bluuebunny/crossref_metadata_2025 huggingface dataset:
Community Outreach through Genomics Education Partnership
Authors: Madupu Ramana , Rosenwald Anne , Campbell A. Malcolm , Bhalla Satish , Sutton Granger
Published: April 2009

The J Craig Venter Institute (JCVI) has recently partnered with undergraduate university faculty to expand the scope of education and outreach program as part of the NIAID’s BRC initiative, by joining forces with faculty members participating in the Genomics Education Partnership (GEP). The goal of the GEP is to provide opportunities for undergraduate students to participate in genomics research and gain hands on experience. Faculty members trained on annotation methodologies and tools during the Prokaryotic Annotation Workshop conducted at JCVI, impart their knowledge in the classroom as part of the semester course. As a pilot project, we are currently collaborating with 3 groups lead by a faculty member, spread across 3 universities in the community curation of bacterial genomes. Each participating undergraduate group collectively annotates a specific bacterial genome that was sequenced at JCVI and run through the automatic annotation pipeline. Remote access to genome sequence data, pre-computed gene predictions, search results, automatic annotation and bioinformatics analysis is provided through our web-based manual annotation tool, MANATEE. The students log into JCVI genome databases with user specific ids and password and learn to annotate single genes, entire metabolic pathways leading to analysis of a question that may be unique to the genome being analyzed. Users of the genome data receive dedicated support and guidance from our in house annotation experts on the usage of JCVI’s tools and annotation methodologies. Through this exercise, the undergraduate students are introduced to concepts of genomics and bioinformatics and gain deeper understanding of the concepts of cellular metabolism and disease pathology, which may lead them to making scientific research their career path. Some groups are focusing on genome specific pathways and plan to conduct wet lab experiments to understand unique genome features. We are highly encouraged that this model of web based, remote access, community annotation has been successful and propose to leverage the community of annotators to update annotations of pathogen genomes in Pathema-BRC.
The Eukaryotic Linear Motif Resource (ELM): Regulatory Sites in Proteins
Authors: Diella Francesca , Via Allegra , Chica Claudia , Luck Katja , Gould Catherin , Gibson Toby
Published: April 2009

Linear motifs are short and evolutionarily variable sequence patterns associated with particular functions often involving post-translational modifications, such as phosphorylation, acetylation, glycosylation, targeting signals for cellular compartments, protein cleavage sites and protein–protein interaction.Experimentally they are often neglected because their short length (4-10 residues long), and the fact that they often reside in disordered regions in proteins makes them difficult to detect. For a similar reason, using the sole regular expression to detect linear motifs matches in sequences has almost no predictive power because they are both statistically insignificant and prone to massive over-prediction.The Eukaryotic Linear Motif resource (ELM - "http://elm.eu.org":http://elm.eu.org) is a bioinformatics facility for investigating candidate short functional motifs in eukaryotic proteins. The ELM database to date has collected more than 140 motifs and their regular expressions patterns as well as information about their instances of occurrence, distribution, crystal structure, publications, etc.In order to reduce the over-prediction inherent to pattern matching against protein sequences and to discriminate true from false positive motif matches, context-based rules and logical filters are applied. The current version includes cell compartment, phylogeny, globular domain clash filters and the more recent structural filter based on known three-dimensional information that relies on structural information, such as residue solvent accessibility and secondary structure features. This implies that a candidate motif can be excluded from further consideration if the protein resides in the wrong cellular compartment or the motif is buried in the core of a globular domain. By considering additional types of context information, we expect that prediction of functional sites by ELM can be considerably improved. In cases where the user cannot provide relevant context information, we consider providing predictions of contextual information in order to improve the ELM performance. For example, since the ELM motif database has been annotated with biological process GO terms, the system could be prepared for addition of a new context filter using biological process.
The Gene Ontology Annotation (GOA) Database
Authors: Huntley Rachael , Dimmer Emily , Barrell Daniel , Binns David , Apweiler Rolf
Published: April 2009

The Gene Ontology (GO) is a well-established, structured vocabulary that has been successfully used for 10 years in the annotation of proteins. GO terms, created in consultation with the biology community, are used to replace the multiple nomenclatures used by scientific databases that can hamper data integration. Currently GO consists of more than 26,500 terms distributed over three ontologies that describe the molecular function, biological process and subcellular location of a protein in a generic cell.The Gene Ontology Annotation (GOA) database ("http://www.ebi.ac.uk/GOA":http://www.ebi.ac.uk/GOA) aims to provide high-quality manual and electronic GO annotations to proteins within the UniProt Knowledgebase (UniProtKB). By annotating all ‘known’ proteins with GO terms and transferring this knowledge to highly similar ‘unknown’ proteins, GOA offers a valuable contribution to the understanding of all proteomes.As well as generating manual annotation, made by extracting experimental evidence from full text peer-reviewed publications, GOA produces electronic annotation by making large-scale assignments of GO terms to proteins using computational methods. To date we have six electronic annotation methods including; InterPro2GO, Swiss-Prot Keyword2GO and the projection of annotations between orthologous species using Ensembl Compara.GOA provides annotated entries for over 180,000 species and is the largest and most comprehensive open-source contributor of annotations to the GO Consortium annotation effort. In addition, by integrating GO annotations from model organism groups (e.g. FlyBase, GeneDB, MGI, RGD, SGD and TAIR), GOA ensures the dataset remains a key reference. GOA prioritises the annotation of the human proteome and provides this annotation to the GO Consortium’s Reference Genome project.GOA produces monthly releases of annotations to the human, mouse, rat, zebrafish, cow, chicken and Arabidopsis proteomes as well as a file for the multiple species within UniProtKB. The GOA dataset can be queried through a user-friendly web interface via our QuickGO browser("http://www.ebi.ac.uk/QuickGO":http://www.ebi.ac.uk/QuickGO) or downloaded in a parsable format via the EBI("ftp://ftp.ebi.ac.uk/pub/databases/GO/goa":ftp://ftp.ebi.ac.uk/pub/databases/GO/goa) and GO FTP sites. The GOA dataset has increasingly been integrated into tools that aid in the analysis of large datasets resulting from high-throughput experiments thus assisting researchers in biological interpretation of their results.
Interplay Between Weight Loss and Gut Microbiota Composition in Overweight Adolescents
Authors: Santacruz Arlette , Marcos Ascensión , Wärnberg Julia , Martí Amelia , Martin‐Matillas Miguel , Campoy Cristina , Moreno Luis A. , Veiga Oscar , Redondo‐Figuero Carlos , Garagorri Jesús M. , Azcona Cristina , Delgado Manuel , García‐Fuentes Miguel , Collado Maria C. , Sanz Yolanda ,   EVASYON Study Group
Published: April 2009

The aim of this study was to determine the influence of an obesity treatment program on the gut microbiota and body weight of overweight adolescents. Thirty‐six adolescents (13–15 years), classified as overweight according to the International Obesity Task Force BMI criteria, were submitted to a calorie‐restricted diet (10–40%) and increased physical activity (15–23 kcal/kg body weight/week) program over 10 weeks. Gut bacterial groups were analyzed by quantitative real‐time PCR before and after the intervention. A group of subjects (n = 23) experienced >4.0 kg weight loss and showed significant BMI (P = 0.030) and BMI z‐score (P = 0.035) reductions after the intervention, while the other group (n = 13) showed <2.0 kg weight loss. No significant differences in dietary intake were found between both groups. In the whole adolescent population, the intervention led to increased Bacteroides fragilis group (P = 0.001) and Lactobacillus group (P = 0.030) counts, and to decreased Clostridium coccoides group (P = 0.028), Bifidobacterium longum (P = 0.031), and Bifidobacterium adolescentis (P = 0.044) counts. In the high weight–loss group, B. fragilis group and Lactobacillus group counts also increased (P = 0.001 and P = 0.007, respectively), whereas C. coccoides group and B. longum counts decreased (P = 0.001 and P = 0.044, respectively) after the intervention. Total bacteria, B. fragilis group and Clostridium leptum group, and Bifidobacterium catenulatum group counts were significantly higher (P < 0.001–0.036) while levels of C. coccoides group, Lactobacillus group, Bifidobacterium, Bifidobacterium breve, and Bifidobacterium bifidum were significantly lower (P < 0.001–0.008) in the high weight–loss group than in the low weight–loss group before and after the intervention. These findings indicate that calorie restriction and physical activity have an impact on gut microbiota composition related to body weight loss, which also seem to be influenced by the individual's microbiota.
Changes in Health State Utilities With Changes in Body Mass in the Diabetes Prevention Program
Authors: Ackermann Ronald T. , Edelstein Sharon L. , Narayan K.M. Venkat , Zhang Ping , Engelgau Michael M. , Herman William H. , Marrero David G. ,   Diabetes Prevention Program Research Group
Published: April 2009

Health utilities are measures of health‐related quality of life (HRQL) used in cost‐effectiveness research. We evaluated whether changes in body weight were associated with changes in health utilities in the Diabetes Prevention Program (DPP) and whether associations differed by treatment assignment (lifestyle intervention, metformin, placebo) or baseline obesity severity. We constructed physical (PCS‐36) and mental component summary (MCS‐36) subscales and short‐form‐6D (SF‐6D) health utility index for all DPP participants completing a baseline 36‐item short form (SF‐36) HRQL assessment (N = 3,064). We used linear regression to test associations between changes in body weight and changes in HRQL indicators, while adjusting for other demographic and behavioral variables. Overall differences in HRQL between treatment groups were highly statistically significant but clinically small after 1 year. In multivariable models, weight change was independently associated with change in SF‐6D score (increase of 0.007 for every 5 kg weight loss; P < 0.001), but treatment effects independent of weight loss were not. We found no significant interaction between baseline obesity severity and changes in SF‐6D with changes in body weight. However, increases in physical function (PCS‐36) with weight loss were greater in persons with higher baseline obesity severity. In summary, improvements in HRQL are associated with weight loss but not with other effects of obesity treatments that are unrelated to weight loss. Although improvements in the SF‐6D did not exceed commonly reported thresholds for a minimally important difference (0.04), these changes, if causal, could still have a significant impact on clinical cost‐effectiveness estimates if sustained over multiple years.
Sedentariness at Work: How Much Do We Really Sit?
Authors: McCrady Shelly K. , Levine James A.
Published: April 2009

Sedentariness is associated with obesity. We examined whether people with sedentary jobs are equally inactive during their work days and leisure days. We enrolled 21 subjects of varying weight and body fat (11 men:10 women, 38 ± 8 years, 83 ± 17 kg, BMI 28 ± 5 kg/m2, 29 ± 11 fat kg, 35 ± 9% fat). All subjects continued their usual work and leisure‐time activities whilst we measured daily activity and body postures for 10 days. The data supported our hypothesis that people sit more at work compared to leisure (597 ± 122 min/day cf 484 ± 83 min/day; P < 0.0001). The mean difference was 110 ± 99 min/day. Similarly, work days were associated with less standing (341 ± 97 min/day; P = 0.002) than leisure days (417 ± 101 min/day). Although the walking bouts did not differ significantly between work and leisure (46 ± 9 vs. 42 ± 9 walking bouts/day); the mean free‐living velocity of a walk at work was 1.08 ± 0.28 mph and on leisure days was 0.94 ± 0.24 mph (P = 0.03) and the average time spent walking was 322 ± 91 min on work days and 380 ± 108 min on leisure days (P = 0.03). Estimates of the daily energetic cost of walking approximated 527 ± 220 kcal/day for work days and 586 ± 326 kcal/day for leisure days (r = 0.72, P < 0.001). Work days are associated with more sitting and less walking/standing time than leisure days. We suggest a need to develop approaches to free people from their chairs and render them more active.
Influence of BMI on Health‐related Quality of Life: Comparison Between an Obese Adult Cohort and Age‐matched Population Norms
Authors: Anandacoomarasamy Ananthila , Caterson Ian D. , Leibman Steven , Smith Garett S. , Sambrook Phillip N. , Fransen Marlene , March Lyn M.
Published: April 2009

The aim of this study was to determine health‐related quality of life and fatigue measures in obese subjects and to compare scores with age‐ and gender‐matched population norms. A total of 163 obese subjects were recruited from laparoscopic‐adjustable gastric banding or exercise and diet weight loss programs between March 2006 and December 2007. All subjects completed the Medical Outcomes Study Short Form 36 (SF‐36), Assessment of Quality of Life (AQoL), and Multidimensional Assessment of Fatigue (MAF) questionnaires. One‐sample t‐tests were used to compare transformed scores with age‐ and gender‐matched population norms and controls. Obese subjects have significantly lower SF‐36 physical and emotional component scores, significantly lower AQoL utility scores and significantly higher fatigue scores compared to age‐matched population norms. Within the study cohort, the SF‐36 physical functioning, role physical and bodily pain scores, and AQoL utility index were even lower in subjects with clinical knee osteoarthritis (OA). However, obese individuals without OA still had significantly lower scores compared to population norms. Obesity is associated with impaired health‐related quality of life and disability as measured by the SF‐36, AQoL, and fatigue score (MAF) compared to matched population norms.
Study of nonlinear spectral energy transfer in frequency domain
Authors: Xu M. , Tynan G. R. , Holland C. , Yan Z. , Muller S. H. , Yu J. H.
Published: April 2009

A method for measuring nonlinear energy transfer in the frequency domain using a two-field model of drift turbulence is proposed, and the theoretical motivation and experimental results are presented. The approach is based on the cross-bispectral analysis of quadratic nonlinearities in the turbulent internal and kinetic energy balance equations directly derived from the fluid plasma continuity and momentum equations. Application of the technique to data from a laboratory plasma experiment reveals the nonlinear energy transfer in weak collisional plasma drift turbulence; the results show a transfer of density fluctuation energy toward higher frequency (which correspond to smaller azimuthal spatial scales) and a transfer of kinetic energy to lower frequencies (corresponding to larger azimuthal scales).
Dielectric and ferroelectric properties of lead zirconate titanate-lead nickel niobate ceramics under compressive stress
Authors: Unruan M. , Prasartketrakarn A. , Ngamjarurojana A. , Laosiritaworn Y. , Ananta S. , Yimnirun R.
Published: April 2009

Dielectric and ferroelectric properties of complex perovskite lead zirconate titanate-lead nickel niobate ceramic system were investigated under the influence of the compressive stress. The results showed that the dielectric properties, i.e., dielectric constant (εr) and dielectric loss (tan δ), and the ferroelectric characteristics, i.e., the area of the ferroelectric hysteresis (P-E) loops, the maximum polarization (Pmax), and the remanent polarization (Pr) changed significantly with increasing compressive stress. These changes depended greatly on the ceramic compositions. The experimental results on the dielectric properties could be explained by the deaging phenomenon. The stress-induced domain wall motion suppression and non-180° ferroelectric domain switching processes were responsible for the changes observed for the ferroelectric parameters. In addition, a significant decrease in those parameters after a cycle of stress was observed and attributed to the stress-induced decrease in switchable part of spontaneous polarization. This study clearly showed that the applied stress has significant influence on the electrical properties of complex perovskite ceramics.
In situ x-ray diffraction study of metal induced crystallization of amorphous germanium
Authors: Knaepen W. , Gaudet S. , Detavernier C. , Van Meirhaeghe R. L. , Sweet J. Jordan , Lavoie C.
Published: April 2009

Metal induced crystallization (MIC) is a technique that lowers the crystallization temperature of amorphous semiconductors. The process has mainly been used to influence the crystallization of amorphous silicon (a-Si) and multiple studies on this subject have already been performed. The research of the MIC of amorphous Ge (a-Ge) has been mostly limited to the use of a Ni or Al film. This paper focuses on the characterization of the crystallization behavior of a-Ge films in the presence of 20 transition metals (Ti, Zr, Hf, V, Nb, Ta, Cr, Mo, W, Mn, Re, Fe, Ru, Co, Rh, Ir, Ni, Pd, Pt, Cu, Ag, Au, and Al). The kinetics of the crystallization process are also systematically studied for the seven metals that lower the initial crystallization temperature the most. In addition, the influence of the thickness of the metal film was determined for the case of a Au and Al film. A comparison of the influence of the various metals on a-Ge and a-Si is made and the similarities and differences are discussed using existing models for the MIC process.
Magnetoelectric coupling in BaTiO3/(NiFe2O4/BaTiO3)n (n=1,2,3,4) multilayered thin films
Authors: Liu Jing , Zhang Yi , Lin Yuanhua , Nan C. W.
Published: April 2009

Multilayered heterostructures, BaTiO3/(NiFe2O4/BaTiO3)n (n=1,2,3,4), with alternating ferroelectric BaTiO3 and ferrimagnetic NiFe2O4 layers were epitaxially grown on (001)-SrTiO3 substrates via pulsed laser deposition technique. The multilayered heterostructures with a total thickness of about 120 nm preserved ferromagnetic and ferroelectric properties at room temperature, strongly depending on the number n due to interface and thickness size effect. The influence of the interface on the magnetoelectric coupling effect in the multilayered thin films were further confirmed by observed increasing magnetoelectric coefficients with the number n.
Numerical study of eigenmode forcing effects on jet flow development and noise generation mechanisms
Authors: Keiderling Felix , Kleiser Leonhard , Bogey Christophe
Published: April 2009

The effect of nonlinear interaction of instability eigenmodes on jet flow transition and its near acoustic field for a high-subsonic round jet at a Reynolds number of Re=4.5×105 and a Mach number of Ma=0.9 is investigated using large-eddy simulations. At the inflow, helical perturbations of azimuthal wavenumbers |n|=4,…,8 determined from linear stability theory are superimposed on a laminar base flow in order to trigger transition to turbulence. The disturbance amplitude is varied parametrically in the range from 1.5% to 4.5% of the jet exit velocity Uj. Thereby we aim to characterize sources of noise generation and, in particular, underlying mode interactions. With increasing forcing amplitude, the transitional behavior of the jet changes which affects the mean flow and also the acoustic near-field, which are both analyzed in detail. As the forcing amplitude is increased, the axial root-mean-square peak levels along the jet centerline are reduced by approximately 7%. Simultaneously, pronounced dual-peak distributions are generated along the jet lip line which are related to the localization of vortex pairings of the jet column mode. For low-amplitude excitation the azimuthal turbulent kinetic energy spectra show that the unexcited, naturally least stable axisymmetric mode n=0 and the helical mode n=1 dominate the early nonlinear regimes between z≈6r0 and 9r0 where r0 is the jet radius. An analysis of the Fourier mode amplitude clarifies that this energy rise is linked to the helical mode n=1. For higher forcing amplitudes, in addition to the varicose mode n=0 interactions between the excited even mode n=4 and higher azimuthal harmonics thereof dominate the azimuthal energy spectra. These differences in the early nonlinear development of the eigenmodes are found to alter the acoustic near-field. At small angles from the downstream jet axis, the peak acoustic frequency occurs at a Strouhal number based on the angular frequency ω and the jet diameter Dj of St=ωDj/(2πUj)≈0.4. For low-amplitude forcing sound pressure levels are slightly enhanced which can be linked to the dominant low azimuthal wavenumbers identified in the transitional region. In the sideline direction, regardless of the excitation level, broadbanded spectra with maxima in the band 0.7≤St≤0.8 are found which is maintained at intermediate observer angles. For high forcing amplitude, however, a tonal component outside the initially excited frequency range is observed. This peak at St≈0.88 can be explained by weakly nonlinear interactions of initially forced eigenmodes n=4 and n=8 together with the jet column mode.
Some applications of the Pohozaev identity
Authors: Shirai Shin-ichi
Published: April 2009

We apply the Pohozaev identity to show the nonexistence of nontrivial solutions to a semilinear equation of the form (H−E)u=f(x,∣u∣)u, where E is a real constant lying on the essential spectrum of H. The self-adjoint operators H under consideration are the Schrödinger operator with Coulomb-type potentials, the Stark-like Hamiltonian, and the semirelativistic Hamiltonian.
Modified atomic scattering amplitudes and size effects on the 002 and 220 electron structure factors of multiple Ga1−xInxAs/GaAs quantum wells
Authors: Titantah J. T. , Lamoen D. , Schowalter M. , Rosenauer A.
Published: April 2009

The modified atomic scattering amplitudes (MASAs) of mixed Ga1−xInxAs, GaAs1−xNx, and InAs1−xNx are calculated using the density functional theory approach and the results are compared with those of the binary counterparts. The MASAs of N, Ga, As, and In for various scattering vectors in various chemical environments and in the zinc-blende structure are compared with the frequently used Doyle and Turner values. Deviation from the Doyle and Turner results is found for small scattering vectors (s<0.3 Å−1) and for these scattering vectors the MASAs are found to be sensitive to the orientation of the scattering vector and on the chemical environment. The chemical environment sensitive MASAs are used within zero pressure classical Metropolis Monte Carlo, finite temperature calculations to investigate the effect of well size on the electron 002 and 220 structure factors (SFs). The implications of the use of the 002 (200) spot for the quantification of nanostructured Ga1−xInxAs systems are examined while the 220 SF across the well is evaluated and is found to be very sensitive to the in-plane static displacements.
Surface layer magneto-optical effect on one-dimensional magneto-photonic crystal
Authors: Nishino Reina , Yamada Shigeki
Published: April 2009

Surface-layer magneto-optical effects of propagating and reflected light were calculated for photonic crystals of magnetic materials using a finite-difference time-domain algorithm. The magneto-optical effect of the reflected light on the photonic band-gap range strongly depended on the dielectric constant of the surface layer, although no such surface effect was observed near the first photonic band edge. When the dielectric constant of the surface layer was low, the polarization rotation angle of the reflected light increased with the frequency of the light, and reached a maximum value just below the second photonic band. This frequency dependence should be associated with the group delay time of the reflected light, and thus the large delay time just below the second photonic band should be caused by the localization mode in the surface layer. Due to the localized surface mode, the influence of the absorption of the medium on the polarization rotation angle strongly depends on the dielectric constant of the surface layer.
Theoretical study of proton tunneling in the excited state of tropolone
Authors: Wójcik Marek J. , Boda Łukasz , Boczar Marek
Published: April 2009

Ab initio CIS/6-311++G(d,p) calculations of geometry and vibrational frequencies have been carried out in the Ã state of tropolone. The grids of potential energy surfaces along the coordinates of high frequency tunneling vibration and the low-frequency coupled vibration have been calculated. Two-dimensional model potentials, formed from symmetric mode coupling potential and squeezed double well potential, have been fitted to the calculated potential energy surfaces and used to analyze proton dynamics. The tunneling splittings for different vibrationally excited states have been calculated and compared with the available experimental data. The model potential energy surfaces, based on the CIS/6-311++G(d,p) calculations, give good estimation of the tunneling energy splittings in the vibrationally ground and excited states of tropolone and explain monotonic decrease in tunneling splittings with the excitation of low-frequency out-of-plane modes and increase in the tunneling splittings with the excitation of low-frequency planar modes.
Droplet formation and stability of flows in a microfluidic T-junction
Authors: Gupta Amit , Murshed S. M. Sohel , Kumar Ranganathan
Published: April 2009

Flow regimes obtained as a consequence of two immiscible fluids interacting at a T-junction are presented for high Capillary numbers and different flow rates of the continuous and dispersed phases. Through lattice Boltzmann based simulations, a regime map is created that distinguishes parallel flows from droplet flows. Simulations show the dependence of flow rates and viscosity ratio on the volume of droplets formed, which is compared with existing experimental data. At high Capillary numbers, the transition zone which separates parallel and droplet flows shrinks, and is influenced by the viscosity ratio as well.
Development of a compact electron ion coincidence analyzer using a coaxially symmetric mirror electron energy analyzer and a miniature polar-angle-resolved time-of-flight ion mass spectrometer with four concentric anodes
Authors: Kobayashi Eiichi , Nambu Akira , Mase Kazuhiko , Isari Kouji , Tanaka Kenichiro , Mori Masanobu , Okudaira Koji K. , Ueno Nobuo
Published: April 2009

A compact electron ion coincidence (EICO) analyzer that uses a coaxially symmetric mirror electron energy analyzer and a miniature polar-angle-resolved time-of-flight ion mass spectrometer with four concentric anodes was developed for surface science and surface analysis. The apparatus is especially useful in the study of ion desorption stimulated by an Auger process because information on the mass, yield, desorption polar angle, and kinetic energy of ions can be obtained for the selected core-ionization-final-states or the selected Auger-final-states. The analyzer can be used also for analysis of the configuration of specific surface molecules because the desorption polar angles reflect the direction of surface bonds. The EICO analyzer was evaluated by measuring polar-angle-resolved-ion yield spectra and coincidence spectra of Auger-electron and polar-angle-resolved H+ from condensed water.
Theoretical prediction of shape memory behavior and ferrimagnetism in Mn2NiIn
Authors: Chakrabarti Aparna , Barman S. R.
Published: April 2009

Using density functional theory, we show that in Mn2NiIn a phase transition from cubic to tetragonal structure results in a lowering of the total energy, indicating occurrence of martensitic phase transition. The structural phase transition is nearly volume conserving, which is a characteristic of a shape memory alloy. The magnetic ground state is ferrimagnetic with antiparallel Mn spin moments and the total spin magnetization is 0.51μB in the martensitic phase. Thus, we predict that Mn2NiIn would behave like a magnetic shape memory alloy. The electronic structure and magnetic properties are explained by the spin polarized density of states.
First principles band structure calculations based on self-consistent screened Hartree–Fock exchange potential
Authors: Shimazaki Tomomi , Asai Yoshihiro
Published: April 2009

A screened Hartree–Fock (HF) exchange potential with the dielectric constant was previously reported by Shimazaki and Asai [Chem. Phys. Lett. 466, 91 (2008)], in which the inverse of the dielectric constant was used to represent a fraction of the HF exchange term. In that report, the experimentally obtained value for the dielectric constant was employed. Herein, we discuss a self-consistent technique, in which the value of the dielectric constant can be automatically determined. This technique enables the energy band structure to be determined without using the experimental value. The band energy structure of diamond is calculated, a self-consistent procedure is determined to give closer bandgaps compared with the local density approximation and the generalized gradient approximation.
Efficient approach to nucleation and growth dynamics: Stationary diffusion flux model
Authors: van Putten Dennis S. , Kalikmanov Vitaly I.
Published: April 2009

A new model describing the evolution of clusters in the processes of nucleation and growth is proposed. The diffusion flux in the nonstationary Fokker–Planck equation with an unknown distribution function is approximated by the closed form expression containing the steady-state solution of the Zeldovich–Frenkel equation. This is justified due to the smallness of induction time of cluster formation compared to the time scale observed in experiments. The resulting stationary diffusion flux model is valid for all cluster sizes, computationally efficient and applicable to various types of cluster formation processes. Its application to a nucleation pulse experiment shows an excellent agreement with the solution of the set of formally exact Becker–Döring equations.
Nitrous oxide dimer: An ab initio coupled-cluster study of isomers, interconversions, and infrared fundamental bands, and experimental observation of a new fundamental for the polar isomer
Authors: Berner G. M. , East A. L. L. , Afshari Mahin , Dehghany M. , Moazzen-Ahmadi N. , McKellar A. R. W.
Published: April 2009

Improved quantum chemistry (coupled-cluster) results are presented for spectroscopic parameters and the potential energy surface for the N2O dimer. The calculations produce three isomer structures, of which the two lowest energy forms are those observed experimentally: a nonpolar C2h-symmetry planar slipped-antiparallel geometry (with inward-located O atoms) and a higher-energy polar Cs-symmetry planar slipped-parallel geometry. Harmonic vibrational frequencies and infrared intensities for these isomers are calculated. The low-frequency intermolecular vibrational mode predictions should be useful for future spectroscopic searches, and there is good agreement in the one case where an experimental value is available. The frequency shifts for the high-frequency intramolecular stretching vibrations, relative to the monomer, were calculated and used to help locate a new infrared band of the polar isomer, which corresponds to the weaker out-of-phase combination of the ν1 antisymmetric stretch of the individual monomers. The new band was observed in the region of the monomer ν1 fundamental for both (N142O)2 and (N152O)2 using a tunable infrared diode laser to probe a pulsed supersonic jet expansion, and results are presented.
Detection of fluorescently labeled biomolecules immobilized on a detachable substrate using an integrated amorphous silicon photodetector
Authors: Pimentel A. C. , Pereira A. T. , Prazeres D. M. F. , Chu V. , Conde J. P.
Published: April 2009

An integrated platform for biomolecular detection is described comprising two parts: (1) an a-Si:H p-i-n photodiode with an integrated filter for fluorescence detection, and (2) a detachable layer (a glass slide) where the biological molecular recognition reaction takes place. The distance between the photodetector and the layer with the fluorescently labeled biomolecules must be accurately controlled to ensure adequate sensitivity. A spacer 400 μm thick was used to separate the photodetector from the molecular layer. The minimum surface density of quantum dot Evitag 604 nm detected was 8 fmol/cm2. The detection of an antibody-antigen molecular recognition reaction is presented.
Contact resistance in carbon nanostructure via interconnects
Authors: Wu Wen , Krishnan Shoba , Yamada Toshishige , Sun Xuhui , Wilhite Patrick , Wu Raymond , Li Ke , Yang Cary Y.
Published: April 2009

We present an in-depth electrical characterization of contact resistance in carbon nanostructure via interconnects. Test structures designed and fabricated for via applications contain vertically aligned arrays of carbon nanofibers (CNFs) grown on a thin titanium film on silicon substrate and embedded in silicon dioxide. Current-voltage measurements are performed on single CNFs using atomic force microscope current-sensing technique. By analyzing the dependence of measured resistance on CNF diameter, we extract the CNF resistivity and the metal-CNF contact resistance.
Multiple magnetic microrobot control using electrostatic anchoring
Authors: Pawashe Chytra , Floyd Steven , Sitti Metin
Published: April 2009

Addressing power and control to individual untethered microrobots is a challenge for small-scale robotics. We present a 250×130×100 μm3 magnetic robot wirelessly driven by pulsed external magnetic fields. An induced stick-slip motion results in translation speeds over 8 mm/s. Control of multiple robots is achieved by an array of addressable electrostatic anchoring pads on the surface, which selectively fixes microrobots, preventing translation. We demonstrate control of two microrobots in both uncoupled individual motion and coupled symmetric motion. An estimated anchoring force of 23.0 μN is necessary to effectively fix each microrobot.
Suspending single-wall carbon nanotube thin film infrared bolometers on microchannels
Authors: Lu Rongtao , Li Zhuangzhi , Xu Guowei , Wu Judy Z.
Published: April 2009

Suspended single-wall carbon nanotube (SWCNT) thin film bolometers have been fabricated on microchannels patterned on Si substrates using electron-beam lithography. The much improved bolometric photoresponse is attributed to the reduced thermal link between SWCNT bolometer and substrate, which can be controlled by tuning the width and spacing of the microchannels. The detectivity D∗ up to 4.5×105 cm Hz1/2/W has been obtained at room temperature, which is at least five times better than that of the unsuspended counterpart and may be further improved via elimination of metallic SWCNTs and improvement of the charge and heat transport across the intertube junctions.
Specific function of phosphoinositide 3-kinase beta in the control of DNA replication
Authors: Marqués Miriam , Kumar Amit , Poveda Ana M. , Zuluaga Susana , Hernández Carmen , Jackson Shaun , Pasero Philippe , Carrera Ana C.
Published: April 2009

Class I
A
phosphoinositide 3-kinase (PI3K) are enzymes comprised of a p85 regulatory and a p110 catalytic subunit that induce formation of 3-polyphosphoinositides, which activate numerous downstream targets. PI3K controls cell division. Of the 2 ubiquitous PI3K isoforms, α has selective action in cell growth and cell cycle entry, but no specific function in cell division has been described for β. We report here a unique function for PI3Kβ in the control of DNA replication. PI3Kβ regulated DNA replication through kinase-dependent and kinase-independent mechanisms. PI3Kβ was found in the nucleus, where it associated PKB. Modulation of PI3Kβ activity altered the DNA replication rate by controlling proliferating cell nuclear antigen (PCNA) binding to chromatin and to DNA polymerase δ. PI3Kβ exerted this action by regulating the nuclear activation of PKB in S phase, and in turn phosphorylation of PCNA negative regulator p21
Cip
. Also, p110β associated with PCNA and controlled PCNA loading onto chromatin in a kinase-independent manner. These results show a selective function of PI3Kβ in the control of DNA replication.
Quantitative genome-scale analysis of protein localization in an asymmetric bacterium
Authors: Werner John N. , Chen Eric Y. , Guberman Jonathan M. , Zippilli Angela R. , Irgon Joseph J. , Gitai Zemer
Published: April 2009

Despite the importance of subcellular localization for cellular activities, the lack of high-throughput, high-resolution imaging and quantitation methodologies has limited genomic localization analysis to a small number of archival studies focused on C-terminal fluorescent protein fusions. Here, we develop a high-throughput pipeline for generating, imaging, and quantitating fluorescent protein fusions that we use for the quantitative genomic assessment of the distributions of both N- and C-terminal fluorescent protein fusions. We identify nearly 300 localized
Caulobacter crescentus
proteins, up to 10-fold more than were previously characterized. The localized proteins tend to be involved in spatially or temporally dynamic processes and proteins that function together and often localize together as well. The distributions of the localized proteins were quantitated by using our recently described projected system of internal coordinates from interpolated contours (PSICIC) image analysis toolkit, leading to the identification of cellular regions that are over- or under-enriched in localized proteins and of potential differences in the mechanisms that target proteins to different subcellular destinations. The
Caulobacter
localizome data thus represent a resource for studying both global properties of protein localization and specific protein functions, whereas the localization analysis pipeline is a methodological resource that can be readily applied to other systems.
Identifying language impairment in children: combining language test scores with parental report
Authors: Bishop Dorothy V. M. , McDonald David
Published: April 2009

Background: Children who meet language test criteria for specific language impairment (SLI) are not necessarily the same as those who are referred to a speech and language therapist.

Aims: To consider how far this discrepancy reflects insensitivity of traditional language tests to clinically important features of language impairment.

Methods & Procedures: A total of 245 twin children, 52 of whom had been referred to a speech and language therapist for assessment or intervention, were studied. They were given a battery of language tests and their parents completed the Children's Communication Checklist — 2 (CCC‐2).

Results: Language tests that stressed verbal short‐term memory were best at distinguishing clinically referred from other cases; narrative and vocabulary tasks were less effective. A discriminant function analysis identified a combination of language test and parental report measures as giving the best discrimination between referred and non‐referred cases. Nevertheless, of 82 children classified as language impaired by the discriminant function, 44 had never been referred to a speech and language therapist. These did not appear to be false‐positives; they scored at least as poorly as referred cases on literacy tests. They had significantly lower socio‐economic backgrounds than referred cases.

Conclusions & Implications: Language test scores provide important information about which children are at risk of academic failure, though this varies from test to test. Reliance on language tests alone, however, is insufficient; a parental report provides important complementary information in the diagnostic process. Children of low socio‐economic status with language problems are particularly likely to have no contact with speech and language therapist services.
The limits of visual mass perception
Authors: Shim Jaeho , Hecht Heiko , Lee Jung-Eun , Yook Dong-Won , Kim Ji-Tae
Published: April 2009

The theory of direct perception suggests that observers can accurately judge the mass of a box picked up by a lifter shown in a point-light display. However, accurate perceptual performance may be limited to specific circumstances. The purpose of the present study was to systematically examine the factors that determine perception of mass, including display type, lifting speed, response type, and lifter's strength. In contrast to previous research, a wider range of viewing manipulations of point-light display conditions was investigated. In Experiment 1, we first created a circumstance where observers could accurately judge lifts of five box masses performed by a lifter of average strength. In Experiments 2–5, we manipulated the spatial and temporal aspects of the lift, the judgement type, and lifter's strength, respectively. Results showed that mass judgement gets worse whenever the context deviates from ideal conditions, such as when only the lifted object was shown, when video play speed was changed, or when lifters of different strength performed the same task. In conclusion, observers’ perception of kinetic properties is compromised whenever viewing conditions are not ideal.
Short article: Is verbal–spatial binding in working memory impaired by a concurrent memory load?
Authors: Elsley Jane V. , Parmentier Fabrice B. R.
Published: April 2009

Binding processes play a critical role in memory. We investigated whether the binding of (visually presented) verbal and spatial (locations) information involves general attentional resources, as stipulated in the revised working memory model, by comparing measures of binding in the presence and absence of a concurrent memory load. Using an adaptation of a probe recognition task contrasting performance between intact and recombined conditions, we found that the concurrent retention of a sequence of three pure tones eliminated verbal–spatial binding. The present study constitutes the first to directly measure the impact of a concurrent memory load on verbal–spatial binding and suggests that such binding may indeed recruit attentional resources, consistent with some recent findings in the visual–spatial binding literature.
Vimentin Regulates Scribble Activity by Protecting It from Proteasomal Degradation
Authors: Phua Dominic C.Y. , Humbert Patrick O. , Hunziker Walter
Published: April 2009

Scribble (Scrib), Discs large, and Lethal giant larvae form a protein complex that regulates different aspects of cell polarization, including apical–basal asymmetry in epithelial cells and anterior–posterior polarity in migrating cells. Here, we show that Scrib interacts with the intermediate filament cytoskeleton in epithelial Madin-Darby canine kidney (MDCK) cells and endothelial human umbilical vein endothelial cells. Scrib binds vimentin via its postsynaptic density 95/disc-large/zona occludens domains and in MDCK cells redistributes from filaments to the plasma membrane during the establishment of cell–cell contacts. RNA interference-mediated silencing of Scrib, vimentin, or both in MDCK cells results in defects in the polarization of the Golgi apparatus during cell migration. Concomitantly, wound healing is delayed due to the loss of directional movement. Furthermore, cell aggregation is dependent on both Scrib and vimentin. The similar phenotypes observed after silencing either Scrib or vimentin support a coordinated role for the two proteins in cell migration and aggregation. Interestingly, silencing of vimentin leads to an increased proteasomal degradation of Scrib. Thus, the upregulation of vimentin expression during epithelial to mesenchymal transitions may stabilize Scrib to promote directed cell migration.
Specificity of Cytoplasmic Dynein Subunits in Discrete Membrane-trafficking Steps
Authors: Palmer Krysten J. , Hughes Helen , Stephens David J.
Published: April 2009

The cytoplasmic dynein motor complex is known to exist in multiple forms, but few specific functions have been assigned to individual subunits. A key limitation in the analysis of dynein in intact mammalian cells has been the reliance on gross perturbation of dynein function, e.g., inhibitory antibodies, depolymerization of the entire microtubule network, or the use of expression of dominant negative proteins that inhibit dynein indirectly. Here, we have used RNAi and automated image analysis to define roles for dynein subunits in distinct membrane-trafficking processes. Depletion of a specific subset of dynein subunits, notably LIC1 (DYNC1LI1) but not LIC2 (DYNC1LI2), recapitulates a direct block of ER export, revealing that dynein is required to maintain the steady-state composition of the Golgi, through ongoing ER-to-Golgi transport. Suppression of LIC2 but not of LIC1 results in a defect in recycling endosome distribution and cytokinesis. Biochemical analyses also define the role of each subunit in stabilization of the dynein complex; notably, suppression of DHC1 or IC2 results in concomitant loss of Tctex1. Our data demonstrate that LIC1 and LIC2 define distinct dynein complexes that function at the Golgi versus recycling endosomes, respectively, suggesting that functional populations of dynein mediate discrete intracellular trafficking pathways.
Swimbladders under pressure: anatomical and acoustic responses by walleye pollock
Authors: Horne John K. , Sawada Kouichi , Abe Koki , Kreisberg Richard B. , Barbee David H. , Sadayasu Kazuhiro
Published: April 2009

Horne, J. K., Sawada, K., Abe, K., Kreisberg, R. B., Barbee, D. H., and Sadayasu, K. 2009. Swimbladders under pressure: anatomical and acoustic responses by walleye pollock. – ICES Journal of Marine Science, 66: 1162–1168. Pressure influences echo intensities from fish through changes in swimbladder volumes and surface areas. Volume reduction is expected to correspond to Boyle’s law (volume α pressure−1), but the effects of deforming the dorsal-aspect surface area of the swimbladder on the target strength (TS) of a physoclist have not been quantified at geometric scattering frequencies. Dorsal and lateral radiographs of three juvenile walleye pollock (Theragra chalcogramma) in a pressure chamber were used to image swimbladders from ambient to a maximum of 4.9 × 105 Pa (i.e. 5 atm). Radiographs from an additional 16 0-group, 21 juvenile, and 28 adult fish were used to compare swimbladder sizes and shapes across life-history stages. The directional elliptical eccentricity, which describes the relative compression in dorsal and lateral planes, was formulated to define swimbladder shapes and their variation. As pressure increased, dorsal-aspect surface areas of the swimbladder decreased at a constant rate. Swimbladder-volume reductions were similar among individuals, but less than those predicted by Boyle’s law. Compression was greatest in the dorsal–ventral plane and asymmetric anterior to posterior. The Kirchhoff-ray mode backscatter model predicted that TS at 38 and 120 kHz decreased by ∼4 dB as pressure increased from ambient to 4.9 × 105 Pa.