bluuebunny/crossref_metadata_2025 huggingface dataset:
Ridging, strength, and stability in high‐resolution sea ice models
Authors: Lipscomb William H. , Hunke Elizabeth C. , Maslowski Wieslaw , Jakacki Jaromir
Published: March 2007

In multicategory sea ice models the compressive strength of the ice pack is often assumed to be a function of the potential energy of pressure ridges. This assumption, combined with other standard features of ridging schemes, allows the ice strength to change dramatically on short timescales. In high‐resolution (∼10 km) sea ice models with a typical time step (∼1 hour), abrupt strength changes can lead to large internal stress gradients that destabilize the flow. The unstable flow is characterized by large oscillations in ice concentration, thickness, strength, velocity, and strain rates. Straightforward, physically motivated changes in the ridging scheme can reduce the likelihood of abrupt strength changes and improve stability. In simple test problems with flow toward and around topography, stability is significantly enhanced by eliminating the threshold fraction G* in the ridging participation function. Use of an exponential participation function increases the maximum stable time step at 10‐km resolution from less than 30 min to about 2 hours. Modifying the redistribution function to build thinner ridges modestly improves stability and also gives better agreement between modeled and observed thickness distributions. Allowing the ice strength to increase linearly with the mean ice thickness improves stability but probably underestimates the maximum stresses.
Amplitude loss of sonic waveform due to source coupling to the medium
Authors: Lee Myung W. , Waite William F.
Published: March 2007

In contrast to hydrate‐free sediments, sonic waveforms acquired in gas hydrate‐bearing sediments indicate strong amplitude attenuation associated with a sonic velocity increase. The amplitude attenuation increase has been used to quantify pore‐space hydrate content by attributing observed attenuation to the hydrate‐bearing sediment's intrinsic attenuation. A second attenuation mechanism must be considered, however. Theoretically, energy radiation from sources inside fluid‐filled boreholes strongly depends on the elastic parameters of materials surrounding the borehole. It is therefore plausible to interpret amplitude loss in terms of source coupling to the surrounding medium as well as to intrinsic attenuation. Analyses of sonic waveforms from the Mallik 5L‐38 well, Northwest Territories, Canada, indicate a significant component of sonic waveform amplitude loss is due to source coupling. Accordingly, all sonic waveform amplitude analyses should include the effect of source coupling to accurately characterize a formation's intrinsic attenuation.
Comprehensive analysis of MHC‐II expression in healthy human skin
Authors: Angel Catherine E , George Elizabeth , Ostrovsky Lena L , Dunbar P Rod
Published: March 2007

A number of antigen‐presenting cells (APCs) expressing major histocompatibility complex class II (MHC‐II) have been identified in healthy human skin including the Langerhans cells of the epidermis and the three recently defined dermal APC subsets. It is well documented that in other tissues HLA‐DR expression is not exclusive to APCs. Following a comprehensive analysis of the cells in human skin using flow cytometry and fluorescence immunohistochemistry, we have identified additional cell subsets that express HLA‐DR. Using markers exclusive for blood and lymphatic endothelium, we demonstrated that both of these cell populations have the capacity to express HLA‐DR. In addition, a small subset of dermal T lymphocytes was found to express low‐level HLA‐DR suggesting an activated phenotype. Dermal T lymphocytes were often in intimate contact with either CD1a+ CD207− dermal APCs or CD1a+ CD207+ dermal Langerhans cells, possibly explaining the activated phenotype of a subset of dermal T lymphocytes.
Strain relief and dislocation motion in III-nitride films grown on stepped and step-free 4H-SiC mesas
Authors: Twigg M. E. , Bassim N. D. , Mastro M. A. , Eddy C. R. , Henry R. L. , Culbertson J. C. , Holm R. T. , Neudeck P. , Powell J. A. , Trunek A. J.
Published: March 2007

The impetus for dislocation motion in thin films is generally understood in terms of Peach-Koehler forces. For the case of III-nitride films grown on step-free 4H-SiC mesas, however, it is the gradient of the strain energy from the mesa edge that is capable of driving misfit dislocations. Using the strain profile as a function of the distance from the mesa edge and the line tension of the c-plane threading arms, we have calculated the excess stress driving the half loop from the mesa edge into the mesa interior. We have also compared the half-loop excess stress with the excess stress driving the tilt of threading edge dislocations, which has been proposed as one of the principal strain relief mechanisms in III-nitride films. The excess stress driving c-plane half loops ranges from a few 1000MPa at the mesa edge to few 100MPa towards the mesa interior, while the excess stress driving the tilt of threading edge dislocations is in excess of 20000MPa. The greater excess stress driving dislocation tilt, however, does not dominate strain relief for III-nitride films on step-free SiC mesas due to the difficulty in nucleating threading dislocations in the absence of interfacial steps.
On recovering continuum topology from a causal set
Authors: Major Seth , Rideout David , Surya Sumati
Published: March 2007

An important question that discrete approaches to quantum gravity must address is how continuum features of space-time can be recovered from the discrete substructure. Here, we examine this question within the causal set approach to quantum gravity, where the substructure replacing the space-time continuum is a locally finite partial order. A new topology on causal sets using “thickened antichains” is constructed. This topology is then used to recover the homology of a globally hyperbolic space-time from a causal set which faithfully embeds into it at sufficiently high sprinkling density. This implies a discrete-continuum correspondence which lends support to the fundamental conjecture or “Hauptvermutung” of causal set theory.
Intermolecular potential and second virial coefficient of the water-nitrogen complex
Authors: Tulegenov Akyl S. , Wheatley Richard J. , Hodges Matthew P. , Harvey Allan H.
Published: March 2007

The authors construct a rigid-body (five-dimensional) potential energy surface for the water-nitrogen complex using the systematic intermolecular potential extrapolation routine. The intermolecular potential is then extrapolated to the limit of a complete basis set. An analytic fit of this surface is obtained, and, using this, the global minimum energy is found. The minimum is located in an arrangement in which N2 is near the H atom of H2O, almost collinear with the OH bond. The best estimate of the binding energy is 441cm−1 (1cm−1≈1.98643×10−23J). The extrapolated potential is then used to calculate the second cross virial coefficient over a wide temperature range (100–3000K). These calculated second virial coefficients are generally consistent with experimental data, but for the most part the former have smaller uncertainties.
Free energy of water permeation into hydrophobic core of sodium dodecyl sulfate micelle by molecular dynamics calculation
Authors: Yoshii Noriyuki , Okazaki Susumu
Published: March 2007

In our previous analysis of the structural stability of a sodium dodecyl sulfate (SDS) micelle based on molecular dynamics calculation, vacancies were found in the center of the micelles [N. Yoshii and S. Okazaki, Chem. Phys. Lett.425, 58 (2006)]. It is very interesting to clarify whether a water molecule is expected in the vacancy in thermodynamic equilibrium at room temperature. In order to investigate the stability of water in the core of micelle, free energy of transfer of water from bulk to the core has been calculated for the SDS micelle in water for two micelle sizes, N=61 and 121, at temperature T=300 K and pressure P=1 atm. The calculated free energy of transfer, ΔGc←b, from the bulk to the core is about 28±4 kJ∕mol and 26±4 kJ∕mol for the micelle of the size N=61 and 121, respectively, where the corresponding Boltzmann factor, exp(−ΔGc←b∕kT), is in the order of one over several ten thousands. Thus, a water molecule hardly permeates into the core of the micelle.
Numerical analysis of magnetic fluid dynamics behaviors during resistance spot welding
Authors: Li Yong Bing , Lin Zhong Qin , Hu S. Jack , Chen Guan Long
Published: March 2007

Magnetic fluid dynamic behaviors during resistance spot welding have important influences on weld nugget formation. In this paper, a coupled multiphysics finite element model, which realizes the coupling of mass conservation, momentum conservation, energy conservation, and the Maxwell system of equations, is proposed to systematically investigate the fluid flow and heat transfer behaviors in a spot weld nugget. It is found that the flow field in the spot weld nugget evolves through five consecutive stages: incubation, fluctuation, rapid growth, rapid attenuation, and termination. Molten metal in the nugget makes regular rotational flow in four symmetrical loops, which changes the temperature gradient in weld nugget during heating and holding, and also yields significant effects on the shape and thickness of weld nugget.
Denaturation of hen egg white lysozyme in electromagnetic fields: A molecular dynamics study
Authors: English Niall J. , Mooney Damian A.
Published: March 2007

Nonequilibrium molecular dynamics simulations of hen egg white lysozyme have been performed in the canonical ensemble at 298K in the presence of external electromagnetic fields of varying intensity in the microwave to far-infrared frequency range. Significant nonthermal field effects were noted, such as marked changes in the protein’s secondary structure which led to accelerated incipient local denaturation relative to zero-field conditions. This occurred primarily as a consequence of alignment of the protein’s total dipole moment with the external field, although the enhanced molecular mobility and dipolar alignment of water molecules is influential on sidechain motion in solvent-exposed regions. The applied field intensity was found to be highly influential on the extent of denaturation in the frequency range studied, and 0.25–0.5VÅrms−1 fields were found to induce initial denaturation to a comparable extent to thermal denaturation in the 400 to 500K range. In subsequent zero-field simulations following exposure to the e/m field, the extent of perturbation from the native fold and the degree of residual dipolar alignment were found to be influential on incipient folding.
Diffusion on (110) surface of molecular crystal pentaerythritol tetranitrate
Authors: Wang Jian , Golfinopoulos Ted , Gee Richard H. , Huang Hanchen
Published: March 2007

Using classical molecular dynamics simulations, the authors investigate the diffusion mechanisms of admolecules on the (110) surface of molecular crystal pentaerythritol tetranitrate. The results show that admolecules (1) are stable at off-lattice sites, (2) diffuse along close-packed [11¯1] and [1¯11] directions, and (3) detach from the surface at 350K and above. Based on the number of diffusion jumps as a function of temperature, The authors estimate the jump frequency to be v=1.14×1012e−0.08eV∕kT∕s.
Atomistic treatment of interface roughness in Si nanowire transistors with different channel orientations
Authors: Luisier Mathieu , Schenk Andreas , Fichtner Wolfgang
Published: March 2007

Nanowire transistors with a perfect crystal structure and a well-defined Si–SiO2 interface cannot be grown with the actual technology. The shape of the semiconducting channel varies from source to drain. By self-consistently coupling the three-dimensional Schrödinger and Poisson equations, interface roughness (IR) effects are studied in Si triple-gate nanowire transistors with [100], [110], [111], and [112] oriented channels. The full-band electronic transport is computed in the nearest-neighbor sp3d5s* tight-binding model. IR is included by adding or removing atoms at the Si surface. A comparison of the different channel orientations is achieved by calculating the variations of the transistor threshold voltage.
Fabrication and characterization of a GaAs-based three-terminal nanowire junction device controlled by double Schottky wrap gates
Authors: Nakamura Tatsuya , Kasai Seiya , Shiratori Yuta , Hashizume Tamotsu
Published: March 2007

A three-terminal nanowire junction device controlled by double nanometer-sized Schottky wrap gates (WPGs), which control left and right branches independently, are fabricated utilizing AlGaAs∕GaAs etched nanowires and characterized experimentally. Fabricated device exhibits clear nonlinear characteristics of output voltage at the center terminal by applying voltages to left and right terminals in push-pull fashion. Applying asymmetric gate voltages to left and right WPGs provides clear asymmetry in the output voltage. The nonlinearity in the low voltage regions is greatly enhanced by squeezing both left and right branches using WPGs.
Modified photoluminescence properties of rare-earth complex/polymer composite fibers prepared by electrospinning
Authors: Zhang Hui , Song Hongwei , Yu Hongquan , Li Suwen , Bai Xue , Pan Guohui , Dai Qilin , Wang Tie , Li Wenlian , Lu Shaozhe , Ren Xinguang , Zhao Haifeng , Kong Xianggui
Published: March 2007

Efficiently luminescent composite fibers of poly (vinyl pyrrolidone) (Mw≈1300000) and europium complex Eu(TTA)3(TPPO)2 (TTA is thenoyltrifluoroacetone; TPPO is triphenylphosphine oxide) were prepared by electrospinning, with average diameters of 200–500nm and lengths of several tens of micrometers. Their photoluminescence properties were studied in comparison to the pure Eu(TTA)3(TPPO)2 complex. It was significant to observe that the thermal stability of photoluminescence in the composite fibers was improved considerably over the pure complex.
Self-assembled magnetic nanowire arrays
Authors: Liu Ming , Lagdani Jalal , Imrane Hassan , Pettiford Carl , Lou Jing , Yoon Soak , Harris Vincent G. , Vittoria Carmine , Sun Nian. X
Published: March 2007

Different self-assembled magnetic nanowire arrays were achieved with ∼100% trapping rate on templates with nanomagnet arrays under a low external magnetic field (∼10Oe). The principles of magnetic charge matching and dimension matching between the magnetic nanowires to be assembled and the gaps between two nanomagnets were proposed and demonstrated to be crucial for achieving low magnetostatic energy and high trapping rate. This templated self-assembly technique and the proposed template design principles have great potential for nanomanufacturing of regular arrays of magnetic nanostructures.
Optical enhancement in semitransparent polymer photovoltaic cells
Authors: Ng Ging-Meng , Kietzke Elizabeth Lekha , Kietzke Thomas , Tan Li-Wei , Liew Pooi-Kwan , Zhu Furong
Published: March 2007

This letter reports our efforts to improve the power conversion efficiency (PCE) and the optical transparency of semitransparent poly(3-hexylthiophene) (P3HT):1-(3-methoxycarbonyl)-propyl-1-phenyl-(6,6)C60 (PCBM) based photovoltaic (PV) cells. Semitransparent P3HT:PCBM based solar cells were prepared based on parameters obtained by optical admittance analysis. The performance of structurally identical polymer PV cells made with a reflective calcium/silver cathode and a semitransparent Ca(10nm)∕Ag(10nm)/indium tin oxide cathode are compared. For semitransparent polymer PV cells with a 75nm thick active P3HT:PCBM blend layer, an average transmission of more than 30% was achieved with a high PCE of 1.7% under simulated AM1.5G illumination of 100mW∕cm2.
Technique for azimuthal anchoring measurement of nematic liquid crystals using magnetic field induced deformation
Authors: Kim Jong-Hyun , Choi Hyunchul
Published: March 2007

The authors devised a technique for measuring the azimuthal anchoring coefficient of nematic liquid crystals. The coefficient was estimated calculating the varying ratio of magnetic coherence length to extrapolation length using light transmission to magnetic field. The paralleled control of the directors on the entrance surface, polarizer axis and magnetic field enables the transmission to sensitively reflect the anchoring. The extrapolation length was 0.48μm for polyimide rubbed surface, 0.56μm for rubbed poly-vinyl alcohol and 5.6μm for photo-aligned polyimide. This technique has advantages such as insensitiveness to sample adjustment, covering wide range of anchoring and independence on the cell gap, electrodes and impurity.
Impact of Joule heating on the brightness homogeneity of organic light emitting devices
Authors: Gärditz C. , Winnacker A. , Schindler F. , Paetzold R.
Published: March 2007

Joule heating and its impact on the brightness homogeneity are investigated since the luminance distribution is a key issue in large area organic light emitting diodes. In addition to previous reports, it is also important to consider the device temperature as a main factor for determining the luminance homogeneity. At a luminance of 1000cd∕m2 the active area reaches an average temperature of 40.6°C and a peak of 46.2°C. The increased device temperature is leading to higher local current densities resulting in a reduced brightness homogeneity. Modeling confirms these results and can be used for further device layout optimization.
Fixed p-i-n junction polymer light-emitting electrochemical cells based on charged self-assembled monolayers
Authors: Simon D. T. , Stanislowski D. B. , Carter S. A.
Published: March 2007

The authors report on enhanced efficiency of polymer light-emitting electrochemical cells (LECs) by means of forming a n-doping self-assembled monolayer (SAM) at the cathode-polymer interface. The addition of the SAM, a silane-based salt with structural similarity to the commonly used LEC n-dopant tetra-n-butylammonium, caused a twofold increase in quantum efficiency. Photovoltaic analysis indicates that the SAM increases both the open-circuit voltage and short-circuit current. Current versus voltage data are presented which indicate that the SAM does not simply introduce an interfacial dipole layer, but rather provides a fixed doping region, and thus a more stable p-i-n structure.
Noncell-autonomous photoreceptor degeneration in a zebrafish model of choroideremia
Authors: Krock Bryan L. , Bilotta Joseph , Perkins Brian D.
Published: March 2007

Choroideremia is an X-linked hereditary retinal degeneration resulting from mutations in the Rab escort protein-1 (
REP1
). The Rep1 protein facilitates posttranslational modification of Rab proteins, which regulate intracellular trafficking in the retinal pigment epithelium (RPE) and photoreceptors and are likely involved in the removal of outer segment disk membranes by the RPE. A critical question for potential treatment of choroideremia is whether photoreceptor degeneration results from autonomous defects in opsin transport within the photoreceptor or as a nonautonomous and secondary consequence of RPE degeneration. To address this question, we have characterized the retinal pathology in zebrafish
rep1
mutants, which carry a recessive nonsense mutation in the
REP1
gene. Zebrafish
rep1
mutants exhibit degeneration of the RPE and photoreceptors and complete loss of visual function as measured by electroretinograms. In the mutant RPE, photoreceptor outer segment material was not effectively eliminated, and large vacuoles were observed. However, opsin trafficking in photoreceptors occurred normally. Mosaic analysis revealed that photoreceptor degeneration was nonautonomous and required contact with the mutant RPE as mutant photoreceptors were rescued in wild-type hosts and wild-type photoreceptors degenerated in mutant hosts. We conclude that mutations in
REP1
disrupt cellular processes in the RPE, which causes photoreceptor death as a secondary consequence. These results suggest that therapies that correct the RPE may successfully rescue photoreceptor loss in choroideremia.
Predicting protein–protein interactions based only on sequences information
Authors: Shen Juwen , Zhang Jian , Luo Xiaomin , Zhu Weiliang , Yu Kunqian , Chen Kaixian , Li Yixue , Jiang Hualiang
Published: March 2007

Protein–protein interactions (PPIs) are central to most biological processes. Although efforts have been devoted to the development of methodology for predicting PPIs and protein interaction networks, the application of most existing methods is limited because they need information about protein homology or the interaction marks of the protein partners. In the present work, we propose a method for PPI prediction using only the information of protein sequences. This method was developed based on a learning algorithm-support vector machine combined with a kernel function and a conjoint triad feature for describing amino acids. More than 16,000 diverse PPI pairs were used to construct the universal model. The prediction ability of our approach is better than that of other sequence-based PPI prediction methods because it is able to predict PPI networks. Different types of PPI networks have been effectively mapped with our method, suggesting that, even with only sequence information, this method could be applied to the exploration of networks for any newly discovered protein with unknown biological relativity. In addition, such supplementary experimental information can enhance the prediction ability of the method.
Induced mitotic recombination of
p53
in vivo
Authors: Wang Wei , Warren Madhuri , Bradley Allan
Published: March 2007

Genetic mosaics produced by

FLP
/
FRT

induced mitotic recombination have been widely used in
Drosophila
to study gene function in development. Recently, the Cre/
lox
P system has been applied to induce mitotic recombination in mouse embryonic stem cells and in many adult mouse tissues. We have used this strategy to generate a previously undescribed
p53
mouse model in which expression of a ubiquitously expressed recombinase in a heterozygous
p53
knockout animal produces mitotic recombinant clones homozygous for the
p53
mutation. The induction of loss of heterozygosity in a few cells in an otherwise normal tissue mimics genetic aspects of tumorigenesis more closely than existing models and has revealed the possible cell autonomous nature of
Wnt3
. Our results suggest that inducible mitotic recombination can be used for clonal analysis of mutants in the mouse.
Crystal structure of a conserved N-terminal domain of histone deacetylase 4 reveals functional insights into glutamine-rich domains
Authors: Guo Liang , Han Aidong , Bates Darren L. , Cao Jue , Chen Lin
Published: March 2007

Glutamine-rich sequences exist in a wide range of proteins across multiple species. A subset of glutamine-rich sequences has been shown to form amyloid fibers implicated in human diseases. The physiological functions of these sequence motifs are not well understood, partly because of the lack of structural information. Here we have determined a high-resolution structure of a glutamine-rich domain from human histone deacetylase 4 (HDAC4) by x-ray crystallography. The glutamine-rich domain of HDAC4 (19 glutamines of 68 residues) folds into a straight α-helix that assembles as a tetramer. In contrast to most coiled coil proteins, the HDAC4 tetramer lacks regularly arranged apolar residues and an extended hydrophobic core. Instead, the protein interfaces consist of multiple hydrophobic patches interspersed with polar interaction networks, wherein clusters of glutamines engage in extensive intra- and interhelical interactions. In solution, the HDAC4 tetramer undergoes rapid equilibrium with monomer and intermediate species. Structure-guided mutations that expand or disrupt hydrophobic patches drive the equilibrium toward the tetramer or monomer, respectively. We propose that a general role of glutamine-rich motifs be to mediate protein–protein interactions characteristic of a large component of polar interaction networks that may facilitate reversible assembly and disassembly of protein complexes.
Embryonic chimerism does not induce tolerance in an invertebrate model organism
Authors: Poudyal Monita , Rosa Sabrina , Powell Anahid E. , Moreno Maria , Dellaporta Stephen L. , Buss Leo W. , Lakkis Fadi G.
Published: March 2007

In colonial marine invertebrates, allorecognition restricts somatic fusion and thus, chimerism, to histocompatible individuals. Little is understood, however, about how invertebrates respond to chimerism formed across histocompatibility barriers or whether embryonic exposure to histoincompatible cells induces allotolerance. We here evaded natural allorecognition barriers by generating well mixed embryonic chimeras of
Hydractinia symbiolongicarpus
(Cnidaria:Hydrozoa) and developed molecular markers to detect chimerism in both histocompatible and histoincompatible settings. Histocompatible chimeras exhibited markedly higher growth rates and survivorship than histoincompatible pairings. Histoincompatible chimeras were unstable, with chimerism being undetectable by 4 wk of age. In contrast, colonies generated from histocompatible pairings remained chimeric at markedly higher frequencies and longer durations. Histoincompatible chimeras that lost detectable chimerism retained the fusibility/rejection characteristics of the remaining component of the chimera but not that of the lost component. Chimerism across histocompatibility barriers in an invertebrate model organism was unstable and did not induce tolerance.
Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polymerases
Authors: Castro Christian , Smidansky Eric , Maksimchuk Kenneth R. , Arnold Jamie J. , Korneeva Victoria S. , Götte Matthias , Konigsberg William , Cameron Craig E.
Published: March 2007

The rate-limiting step for nucleotide incorporation in the pre-steady state for most nucleic acid polymerases is thought to be a conformational change. As a result, very little information is available on the role of active-site residues in the chemistry of nucleotidyl transfer. For the poliovirus RNA-dependent RNA polymerase (3D
pol
), chemistry is partially (Mg
2+
) or completely (Mn
2+
) rate limiting. Here we show that nucleotidyl transfer depends on two ionizable groups with pK
a
values of 7.0 or 8.2 and 10.5, depending upon the divalent cation used in the reaction. A solvent deuterium isotope effect of three to seven was observed on the rate constant for nucleotide incorporation in the pre-steady state; none was observed in the steady state. Proton-inventory experiments were consistent with two protons being transferred during the rate-limiting transition state of the reaction, suggesting that both deprotonation of the 3′-hydroxyl nucleophile and protonation of the pyrophosphate leaving group occur in the transition state for phosphodiester bond formation. Importantly, two proton transfers occur in the transition state for nucleotidyl-transfer reactions catalyzed by RB69 DNA-dependent DNA polymerase, T7 DNA-dependent RNA polymerase and HIV reverse transcriptase. Interpretation of these data in the context of known polymerase structures suggests the existence of a general base for deprotonation of the 3′-OH nucleophile, although use of a water molecule cannot be ruled out conclusively, and a general acid for protonation of the pyrophosphate leaving group in all nucleic acid polymerases. These data imply an associative-like transition-state structure.
Domain-swapped dimerization of the HIV-1 capsid C-terminal domain
Authors: Ivanov Dmitri , Tsodikov Oleg V. , Kasanov Jeremy , Ellenberger Tom , Wagner Gerhard , Collins Tucker
Published: March 2007

Assembly of the HIV and other retroviruses is primarily driven by the oligomerization of the Gag polyprotein, the major viral structural protein capable of forming virus-like particles even in the absence of all other virally encoded components. Several critical determinants of Gag oligomerization are located in the C-terminal domain of the capsid protein (CA-CTD), which encompasses the most conserved segment in the highly variable Gag protein called the major homology region (MHR). The CA-CTD is thought to function as a dimerization module, although the existing model of CA-CTD dimerization does not readily explain why the conserved residues of the MHR are essential for retroviral assembly. Here we describe an x-ray structure of a distinct domain-swapped variant of the HIV-1 CA-CTD dimer stabilized by a single amino acid deletion. In the domain-swapped structure, the MHR-containing segment forms a major part of the dimerization interface, providing a structural mechanism for the enigmatic function of the MHR in HIV assembly. Our observations suggest that swapping of the MHR segments of adjacent Gag molecules may be a critical intermediate in retroviral assembly.
A gene essential for hydrotropism in roots
Authors: Kobayashi Akie , Takahashi Akiko , Kakimoto Yoko , Miyazawa Yutaka , Fujii Nobuharu , Higashitani Atsushi , Takahashi Hideyuki
Published: March 2007

Roots display hydrotropism in response to moisture gradients, which is thought to be important for controlling their growth orientation, obtaining water, and establishing their stand in the terrestrial environment. However, the molecular mechanism underlying hydrotropism remains unknown. Here, we report that roots of the
Arabidopsis
mutant
mizu-kussei1
(
miz1
), which are impaired in hydrotropism, show normal gravitropism and elongation growth. The roots of
miz1
plants showed reduced phototropism and a modified wavy growth response. There were no distinct differences in morphological features and root structure between
miz1
and wild-type plants. These results suggest that the pathway inducing hydrotropism is independent of the pathways used in other tropic responses. The phenotype results from a single recessive mutation in
MIZ1
, which encodes a protein containing a domain (the MIZ domain) that is highly conserved among terrestrial plants such as rice and moss. The MIZ domain was not found in known genomes of organisms such as green algae, red algae, cyanobacteria, or animals. We hypothesize that
MIZ1
has evolved to play an important role in adaptation to terrestrial life because hydrotropism could contribute to drought avoidance in higher plants. In addition, a
pMIZ1
::
GUS
fusion gene was expressed strongly in columella cells of the root cap but not in the elongation zone, suggesting that MIZ1 functions in the early phase of the hydrotropic response.
Modulating seed β-ketoacyl-acyl carrier protein synthase II level converts the composition of a temperate seed oil to that of a palm-like tropical oil
Authors: Pidkowich Mark S. , Nguyen Huu Tam , Heilmann Ingo , Ischebeck Till , Shanklin John
Published: March 2007

β-Ketoacyl-acyl carrier protein (ACP) synthase II (KASII) elongates 16:0-ACP to 18:0-ACP in the plastid, where it competes with three other enzymes at the first major branch point in fatty acid biosynthesis. Despite its key metabolic location, the influence of KASII in determining seed oil composition remains unclear, in part because the biochemical consequences of the
fab1-1
mutation were unresolved. Thus,
fab1-1
, and a newly identified knockout allele,
fab1-2
, were analyzed in the context of the hypothesis that modulating KASII activity is sufficient to convert the composition of a temperate seed oil into that of a palm-like tropical oil. No homozygous
fab1-2
individuals were identified in progeny of self-fertilized heterozygous
fab1-2
plants, ≈1/4 of which aborted before the torpedo stage, suggesting that
fab1-2
represents a complete loss of function and results in lethality when homozygous. Consistent with this hypothesis, homozygous
fab1-2
plants were identified when a
fab1-1
transgene was introduced, demonstrating that
fab1-1
encodes an active KASII. Strong seed-specific hairpin-RNAi reductions in
FAB1
expression resulted in abortion of ≈1/4 of the embryos in an apparent phenocopy of
fab1-2
homozygosity. In less severe
FAB1
hairpin-RNAi individuals, embryos developed normally and exhibited a 1:2:1 segregation ratio for palmitate accumulation. Thus, early embryo development appears sensitive to elevated 16:0, whereas at later stages, up to 53% of 16:0, i.e., a 7-fold increase over wild-type levels, is tolerated. These results resolve the role of KASII in seed metabolism and demonstrate that modulation of
Arabidopsis
KASII levels is sufficient to convert its temperate oilseed composition to that of a palm-like tropical oil.
Microparticle-based delivery of oxytocin receptor antisense DNA in the medial amygdala blocks social recognition in female mice
Authors: Choleris Elena , Little Steven R. , Mong Jessica A. , Puram Sidharth V. , Langer Robert , Pfaff Donald W.
Published: March 2007

Social recognition constitutes the basis of social life. In male mice and rats, social recognition is known to be governed by the neuropeptide oxytocin (OT) through its action on OT receptors (OTRs) in the medial amygdala. In female rats and mice, which have sociosexual behaviors controlling substantial investment in reproduction, an important role for OT in sociosexual behaviors has also been shown. However, the site in the female brain for OT action on social recognition is still unknown. Here we used a customized, controlled release system of biodegradable polymeric microparticles to deliver, in the medial amygdala of female mice, “locked nucleic acid” antisense (AS) oligonucleotides with sequences specific for the mRNA of the OTR gene. We found that single bilateral intraamygdala injections of OTR AS locked nucleic acid oligonucleotides several days before behavioral testing reduced social recognition. Thus, we showed that gene expression for OTR specifically in the amygdala is required for normal social recognition in female mice. Importantly, during the same experiment, we performed a detailed ethological analysis of mouse behavior revealing that OTR AS-treated mice underwent an initial increase in ambivalent risk-assessment behavior. Other behaviors were not affected, thus revealing specific roles for amygdala OTR in female social recognition potentially mediated by anxiety in a social context. Understanding the functional genomics of OT and OTR in social recognition should help elucidate the neurobiological bases of human disorders of social behavior (e.g., autism).
Fork head controls the timing and tissue selectivity of steroid-induced developmental cell death
Authors: Cao Chike , Liu Yanling , Lehmann Michael
Published: March 2007

Cell death during Drosophila melanogaster metamorphosis is controlled by the steroid hormone 20-hydroxyecdysone (20E). Elements of the signaling pathway that triggers death are known, but it is not known why some tissues, and not others, die in response to a particular hormone pulse. We found that loss of the tissue-specific transcription factor Fork head (Fkh) is both required and sufficient to specify a death response to 20E in the larval salivary glands. Loss of fkh itself is a steroid-controlled event that is mediated by the 20E-induced BR-C gene, and that renders the key death regulators hid and reaper hormone responsive. These results implicate the D. melanogaster FOXA orthologue Fkh with a novel function as a competence factor for steroid-controlled cell death. They explain how a specific tissue is singled out for death, and why this tissue survives earlier hormone pulses. More generally, they suggest that cell identity factors like Fkh play a pivotal role in the normal control of developmental cell death.
Propagation of centromeric chromatin requires exit from mitosis
Authors: Jansen Lars E.T. , Black Ben E. , Foltz Daniel R. , Cleveland Don W.
Published: March 2007

Centromeres direct chromosomal inheritance by nucleating assembly of the kinetochore, a large multiprotein complex required for microtubule attachment during mitosis. Centromere identity in humans is epigenetically determined, with no DNA sequence either necessary or sufficient. A prime candidate for the epigenetic mark is assembly into centromeric chromatin of centromere protein A (CENP-A), a histone H3 variant found only at functional centromeres. A new covalent fluorescent pulse-chase labeling approach using SNAP tagging has now been developed and is used to demonstrate that CENP-A bound to a mature centromere is quantitatively and equally partitioned to sister centromeres generated during S phase, thereby remaining stably associated through multiple cell divisions. Loading of nascent CENP-A on the megabase domains of replicated centromere DNA is shown to require passage through mitosis but not microtubule attachment. Very surprisingly, assembly and stabilization of new CENP-A–containing nucleosomes is restricted exclusively to the subsequent G1 phase, demonstrating direct coupling between progression through mitosis and assembly/maturation of the next generation of centromeres.
Centromeric chromatin gets loaded
Authors: Carroll Christopher W. , Straight Aaron F.
Published: March 2007

Centromeric nucleosomes contain a histone H3 variant called centromere protein A (CENP-A) that is required for kinetochore assembly and chromosome segregation. Two new studies, Jansen et al. (see p. 795 of this issue) and Maddox et al. (see p. 757 of this issue), address when CENP-A is deposited at centromeres during the cell division cycle and identify an evolutionally conserved protein required for CENP-A deposition. Together, these studies advance our understanding of centromeric chromatin assembly and provide a framework for investigating the molecular mechanisms that underlie the centromere-specific loading of CENP-A.
To die or not to die—a role for Fork head
Authors: Thummel Carl S.
Published: March 2007

The precise determination of when and where cells undergo programmed cell death is critical for normal development and tissue homeostasis. Cao et al. (2007; see p. 843 of this issue) report that the Fork head (Fkh) transcription factor, which is essential for the early development and function of the larval salivary glands in Drosophila melanogaster, also contributes to its demise. These authors show that fkh expression in the salivary glands is normally lost at puparium formation, which is ∼12 h before they undergo massive cell death triggered by the steroid hormone ecdysone, making room for their developing adult counterparts. The loss of Fkh eliminates its role in blocking cell death, allowing for subsequent ecdysone-induced reaper and head involution defective death activator expression and tissue destruction. This study provides new insights into the transcriptional regulation of programmed cell death and the mechanisms that underlie the precise spatial and temporal control of hormone responses during development.
Succinimidyl 7-methoxy-2H-chromene-3-carboxylate
Authors: Bardajee Ghasem Rezanejade , Winnik Mitchell A. , Lough Alan J.
Published: March 2007

In the title molecule, C15H11NO7, the dihedral angle between the coumarin unit and the succinimide unit is 72.36 (4)°. The crystal structure is stabilized by weak intermolecular C—H...O hydrogen bonds and π–π stacking interactions.
Living with uncertainty: concept advancement
Authors: Penrod Janice
Published: March 2007

Aim. This paper reports a study to demonstrate how the scientific understanding of the concept of uncertainty was advanced through a phenomenological study of living with uncertainty.

Background. Techniques for concept analysis have evolved to subsume strategies for advancing a concept towards greater clarity and utility for research and practice. Recently, it has been argued that a clear delineation of techniques for concept analysis as separate and distinct from techniques of concept advancement is warranted. This article applies such delineated processes to demonstrate the advancement of the concept of uncertainty.

Method. Concept analysis was used to establish an integrated understanding of the state of the science. Gaps in understanding were carefully analysed, resulting in the research question guiding the next phase of concept advancement: what is the nature of the lived experience of uncertainty? A phenomenological investigation of the experience of uncertainty among family caregivers was conducted. Then, using methods of template comparison, the conceptual attributes identified through the phenomenological study were compared and contrasted with the theoretical definition derived through concept analysis. Finally, a new conceptual definition of higher order abstraction, with greater pragmatic utility, was derived.

Findings. Uncertainty is rooted in the individual's perception of outcomes or meaning of a situation. Such perceptions challenge one's sense of confidence and/or control to yield varied types and modes of uncertainty. Uncertainty is present oriented. Both cognitive and precognitive ways of knowing are influential in ascribing meaning, anticipating outcomes and adapting strategies.

Conclusions. One's sense of confidence and sense of control are primary essences that determine the nature of the experience of uncertainty. The experience of living with uncertainty is dynamic, with fluctuations in the types and modes of uncertainty in response to precognitive and cognitive ways of knowing. Probabilistic paradigms preclude existential and situational modes of uncertainty for which probabilities cannot be appreciated.
Cancer survivors' experience of time – time disruption and time appropriation
Authors: Rasmussen Dorte M. , Elverdam Beth
Published: March 2007

Aim.  This paper reports a study to explore how cancer survivors talk about, experience and manage time in everyday life.

Background.  There is an increasing interest in specific physical and psychosocial aspects of life after cancer diagnosis and treatment, but hardly any research follows cancer survivors over time to explore how perceptions and experiences change.

Methods.  An exploratory study was carried out in 2002–2004 with a purposive sample of adults who had experienced various forms of cancer. Data collection included 9 weeks of participant observation at a Cancer Rehabilitation Centre and ethnographic interviews with 23 informants. Ten men and 13 women were interviewed twice: 2 weeks after their stay and 18 months later.

Findings.  Data were analysed from a culture‐analytical perspective. Three main themes regarding the survivors’ handling and perception of time were found: (1) cancer disrupts time and life; (2) awareness of time increases, time is verbalized and reflected; and (3) the informants appropriate time. A diagnosis of cancer, even for a survivor, means a confrontation with death. It means a disruption of continuous clock and calendar time. Survivors appropriate time, and prioritize how and with whom they want to spend their time.

Conclusion.  With an increasing number of people being cured following a cancer diagnosis, nurses and oncology nurse specialists who work with cancer survivors must be aware of the fact that time is a central theme in understanding cancer survivors’ lives, and they must know how to guide these survivors in their new lives and take care of their well‐being.
Patients’ conceptions of how the spiritual dimension is addressed in mental health care: a qualitative study
Authors: Koslander Tiburtius , Arvidsson Barbro
Published: March 2007

Aim.  This paper reports a study to describe patients’ conceptions of how the spiritual dimension is addressed in mental health care.

Background.  Spirituality is a broad concept, and is highly subjective, multidimensional and difficult to define. Spirituality and religiousness are two separate concepts but have several common features. In mental health care, it is essential that nursing care be built on a holistic view, and the spiritual dimension has an important function in nursing care. The notion of spirituality is full of nuances, and in a multi‐cultural society patients express their spirituality in different ways.

Method.  Data were collected by interviewing 12 strategically selected patients in mental health care and analysed according to a qualitative method inspired by the phenomenographic approach. The data were collected in 2003 in Sweden.

Findings.  Three descriptive categories emerged: patients wish to have their spiritual needs addressed; patients must see to it that their spiritual needs are addressed; patients lack confidence in nurses with regard to discussing spirituality. The findings show that patients actively sought the assistance of nurses to meet their spiritual needs. They turned their thoughts inwards and found community with other patients, while nurses often avoided addressing the spiritual dimension.

Conclusion.  Nurses should work actively to seek new knowledge about how they can address patients’ spiritual needs. It is also important that there be scope for discussing and reflecting on spiritual questions at the workplace. Additional research is needed to explore how knowledge about spirituality should be implemented in mental health care and nursing education.
Pharmacokinetics of florfenicol, thiamphenicol, and chloramphenicol in turkeys
Authors: SWITAŁA M. , HRYNYK R. , SMUTKIEWICZ A. , JAWORSKI K. , PAWLOWSKI P. , OKONIEWSKI P. , GRABOWSKI T. , DEBOWY J.
Published: March 2007

The pharmacokinetics of florfenicol (FF), thiamphenicol (TP) and chloramphenicol (CP) after single intravenous (i.v.) or oral (p.o.) administration was studied in an independent cross‐over study in broiler turkeys. All the fenicol antibiotics were administered at a dose of 30 mg/kg b.w. and their concentrations in plasma samples were assayed using the same validated high‐performance liquid chromatography method. Pharmacokinetic parameters were calculated by a noncompartmental method. The kinetic profiles of the compounds were compared with the results of the structure–activity relationship. According to the proposed mathematical description, no differences in plasma clearance values for the studied antibiotics were observed. The mean residence time values of FF, TF, and CP after i.v. injection were 3.37 ± 0.63, 2.43 ± 0.29, and 2.12 ± 0.21 h, respectively. The mean values of Varea for FF (1.39 ± 0.31 L/kg) and TP (1.31 ± 0.19 L/kg) were similar, but significantly different from that of CP (1.04 ± 0.12 L/kg). The bioavailabilities of FF, TP, and CP after oral administration were 82%, 69%, and 45%, respectively. Differences in the bioavailability values of the compared fenicol antibiotics correspond to the ratio of the apolar/polar surface areas of their particles.
Pesticides and the intoxication of wild animals
Authors: BERNY P.
Published: March 2007

Pesticides are widely used to control agricultural pests. Unfortunately, because of their biological activity, they may have detrimental effects on nontarget species. Acute toxicity, resulting in death, is reported worldwide. Although chronic and indirect effects may be even more hazardous for animal populations on a long‐term basis, they are usually evaluated as parts of research programs. The purpose of this paper was to review the wildlife‐poisoning surveillance systems and their results regarding the circumstances of exposure of wild animals, the pesticides involved and the species exposed. Most data are retrieved from the British and French pesticide poisoning surveillance systems in wildlife, with some data from other European structures.