A comprehensive functional map of the hepatitis C virus genome provides a resource for probing viral proteins.

UnlabelledPairing high-throughput sequencing technologies with high-throughput mutagenesis enables genome-wide investigations of pathogenic organisms. Knowledge of the specific functions of protein domains encoded by the genome of the hepatitis C virus (HCV), a major human pathogen that contributes to liver disease worldwide, remains limited to insight from small-scale studies. To enhance the capabilities of HCV researchers, we have obtained a high-resolution functional map of the entire viral genome by combining transposon-based insertional mutagenesis with next-generation sequencing. We generated a library of 8,398 mutagenized HCV clones, each containing one 15-nucleotide sequence inserted at a unique genomic position. We passaged this library in hepatic cells, recovered virus pools, and simultaneously assayed the abundance of mutant viruses in each pool by next-generation sequencing. To illustrate the validity of the functional profile, we compared the genetic footprints of viral proteins with previously solved protein structures. Moreover, we show the utility of these genetic footprints in the identification of candidate regions for epitope tag insertion. In a second application, we screened the genetic footprints for phenotypes that reflected defects in later steps of the viral life cycle. We confirmed that viruses with insertions in a region of the nonstructural protein NS4B had a defect in infectivity while maintaining genome replication. Overall, our genome-wide HCV mutant library and the genetic footprints obtained by high-resolution profiling represent valuable new resources for the research community that can direct the attention of investigators toward unidentified roles of individual protein domains.ImportanceOur insertional mutagenesis library provides a resource that illustrates the effects of relatively small insertions on local protein structure and HCV viability. We have also generated complementary resources, including a website (http://hangfei.bol.ucla.edu) and a panel of epitope-tagged mutant viruses that should enhance the research capabilities of investigators studying HCV. Researchers can now detect epitope-tagged viral proteins by established antibodies, which will allow biochemical studies of HCV proteins for which antibodies are not readily available. Furthermore, researchers can now quickly look up genotype-phenotype relationships and base further mechanistic studies on the residue-by-residue information from the functional profile. More broadly, this approach offers a general strategy for the systematic functional characterization of viruses on the genome scale

Diffuse X-ray Emissions from Dynamic Planetary Nebulae

We present theoretical results of a piecewise isothermal shock wind model devised for predicting the luminosity and surface brightness profile of diffuse X-ray emissions primarily from the inner shocked downstream wind zone of a planetary nebula (PN) surrounded by self-similar shocked dense shell and outer slow AGB wind envelope involving self-gravity and compare/fit our computational model results with available observations of a few grossly spherical X-ray emitting PNe. Matching shocked piecewise isothermal self-similar void (ISSV) solutions with self-gravity of Lou & Zhai (LZ) for the outer zone and a stationary isothermal fast tenuous wind with a reverse shock for the inner zone across an expanding contact discontinuity, we can consistently construct dynamic evolution models of PNe with diffuse X-ray emissions. On the basis of such a chosen dynamic wind interaction model, both X-ray luminosity and radial X-ray brightness profile are determined by three key parameters, namely the so-called X-ray parameter $X$, two radii $R_{rs}$ and $R_c$ of the reverse shock and the contact discontinuity. We find that morphologies of X-ray emissions would appear in the forms of either a central luminous sphere or a bright ring embedded within optically bright shells. In contrast to previous adiabatic models, the X-ray brightness peaks around the reverse shock, instead of the contact discontinuity surface just inside the outer shocked dense shell. Diffuse X-ray emissions of a few observed PNe appear to support this wind-wind dynamic interaction scenario.Comment: 13 pages, 8 figures, accepted by Mon. Not. R. Astron. Soc. Accepted 2010 June 2. Received 2010 May 28; in original form 2010 May

Clinical Study of Uric Acid Urolithiasis

Uric acid urolithiasis develops from various causes. To investigate the clinical and biochemical presentation of patients with uric acid urolithiasis, a retrospective study was designed. A total of 46 cases were enrolled between January 2004 and December 2005. The compositions of the stones were analyzed by infrared spectrophotometry. There were 39 males (84.8%) and seven females (15.2%), with a mean age of 61.5 ± 10.6 years and mean body mass index (BMI) of 26.7 ± 3.1 kg/m2. The stone location was kidney in 10 (21.7%), ureter in 22 (41.8%), and bladder in 14 (30.5%). Multiple stones were diagnosed in 36 patients (78.3%). Pre-existing comorbidities included diabetes mellitus in 11 patients (23.9%), hypertension in 23 (50%), gout in 13 (28.2%), and benign prostatic hyperplasia in 14 (30.4%). Mean serum creatinine and uric acid was 1.6 ± 0.6 mg/dL and 7.6 ± 1.8 mg/dL, respectively. There were 27 patients (58%) with creatinine > 1.4 mg/dL. The mean urinary pH was 5.42 ± 0.46. Patients with uric acid urolithiasis were predominantly male, older, with higher BMI, multiple stone presentation, with lower urinary pH, and hyperuricemia. Exacerbation of the renal function should also be of concern because of the high proportion of patients with renal insufficiency diagnosed in this study

Developmental changes in the role of different metalinguistic awareness skills in Chinese reading acquisition from preschool to third grade

Copyright @ 2014 Wei et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.The present study investigated the relationship between Chinese reading skills and metalinguistic awareness skills such as phonological, morphological, and orthographic awareness for 101 Preschool, 94 Grade-1, 98 Grade-2, and 98 Grade-3 children from two primary schools in Mainland China. The aim of the study was to examine how each of these metalinguistic awareness skills would exert their influence on the success of reading in Chinese with age. The results showed that all three metalinguistic awareness skills significantly predicted reading success. It further revealed that orthographic awareness played a dominant role in the early stages of reading acquisition, and its influence decreased with age, while the opposite was true for the contribution of morphological awareness. The results were in stark contrast with studies in English, where phonological awareness is typically shown as the single most potent metalinguistic awareness factor in literacy acquisition. In order to account for the current data, a three-stage model of reading acquisition in Chinese is discussed.National Natural Science Foundation of China and Knowledge Innovation Program of the Chinese Academy of Sciences

Lattice Calculation of the Intrinsic Soft Function and the Collins-Soper Kernel

We calculate the soft function using lattice QCD in the framework of large momentum effective theory incorporating the one-loop perturbative contributions. The soft function is a crucial ingredient in the lattice determination of light cone objects using transverse-momentum-dependent (TMD) factorization. It consists of a rapidity-independent part called intrinsic soft function and a rapidity-dependent part called Collins-Soper kernel. We have adopted appropriate normalization when constructing the pseudo-scalar meson form factor that is needed in the determination of the intrinsic part and applied Fierz rearrangement to suppress the higher-twist effects. In the calculation of CS kernel we consider a CLS ensemble other than the MILC ensemble used in a previous study. We have also compared the applicability of determining the CS kernel using quasi TMDWFs and quasi TMDPDFs. As an example, the determined soft function is used to obtain the physical TMD wave functions (WFs) of pion and unpolarized iso-vector TMD parton distribution functions (PDFs) of proton.Comment: 24 pages, 19 figures, published versio

AMiBA: Broadband Heterodyne CMB Interferometry

The Y. T. Lee Array for Microwave Background (AMiBA) has reported the first science results on the detection of galaxy clusters via the Sunyaev Zel'dovich effect. The science objectives required small reflectors in order to sample large scale structures (20') while interferometry provided modest resolutions (2'). With these constraints, we designed for the best sensitivity by utilizing the maximum possible continuum bandwidth matched to the atmospheric window at 86-102GHz, with dual polarizations. A novel wide-band analog correlator was designed that is easily expandable for more interferometer elements. MMIC technology was used throughout as much as possible in order to miniaturize the components and to enhance mass production. These designs will find application in other upcoming astronomy projects. AMiBA is now in operations since 2006, and we are in the process to expand the array from 7 to 13 elements.Comment: 10 pages, 6 figures, ApJ in press; a version with high resolution figures available at http://www.asiaa.sinica.edu.tw/~keiichi/upfiles/AMiBA7/mtc_highreso.pd

Establishing a nationwide emergency department-based syndromic surveillance system for better public health responses in Taiwan

Background. With international concern over emerging infectious diseases (EID) and bioterrorist attacks, public health is being required to have early outbreak detection systems. A disease surveillance team was organized to establish a hospital emergency department-based syndromic surveillance system (ED-SSS) capable of automatically transmitting patient data electronically from the hospitals responsible for emergency care throughout the country to the Centers for Disease Control in Taiwan (Taiwan-CDC) starting March, 2004. This report describes the challenges and steps involved in developing ED-SSS and the timely information it provides to improve in public health decision-making. Methods. Between June 2003 and March 2004, after comparing various surveillance systems used around the world and consulting with ED physicians, pediatricians and internal medicine physicians involved in infectious disease control, the Syndromic Surveillance Research Team in Taiwan worked with the Real-time Outbreak and Disease Surveillance (RODS) Laboratory at the University of Pittsburgh to create Taiwan's ED-SSS. The system was evaluated by analyzing daily electronic ED data received in real-time from the 189 hospitals participating in this system between April 1, 2004 and March 31, 2005. Results. Taiwan's ED-SSS identified winter and summer spikes in two syndrome groups: influenza-like illnesses and respiratory syndrome illnesses, while total numbers of ED visits were significantly higher on weekends, national holidays and the days of Chinese lunar new year than weekdays (p < 0.001). It also identified increases in the upper, lower, and total gastrointestinal (GI) syndrome groups starting in November 2004 and two clear spikes in enterovirus-like infections coinciding with the two school semesters. Using ED-SSS for surveillance of influenza-like illnesses and enteroviruses-related infections has improved Taiwan's pandemic flu preparedness and disease control capabilities. Conclusion. Taiwan's ED-SSS represents the first nationwide real-time syndromic surveillance system ever established in Asia. The experiences reported herein can encourage other countries to develop their own surveillance systems. The system can be adapted to other cultural and language environments for better global surveillance of infectious diseases and international collaboration. © 2008 Wu et al; licensee BioMed Central Ltd

One-pot synthesis of nano-crystalline MCM-22

[EN] Nano-crystalline MCM-22 zeolite was synthesized in a one-pot procedure by the use of an organosilane (dimethyl-octadecyl-(3-trimethoxysilylpropyl)-ammonium chloride, TPOAC) in the zeolite synthesis gel. This crystal growth inhibition procedure introduced mesopores in the MCM-22 crystallites. The lower mechanical stability of the nano-crystalline MCM-22 zeolite compared with bulk MCM-22 can be countered to some extent by pillaring. The increased external surface of the microporous zeolite domains resulted in increased accessibility of the Bronsted acid sites, as followed from the better performance in liquid-phase benzene alkylation with propylene as compared with bulk MCM-22. The increased accessibility of the internal acid sites in Mo-loaded hierarchical MCM-22 was also evident from the improved benzene selectivity during methane aromatization. Silylation of hierarchical Mo/MCM-22 was detrimental for the catalytic performance in MDA. The nano-crystalline MCM-22 has physico-chemical and catalytic properties intermediate between those of MCM-22 and ITQ-2 with the benefit over ITQ-2 that it can be synthesized in a single step. (C) 2015 Elsevier Inc. All rights reserved.Funding from the 7th Framework Program of the European Commission through the Collaborative Project Next-GTL (agreement no 229183) and financial support by the Spanish Government-MINECO through "Severo Ochoa" (SEV 2012-0267), Consolider Ingenio 2010-Multicat (CSD2009-00050) and MAT2012-31657 are acknowledged. Marta E. Martinez Armero thanks MINECO for economical support through pre-doctoral fellowship for doctors training (BES-2013-066800). The authors thank B. Esparcia for technical assistance.Tempelman, CHL.; Portilla Ovejero, MT.; Martínez Armero, ME.; Mezari, B.; De Caluwe, NGR.; Martínez, C.; Hensen, EJM. (2016). One-pot synthesis of nano-crystalline MCM-22. Microporous and Mesoporous Materials. 220:28-38. https://doi.org/10.1016/j.micromeso.2015.08.018S283822

The Yuan-Tseh Lee Array for Microwave Background Anisotropy

The Yuan-Tseh Lee Array for Microwave Background Anisotropy (AMiBA) is the first interferometer dedicated to studying the cosmic microwave background (CMB) radiation at 3mm wavelength. The choice of 3mm was made to minimize the contributions from foreground synchrotron radiation and Galactic dust emission. The initial configuration of seven 0.6m telescopes mounted on a 6-m hexapod platform was dedicated in October 2006 on Mauna Loa, Hawaii. Scientific operations began with the detection of a number of clusters of galaxies via the thermal Sunyaev-Zel'dovich effect. We compare our data with Subaru weak lensing data in order to study the structure of dark matter. We also compare our data with X-ray data in order to derive the Hubble constant.Comment: accepted for publication in ApJ (13 pages, 7 figures); a version with high resolution figures available at http://www.asiaa.sinica.edu.tw/~keiichi/upfiles/AMiBA7/pho_highreso.pd

Sorption of hydrophobic organic compounds on natural sorbents and organoclays from aqueous and non-aqueous solutions: a mini-review

Renewed focus on the sorption of hydrophobic organic chemicals (HOCs) onto mineral surfaces and soil components is required due to the increased and wider range of organic pollutants being released into the environment. This mini-review examines the possibility of the contribution and mechanism of HOC sorption onto clay mineral sorbents such as kaolinite, and soil organic matter and the possible role of both in the prevention of environmental contamination by HOCs. Literature data indicates that certain siloxane surfaces can be hydrophobic. Therefore soils can retain HOCs even at low soil organic levels and the extent will depend on the structure of the pollutant and the type and concentration of clay minerals in the sorbent. Clay minerals are wettable by nonpolar solvents and so sorption of HOCs onto them from aqueous and non-aqueous solutions is possible. This is important for two reasons: firstly, the movement and remediation of soil environments will be a function of the concentration and type of clay minerals in the soil. Secondly, low-cost sorbents such as kaolinite and expandable clays can be added to soils or contaminated environments as temporary retention barriers for HOCs. Inorganic cations sorbed onto the kaolinite have a strong influence on the rate and extent of sorption of hydrophobic organic pollutants onto kaolinite. Structural sorbate classes that can be retained by the kaolinite matrix are limited by hydrogen bonding between hydroxyl groups of the octahedral alumosilicate sheet and the tetrahedral sheet with silicon. Soil organic carbon plays a key role in the sorption of HOCs onto soils, but the extent will be strongly affected by the structure of the organic soil matter and the presence of soot. Structural characterisation of soil organic matter in a particular soil should be conducted during a particular contamination event. Contamination by mining extractants and antibiotics will require renewed focus on the use of the QSAR approaches in the context of the sorption of HOCs onto clay minerals from aqueous and non-aqueous solutions