bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expansion Mechanisms and Functional Annotations of Hypothetical Genes in the Rice Genome
Authors: Jiang Shu-Ye , Christoffels Alan , Ramamoorthy Rengasamy , Ramachandran Srinivasan 
Published: June 2009

Abstract
In each completely sequenced genome, 30% to 50% of genes are annotated as uncharacterized hypothetical genes. In the rice (Oryza sativa) genome, 10,918 hypothetical genes were annotated in the latest version (release 6) of the Michigan State University rice genome annotation. We have implemented an integrative approach to analyze their duplication/expansion and function. The analyses show that tandem/segmental duplication and transposition/retrotransposition have significantly contributed to the expansion of hypothetical genes despite their different contribution rates. A total of 3,769 hypothetical genes have been detected from retrogene, tandem, segmental, Pack-MULE, or long terminated direct repeat-related duplication/expansion. The nonsynonymous substitutions per site and synonymous substitutions per site analyses showed that 21.65% of them were still functional, accounting for 7.47% of total hypothetical genes. Global expression analyses have identified 1,672 expressed hypothetical genes. Among them, 415 genes might function in a developmental stage-specific manner. Antisense strand expression and small RNA analyses have demonstrated that a high percentage of these hypothetical genes might play important roles in negatively regulating gene expression. Homologous searches against Arabidopsis (Arabidopsis thaliana), maize (Zea mays), sorghum (Sorghum bicolor), and indica rice genomes suggest that most of the hypothetical genes could be annotated from recently evolved genomic sequences. These data advance the understanding of rice hypothetical genes as being involved in lineage-specific expansion and that they function in a specific developmental stage. Our analyses also provide a valuable means to facilitate the characterization and functional annotation of hypothetical genes in other organisms.
The Magnesium-Chelatase H Subunit Binds Abscisic Acid and Functions in Abscisic Acid Signaling: New Evidence in Arabidopsis
Authors: Wu Fu-Qing , Xin Qi , Cao Zheng , Liu Zhi-Qiang , Du Shu-Yuan , Mei Chao , Zhao Chen-Xi , Wang Xiao-Fang , Shang Yi , Jiang Tao , Zhang Xiao-Feng , Yan Lu , Zhao Rui , Cui Zi-Ning , Liu Rui , Sun Hai-Li , Yang Xin-Ling , Su Zhen , Zhang Da-Peng 
Published: June 2009

AbstractUsing a newly developed abscisic acid (ABA)-affinity chromatography technique, we showed that the magnesium-chelatase H subunit ABAR/CHLH (for putative abscisic acid receptor/chelatase H subunit) specifically binds ABA through the C-terminal half but not the N-terminal half. A set of potential agonists/antagonists to ABA, including 2-trans,4-trans-ABA, gibberellin, cytokinin-like regulator 6-benzylaminopurine, auxin indole-3-acetic acid, auxin-like substance naphthalene acetic acid, and jasmonic acid methyl ester, did not bind ABAR/CHLH. A C-terminal C370 truncated ABAR with 369 amino acid residues (631–999) was shown to bind ABA, which may be a core of the ABA-binding domain in the C-terminal half. Consistently, expression of the ABAR/CHLH C-terminal half truncated proteins fused with green fluorescent protein (GFP) in wild-type plants conferred ABA hypersensitivity in all major ABA responses, including seed germination, postgermination growth, and stomatal movement, and the expression of the same truncated proteins fused with GFP in an ABA-insensitive cch mutant of the ABAR/CHLH gene restored the ABA sensitivity of the mutant in all of the ABA responses. However, the effect of expression of the ABAR N-terminal half fused with GFP in the wild-type plants was limited to seedling growth, and the restoring effect of the ABA sensitivity of the cch mutant was limited to seed germination. In addition, we identified two new mutant alleles of ABAR/CHLH from the mutant pool in the Arabidopsis Biological Resource Center via Arabidopsis (Arabidopsis thaliana) Targeting-Induced Local Lesions in Genomes. The abar-2 mutant has a point mutation resulting in the N-terminal Leu-348→Phe, and the abar-3 mutant has a point mutation resulting in the N-terminal Ser-183→Phe. The two mutants show altered ABA-related phenotypes in seed germination and postgermination growth but not in stomatal movement. These findings support the idea that ABAR/CHLH is an ABA receptor and reveal that the C-terminal half of ABAR/CHLH plays a central role in ABA signaling, which is consistent with its ABA-binding ability, but the N-terminal half is also functionally required, likely through a regulatory action on the C-terminal half.
Truffles Regulate Plant Root Morphogenesis via the Production of Auxin and Ethylene
Authors: Splivallo Richard , Fischer Urs , Göbel Cornelia , Feussner Ivo , Karlovsky Petr 
Published: June 2009

AbstractTruffles are symbiotic fungi that form ectomycorrhizas with plant roots. Here we present evidence that at an early stage of the interaction, i.e. prior to physical contact, mycelia of the white truffle Tuber borchii and the black truffle Tuber melanopsorum induce alterations in root morphology of the host Cistus incanus and the nonhost Arabidopsis (Arabidopsis thaliana; i.e. primary root shortening, lateral root formation, root hair stimulation). This was most likely due to the production of indole-3-acetic acid (IAA) and ethylene by the mycelium. Application of a mixture of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid and IAA fully mimicked the root morphology induced by the mycelium for both host and nonhost plants. Application of the single hormones only partially mimicked it. Furthermore, primary root growth was not inhibited in the Arabidopsis auxin transport mutant aux1-7 by truffle metabolites while root branching was less effected in the ethylene-insensitive mutant ein2-LH. The double mutant aux1-7;ein2-LH displayed reduced sensitivity to fungus-induced primary root shortening and branching. In agreement with the signaling nature of truffle metabolites, increased expression of the auxin response reporter DR5∷GFP in Arabidopsis root meristems subjected to the mycelium could be observed, confirming that truffles modify the endogenous hormonal balance of plants. Last, we demonstrate that truffles synthesize ethylene from l-methionine probably through the α-keto-γ-(methylthio)butyric acid pathway. Taken together, these results establish the central role of IAA and ethylene as signal molecules in truffle/plant interactions.
Level-raising for Saito–Kurokawa forms
Authors: Sorensen Claus M. 
Published: June 2009

AbstractThis paper provides congruences between unstable and stable automorphic forms for the symplectic similitude group GSp(4). More precisely, we raise the level of certain CAP representations Π arising from classical modular forms. We first transfer Π toπon a suitable inner formG; this is achieved byθ-lifting. Forπ, we prove a precise level-raising result that is inspired by the work of Bellaiche and Clozel and which relies on computations of Schmidt. We thus obtain a$\tilde {\pi }$congruent toπ, with a local component that is irreducibly induced from an unramified twist of the Steinberg representation of the Klingen parabolic. To transfer$\tilde {\pi }$back to GSp(4), we use Arthur’s stable trace formula. Since$\tilde {\pi }$has a local component of the above type, all endoscopic error terms vanish. Indeed, by results due to Weissauer, we only need to show that such a component does not participate in theθ-correspondence with any GO(4); this is an exercise in using Kudla’s filtration of the Jacquet modules of the Weil representation. We therefore obtain a cuspidal automorphic representation$\tilde {\Pi }$of GSp(4), congruent to Π, which is neither CAP nor endoscopic. It is crucial for our application that we can arrange for$\tilde {\Pi }$to have vectors fixed by the non-special maximal compact subgroups at all primes dividingN. SinceGis necessarily ramified at some primer, we have to show a non-special analogue of the fundamental lemma atr. Finally, we give an application of our main result to the Bloch–Kato conjecture, assuming a conjecture of Skinner and Urban on the rank of the monodromy operators at the primes dividingN.
Fully Lagrangian Modeling of Dynamics of MEMS With Thin Beams—Part II: Damped Vibrations
Authors: Ghosh Ranajay , Mukherjee Subrata 
Published: June 2009

AbstractMicro-electro-mechanical systems (MEMS) often use beam or plate shaped conductors that are very thin with h/L≈O(10−2–10−3) (in terms of the thickness h and length L of a beam or side of a square plate). A companion paper (Ghosh and Mukherjee, 2009, “Fully Lagrangian Modeling of Dynamics of MEMS With Thin Beams—Part I: Undamped Vibrations,” ASME J. Appl. Mech., 76, p. 051007) addresses the coupled electromechanical problem of MEMS devices composed of thin beams. A new boundary element method (BEM) is coupled with the finite element method (FEM) by Ghosh and Mukherjee, and undamped vibrations are addressed there. The effect of damping due to the surrounding fluid modeled as Stokes flow is included in the present paper. Here, the elastic field modeled by the FEM is coupled with the applied electric field and the fluid field, both modeled by the BEM. As for the electric field, the BEM is adapted to efficiently handle narrow gaps between thin beams for the Stokes flow problem. The coupling of the various fields is carried out using a Newton scheme based on a Lagrangian description of the various domains. Numerical results are presented for damped vibrations of MEMS beams.
Confined Thin Film
Delamination in the Presence of Intersurface Forces With Finite Range and
Magnitude
Authors: Wan Kai-tak , Julien Scott
E. 
Published: June 2009

Abstract
A circular membrane clamped at the periphery is allowed to adhere to or to delaminate from a planar surface of a cylindrical punch in the presence of intersurface forces with finite range and magnitude. Assuming a uniform disjoining pressure within the cohesive zone at the delamination front, the adhesion-delamination mechanics is obtained by a thermodynamic energy balance. Interrelations between the instantaneous applied load, punch displacement, and contact circle, and the resulting critical thresholds of “pinch-off,” “pull-off,” and “pull-in” are derived from the first principles. Two limiting cases are obtained: (i) intersurface force with long range and small magnitude in reminiscence of the classical Derjaguin–Muller–Toporov (DMT) model and (ii) short range and large magnitude alluding to the Johnson–Kendall–Roberts (JKR) model. The DMT-JKR transitional behavior has significant impacts on adhesion measurements, micro-electromechanical systems, and life-sciences.
Finite Element
Analysis of Plugging Failure in Steel Plates Struck by Blunt
Projectiles
Authors: Kane A. , Børvik T. , Hopperstad O.
S. , Langseth M. 
Published: June 2009

Abstract
In this paper, the influence of mesh sensitivity on the fracture predictions during penetration and perforation of hardened blunt-nose cylindrical steel projectiles in plates of Weldox 460E, Weldox 700E, and Weldox 900E steel has been studied. The main objective is to try to describe the experimentally obtained trend of a decrease in ballistic limit velocity with increased target strength when the plates are impacted by blunt projectiles. This behavior is due to the occurrence of highly localized shear bands as the target strength increases. The impact tests are analyzed using the explicit solver of a nonlinear finite element code. A thermoelastic-thermoviscoplastic constitutive model with coupled or uncoupled ductile damage was used in the simulations. It was found that the residual velocity continuously increases when the element size is decreased from 125 μm to 15 μm in the shear zone, and that this increase is significantly stronger for impact velocities close to the ballistic limit. The ballistic limit decreases by up to 25% when the size of the element is decreased from 125 μm to 30 μm; the decrease being somewhat greater for the two steels with the highest strength. Even with the finest mesh, the experimental trend of a decreasing ballistic limit with increasing target strength was not predicted in the simulations, neither with coupled nor uncoupled damage. Nonlocal simulations based on smoothing of the damage and temperature fields, which are the two variables causing the softening, were carried out for the Weldox steels and a mesh size of 30 μm. These simulations indicate a reduction in the mesh sensitivity for both the coupled and uncoupled damage approaches when nonlocal averaging is employed.
The Influence of
Material Properties and Confinement on the Dynamic Penetration of Alumina by Hard
Spheres
Authors: Wei Z. , Evans A.
G. , Deshpande V. S. 
Published: June 2009

Abstract
The ability of a ceramic to resist penetration by projectiles depends, in a coupled manner, on its confinement and its mechanical properties. In order to explore the fundamental inter-relationships, a simulation protocol is required that permits the microstructure and normative properties (hardness and toughness) to be used as input parameters. Potential for attaining this goal has been provided by a recent constitutive model, devised by Deshpande and Evans (DE) [2008, “Inelastic Deformation and Energy Dissipation in Ceramics: A Mechanics-Based Dynamic Constitutive Model,” J. Mech. Phys. Solids, 56, pp. 3077–3100] that incorporates the contributions to the inelastic strain from both plasticity and microcracking. Before implementing the DE model, various comparisons with experimental measurements are required. Previously, the model has been successfully used to predict the quasistatic penetration of alumina by hard spheres. In the present assessment, simulations of the dynamic penetration of confined alumina cylinders are presented as a function of microstructure and properties and compared with literature measurements of the ballistic mass efficiency. It is shown that the model replicates the measured trends with hardness and grain size. Motivated by this comparison, further simulations are used to gain a basic understanding of the respective roles of plasticity and microcracking on penetration and to elucidate the phenomena governing projectile defeat.
Beneficial Effects of a Combination of Korean Red Ginseng and Highly Active Antiretroviral Therapy in Human Immunodeficiency Virus Type 1-Infected Patients
Authors: Sung Heungsup , Jung You-Sun , Cho Young-Keol 
Published: June 2009

ABSTRACT

To determine whether Korean red ginseng (KRG) has beneficial effects on human immunodeficiency virus type 1 (HIV-1)-infected patients administered highly active antiretroviral therapy (HAART), we analyzed the CD4 T-cell count, viral load, and resistance mutations to HAART in 46 individuals. Thirteen patients harbored resistance mutations at baseline. The study population was divided into two groups: specifically, a group treated with a combination of HAART plus KRG (23 patients) and a group treated with HAART alone (23 patients). The annual increase in CD4 T-cell count in the combination group was significantly higher than that in the group treated with HAART alone (
P
< 0.05). Overall, 21 patients harbored resistance mutations after 3 years of therapy. Following exclusion of 13 patients displaying baseline resistance mutations, 7.1% of patients (1/14) in the combination group and 42.1% (8/19) in the HAART group were identified with resistance mutations. One patient with baseline resistance mutations in the combination group did not display resistance mutations 3 years after HAART therapy. High-level resistance mutations were significantly lower in the combination group than in the group treated with HAART alone. Five patients showed no improvement in viral copy number (26.3% [5/19]) in the combination group and 9 (45.0% [9/20]) showed no improvement in the HAART-only group. Our data support the clinical utility of KRG intake during HAART therapy.
Statistical Approach To Estimate Vaccinia-Specific Neutralizing Antibody Titers Using a High-Throughput Assay
Authors: Kennedy Richard , Pankratz V. Shane , Swanson Eric , Watson David , Golding Hana , Poland Gregory A. 
Published: June 2009

ABSTRACT
Because of the bioterrorism threat posed by agents such as variola virus, considerable time, resources, and effort have been devoted to biodefense preparation. One avenue of this research has been the development of rapid, sensitive, high-throughput assays to validate immune responses to poxviruses. Here we describe the adaptation of a β-galactosidase reporter-based vaccinia virus neutralization assay to large-scale use in a study that included over 1,000 subjects. We also describe the statistical methods involved in analyzing the large quantity of data generated. The assay and its associated methods should prove useful tools in monitoring immune responses to next-generation smallpox vaccines, studying poxvirus immunity, and evaluating therapeutic agents such as vaccinia virus immune globulin.
Detection of Cryptic Genospecies Misidentified as
Haemophilus influenzae
in Routine Clinical Samples by Assessment of Marker Genes
fucK
,
hap
, and
sodC
Authors: Nørskov-Lauritsen Niels 
Published: June 2009

ABSTRACT

Clinical isolates of
Haemophilus influenzae
were assessed for the presence of
fucK
,
hap
, and
sodC
by hybridization with gene-specific probes, and isolates diverging from the expected
H. influenzae
genotype were characterized by phenotype and 16S rRNA gene sequencing. Two of 480 isolates were finally classified as variant strains (“nonhemolytic
Haemophilus haemolyticus
”).
Assessment of the Ability of a Fourth-Generation Immunoassay for Human Immunodeficiency Virus (HIV) Antibody and p24 Antigen To Detect both Acute and Recent HIV Infections in a High-Risk Setting
Authors: Pandori Mark W. , Hackett John , Louie Brian , Vallari Ana , Dowling Teri , Liska Sally , Klausner Jeffrey D. 
Published: June 2009

ABSTRACT
An immunoassay (IA) that simultaneously detects both antibody to human immunodeficiency virus (HIV) and HIV p24 antigen (Architect HIV Ag/Ab Combo) was evaluated for its ability to detect HIV infection by using a panel of specimens collected from individuals recently infected with HIV type 1 (HIV-1). This IA was found to be capable of detecting the majority (89%) of infections, including 80% of those considered acute infections based on the presence of HIV RNA and the lack of detectable antibody to HIV. Substantial improvements in detection of recent infections by the Architect HIV Ag/Ab Combo relative to previous generations of IAs as well as the capacity to detect acute infections have important implications for HIV prevention strategies.
CagA and VacA Polymorphisms Do Not Correlate with Severity of Histopathological Lesions inHelicobacter pylori-Infected Greek Children
Authors: Sgouras Dionyssios N. , Panayotopoulou Effrosini G. , Papadakos Konstantinos , Martinez-Gonzalez Beatriz , Roumbani Aikaterini , Panayiotou Joanna , vanVliet-Constantinidou Cathy , Mentis Andreas F. , Roma-Giannikou Eleftheria 
Published: June 2009

ABSTRACTThe presence of various numbers of EPIYA tyrosine phosphorylation motifs in the CagA protein ofHelicobacter pylorihas been suggested to contribute to pathogenesis in adults. In this prospective study, we characterizedH. pyloriisolates from symptomatic children, with reference to the diversity of functional EPIYA motifs in the CagA protein andvacAisotypes, and assessed the potential correlation with the histopathological manifestations of the infection. We analyzed 105H. pyloriisolates from 98 children and determined the diversity of EPIYA motifs in CagA by amplification and sequencing of the 3′ variable region of thecagAgene as well asvacAisotypes for the signal, middle, and intermediate regions. CagA phosphorylation and levels of secreted IL-8 were determined following in vitro infection of AGS gastric epithelial cells. Histopathological evaluation ofH. pyloricolonization, activity, and severity of the associated gastritis was performed according to the updated Sydney criteria. EPIYA A (GLKN[ST]EPIYAKVNKKK), EPIYA B (Q[V/A]ASPEPIY[A/T]QVAKKVNAKI), and EPIYA C (RS[V/A]SPEPIYATIDDLG) motifs were detected in the ABC (46.6%) and ABCC (17.1%) combinations. No isolates harboring more than two EPIYA C motifs in CagA were found. The presence of isogenic strains with variable numbers of CagA EPIYA C motifs within the same patient was detected in seven cases. Occurrence of increasing numbers of EPIYA C motifs correlated strongly with presence of a high-vacuolation (s1 or s2/i1/m1) phenotype and age. A weak positive correlation was observed between vacuolatingvacAgenotypes and presence of nodular gastritis. However, CagA- and VacA-dependent pathogenicities were not found to contribute to severity of histopathology manifestations inH. pylori-infected children.
Simple, Accurate, Serotype-Specific PCR Assay To Differentiate
Streptococcus pneumoniae
Serotypes 6A, 6B, and 6C
Authors: Jin Ping , Xiao Meng , Kong Fanrong , Oftadeh Shahin , Zhou Fei , Liu Chunyi , Gilbert Gwendolyn L. 
Published: June 2009

ABSTRACT

In this study, we developed a simple, reliable, serotype-specific PCR method to differentiate
Streptococcus pneumoniae
serotypes 6A, 6B, and 6C. It was more efficient and practical than the assays currently being used to identify serotypes 6A, 6B, and 6C. Of 120 selected serogroup 6 isolates from subjects with invasive (
n
= 101) and noninvasive (
n
= 19) pneumococcal disease, most of which were collected after 2003 in New South Wales, 45 had been identified as 6A and 75 had been identified as 6B by the Quellung reaction. PCR analysis confirmed the results for serotype 6B isolates and identified two different subtypes. Fourteen of 45 isolates that had been identified as serotype 6A actually belonged to serotype 6C.
Mycobacterium microti
: More Diverse than Previously Thought
Authors: Smith N. H. , Crawshaw T. , Parry J. , Birtles R. J. 
Published: June 2009

ABSTRACT

Mycobacterium microti
is a member of the
Mycobacterium tuberculosis
complex of bacteria. This species was originally identified as a pathogen of small rodents and shrews and was associated with limited diversity and a much reduced spoligotype pattern. More recently, specific deletions of chromosomal DNA have been shown to define this group of organisms, which can be identified by the absence of chromosomal region RD1
mic
. We describe here the molecular characteristics of 141 strains of the
Mycobacterium tuberculosis
complex isolated in Great Britain over a 14-year period. All strains have characteristic loss of some spoligotype spacers and characteristic alleles at the ETR-E and ETR-F variable-number tandem-repeat (VNTR) loci, and a sample of these strains was deleted for regions RD7, RD9, and RD1
mic
but intact for regions RD4 and RD12. We therefore identified these strains as
M. microti
and show that they have much more diverse spoligotype patterns and VNTR types than previously thought. The most common source of these strains was domestic cats, and we show that the molecular types of
M. microti
are geographically localized in the same way that molecular types of
Mycobacterium bovis
are geographically localized in cattle in the United Kingdom. We describe the pathology of
M. microti
infection in cats and suggest that the feline disease is a spillover from a disease maintained in an unknown wild mammal, probably field voles. The location of the cats with
M. microti
infection suggests that they do not overlap geographically with the strains of
Mycobacterium bovis
in Great Britain.
Evaluation of New Preanalysis Sample Treatment Tools and DNA Isolation Protocols To Improve Bacterial Pathogen Detection in Whole Blood
Authors: Hansen Wendy L. J. , Bruggeman Cathrien A. , Wolffs Petra F. G. 
Published: June 2009

ABSTRACT
Two novel preanalysis sample treatment tools were evaluated in combination with four DNA extraction kits for the selective isolation of bacterial DNA from whole blood. The combination of performing a preanalysis sample treatment and using a larger sample volume increased the detection limit to 50 CFU per ml.