bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacteriophage-Mediated Toxin Gene Regulation in
Clostridium difficile
Authors: Govind Revathi , Vediyappan Govindsamy , Rolfe Rial D. , Dupuy Bruno , Fralick Joe A.
Published: September 2009

Clostridium difficile
has been identified as the most important single identifiable cause of nosocomial antibiotic-associated diarrhea and colitis. Virulent strains of
C. difficile
produce two large protein toxins, toxin A and toxin B, which are involved in pathogenesis. In this study, we examined the effect of lysogeny by ΦCD119 on
C. difficile
toxin production. Transcriptional analysis demonstrated a decrease in the expression of pathogenicity locus (PaLoc) genes
tcdA
,
tcdB
,
tcdR
,
tcdE
, and
tcdC
in ΦCD119 lysogens. During this study we found that
repR
, a putative repressor gene of ΦCD119, was expressed in
C. difficile
lysogens and that its product, RepR, could downregulate
tcdA
::
gusA
and
tcdR
::
gusA
reporter fusions in
Escherichia coli
. We cloned and purified a recombinant RepR containing a C-terminal six-His tag and documented its binding to the upstream regions of
tcdR
in
C. difficile
PaLoc and in
repR
upstream region in ΦCD119 by gel shift assays. DNA footprinting experiments revealed similarities between the RepR binding sites in
tcdR
and
repR
upstream regions. These findings suggest that presence of a CD119-like temperate phage can influence toxin gene regulation in this nosocomially important pathogen.
Structure-Function Analysis of Human Immunodeficiency Virus Type 1 gp120 Amino Acid Mutations Associated with Resistance to the CCR5 Coreceptor Antagonist Vicriviroc
Authors: Ogert Robert A. , Ba Lei , Hou Yan , Buontempo Catherine , Qiu Ping , Duca Jose , Murgolo Nicholas , Buontempo Peter , Ralston Robert , Howe John A.
Published: September 2009

Vicriviroc (VCV) is a small-molecule CCR5 coreceptor antagonist currently in clinical trials for treatment of R5-tropic human immunodeficiency virus type 1 (HIV-1) infection. With this drug in development, identification of resistance mechanisms to VCV is needed to allow optimal outcomes in clinical practice. In this study we further characterized VCV resistance in a lab-adapted, VCV-resistant RU570 virus (RU570-VCV
res
). We show that K305R, R315Q, and K319T amino acid changes in the V3 loop, along with P437S in C4, completely reproduced the resistance phenotype in a chimeric ADA envelope containing the C2-V5 region from RU570 passage control gp120. The K305R amino acid change primarily impacted the degree of resistance, whereas K319T contributed to both resistance and virus infectivity. The P437S mutation in C4 had more influence on the relative degree of virus infectivity, while the R315Q mutation contributed to the virus concentration-dependent phenotypic resistance pattern observed for RU570-VCV
res
. RU570-VCV
res
pseudovirus entry with VCV-bound CCR5 was dramatically reduced by Y10A, D11A, Y14A, and Y15A mutations in the N terminus of CCR5, whereas these mutations had less impact on entry in the absence of VCV. Notably, an additional Q315E/I317F substitution in the crown region of the V3 loop enhanced resistance to VCV, resulting in a stronger dependence on the N terminus for viral entry. By fitting the envelope mutations to a molecular model of a recently described docked N-terminal CCR5 peptide consisting of residues 2 to 15 in complex with HIV-1 gp120 CD4, potential new interactions in gp120 with the N terminus of CCR5 were uncovered. The cumulative results of this study suggest that as the RU570 VCV-resistant virus adapted to use the drug-bound receptor, it also developed an increased reliance on the N terminus of CCR5.
Functional Analysis and Structural Modeling of Human APOBEC3G Reveal the Role of Evolutionarily Conserved Elements in the Inhibition of Human Immunodeficiency Virus Type 1 Infection and
Alu
Transposition
Authors: Bulliard Yannick , Turelli Priscilla , Röhrig Ute F. , Zoete Vincent , Mangeat Bastien , Michielin Olivier , Trono Didier
Published: September 2009

Retroelements are important evolutionary forces but can be deleterious if left uncontrolled. Members of the human APOBEC3 family of cytidine deaminases can inhibit a wide range of endogenous, as well as exogenous, retroelements. These enzymes are structurally organized in one or two domains comprising a zinc-coordinating motif. APOBEC3G contains two such domains, only the C terminal of which is endowed with editing activity, while its N-terminal counterpart binds RNA, promotes homo-oligomerization, and is necessary for packaging into human immunodeficiency virus type 1 (HIV-1) virions. Here, we performed a large-scale mutagenesis-based analysis of the APOBEC3G N terminus, testing mutants for (i) inhibition of
vif
-defective HIV-1 infection and
Alu
retrotransposition, (ii) RNA binding, and (iii) oligomerization. Furthermore, in the absence of structural information on this domain, we used homology modeling to examine the positions of functionally important residues and of residues found to be under positive selection by phylogenetic analyses of primate APOBEC3G genes. Our results reveal the importance of a predicted RNA binding dimerization interface both for packaging into HIV-1 virions and inhibition of both HIV-1 infection and
Alu
transposition. We further found that the HIV-1-blocking activity of APOBEC3G N-terminal mutants defective for packaging can be almost entirely rescued if their virion incorporation is forced by fusion with Vpr, indicating that the corresponding region of APOBEC3G plays little role in other aspects of its action against this pathogen. Interestingly, residues forming the APOBEC3G dimer interface are highly conserved, contrasting with the rapid evolution of two neighboring surface-exposed amino acid patches, one targeted by the Vif protein of primate lentiviruses and the other of yet-undefined function.
Identification and Mutational Analysis of a Rej Response Element in Jaagsiekte Sheep Retrovirus RNA
Authors: Nitta Takayuki , Hofacre Andrew , Hull Stacey , Fan Hung
Published: September 2009

Jaagsiekte sheep retrovirus (JSRV) is a simple betaretrovirus causing a contagious lung cancer of sheep. JSRV encodes unspliced and spliced viral RNAs, among which unspliced RNA encodes Gag and Pol proteins and a singly spliced mRNA encodes Env protein. In another study we found that JSRV encodes a regulatory protein, Rej, that is responsible for synthesis of Gag polyprotein from unspliced viral RNA. Rej is encoded in the 5′ end of
env
, and it enhances nuclear export or accumulation of cytoplasmic unspliced viral RNA in 293T cells but not in most other cell lines (A. Hofacre, T. Nitta, and H. Fan, J. Virol. 83:12483-12498, 2009). In this study, we found that mutations in the 3′ end of
env
in the context of a cytomegalovirus-driven full-length JSRV expression construct abolished Gag protein synthesis and released viruses in 293T cells. These mutants also showed deficits in accumulation of unspliced viral RNA in the cytoplasm. These mutants defined a Rej-responsive element (RejRE). Inhibition of CRM1 but not Tap function prevented nuclear export/accumulation of cytoplasmic unspliced RNA in 293T cells, similarly to other complex retroviruses that express analogous regulator proteins (e.g., human immunodeficiency virus Rev). Structural modeling of the RejRE with Zuker M-fold indicated a region with a predicted stable secondary structure. Mutational analysis in this region indicated the importance of both secondary structures and primary nucleotide sequences in a central stem-bulge-stem structure. In contrast to 293T cells, mutations in the RejRE did not affect the levels of cytoplasmic unspliced RNA in 293 cells, although the unspliced RNA showed partial degradation, perhaps due to lack of translation. RejRE-containing RNA relocalized Rej protein from the nucleus to the cytoplasm in 293 and rat 208F cells, suggesting binding of Rej to the RejRE.
Rotational and Vibrational Analysis of the First Singlet Transition (1B2 ← 1A1) of Isobenzofuran
Authors: Robey M. J. , Ross I. G.
Published: September 2009

The absorption spectrum of isobenzofuran vapor has been photographed at resolving powers in excess of 300 000. The vibrational structure is straightforward, involving totally symmetric vibrations only. The rotational structure of a band at 0 + 858 cm−1 has been analyzed as a type B band, leading to the assignment of the transition as 1B2 ← 1A1. The detailed structure of the band is described. The changes in the rotational constants are ΔA + 0.000124, ΔB −0.000122, and ΔC −0.00052 cm−1. A calculated excited state structure compatible with these results is proposed.
High Resolution Infrared Spectra of the ν2 and 2ν1 Bands of 14N16O2
Authors: Cabana Aldée , Laurin Michel , Lafferty Walter J. , Sams Robert L.
Published: September 2009

The infrared spectra of two B type bands, ν2 and 2ν1, of 14N16O2 have been recorded under high resolution. Ground state combination differences from these bands have been combined with combination differences obtained in previous studies and eight pure rotational microwave transitions to yield improved ground state rotational constants. Upper state constants and band centers for the ν2 and 2ν1 bands are also reported. The 2ν1 band contains internal intensity anomalies believed to arise from a weak Coriolis interaction with the much stronger ν1 + ν3 band. Equilibrium rotational constants have been calculated. The equilibrium structure of the molecule is: rc = 1.1945 ± 0.0005 Å and Θc = 133.85 ± 0.10°. For the sake of comparison, effective, substitution, and average structures are also reported.
Laser Magnetic Resonance Spectra of 14NO2 and 15NO2 near 1600 cm−1
Authors: Freund S. M. , Hougen J. T. , Lafferty W. J.
Published: September 2009

Two laser magnetic resonance patterns for 14NO2 and six patterns for 15NO2, observed using six CO laser transitions, have been analyzed to yield spin corrected zero-field vibration–rotation transition wave numbers and zero-field spin–rotation splittings. The 14NO2 results are in good agreement with results obtained from conventional infrared grating studies. The 15NO2 results allow new values of ν0 = 1582.107 ± 0.008, A′ − A″ = −0.2116 ± 0.0011, and DK′ − DK″ = −1.39 ± 0.20 × 10−4 cm−1 to be determined for the ν3 fundamental of that molecule (errors are 3 standard deviations). Two spectral figures and a list of assigned Zeeman lines are presented to permit using this stable molecule as an aid in adjusting newly constructed instruments. Closed form approximate intensity expressions are given for Zeeman transitions of the type observed in this work, i.e., for sharp partially spin forbidden Zeeman transitions in A type bands of near prolate asymmetric rotors.
Ground State D2 Dissociation Energy from the Near-dissociation Behavior of Rotational Level Spacings
Authors: Roy Robert J. Le , Barwell Margaret G.
Published: September 2009

A method of determining the dissociation energy of a diatomic molecule from the rotational term value(s)of a single vibrational level lying near dissociation is derived and tested. It is based on expressions relating the characteristic near-dissociation behavior of the rotational constants Bv, Dv, Hv,… etc., to the asymptotically dominant inverse power contribution to the long range intermolecular potential. Application of this procedure to data for ground state D2 yields a dissociation energy of D0 = 36 748.88(±0.3)cm−1, in essentially exact agreement with the value Herzberg determined from the onset of continuum absorption in the vacuum u.v., 36 748.9(±0.4) cm−1. This agreement between results obtained from completely different observables appears to confirm the existence of a small discrepancy between experiment and the most recent theoretical nonadiabatic dissociation energy of Kolos and Wolniewicz, 36 748.2 cm−1.
Microwave Spectrum of Methane-d2, CH2D2
Authors: Hirota Eizi , Imachi Misako
Published: September 2009

Three rotational transitions of methane-d2 were observed by a source-modulation microwave spectrometer. The two differences in the rotational constants, A – C and B – C, were determined to be 37 555.758 and 13 664.280 MHz, respectively, from the observed frequencies of 110 ← 101 and 211 ← 202 after correcting for the centrifugal distortion effects. The centrifugal distortion constants were evaluated by a normal coordinate analysis. The dipole moment of CH2D2 was determined to be 0.014 ± 0.005 D, by comparing the intensity of 211 ← 202 with that of an oxygen line.
Energy Band Models for Spatially Dispersive Dielectric Media
Authors: Sipe J. E. , Kranendonk J. Van
Published: September 2009

The effects of spatial dispersion on the optical properties of dielectric crystals, arising from the broadening of the molecular energy levels into energy bands by the intermolecular interaction, are discussed both in the microscopic and the macroscopic theory. The microscopic equations of motion for the internal degrees of freedom describing the molecular excitations are derived using semiclassical radiation theory, and the conditions are given under which a description in terms of only the dipole moment is possible. The corresponding macroscopic equations are derived and the nature of the boundary conditions and integral relations appearing in the theory are discussed. The characterization of spatially dispersive media as nonlocal is shown to be based on a misinterpretation of the meaning of the integral kernels relating to infinite media. The breakdown of the macroscopic theory due to the previously predicted onset of an antiresonant response is explicitly demonstrated for slab geometries for which rigorous solutions are given of both the macroscopic and the microscopic equations. Finally, we introduce a mechanical coupling varying exponentially with the intermolecular separation, which provides a two parameter model for the exciton bands and which prevents the proliferation of microscopic refractive indices occurring in other models. The exp model is shown to be useful to study the dependence of the optical properties for example on the effective mass and the width of an exciton band.
The a4Σ3/2+ and the D2Π1/2 States of YbH and YbD
Authors: Kopp I. , Hagland L. , Rydh B.
Published: September 2009

The region of 7000–11 000 Å of the spectra of YbH and YbD has been studied and bands of the transitions a4Σ3/2+–X2Σ+ and D2Π1/2–X2Σ+ have been rotationally analyzed. Equilibrium values of the constants for the a and D states of YbD have been derived:[Formula: see text]
TEMPERATURE GRADIENT CAUSED BY GRAVITATION
Authors: LIAO CHUANPING
Published: September 2009

Thermodynamic deduction and experimental results both demonstrate that gravitation causes temperature gradient in an adiabatic system, i.e., gravithermal effect: The higher altitude the lower temperature.
SUBSTITUTIONAL EFFECT OF Zn AND Pr IN YBa2Cu3O7-δ
Authors: NAIK MISKIL S. , PRABHU R. B. , SARODE P. R. , PRIOLKAR K. R. , VASANTHACHARYA N. Y.
Published: September 2009

The co-doping effect of Zn and Pr impurities in the compounds of composition Y 1-x Pr x Ba 2[ Cu 1-y Zn y]3 O 7-δ with x = 0.1, x = 0.2 and 0 ≤ y ≤ 0.1 has been investigated by analyzing the results of electrical resistivity measurements. It is found that for Pr substitution at x = 0.1, there is a minimal influence on in-plane processes, thereby slightly affecting Tc and residual resistivity ρ0, but with the resistivity slope dρ/dT becoming large for the range of y from 0.03 to 0.06, leading to a larger depinning effect. For x = 0.2 a drastic change is observed whereby ρ0 becomes abnormally large, and dρ/dT becomes negative, implying totally pinned charge stripes and no depinning. This second observation therefore suggests that Pr substitution converts the overdoped system to an optimally doped system, leading to the universal superconductor–insulator transition.
SYNTHESIS, GROWTH AND CHARACTERIZATION OF GLYCINE THIOUREA: A NOVEL NONLINEAR OPTICAL MATERIAL
Authors: PRAKASH J. THOMAS JOSEPH , KUMARARAMAN S. , THAILA T.
Published: September 2009

A novel mixed organic single crystal of glycine thiourea (GTU), which is a potential material for nonlinear optical applications, has been grown by solvent evaporation method at room temperature. The grown single crystal has been analyzed using different characterization methods. X-ray diffraction studies show that it belongs to an orthorhombic crystal system having lattice dimensions a = 5.546 Å, b = 7.774 Å and c = 8.637 Å. The formation of the compound was verified by FTIR analysis. Its optical behavior was analyzed using UV-vis analysis and it was found that it had good optical transmission in the entire visible region. The mechanical properties of grown crystals were studied using Vickers microhardness tester. The surface defects were examined by adopting an etching technique. Its nonlinear optical property was tested using Kurtz powder method and found to have better SHG efficiency than that of potassium dihydrogen phosphate (KDP) single crystal.
THE PURE DEPHASING FACTOR OF COULOMB BOUND POLARON IN AN ANISOTROPIC QUANTUM DOT
Authors: LI HONG-JUAN , SUN JIA-KUI , XIAO JING-LIN
Published: September 2009

On the condition of electron–LO-phonon strong coupling in an anisotropic qunntum dot (QD), the eigenenergies of the ground-state and the first excited state, the eigenfunctions of the ground-state and the first excited state are obtained by using a variational method of Pekar type. This system in QD may be employed as a quantum system-qubit. Numerical calculations are performed on the pure dephasing factor. The relations of the pure dephasing factor on the temperature, the Coulomb binding parameter, the electron–LO-phonon coupling strength and the effective confinement length are derived.
EXACT DARK SOLITON SOLUTION OF THE GENERALIZED NONLINEAR SCHRÖDINGER EQUATION
Authors: ZHANG YI , CAI XIAO-NA , YAO CAI-ZHEN , XU HONG-XIAN
Published: September 2009

The generalized nonlinear Schrödinger equation with the variable coefficient is discussed, and the exact dark N-soliton solution is presented by using the Hirota bilinear method, from finding the 1-soliton to 2-soliton, and then we obtain the N-soliton solution. With the aid of Maple, a few figures of solutions under several different cases are shown when aleatoric constants and variables are given exact values.
DYNAMIC RELAXATION OF FINANCIAL INDICES
Authors: SHEN J. , ZHENG B. , LIN H. , QIU T.
Published: September 2009

The dynamic relaxation of the German DAX both before and after a large price-change is investigated. The dynamic behavior is characterized by a power law. At the minutely time scale, the exponent p governing the power-law behavior takes a same value before and after the large price change, while at the daily time scale, it is different. Numerical simulations of an interacting EZ herding model are performed for comparison.
Insulin-like growth factor-II regulates maternal hemodynamic adaptation to pregnancy in rats
Authors: Van Mieghem Tim , van Bree Rita , Van Herck Erik , Deprest Jan , Verhaeghe Johan
Published: September 2009

The relationship between maternal plasma volume (PV) expansion and fetal growth is well established, but the underlying mechanisms remain unclear. Here, we examined the influence of maternal body weight and fetoplacental mass on gestational PV increment in the rat. Because IGF-I and IGF-II have growth-promoting and vasoactive properties, their relationship to PV expansion and fetoplacental growth was also studied. In normal rats, the gradual expansion of PV (+35% at day 22, i.e., term) was accompanied by a rise in circulating IGF-II (+45%) and a considerable drop in IGF-I (−73%). Increased maternal body weight induced by an obesogenic diet did not influence PV and circulating IGFs compared with rats on the standard diet. Combining the results from both diets, circulating IGF-II was the principal correlate of PV. A second experiment examined the effect of fetoplacental mass reduction by surgically removing half of the gestational sacs at day 16. This procedure reduced maternal PV and circulating IGF-II at term by 14% and 20%, respectively. We then investigated the effect of a constant infusion of IGF-II (1 mg·kg−1·day−1) from day 16, which raised circulating IGF-II by 38% and found increased PV (+19%) and a larger placental trophospongial area (+29%) at term. Our results indicate that the placenta, the primary source of IGF-II synthesis in pregnancy, drives PV expansion, and that IGF-II is among the regulatory factors of the gestational PV increment. Further studies should clarify whether IGF-II directly affects vascular function and/or indirectly promotes the secretion of placenta-derived vasoactive substances.
The farnesoid X receptor modulates renal lipid metabolism and diet-induced renal inflammation, fibrosis, and proteinuria
Authors: Wang Xiaoxin X. , Jiang Tao , Shen Yan , Adorini Luciano , Pruzanski Mark , Gonzalez Frank J. , Scherzer Pnina , Lewis Linda , Miyazaki-Anzai Shinobu , Levi Moshe
Published: September 2009

Diet-induced obesity is associated with proteinuria and glomerular disease in humans and rodents. We have shown that in mice fed a high-fat diet, increased renal expression of the transcriptional factor sterol-regulatory element binding protein-1 (SREBP-1) plays a critical role in renal lipid accumulation and increases the activity of proinflammatory cytokines and profibrotic growth factors. In the current study, we have determined a key role of the farnesoid X receptor (FXR) in modulating renal SREBP-1 activity, glomerular lesions, and proteinuria. We found that feeding a Western-style diet to DBA/2J mice results in proteinuria, podocyte loss, mesangial expansion, renal lipid accumulation, and increased expression of proinflammatory factors, oxidative stress, and profibrotic growth factors. Treatment of these mice with the highly selective and potent FXR-activating ligand 6-α-ethyl-chenodeoxycholic acid (INT-747) ameliorates triglyceride accumulation by modulating fatty acid synthesis and oxidation, improves proteinuria, prevents podocyte loss, mesangial expansion, accumulation of extracellular matrix proteins, and increased expression of profibrotic growth factors and fibrosis markers, and modulates inflammation and oxidative stress. Our results therefore indicate that FXR activation could represent an effective therapy for treatment of abnormal renal lipid metabolism with associated inflammation, oxidative stress, and kidney pathology in patients affected by obesity.
Pulse mTOR inhibitor treatment effectively controls cyst growth but leads to severe parenchymal and glomerular hypertrophy in rat polycystic kidney disease
Authors: Wu Ming , Arcaro Alexandre , Varga Zsuzsanna , Vogetseder Alexander , Le Hir Michel , Wüthrich Rudolf P. , Serra Andreas L.
Published: September 2009

The efficacy of mammalian target of rapamycin (mTOR) inhibitors is currently tested in patients affected by autosomal dominant polycystic kidney disease. Treatment with mTOR inhibitors has been associated with numerous side effects. However, the renal-specific effect of mTOR inhibitor treatment cessation in polycystic kidney disease is currently unknown. Therefore, we compared pulse and continuous everolimus treatment in Han:SPRD rats. Four-week-old male heterozygous polycystic and wild-type rats were administered everolimus or vehicle by gavage feeding for 5 wk, followed by 7 wk without treatment, or continuously for 12 wk. Cessation of everolimus did not result in the appearance of renal cysts up to 7 wk postwithdrawal despite the reemergence of S6 kinase activity coupled with an overall increase in cell proliferation. Pulse everolimus treatment resulted in striking noncystic renal parenchymal enlargement and glomerular hypertrophy that was not associated with compromised kidney function. Both treatment regimens ameliorated kidney function, preserved the glomerular-tubular connection, and reduced proteinuria. Pulse treatment at an early age delays cyst development but leads to striking glomerular and parenchymal hypertrophy. Our data might have an impact when long-term treatment using mTOR inhibitors in patients with autosomal dominant polycystic kidney disease is being considered.
LTD and LTP at the Developing Retinogeniculate Synapse
Authors: Žiburkus Jokūbas , Dilger Emily K. , Lo Fu-Sun , Guido William
Published: September 2009

The purpose of the present study was to determine whether retinal activity can support long-term changes in synaptic strength in the developing dorsal lateral geniculate nucleus (LGN) of thalamus. To test for this we made use of a rodent in vitro explant preparation in which retinal afferents and the intrinsic circuitry of the LGN remain intact. We repetitively stimulated the optic tract with a tetanus protocol that approximated the temporal features of spontaneous retinal waves. We found the amplitude of extracellular field potentials evoked by retinal stimulation changed significantly after tetanus and that the polarity of these alterations was related to postnatal age. At a time when substantial pruning of retinal connections occurs (postnatal day 1 [P1] to P14), high-frequency stimulation led to an immediate and long-term depression (LTD). However, at times when pruning wanes and adultlike patterns of connectivity are stabilizing (P16 to P30), the identical form of stimulation produced a modest form of potentiation (long-term potentiation [LTP]). The LTD was unaffected by the bath application of γ-aminobutyric acid type A and N-methyl-d-aspartate receptor antagonists. However, both LTD and LTP were blocked by L-type Ca2+-channel antagonists. Thus the Ca2+ influx associated with L-type channel activation mediates the induction of synaptic plasticity and may signal the pruning and subsequent stabilization of developing retinogeniculate connections.
The Influence of Motor Training on Human Express Saccade Production
Authors: Bibi Raquel , Edelman Jay A.
Published: September 2009

Express saccadic eye movements are saccades of extremely short latency. In monkey, express saccades have been shown to occur much more frequently when the monkey has been trained to make saccades in a particular direction to targets that appear in predictable locations. Such results suggest that express saccades occur in large number only under highly specific conditions, leading to the view that vector-specific training and motor preparatory processes are required to make an express saccade of a particular magnitude and direction. To evaluate this hypothesis in humans, we trained subjects to make saccades quickly to particular locations and then examined whether the frequency of express saccades depended on training and the number of possible target locations. Training significantly decreased saccade latency and increased express saccade production to both trained and untrained locations. Increasing the number of possible target locations (two vs. eight possible targets) led to only a modest increase of saccade latency. For most subjects, the probability of express saccade occurrence was much higher than that expected if vector-specific movement preparation were necessary for their production. These results suggest that vector-specific motor preparation and vector-specific saccade training are not necessary for express saccade production in humans and that increases in express saccade production are due in part to a facilitation in fixation disengagement or else a general enhancement in the ability of the saccadic system to respond to suddenly appearing visual stimuli.
An Evolutionary Formulation of the Crossing Number Problem
Authors: Gan Che Sheng , Alan Tan Wee Chiat , Koo Voon Chet , Mak Kwang Hwai
Published: September 2009

A graph drawing algorithm is presented which results in complete graphs having minimum crossings equal to that of Guy′s conjecture. It is then generalized and formulated in an evolutionary algorithm (EA) to perform constrained search for the crossing numbers. The main objective of this work is to present a suitable two‐dimensional scheme which can greatly reduce the complexity of finding crossing numbers by using computer. Program performance criteria are presented and discussed. It is shown that the EA implementation provides good confirmation of the predicted crossing numbers.
FlowFP: A Bioconductor Package for Fingerprinting Flow Cytometric Data
Authors: Rogers Wade T. , Holyst Herbert A.
Published: September 2009

A new software package called flowFP for the analysis of flow cytometry data is introduced. The package, which is tightly integrated with other Bioconductor software for analysis of flow cytometry, provides tools to transform raw flow cytometry data into a form suitable for direct input into conventional statistical analysis and empirical modeling software tools. The approach of flowFP is to generate a description of the multivariate probability distribution function of flow cytometry data in the form of a “fingerprint.” As such, it is independent of a presumptive functional form for the distribution, in contrast with model-based methods such as Gaussian Mixture Modeling. FlowFP is computationally efficient and able to handle extremely large flow cytometry data sets of arbitrary dimensionality. Algorithms and software implementation of the package are described. Use of the software is exemplified with applications to data quality control and to the automated classification of Acute Myeloid Leukemia.
Megacystis-Microcolon-Intestinal Hypoperistalsis Syndrome: A Case Report
Authors: Melek Mehmet , Edirne Yesim , Beger Burhan , Cetin Mecnun
Published: September 2009

Megacystis Microcolon Intestinal Hypoperistalsis Syndrom (MMIHS) is a quite rare congenital and fatal disease which was firstly defined by Berdon and his colleagues. It appears through a widely enlarged bladder and microcolon and its cause is unknown (Berdon et al., 1976; Carmelo et al., 2005; Makhija et al., 1999; Loening-Baucke and Kimura 1999; Redman et al., 1984; Hsu et al., 2003; Yigit et al., 1996; Srikanth et al., 1993). The disease is found in females three or four times more than in males (Srikanth et al., 1993; Sen et al., 1993; Hirato et al., 2003). Most of the cases die within the early months of their lives (Yigit et al., 1996; Srikanth et al., 1993; Sen et al., 1993; Hirato et al., 2003). We present the case of a female newborn with antenatal ultrasound revealing intestinal mass and bilateral hydroureteronephrosis. The case was admitted for intestinal obstruction after birth.
Low-Profile Array of Wire Patch Antennas
Authors: Zhang H. , Chantalat R. , Torres F. , Thevenot M. , Monediere T. , Jecko B.
Published: September 2009

A low-profile antenna over a ground plane that radiates a directive lobe in the end fire direction is described in this paper. An array of 16 wire patch antenna (WPA) fed by an integrated 16 ways power divider has been designed. Owing to its low height, low cost, high robustness, and monopolar radiation pattern, the WPA has been chosen as unit cell of the array that must be placed on the vehicle roof. A gain higher than 18.9 dB was achieved in the end fire direction over a 4.5% bandwidth. However, the antenna has been tilted in order to compensate the beam deviation caused by the edge diffraction. Moreover, a vertical metallic plane has been inserted to eliminate the back fire radiation. Its position and the disposition of the WPAs are explained in this paper. A prototype with four elements has been manufactured in order to validate the antenna principle. A gain difference lower than 0.5 dB is achieved between the measurements and the simulations.
Esophageal Clearance Patterns in Normal Older Adults as Documented with Videofluoroscopic Esophagram
Authors: Jou Janice , Radowsky Jason , Gangnon Ronald , Sadowski Elizabeth , Kays Stephanie , Hind Jacqueline , Gaumnitz Eric , Taylor Andrew , Robbins JoAnne
Published: September 2009

Normal esophageal bolus transport in asymptomatic healthy older adults has not been well defined,potentiallyleading to ambiguity in differentiating esophageal swallowing patterns of dysphagic and healthy individuals. This pilot study of 24 young (45–64 years) and old (65+years) men and women was designed to assess radiographic esophageal bolus movement patterns in healthy adults using videofluoroscopic recording. Healthy, asymptomatic adults underwent videofluoroscopic esophagram to evaluate for the presence of ineffective esophageal clearance, namely, intraesophageal stasis and intraesophageal reflux. Intraesophageal stasis and intraesophageal reflux were visualized radiographically in these normal subjects. Intraesophageal stasis occurred significantly more frequently with semisolid (96%) compared with liquid (16%) barium, suggesting that a variety of barium consistencies, as opposed to only the traditional fluids, would better define the spectrum of esophageal transport. Intraesophageal reflux was observed more frequently in older males than in their younger counterparts. The rates of intraesophageal stasis and intraesophageal reflux were potentially high given that successive bolus presentations were spaced 10 seconds apart. These findings suggest a need for a more comprehensive definition regarding the range of normal esophageal bolus transport to (a) prevent misdiagnosis of dysphagia and (b) to enhance generalization to functional eating, which involves solid foods in addition to liquids.
Navigating Policy Responses at the National Level in the Midst of the Global Financial Crisis: The Experience of Indonesia
Authors: Basri Muhammad Chatib , Siregar Reza Yamora
Published: September 2009

While the global financial crisis (GFC) deepens with no clear signs of abatement, it is almost impossible to assess its full impacts on any economies, including that of Indonesia. Nonetheless, it is important to take stock of the impacts of the GFC on Indonesia and to assess the implementation and the progress of ongoing policy responses. In particular, our study scrutinizes policy responses from two key fronts, namely fiscal and monetary policies, and highlights challenges and potential shortcomings.
The Philippine Economy in the Face of External Shocks
Authors: Gochoco-Bautista Maria Socorro
Published: September 2009

The Philippines has a unique economic history relative to its neighbors. It is less open to trade and has been unable to attain and sustain high rates of growth. Today, globalization and participation in the global economy primarily means the export of labor rather than goods. The Philippines' reliance on remittances from its cadre of overseas Filipino workers has become the main pillar of its growth and development strategy. Going into the period of the global crisis, the Philippines had robust growth relative to its historical average and a strengthened banking system. The effects on the real sector intensified in the last quarter of 2008. While there are continuing attempts to use expansionary monetary and fiscal policy to spur the economy, the ability of the Philippines to pursue such expansionary policies may be limited by the still relatively high inflation and the government's historically weak fiscal position. Although it appears that the Philippines will muddle through and survive the current global crisis, it will continue to face the daunting task of effectively leveraging for long-term growth and development.
A 1–10-Day Ensemble Forecasting Scheme for the Major River Basins of Bangladesh: Forecasting Severe Floods of 2003–07*
Authors: Hopson Thomas M. , Webster Peter J.
Published: September 2009

This paper describes a fully automated scheme that has provided calibrated 1–10-day ensemble river discharge forecasts and predictions of severe flooding of the Brahmaputra and Ganges Rivers as they flow into Bangladesh; it has been operational since 2003. The Bangladesh forecasting problem poses unique challenges because of the frequent life-threatening flooding of the country and because of the absence of upstream flow data from India means that the Ganges and Brahmaputra basins must be treated as if they are ungauged. The meteorological–hydrological forecast model is a hydrologic multimodel initialized by NASA and NOAA precipitation products, whose states and fluxes are forecasted forward using calibrated European Centre for Medium-Range Weather Forecasts ensemble prediction system products, and conditionally postprocessed to produce calibrated probabilistic forecasts of river discharge at the entrance points of the Ganges and Brahmaputra into Bangladesh. Forecasts with 1–10-day horizons are presented for the summers of 2003–07. Objective verification shows that the forecast system significantly outperforms both a climatological and persistence forecast at all lead times. All severe flooding events were operationally forecast with significant probability at the 10-day horizon, including the extensive flooding of the Brahmaputra in 2004 and 2007, with the latter providing advanced lead-time warnings for the evacuation of vulnerable residents.
Interference Pattern and Propagation of the M2 Internal Tide South of the Hawaiian Ridge
Authors: Rainville Luc , Johnston T. M. Shaun , Carter Glenn S. , Merrifield Mark A. , Pinkel Robert , Worcester Peter F. , Dushaw Brian D.
Published: September 2009

Most of the M2 internal tide energy generated at the Hawaiian Ridge radiates away in modes 1 and 2, but direct observation of these propagating waves is complicated by the complexity of the bathymetry at the generation region and by the presence of interference patterns. Observations from satellite altimetry, a tomographic array, and the R/P FLIP taken during the Farfield Program of the Hawaiian Ocean Mixing Experiment (HOME) are found to be in good agreement with the output of a high-resolution primitive equation model, simulating the generation and propagation of internal tides. The model shows that different modes are generated with different amplitudes along complex topography. Multiple sources produce internal tides that sum constructively and destructively as they propagate. The major generation sites can be identified using a simplified 2D idealized knife-edge ridge model. Four line sources located on the Hawaiian Ridge reproduce the interference pattern of sea surface height and energy flux density fields from the numerical model for modes 1 and 2. Waves from multiple sources and their interference pattern have to be taken into account to correctly interpret in situ observations and satellite altimetry.
Impact of Phased-Array Radar Observations over a Short Assimilation Period: Observing System Simulation Experiments Using an Ensemble Kalman Filter
Authors: Yussouf Nusrat , Stensrud David J.
Published: September 2009

The conventional Weather Surveillance Radar-1988 Doppler (WSR-88D) scans a given weather phenomenon in approximately 5 min, and past results suggest that it takes 30–60 min to establish a storm into a model assimilating these data using an ensemble Kalman filter (EnKF) data assimilation technique. Severe-weather events, however, can develop and evolve very rapidly. Therefore, assimilating observations for a 30–60-min period prior to the availability of accurate analyses may not be feasible in an operational setting. A shorter assimilation period also is desired if forecasts are produced to increase the warning lead time. With the advent of the emerging phased-array radar (PAR) technology, it is now possible to scan the same weather phenomenon in less than 1 min. Therefore, it is of interest to see if the faster scanning rate of PAR can yield improvements in storm-scale analyses and forecasts from assimilating over a shorter period of time. Observing system simulation experiments are conducted to evaluate the ability to quickly initialize a storm into a numerical model using PAR data in place of WSR-88D data. Synthetic PAR and WSR-88D observations of a splitting supercell storm are created from a storm-scale model run using a realistic volume-averaging technique in native radar coordinates. These synthetic reflectivity and radial velocity observations are assimilated into the same storm-scale model over a 15-min period using an EnKF data assimilation technique followed by a 50-min ensemble forecast. Results indicate that assimilating PAR observations at 1-min intervals over a short 15-min period yields significantly better analyses and ensemble forecasts than those produced using WSR-88D observations. Additional experiments are conducted in which the adaptive scanning capability of PAR is utilized for thunderstorms that are either very close to or far away from the radar location. Results show that the adaptive scanning capability improves the analyses and forecasts when compared with the nonadaptive PAR data. These results highlight the potential for flexible rapid-scanning PAR observations to help to quickly and accurately initialize storms into numerical models yielding improved storm-scale analyses and very short range forecasts.
On the Predictability of Mesoscale Convective Systems: Three-Dimensional Simulations
Authors: Wandishin Matthew S. , Stensrud David J. , Mullen Steven L. , Wicker Louis J.
Published: September 2009

Mesoscale convective systems (MCSs) are a dominant climatological feature of the central United States and are responsible for a substantial fraction of warm-season rainfall. Yet very little is known about the predictability of MCSs. To help address this situation, a previous paper by the authors examined a series of ensemble MCS simulations using a two-dimensional version of a storm-scale (Δx = 1 km) model. Ensemble member perturbations in the preconvective environment, namely, wind speed, relative humidity, and convective instability, are based on current 24-h forecast errors from the North American Model (NAM). That work is now extended using a full three-dimensional model.

Results from the three-dimensional simulations of the present study resemble those found in two dimensions. The model successfully produces an MCS within 100 km of the location of the control run in around 70% of the ensemble runs using perturbations to the preconvective environment consistent with 24-h forecast errors, while reducing the preconvective environment uncertainty to the level of current analysis errors improves the success rate to nearly 85%. This magnitude of improvement in forecasts of environmental conditions would represent a radical advance in numerical weather prediction. The maximum updraft and surface wind forecast uncertainties are of similar magnitude to their two-dimensional counterparts. However, unlike the two-dimensional simulations, in three dimensions, the improvement in the forecast uncertainty of storm features requires the reduction of preconvective environmental uncertainty for all perturbed variables. The MCSs in many of the runs resemble bow echoes, but surface winds associated with these solutions, and the perturbation profiles that produce them, are nearly indistinguishable from the nonbowing solutions, making any conclusions about the bowlike systems difficult.
Re-Ordering Justice: Towards A New Methodological Approach to Studying Transitional Justice
Authors: Grodsky Brian
Published: September 2009

Scholars and policymakers have turned increasing attention to questions of transitional justice, those legal responses to a former regime’s repressive acts following a change in political systems. Although there is a rich, interdisciplinary literature that addresses the value of various transitional justice measures, theoretical arguments for how and under what conditions we should expect to see these measures implemented tend to gravitate to intuitively appealing relative power considerations. But attempts at parsimony have tended to leave the dependent variable either overly restrictive or poorly defined, yielding theories that are difficult to test. In this article, the author proposes a ‘transitional justice spectrum’ based on a hierarchical series of possible accountability mechanisms and designed to allow researchers to conduct more rigorous, cross-national tests of justice arguments. The objective here is not to posit a broad theory of transitional justice, but to open the debate into a methodological weakness in the transitional justice literature. The article includes seven accountability mechanisms: cessation and codification of human rights violations; condemnation of the old system; rehabilitation and compensation for victims; creation of a truth commission; purging human rights abusers from public function; criminal prosecution of ‘executors’ (those lower on the chain-of-command); criminal prosecution of commanders (those higher on the chain-of-command).
Predicting the Military Career Success of United States Air Force Academy Cadets
Authors: Rodriguez Jacob
Published: September 2009

The purpose of this study was to determine the factors that best predicted the military career success (twenty years of service and the achievement of the rank of lieutenant colonel) of Air Force Academy cadets. The Department of Institutional Research at the Air Force Academy provided the data. The sample included admitted cadets between 1982 and 1990. Three hypotheses were tested using probit regression: (1) admissions variables, (2) Academy variables, and (3) aeronautical status had a statistically significant impact on career success. The model was 97.34 percent accurate in predicting career failure, 12.50 percent accurate in predicting career success, and 75.57 percent accurate overall. These results suggest determinates of career success largely occur after graduation. They also suggest the possibility to identify those less likely to achieve career success using admissions and Academy variables. Academy leadership may design interventions to increase the likelihood cadets will achieve career success.
The Illusion of Will in Organizational Behavior Research: Nonconscious Processes and Job Design
Authors: George Jennifer M.
Published: September 2009

Theorizing and research in organizational behavior implicitly or explicitly assumes that behavior is the product of conscious will. However, an extensive body of literature suggests that much of human behavior is automatic and that nonconscious thoughts and feelings are primary drivers of reactions and behavior. Relying on propositions in use in job design theory and research as a critical case in point, the author reviews the literatures on automatic thought and nonconscious emotions and their implications. Based on these literatures, the author develops alternative propositions for job design theory and research that are based on more realistic assumptions about the mind and human functioning. In addition to discussing implications of nonconscious processes for job design, the author draws broader implications for the field of organizational behavior.
Leadership in Teams: A Functional Approach to Understanding Leadership Structures and Processes
Authors: Morgeson Frederick P. , DeRue D. Scott , Karam Elizabeth P.
Published: September 2009

As the use of teams has increased in organizations, research has begun to focus on the role of leadership in fostering team success. This review sought to summarize this literature and advance research and theory by focusing on leadership processes within a team and describing how team leadership can arise from four distinct sources inside and outside a team. Then, drawing from this inclusive, team-centric view of leadership, the authors describe 15 team leadership functions that help teams satisfy their critical needs and regulate their behavior in the service of goal accomplishment. This integrative view of team leadership enables the summarization of past research and identification of promising areas of future research.
An insurrection in words: East End voices in the 1970s
Authors: Harcup Tony
Published: September 2009

From 1971 to 1976, Chris Searle was at the centre of a number of events in the East End of London that, nearly four decades on, continue to resonate. This article uses a combination of reminiscence, reflection, contemporaneous and retrospective accounts, and engagement with the writings of Searle himself, to explore the meanings of the ‘Stepney Words insurrection’ and the creation of the Basement Writers. The article is informed by ideas of critical literacy, including Paulo Freire’s ‘pedagogy of the oppressed’, and argues that community publishing can be seen as an expression of working-class agency and active citizenship within an alternative or ‘plebeian public sphere’.