bluuebunny/crossref_metadata_2025 huggingface dataset:
Tunable continuous wave and femtosecond mode-locked Yb3+ laser operation in NaLu(WO4)2
Authors: García-Cortés A. , Cano-Torres J. M. , Han X. , Cascales C. , Zaldo C. , Mateos X. , Rivier S. , Griebner U. , Petrov V. , Valle F. J.
Published: March 2007

Continuous wave and femtosecond mode-locked laser operation of Yb3+ in the tetragonal NaLu(WO4)2 crystal host is demonstrated by pumping with a Ti:sapphire laser. Pumping with 1.8W at 974nm, a maximum output power of 650mW was achieved at 1029.6nm. The slope efficiency was in excess of 60%. The laser performance was similar for the two polarizations. By inserting a birefringent filter the output wavelength was tunable from 1010to1055nm. Pulses as short as 90fs with an average power of 50mW were generated by passive mode locking at a repetition rate of 95MHz. These attractive laser properties of NaLu1−xYbx(WO4)2 are related to the inhomogeneous broadening of the Yb3+ spectral features resulting from the local disorder of the host crystal. We report the spectroscopic properties of Yb3+ in the 5–300K temperature range and the optical properties of the host at room temperature.
Crystal field excitations in the singlet ground state compound Pr3In
Authors: Christianson A. D. , Lawrence J. M. , Littrell K. C. , Goremychkin E. A. , Kolesnikov A. I. , Thompson J. D. , Sarrao J. L.
Published: March 2007

Pr 3 In exhibits an antiferromagnetic transition at ∼12K. This transition appears to occur due to the exchange-generated admixture of higher lying crystal field levels into the singlet ground state. It is thus an example of an induced moment antiferromagnet. To provide detailed understanding of the magnetic behavior of Pr3In, we have measured the magnetic excitation spectrum with inelastic neutron scattering experiments. We observe a clear dispersion of a crystal field excitation at 4K. Above 100K, the dispersion of the crystal field excitation has largely vanished and a crystal field scheme for Pr in a cubic site symmetry (in which the lowest states are a Γ1 singlet and a Γ4 triplet) provides a good approximation to the data.
Low-loss barium ferrite quasi-single-crystals for microwave application
Authors: Chen Yajie , Geiler Anton L. , Chen Taiyang , Sakai Tomokazu , Vittoria C. , Harris V. G.
Published: March 2007

Barium hexaferrites (BaFe12O19) are especially useful for microwave/millimeter devices. Due to large ferromagnetic resonance (FMR) loss (linewidths >2kOe), traditional compacts of polycrystalline Ba ferrites indeed hinder the utilization of the materials for practical devices. The present experiment demonstrates that the quasi-single-crystal Ba ferrite disks can be fabricated by a single solid-state reaction technique without liquid phase participation, combining with a processing of alignment for the ferrite seed crystals. The ferrite bulks show a pure hexagonal Ba ferrite phase, an expected 4πMs of 4.48kG, and coercivity of 10∼20Oe along the c axis, similar to the results of a typical single crystal. The FMR measurement indicates that the sample yields an anisotropy field of 16.0kOe and a linewidth of about 300Oe at U-band frequencies. Although the linewidth is broader than ideal Ba ferrite single crystals (ΔH<100Oe), it may be possible to reduce to 100Oe by eliminating pores, cracks, local grain boundary, and nonuniformity. In terms of material preparation, we believe that it is cost effective in the production of future microwave devices.
Structure and optical characterization of sulfur incorporated As2Se3 crystals
Authors: Wu Ching-Cherng
Published: March 2007

In this study, structural and optical properties of crystalline sulfur incorporated As2Se3 have been characterized using x-ray diffraction and thermoreflectance (TR) measurements at 300K. The crystalline layer compounds of As2(Se1−xSx)3 (0⩽x⩽0.4) [c-As2(Se1−xSx)3] were grown by vertical Bridgman method. The lattice parameters were determined by x-ray diffraction measurements. The band structure of c-As2(Se1−xSx)3 was characterized experimentally by TR measurements in the energy range of 1.25–6eV. TR spectra of the c-As2(Se1−xSx)3 (0⩽x⩽0.4) exhibit a multitude of derivativelike features in the vicinity of band edge as well as the higher lying interband transition regions. Interband transition features of the c-As2(Se1−xSx)3 (0⩽x⩽0.4) are analyzed and the proper transition origins are assigned. Based on the experimental analyses and on the previous band-structure calculations of As2X3 (X=S,Se), a probable experimental band scheme near the fundamental edge of As2(Se1−xSx)3 is then constructed.
Study on constitutive relations and spall models for oxygen-free high-conductivity copper under planar shock tests
Authors: Danian Chen , Chunlei Fan , Shugang Xie , Jinwei Hu , Shanxing Wu , Huanran Wang , Hua Ta , Yuying Yu
Published: March 2007

It is indicated that the constitutive relations for shear modulus G as functions of thermodynamic state were not given in the Johnson-Cook model and the Zerilli-Armstrong model while the constitutive relations for yield strength Y as functions of strain and strain rate were not given in the Wallace model and the Straub model. Seven constitutive models are constructed based on Y∕G=constant and on G∕B=constant (B-bulk modulus), respectively. The variations of longitudinal stress, transverse stress, and yield strength of oxygen-free high-conductive (OFHC) copper with time under planar shock loading are obtained using the manganin stress gauges and compared with the predicted results by the constructed seven constitutive models. It seems that the pressure, density, temperature, and plastic strain dependence of the yield strength for OFHC copper subjected to planar shock loading is essential to the constitutive description. Planar spall tests for OFHC copper are also performed and the void coalescence-based spall model presented by the authors are applied to numerical simulations of planar spall tests including tests given by Seaman et al. [Phys. Rep. 147, 253 (1987)]. The Steinberg-Cochran-Guinan constitutive model is proved appropriate to the planar shock loading and is adopted in the numerical simulations of planar spall tests.
Optimum charge carrier mobility in organic solar cells
Authors: Mandoc M. M. , Koster L. J. A. , Blom P. W. M.
Published: March 2007

In organic semiconductors the recombination mechanism is of the Langevin type, controlled by the mobility of the charge carriers. As a result, in organic solar cells the mobility simultaneously controls both the carrier extraction and the losses via carrier recombination. The authors demonstrate that the balance between carrier losses by extraction and by recombination leads to a distinct optimum in the carrier mobility with regard to the efficiency of organic solar cells. For low mobilities recombination losses limit the performance, whereas the efficient extraction at high mobilities leads to a reduction of the open-circuit voltage.
Bifurcation analysis of bubble dynamics in fluidized beds
Authors: Blomgren Peter , Palacios Antonio , Zhu Bing , Daw Stuart , Finney Charles , Halow John , Pannala Sreekanth
Published: March 2007

We use a low-dimensional, agent-based bubble model to study the changes in the global dynamics of fluidized beds in response to changes in the frequency of the rising bubbles. The computationally based bifurcation analysis shows that at low frequencies, the global dynamics is attracted towards a fixed point since the bubbles interact very little with one another. As the frequency of injection increases, however, the global dynamics undergoes a series of bifurcations to new behaviors that include highly periodic orbits, chaotic attractors, and intermittent behavior between periodic orbits and chaotic sets. Using methods from time-series analysis, we are able to approximate nonlinear models that allow for long-term predictions and the possibility of developing control algorithms.
Thermophoresis of a slightly deformed aerosol sphere
Authors: Senchenko Sergey , Keh Huan J.
Published: March 2007

An analytical study is presented for the thermophoretic motion of a freely suspended aerosol particle with an arbitrary, slightly deformed spherical surface in a uniformly prescribed temperature gradient. The Knudsen number is assumed to be small so that the fluid flow is described by a continuum model with a temperature jump, a thermal slip, and a frictional slip at the surface of the particle. A first attempt is made to obtain analytical approximations for the thermophoretic velocity of the particle in the limit of vanishing Peclet and Reynolds numbers. To the first order in the small parameter characterizing the deformation of the spherical shape of the particle, explicit expressions are derived for its drift and rotational velocities. The angular velocity of a particle undergoing thermophoresis is found to be zero for any shape, which is the first indication that the fluid motion around a single thermophoretic particle of an arbitrary shape is irrotational, as is known to be in the case of thin-double-layer electrophoresis. A comparison of our first-order approximation for the thermophoretic velocity of a spheroid with the available exact solution shows that the agreement is quite good, even for relatively large deformations of the spherical shape of the particle. Our results for the motion of a spheroid demonstrate that its relative physical and surface properties, its aspect ratio, and its orientation relative to the imposed temperature gradient can have significant effects on its thermophoretic mobility.
Structural transition of ferromagnetic Ni2MnGa nanoparticles
Authors: Wang Y. D. , Ren Y. , Nie Z. H. , Liu D. M. , Zuo L. , Choo H. , Li H. , Liaw P. K. , Yan J. Q. , McQueeney R. J. , Richardson J. W. , Huq A.
Published: March 2007

We report here that the ball-milling process induces the phase transformation from the tetragonal structure to the disordered face-centered-cubic structure in Ni2MnGa ferromagnetic shape-memory alloys. The in situ high-energy x-ray diffraction analyses reveal that an intermediate phase, which is characterized by amorphous structure, controls the transformation kinetics during the postannealing process. Completely different from their coarse-grained counterparts, the ferromagnetic Ni2MnGa nanoparticles undergo various sequences of structural transitions that are tailored by the crystallite size, atomic order, and intrinsic magnetic structure.
Interlayer segregation of nonmagnetic metal spacers and its influence on exchange coupling in magnetic multilayers
Authors: Li M. H. , Yu G. H. , Zhu F. W. , Lai W. Y.
Published: March 2007

Two sets of NiFe∕FeMn films with Ta and Ta∕Cu buffer layers were prepared by magnetron sputtering to study the influence of different buffers on the exchange coupling process. The results show that the exchange bias field (Hex) of NiFe∕FeMn films with a Ta∕Cu buffer is lower than that of films with a Ta buffer. There is no apparent difference in the texture and roughness of films both with Ta and Ta∕Cu buffers. However, the segregation of Cu atoms on the surface of NiFe in the trilayer of Ta∕Cu∕NiFe was found by using angle-resolved x-ray photoelectron spectroscopy (XPS). A decrease of Hex for NiFe∕FeMn films with a Ta∕Cu buffer layer is primarily caused by the segregation of Cu atoms to the interface of the NiFe and FeMn layers. In order to suppress the Cu segregation, we deposited Bi insetting layers at the interface of Cu and NiFe in Ta∕Cu∕NiFe∕FeMn∕Ta films and found that Hex of NiFe∕FeMn can be doubled when the proper quantity of Bi is deposited. XPS analysis shows that Bi insetting layers deposited at the interface of Cu and NiFe effectively suppress the Cu segregation on the NiFe layer. As a result, Hex is increased. However, if the insetting Bi is deposited excessively, it will partially migrate to the FeMn layer, damaging the antiferromagnetic property of the FeMn layer, thereby resulting in decreased Hex. When Ag and Pb were deposited at the interface of Cu and NiFe in Ta∕Cu∕NiFe∕FeMn∕Ta films, similar experimental results were obtained.
Critical temperatures of 70%Pb(Mg1∕3Nb2∕3)O3–30%PbTiO3 thin films investigated by dielectric, ferroelectric, and structural measurements
Authors: Meng X. J. , Rémiens D. , Detalle M. , Dkhil B. , Sun J. L. , Chu J. H.
Published: March 2007

The authors have investigated the temperature dependence of the ferroelectric, dielectric, and structural properties of 70%Pb(Mg1∕3Nb2∕3)O3–30%PbTiO3 thin films. Two critical temperatures were evidenced. The first one occurring around 410K corresponds to the bulk paraelectric-ferroelectric phase transition and the second one around 200K is rather related to a self-arrangement of small domains into macrodomains in order to minimize elastic energies. A multiscale domainlike structure is induced and the temperature evolution of such complex structure can be revealed through pronounced changes occurring in the nonlinear dielectric susceptibility.
Molecular statics calculation of the formation enthalpy for ternary metal systems based on the long-range empirical interatomic potentials
Authors: Dai X. D. , Li J. H. , Liu B. X.
Published: March 2007

A scheme is proposed in the present study to predict the formation enthalpy of the ternary metal system. Based on the long-range empirical potential model, the interatomic potentials are first constructed for the Cu–Ag–Au, Cu–Ag–Ni, Ag–Au–Ni, and Cu–Au–Ni systems, and then molecular statics calculations are performed to predict the formation enthalpies of the four systems. It is found that the predicted results by the present scheme match well with those obtained by experiments or ab initio calculations, exhibiting a more precise feature than Miedema’s model.
Ferroelectric domains and piezoelectricity in monocrystalline Pb(Zr,Ti)O3 nanowires
Authors: Wang J. , Sandu C. S. , Colla E. , Wang Y. , Ma W. , Gysel R. , Trodahl H. J. , Setter N. , Kuball M.
Published: March 2007

Monocrystalline lead zirconate titanate nanowires were grown by a polymer assisted solvothermal technique. X-ray and electron diffractions confirmed tetragonal perovskite structure and a [001] orientation along the wire axis, respectively. Raman scattering was used to analyze the structure and composition of single wires. Ferroelectric/ferroelastic domain walls were imaged by transmission electron microscopy, showing some domains with polarization directions along the wire axis and some perpendicular to it. The domain walls disappeared upon heating above the ferroelectric phase transition at 460°C. Ferroelectric switching, as well as piezoelectric activity and hysteresis, were shown locally using piezoelectric force microscopy.
Valence band offset of InN∕AlN heterojunctions measured by x-ray photoelectron spectroscopy
Authors: King P. D. C. , Veal T. D. , Jefferson P. H. , McConville C. F. , Wang T. , Parbrook P. J. , Lu Hai , Schaff W. J.
Published: March 2007

The valence band offset of wurtzite-InN∕AlN (0001) heterojunctions is determined by x-ray photoelectron spectroscopy to be 1.52±0.17eV. Together with the resulting conduction band offset of 4.0±0.2eV, a type-I heterojunction forms between InN and AlN in the straddling arrangement.
Vertically coupled quantum wires in a longitudinal magnetic field
Authors: Mourokh Lev G. , Smirnov Anatoly Yu. , Fischer Saskia F.
Published: March 2007

The authors examine analytically the energy subband structure for two vertically stacked quantum wires separated by a tunneling barrier in the presence of a longitudinal magnetic field. For identical harmonic confining potentials, they show that the tunnel splitting between formed symmetric and antisymmetric subbands decreases exponentially with increasing magnetic field and, moreover, the tunnel coupling disappears at appropriate values of the magnetic field in agreement with experimental data. They propose to achieve a controllable coupling of quantum wires with the decoupling magnetic field and with nanomagnets providing coupling windows, which can be used for quantum computation purposes.
Near-diffraction-limited passively Q-switched Yb:Y3Al5O12 ceramic lasers with peak power >150kW
Authors: Dong Jun , Shirakawa Akira , Ueda Ken-ichi , Yagi Hideki , Yanagitani Takagimi , Kaminskii Alexander A.
Published: March 2007

Laser-diode pumped nearly diffraction-limited beam quality (M2<1.05), high peak power, subnanosecond passively Q-switched Yb:Y3Al5O12 ceramic miniature laser with Cr4+:Y3Al5O12 ceramic as saturable absorber has been achieved. The slope efficiency is as high as 36% for 80% initial transmission of Cr4+:Y3Al5O12 ceramic. The pulse width of 335ps and peak power of over 150kW at repetition rate of 5kHz were obtained. Laser oscillates at single-longitudinal-mode oscillation and wide-separated multilongitudinal-mode oscillation due to the combined etalon effect of the Cr4+:YAG thin plate and thin glass plate as output coupler.
Relating species traits to environmental variables in Indonesian coral reef sponge assemblages
Authors: de Voogd Nicole J. , Cleary Daniel F. R.
Published: March 2007

A key goal in ecology is to understand how species with given traits vary with changing environmental conditions. In the Spermonde Archipelago, Indonesia, we identified environmental gradients associated with significant variation in sponge species traits. These were (1) an on-to-offshore gradient, (2) a gradient from locally perturbed reef sites characterised by fluctuating sediment load concentrations and poor water transparency to locally pristine sites characterised by good water transparency and (3) a depth gradient. Species with a massive growth form were associated with inshore reef environments, whereas species with a cup growth form were linked to offshore reefs with a high coral cover. Weakly bioactive species and species with a globular, fan or fistulose growth form were associated with locally perturbed reef environments as indicated by fluctuating sediment levels and reduced water transparency, whereas strongly bioactive species and species with a massive-encrusting and tube growth form were associated with more pristine reef environments with good water transparency. With respect to depth, oviparous species and species with a cup and massive growth form were most strongly associated with deeper transects, whereas species with a ramose, massive creeping and massive-encrusting growth form were most strongly associated with shallower transects. Results of the present study indicate that environmental conditions and species traits interact to determine the composition of sponges across coral reefs.
Local structural disorder imparts plasticity on linear motifs
Authors: Fuxreiter Monika , Tompa Peter , Simon István
Published: March 2007

Motivation: The dynamic nature of protein interaction networks requires fast and transient molecular switches. The underlying recognition motifs (linear motifs, LMs) are usually short and evolutionarily variable segments, which in several cases, such as phosphorylation sites or SH3-binding regions, fall into locally disordered regions. We probed the generality of this phenomenon by predicting the intrinsic disorder of all LM-containing proteins enlisted in the Eukaryotic Linear Motif (ELM) database.

Results: We demonstrated that LMs in average are embedded in locally unstructured regions, while their amino acid composition and charge/hydropathy properties exhibit a mixture characteristic of folded and disordered proteins. Overall, LMs are constructed by grafting a few specificity-determining residues favoring structural order on a highly flexible carrier region. These results establish a connection between LMs and molecular recognition elements of intrinsically unstructured proteins (IUPs), which realize a non-conventional mode of partner binding mostly in regulatory functions.

Contact:  simon@enzim.hu

Supplementary information: Supplementary data are available at Bioinformatics online.
A sequential Monte Carlo EM approach to the transcription factor binding site identification problem
Authors: Jackson Edmund S. , Fitzgerald William J.
Published: March 2007

Motivation: A significant and stubbornly intractable problem in genome sequence analysis has been the de novo identification of transcription factor binding sites in promoter regions. Although theoretically pleasing, probabilistic methods have faced difficulties due to model mismatch and the nature of the biological sequence. These problems result in inference in a high dimensional, highly multimodal space, and consequently often display only local convergence and hence unsatisfactory performance.

Algorithm: In this article, we derive and demonstrate a novel method utilizing a sequential Monte Carlo-based expectation-maximization (EM) optimization to improve performance in this scenario. The Monte Carlo element should increase the robustness of the algorithm compared to classical EM. Furthermore, the parallel nature of the sequential Monte Carlo algorithm should be more robust than Gibbs sampling approaches to multimodality problems.

Results: We demonstrate the superior performance of this algorithm on both semi-synthetic and real data from Escherichia coli.

Availability: http://sigproc-eng.cam.ac.uk/∼ej230/smc_em_tfbsid.tar.gz

Contact: ej230@cam.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
Regression analysis and modelling of data acquisition for SELDI-TOF mass spectrometry
Authors: Sköld Martin , Rydén Tobias , Samuelsson Viktoria , Bratt Charlotte , Ekblad Lars , Olsson Håkan , Baldetorp Bo
Published: March 2007

Motivation: Pre-processing of SELDI-TOF mass spectrometry data is currently performed on a largel y ad hoc basis. This makes comparison of results from independent analyses troublesome and does not provide a framework for distinguishing different sources of variation in data.

Results: In this article, we consider the task of pooling a large number of single-shot spectra, a task commonly performed automatically by the instrument software. By viewing the underlying statistical problem as one of heteroscedastic linear regression, we provide a framework for introducing robust methods and for dealing with missing data resulting from a limited span of recordable intensity values provided by the instrument. Our framework provides an interpretation of currently used methods as a maximum-likelihood estimator and allows theoretical derivation of its variance. We observe that this variance depends crucially on the total number of ionic species, which can vary considerably between different pooled spectra. This variation in variance can potentially invalidate the results from naive methods of discrimination/classification and we outline appropriate data transformations. Introducing methods from robust statistics did not improve the standard errors of the pooled samples. Imputing missing values however—using the EM algorithm—had a notable effect on the result; for our data, the pooled height of peaks which were frequently truncated increased by up to 30%.

Contact: martins@maths.lth.se

Supplementary information: Supplementary data are available at Bioinformatics online.
Stability and value of male care for offspring: is it worth only half the trouble?
Authors: Fromhage Lutz , McNamara John M , Houston Alasdair I
Published: March 2007

Models of parental investment often assume a trade-off for males between providing care and seeking additional mating opportunities. It is not obvious, however, how such additional matings should be accounted for in a consistent population model, because deserting males might increase their fertilization success at the cost of either caring males, other deserting males or both. Here, we present a game theory model that addresses all of these possibilities in a general way. In contrast to earlier work, we find that the source of deserting males' additional matings is irrelevant to the evolutionary stability of male care. We reject the claim that fitness gains through male care are intrinsically less valuable than those through desertion, and that the former must therefore be down-weighted by 1/2 when compared with the latter.
John Freind: physician, chemist, Jacobite, and friend of Voltaire's
Authors: Rowlinson J.S
Published: March 2007

John Freind (1675/76–1728) achieved distinction in several walks of life, first as a classical scholar, then as a physician and as a chemist who advocated Newtonian philosophy. His clinical practice was generally conservative and he was against the newly introduced practice of inoculating the smallpox. His principles were Tory and High Church; his loyalty to the house of Stuart involved him in the Jacobite plot of 1722, and a spell in the Tower of London. His money was part of the foundation of Dr Lee's benefaction to Christ Church, which still survives in name in scientific posts in Oxford. He was among the circle of friends that Voltaire formed during his two-year stay in England and, 50 years later, Voltaire took him and his son as the principal characters in a
conte philosophique
defending a deistic attitude against both atheism and revealed religion.
The legacy of Professor John Stanley Gardiner FRS to reef science
Authors: Brown Barbara E
Published: March 2007

John Stanley Gardiner is best known for his extensive expeditions into the Indian Ocean to study the flora and fauna of coral reefs and islands in the early 1900s. His contributions to reef origins and reef morphology have been discussed by others but little has been made of his zoological studies, which were well ahead of their time, and his significant influence on the Great Barrier Reef Expedition of 1928–29, which proved to be a major breakthrough in the study of coral reefs. This paper reviews his important legacy in this regard.
Experimental computation of real numbers by Newtonian machines
Authors: Beggs E.J , Tucker J.V
Published: March 2007

Following a methodology we have proposed for analysing the nature of experimental computation, we prove that there is a three-dimensional Newtonian machine which given
any
point
x
∈[0, 1] can generate an infinite sequence [
p

n

,
q

n

], for
n
=1, 2, …, of rational number interval approximations, that converges to
x
as
n
→∞. The machine is a system for scattering and collecting particles. The theorem implies that every point x∈[0, 1] is computable by a simple Newtonian kinematic system that is bounded in space and mass and for which the calculation of the nth approximation of x takes place in
O
(
n
) time with
O
(
n
) energy. We describe variants of the scatter machine which explain why our machine is non-deterministic.
Birds prefer to breed in sites with low radioactivity in Chernobyl
Authors: Møller A.P , Mousseau T.A
Published: March 2007

Low-level radioactive contamination may affect choice of breeding site and life-history decisions if (i) radioactivity directly affects body condition or (ii) it affects resource abundance that then secondarily influences reproductive decisions. We tested the effects of radioactive contamination on nest-site choice and reproduction in a community of hole nesting birds by putting up nest boxes in areas differing in levels of background radiation. Great tit
Parus major
and pied flycatcher
Ficedula hypoleuca
significantly avoided nest boxes in heavily contaminated areas, with a stronger effect in flycatchers than in tits. These preferences could not be attributed to variation in habitat quality or resource abundance, as determined by analyses of habitat use and the relationship between radiation and life-history characters. Likewise, none of these effects could be attributed to individuals of a specific age breeding in the most contaminated areas. Laying date and clutch size were not significantly related to dose rate in either species. Hatching success was depressed by elevated radioactive contamination, interacting with habitat in the great tit and with laying date in the pied flycatcher. Interspecific differences in effects of radiation on nest-site choice suggest that species respond in a species-specific manner to radiation, perhaps related to differences in migratory habits. We suggest that individual body condition rather than secondary effects of radiation on resource abundance account for the effects on nest box use and hatching success.
Perception of visual texture and the expression of disruptive camouflage by the cuttlefish,Sepia officinalis
Authors: Kelman E.J , Baddeley R.J , Shohet A.J , Osorio D
Published: March 2007

Juvenile cuttlefish (Sepia officinalis)camouflage themselves by changing their body pattern according to the background. This behaviour can be used to investigate visual perception in these molluscs and may also give insight into camouflage design. Edge detection is an important aspect of vision, and here we compare the body patterns that cuttlefish produced in response to checkerboard backgrounds with responses to backgrounds that have the same spatial frequency power spectrum as the checkerboards, but randomized spatial phase. For humans, phase randomization removes visual edges. To describe the cuttlefish body patterns, we scored the level of expression of 20 separate pattern ‘components’, and then derived principal components (PCs) from these scores. After varimax rotation, the first component (PC1) corresponded closely to the so-called disruptive body pattern, and the second (PC2) to the mottle pattern. PC1 was predominantly expressed on checkerboards, and PC2 on phase-randomized backgrounds. Thus, cuttlefish probably have edge detectors that control the expression of disruptive pattern. Although the experiments used unnatural backgrounds, it seems probable that cuttlefish display disruptive camouflage when there are edges in the visual background caused by discrete objects such as pebbles. We discuss the implications of these findings for our understanding of disruptive camouflage.
Microlunatus ginsengisoli sp. nov., isolated from soil of a ginseng field
Authors: Cui Ying-Shun , Im Wan-Taek , Yin Cheng-Ri , Yang Deok-Chun , Lee Sung-Taik
Published: March 2007

A Gram-positive, aerobic, coccus-shaped, non-endospore-forming bacterium (Gsoil 633T) was isolated from soil from a ginseng field in Pocheon province in South Korea. The novel isolate was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarities, strain Gsoil 633T was shown to belong to the family Propionibacteriaceae. The closest phylogenetic relative was Microlunatus phosphovorus DSM 19555T, with 96.1 % sequence similarity; the sequence similarity to other members of the family was less than 95.4 %. The isolate was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-9(H4) as the predominant menaquinone and anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0 as the major fatty acids. The G+C content of the genomic DNA was 69.8 mol%. The morphological and chemotaxonomic properties of the isolate were consistent with those of M. phosphovorus, but the results of physiological and biochemical tests allowed the phenotypic differentiation of strain Gsoil 633T from this species. Therefore, strain Gsoil 633T represents a novel species, for which the name Microlunatus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 633T (=KCTC 13940T=DSM 17942T).
Nocardia ninae sp. nov., isolated from a bronchial aspirate
Authors: Laurent Frédéric , Rodríguez-Nava Verónica , Noussair Latifa , Couble Andrée , Nicolas-Chanoine Marie-Hélène , Boiron Patrick
Published: March 2007

A Gram-positive and acid-fast filamentous bacterium (OFN 02.72T) was isolated from a bronchial aspirate from a 53-year-old patient. Chemotaxonomic data supported the affiliation of this organism to the genus Nocardia, and the phenotypic characteristics demonstrated that the strain differed from all previously described Nocardia species. Restriction enzyme analysis of the hsp65 gene (encoding the 65 kDa heat-shock protein) and sequencing of the 16S rRNA and hsp65 genes confirmed that this isolate is unique. The most closely related type strains were Nocardia alba YIM 30243T (=DSM 44684T) and Nocardia jejuensis N3-2T (=JCM 13281T) (with 16S rRNA gene sequence similarities of 98.3 and 97.2 %, respectively). On the basis of this polyphasic study, strain OFN 02.72T represents a novel species within the genus Nocardia, for which the name Nocardia ninae sp. nov. is proposed. The type strain is OFN 02.72T (=CIP 108955T=DSM 44978T).
Taxonomic evaluation of the genera Ruegeria and Silicibacter: a proposal to transfer the genus Silicibacter Petursdottir and Kristjansson 1999 to the genus Ruegeria Uchino et al. 1999
Authors: Yi Hana , Lim Young Woon , Chun Jongsik
Published: March 2007

The taxonomic positions of the genera Ruegeria and Silicibacter were evaluated by a polyphasic investigation. It was evident from 16S rRNA gene sequence analysis that both genera are closely related as they formed a monophyletic clade with high sequence similarities (96.9–98.2 %). Several properties commonly found in these taxa strongly suggest that they should be classified in the same genus. Further, a comparative study based on DNA–DNA hybridization, phenotypic characterization and chemotaxonomic analysis indicated that the members of this clade, namely Ruegeria atlantica, Silicibacter lacuscaerulensis and Silicibacter pomeroyi, can be readily differentiated from each other. On the basis of the polyphasic data obtained in this study, all species of the genus Silicibacter should be transferred to the genus Ruegeria, since the latter has nomenclatural priority. It is therefore proposed that Silicibacter lacuscaerulensis and Silicibacter pomeroyi are transferred to the genus Ruegeria as Ruegeria lacuscaerulensis comb. nov. and Ruegeria pomeroyi comb. nov.
Haloplanus natans gen. nov., sp. nov., an extremely halophilic, gas-vacuolate archaeon isolated from Dead Sea–Red Sea water mixtures in experimental outdoor ponds
Authors: Bardavid Rahel Elevi , Mana Lily , Oren Aharon
Published: March 2007

To study biological phenomena in the Dead Sea and to simulate the effects of mixing Dead Sea water with Red Sea water, experimental mesocosms were operated at the Dead Sea Works at Sedom, Israel. Dense communities of red halophilic archaea developed in mesocosms filled with 80 % Dead Sea water and 20 % Red Sea water after enrichment with phosphate. The most common type of colonies isolated from these brines belonged to the genus Halorubrum. A few white–pinkish opaque colonies contained pleomorphic flat cells with gas vesicles. Three strains isolated from the latter colonies were characterized in depth. Their 16S rRNA gene sequences showed only 91 % similarity to the closest cultured relative (Haloferax mediterranei), indicating that the new strains represent a novel species of a new genus. The name Haloplanus natans gen. nov., sp. nov. is proposed for this novel organism. The type strain of Haloplanus natans is RE-101T (=DSM 17983T=JCM 14081T).
Enterobacter turicensis sp. nov. and Enterobacter helveticus sp. nov., isolated from fruit powder
Authors: Stephan Roger , Van Trappen Stefanie , Cleenwerck Ilse , Vancanneyt Marc , De Vos Paul , Lehner Angelika
Published: March 2007

Four Gram-negative, facultatively anaerobic, non-spore-forming isolates of coccoid rods were obtained from fruit powder and investigated in a polyphasic taxonomic study. Comparative 16S rRNA gene sequence analysis allocated the isolates to the family Enterobacteriaceae. Their phylogenetic position within the family Enterobacteriaceae was confirmed by rpoB sequence analysis and as the highest rpoB sequence similarities were obtained with Enterobacter radicincitans, Enterobacter cowanii and Enterobacter sakazakii, the isolates clearly belong to the genus Enterobacter. Biochemical data revealed that the isolates can be separated into two distinct groups that represent two novel species, as confirmed by DNA–DNA hybridizations. The two novel species can be differentiated from their nearest neighbours by the following characteristics: the utilization of sucrose, d-sorbitol, putrescine and mucate, the hydrolysis of aesculin and a negative result in the Voges–Proskauer reaction. It is therefore proposed that these novel isolates are classified as Enterobacter turicensis sp. nov. (type strain 508/05T=LMG 23730T=DSM 18397T) and Enterobacter helveticus sp. nov. (type strain 513/05T=LMG 23732T=DSM 18396T).
Paenibacillus zanthoxyli sp. nov., a novel nitrogen-fixing species isolated from the rhizosphere of Zanthoxylum simulans
Authors: Ma Yuchao , Zhang Jian , Chen Sanfeng
Published: March 2007

Five endospore-forming, nitrogen-fixing strains were isolated from rhizosphere soils ofZanthoxylum simulansplanted in Beijing, China. Phylogenetic analysis based on full-length 16S rRNA gene sequences revealed that the five strains formed a distinct cluster within the genusPaenibacillus. High levels of 16S rRNA gene sequence similarity were found between these novel strains andPaenibacillus azotofixansATCC 35681T(97.8–98.5 % similarity) andPaenibacillus stelliferDSM 14472T(95.4–96.3 %). Levels of 16S rRNA gene sequence similarity between the novel isolates and other species of the genusPaenibacilluswere less than 95.0 %. Levels of 16S rRNA gene sequence similarity among the isolates were more than 98.0 %. DNA–DNA relatedness between the five novel isolates andP. azotofixansATCC 35681Twas 45.50–47.45 % and relatedness among the five novel strains was 95.8–99.6 %. A significant feature of the novel strains that differentiated them fromP. azotofixansand otherPaenibacillusspecies was that none of the novel strains could produce acid or gas from the following various carbohydrates: glucose, sucrose, lactose, fructose, glycerol, xylose, maltose,d-sorbitol, sodium succinate, sodium citrate, glycine orl-aspartate. Anteiso-branched C15 : 0was the major fatty acid component (36.59 %) of novel strain JH29T. On the basis of phenotypic properties, 16S rRNA gene sequences, DNA G+C content, DNA–DNA hybridization, chemotaxonomic properties and thenifHgene sequence, the five novel strains form a very homogeneous group which is different from other related species within the genusPaenibacillus. Therefore, the five novel strains are considered to represent a novel species of the genusPaenibacillus, for which the namePaenibacillus zanthoxylisp. nov. is proposed. The type strain is JH29T(=CCBAU 10243T=DSM 18202T).
Granulicoccus phenolivorans gen. nov., sp. nov., a Gram-positive, phenol-degrading coccus isolated from phenol-degrading aerobic granules
Authors: Maszenan Abdul Majid , Jiang He Long , Tay Joo-Hwa , Schumann Peter , Kroppenstedt Reiner M. , Tay Stephen Tiong-Lee
Published: March 2007

A Gram-positive bacterium, designated strain PG-02T, was isolated by serial dilution from aerobic granules obtained from a laboratory-scale sequencing batch reactor for bioremediation of phenolic wastewater. Strain PG-02T grew axenically as cocci and is an oxidase-negative and catalase-positive, non-motile facultative anaerobe. It does not reduce nitrate and grows between 15 and 37 °C, with an optimum temperature of 30 °C. The pH range for growth is between 5.0 and 8.5, with an optimum pH of 7.0. Strain PG-02T contains type A3γ peptidoglycan (ll-A2pm←Gly with alanine at position 1 of the peptide subunit). The G+C content of the DNA is 69 mol%. Menaquinone MK-9(H4) was the major isoprenoid quinone. The polar lipids included diphosphatidylglycerol and phosphatidylglycerol, while 13-methyltetradecanoic acid (i-C15 : 0) and 1,1-dimethoxy-iso-pentadecane (i-C15 : 0 DMA) were the major components in whole-cell methanolysates. PG-02T stained positively for intracellular polyphosphate granules but not poly-β-hydroxyalkanoates. It produces capsular material and possesses an autoaggregation capability. Phenotypic and 16S rRNA gene sequence analyses showed that PG-02T differed from its closest phylogenetic relatives, namely members of the suborder Propionibacterineae, which includes the genera Tessaracoccus, Microlunatus, Luteococcus, Micropruina, Propionibacterium, Propioniferax, Nocardioides, Friedmanniella and Aeromicrobium, and that it should be placed in a new genus and species as Granulicoccus phenolivorans gen. nov., sp. nov. The type strain of Granulicoccus phenolivorans is PG-02T (=ATCC BAA-1292T=DSM 17626T).
Leucobacter iarius sp. nov., in the family Microbacteriaceae
Authors: Somvanshi Vishal S. , Lang Elke , Schumann Peter , Pukall Rüdiger , Kroppenstedt R. M. , Ganguly Sudershan , Stackebrandt Erko
Published: March 2007

A novel Gram-positive bacterium, strain 40T, was isolated in the course of identifying bacteria from infective juveniles of the entomopathogenic nematode Steinernema thermophilum. Based on 16S rRNA gene analysis, strain 40T was found to be related to the type strains of recognized species of the genus Leucobacter, family Microbacteriaceae. The 16S rRNA gene sequence similarity values of strain 40T and Leucobacter albus IAM 14851T, Leucobacter luti LMG 23118T, Leucobacter alluvii LMG 23117T, Leucobacter komagatae DSM 8803T, Leucobacter chromiireducens CIP 108389T and Leucobacter aridicollis CIP 108388T, respectively, were 97.3, 97.5, 97.6, 97.6, 97.6 and 98.5 %. Chemotaxonomic analysis also supported the affiliation of strain 40T to the genus Leucobacter: the major menaquinone was MK-11, the peptidoglycan cross-linkage was of the B-type, the cell wall diamino acid was l-diaminobutyric acid and the major fatty acids were anteiso-C15 : 0 (42 %), anteiso-C17 : 0 (34 %) and iso-C16 : 0 (16 %). Based upon the biochemical and genomic analyses, strain 40T is sufficiently distinct from the type strains of recognized Leucobacter species to warrant the description of a novel species, for which the name Leucobacter iarius sp. nov. is proposed. The type strain is strain 40T (=DSM 17402T=CIP 108831T).
Aeromicrobium panaciterrae sp. nov., isolated from soil of a ginseng field in South Korea
Authors: Cui Ying-Shun , Im Wan-Taek , Yin Cheng-Ri , Lee Jung-Sook , Lee Keun Chul , Lee Sung-Taik
Published: March 2007

A Gram-positive, rod-shaped, non-spore-forming and strictly aerobic bacterium (Gsoil 161T) was isolated from soil of a ginseng field in Pocheon Province, South Korea. The novel isolate was characterized using a polyphasic approach in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 161T was shown to belong to the family Nocardioidaceae and was related to Aeromicrobium marinum (98.0 % similarity to the type strain), Aeromicrobium alkaliterrae (97.6 %), Aeromicrobium fastidiosum (97.0 %) and Aeromicrobium erythreum (96.7 %); the sequence similarity with other species within the family was less than 94.4 %. It was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-9(H4) as the predominant menaquinone and C16 : 0, 10-methyl C18 : 0 (tuberculostearic acid), C16 : 0 2-OH, 10-methyl C17 : 0 and 10-methyl-C16 : 0 as the major fatty acids. The G+C content of the genomic DNA was 65.5 mol%. These chemotaxonomic properties and phenotypic characteristics support the affiliation of strain Gsoil 161T to the genus Aeromicrobium. Results of physiological and biochemical tests enabled strain Gsoil 161T to be differentiated genotypically and phenotypically from currently known Aeromicrobium species. Therefore, strain Gsoil 161T represents a novel species, for which the name Aeromicrobium panaciterrae sp. nov. is proposed. The type strain is strain Gsoil 161T (=KCTC 19131T=DSM 17939T=CCUG 52476T).
Lechevalieria fradiae sp. nov., a novel actinomycete isolated from soil in China
Authors: Zhang Jianli , Xie Qiong , Liu Zhiheng , Goodfellow Michael
Published: March 2007

The taxonomic position of a soil isolate, strain Z6T, was established using a polyphasic approach. The organism showed a range of chemical and morphological properties consistent with its classification in the genusLechevalieria. An almost complete 16S rRNA gene sequence determined for the strain was aligned with corresponding sequences of representatives of the genusLechevalieriaand related taxa using three tree-making algorithms. The organism formed a distinct phyletic line within the evolutionary radiation occupied by the genusLechevalieriaand was more closely related to the type strain ofLechevalieria aerocolonigenesthan to that ofLechevalieria flava. Strain Z6Tcould be distinguished from both these strains using DNA–DNA relatedness data and by a combination of phenotypic properties. The combined genotypic and phenotypic data show that strain Z6Tshould be assigned to the genusLechevalieriaas a representative of a novel species. The name proposed for this new taxon isLechevalieria fradiaesp. nov. The type strain is Z6T(=CGMCC 4.3506T=JCM 14205T).
Phaeobacter daeponensis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea
Authors: Yoon Jung-Hoon , Kang So-Jung , Lee Soo-Young , Oh Tae-Kwang
Published: March 2007

A Gram-negative, motile and egg-shaped bacterium, strain TF-218T, was isolated from a tidal flat at Daepo Beach (Yellow Sea), Korea, and subjected to a polyphasic taxonomic analysis. Strain TF-218T grew optimally at pH 7.0–8.0 and 37 °C in the presence of 2 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C18 : 1
ω7c and 11-methyl C18 : 1
ω7c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified lipids and an aminolipid. The DNA G+C content was 64.9 mol%. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain TF-218T is phylogenetically closely related to the genera Phaeobacter, Leisingera and Marinovum of the Alphaproteobacteria. The phylogenetic and chemotaxonomic similarities suggest that strain TF-218T represents a member of the genus Phaeobacter. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain TF-218T differs from the recognized Phaeobacter species. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain TF-218T represents a novel species of the genus Phaeobacter, for which the name Phaeobacter daeponensis sp. nov. is proposed. The type strain is TF-218T (=KCTC 12794T=JCM 13606T).
The modifier ofMin2 (Mom2) locus: Embryonic lethality of a mutation in theAtp5a1gene suggests a novel mechanism of polyp suppression
Authors: Baran Amy A. , Silverman Karen A. , Zeskand Joseph , Koratkar Revati , Palmer Ashley , McCullen Kristen , Curran Walter J. , Edmonston Tina Bocker , Siracusa Linda D. , Buchberg Arthur M.
Published: March 2007

Inactivation of theAPCgene is considered the initiating event in human colorectal cancer. Modifier genes that influence the penetrance of mutations in tumor-suppressor genes hold great potential for preventing the development of cancer. The mechanism by which modifier genes alter adenoma incidence can be readily studied in mice that inherit mutations in theApcgene. We identified a new modifier locus ofApcMin-induced intestinal tumorigenesis calledModifierofMin2(Mom2). The polyp-resistantMom2Rphenotype resulted from a spontaneous mutation and linkage analysis localizedMom2to distal chromosome 18. To obtain recombinant chromosomes for use in refining theMom2interval, we generated congenic DBA.B6ApcMin/+,Mom2R/+mice. An intercross revealed thatMom2Rencodes a recessive embryonic lethal mutation. We devised an exclusion strategy for mapping theMom2locus using embryonic lethality as a method of selection. Expression and sequence analyses of candidate genes identified a duplication of four nucleotides within exon 3 of the α subunit of the ATP synthase (Atp5a1) gene. Tumor analyses revealed a novel mechanism of polyp suppression byMom2RinMinmice. Furthermore, we show that more adenomas progress to carcinomas inMinmice that carry theMom2Rmutation. The absence of loss of heterozygosity (LOH) at theApclocus, combined with the tendency of adenomas to progress to carcinomas, indicates that the sequence of events leading to tumors inApcMin/+Mom2R/+mice is consistent with the features of human tumor initiation and progression.