Molecular signature of clinical severity in recovering patients with severe acute respiratory syndrome coronavirus (SARS-CoV)

BACKGROUND: Severe acute respiratory syndrome (SARS), a recent epidemic human disease, is caused by a novel coronavirus (SARS-CoV). First reported in Asia, SARS quickly spread worldwide through international travelling. As of July 2003, the World Health Organization reported a total of 8,437 people afflicted with SARS with a 9.6% mortality rate. Although immunopathological damages may account for the severity of respiratory distress, little is known about how the genome-wide gene expression of the host changes under the attack of SARS-CoV. RESULTS: Based on changes in gene expression of peripheral blood, we identified 52 signature genes that accurately discriminated acute SARS patients from non-SARS controls. While a general suppression of gene expression predominated in SARS-infected blood, several genes including those involved in innate immunity, such as defensins and eosinophil-derived neurotoxin, were upregulated. Instead of employing clustering methods, we ranked the severity of recovering SARS patients by generalized associate plots (GAP) according to the expression profiles of 52 signature genes. Through this method, we discovered a smooth transition pattern of severity from normal controls to acute SARS patients. The rank of SARS severity was significantly correlated with the recovery period (in days) and with the clinical pulmonary infection score. CONCLUSION: The use of the GAP approach has proved useful in analyzing the complexity and continuity of biological systems. The severity rank derived from the global expression profile of significantly regulated genes in patients may be useful for further elucidating the pathophysiology of their disease

Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

<p>Abstract</p> <p>Background</p> <p>The black tiger shrimp (<it>Penaeus monodon</it>) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the <it>P. monodon </it>genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the <it>P. monodon </it>genome were obtained for repetitive and protein-coding sequence analyses.</p> <p>Results</p> <p>We found that microsatellite sequences were highly abundant in the <it>P. monodon </it>genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, <it>via </it>self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, <it>i.e</it>., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the <it>P. monodon </it>genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the <it>P. monodon </it>genome.</p> <p>Conclusions</p> <p>The redundancy of various repeat types in the <it>P. monodon </it>genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.</p

Search for eccentric black hole coalescences during the third observing run of LIGO and Virgo

Despite the growing number of confident binary black hole coalescences observed through gravitational waves so far, the astrophysical origin of these binaries remains uncertain. Orbital eccentricity is one of the clearest tracers of binary formation channels. Identifying binary eccentricity, however, remains challenging due to the limited availability of gravitational waveforms that include effects of eccentricity. Here, we present observational results for a waveform-independent search sensitive to eccentric black hole coalescences, covering the third observing run (O3) of the LIGO and Virgo detectors. We identified no new high-significance candidates beyond those that were already identified with searches focusing on quasi-circular binaries. We determine the sensitivity of our search to high-mass (total mass M&gt;70 M⊙) binaries covering eccentricities up to 0.3 at 15 Hz orbital frequency, and use this to compare model predictions to search results. Assuming all detections are indeed quasi-circular, for our fiducial population model, we place an upper limit for the merger rate density of high-mass binaries with eccentricities 0&lt;e≤0.3 at 0.33 Gpc−3 yr−1 at 90\% confidence level

Ultralight vector dark matter search using data from the KAGRA O3GK run

Among the various candidates for dark matter (DM), ultralight vector DM can be probed by laser interferometric gravitational wave detectors through the measurement of oscillating length changes in the arm cavities. In this context, KAGRA has a unique feature due to differing compositions of its mirrors, enhancing the signal of vector DM in the length change in the auxiliary channels. Here we present the result of a search for U(1)B−L gauge boson DM using the KAGRA data from auxiliary length channels during the first joint observation run together with GEO600. By applying our search pipeline, which takes into account the stochastic nature of ultralight DM, upper bounds on the coupling strength between the U(1)B−L gauge boson and ordinary matter are obtained for a range of DM masses. While our constraints are less stringent than those derived from previous experiments, this study demonstrates the applicability of our method to the lower-mass vector DM search, which is made difficult in this measurement by the short observation time compared to the auto-correlation time scale of DM

Low-Temperature Transport Study of Transition Metal Dichalcogenide Heterostructures

The electron-electron interaction is the origin of many interesting phenomena in condensed matter. These phenomena post challenges to theoretical physics and can lead to important future applications. Transition metal dichalcogenide heterostructures provide excellent platforms to study these phenomena because of the two-dimensional nature, large effective mass and tunable bandwidth with moiré potential. As electron bands become narrower such that the Coulomb interaction energy becomes comparable to the bandwidth, interactions can drive new quantum phases. This dissertation describes the realization of this platform and probing of correlated phenomena with low- temperature transport measurements. As the first step, the electrical contact problem of few-layer transition metal dichalcogenides, which prohibits low-temperature transport measurements, needs to be solved. Two different contact schemes have been used to attack this problem. For p-type transition metal dichalcogenide, prepatterned platinum is used to bottom contact transition metal dichalcogenides. This method prevents channel from deterioration due to electron beam evaporation and the high workfunction platinum can place the Fermi level underneath the material valence band. Alternatively, for n-type transition metal dichalcogenides, a single layer of boron nitride is put on transition metal dichalcogenide before cobalt evaporation. This way, the boron nitride layer protects the transition metal dichalcogenide from the process of evaporation and can decrease the work function of cobalt thus putting Fermi level above the conduction band. With these contact methods, Ohmic contacts can be achieved at cryogenic temperature and probing the transition metal dichalcogenide heterostructures with transport measurements become accessible. Then, the magnetotransport properties of monolayer molybdenum disulphide and bilayer tungsten diselenide encapsulated with boron nitride with graphite dual-gate were measured. There are three unique features underlie this two dimensional electron gas system. First, the system is strong correlated. The Landau level spectrum reveals strong correlated signatures, such as enhanced spin-orbit coupling splitting and enhanced effective g-factor. Second, the longitudinal resistance/conductance at half-filling of Landau levels are found to depend on the spin orientation. The minority spin Landau level become totally localized at higher magnetic field. Third, in bilayer device the two layers are weak coupled and can be independently controlled by two gates. All this features establish transition metal dichalcogenide a unique platform for studying correlated physics. Finally, to achieve higher level of correlation, two layers of tungsten diselenide are stacked together with a small twist angle. With the help of moiré potential and layer hybridization, the bandwidth can be continuously tuned by the twist angle. In the range of 3 degree to 5.1degree, with moderate correlation strength, correlated insulating states are shown at half-filled flatband and are highly tunable with vertical electric field

Helicobacter pylori infection concomitant with metabolic syndrome further increase risk of colorectal adenomas

AIM: To investigate the association of colorectal adenomas with both Helicobacter pylori (H. pylori) infection and metabolic syndrome

Biomechanical Comparison of a Novel Implant and Commercial Fixation Devices for AO/OTA 43-C1 Type Distal Tibial Fracture

This study compares the novel Asia Distal Lateral Tibial Locking Plate mechanical stability to that of the current anterolateral and medial tibial plates based on finite element analysis. Four-part fracture fragment model of the distal tibia was reconstructed using CAD software. A load was applied to simulate the swing phase of gait. The implant stress and the construct stiffness were compared. The results of the anterolateral plate and the medial plate were similar and the displacement values were determined lower than those in the medial plate. In the simulated distal tibia fracture, the Aplus Asia Distal Lateral Tibial Locking Plate and medial distal tibial plate tibia fixations will lead to a stiffer bone-implant construct compared to the anterolateral distal tibial plate. Moreover, the stress in the Aplus Asia Distal Lateral Tibial Locking Plate was lower than those for the medial distal tibial plate and anterolateral bone plates. The Aplus Asia Distal Lateral Tibial Locking Plate has better stabilization and is an anterolateral plate that avoids more soft tissue damage than other bone plates. The Aplus Asia Distal Lateral Tibial Locking Plate could be one of a suitable design in tibia distal fracture fixation

Supercritical carbon dioxide anti-solvent precipitation of anti-oxidative zeaxanthin highly recovered by elution chromatography from Nannochloropsis oculata

Zeaxanthin, a kind of xanthophylls, rich in Marigold flowers and a few micro algae, acts as a strong antioxidant capable of protecting human eye-sight from age-related macular degeneration. This study examined elution chromatography coupled with supercritical anti-solvent precipitation applied for generation of zeaxanthin-rich particulates from micro-algal Nannochloropsis oculata species. Crude of the ultrasonic acetone extract subjected to the column fractionation successfully yields a fraction containing 303.02 mg/g (30%) of zeaxanthin with recovery of 90%. Supercritical anti-solvent precipitation of the algal solution at 200 bar and 313 K was used in producing submicron-sized particulates of 50% zeaxanthin. These extracts were subjected to tests of antioxidant capacities in 2,2-diphenyl-2-picrylhydrazyl hydrate free-radical assay and human adult retinal pigment epithelium-19 cells. This work provided a fast and environmental benign process to generate anti-oxidative capable algal micronized powders from the N. oculata