 16SrV-C or -D. During the official GY survey in 2009, 40 symptomatic grapevines (Vitis vinifera L.) were sampled throughout grapevine-growing regions in Croatia. Typical GY symptoms of leaf yellowing or reddening were evident on white and red varieties, respectively. Leaf rolling as well as irregular lignification of the shoots and withering of clusters were also observed. Phloem tissue from cuttings and leaf veins from mature vines were sampled for total DNA extraction and amplification of phytoplasma 16S rRNA gene by using generic primers P1/P7 in a direct PCR assay followed by a nested PCR using primer pair R16F2n/R2 (2). Phytoplasma ribosomal group affiliation was determined by restriction fragment length polymorphism (RFLP) analysis of the nested PCR products with enzyme Tru1I (Fermentas, Vilnius, Lithuania). These initial findings were validated and augmented by a triplex real-time PCR assay targeting the nonribosomal map gene. This assay enables simultaneous detection of BN and FD (16SrV-C and -D) phytoplasmas in grapevine (3). Assay results revealed the majority of GY positive vines (19 of 40) contained BN phytoplasma which is widespread. For the first time in Croatia, two red variety samples, Pinot Noir and Plemenka Crvena, from the vicinity of Ozalj (Vivodina) and Zagreb (Brezje), respectively, were found to harbor FD-related phytoplasmas. Fragments amplified by P1/P7 primers from latter samples were cloned and sequenced. Sequence analyses using online interactive tool iPhyClassifier (4) revealed that the phytoplasma under study from Pinot Noir sample (GenBank Accession No. HQ712064) is a member of 16SrV-C subgroup and shares 99.87% similarity with 16S rDNA sequence of the reference strain (GenBank Accession No. AF176319). The sequence from the Plemenka Crvena sample (GenBank Accession No. HQ712065) shares 99.54% similarity with the reference strain and has the most similar virtual RFLP pattern to the one of the 16SrV-C subgroup (GenBank Accession No. AY197642). These findings are currently limited to vineyards in northwestern Croatia. Even so, the presence of FD principal cicadellid vector Scaphoideus titanus in the country and the occurrence and distribution of FD in neighboring countries (1,2) are factors indicating that the spread of FD in Croatia is highly probable.

References: (1) L. Filippin et al. Plant Pathol. 58:826, 2009. (2) S. Kuzmanović et al. Vitis 47:105, 2008. (3) C. Pelletier et al. Vitis 48:87, 2009. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.
In Planta and Soil Quantification of Fusarium oxysporum f. sp. ciceris and Evaluation of Fusarium Wilt Resistance in Chickpea with a Newly Developed Quantitative Polymerase Chain Reaction Assay
Authors: Jiménez-Fernández Daniel , Montes-Borrego Miguel , Jiménez-Díaz Rafael M. , Navas-Cortés Juan A. , Landa Blanca B.
Published: January 2011

Fusarium wilt of chickpea caused by Fusarium oxysporum f. sp. ciceris can be managed by risk assessment and use of resistant cultivars. A reliable method for the detection and quantification of F. oxysporum f. sp. ciceris in soil and chickpea tissues would contribute much to implementation of those disease management strategies. In this study, we developed a real-time quantitative polymerase chain reaction (q-PCR) protocol that allows quantifying F. oxysporum f. sp. ciceris DNA down to 1 pg in soil, as well as in the plant root and stem. Use of the q-PCR protocol allowed quantifying as low as 45 colony forming units of F. oxysporum f. sp. ciceris per gram of dry soil from a field plot infested with several races of the pathogen. Moreover, the q-PCR protocol clearly differentiated susceptible from resistant chickpea reactions to the pathogen at 15 days after sowing in artificially infested soil, as well as the degree of virulence between two F. oxysporum f. sp. ciceris races. Also, the protocol detected early asymptomatic root infections and distinguished significant differences in the level of resistance of 12 chickpea cultivars that grew in that same field plot infested with several races of the pathogen. Use of this protocol for fast, reliable, and cost-effective quantification of F. oxysporum f. sp. ciceris in asymptomatic chickpea tissues at early stages of the infection process can be of great value for chickpea breeders and for epidemiological studies in growth chambers, greenhouses and field-scale plots.
Life in the lithosphere, kinetics and the prospects for life elsewhere
Authors: Cockell Charles S.
Published: January 2011

The global contiguity of life on the Earth today is a result of the high flux of carbon and oxygen from oxygenic photosynthesis over the planetary surface and its use in aerobic respiration. Life’s ability to directly use redox couples from components of the planetary lithosphere in a pre-oxygenic photosynthetic world can be investigated by studying the distribution of organisms that use energy sources normally bound within rocks, such as iron. Microbiological data from Iceland and the deep oceans show the kinetic limitations of living directly off igneous rocks in the lithosphere. Using energy directly extracted from rocks the lithosphere will support about six orders of magnitude less productivity than the present-day Earth, and it would be highly localized. Paradoxically, the biologically extreme conditions of the interior of a planet and the inimical conditions of outer space, between which life is trapped, are the locations from which volcanism and impact events, respectively, originate. These processes facilitate the release of redox couples from the planetary lithosphere and might enable it to achieve planetary-scale productivity approximately one to two orders of magnitude lower than that produced by oxygenic photosynthesis. The significance of the detection of extra-terrestrial life is that it will allow us to test these observations elsewhere and establish an understanding of universal relationships between lithospheres and life. These data also show that the search for extra-terrestrial life must be accomplished by ‘following the kinetics’, which is different from following the water or energy.
Chemical methods for searching for evidence of extra-terrestrial life
Authors: Pillinger Colin
Published: January 2011

This paper describes the chemical concepts used for the purpose of detecting life in extra-terrestrial situations. These methods, developed initially within the oil industry, have been used to determine when life began on Earth and for investigating the Moon and Mars via space missions. In the case of Mars, the Viking missions led to the realization that we had meteorites from Mars on Earth. The study of Martian meteorites in the laboratory provides tantalizing clues for life on Mars in both the ancient and recent past. Meteorite analyses led to the launch of the Beagle 2 spacecraft, which was designed to prove that life-detection results obtained on Earth were authentic and not confused by terrestrial contamination. Some suggestions are made for future work.
Predicting what extra-terrestrials will be like: and preparing for the worst
Authors: Morris Simon Conway
Published: January 2011

It is difficult to imagine evolution in alien biospheres operating in any manner other than Darwinian. Yet, it is also widely assumed that alien life-forms will be just that: strange, un-nerving and probably repulsive. There are two reasons for this view. First, it is assumed that the range of habitable environments available to extra-terrestrial life is far wider than on Earth. I suggest, however, that terrestrial life is close to the physical and chemical limits of life anywhere. Second, it is a neo-Darwinian orthodoxy that evolution lacks predictability; imagining what extra-terrestrial life would look like in any detail is a futile exercise. To the contrary, I suggest that the outcomes of evolution are remarkably predictable. This, however, leads us to consider two opposites, both of which should make our blood run cold. The first, and actually extremely unlikely, is that alien biospheres will be strikingly similar to our terrestrial equivalent and that in such biospheres intelligence will inevitably emerge. The reasons for this revolve around the ubiquity of evolutionary convergence, the determinate structure of the Tree of Life and molecular inherency. But if something like a human is an inevitability, why do I also claim that the first possibility is ‘extremely unlikely’? Simply because the other possibility is actually the correct answer. Paradoxically, we and our biosphere are completely alone. So which is worse? Meeting ourselves or meeting nobody?
Modulation of JAK2 V617F allele burden dynamics by hydroxycarbamide in polycythaemia vera and essential thrombocythaemia patients
Authors: Besses Carlos , Álvarez‐Larrán Alberto , Martínez‐Avilés Luz , Mojal Sergi , Longarón Raquel , Salar Antonio , Florensa Lourdes , Serrano Sergi , Bellosillo Beatriz
Published: January 2011

The modulation of JAK2 V617F allele burden dynamics was prospectively analysed in 47 patients (26 polycythaemia vera [PV] and 21 essential thrombocythaemia [ET]) treated with first‐line hydroxyurea (HU) and compared with the JAK2 V617F dynamics of a control group of 45 PV and ET patients. A partial molecular response (PMR), according to European Leukaemia Net criteria, was observed in 27/47 (57%) patients. Median time to PMR was 14 months (3–66) with a probability of PMR at 3 years of 57%. A significant decrease in JAK2 V617F allele load was observed at 36 months both in PV and ET patients, being the reduction in PV higher than in ET patients (P = 0·01). A haematocrit ≥0·45 L/L was associated with a higher probability of attaining a PMR (HR:3·4; 95%CI:1·02–11·6, P = 0·04). Control group showed a slight increase of JAK2 V617F allele burden over time. The reduction in the mutated allele load comparing treated patients versus controls was highly significant both in PV and ET, demonstrating a clear effect of HU on the JAK2 V617F allele burden. In conclusion, first‐line HU can attain PMR in more than 50% of newly diagnosed PV and ET patients, with a continuous decrease of the JAK2 V617F allele burden in PV patients during treatment.
Variability in salt tolerance of native populations of Elymus scabrifolius (Döll) J. H. Hunz from Argentina
Authors: Zabala J. M. , Taleisnik E. , Giavedoni J. A. , Pensiero J. F. , Schrauf G. E.
Published: January 2011

Elymus scabrifolius is a native C3 South American grass species. It is valued as forage species adapted to various environments in Argentina and is also a potential source of traits for wheat‐breeding programmes. Efficient utilization of native genetic resources requires extensive collection and characterization of available material. The purpose of this study was to identify and characterize variability in salt tolerance within E. scabrifolius populations in Argentina. Specimens of E. scabrifolius were collected from a wide range of soils in Argentina, and most populations were found in saline environments with high sodium levels. Intraspecific variability in salt tolerance was estimated, and its relation to the salinity level of the populations’ natural environment was assessed. A principal component analysis based on growth data distinguished lines from saline and non‐saline habitats only under salt conditions. Results suggest that selecting under stressed environments is a reasonable strategy for breeding E. scabrifolius. Lines of saline origin had higher biomass under both control and saline conditions, suggesting that higher gains from selection would be obtained if germplasm from this origin was used, and tillering may be the most useful indirect selection criterion for improving salt tolerance. The association between salt tolerance, ion content and osmotic adjustment was also assessed. Salt‐sensitive lines accumulated high sodium levels in leaves. However, osmotic adjustment did not correlate with the maintenance of leaf elongation rates under salinity in the genotypes included in this study.