Measurement of the Forward-Backward Charge Asymmetry in Top-Quark Pair Production in Proton-Antiproton Collisions at D0

A measurement of the forward-backward charge asymmetry in top-antitop (t\bar{t}) pair production in proton-antiproton (p\bar{p}) collisions is presented. The asymmetry is measured for different jet multiplicities in the lepton+jets final state on 0.9 fb^{-1} of data collected by the D0 experiment at the Fermilab Tevatron Collider. The result is sensitive to new physics, which is demonstrated by setting an upper limit on t\bar{t} production via heavy neutral gauge bosons (Z^{\prime}).Comment: Presented at 16th International Conference on Supersymmetry and the Unification of Fundamental Interactions (SUSY08), Seoul, Korea, 16-21 Jun 200

Metal-Insulator Phase Transition in Quasi-One-Dimensional VO₂Structures

The metal-insulator transition (MIT) in strongly correlated oxides has attracted considerable attention from both theoretical and experimental researchers. Among the strongly correlated oxides, vanadium dioxide (VO2) has been extensively studied in the last decade because of a sharp, reversible change in its optical, electrical, and magnetic properties at approximately 341 K, which would be possible and promising to develop functional devices with advanced technology by utilizing MITs. However, taking the step towards successful commercialization requires the comprehensive understanding of MIT mechanisms, enabling us to manipulate the nature of transitions. In this regard, recently, quasi-one-dimensional (quasi-1D) VO2structures have been intensively investigated due to their attractive geometry and unique physical properties to observe new aspects of transitions compared with their bulk counterparts. Thus, in this review, we will address recent research progress in the development of various approaches for the modification of MITs in quasi-1D VO2structures. Furthermore, we will review recent studies on realizing novel functional devices based on quasi-1D VO2structures for a wide range of applications, such as a gas sensor, a flexible strain sensor, an electrical switch, a thermal memory, and a nonvolatile electrical memory with multiple resistance.</jats:p

Carpal Tunnel Syndrome Caused by Space Occupying Lesions

PURPOSE: To evaluate the diagnosis and treatment of the carpal tunnel syndrome (CTS) due to space occupying lesions (SOL). MATERIALS and METHODS: Eleven patients and 12 cases that underwent surgery for CTS due to SOL were studied retrospectively. We excluded SOL caused by bony lesions, such as malunion of distal radius fracture, volar lunate dislocation, etc. the average age was 51 years. There were 3 men and 8 women. Follow-up period was 12 to 40 months with an average of 18 months. the diagnosis of CTS was made clinically and electrophysiologically. in patients with swelling or tenderness on the area of wrist flexion creases, magnetic resonance imaging (MRI) and/or computed tomogram (CT) were additionally taken as well as the carpal tunnel view. We performed conventional open transverse carpal ligament release and removal of SOL. RESULTS: the types of lesion confirmed by pathologic examination were; tuberculosis tenosynovitis in 3 cases, nonspecific tenosynovitis in 2 cases, and gout in one case. Other SOLs were tumorous condition in five cases, and abnormal palmaris longus hypertrophy in 1 case. Tumorous conditions were due to calcifying mass in 4 cases and ganglion in 1 case. Following surgery, all cases showed alleviation of symptom without recurrence or complications. CONCLUSION: in cases with swelling or tenderness on the area of wrist flexion creases, it is important to obtain a carpal tunnel view, and MRI and/or CT should be supplemented in order to rule out SOLs around the carpal tunnel, if necessary.ope

Phylogenomics databases for facilitating functional genomics in rice

The completion of whole genome sequence of rice (Oryza sativa) has significantly accelerated functional genomics studies. Prior to the release of the sequence, only a few genes were assigned a function each year. Since sequencing was completed in 2005, the rate has exponentially increased. As of 2014, 1,021 genes have been described and added to the collection at The Overview of functionally characterized Genes in Rice online database (OGRO). Despite this progress, that number is still very low compared with the total number of genes estimated in the rice genome. One limitation to progress is the presence of functional redundancy among members of the same rice gene family, which covers 51.6 % of all non-transposable element-encoding genes. There remain a significant portion or rice genes that are not functionally redundant, as reflected in the recovery of loss-of-function mutants. To more accurately analyze functional redundancy in the rice genome, we have developed a phylogenomics databases for six large gene families in rice, including those for glycosyltransferases, glycoside hydrolases, kinases, transcription factors, transporters, and cytochrome P450 monooxygenases. In this review, we introduce key features and applications of these databases. We expect that they will serve as a very useful guide in the post-genomics era of research

Localizing Gravitational Wave Sources with Single-Baseline Atom Interferometers

Localizing sources on the sky is crucial for realizing the full potential of gravitational waves for astronomy, astrophysics, and cosmology. We show that the mid-frequency band, roughly 0.03 to 10 Hz, has significant potential for angular localization. The angular location is measured through the changing Doppler shift as the detector orbits the Sun. This band maximizes the effect since these are the highest frequencies in which sources live several months. Atom interferometer detectors can observe in the mid-frequency band, and even with just a single baseline can exploit this effect for sensitive angular localization. The single baseline orbits around the Earth and the Sun, causing it to reorient and change position significantly during the lifetime of the source, and making it similar to having multiple baselines/detectors. For example, atomic detectors could predict the location of upcoming black hole or neutron star merger events with sufficient accuracy to allow optical and other electromagnetic telescopes to observe these events simultaneously. Thus, mid-band atomic detectors are complementary to other gravitational wave detectors and will help complete the observation of a broad range of the gravitational spectrum.Comment: 16 pages, 3 figures, 2 table

Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research

Glycoside hydrolases (GH) catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/). This database integrates multiple data types including the structural features, orthologous relationships, mutant availability, and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification

The Rice Oligonucleotide Array Database: an atlas of rice gene expression

BACKGROUND: Microarray technologies facilitate high-throughput gene expression analysis. However, the diversity of platforms for rice gene expression analysis hinders efficient analysis. Tools to broadly integrate microarray data from different platforms are needed. RESULTS: In this study, we developed the Rice Oligonucleotide Array Database (ROAD,http://www.ricearray.org) to explore gene expression across 1,867 publicly available rice microarray hybridizations. The ROAD’s user-friendly web interface and variety of visualization tools facilitate the extraction of gene expression profiles using gene and microarray element identifications. The ROAD supports meta-analysis of genes expressed in different tissues and at developmental stages. Co-expression analysis tool provides information on co-regulation between genes under general, abiotic and biotic stress conditions. Additionally, functional analysis tools, such as Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology, are embedded in the ROAD. These tools facilitate the identification of meaningful biological patterns in a list of query genes. CONCLUSIONS: The Rice Oligonucleotide Array Database provides comprehensive gene expression profiles for all rice genes, and will be a useful resource for researchers of rice and other grass species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1939-8433-5-17) contains supplementary material, which is available to authorized users

bZIPDB : A database of regulatory information for human bZIP transcription factors

<p>Abstract</p> <p>Background</p> <p>Basic region-leucine zipper (bZIP) proteins are a class of transcription factors (TFs) that play diverse roles in eukaryotes. Malfunctions in these proteins lead to cancer and various other diseases. For detailed characterization of these TFs, further public resources are required.</p> <p>Description</p> <p>We constructed a database, designated bZIPDB, containing information on 49 human bZIP TFs, by means of automated literature collection and manual curation. bZIPDB aims to provide public data required for deciphering the gene regulatory network of the human bZIP family, e.g., evaluation or reference information for the identification of regulatory modules. The resources provided by bZIPDB include (1) protein interaction data including direct binding, phosphorylation and functional associations between bZIP TFs and other cellular proteins, along with other types of interactions, (2) bZIP TF-target gene relationships, (3) the cellular network of bZIP TFs in particular cell lines, and (4) gene information and ontology. In the current version of the database, 721 protein interactions and 560 TF-target gene relationships are recorded. bZIPDB is annually updated for the newly discovered information.</p> <p>Conclusion</p> <p>bZIPDB is a repository of detailed regulatory information for human bZIP TFs that is collected and processed from the literature, designed to facilitate analysis of this protein family. bZIPDB is available for public use at <url>http://biosoft.kaist.ac.kr/bzipdb</url>.</p

TAZ Suppresses NFAT5 Activity through Tyrosine Phosphorylation

Transcriptional coactivator with PDZ-binding motif (TAZ) physically interacts with a variety of transcription factors and modulates their activities involved in cell proliferation and mesenchymal stem cell differentiation. TAZ is highly expressed in the kidney, and a deficiency of this protein results in multiple renal cysts and urinary concentration defects; however, the molecular functions of TAZ in renal cells remain largely unknown. In this study, we examined the effects of osmotic stress on TAZ expression and activity in renal cells. We found that hyperosmotic stress selectively increased protein phosphorylation at tyrosine 316 of TAZ and that this was enhanced by c-Abl activation in response to hyperosmotic stress. Interestingly, phosphorylated TAZ physically interacted with nuclear factor of activated T cells 5 (NFAT5), a major osmoregulatory transcription factor, and subsequently suppressed DNA binding and transcriptional activity of NFAT5. Furthermore, TAZ deficiency elicited an increase in NFAT5 activity in vitro and in vivo, which then reverted to basal levels following restoration of wild-type TAZ but not mutant TAZ (Y316F). Collectively, the data suggest that TAZ modulates cellular responses to hyperosmotic stress through fine-tuning of NFAT5 activity via tyrosine phosphorylation.open3