bluuebunny/crossref_metadata_2025 huggingface dataset:
Parameter study of the diamagnetic relativistic pulse accelerator in slab geometry. I. Dependence on initial frequency ratio and slab width
Authors: Nishimura Kazumi , Liang Edison
Published: September 2004

Two-and-a-half-dimensional particle-in-cell plasma simulations are used to study the particle energization in expanding magnetized electron-positron plasmas with slab geometry. When the magnetized relativistic plasma with high temperature (electron and positron temperature are kBTe=kBTp=5 MeV) is expanding into a vacuum, the electromagnetic (EM) pulse with large amplitude is formed and the surface plasma particles are efficiently accelerated in the forward direction owing to the energy conversion from the EM field to the plasma particles. The behavior of the diamagnetic relativistic pulse accelerator depends strongly on the ratio of the electron plasma frequency to the cyclotron frequency ωpe/Ωe and the initial plasma thickness. In the high ωpe/Ωe case, the EM pulse is rapidly damped and the plasma diffuses uniformly without forming density peaks because the initial thermal energy of the plasma is much larger than the field energy. On the contrary, in the low ωpe/Ωe case, the field energy becomes large enough to energize all the plasma particles, which are confined in the EM pulse and efficiently accelerated to ultrarelativistic energies. It is also found that a thicker initial plasma increases the maximum energy of the accelerated particles.
Dynamic radiography using a carbon-nanotube-based field-emission x-ray source
Authors: Cheng Y. , Zhang J. , Lee Y. Z. , Gao B. , Dike S. , Lin W. , Lu J. P. , Zhou O.
Published: September 2004

We report a dynamic radiography system with a carbon nanotube based field-emission microfocus x-ray source. The system can readily generate x-ray radiation with continuous variation of temporal resolution as short as nanoseconds. Its potential applications for dynamic x-ray imaging are demonstrated. The performance characteristics of this compact and versatile system are promising for noninvasive imaging in biomedical research and industrial inspection.
An in situ cell for characterization of solids by soft x-ray absorption
Authors: Drake Ian J. , Liu Teris C. N. , Gilles Mary , Tyliszczak Tolek , Kilcoyne A. L. David , Shuh David K. , Mathies Richard A. , Bell Alexis T.
Published: September 2004

A cell has been designed and fabricated for in situ characterization of catalysts and environmental materials using soft x-ray absorption spectroscopy and spectromicroscopy at photon energies above 250 eV. “Lab-on-a-chip” technologies were used to fabricate the cell on a glass wafer. The sample compartment is 1.0 mm in diameter and has a gas path length of 0.8 mm to minimize x-ray absorption in the gas phase. The sample compartment can be heated to 533 K by an Al resistive heater and gas flows up to 5.0 cm3 min−1 can be supplied to the sample compartment through microchannels. The performance of the cell was tested by acquiring Cu L3-edge x-ray appearance near-edge structure (XANES) data during the reduction and oxidation of a silica-supported Cu catalyst using the beam line 11.0.2 scanning transmission x-ray microscope (STXM) at the Advanced Light Source of Lawrence Berkeley National Laboratory (Berkeley, CA). Two-dimensional images of individual catalyst particles were recorded at photon energies between 926 and 937 eV, the energy range in which the Cu(II) and Cu(I) L3 absorption edges are observed. Oxidation state specific images of the catalyst clearly show the disappearance of Cu(II) species during the exposure of the oxidized sample to 4% CO in He while increasing the temperature from 308 to 473 K. Reoxidation restores the intensity of the image associated with Cu(II). Cu L3-edge XANES spectra obtained from stacks of STXM images show that with increasing temperature the Cu(II) peak intensity decreases as the Cu(I) peak intensity increases.
Lasing action and photodegradation of Disperse Orange 11 dye in liquid solution
Authors: Howell Brent F. , Kuzyk Mark G.
Published: September 2004

We report optically pumped lasing action near 650nm of 1-amino-2-methylanthraquinone (known as Disperse Orange 11 or DO11) in the common laser dye solvents dimethylformamide and dimethylsulfoxide. Amplified spontaneous emission (ASE) was studied under second-harmonic Nd:YAG laser excitation in a transverse pumping configuration. ASE conversion efficiency is found to be comparable to other laser dyes. Photodegradation of dye solution in a micro-cuvette was investigated. While DO11 in poly(methyl methacrylate) polymer shows reversible photodegradation, in liquid solution, degradation is permanent.
Optical fiber gas sensor based on thermal lens spectroscopy
Authors: Yarai Atsushi , Nakanishi Takuji
Published: September 2004

This article describes how to design an optical fiber gas sensor based on a thermal lens (TL) spectroscopy instrument composed of spherical lensed fibers. This sensor features a detection head composed of two spherical lensed fibers assembled across from each other. The distance between the two fibers is just under 100 μm, with the gas in between. In other words, the optical absorption path length for our gas sensor is extremely short compared with that for other optical spectroscopic techniques (e.g., 10–20 mm∼1–2 m). In addition, our gas sensor is extremely simple, small (e.g., 20 mm in length), adjustment-free and robust. These points are extremely important for actual use in the field. The measurement principle and theoretical analysis of the design are first described. Acetylene (12C2H2) gas is used as a sample gas to evaluate the sensitivity of our sensor. The limit of detection was estimated to be approximately 5200 Pa in our experimental condition. In the conclusion, the capability of our technique is discussed, and a technique for enhancing the sensitivity in our TL technique is proposed.
Absorption, emission spectrum properties, and efficient laser performances of Yb:Y3ScAl4O12 ceramics
Authors: Saikawa J. , Sato Y. , Taira T. , Ikesue A.
Published: September 2004

We report on the continuous-wave laser performances of Yb3+-doped disordered Y3Al5O12∕Y3Sc2Al4O12(YAG∕YSAG) ceramics fabricated by sintering method. These materials exhibit relatively low minimum pump intensity (Imin) and broad emission bandwidth even in the yttrium aluminum garnet systems. The value of Imin in the Yb:Y3ScAl4O12 ceramics was found to be 2∕3 compared with the Yb:YAG single crystal under 970nm zero-line pumping. Efficient laser oscillation of 72% slope efficiency was obtained for input pump power. These materials attract great interest for high power femtosecond microchip lasers and amplifier applications.
High-spatial-resolution scanning capacitance microscope using all-metal probe with quartz tuning fork
Authors: Naitou Yuichi , Ookubo Norio
Published: September 2004

The scanning capacitance microscope (SCM) reported here uses a frequency modulation (FM) technique to control the distance between the sample and an all-metal probe. The probe was attached to a quartz tuning fork in a configuration minimizing the perturbation due to the probe. The FM-SCM yields two images of ∂C∕∂V and ∂C∕∂Z signals, where C is capacitance sensed by the probe, Z the probe–sample distance, and V a bias voltage, respectively. On a cross section of a field effect transistor, the two-dimensional p–n junction locus was observed with a spatial resolution better than 5nm in the ∂C∕∂V image. The ∂C∕∂Z images of polysilicon gate electrodes and highly doped source/drain regions have higher contrast than the ∂C∕∂V images.
Collisionless magnetic reconnection with arbitrary guide field
Authors: Fitzpatrick Richard , Porcelli Franco
Published: September 2004

A set of reduced equations governing nonlinear, two-dimensional, two-fluid, collisionless magnetic reconnection with arbitrary guide field is derived. These equations represent an improvement on the existing nonlinear reduced equations generally used to investigate collisionless reconnection, which are only valid in the large guide-field limit. The improved equations are used to calculate the linear growth rate of a strongly unstable, spontaneously reconnecting, plasma instability, as well as the general linear dispersion relation for such an instability.
Front-coupling of a prefocused x-ray beam into a monomodal planar waveguide
Authors: Fuhse Christian , Jarre Ansgar , Ollinger Christoph , Seeger Jens , Salditt Tim , Tucoulou Remi
Published: September 2004

A hard x-ray beam of photon energy E=12.5keV has been focused by a Kirkpatrick–Baez mirror system and coupled into the front side of a single-mode x-ray waveguide. The beam dimensions of 3.8×2.5μm2 in the focus of the mirror system have thus been reduced in one direction to 32nm, corresponding to the guiding layer thickness of the waveguide. At the same time the waveguide acts as a coherence filter and leads to a well-defined intensity distribution with steep tails in the near- and far-field regions. The total flux transmitted by the waveguide exceeded 108 photons/s while no significant contributions of radiation transmitted through the absorbing waveguide cladding have been observed.
Observation of instability in presence of E×B flow in a direct current cylindrical magnetron discharge plasma
Authors: Pal Arup Ratan , Chutia Joyanti , Bailung Heremba
Published: September 2004

An electrostatic instability with an intermediate frequency range (50–100 MHz) between the electron collision frequency and electron cyclotron frequency has been observed in presence of crossed electric and magnetic fields in a dc cylindrical magnetron plasma. The amplitude of the instability becomes maximum at particular values of the magnetic field and the discharge voltage. It is seen that when the magnetic field is increased the instability peaks at lower discharge voltages. The different modes of instability are prominent only when the neutral gas pressure is sufficiently low (∼4×10−3 mbar). The instability becomes suppressed when the magnetic field is high (>200 G). A constant amplitude test signal applied to the plasma through the cathode grows when its frequency matches with the frequency of the instability. The current-voltage characteristics form hysteresis loop in the instability excitation region.
Terahertz plasma wave resonance of two-dimensional electrons in InGaP∕InGaAs∕GaAs high-electron-mobility transistors
Authors: Otsuji Taiichi , Hanabe Mitsuhiro , Ogawara Osamu
Published: September 2004

We have observed the frequency dependence of the plasma resonant intensity in the terahertz range for a short gate-length InGaP∕InGaAs∕GaAs pseudomorphic high-electron-mobility transistor. The plasma resonance excitation was performed by means of interband photoexcitation using the difference-frequency component of a photomixed laser beam. Under sufficient density of two-dimensional (2D) conduction electrons (>1012cm−2) and a moderate modulation index (the ratio of the density of photoexcited electrons to the initial density of the 2D electrons) we clearly observed the plasma-resonant peaks at 1.9 and 5.8THz corresponding to the fundamental and third-harmonic resonance at room temperature, which is in good agreement with theory.
Photoconductivity from PbS-nanocrystal∕semiconducting polymer composites for solution-processible, quantum-size tunableinfrared photodetectors
Authors: McDonald S. A. , Cyr P. W. , Levina L. , Sargent E. H.
Published: September 2004

We report photoconductivity at infrared wavelengths, 975–1300nm, from a polymer∕nanocrystal quantum dot composite. Biased films of the conjugated polymer poly[2-methoxy-5-(2′-ethylhexyloxy-p-phenylenevinylene)] (MEH-PPV) sensitized with PbS nanocrystals (∼5nm diameter) demonstrate photocurrent at wavelengths beyond the response of the polymer and corresponding to the absorption of the nanocrystals. The photocurrent is attributed to absorption in the nanocrystals with subsequent hole transfer to the polymer and had an internal quantum efficiency of ∼5×10−6to∼10−5charges∕photon at 5V bias.
Electrostatic vortices associated with ion-temperature-gradient driven drift modes in electron-positron-ion plasmas
Authors: Azeem M. , Mirza Arshad M.
Published: September 2004

A set of nonlinear equations governing the dynamics of low-frequency electrostatic waves in the presence of equilibrium density, temperature, magnetic field and electrostatic potential gradients has been derived. In the linear limit, it is shown that nonzero equilibrium ion-temperature-gradient and the presence of positrons modify the basic drift modes. On the other hand, in the nonlinear case, it is shown that under certain conditions possible stationary solutions of the same set of nonlinear equations are reduced in the form of various types of vortex patterns. The results of the present investigation should be useful to understand the wave phenomena in laboratory and astrophysical e-p-i plasmas.
Direct laser writing and characterization of “Slanted Pore” Photonic Crystals
Authors: Deubel Markus , Wegener Martin , Kaso Artan , John Sajeev
Published: September 2004

We report the fabrication and characterization of the recently proposed Slanted Pore Photonic Crystals. The Photonic Crystals fabricated via direct laser writing by multiphoton polymerization are characterized by electron microscopy as well as by optical spectroscopy. The latter is compared with band structure calculations. We show that this Slanted Pore geometry allows for controlling the surface termination of the Photonic Crystal.
Ambipolar pentacene field-effect transistors with calcium source-drain electrodes
Authors: Yasuda Takeshi , Goto Takeshi , Fujita Katsuhiko , Tsutsui Tetsuo
Published: September 2004

Field-effect transistors consisted of vacuum-sublimed polycrystalline pentacene films and calcium source-drain electrodes were prepared and device characteristics were evaluated in an oxygen-free condition. The field-effect transistor showed typical ambipolar characteristics and field-effect hole mobility of 4.5×10−4cm2/Vs and field-effect electron mobility of 2.7×10−5cm2∕Vs were estimated from saturation currents. Appearance of an electron enhancement mode in pentacene field-effect transistors was ascribed to the lowering of barrier for electron injection at source-drain electrodes. Effective elimination of electron traps using an oxygen-free condition was found to be another requirement for the observation of ambipolar behavior in pentacene.
Optical properties of InP∕GaInP quantum-dot laser structures
Authors: Lewis G. M. , Lutti J. , Smowton P. M. , Blood P. , Krysa A. B. , Liew S. L.
Published: September 2004

We have grown InP quantum dots with different rates and on substrates with different orientations. The growth conditions have a major influence on the form of the gain spectrum. Using a high growth rate on a 10° off (100) substrate we obtain a broad gain spectrum due to contributions from a bimodal dot size distribution whereas a sample containing mostly small dots, produced using (211)B substrates, has a narrower gain spectrum centered at a shorter wavelength of ∼700–710nm. The modal gain saturates at a magnitude significantly smaller than the modal absorption, nevertheless the measured values of modal gain are sufficient to sustain laser action, and structures grown at high growth rate on 10° off (100) substrates are capable of providing laser devices operating in the region of 750nm.
Multilevel conductance and memory in ultrathin organic films
Authors: Mukherjee Biswanath , Pal Amlan J.
Published: September 2004

The present letter reports conductance switching in Langmuir–Blodgett films of an organic semiconductor. We have achieved multiple conducting levels in devices based on ultrathin films for increased density of memory bits in the same space. We have shown that multiple conducting levels in a device can be achieved by controlling the density of high-conducting molecules in the structures. We have observed one low- and three high-conducting states of the devices. All four states have associated memory for data-storage applications. Any of the four states, namely 00, 01, 10, and 11, can be “read” for several hours for read-only memory applications. We could “erase” a state, “write” another, and “read” the state for multibit random-access-memory applications.
Dielectric properties and space charge behavior in SiC ceramic capacitor
Authors: Zhang Rui , Gao Lian , Wang Hailong , Guo Jingkun
Published: September 2004

Strong space charge response is observed in SiC ceramic capacitors at low frequencies up to 0.1MHz. It leads to a dielectric constant of 2 910 000 at 100Hz. The critical temperature is observed near 773K. The losses decrease with increasing temperature. Strong frequency dependence of the dielectric properties is also detected. The SiC ceramic capacitor might be suitable as high-temperature by-pass capacitor in low voltage circuits.
Circular box C/D RNAs in
Pyrococcus furiosus
Authors: Starostina Natalia G. , Marshburn Sarah , Johnson L. Steven , Eddy Sean R. , Terns Rebecca M. , Terns Michael P.
Published: September 2004

Box C/D RNAs are small, noncoding RNAs that function in RNA modification in eukaryotes and archaea. Here, we report that box C/D RNAs exist in the rare biological form of RNA circles in the hyperthermophilic archaeon
Pyrococcus furiosus
. Northern analysis of box C/D RNAs reveals two prominent RNA species of different electrophoretic mobilities in total
P. furiosus
RNA preparations. Together, the results of Northern, ribozyme, RT-PCR, and lariat debranching analyses indicate that the two species are circular and linear RNAs of similar length and abundance. It seems that most, if not all, species of box C/D RNAs exist as circles in
P. furiosus
. In addition, the circular RNAs are found in complexes with proteins required for box C/D RNA function. Our finding places box C/D RNAs among the extremely few circular RNAs known to exist in nature. Moreover, the unexpected discovery of circular box C/D RNAs points to the existence of a previously unrecognized biogenesis pathway for box C/D RNAs in archaea.
Laboratory evidence for a key intermediate in the Venus atmosphere: Peroxychloroformyl radical
Authors: Pernice Holger , Garcia Placido , Willner Helge , Francisco Joseph S. , Mills Franklin P. , Allen Mark , Yung Yuk L.
Published: September 2004

For two decades, the peroxychloroformyl radical, ClC(O)OO, has played a central role in models of the chemical stability of the Venus atmosphere. No confirmation, however, has been possible in the absence of laboratory measurements for ClC(O)OO. We report the isolation of ClC(O)OO in a cryogenic matrix and its infrared and ultraviolet spectral signatures. These experiments show that ClC(O)OO is thermally and photolytically stable in the Venus atmosphere. These experimental discoveries validate the existence of ClC(O)OO, confirm several longstanding model assumptions, and provide a basis for the astronomical search for this important radical species.
A phosphorylation site in Bruton's tyrosine kinase selectively regulates B cell calcium signaling efficiency by altering phospholipase C-γ activation
Authors: Guo Shuling , Ferl Gregory Z. , Deora Rajendar , Riedinger Mireille , Yin Sheng , Kerwin James L. , Loo Joseph A. , Witte Owen N.
Published: September 2004

Loss of function of Bruton's tyrosine kinase (Btk) causes X-linked agammaglobulinemia (XLA) in humans and X-linked immunodeficiency in mice (xid). By using MS analysis and phosphopeptide-specific antibodies, we identified a tyrosine phosphorylation site (Y617) near the carboxyl terminus of the Btk domain from Btk expressed in 293T as well as DT-40 cells. Y617 is conserved in all Tec family kinases except murine Tec. Replacement of Y617 with a negatively charged glutamic acid (E) suppressed Btk-mediated phospholipase Cγ2 activation and calcium response in DT-40 cells, whereas Akt activation was not affected. The Btk Y617E mutant could partially restore conventional B cell development and proliferation in Btk
–
/Tec
–
mice but failed to rescue CD5
+
B-1 cell development and the TI-II immune response to 2,4,6,-trinitrophenyl-Ficoll. These data suggest that Y617 phosphorylation or a negative charge at this site may down-regulate the function of Btk by selectively suppressing the B cell calcium signaling pathway.
Identification of Mushroom body miniature, a zinc-finger protein implicated in brain development of
Drosophila
Authors: Raabe Thomas , Clemens-Richter Susanne , Twardzik Thomas , Ebert Anselm , Gramlich Gertrud , Heisenberg Martin
Published: September 2004

The mushroom bodies are bilaterally arranged structures in the protocerebrum of
Drosophila
and most other insect species. Mutants with altered mushroom body structure have been instrumental not only in establishing their role in distinct behavioral functions but also in identifying the molecular pathways that control mushroom body development. The

mushroom body miniature
1

(

mbm
1

) mutation results in grossly reduced mushroom bodies and odor learning deficits in females. With a survey of genomic rescue constructs, we have pinpointed

mbm
1

to a single transcription unit and identified a single nucleotide exchange in the 5′ untranslated region of the corresponding transcript resulting in a reduced expression of the protein. The most obvious feature of the Mbm protein is a pair of C
2
HC zinc fingers, implicating a function of the protein in binding nucleic acids. Immunohistochemical analysis shows that expression of the Mbm protein is not restricted to the mushroom bodies. BrdUrd labeling experiments indicate a function of Mbm in neuronal precursor cell proliferation.
Microarray Analysis in Alzheimer's Disease and Normal Aging
Authors: Ricciarelli Roberta , d'Abramo Cristina , Massone Sara , Marinari Umberto M. , Pronzato Maria A. , Tabaton Massimo
Published: September 2004

The purpose of this study was to investigate gene expression in Alzheimer's disease (AD), the most common form of senile dementia. We utilized the microarray technology to simultaneously compare the expression profile of 12,000 human genes in cerebral cortex of AD and normal aging. To identify gene expression related to neurodegeneration, beside the presence of amyloid deposition, we used control brains with abundant amyloid plaques, derived from cognitively normal elderly subjects. The microarray analysis indicated that 314 genes were differentially expressed in AD cerebral cortex, with differences greater than 5 folds in 25 genes. RT‐PCR performed on a selected group of genes confirmed the increased expression of the interferon‐induced protein 3 in AD brain. This protein, which is highly inducible by both type I and type II interferons, was not previously associated with the neurodegenerative disease.
IUBMB Life, 56: 349‐354, 2004
A memory-efficient algorithm for multiple sequence alignment with constraints
Authors: Lu Chin Lung , Huang Yen Pin
Published: September 2004

Motivation: Recently, the concept of the constrained sequence alignment was proposed to incorporate the knowledge of biologists about structures/functionalities/consensuses of their datasets into sequence alignment such that the user-specified residues/nucleotides are aligned together in the computed alignment. The currently developed programs use the so-called progressive approach to efficiently obtain a constrained alignment of several sequences. However, the kernels of these programs, the dynamic programming algorithms for computing an optimal constrained alignment between two sequences, run in 𝒪(γn2) memory, where γ is the number of the constraints and n is the maximum of the lengths of sequences. As a result, such a high memory requirement limits the overall programs to align short sequences~only.

Results: We adopt the divide-and-conquer approach to design a memory-efficient algorithm for computing an optimal constrained alignment between two sequences, which greatly reduces the memory requirement of the dynamic programming approaches at the expense of a small constant factor in CPU time. This new algorithm consumes only 𝒪(αn) space, where α is the sum of the lengths of constraints and usually α ≪ n in practical applications. Based on this algorithm, we have developed a memory-efficient tool for multiple sequence alignment with constraints.

Availability:  http://genome.life.nctu.edu.tw/MUSICME

Contact:  cllu@mail.nctu.edu.tw
PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics
Authors: Kahraman Abdullah , Avramov Andrey , Nashev Lyubomir G. , Popov Dimitar , Ternes Rainer , Pohlenz Hans-Dieter , Weiss Bertram
Published: September 2004

Summary: We have created PhenomicDB, a multi-species genotype/phenotype database by merging public genotype/phenotype data from a wide range of model organisms and Homo sapiens. Until now these data were available in distinct organism-specific databases (e.g. WormBase, OMIM, FlyBase and MGI). We compiled this wealth of data into a single integrated resource by coarse-grained semantic mapping of the phenotypic data fields, by including common gene indices (NCBI Gene), and by the use of associated orthology relationships. With its use-case-oriented user interface, PhenomicDB allows scientists to compare and browse known phenotypes for a given gene or a set of genes from different organisms simultaneously.

Availability: PhenomicDB has been implemented at Schering AG as described below. A PhenomicDB implementation differing in some technical details has been set up for the public at Metalife AG http://www.phenomicDB.de

Contact:  bertram.weiss@schering.de

Supplementary information: database model, semantic mapping table.
Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets
Authors: Li Haiquan , Li Jinyan
Published: September 2004

Motivation: Discovery of binding sites is important in the study of protein–protein interactions. In this paper, we introduce stable and significant motif pairs to model protein-binding sites. The stability is the pattern’s resistance to some transformation. The significance is the unexpected frequency of occurrence of the pattern in a sequence dataset comprising known interacting protein pairs. Discovery of stable motif pairs is an iterative process, undergoing a chain of changing but converging patterns. Determining the starting point for such a chain is an interesting problem. We use a protein complex dataset extracted from the Protein Data Bank to help in identifying those starting points, so that the computational complexity of the problem is much released.

Results: We found 913 stable motif pairs, of which 765 are significant. We evaluated these motif pairs using comprehensive comparison results against random patterns. Wet-experimentally discovered motifs reported in the literature were also used to confirm the effectiveness of our method.

Contact  haiquan@i2r.a-star.edu.sg

Supplementary information  http://sdmc.i2r.a-star.edu.sg/BindingMotifPairs
MAP-O-MAT: internet-based linkage mapping
Authors: Kong X. , Matise T. C.
Published: September 2004

Summary: MAP-O-MAT is a web-based server for automated linkage mapping of human polymorphic DNA markers. MAP-O-MAT facilitates the verification of order and map distances for custom mapping sets using genotype data from the CEPH database, and from the Marshfield, SNP Consortium and Rutgers linkage maps (exclusive to the deCODE genotyping data). The CRI-MAP program is used for likelihood calculations and some mapping algorithms, and physical map positions are provided from the human genome assembly.

Availability: MAP-O-MAT is located at http://compgen.rutgers.edu/mapomat/

Contact:  matise@biology.rutgers.edu
Improving genome annotations using phylogenetic profile anomaly detection
Authors: Mikkelsen Tarjei S. , Galagan James E. , Mesirov Jill P.
Published: September 2004

Motivation: A promising strategy for refining genome annotations is to detect features that conflict with known functional or evolutionary relationships between groups of genes. Previous work in this area has been focused on investigating the absence of ‘housekeeping’ genes or components of well-studied pathways. We have sought to develop a method for improving new annotations that can automatically synthesize and use the information available in a database of other annotated genomes.

Results: We show that a probabilistic model of phylogenetic profiles, trained from a database of curated genome annotations, can be used to reliably detect errors in new annotations. We use our method to identify 22 genes that were missed in previously published annotations of prokaryotic genomes.

Availability: The method was evaluated using MATLAB and open source software referenced in this work. Scripts and datasets are available from the authors upon request.

Contact:  tarjei@broad.mit.edu
SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks
Authors: Sachdeva Gaurav , Kumar Kaushal , Jain Preti , Ramachandran Srinivasan
Published: September 2004

Motivation: The adhesion of microbial pathogens to host cells is mediated by adhesins. Experimental methods used for characterizing adhesins are time-consuming and demand large resources. The availability of specialized software can rapidly aid experimenters in simplifying this problem. We have employed 105 compositional properties and artificial neural networks to develop SPAAN, which predicts the probability of a protein being an adhesin (Pad).

Results: SPAAN had optimal sensitivity of 89% and specificity of 100% on a defined test set and could identify 97.4% of known adhesins at high Pad value from a wide range of bacteria. Furthermore, SPAAN facilitated improved annotation of several proteins as adhesins. Novel adhesins were identified in 17 pathogenic organisms causing diseases in humans and plants. In the severe acute respiratory syndrome (SARS) associated human corona virus, the spike glycoprotein and nsps (nsp2, nsp5, nsp6 and nsp7) were identified as having adhesin-like characteristics. These results offer new lead for rapid experimental testing.

Availability: SPAAN is freely available through ftp://203.195.151.45

Contact:  ramu@igib.res.in
tPatternHunter: gapped, fast and sensitive translated homology search
Authors: Kisman Derek , Li Ming , Ma Bin , Wang Li
Published: September 2004

Summary: New ideas, spaced seeds and gapped alignment before 6-frame translation are implemented for translated homology search in tPatternHunter. The new software compares favorably with tBLASTx.

Availability: The software is free to academics at http://www.bioinformaticssolutions.com/downloads/ph-academic/

Contact:  bma@csd.uwo.ca
Online synonymous codon usage analyses with the ade4 and seqinR packages
Authors: Charif D. , Thioulouse J. , Lobry J. R. , Perrière G.
Published: September 2004

Summary: Correspondence analysis of codon usage data is a widely used method in sequence analysis, but the variability in amino acid composition between proteins is a confounding factor when one wants to analyse synonymous codon usage variability. A simple and natural way to cope with this problem is to use within-group correspondence analysis. There is, however, no user-friendly implementation of this method available for genomic studies. Our motivation was to provide to the community a Web facility to easily study synonymous codon usage on a subset of data available in public genomic databases.

Availability: Availability through the Pôle Bioinformatique Lyonnais (PBIL) Web server at http://pbil.univ-lyon1.fr/datasets/charif04/ with a demo allowing us to reproduce the figure in the present application note. All underlying software is distributed under a GPL licence.

Contact:  http://pbil.univ-lyon1.fr/members/lobry
Expression-based monitoring of transcription factor activity: the TELiS database
Authors: Cole Steve W. , Yan Weihong , Galic Zoran , Arevalo Jesusa , Zack Jerome A.
Published: September 2004

Motivation: In microarray studies it is often of interest to identify upstream transcription control pathways mediating observed changes in gene expression. The Transcription Element Listening System (TELiS) combines sequence-based analysis of gene regulatory regions with statistical prevalence analyses to identify transcription-factor binding motifs (TFBMs) that are over-represented among the promoters of up- or down-regulated genes. Efficiency is maximized by decomposing the problem into two steps: (1) a priori compilation of prevalence matrices specifying the number of putative binding sites for a variety of transcription factors in promoters from all genes assayed by a given microarray, and (2) real-time statistical analysis of pre-compiled prevalence matrices to identify TFBMs that are over- or under-represented in promoters of differentially expressed genes. The interlocking JAVA applications namely, PromoterScan and PromoterStats carry out these tasks, and together constitute the TELiS database for reverse inference of transcription factor activity.

Results: In two validation studies, TELiS accurately detected in vivo activation of NF-κB and the Type I interferon system by HIV-1 infection and pharmacologic activation of the glucocorticoid receptor in peripheral blood mononuclear cells. The population-based statistical inference underlying TELiS out-performed conventional statistical tests in analytic sensitivity, with parametric studies demonstrating accurate identification of transcription factor activity from as few as 20 differentially expressed genes. TELiS thus provides a simple, rapid and sensitive tool for identifying transcription control pathways mediating observed gene expression dynamics.

Availability:  http://www.telis.ucla.edu

Contact:  coles@ucla.edu
RAP: a new computer program for de novo identification of repeated sequences in whole genomes
Authors: Campagna Davide , Romualdi Chiara , Vitulo Nicola , Del Favero Micky , Lexa Matej , Cannata Nicola , Valle Giorgio
Published: September 2004

Motivation: DNA repeats are a common feature of most genomic sequences. Their de novo identification is still difficult despite being a crucial step in genomic analysis and oligonucleotides design. Several efficient algorithms based on word counting are available, but too short words decrease specificity while long words decrease sensitivity, particularly in degenerated repeats.

Results: The Repeat Analysis Program (RAP) is based on a new word-counting algorithm optimized for high resolution repeat identification using gapped words. Many different overlapping gapped words can be counted at the same genomic position, thus producing a better signal than the single ungapped word. This results in better specificity both in terms of low-frequency detection, being able to identify sequences repeated only once, and highly divergent detection, producing a generally high score in most intron sequences.

Availability: The program is freely available for non-profit organizations, upon request to the authors.

Contact:  giorgio.valle@unipd.it

Supplementary information: The program has been tested on the Caenorhabditis elegans genome using word lengths of 12, 14 and 16 bases. The full analysis has been implemented in the UCSC Genome Browser and is accessible at http://genome.cribi.unipd.it.
A conserved protein network controls assembly of the outer kinetochore and its ability to sustain tension
Authors: Cheeseman Iain M. , Niessen Sherry , Anderson Scott , Hyndman Francie , Yates John R. , Oegema Karen , Desai Arshad
Published: September 2004

Kinetochores play an essential role in chromosome segregation by forming dynamic connections with spindle microtubules. Here, we identify a set of 10 copurifying kinetochore proteins from Caenorhabditis elegans, seven of which were previously uncharacterized. Using in vivo assays to monitor chromosome segregation, kinetochore assembly, and the mechanical stability of chromosome-microtubule attachments, we show that this copurifying protein network plays a central role at the kinetochore-microtubule interface. In addition, our analysis suggests that the network is comprised of three groups of proteins that contribute in distinct ways to this interface: KNL proteins act after the assembly of centromeric chromatin to generate the core of the microtubule-binding interface, MIS proteins control the rate and extent of formation of this interface, and NDC proteins are necessary to sustain tension during interactions with spindle microtubules. We also purify a similar set of associated proteins from human cells that includes four novel proteins and has recognizable homologs from each functional class. Thus, this protein network is a conserved constituent of the outer kinetochore, and the functions defined by our analysis in C. elegans are likely to be widely relevant.
The biology of hypoxia: the role of oxygen sensing in development, normal function, and disease
Authors: Giaccia Amato J. , Simon M. Celeste , Johnson Randall
Published: September 2004

The ability to sense and respond to changes in oxygen is essential for the survival of prokaryotic and eukaryotic organisms. Oxygen-sensing mechanisms have been developed to maintain cell and tissue homeostasis, as well as to adapt to the chronic low-oxygen conditions found in diseases such as cancer. This report on the first Keystone Meeting on the Biology of Hypoxia will summarize our current understanding of key genes and pathways involved in oxygen sensing that are required for normal development and that are dysregulated in disease states. It will also comment on future directions for this exciting field.
Exploratory orientation data analysis with ω sections
Authors: van den Boogaart K. Gerald , Schaeben Helmut
Published: September 2004

Since the domain of crystallographic orientations is three-dimensional and spherical, insightful visualization of them or visualization of related probability density functions requires (i) exploitation of the effect of a given orientation on the crystallographic axes, (ii) consideration of spherical means of the orientation probability density function, in particular with respect to one-dimensional totally geodesic submanifolds, and (iii) application of projections from the two-dimensional unit sphere S^2 \subset I\!R^3 onto the unit disk D \subset I\!R^2. The familiar crystallographic `pole figures' are actually mean values of the spherical Radon {\cal R}_1 transform. The mathematical Radon {\cal R}_1 transform associates a real-valued functionfdefined on a sphere with its mean values {\cal R}_{1}f along one-dimensional circles with centre {\cal O}, the origin of the coordinate system, and spanned by two unit vectors. The family of views suggested here defines ω sections in terms of simultaneous orientational relationships of two different crystal axes with two different specimen directions, such that their superposition yields a user-specified pole probability density function. Thus, the spherical averaging and the spherical projection onto the unit disk determine the distortion of the display. Commonly, spherical projections preserving either volume or angle are favoured. This rich family displaysfcompletely,i.e.iffis given or can be determined unambiguously, then it is uniquely represented by several subsets of these views. A computer code enables the user to specify and control interactively the display of linked views, which is comprehensible as the user is in control of the display.
Structure and order in lamellar phases determined by small-angle scattering
Authors: Frühwirth Thomas , Fritz Gerhard , Freiberger Norbert , Glatter Otto
Published: September 2004

Multilamellar phases can be identified and characterized by small-angle scattering of X-rays (SAXS) or neutrons (SANS). Equidistant peaks are the typical signature and their spacing allows the fast determination of the repeat distance,i.e.the mean distance between the midplane of neighbouring bilayers. The scattering function can be described as the product of a structure factor and a form factor. The structure factor is related to the ordering of the bilayers and is responsible for the typical equidistant peaks, but it also contains information about the bilayer flexibility and the number of coherently scattering bilayers. The form factor depends on the thickness and the internal structure (scattering length density distribution) of a single bilayer. The recently developed generalized indirect Fourier transformation (GIFT) method is extended to such systems. This method allows the simultaneous determination of the structure factor and the form factor of the system, including the correction of instrumental broadening effects. A few-parameter model is used for the structure factor, while the determination of the form factor is completely model-free. The method has been tested successfully with simulated scattering data and by application to experimental data sets.
Re-thinking the role of the beamstop at a synchrotron-based protein crystallography beamline
Authors: Alkire R. W. , Schuessler R. , Rotella F. J. , Gonczy J. D. , Rosenbaum G.
Published: September 2004

A 1 mm vertical-profile X-ray beamstop has been designed to operate in the energy range 6–20 keV. The relationship between the beamstop-to-sample distance and air scatter is discussed with the intent of establishing criteria for optimal beamstop positioning during an experiment. Different choices for beamstop materials are described with respect to stopping power, fluorescence and scattering from the surface. Suggestions for improvements in beamstop design are presented which are applicable for future automation and equipment safety. All work was performed on the Structural Biology Center insertion-device beamline, 19ID, at the Advanced Photon Source.
Study of geometrical local order in a non-ideal solid solution: an intermediary structure
Authors: Laridjani M. , Dénoyer F.
Published: September 2004

One of the key obstacles in the progress of certain aspects of solid-state physics is the determination of the nature of irregularities in the atomic network of matter and their correlation with macroscopic properties. In this work, an original structural result is presented, namely the presence of icosahedral clusters in an Al solid solution, as deduced from the analysis of the total Fourier-space image. This work has led to the belief that these non-crystalline clusters create a fundamental irregularity in the network of a non-ideal solid solution.
Full-profile refinement by derivative difference minimization
Authors: Solovyov Leonid A.
Published: September 2004

A new method of full-profile refinement is developed on the basis of the minimization of the derivatives of the profile difference curve. The use of the derivatives instead of the absolute difference between the observed and calculated profile intensities allows refinement independently of the background. The procedure is tested on various powder diffraction data sets and is shown to be fully functional. Besides having the capability of powder diffraction structure analysis without modelling the background curve, the method is shown to allow the derivation of structure parameters of even higher quality than those obtained by Rietveld refinement in the presence of systematic errors in the model background function. The derivative difference minimization principles may be used in many different areas of powder diffraction and beyond.
X-ray diffuser
Authors: Matsuura Yoshiki , Yoshizaki Izumi , Tanaka Masahiko
Published: September 2004

Amorphous boron powder was used as an X-ray diffuser, making the beam divergence of synchrotron radiation broader by simple insertion of the diffuser into the beam. The diffuser has been used successfully for the purpose of easy peak finding on a four-circle diffractometer. The diffuser effect is considered to be brought about by small-angle scattering from the boron powder.
HELIX: a helical diffraction simulation program
Authors: Knupp Carlo , Squire John M.
Published: September 2004

The programHELIXhas been devised as a simple aid to understanding the origin and appearance of fibre diffraction patterns from helical structures. Helices are common as preferred conformations in both natural and synthetic macromolecules (e.g.DNA, α-helices, polysaccharides, synthetic polymers), and occur frequently in extended macromolecular aggregates (e.g.actin filaments, myosin filaments, microtubules, amyloid filamentsetc.). For this reason, a simple way of visualizing the kinds of diffraction patterns that these structures can give should have educational value and should also be useful as a quick means of testing possible symmetries in structural investigations before embarking on full helical diffraction analysis. Despite its simplicity, there is no other public program that provides these possibilities. TheHELIXprogram, running under Microsoft Windows, is freely available from the CCP13 website (http://www.ccp13.ac.uk).
Disordered quasicrystals: diffuse scattering in decagonal Al–Ni–Fe
Authors: Weidner E. , Frey F. , Lei J.-L. , Pedersen B. , Paulmann C. , Morgenroth W.
Published: September 2004

High-resolution synchrotron data of near-Bragg diffuse scattering from decagonal Al71.5Ni23.5Fe5quasicrystals were recorded. A dominant phasonic origin is ruled out because of the absence of a significantG⊥dependence. An analysis solely in the frame of thermal diffuse scattering (TDS) theory (phonon scattering) showed a good match between experimental and calculated data in the quasiperiodic layers, but with an improbable ratio of elastic constants,c66/c11 = 4.0.In situhigh-temperature measurements up to 1000 K revealed an increase of the intensity distribution perpendicular to the scattering vectorG. Huang diffuse scattering (HDS) arising from quenched local defects has a general appearance that qualitatively reproduces the observed symmetry and anisotropy. An interpretation based on both TDS and HDS contributions is given.
Contribution of powder diffraction for structure refinements of aperiodic misfit cobalt oxides
Authors: Grebille Dominique , Lambert Sébastien , Bourée Françoise , Petříček Václav
Published: September 2004

Two families of misfit cobalt oxides have been reinvestigated using neutron and synchrotron powder diffraction data and Rietveld structure refinements in the four-dimensional formalism for aperiodic structures. In the first system [Ca2CoO3][CoO2]1.62, the structure-specific features of two complex polytypic phases previously described from single-crystal diffraction data have been confirmed for the main term of the series and are described with theC2/m(1,δ,0)s0 superspace symmetry (Rp= 0.026,Rwp= 0.031,RB= 0.014). The high-resolution synchrotron diffraction experiments have been interpreted with a triclinic distortion of the structure, probably related to an intrinsic modulation of the [Ca2CoO3] sublattice in relation with Co and O split atomic sites. In the second system Ca0.82(Cu0.65Co0.35O2), a new occupation modulation of the metallic site is shown with theFmmm(α11)0sssuperspace symmetry (Rp= 0.031,Rwp= 0.039,RB= 0.027) and is interpreted in relation with the modulated interatomic distances of the square coordination of the cationic site. In both cases, recently developed tools for structure refinements of aperiodic systems using powder diffraction data (in theJANA2000package) have proved their efficiency, in particular as specific complements to previous single-crystal structure refinements.
Experimental electron density study of the supramolecular aggregation between 4,4′-dipyridyl-N,N′-dioxide and 1,4-diiodotetrafluorobenzene at 90 K
Authors: Bianchi Riccardo , Forni Alessandra , Pilati Tullio
Published: September 2004

The electron density of the halogen-bonded complex of 4,4′-dipyridyl-N,N′-dioxide (bpNO) with 1,4-diiodotetrafluorobenzene (F4dIb) at 90 K has been determined by X-ray diffraction and analysed. The nature of the I...O intermolecular bond connecting the bpNO and F4dIb molecules into one-dimensional infinite chains, as well as the other non-covalent interactions present in the crystal, such as C—H...O, C—H...F and C—H...I hydrogen bonds and C...C, C...N, C...I and F...F interactions, have been investigated. The integration of electron density over the atomic basins reveals the electrostatic nature of the I...O halogen bond, which is very similar to a previously analysed I...N halogen bond.