593 research outputs found

    VNTRDB: a bacterial variable number tandem repeat locus database

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    Variable number tandem repeat-PCR (VNTR-PCR) is a novel method developed for molecular typing of microorganisms. This method has proven useful in epidemiological studies in medical microbiology. Although hundreds of bacterial genomes have been sequenced, variable number tandem repeats (TRs) derived from comparative genome analyses are scarce. This may hamper their application to the surveillance of bacteria in molecular epidemiology. Here, we present a freely accessible variable number tandem repeat database (VNTRDB) that is intended to be a resource for helping in the discovery of putatively polymorphic tandem repeat loci and to aid with assay design by providing the flanking sequences that can be used in subsequent PCR primer design. In order to reveal possible polymorphism, each TR locus was obtained by comparing the sequences between different sets of bacterial genera, species or strains. Through this comparison, TRs which are unique to a genus can also be identified. Moreover, a visualization tool is provided to ensure that the copy number and locus length of repeats are correct. The VNTRDB is available at

    Domino Rh-catalyzed hydroformylation–doublecyclization of o-amino cinnamyl derivatives:applications to the formal total syntheses ofphysostigmine and physovenine

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    A parallel, versatile and efficient route to synthesis of pyrrolidinoindoline and tetrahydrofuranoindoline alkaloids from cinnamyl derivatives has been developed, featuring a domino Rh-catalyzed hydroformylation–double cyclization sequence. This method can be applied to the syntheses of anti-Alzheimer drugs such as physostigmine and physovenine

    A Multichannel MAC Protocol for IoT-enabled Cognitive Radio Ad Hoc Networks

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    Cognitive radios have the ability to dynamically sense and access the wireless spectrum, and this ability is a key factor in successfully building Internet-of-Things (IoT)-enabled mobile ad hoc networks. This paper proposes a contention-free token-based multichannel MAC protocol for IoT-enabled Cognitive Radio Ad Hoc Networks (CRAHNs). In this, secondary users of CRAHNs detect activity on the wireless spectrum and then access idle channels licensed by primary users. CRAHNs are divided into clusters, and the channel to use for transmission is determined dynamically from the probability of finding idle primary-user channels. The token-based MAC window size is adaptive, with adjustment according to actual traffic, which reduces both end-to-end MAC contention delay and energy consumption. High throughput and spatial reuse of channels can also be achieved using a dynamic control channel and dynamic schemes for contention windows. We performed extensive simulations to verify that the proposed method can achieve better performance in mobile CRAHNs than other MAC schemes can

    The Liquid Sensor Using Thin Film Bulk Acoustic Resonator with C-Axis Tilted AlN Films

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    Dual-mode thin film bulk acoustic resonator (TFBAR) devices are fabricated with c-axis tilted AlN films. To fabricate dual-mode TFBAR devices, the off-axis RF magnetron sputtering method for the growth of tilted piezoelectric AlN thin films is adopted. In this report, the AlN thin films are deposited with tilting angles of 15° and 23°. The frequency response of the TFBAR device with 23° tilted AlN thin film is measured to reveal its ability to provide dual-mode resonance. The sensitivities of the longitudinal and shear modes to mass loading are calculated to be 2295 Hz cm2/ng and 1363 Hz cm2/ng with the mechanical quality factors of 480 and 287, respectively. The sensitivities of the longitudinal and shear modes are calculated to be 0 and 15 Hz cm2/μg for liquid loading

    Perforated Sigmoid Colon Cancer within an Irreducible Inguinal Hernia: a Case Report

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    A perforated sigmoid colon cancer within an inguinal hernia is extremely rare. This unexpected finding is usually discovered during surgery and causes an unavoidable septic evolution. Here, we describe the case of an 84-year-old man who presented with fever, abdominal distension, and a painful, enlarged, left scrotum. A CT showed a left, incarcerated, inguinal hernia containing a perforated sigmoid adenocarcinoma (which was confirmed by histopathology). The possibility of an irreducible inguinal hernia in association with perforated sigmoid colon cancer should be considered in the array of diagnoses. A pre-operative CT scan would be helpful in facilitating an accurate diagnosis

    High pressure evolution of Fe2_{2}O3_{3} electronic structure revealed by X-ray absorption

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    We report the first high pressure measurement of the Fe K-edge in hematite (Fe2_2O3_3) by X-ray absorption spectroscopy in partial fluorescence yield geometry. The pressure-induced evolution of the electronic structure as Fe2_2O3_3 transforms from a high-spin insulator to a low-spin metal is reflected in the x-ray absorption pre-edge. The crystal field splitting energy was found to increase monotonically with pressure up to 48 GPa, above which a series of phase transitions occur. Atomic multiplet, cluster diagonalization, and density-functional calculations were performed to simulate the pre-edge absorption spectra, showing good qualitative agreement with the measurements. The mechanism for the pressure-induced phase transitions of Fe2_2O3_3 is discussed and it is shown that ligand hybridization significantly reduces the critical high-spin/low-spin pressure.Comment: 5 pages, 4 figures and 1 tabl

    Inferring nonneutral evolution from contrasting patterns of polymorphisms and divergences in different protein coding regions of enterovirus 71 circulating in Taiwan during 1998-2003

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    <p>Abstract</p> <p>Background</p> <p>Enterovirus (EV) 71 is one of the common causative agents for hand, foot, and, mouth disease (HFMD). In recent years, the virus caused several outbreaks with high numbers of deaths and severe neurological complications. Despite the importance of these epidemics, several aspects of the evolutionary and epidemiological dynamics, including viral nucleotide variations within and between different outbreaks, rates of change in immune-related structural regions vs. non-structural regions, and forces driving the evolution of EV71, are still not clear.</p> <p>Results</p> <p>We sequenced four genomic segments, i.e., the 5' untranslated region (UTR), VP1, 2A, and 3C, of 395 EV71 viral strains collected from 1998 to 2003 in Taiwan. The phylogenies derived from different genomic segments revealed different relationships, indicating frequent sequence recombinations as previously noted. In addition to simple recombinations, exchanges of the P1 domain between different species/genotypes of human enterovirus species (HEV)-A were repeatedly observed. Contrasting patterns of polymorphisms and divergences were found between structural (VP1) and non-structural segments (2A and 3C), i.e., the former was less polymorphic within an outbreak but more divergent between different HEV-A species than the latter two. Our computer simulation demonstrated a significant excess of amino acid replacements in the VP1 region implying its possible role in adaptive evolution. Between different epidemic seasons, we observed high viral diversity in the epidemic peaks followed by severe reductions in diversity. Viruses sampled in successive epidemic seasons were not sister to each other, indicating that the annual outbreaks of EV71 were due to genetically distinct lineages.</p> <p>Conclusions</p> <p>Based on observations of accelerated amino acid changes and frequent exchanges of the P1 domain, we propose that positive selection and subsequent frequent domain shuffling are two important mechanisms for generating new genotypes of HEV-A. Our viral dynamics analysis suggested that the importation of EV71 from surrounding areas likely contributes to local EV71 outbreaks.</p

    Be Stars in the Open Cluster NGC 6830

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    We report the discovery of 2 new Be stars, and re-identify one known Be star in the open cluster NGC 6830. Eleven H-alpha emitters were discovered using the H-alpha imaging photometry of the Palomar Transient Factory Survey. Stellar membership of the candidates was verified with photometric and kinematic information using 2MASS data and proper motions. The spectroscopic confirmation was carried out by using the Shane 3-m telescope at Lick observatory. Based on their spectral types, three H-alpha emitters were confirmed as Be stars with H-alpha equivalent widths > -10 Angstrom. Two objects were also observed by the new spectrograph SED-Machine on the Palomar 60 inch Telescope. The SED-Machine results show strong H-alpha emission lines, which are consistent with the results of the Lick observations. The high efficiency of the SED-Machine can provide rapid observations for Be stars in a comprehensive survey in the future.Comment: 11 pages, 8 figures, AJ in pres
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