bluuebunny/crossref_metadata_2025 huggingface dataset:
Dramatic thermal conductivity reduction by nanostructures for large increase in thermoelectric figure-of-merit of FeSb2
Authors: Zhao Huaizhou , Pokharel Mani , Zhu Gaohua , Chen Shuo , Lukas Kevin , Jie Qing , Opeil Cyril , Chen Gang , Ren Zhifeng
Published: October 2011

In this report, thermal conductivity reduction by more than three orders of magnitude over its single crystal counterpart for the strongly correlated system FeSb2 through a nanostructure approach was presented, leading to a significant increase of thermoelectric figure-of-merit (ZT). For the samples processed with the optimal parameters, the thermal conductivity reached 0.34 Wm−1 K−1 at 50 K, leading to a ZT peak of about 0.013, compared to 0.005 for single crystal FeSb2, an increase of about 160%. This work suggests that nanostructure method is effective and can be possibly extended to other strongly correlated low temperature thermoelectric materials, paving the way for future cryogenic temperature cooling applications.
Fractal phononic crystals in aluminum nitride: An approach to ultra high frequency bandgaps
Authors: Kuo Nai-Kuei , Piazza Gianluca
Published: October 2011

This letter reports on the design and experimental demonstration of a microscale fractal-like phononic bandgap (PBG) structure in aluminum nitride (AlN). The micro-fabricated fractal phononic crystals (PnCs) exhibit two frequency stop bands for symmetric lamb waves in the Γ-Χ direction centered about 900 MHz (bandwidth of 11.1%) and 1.10 GHz (bandwidth of 9.1%) with maximum acoustic rejection of 40 dB. Differently from the conventional phononic bandgap designs, the unit cell consists of a center air square scatterer with four side air square scatterers repeating at its corners. The presence of these side squares essentially shortens the scattering distance between the unit cells and translates into the suppression of higher frequency vibrational modes. In other words, this design is capable of extending the frequency of operation of the PBGs for a given unit cell and minimum feature size. For the purpose of the demonstration, AlN lamb wave transducers were utilized to launch symmetric lamb waves into the PBG structure. The evidence of direct in-plane integration between the transducers and the PnC structure operating in the ultra high frequency range lays the foundation for the development of ultrasonic devices based on PBGs.
Fragility of iron-based glasses
Authors: Hyun Na Jong , Demetriou Marios D. , Johnson William L.
Published: October 2011

The viscosity of various iron-based bulk-glass-forming liquids is measured around the glass transition, and the associated fragility is calculated. Fragility is found to vary broadly between compositions, from a low value of ∼43, which indicates fairly “strong” liquid behavior, to ∼65, well within the region of “fragile” behavior. Despite a strong covalent bonding identified in the structure of this class of metal/metalloid glasses, their liquid fragility can be remarkably high, exceeding even the very fragile palladium and platinum bulk-glass formers. An inverse correlation between glass-forming ability and fragility is identified, suggesting that iron-based glasses are effectively “kinetically” stabilized.
Dynamical stability of global vortex strings
Authors: Tho Nguyen Vien , Ha To Ba
Published: October 2011

The time-dependent field equations of the nonlinear field systems, whose static soliton solutions are (global) vortex strings, are studied by a numerical approach. They concern (i) the theory of a single complex scalar field with a spontaneously broken U(1) symmetry, and (ii) the system of a complex scalar field doublet with an approximate U(2) symmetry. The obtained numerical solutions allow to clarify the dynamical behaviors of the systems under fluctuations. The systems are shown to have order-chaos phase transitions, but, despite phase transitions and deformations in field profiles by fluctuations, the shapes of the total field energy density distributions are rather stable.
All the groups of signal analysis from the (1+1)-affine Galilei group
Authors: Chowdhury S. Hasibul Hassan , Ali S. Twareque
Published: October 2011

We study the relationship between the (1+1)-affine Galilei group and four groups of interest in signal analysis and image processing, viz., the wavelet or the affine group of the line, the Weyl-Heisenberg, the shearlet, and the Stockwell groups. We show how all these groups can be obtained either directly as subgroups of the affine Galilei group, or as subgroups of central extensions of a subgroup of the affine Galilei group, namely, the Galilei-Schrödinger group. We also study this at the level of unitary representations of the groups on Hilbert spaces.
Electrical spin injection and detection at Al2O3/n-type germanium interface using three terminal geometry
Authors: Jain A. , Louahadj L. , Peiro J. , Le Breton J. C. , Vergnaud C. , Barski A. , Beigné C. , Notin L. , Marty A. , Baltz V. , Auffret S. , Augendre E. , Jaffrès H. , George J. M. , Jamet M.
Published: October 2011

In this letter, we report on electrical spin injection and detection in n-type germanium-on-insulator using a Co/Py/Al2O3 spin injector and 3-terminal non-local measurements. We observe an enhanced spin accumulation signal of the order of 1 meV consistent with the sequential tunneling process via interface states in the vicinity of the Al2O3/Ge interface. This spin signal is further observable up to 220 K. Moreover, the presence of a strong inverted Hanle effect points out the influence of random fields arising from interface roughness on the injected spins.
Temperature dependent energy level shifts of nitrogen-vacancy centers in diamond
Authors: Chen X.-D. , Dong C.-H. , Sun F.-W. , Zou C.-L. , Cui J.-M. , Han Z.-F. , Guo G.-C.
Published: October 2011

Magnetic resonance and fluorescence spectra of nitrogen-vacancy (NV) color centers ensemble in high purity diamond sample were measured, with temperature ranging from 5.6 K to 295 K. Both microwave and optical transition energies have similar nonlinear temperature dependent changes, which might mainly originate from the local thermal expansion. As the frequency shifts will reduce the fidelity of resonant quantum control, the present results demonstrate the necessity of taking temperature fluctuation into consideration. For temperature below 100 K, the transition energies show tendencies to be constant, which indicate higher stability and performance in applications with NV centers.
Anisotropic response of nanosized bismuth films upon femtosecond laser excitation monitored by ultrafast electron diffraction
Authors: Esmail Ahmed R. , Elsayed-Ali Hani E.
Published: October 2011

The lattice response of 5 nm thick bismuth film to femtosecond laser excitation is probed by ultrafast electron diffraction. The transient decay time after laser excitation is greater for diffraction from (012) lattice planes compared to (110) planes and is reduced for both planes with the increased laser fluence. These results indicate that different energy coupling mechanisms to the lattice occur depending on the crystal direction. The behavior of the diffraction peak width indicates partial disorder of the film upon photoexcitation that increases together with the laser fluence.
Development of the heat treatment system for the 40 T hybrid magnet superconducting outsert
Authors: Chen W. G. , Chen Z. M. , Chen Z. Y. , Huang P. C. , He P. , Zhu J. W.
Published: October 2011

The heat treatment of Nb3Sn coil with the glass fabric insulation is one of the key and critical processes for the outsert solenoids of the 40 T hybrid magnet, which could be wound with cable-in-conduit conductors using the insulation-wind-and-react technique. The manufacturing of the large vertical type vacuum/Ar atmosphere-protection heat treatment system has been completed and recently installed in the High Magnetic Filed Laboratory, Chinese Academy of Sciences. The heat treatment system composed mainly the furnace, the purging gas supply system, the control system, the gas impurities monitoring system, and so on. At present, the regulation and testing of the heat treatment system has been successfully finished, and all of technical parameters meet or exceed specifications.
Ellipticity dependence of 400 nm-driven high harmonic generation
Authors: Khan Sabih D. , Cheng Yan , Möller Max , Zhao Kun , Zhao Baozhen , Chini Michael , Paulus Gerhard. G. , Chang Zenghu
Published: October 2011

We studied the dependence of high harmonic generation efficiency on the ellipticity of 400 nm driving laser pulses at 7.7 × 1014 W/cm2 and compared it with the 800 nm driving laser under the same conditions. The measured decrease of high harmonic yield with the ellipticity of the 400 nm laser is ∼1.5 times slower that of the 800 nm, which agrees well with theoretical predictions based on a semi-classical model. The results indicate that it is feasible to use the generalized double optical gating with 400 nm lasers for extracting single attosecond pulses with high efficiency.
Micromagnetic modelling of L1-FePt/Ag/L1-FePt pseudo spin valves
Authors: Ho P. , Evans R. F. L. , Chantrell R. W. , Han G. C. , Chow G. M. , Chen J. S.
Published: October 2011

A micromagnetic bilayer model, based on the Landau-Lifshitz-Bloch equation, was utilized to study the magnetic, reversal, and spin transport properties of MgO/L10-FePt/Ag/L10-FePt pseudo spin valves. The model simulates a granular bilayer FePt structure and the effects of the Ag spacer were controlled by varying the interlayer exchange strength. Simulation results showed that the reversal of the FePt layers proceeded via reversed domain formation and propagation. Stray fields emanating from the top soft FePt layer reduced the nucleation field of the bottom FePt locally, resulting in the preferential formation of reversed domains at adjacent sites of the bottom hard FePt layer.
Attenuated total reflection GeO2 hollow waveguide for 9.6–11.7 μm infrared light transmission
Authors: Jing Chengbin , Zhang Chuanjian , Li Yi , Shi Yiwei , Chu Junhao
Published: October 2011

We report the preparation and characterization of an attenuated total reflection (ATR) GeO2 hollow waveguide. An internally GeO2-coated silica glass tube (bore size 1.0–1.2 mm, length 1.2 m) was prepared using a homogeneous liquid phase deposition method. Kramers-Kronig analysis reveals that the GeO2 cladding material qualifies as a reflective layer (nr < 1) for the ATR hollow waveguide structure. ATR-transmission of 9.6–11.7 μm light through HE11 mode is confirmed by loss spectrum analysis of the sample. The straight and bending (30°) transmission losses for delivery of a ∼40 W CO2 laser beam (10.6 μm) are 0.56 dB/m and 1.64 dB/m, respectively.
Interfacial charge effects on electron transport in III-Nitride metal insulator semiconductor transistors
Authors: Hung Ting-Hsiang , Esposto Michele , Rajan Siddharth
Published: October 2011

We report on the calculation of the two dimension electron gas (2DEG) mobility in scaled AlGaN/GaN metal-insulator-semiconductor high-electron-mobility-transistors. We investigate the effect of remote impurity and phonon scattering models on the 2DEG mobility of the dielectric/AlGaN/GaN structure and investigate its variation with dielectric/AlGaN interface charge density, 2DEG concentration, and AlGaN thickness. Remote impurity scattering was found to be the dominant mechanism when the 2DEG density is below 5 × 1012 cm−2 and dielectric/AlGaN interface charge density is above 5 × 1012 cm−2. The interfacial charge has significant effect on the mobility as the AlGaN cap layer thickness is scaled down below 5 nm.
Light interference detection on-chip by integrated SNSPD counters
Authors: Cavalier Paul , Villégier Jean-Claude , Feautrier Philippe , Constancias Christophe , Morand Alain
Published: October 2011

A SWIFTS device (Stationary Wave Integrated Fourier Transform Spectrometer) has been realized with an array of 24 Superconducting Nanowire Single Photon Detectors (SNSPD), on-chip integrated under a Si3N4 monomode rib-waveguide interferometer. Colored light around 1.55μm wavelength is introduced through end-fire coupling, producing a counter-propagative stationary interferogram over the 40nm wide, 120nm spaced, 4nm thick epi-NbN nanowire array. Modulations in the source bandwidth have been detected using individual waveguide coupled SNSPDs operating in single photon counting mode, which is a step towards light spectrum reconstruction by inverse Fourier transform of the stationary wave intensity. We report the design, fabrication process and in-situ measurement at 4.2K of light power modulation in the interferometer, obtained with variable laser wavelength. Such micro-SWIFTS configuration with 160nm sampling period over 3.84μm distance allows a spectral bandwidth of 2μm and a wavelength resolution of 170nm. The light interferences direct sampling ability is unique and raises wide interest with several potential applications like fringe-tracking, metrology, cryptography or optical tomography.
Anoctamin 6 is an essential component of the outwardly rectifying chloride channel
Authors: Martins Joana Raquel , Faria Diana , Kongsuphol Patthara , Reisch Barbara , Schreiber Rainer , Kunzelmann Karl
Published: October 2011

Outwardly rectifying chloride channels (ORCC, ICOR) of intermediate single-channel conductance of around 50 pS, are ubiquitously expressed, but have remained a mystery since their description more than 25 y ago. These channels have been shown to be activated on membrane excision and depolarization of the membrane voltage and by cAMP in the presence of the cystic fibrosis transmembrane conductance regulator. We show that anoctamin 6 (Ano6), a member of the recently identified family of putative Cl
−
channels, is the crucial component of ORCC single-channel and whole-cell currents in airway epithelial cells and Jurkat T lymphocytes. Cystic fibrosis transmembrane conductance regulator augmented ORCC produced by Ano6 in A549 airway epithelial cells. Ano6 is activated during membrane depolarization or apoptosis of Jurkat T lymphocytes and epithelial cells, and is inhibited by 5-nitro-2-(3-phenylpropylamino) benzoic acid, 4,4′-diisothio-cyanostilbene-2,2′-disulfonic acid, or AO1. Ano6 belongs to the basic equipment of any cell type, including colonic surface epithelial cells. It forms the essential component of ORCC and seems to have a role for cell shrinkage and programmed cell death.
Inverted selective plane illumination microscopy (
i
SPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in
Caenorhabditis elegans
Authors: Wu Yicong , Ghitani Alireza , Christensen Ryan , Santella Anthony , Du Zhuo , Rondeau Gary , Bao Zhirong , Colón-Ramos Daniel , Shroff Hari
Published: October 2011

The
Caenorhabditis elegans
embryo is a powerful model for studying neural development, but conventional imaging methods are either too slow or phototoxic to take full advantage of this system. To solve these problems, we developed an inverted selective plane illumination microscopy (
i
SPIM) module for noninvasive high-speed volumetric imaging of living samples.
i
SPIM is designed as a straightforward add-on to an inverted microscope, permitting conventional mounting of specimens and facilitating SPIM use by development and neurobiology laboratories.
i
SPIM offers a volumetric imaging rate 30× faster than currently used technologies, such as spinning-disk confocal microscopy, at comparable signal-to-noise ratio. This increased imaging speed allows us to continuously monitor the development of
C, elegans
embryos, scanning volumes every 2 s for the 14-h period of embryogenesis with no detectable phototoxicity. Collecting ∼25,000 volumes over the entirety of embryogenesis enabled in toto visualization of positions and identities of cell nuclei. By merging two-color
i
SPIM with automated lineaging techniques we realized two goals: (
i
) identification of neurons expressing the transcription factor CEH-10/Chx10 and (
ii
) visualization of their neurodevelopmental dynamics. We found that canal-associated neurons use somal translocation and amoeboid movement as they migrate to their final position in the embryo. We also visualized axon guidance and growth cone dynamics as neurons circumnavigate the nerve ring and reach their targets in the embryo. The high-speed volumetric imaging rate of
i
SPIM effectively eliminates motion blur from embryo movement inside the egg case, allowing characterization of dynamic neurodevelopmental events that were previously inaccessible.
Comparing machines and humans on a visual categorization test
Authors: Fleuret François , Li Ting , Dubout Charles , Wampler Emma K. , Yantis Steven , Geman Donald
Published: October 2011

Automated scene interpretation has benefited from advances in machine learning, and restricted tasks, such as face detection, have been solved with sufficient accuracy for restricted settings. However, the performance of machines in providing rich semantic descriptions of natural scenes from digital images remains highly limited and hugely inferior to that of humans. Here we quantify this “semantic gap” in a particular setting: We compare the efficiency of human and machine learning in assigning an image to one of two categories determined by the spatial arrangement of constituent parts. The images are not real, but the category-defining rules reflect the compositional structure of real images and the type of “reasoning” that appears to be necessary for semantic parsing. Experiments demonstrate that human subjects grasp the separating principles from a handful of examples, whereas the error rates of computer programs fluctuate wildly and remain far behind that of humans even after exposure to thousands of examples. These observations lend support to current trends in computer vision such as integrating machine learning with parts-based modeling.
Transformation of stimulus value signals into motor commands during simple choice
Authors: Hare Todd A. , Schultz Wolfram , Camerer Colin F. , O'Doherty John P. , Rangel Antonio
Published: October 2011

Decision-making can be broken down into several component processes: assigning values to stimuli under consideration, selecting an option by comparing those values, and initiating motor responses to obtain the reward. Although much is known about the neural encoding of stimulus values and motor commands, little is known about the mechanisms through which stimulus values are compared, and the resulting decision is transmitted to motor systems. We investigated this process using human fMRI in a task where choices were indicated using the left or right hand. We found evidence consistent with the hypothesis that value signals are computed in the ventral medial prefrontal cortex, they are passed to regions of dorsomedial prefrontal cortex and intraparietal sulcus, implementing a comparison process, and the output of the comparator regions modulates activity in motor cortex to implement the choice. These results describe the network through which stimulus values are transformed into actions during a simple choice task.
Structural reorganization of the antigen-binding groove of human CD1b for presentation of mycobacterial sulfoglycolipids
Authors: Garcia-Alles Luis F. , Collmann Anthony , Versluis Cees , Lindner Buko , Guiard Julie , Maveyraud Laurent , Huc Emilie , Im Jin S. , Sansano Sebastiano , Brando Thérèse , Julien Sylviane , Prandi Jacques , Gilleron Martine , Porcelli Steven A. , de la Salle Henri , Heck Albert J. R. , Mori Lucia , Puzo Germain , Mourey Lionel , De Libero Gennaro
Published: October 2011

The mechanisms permitting nonpolymorphic CD1 molecules to present lipid antigens that differ considerably in polar head and aliphatic tails remain elusive. It is also unclear why hydrophobic motifs in the aliphatic tails of some antigens, which presumably embed inside CD1 pockets, contribute to determinants for T-cell recognition. The 1.9-Å crystal structure of an active complex of CD1b and a mycobacterial diacylsulfoglycolipid presented here provides some clues. Upon antigen binding, endogenous spacers of CD1b, which consist of a mixture of diradylglycerols, moved considerably within the lipid-binding groove. Spacer displacement was accompanied by F’ pocket closure and an extensive rearrangement of residues exposed to T-cell receptors. Such structural reorganization resulted in reduction of the A’ pocket capacity and led to incomplete embedding of the methyl-ramified portion of the phthioceranoyl chain of the antigen, explaining why such hydrophobic motifs are critical for T-cell receptor recognition. Mutagenesis experiments supported the functional importance of the observed structural alterations for T-cell stimulation. Overall, our data delineate a complex molecular mechanism combining spacer repositioning and ligand-induced conformational changes that, together with pocket intricacy, endows CD1b with the required molecular plasticity to present a broad range of structurally diverse antigens.
Iron deficiency drives an autosomal dominant hypophosphatemic rickets (ADHR) phenotype in fibroblast growth factor-23 (Fgf23) knock-in mice
Authors: Farrow Emily G. , Yu Xijie , Summers Lelia J. , Davis Siobhan I. , Fleet James C. , Allen Matthew R. , Robling Alexander G. , Stayrook Keith R. , Jideonwo Victoria , Magers Martin J. , Garringer Holly J. , Vidal Ruben , Chan Rebecca J. , Goodwin Charles B. , Hui Siu L. , Peacock Munro , White Kenneth E.
Published: October 2011

Autosomal dominant hypophosphatemic rickets (ADHR) is unique among the disorders involving Fibroblast growth factor 23 (FGF23) because individuals with R176Q/W and R179Q/W mutations in the FGF23
176
RXXR
179
/S
180
proteolytic cleavage motif can cycle from unaffected status to delayed onset of disease. This onset may occur in physiological states associated with iron deficiency, including puberty and pregnancy. To test the role of iron status in development of the ADHR phenotype, WT and R176Q-Fgf23 knock-in (ADHR) mice were placed on control or low-iron diets. Both the WT and ADHR mice receiving low-iron diet had significantly elevated bone Fgf23 mRNA. WT mice on a low-iron diet maintained normal serum intact Fgf23 and phosphate metabolism, with elevated serum C-terminal Fgf23 fragments. In contrast, the ADHR mice on the low-iron diet had elevated intact and C-terminal Fgf23 with hypophosphatemic osteomalacia. We used in vitro iron chelation to isolate the effects of iron deficiency on Fgf23 expression. We found that iron chelation in vitro resulted in a significant increase in Fgf23 mRNA that was dependent upon Mapk. Thus, unlike other syndromes of elevated FGF23, our findings support the concept that late-onset ADHR is the product of gene–environment interactions whereby the combined presence of an Fgf23-stabilizing mutation and iron deficiency can lead to ADHR.
Determinants of endocytic membrane geometry, stability, and scission
Authors: Kishimoto Takuma , Sun Yidi , Buser Christopher , Liu Jian , Michelot Alphée , Drubin David G.
Published: October 2011

During endocytic vesicle formation, distinct subdomains along the membrane invagination are specified by different proteins, which bend the membrane and drive scission. Bin-Amphiphysin-Rvs (BAR) and Fer-CIP4 homology-BAR (F-BAR) proteins can induce membrane curvature and have been suggested to facilitate membrane invagination and scission. Two F-BAR proteins, Syp1 and Bzz1, are found at budding yeast endocytic sites. Syp1 arrives early but departs from the endocytic site before formation of deep membrane invaginations and scission. Using genetic, spatiotemporal, and ultrastructural analyses, we demonstrate that Bzz1, the heterodimeric BAR domain protein Rvs161/167, actin polymerization, and the lipid phosphatase Sjl2 cooperate, each through a distinct mechanism, to induce membrane scission in yeast. Additionally, actin assembly and Rvs161/167 cooperate to drive formation of deep invaginations. Finally, we find that Bzz1, acting at the invagination base, stabilizes endocytic sites and functions with Rvs161/167, localized along the tubule, to achieve proper endocytic membrane geometry necessary for efficient scission. Together, our results reveal that dynamic interplay between a lipid phosphatase, actin assembly, and membrane-sculpting proteins leads to proper membrane shaping, tubule stabilization, and scission.
Bis-(3′-5′)-cyclic dimeric GMP-linked quorum sensing controls swarming in
Vibrio parahaemolyticus
Authors: Trimble Michael J. , McCarter Linda L.
Published: October 2011

Movement over and colonization of surfaces are important survival strategies for bacteria, and many find it advantageous to perform these activities as a group, using quorum sensing to sample population size and synchronize behavior. It is puzzling however, that swarming-proficient and virulent strains of
Vibrio parahaemolyticus
are silenced for the vibrio archetypal pathway of quorum sensing. Here we describe the S-signal, a pheromone that can be communicated between cells in coculture to regulate surface colonization. This signal was harvested in cell-free supernatants and demonstrated to stimulate swarming gene expression at low cell density. The S-signal was generated by the pyridoxal phosphate-dependent aminotransferase ScrA; signal reception required the periplasmic binding protein ScrB and the membrane-bound GGDEF-EAL domain-containing protein ScrC. ScrC is a bifunctional enzyme that has the ability to form and degrade the second messenger bis-(3′-5′) cyclic dimeric GMP (c-di-GMP). ScrA in neighboring cells was able to alter the activity of ScrC in a ScrB-dependent manner, transforming ScrC’s repressing ability to inducing activity with respect to swarming. Conversely, cell–cell signaling repressed capsule gene expression. In summary, we report that quorum sensing can stimulate swarming in
V. parahaemolyticus
; it does so via an alternative pathway capable of generating an autoinducing signal that influences c-di-GMP, thereby expanding the lexicon and language of cell–cell communication.
Physical limits of cells and proteomes
Authors: Dill Ken A. , Ghosh Kingshuk , Schmit Jeremy D.
Published: October 2011

What are the physical limits to cell behavior? Often, the physical limitations can be dominated by the proteome, the cell’s complement of proteins. We combine known protein sizes, stabilities, and rates of folding and diffusion, with the known protein-length distributions
P
(
N
) of proteomes (
Escherichia coli
, yeast, and worm), to formulate distributions and scaling relationships in order to address questions of cell physics. Why do mesophilic cells die around 50 °C? How can the maximal growth-rate temperature (around 37 °C) occur so close to the cell-death temperature? The model shows that the cell’s death temperature coincides with a denaturation catastrophe of its proteome. The reason cells can function so well just a few degrees below their death temperature is because proteome denaturation is so cooperative. Why are cells so dense-packed with protein molecules (about 20% by volume)? Cells are packed at a density that maximizes biochemical reaction rates. At lower densities, proteins collide too rarely. At higher densities, proteins diffuse too slowly through the crowded cell. What limits cell sizes and growth rates? Cell growth is limited by rates of protein synthesis, by the folding rates of its slowest proteins, and—for large cells—by the rates of its protein diffusion. Useful insights into cell physics may be obtainable from scaling laws that encapsulate information from protein knowledge bases.
Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis
Authors: Wang Weina , Hellinga Homme W. , Beese Lorena S.
Published: October 2011

Even though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. Using high-resolution X-ray crystallographic analysis of a DNA polymerase that catalyzes replication in crystals, we observe that a C•A mismatch can mimic the shape of cognate base pairs at the site of incorporation. This shape mimicry enables the mismatch to evade the error detection mechanisms of the polymerase, which would normally either prevent mismatch incorporation or promote its nucleolytic excision. Movement of a single proton on one of the mismatched bases alters the hydrogen-bonding pattern such that a base pair forms with an overall shape that is virtually indistinguishable from a canonical, Watson-Crick base pair in double-stranded DNA. These observations provide structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis, a long-standing concept that has been difficult to demonstrate directly.
Involvement of O-glycosylation defining oncofetal fibronectin in epithelial-mesenchymal transition process
Authors: Freire-de-Lima Leonardo , Gelfenbeyn Kirill , Ding Yao , Mandel Ulla , Clausen Henrik , Handa Kazuko , Hakomori Sen-itiroh
Published: October 2011

The process termed “epithelial–mesenchymal transition” (EMT) was originally discovered in ontogenic development, and has been shown to be one of the key steps in tumor cell progression and metastasis. Recently, we showed that the expression of some glycosphingolipids (GSLs) is down-regulated during EMT in human and mouse cell lines. Here, we demonstrate the involvement of GalNAc-type (or mucin-type) O-glycosylation in EMT process, induced with transforming growth factor β (TGF-β) in human prostate epithelial cell lines. We found that: (
i
) TGF-β treatment caused up-regulation of oncofetal fibronectin (onfFN), which is defined by mAb FDC6, and expressed in cancer or fetal cells/tissues, but not in normal adult cells/tissues. The reactivity of mAb FDC6 requires the addition of an O-glycan at a specific threonine, inside the type III homology connective segment (IIICS) domain of FN. (
ii
) This change is associated with typical EMT characteristics; i.e., change from epithelial to fibroblastic morphology, enhanced cell motility, decreased expression of a typical epithelial cell marker, E-cadherin, and enhanced expression of mesenchymal markers. (
iii
) TGF-β treatment up-regulated mRNA level of FN containing the IIICS domain and GalNAc-T activity for the IIICS domain peptide substrate containing the FDC6 onfFN epitope. (
iv
) Knockdown of GalNAc-T6 and T3 inhibited TGF-β–induced up-regulation of onfFN and EMT process. (
v
) Involvement of GSLs was not detectable with the EMT process in these cell lines. These findings indicate the important functional role of expression of onfFN, defined by site-specific O-glycosylation at IIICS domain, in the EMT process.
Beyond a unitary conception of pedagogic pace: quantitative measurement and ethnographic experience
Authors: Lefstein Adam , Snell Julia
Published: October 2011

English education policy‐makers have targeted classroom time as a key area for regulation and intervention, with ‘brisk pace’ widely accepted as a feature of good teaching practice. We problematise this conventional wisdom through an exploration of objective and subjective dimensions of lesson pace in a corpus of 30 Key Stage 2 literacy lessons from three classrooms in one London school. Systematic classroom observation produced an anomaly: the lessons we experienced as fast‐paced were rated objectively as slowest, and vice‐versa. We contrasted the fastest and slowest episodes in the corpus, demonstrating that for these episodes the accepted measure of pace primarily reflected differences in utterance length. Linguistic ethnographic micro‐analysis of the episodes highlighted predictability, stakes, meaning and dramatic performance as key factors contributing to pace as experienced. We argue, among other claims, that sometimes accelerating pupils' experience—and learning—necessitates slowing down the pace of teaching, and that government calls for urgency may, perversely, make lessons slower.
Osteoclasts are dispensable for hematopoietic stem cell maintenance and mobilization
Authors: Miyamoto Kana , Yoshida Shigeyuki , Kawasumi Miyuri , Hashimoto Kazuaki , Kimura Tokuhiro , Sato Yuiko , Kobayashi Tami , Miyauchi Yoshiteru , Hoshi Hiroko , Iwasaki Ryotaro , Miyamoto Hiroya , Hao Wu , Morioka Hideo , Chiba Kazuhiro , Kobayashi Takashi , Yasuda Hisataka , Penninger Josef M. , Toyama Yoshiaki , Suda Toshio , Miyamoto Takeshi
Published: October 2011

Hematopoietic stem cells (HSCs) are maintained in a specific bone marrow (BM) niche in cavities formed by osteoclasts. Osteoclast-deficient mice are osteopetrotic and exhibit closed BM cavities. Osteoclast activity is inversely correlated with hematopoietic activity; however, how osteoclasts and the BM cavity potentially regulate hematopoiesis is not well understood. To investigate this question, we evaluated hematopoietic activity in three osteopetrotic mouse models: op/op, c-Fos-deficient, and RANKL (receptor activator of nuclear factor kappa B ligand)-deficient mice. We show that, although osteoclasts and, by consequence, BM cavities are absent in these animals, hematopoietic stem and progenitor cell (HSPC) mobilization after granulocyte colony-stimulating factor injection was comparable or even higher in all three lines compared with wild-type mice. In contrast, osteoprotegerin-deficient mice, which have increased numbers of osteoclasts, showed reduced HSPC mobilization. BM-deficient patients and mice reportedly maintain hematopoiesis in extramedullary spaces, such as spleen; however, splenectomized op/op mice did not show reduced HSPC mobilization. Interestingly, we detected an HSC population in osteopetrotic bone of op/op mice, and pharmacological ablation of osteoclasts in wild-type mice did not inhibit, and even increased, HSPC mobilization. These results suggest that osteoclasts are dispensable for HSC mobilization and may function as negative regulators in the hematopoietic system.
Flexible resistive switching memory based on Mn0.20Zn0.80O/HfO2 bilayer structure
Authors: Zhou Hai , Fang Guo-Jia , Zhu Yongdan , Liu Nishuang , Li Meiya , Zhao Xing-Zhong
Published: October 2011

We have investigated Mn0.20Zn0.80O/HfO2 bilayer structure resistance memory fabricated on flexible Kapton substrates. The Mn0.20Zn0.80O/HfO2 bilayer structure shows a steady and bipolar resistive switching characteristic with an on/off ratio of ∼70 at 0.5 V. Through the bending investigation, our flexible memory exhibits no degradation in switching property, even when the substrate is bent up to 11 mm radius. The resistive switching mechanism of the Mn0.20Zn0.80O/HfO2 bilayer structure can be attributed to the control of oxygen vacancies in HfO2 through the forward or reverse bias.
Synthesis of fly-ash cenospheres coated with polypyrrole using a layer-by-layer method
Authors: Li Qin , Wang Bing , Li Chuang , Pang Jianfeng , Zhai Jianping
Published: October 2011

Uniform polypyrrole (PPy) films, of controlled thickness, were successfully synthesized and immobilized on polyelectrolyte (PE) multilayer-assembled fly-ash cenospheres (FACs) using a simple and versatile method. In this approach, FACs were assembled with multilayers of poly(diallyldimethylammonium chloride) (PDDA) and poly(sodium 4-styrenesulfonate) (PSS) using a layer-by-layer self-assembly procedure. The FACs were used as templates for the subsequent deposition of PPy. The deposition behaviours of PEs on the surfaces of the FACs were examined, and the results could be fitted to a first-order exponential decay model at pH 6. The surfaces of the PE-deposited FACs (FAC-(PDDA-PSS)
n
, n is the number of PE layers) became more homogeneous as n increased. Their properties were determined mainly by the PE, not by the FAC itself, after n = 4. PPy-coated FACs with PE precursor layers [(PPy/FAC-(PDDA-PSS)
n
] had different morphologies for different numbers of PE layers. The PPy loading amount on the FACs and the conductivities of the composites reached plateaus after the PE layer deposition number exceeded six.
Sodium deoxycholate functionalized graphene and its composites with polyvinyl alcohol
Authors: Wang Lanwei , Liao Ruijuan , Tang Zhenghai , Lei Yanda , Guo Baochun
Published: October 2011

Sodium deoxycholate (SDC), a kind of bile derivative, is used to noncovalently functionalize graphene. Stable and high concentration (up to 20 mg ml−1) of graphene colloid is obtained. The stabilization mechanism is revealed to be hydrophobic interaction, electrostatic repulsion and hydrogen bonding. Single-layer and few-layer graphene are obtained in the colloid. Subsequently, the obtained graphene sheets are incorporated into a polyvinyl alcohol (PVA) matrix by solution casting to fabricate PVA/graphene composites. Morphological observations substantiate the homogeneous dispersion of graphene in the PVA matrix and strong interfacial adhesion between them. Significant improvements in tensile strength and modulus of the composite films are observed.
A simple methodology for predicting laser-weld properties from material and laser parameters
Authors: Hann D B , Iammi J , Folkes J
Published: October 2011

In laser material processing, understanding the laser interaction and the effect of processing parameters on this interaction is fundamental to any process if the system is to be optimized. Expanding this to different materials or other laser systems with different beam characteristics makes this interaction more complex and difficult to resolve. This work presents a relatively simple physical model to understand these interactions in terms of mean surface enthalpy values derived from both material parameters and laser parameters. From these fundamental properties the melt depth and width for any material can be predicted using a simple theory. By considering the mean enthalpy of the surface, the transition from conduction limited melting to keyholing can also be accurately predicted. The theory is compared to experimental results and the predicted and observed data are shown to correspond well for these experimental results as well as for published results for stainless steel and for a range of metals. The results suggest that it is important to keep the Fourier number of the weld much smaller than one to make it efficient. It is also discussed that the surface enthalpy could be used to prodict other effects in the weld such as porosity and material expulsion.
Mapping personal functional data to personal genomes
Authors: Rivas-Astroza Marcelo , Xie Dan , Cao Xiaoyi , Zhong Sheng
Published: October 2011

Motivation: The sequencing of personal genomes enabled analysis of variation in transcription factor (TF) binding, chromatin structure and gene expression and indicated how they contribute to phenotypic variation. It is hypothesized that using the reference genome for mapping ChIP-seq or RNA-seq reads may introduce errors, especially at polymorphic genomic regions.

Results: We developed a Personal Genome Editor (perEditor) that changes the reference human genome (NCBI36/hg18) into an individual genome, taking into account single nucleotide polymorphisms (SNPs), insertions and deletions, copy number variation, and chromosomal rearrangements. perEditor outputs two alleles (maternal, paternal) of the individual genome that is ready for mapping ChIP-seq and RNA-seq reads, and enabling the analyses of allele specific binding, chromatin structure and gene expression.

Availability: perEditor is available at http://biocomp.bioen.uiuc.edu/perEditor.

Contact:  szhong@illinois.edu
Glutathione Is Required by Rhizobium etli for Glutamine Utilization and Symbiotic Effectiveness
Authors: Taté Rosarita , Cermola Michele , Riccio Anna , Diez-Roux Graciana , Patriarca Eduardo J.
Published: October 2011

Here, we provide genetic and biochemical evidence indicating that the ability of Rhizobium etli bacteria to efficiently catabolize glutamine depends on its ability to produce reduced glutathione (l-γ-glutamyl-l-cysteinylglycine [GSH]). We find that GSH-deficient strains, namely a gshB (GSH synthetase) and a gor (GSH reductase) mutant, can use different amino acids, including histidine, alanine, and asparagine but not glutamine, as sole source of carbon, energy, and nitrogen. Moreover, l-buthionine(S,R)-sulfoximine, a GSH synthesis inhibitor, or diamide that oxidizes GSH, induced the same phenotype in the wild-type strain. Among the steps required for its utilization, glutamine uptake, occurring through the two well-characterized carriers (Aap and Bra systems) but not glutamine degradation or respiration, was largely reduced in GSH-deficient strains. Furthermore, GSH-deficient mutants of R. etli showed a reduced symbiotic efficiency. Exogenous GSH was sufficient to rescue glutamine uptake or degradation ability, as well as the symbiotic effectiveness of GSH mutants. Our results suggest a previously unknown GSH–glutamine metabolic relationship in bacteria.
Photorespiratory Metabolism and Nodule Function: Behavior ofLotus japonicusMutants Deficient in Plastid Glutamine Synthetase
Authors: García-Calderón Margarita , Chiurazzi Maurizio , Espuny M. Rosario , Márquez Antonio J.
Published: October 2011

Two photorespiratory mutants of Lotus japonicus deficient in plastid glutamine synthetase (GS2) were examined for their capacity to establish symbiotic association with Mesorhizobium loti bacteria. Biosynthetic glutamine synthetase (GS) activity was reduced by around 40% in crude nodule extracts from mutant plants as compared with the wild type (WT). Western blot analysis further confirmed the lack of GS2polypeptide in mutant nodules. The decrease in GS activity affected the nodular carbon metabolism under high CO2(suppressed photorespiration) conditions, although mutant plants were able to form nodules and fix atmospheric nitrogen. However, when WT and mutant plants were transferred to an ordinary air atmosphere (photorespiratory active conditions) the nodulation process and nitrogen fixation were substantially affected, particularly in mutant plants. The number and fresh weight of mutant nodules as well as acetylene reduction activity showed a strong inhibition compared with WT plants. Optical microscopy studies from mutant plant nodules revealed the anticipated senescence phenotype linked to an important reduction in starch and sucrose levels. These results show that, in Lotus japonicus, photorespiration and, particularly, GS2deficiency result in profound limitations in carbon metabolism that affect the nodulation process and nitrogen fixation.
Roles of Infected Seed Tubers and Soilborne Inoculum on Verticillium Wilt of ‘Russet Burbank’ Potato
Authors: Dung Jeremiah K. S. , Johnson Dennis A.
Published: October 2011

Verticillium dahliae, causal agent of Verticillium wilt of potato, persists in soil as microsclerotia and can be found in infected tubers used for seed. The effects of naturally infected tubers and soilborne inoculum on Verticillium wilt symptoms were compared in the greenhouse. Infected and noninfected tubers were grown in infested and noninfested potting soil. Chlorosis and necrosis were measured and converted to area under senescence progress curves (AUSPC). Aboveground stems and progeny tubers were assayed for V. dahliae. Plants from infested soils exhibited significantly greater AUSPC than plants from noninfested soil. Plants grown from infected and noninfected tubers had similar AUSPC and interactions between infected tubers and infested soil were not observed. The pathogen was isolated from the vascular system of 94% of plants grown in infested soils and 8% of plants grown from infected tubers in noninfested soil. Plants grown in infested soil contained microsclerotia on 46% of stems while plants grown from infected tubers in noninfested soils exhibited microsclerotia on <1% of stems. Infected progeny tubers were only recovered from plants grown in infested soil. Seed tuber infection did not contribute to premature senescence or potential inoculum production, indicating that management efforts should focus on reducing soilborne inoculum.
First Report of the Root-Knot Nematode Meloidogyne arenaria on Cheeseweed Mallow (Malva parviflora) in the United States
Authors: Kokalis-Burelle N. , Rosskopf E. N. , Holzinger J.
Published: October 2011

During a 2010 field trial for examining alternatives to methyl bromide soil fumigation for the production of field-grown cut flowers, weeds were collected for identification and evaluated for their potential as hosts for plant pathogenic nematodes. In one cut flower field located in Martin County, FL, six cheeseweed mallow (Malva parviflora L.) plants were collected that had root-galling typical of infection by a root-knot nematode (Meloidogyne spp.). Field collected plants were used for species identification of the weed and maintained in the greenhouse for seed production. Several gravid female nematodes were extracted from field collected mallow roots and individually identified as Meloidogyne arenaria based on their esterase phenotype (PhastSystem, GE Healthcare) (1). A single egg mass was then extracted from the field collected mallow roots and inoculated onto a tomato plant (Solanum lycopersicum, ‘Rutgers’) grown in steamed builders sand in the greenhouse. The single egg mass culture was increased for 8 weeks, until galling was sufficient to produce adequate nematode inoculum to complete Koch's postulates on the original mallow host. Ten mallow plants were inoculated with single egg masses originally isolated from mallow and increased on tomato. Ten additional plants were maintained in the greenhouse as uninoculated controls. Inoculated and control mallow plants were grown in the greenhouse for 8 weeks, after which the roots were evaluated for galling, and root-knot nematode J2 were extracted from roots and soil and counted. All inoculated plants produced galled roots and control plants did not. Gravid females were extracted from mallow roots and identified as M. arenaria based on esterase phenotype as previously described. Ten gravid females for each DNA extraction were collected from mallow roots and DNA was isolated with the PowerSoil DNA Isolation Kit (MO BIO Laboratories, Inc., Carlsbad, CA). Identification of M. arenaria was confirmed by using species-specific primers F5′-TCGAGGGCATCTAATAAAGG-3′ and R5′-GGGCTGAATAATCAAAGGAA-3′ (2) and F5′-TCGGCGATAGAGGTAAATGAC-3′ and R5′-TCGGCGATAGACACTACAACT-3′ (4), which produced single amplicon bands of the expected size of 420 and 950 bp, respectively. This weed species has been reported as a host for M. javanica in Algeria and as an experimental host in Egypt (3), but this report, to our knowledge, constitutes the first documentation of Malva parviflora as a natural host of M. arenaria. The importance of weeds as hosts for plant parasitic nematodes cannot be over emphasized. As growers, particularly in Florida and California, continue to lose tools for broad-spectrum pest control, the ability of nematodes to reproduce on uncontrolled weeds will become increasingly important.

References: (1) J. A. Brito et al. Nematology 10:757, 2008. (2) K. Dong et al. Nematropica 31:273, 2001. (3) M. Quader et al. Australas. Plant Pathol. 30:357, 2001. (4) C. Zijlstra et al. Nematology 2:847, 2000.