bluuebunny/crossref_metadata_2025 huggingface dataset:
Gray hematite distribution and formation in Ophir and Candor chasmata
Authors: Weitz Catherine M. , Lane Melissa D. , Staid Matthew , Dobrea Eldar Noe
Published: February 2008

We have studied eight of the spatially largest locations in Ophir and Candor chasmata that have the highest abundances of coarse‐grained gray hematite, as measured by the Mars Global Surveyor Thermal Emission Spectrometer (TES). All of the eight hematite locations correspond to relatively smooth dark units that overlie or are adjacent to light‐toned rock units. Linear modeling of TES spectra sampled in the eight hematite locations shows mostly mafic associations with the hematite, dominated by pyroxene and feldspar, with a lower abundance of sulfates. The spectral and morphologic similarity between the hematite‐bearing units at Ophir and Candor to those at Meridiani Planum lead us to favor a similar aqueous origin for the hematite in Valles Marineris. Water that may have infiltrated the light‐toned rocks by an increase in the water table or when lakes may have existed within the canyons could have resulted in the formation of hematite‐rich grains in a scenario similar to that proposed for Meridiani Planum. Erosion by wind of the formerly overlying or adjacent friable light‐toned rocks that contain the hematite‐rich grains enabled the more resistant hematite grains to be concentrated in sufficient abundances along the surface to be detected by TES. A more limited supply of hematite grains within the light‐toned rocks, inadequate winds, subsequent burial beneath dust or sand, and fewer low‐lying terrains upon which the grains could form a lag deposit may explain why there are smaller exposures of hematite within Valles Marineris compared to Meridiani Planum and Aram Chaos.
Nitrogen fixation in an anticyclonic eddy in the oligotrophic North Pacific Ocean
Authors: Fong Allison A , Karl David M , Lukas Roger , Letelier Ricardo M , Zehr Jonathan P , Church Matthew J
Published: February 2008

Mesoscale physical processes (for example eddies, frontal meanders and planetary waves) can play important roles in controlling ocean biogeochemistry. We examined spatial variations in upper ocean (0–100 m) nutrient inventories, N2 fixing microorganism diversity and abundance, and rates of N2 fixation in an anticyclonic eddy near Station ALOHA (22° 45′ N, 158° 00′ W) in the North Pacific Subtropical Gyre (NPSG). In July 2005, satellite-based sea surface altimetry and ocean color observation revealed an anticyclonic eddy with enhanced chlorophyll in the upper ocean in the vicinity of Station ALOHA. Within the eddy, near-surface ocean chlorophyll concentrations were ∼5-fold greater than in the surrounding waters. Inventories of nitrate and phosphate in the eddy were similar to the concentrations historically observed at Station ALOHA, while silicic acid inventories were significantly depleted (one-way analysis of variance, P<0.01). Quantitative PCR determinations of nifH gene copies revealed relatively high abundances of several N2 fixing cyanobacteria, including Trichodesmium spp., Crocosphaera watsonii and Richelia intracellularis. Reverse transcriptase PCR (RT-PCR) amplified nitrogenase (nifH) gene transcripts were cloned and sequenced to examine the diversity of active N2 fixing microorganisms; these clone libraries were dominated by sequence-types 97%–99% identical to the filamentous cyanobacteria Trichodesmium spp. Near-surface ocean rates of N2 fixation were 2–18 times greater (averaging 8.6±5.6 nmol N per l per day) than previously reported measurements at Station ALOHA. These results suggest that mesoscale physical variability can play an important role in modifying the abundances of N2 fixing microorganisms and associated rates of N2 fixation in open ocean ecosystems.
Maintenance of Weight Loss in Overweight Middle‐aged Women Through the Internet
Authors: Cussler Ellen C. , Teixeira Pedro J. , Going Scott B. , Houtkooper Linda B. , Metcalfe Lauve L. , Blew Robert M. , Ricketts Jennifer R. , Lohman J'Fleur , Stanford Vanessa A. , Lohman Timothy G.
Published: February 2008

Objective: The purpose of this study was to compare weight regain in a group of perimenopausal women (48.0 ± 4.4 years old), randomized to a 12‐month weight maintenance Internet intervention or to self‐directed weight maintenance after a 4‐month weight loss treatment.

Methods and Procedures: After a 4‐month behavioral weight loss program, 135 women were randomized to either Internet or self‐directed groups. The Internet group (n = 66) used a website to gain information and complete logs concerning their weight, diet, and exercise progress over a 12‐month follow‐up. The 69 self‐directed women had no contact with study staff. All women were measured for weight and body composition, and diet intake, and were interviewed using the 7‐day physical activity questionnaires at baseline, 4 months, and 16 months.

Results: At the end of the 12‐month follow‐up, the Internet and self‐directed groups had regained on average 0.4 ± 5.0 kg and 0.6 ± 4.0 kg, respectively (P = 0.5). In within‐group analyses, Internet diet‐log entries were correlated with follow‐up weight change (r = −0.29; P < 0.05) and moderately with change in exercise energy expenditure (EEE; r = 0.44; P < 0.01). Follow‐up weight change was not correlated with change in dietary intake.

Discussion: While significant weight loss was maintained over follow‐up by both groups of women, Internet use did not surpass self‐direction in helping to sustain weight loss. Among Internet users, Internet use was related to weight change and EEE.
Nanocharacterisation
Authors:   Royal Society of Chemistry
Published: February 2008

Chemical characterisation techniques have been essential tools in underpinning the explosion in nanotechnology in recent years and nanocharacterisation is a rapidly developing field. Contributions in this book from leading teams across the globe provide an overview of the different microscopic techniques now in regular use for the characterisation of nanostructures. Essentially a handbook to all working in the field this indispensable resource provides a survey of microscopy based techniques with experimental procedures and extensive examples of state of the art characterisation methods including, Transmission Electron Microscopy, Electron Tomography, Tunneling Microscopy, Electron Holography, Electron Energy Loss Spectroscopy This timely publication will appeal to academics, professionals and anyone working fields related to the research and development of nanocharacterisation and nanotechnology.
First plasma of the A-PHOENIX electron cyclotron resonance ion source
Authors: Thuillier T. , Lamy T. , Latrasse L. , Angot J.
Published: February 2008

A-PHOENIX is a new compact hybrid electron cyclotron resonance ion source using a large permanent magnet hexapole (1.92T at the magnet surface) and high temperature superconducting Solenoids (3T) to make min-∣B∣ structure suitable for 28GHz cw operation. The final assembly of the source was achieved at the end of June 2007. The first plasma of A-PHOENIX at 18GHz was done on the 16th of August, 2007. The technological specificities of A-PHOENIX are presented. The large hexapole built is presented and experimental magnetic measurements show that it is nominal with respect to simulation. A fake plasma chamber prototype including thin iron inserts showed that the predicted radial magnetic confinement can be fulfilled up to 2.15T at the plasma chamber wall. Scheduled planning of experiments until the end of 2008 is presented.
Experimental investigation of the Jahn-Teller effect in the ground and excited electronic states of the tropyl radical. Part II. Vibrational analysis of the ÃE3″2-X̃E2″2 electronic transition
Authors: Sioutis Ilias , Stakhursky Vadim L. , Tarczay György , Miller Terry A.
Published: February 2008

Laser-induced fluorescence (LIF) and laser-excited dispersed fluorescence (LEDF) spectra of the cycloheptatrienyl (tropyl) radical C7H7 have been observed under supersonic jet-cooling conditions. Assignment of the LIF excitation spectrum yields detailed information about the Ã-state vibronic structure. The LEDF emission was collected by pumping different vibronic bands of the ÃE3″2←X̃E2″2 electronic spectrum. Analysis of the LEDF spectra yields valuable information about the vibronic levels of the X̃E2″2 state. The X̃- and Ã-state vibronic structures characterize the Jahn-Teller distortion of the respective potential energy surfaces. A thorough analysis reveals observable Jahn-Teller activity in three of the four e3′ modes for the X̃E2″2 state and two of the three e1′ modes for the ÃE3″2 state and provides values for their deperturbed vibrational frequencies as well as linear Jahn-Teller coupling constants. The molecular parameters characterizing the Jahn-Teller interaction in the X̃ and Ã states of C7H7 are compared to theoretical results and to those previously obtained for C5H5 and C6H6+.
Interface and Mn valence effects in ferromagnetic insulating multilayers based on Mn and tin oxide
Authors: Espinosa A. , Céspedes E. , Prieto C. , García-Hernández M. , Rubio-Zuazo J. , de Andrés A.
Published: February 2008

Several series of Mn based multilayers (Mn∕SnO2,Mn∕Si,andMn∕SiO2)N were prepared by magnetron sputtering on Si(100) substrates at room temperature (RT). A ferromagnetic phase with TC above 300K is detected only for Mn∕SnO2. The highest ferromagnetic signal corresponds to the presence of Mn in a mixed valence state combined with the presence of tin oxide. Grazing incidence high-angle x-ray diffraction revealed the formation of MnO and SnO1+x nanocrystals. After annealing, no traces of metallic Mn or MnO are detected from x-ray absorption near-edge structure (XANES) or diffraction; Mn2O3 and Mn3O4 oxides and polycrystalline SnO2 were identified. A clear ferromagnetic signal below 42K with high coercive field is then detected corresponding to Mn3O4 but the RT ferromagnetic component decreases drastically. No mixed Mn–Sn–O phases are detected in as-grown or annealed samples. The close vicinity of MnO1+x and SnO1+x nanograins at the multilayer interfaces seems to be the condition necessary for the RT ferromagnetism.
Parameterized local hybrid functionals from density-matrix similarity metrics
Authors: Janesko Benjamin G. , Scuseria Gustavo E.
Published: February 2008

We recently proposed a real-space similarity metric comparing the Kohn–Sham one-particle density matrix to the local spin-density approximation model density matrix [Janesko and Scuseria, J. Chem. Phys. 127, 164117 (2007)]. This metric provides a useful ingredient for constructing local hybrid density functionals that locally mix exact exchange and semilocal density functional theory exchange. Here we present two lines of inquiry: An approximate similarity metric comparing exact versus generalized gradient approximation (GGA), exchange and parameterized mixing functions using these similarity metrics. This approach yields significantly improved thermochemistry, including GGA local hybrids whose thermochemical performance approaches GGA global hybrids.
Statistical geometry of lattice chain polymers with voids of defined shapes: Sampling with strong constraints
Authors: Lin Ming , Chen Rong , Liang Jie
Published: February 2008

Proteins contain many voids, which are unfilled spaces enclosed in the interior. A few of them have shapes compatible to ligands and substrates and are important for protein functions. An important general question is how the need for maintaining functional voids is influenced by, and affects other aspects of proteins structures and properties (e.g., protein folding stability, kinetic accessibility, and evolution selection pressure). In this paper, we examine in detail the effects of maintaining voids of different shapes and sizes using two-dimensional lattice models. We study the propensity for conformations to form a void of specific shape, which is related to the entropic cost of void maintenance. We also study the location that voids of a specific shape and size tend to form, and the influence of compactness on the formation of such voids. As enumeration is infeasible for long chain polymer, a key development in this work is the design of a novel sequential Monte Carlo strategy for generating large number of sample conformations under very constraining restrictions. Our method is validated by comparing results obtained from sampling and from enumeration for short polymer chains. We succeeded in accurate estimation of entropic cost of void maintenance, with and without an increasing number of restrictive conditions, such as loops forming the wall of void with fixed length, with additionally fixed starting position in the sequence. Additionally, we have identified the key structural properties of voids that are important in determining the entropic cost of void formation. We have further developed a parametric model to predict quantitatively void entropy. Our model is highly effective, and these results indicate that voids representing functional sites can be used as an improved model for studying the evolution of protein functions and how protein function relates to protein stability.
Approximating correlation effects in multiconfigurational self-consistent field calculations of spin-spin coupling constants
Authors: San Fabián J. , Díez E. , García de la Vega J. M. , Suardíaz R.
Published: February 2008

The multiconfigurational self-consistent field (MCSCF) method in their approximations restricted and complete active spaces (RAS and CAS) provides a theoretically accurate description of the coupling constants of a wide range of molecules. To obtain accurate results, however, very large basis sets and large configuration spaces must be used. Nuclear magnetic resonance coupling constants for the equilibrium geometry have been calculated for a series of small molecules using approximated correlation contributions. The four contributions to the coupling constants (Fermi contact, spin dipolar, orbital paramagnetic, and orbital diamagnetic) have been calculated at the CAS and RAS MCSCF and second-order polarization propagator approximation levels using a large basis set. An additive model that considers the effect on the coupling constants from excitation of more than two electrons and from core-electron correlation is used to estimate the coupling constants. Compared with the experimental couplings, the best calculated values, which correspond to the MCSCF results, present a mean absolute error of 3.6Hz and a maximum absolute deviation of 13.4Hz. A detailed analysis of the different contributions and of the effects of the additive contributions on the coupling constants is carried out.
Influence of wall modes on the onset of bulk convection in a rotating cylinder
Authors: Marques F. , Lopez J. M.
Published: February 2008

The onset of thermal convection in an enclosed rotating cylinder is greatly influenced by the interaction between the Coriolis force and the cylinder sidewall. For temperature differences between the hot bottom and the cool top that are too small to sustain convection throughout the entire cylinder, convection sets in as pairs of wall-bounded hot thermal plumes ascend and cold thermal plumes descend in the sidewall boundary layer, the so-called wall modes of rotating convection. Over an extensive range of parameter space, several wall modes with different numbers of thermal pairs coexist stably, and this multiplicity of states leads to very rich nonlinear dynamics as the temperature difference is increased to a level supporting thermal convection throughout the bulk of the cylinder. The bulk convection takes on characteristics of Küppers–Lortz spatiotemporal chaos, but its interaction with the persistent wall modes also leads to further flow complications which are explored here via numerical simulations.
Precise measurements of radial temperature gradients in the laser-heated diamond anvil cell
Authors: Kavner A. , Nugent C.
Published: February 2008

A new spectroradiometry system specialized for measuring two-dimensional temperature gradients for samples at high pressure in the laser heated diamond anvil cell has been designed and constructed at UCLA. Emitted light intensity from sample hotspots is imaged by a videocamera for real time monitoring, an imaging spectroradiometer for temperature measurement, and a high-dynamic-range camera that examines a magnified image of the two-dimensional intensity distribution of the heated spot, yielding precise measurements of temperature gradients. With this new system, most systematic errors in temperature measurement due to chromatic aberration are bypassed. We use this system to compare several different geometries of temperature measurement found in the literature, including scanning a pinhole aperture, and narrow-slit and wide-slit entrance apertures placed before the imaging spectrometer. We find that the most accurate way of measuring a temperature is to use the spectrometer to measure an average hotspot temperature and to use information from the imaging charge coupled device to calculate the temperature distribution to the hotspot. We investigate the effects of possible wavelength- and temperature-dependent emissivity, and evaluate their errors. We apply this technique to measure the anisotropy in temperature distribution of highly oriented graphite at room temperature and also at high pressures. A comparison between model and experiment demonstrates that this system is capable of measuring thermal diffusivity in anisotropic single crystals and is also capable of measuring relative thermal diffusivity at high pressures and temperatures among different materials. This shows the possibility of using this system to provide information about thermal diffusivity of materials at high pressure and temperature.
Stable harmonic multiplying gyrotron traveling-wave amplifier with distributed wall losses and attenuating severs
Authors: Yeh Y. S. , Cheng J. H. , Chen L. K. , Hung C. W. , Lo C. Y. , Liao C. W.
Published: February 2008

Harmonic multiplying gyrotron traveling-wave amplifiers (gyro-TWTs) provide magnetic field reduction and frequency multiplication. However, spurious oscillations may reduce the amplification of the gyro-TWT. Most distributed-loss structures are stabilized in gyro-TWTs that operate at low beam currents. Attenuating severs are added to the interaction circuit of a distributed-loss gyro-TWT to prevent high beam currents that result in mode competition. This study proposes a Ka-band harmonic multiplying gyro-TWT, using distributed wall losses and attenuating severs, to improve the stability of the amplification and the performance of the amplifier. Simulation results reveal that the absolute instabilities are effectively suppressed by wall losses of the lossy and severed sections, especially in the low-kz and high-order modes. Meanwhile, the severed section, dividing an interaction circuit into several short sections, reduces the effective interaction lengths of the absolute instabilities. The stable harmonic multiplying gyro-TWT is predicted to yield a peak output power of 230kW at 33.65GHz with an efficiency of 30%, a saturated gain of 40dB, and a 3dB bandwidth of 0.8GHz for a 60kV, 13A electron beam with an axial velocity spread of Δvz∕vz=8%. The power/gain scaling and phase relation between the drive and the output waves are elucidated.
A desktop Faraday rotation instrument in the ultraviolet
Authors: Ström Valter , Rao K. V.
Published: February 2008

A simple versatile desktop instrument for the measurement of Faraday rotation in the ultraviolet range has been designed and constructed. A high pressure short arc mercury lamp is used for the light source. By using interference filter for mercury, the desired wavelength of the available lines for mercury (e.g., 365, 405, and 436nm) is selected. Our instrument measures hysteresis loops in magnetic fields up to 900kA∕m within a few minutes. With a light beam intensity monitor, the detrimental effect from fluctuations in the light source has been virtually eliminated. The instrument can operate at photocurrents from the picoampere regime and above with a Faraday rotation sensitivity of around 1millideg. By incorporating a higher order Taylor expansion approach, we improve the linearity of the Faraday rotation to transmitted light relationship by two orders of magnitude. The electronics is custom designed analog type, rendering relaxed dynamic requirements for the analog-to-digital converter. The design is fully protected from ambient light which makes operation with the equipment in darkness superfluous; neither does it need any optical table. The data acquisition and operation of the instrument are fully supported by a LABVIEW program. Measurements on a magnetite thin film and on microscope cover glass are given as examples for the performance and sensitivity of the equipment.
Fourth-generation plasma immersion ion implantation and deposition facility for hybrid surface modification layer fabrication
Authors: Wang Langping , Huang Lei , Xie Zhiwen , Wang Xiaofeng , Tang Baoyin
Published: February 2008

The fourth-generation plasma immersion ion implantation and deposition (PIIID) facility for hybrid and batch treatment was built in our laboratory recently. Comparing with our previous PIIID facilities, several novel designs are utilized. Two multicathode pulsed cathodic arc plasma sources are fixed on the chamber wall symmetrically, which can increase the steady working time from 6h (the single cathode source in our previous facilities) to about 18h. Meanwhile, the inner diameter of the pulsed cathodic arc plasma source is increased from the previous 80to209mm, thus, large area metal plasma can be obtained by the source. Instead of the simple sample holder in our previous facility, a complex revolution-rotation sample holder composed of 24 shafts, which can rotate around its axis and adjust its position through revolving around the center axis of the vacuum chamber, is fixed in the center of the vacuum chamber. In addition, one magnetron sputtering source is set on the chamber wall instead of the top cover in the previous facility. Because of the above characteristic, the PIIID hybrid process involving ion implantation, vacuum arc, and magnetron sputtering deposition can be acquired without breaking vacuum. In addition, the PIIID batch treatment of cylinderlike components can be finished by installing these components on the rotating shafts on the sample holder.
Influence of laser beam size on measurement sensitivity of thermophysical property gradients in layered structures using thermal-wave techniques
Authors: Wang Chinhua , Mandelis Andreas , Qu Hong , Chen Zhuying
Published: February 2008

The influence of the photothermal laser source beam size on the measurement sensitivity of layered systems using photothermal radiometry (PTR) is presented. Based on an appropriate theoretical model, widely different behaviors of the photothermal amplitude and phase in terms of combinations of thermophysical properties (i.e., thermal conductivity and thermal diffusivity) between a thin coating and the substrate are observed. The beam size effect on PTR measurement sensitivity is theoretically examined and experimentally demonstrated using a carbonitrided C1018 steel sample. The experimental results of using a variable size laser beam for the carbonitrided C1018 sample validate the theoretical prediction, in which an expanded beam exhibits a much larger magnitude change in both amplitude and phase as a function of frequency than measurements with a focused beam. The fitted thermal conductivity and thermal diffusivity based on the assumed industrially relevant range of effective hardness case depth gives the approximate range of the change in thermal conductivity and thermal diffusivity of C1018 steels after the carbonitriding process.
Ablation-induced explosion of metal using a high-power Nd:YAG laser
Authors: Yoh Jack J. , Lee Hyunhee , Choi Jihee , Lee Kyung-cheol , Kim Ki-hong
Published: February 2008

The interaction of a high-power pulsed-laser beam with metal targets in air from a 1.06 μm, 5 ns, 3 J/pulse, Nd:YAG pulsed laser is investigated together with hydrodynamic theories of laser-supported blast wave and multimaterial reactive Euler equations. The high-speed blast wave generated by the laser ablation of metal reaches a maximum velocity of several thousand meters per second. The apparently similar flow conditions to those of reactive shock wave allow one to apply the equations of motion for energetic materials and to understand the explosive behavior of metal vaporization upon laser ablation. The characteristic time at which the planar to spherical wave transition occurs is investigated at low (20 mJ/pulse) to high (200 mJ/pulse) beam intensities. The flow structure behind the leading shock wave during the early planar shock state is confirmed by the high-resolution multimaterial hydrocode originally developed for shock compression of condensed matter. A repeatable lab-scale blast wave experiment is conducted at various energy levels with three different ablative targets, and both theoretical and computational analyses are used to verify the flow structures behind the leading shock front that remains spherically symmetric until all the momentum transferred from the absorbed intensity dissipates into open air a few microseconds later.
Electron and hole transport in a wide bandgap organic phosphine oxide for blue electrophosphorescence
Authors: Cai Xiuyu , Padmaperuma Asanga B. , Sapochak Linda S. , Vecchi Paul A. , Burrows Paul E.
Published: February 2008

We report blue phosphorescent organic light-emitting devices (OLEDs) using an ambipolar host, N-(4-diphenylphosphoryl phenyl) carbazole (MPO12), doped with iridium (III) bis[(4,6-difluorophenyl)-pyridinato-N,C2′]picolinate (FIrpic). The external quantum efficiency and operating voltage is 9.1(±0.1)% and 4.8V, respectively, measured at a brightness of 800cd∕m2 with no outcoupling enhancement. By varying the layer structure of the OLEDs, we show that MPO12 is capable of transporting both electrons and holes, in contrast to previous demonstrations using diphosphine oxides, which only transported electrons. The improved hole transport results in improved device efficiency.
Air/vacuum dielectric organic single crystalline transistors of copper-hexadecafluorophthalocyanine ribbons
Authors: Tang Qingxin , Tong Yanhong , Li Hongxiang , Hu Wenping
Published: February 2008

Air/vacuum dielectric organic field-effect transistors (OFETs) based on submicrometer-size copper-hexadecafluorophthalocyanine single crystalline ribbon were fabricated and characterized. The n-type OFETs showed high performance with the electron mobility at ∼0.35cm2V−1s−1 and on/off ratio at >3×105, respectively. The electrical characteristics of the devices were hardly affected by air, illumination, and continuous measurements even though the mobility was thermally activated. The high performance of the air/vacuum dielectric devices showed their potential applications in organic circuits.
Leakage current mechanisms in top-gate nanocrystalline silicon thin film transistors
Authors: Lee Hyun Jung , Sazonov Andrei , Nathan Arokia
Published: February 2008

The leakage current in the top-gate nanocrystalline silicon (nc-Si:H) thin film transistors was examined at various temperatures in an attempt to deduce the underlying off-state conduction mechanisms. Under high gate bias, the leakage current can be attributed to the thermal emission of trapped carriers at the midgap grain boundary states at low drain bias, while the behavior is reminiscent of the Poole–Frenkel emission in the drain depletion region at high drain bias. In contrast, Ohmic conduction through the bulk nc-Si:H channel layer seems to be the dominant mechanism of the leakage current under low gate bias.
Replication timing, chromosomal bands, and isochores
Authors: Costantini Maria , Bernardi Giorgio
Published: February 2008

Chromosome replication timing is biphasic (early–late) in the cell cycle of vertebrates and of most (possibly all) eukaryotes. In the present work we have compared the extended, detailed replication timing maps that are available, namely those of human chromosomes 6, 11q, and 21q, with chromosomal bands as visualized at low (400 bands), high (850 bands), and highest (3,200 isochores) resolution. We have observed that the replicons located in a given isochore practically always show either all early or all late replication timing and that early-replicating isochores are short and GC-rich and late-replicating isochores are long and GC-poor. In the vast majority of cases, replicons are clustered in isochores, which are themselves most often clustered in early- or late-replication timing zones and may often reach the size of high-resolution bands and, very rarely, even that of low-resolution bands. Finally, we show that our results should be representative for the whole human genome and thus help to predict replication timing zones in all chromosomes.
Centroid estimation in discrete high-dimensional spaces with applications in biology
Authors: Carvalho Luis E. , Lawrence Charles E.
Published: February 2008

Maximum likelihood estimators and other direct optimization-based estimators dominated statistical estimation and prediction for decades. Yet, the principled foundations supporting their dominance do not apply to the discrete high-dimensional inference problems of the 21st century. As it is well known, statistical decision theory shows that maximum likelihood and related estimators use data only to identify the single most probable solution. Accordingly, unless this one solution so dominates the immense ensemble of all solutions that its probability is near one, there is no principled reason to expect such an estimator to be representative of the posterior-weighted ensemble of solutions, and thus represent inferences drawn from the data. We employ statistical decision theory to find more representative estimators, centroid estimators, in a general high-dimensional discrete setting by using a family of loss functions with penalties that increase with the number of differences in components. We show that centroid estimates are obtained by maximizing the marginal probabilities of the solution components for unconstrained ensembles and for an important class of problems, including sequence alignment and the prediction of RNA secondary structure, whose ensembles contain exclusivity constraints. Three genomics examples are described that show that these estimators substantially improve predictions of ground-truth reference sets.
Phenylalanine-508 mediates a cytoplasmic–membrane domain contact in the CFTR 3D structure crucial to assembly and channel function
Authors: Serohijos Adrian W. R. , Hegedűs Tamás , Aleksandrov Andrei A. , He Lihua , Cui Liying , Dokholyan Nikolay V. , Riordan John R.
Published: February 2008

Deletion of phenylalanine-508 (Phe-508) from the N-terminal nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR), a member of the ATP-binding cassette (ABC) transporter family, disrupts both its folding and function and causes most cystic fibrosis. Most mutant nascent chains do not pass quality control in the ER, and those that do remain thermally unstable, only partially functional, and are rapidly endocytosed and degraded. Although the lack of the Phe-508 peptide backbone diminishes the NBD1 folding yield, the absence of the aromatic side chain is primarily responsible for defective CFTR assembly and channel gating. However, the site of interdomain contact by the side chain is unknown as is the high-resolution 3D structure of the complete protein. Here we present a 3D structure of CFTR, constructed by molecular modeling and supported biochemically, in which Phe-508 mediates a tertiary interaction between the surface of NBD1 and a cytoplasmic loop (CL4) in the C-terminal membrane-spanning domain (MSD2). This crucial cytoplasmic membrane interface, which is dynamically involved in regulation of channel gating, explains the known sensitivity of CFTR assembly to many disease-associated mutations in CL4 as well as NBD1 and provides a sharply focused target for small molecules to treat CF. In addition to identifying a key intramolecular site to be repaired therapeutically, our findings advance understanding of CFTR structure and function and provide a platform for focused biochemical studies of other features of this unique ABC ion channel.
Decidual expression and maternal serum levels of heme oxygenase 1 are increased in pre‐eclampsia
Authors: EIDE IRINA P. , ISAKSEN CHRISTINA V. , SALVESEN KJELL Å. , LANGAAS METTE , SCHØNBERG SVANHILD A. , AUSTGULEN RIGMOR
Published: February 2008

Background. Pre‐eclampsia (PE) is associated with increased oxidative stress and excessive maternal inflammatory response. Heme oxygenase 1 (HMOX1) is an important stress response enzyme and a mediator of cytoprotection against a wide variety of tissue injuries. Methods. In the present study, microarray technology was used to compare the expression of HMOX1 and other genes involved in stress and inflammatory responses in decidua basalis from 16 pregnancies complicated by PE and 17 healthy controls. In addition, the presence of HMOX1 protein in decidua basalis was examined by means of immunohistochemistry, and ELISA was used to measure the maternal serum concentration of HMOX1. Results. Fifteen transcripts involved in stress response including HMOX1 were up‐regulated in cases, using a cut‐off value at p = 0.01. HMOX1 protein expression in decidua basalis was significantly increased in cases compared to controls reflected by more pronounced intensity of HMOX1 positive decidual cells (1.8±0.3 versus 1.5±0.4, p = 0.02) and an increased proportion of HMOX1 positive decidual leukocytes (31±29 versus 9±6%, p = 0.001). Finally, serum HMOX1 levels were significantly higher among cases compared to controls (3.1±1.3 versus 1.9±0.5 ng/ml, p = 0.008). Conclusions. Increased decidual and serum HMOX1 levels, together with altered decidual expression of some stress‐related genes in cases, support the role of oxidative stress and excessive maternal inflammatory response in the pathogenesis of PE.
Smoking during pregnancy from 1999 to 2004: a study from the Medical Birth Registry of Norway
Authors: KVALVIK LIV GRIMSTVEDT , SKJÆRVEN ROLV , HAUG KJELL
Published: February 2008

Background. The aims of the study were to describe changes in smoking habits and evaluate secular trends among all Norwegian pregnant women during the period 1999–2004. We wanted to investigate whether there was a general decline in smoking habits among pregnant women. We also wanted to identify population subgroups with diverging trends. Methods. The Medical Birth Registry of Norway (MBR) has national coverage of all births of 16 or more gestational weeks. Since 1999, women have been asked about tobacco smoking at the beginning and at the end of pregnancy. We included records from 304,905 women giving birth in the period January 1999 through April 2004. Women born outside Norway were handled separately. The selection left a dataset containing 259,573 Norwegian‐born women. Results. We obtained information on smoking habits from 86% at the end of pregnancy. Among those, the daily smoking prevalence was reduced from 17.3% in 1999–2001 to 13.2% in 2002–2004. Higher smoking prevalence was found among multiparous (3+), teenage mothers, single women, and women with low educational level. Conclusions. From 1999 to 2004, a substantial decline in smoking prevalence among Norwegian pregnant women was identified in all subgroups. However, an increasing social polarisation with regard to education and smoking habits was observed in the study period. In order to reduce the smoking‐related risks for unsuccessful pregnancy outcome, special attention should be paid to smoking habits among multiparous, teenage women, single women and women with low education.
Validation study of the capacity of the reference curves of ultrasonographic measurements of the umbilical cord to identify deviations in estimated fetal weight
Authors: BARBIERI CRISTIANE , GUILHERME CECATTI JOSE , KRUPA FABIANA , FRANCISCO MARUSSI EMILIO , VILTON COSTA JOSE
Published: February 2008

Background. The objective of this study was to evaluate the capacity of the cross‐sectional area and diameter of the umbilical cord, and the area of Wharton's jelly (WJ), to predict abnormalities in estimated fetal weight (EFW) in 20–40 week, low‐risk pregnancies. Methods. A validation study was performed in 1,828 pregnant women. Fetal weight was estimated by ultrasonography and classified as: small for gestational age (SGA), appropriate for gestational age (AGA) or large for gestational age (LGA) according to the 10th and 90th percentiles of the reference curve. Measurements of the parameters of the cord were used to classify it as thin, normal or thick using the 10th and 90th percentiles of the reference curves as limits. The capacity of the diameter and total area of the cord and the area of WJ to predict abnormal EFW was calculated for different gestational ages. Results. The capacity of the diameter of thin cords to predict SGA fetuses (S =8.3%, PPV =16.5%) or thick cords to predict LGA fetuses (S =5.5%, PPV =30.1) was weak, similar to the capacity of the area of the umbilical cord to predict SGA (S =8.3%; PPV =16.3%) or LGA fetuses (S =5.5%; PPV =27.8%). The capacity of the area of WJ to predict SGA fetuses (S =5.7%, PPV =11.7%) was similar to its capacity to predict LGA fetuses (S =4%, PPV =27.1%). Conclusion. Despite the correlation between the diameter and cross‐sectional area of the cord and EFW, these measurements were not found to be useful in predicting alterations in EFW and should not be used for this purpose.
Stathmin Activity Influences Sarcoma Cell Shape, Motility, and Metastatic Potential
Authors: Belletti Barbara , Nicoloso Milena S. , Schiappacassi Monica , Berton Stefania , Lovat Francesca , Wolf Katarina , Canzonieri Vincenzo , D'Andrea Sara , Zucchetto Antonella , Friedl Peter , Colombatti Alfonso , Baldassarre Gustavo
Published: February 2008

The balanced activity of microtubule-stabilizing and -destabilizing proteins determines the extent of microtubule dynamics, which is implicated in many cellular processes, including adhesion, migration, and morphology. Among the destabilizing proteins, stathmin is overexpressed in different human malignancies and has been recently linked to the regulation of cell motility. The observation that stathmin was overexpressed in human recurrent and metastatic sarcomas prompted us to investigate stathmin contribution to tumor local invasiveness and distant dissemination. We found that stathmin stimulated cell motility in and through the extracellular matrix (ECM) in vitro and increased the metastatic potential of sarcoma cells in vivo. On contact with the ECM, stathmin was negatively regulated by phosphorylation. Accordingly, a less phosphorylable stathmin point mutant impaired ECM-induced microtubule stabilization and conferred a higher invasive potential, inducing a rounded cell shape coupled with amoeboid-like motility in three-dimensional matrices. Our results indicate that stathmin plays a significant role in tumor metastasis formation, a finding that could lead to exploitation of stathmin as a target of new antimetastatic drugs.
Tracing evolutionary pressure
Authors: Ye Kai , Vriend Gert , IJzerman Adriaan P.
Published: February 2008

Motivation: Recent advances in sequencing techniques have yielded enormous amounts of protein sequence data from various species. This large dataset allows sequence comparison between paralogous and orthologous proteins to identify motifs or functional positions that account for the differences of functional subgroups (‘specificity’ positions). Algorithms such as SDPpred and the two-entropies analysis (TEA) have been developed to detect such specificity positions from a multiple sequence alignment (MSA) grouped into classes according to certain biological functions. Other algorithms such as TreeDet compute a classification and then predict specificity positions associated with it. However, there are still many unresolved questions: Was the optimal subdivision of a protein family achieved? Do the definitions at different levels of the phylogenetic tree affect the prediction of specificity positions? Can the whole phylogenetic tree be used instead of only one level in it to predict specificity positions?

Results: Here we present a novel method, TEA-O (Two-entropies analysis—Objective), to trace the evolutionary pressure from the root to the branches of the phylogenetic tree. At each level of the tree, a TEA plot is produced to capture the signal of the evolutionary pressure. A consensus TEA-O plot is composed from the whole series of plots to provide a condensed representation. Positions related to functions that evolved early (conserved) or later (specificity) are close to the lower-left or upper-left corner of the TEA-O plot, respectively. This novel approach allows an unbiased, user-independent, analysis of residue relevance in a protein family.

We compared our TEA-O method with various algorithms using both synthetic and real protein sequences. The results show that our method is robust, sensitive to subtle differences in evolutionary pressure during evolution and comprehensive because all positions in the MSA are presented in the consensus plot.

Availability: All computer programs and datasets used in this work are available at http://nava.liacs.nl/kye/TEA-O/ for academic use

Contact:  k.ye@lacdr.leidenuniv.nl
FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors
Authors: Park Jongsun , Park Jaejin , Jang Suwang , Kim Seryun , Kong Sunghyung , Choi Jaeyoung , Ahn Kyohun , Kim Juhyeon , Lee Seungmin , Kim Sunggon , Park Bongsoo , Jung Kyongyong , Kim Soonok , Kang Seogchan , Lee Yong-Hwan
Published: February 2008

Summary: Genomes of more than 60 fungal species have been sequenced to date, yet there has been no systematic approach to analyze fungal transcription factors (TFs) kingdom widely. We developed a standardized pipeline for annotating TFs in fungal genomes. Resulting data have been archived in a new database termed the Fungal Transcription Factor Database (FTFD). In FTFD, 31 832 putative fungal TFs, identified from 62 fungal and 3 Oomycete species, were classified into 61 families and phylogenetically analyzed. The FTFD will serve as a community resource supporting comparative analyses of the distribution and domain structure of TFs within and across species.

Availability: All data described in this study can be browsed through the FTFD web site at http://ftfd.snu.ac.kr/.

Contact:  yonglee@snu.ac.kr
DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra
Authors: Mayampurath Anoop M. , Jaitly Navdeep , Purvine Samuel O. , Monroe Matthew E. , Auberry Kenneth J. , Adkins Joshua N. , Smith Richard D.
Published: February 2008

Summary:  DeconMSn accurately determines the monoisotopic mass and charge state of parent ions from high-resolution tandem mass spectrometry data, offering significant improvement for LTQ_FT and LTQ_Orbitrap instruments over the commercially delivered Thermo Fisher Scientific's extract_msn tool. Optimal parent ion mass tolerance values can be determined using accurate mass information, thus improving peptide identifications for high-mass measurement accuracy experiments. For low-resolution data from LCQ and LTQ instruments, DeconMSn incorporates a support-vector-machine-based charge detection algorithm that identifies the most likely charge of a parent species through peak characteristics of its fragmentation pattern.

Availability:  http://ncrr.pnl.gov/software/ or http://www.proteomicsresource.org/

Contact:  rds@pnl.gov

Supplementary information: PowerPoint presentation/Poster on http://ncrr.pnl.gov/software/.
Metabolic and Developmental Adaptations of Growing Potato Tubers in Response to Specific Manipulations of the Adenylate Energy Status
Authors: Riewe David , Grosman Lukasz , Zauber Henrik , Wucke Cornelia , Fernie Alisdair R. , Geigenberger Peter
Published: February 2008

Heterotrophic carbon metabolism has been demonstrated to be limited by oxygen availability in a variety of plant tissues, which in turn inevitably affects the adenylate status. To study the effect of altering adenylate energy metabolism, without changing the oxygen supply, we expressed a plastidially targeted ATP/ADP hydrolyzing phosphatase (apyrase) in tubers of growing potato (Solanum tuberosum) plants under the control of either inducible or constitutive promoters. Inducible apyrase expression in potato tubers, for a period of 24 h, resulted in a decrease in the ATP-content and the ATP-ADP ratio in the tubers. As revealed by metabolic profiling, this was accompanied by a decrease in the intermediates of sucrose to starch conversion and several plastidially synthesized amino acids, indicating a general depression of tuber metabolism. Constitutive tuber-specific apyrase expression did not lead to a reduction of ATP, but rather a decrease in ADP and an increase in AMP levels. Starch accumulation was strongly inhibited and shifted to the production of amylopectin instead of amylose in these tubers. Furthermore, the levels of almost all amino acids were decreased, although soluble sugars and hexose-Ps were highly abundant. Respiration was elevated in the constitutively expressing lines indicating a compensation for the dramatic increase in ATP hydrolysis. The increase in respiration did not affect the internal oxygen tensions in the tubers. However, the tubers developed a ginger-like phenotype having an elevated surface-volume ratio and a reduced mass per tuber. Decreased posttranslational redox activation of ADP-glucose pyrophosphorylase and a shift in the ratio of soluble starch synthase activity to granule-bound starch synthase activity were found to be partially responsible for the alterations in starch structure and abundance. The activity of alcohol dehydrogenase was decreased and pyruvate decarboxylase was induced, but this was neither reflected by an increase in fermentation products nor in the cellular redox state, indicating that fermentation was not yet induced in the transgenic lines. When taken together the combined results of these studies allow the identification of both short- and long-term adaptation of plant metabolism and development to direct changes in the adenylate status.
Engineering membrane protein overproduction in Escherichia coli
Authors: Molina Daniel Martinez , Cornvik Tobias , Eshaghi Said , Haeggström Jesper Z. , Nordlund Pär , Sabet Marina Ignatushchenko
Published: February 2008

Membrane proteins play a fundamental role in human disease and therapy, but suffer from a lack of structural and functional information compared to their soluble counterparts. The paucity of membrane protein structures is primarily due to the unparalleled difficulties in obtaining detergent‐solubilized membrane proteins at sufficient levels and quality. We have developed an in vitro evolution strategy for optimizing the levels of detergent‐solubilized membrane protein that can be overexpressed and purified from recombinant Escherichia coli. Libraries of random mutants for nine membrane proteins were screened for expression using a novel implementation of the colony filtration blot. In only one cycle of directed evolution were significant improvements of membrane protein yield obtained for five out of nine proteins. In one case, the yield of detergent‐solubilized membrane protein was increased 40‐fold.