Deep sequencing of PRRSV isolates: rapid and large-scale characterization of viral genomes

Porcine reproductive and respiratory syndrome virus (PRRSV) is a single stranded, positive sense RNA virus with a genome size of approximately 15 kb. Much of the genetic characterization or viral genotyping of PRRSV isolates is limited to one or two viral genes only (ORF5 and/or ORF7) for a number of reasons, for example: (1) characterizing one or two ORFs is sufficient for diagnostics; (2) genome characterization is laborious because traditional (Sanger) sequencing yields only a single sequence of 800-1000 bases per reaction; (3) large-scale genome characterization is time-consuming and costly. Collectively, this hinders the study of PRRSV genomic evolution at different levels (host, regional, and global). We demonstrate here the use of 454 technology to rapidly sequence PRRSV genomic nucleic acid from different sources (cell culture and swine tissue), genotypes (type 1 and type 2), and genome structure (non-deletion vs. deletion variants). Samples (n=16) were multiplexed to bring down cost per genome sequence. Assembly of sample specific reads resulted in a single contig in almost all instances (15 out of 16). Average genome coverage was 96.7% with reference to prototype isolates (Lelystad virus for type 1 and ATCC VR2332 for type 2). Average sequence depth was 405 reads per nucleotide position. This high sequence depth allowed characterization of variants from quasispecies that occurred at frequencies even lower than 1%. In summary, next generation sequencing technology offers unparalleled opportunity to quickly and efficiently characterize near complete length PRRSV genomes in an economical manner. This allows experiments to be designed with considerations to viral genomic evolution rather than those with limited insights from select viral genes only.postprin

Comparison of digital signal-signal beat interference compensation techniques in direct-detection subcarrier modulation systems

Single-polarization direct-detection transceivers may offer advantages compared to digital coherent technology for some metro, back-haul, access and inter-data center applications since they offer low-cost and complexity solutions. However, a direct-detection receiver introduces nonlinearity upon photo detection, since it is a square-law device, which results in signal distortion due to signal-signal beat interference (SSBI). Consequently, it is desirable to develop effective and low-cost SSBI compensation techniques to improve the performance of such transceivers. In this paper, we compare the performance of a number of recently proposed digital signal processing-based SSBI compensation schemes, including the use of single- and two-stage linearization filters, an iterative linearization filter and a SSBI estimation and cancellation technique. Their performance is assessed experimentally using a 7 × 25 Gb/s wavelength division multiplexed (WDM) single-sideband 16-QAM Nyquistsubcarrier modulation system operating at a net information spectral density of 2.3 (b/s)/Hz

Bidirectional symmetric 8x10. 7Gb/s WDM-PON over 108 km installed fiber using low complexity polarization-insensitive coherent ONUs

Polarization-time block-coded OFDM-QPSK downstream channels are robustly detected using a polarization-insensitive coherent receiver, consisting of only a 3dB coupler and single balanced PD. 8 x10.7Gb/s channels are bidirectionally transmitted over 108 km installed fiber achieving a 1:16-way passive split

Comparison of low complexity coherent receivers for UDWDM-PONs (λ-to-the-User)

It is predicted that demand in future optical access networks will reach multigigabit/s per user. However, the limited performance of the direct detection receiver technology currently used in the optical network units at the customers' premises restricts data rates per user. Therefore, the concept of coherent-enabled access networks has attracted attention in recent years, as this technology offers high receiver sensitivity, inherent frequency selectivity, and linear field detection enabling the full compensation of linear channel impairments. However, the complexity of conventional (dual-polarization digital) coherent receivers has so far prevented their introduction into access networks. Thus, to exploit the benefits of coherent technology in access networks, low complexity coherent receivers, suitable for implementation in ONUs, are needed. In this paper, the recently proposed low complexity coherent (i.e., polarization-independent Alamouti-coding heterodyne) receiver is, for the first time, compared in terms of its minimum receiver sensitivity with five previously reported receiver designs, including a detailed discussion on their advantages and limitations. It is shown that, of all the configurations considered, the Alamouti-coding based receiver approach allows the lowest number of photons per bit (PPB) transmitted (with a lower bound of 15.5 PPB in an ideal implementation of the system), while requiring the lowest optical receiver hardware complexity (in terms of the optical component count). It also exhibits comparable complexity to the currently deployed direct-detection receivers, which typically require over 1000 PPB. Finally, a comparison of experimentally achieved receiver sensitivities and transmission distances using these receivers is presented. The highest spectral efficiency and longest transmission distance at the highest bit rate (10 Gb/s) was reported using the Alamouti-coding receiver, which is also the only one, to date, to have been demonstrated in a full system bidirectional transmission

Reach Enhancement for WDM Direct-Detection Subcarrier Modulation using Low-Complexity Two-Stage Signal-Signal Beat Interference Cancellation

We describe a novel low-complexity SSBI cancellation scheme, and experimentally investigate its performance in a 7×25 Gb/s WDM direct-detection single-sideband 16QAM Nyquistsubcarrier modulation system. The scheme achieves a doubling of the transmission reach

SSBI Mitigation and the Kramers-Kronig Scheme in Single-Sideband Direct-Detection Transmission With Receiver-Based Electronic Dispersion Compensation

The performance of direct-detection transceivers employing electronic dispersion compensation combined with DSP-based receiver linearization techniques is assessed through experiments on a 4 × 112 Gb/s wavelength-division multiplexing direct-detection single-sideband 16 quadratic-amplitude modulation Nyquist-subcarrier-modulation system operating at a net optical information spectral density of 2.8 b/s/Hz in transmission over standard single mode fiber links of up to 240 km. The experimental results indicate that systems with receiver-based dispersion compensation can achieve similar performance to those utilizing transmitter-based dispersion compensation, provided it is implemented together with an effective digital receiver linearization technique. The use of receiver-based compensation would simplify the operation of a fiber link since knowledge of the link dispersion is not required at the transmitter. The recently proposed Kramers-Kronig receiver scheme was found to be the best performing among the receiver linearization techniques assessed. To the best of our knowledge, this is the first experimental demonstration of the Kramers-Kronig scheme

Effect of WeiJia on carbon tetrachloride induced chronic liver injury

Aim: To study the effect of WeiJia on chronic liver injury using carbon tetrachloride (CCl 4) induced liver injury animal model. Methods: Wista r rats weighing 180-220g were randomly divided into three groups: normal control group (Group A), CCl 4 induced liver injury control group (Group B) and CCl 4 induction with WeiJia treatment group (Group C). Each group consisted of 14 rats. Liver damage and fibrosis was induced by subcutaneous injection with 40% CCl 4 in olive oil at 3 mL/kg body weight twice a week for eight weeks for Groups B and C rats whereas olive oil was used for Group A rats. Starting from the third week, Group C rats also received daily intraperitoneal injection of WeiJia at a dose of 1.25 μg/kg body weight. Animals were sacrificed at the fifth week (4 male, 3 female), and eighth week (4 male, 3 female) respectively. Degree of fibrosis were measured and serological markers for liver fibrosis and function including hyaluronic acid (HA), type IV collagen (CIV), γ-glutamyl transferase (γ-GT), alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were determined. Alpha smooth muscle actin (α-SMA) and proliferating cell nuclear antigen (PCNA) immunohistochemistry were also performed. Results: CCl 4 induction led to the damage of liver and development of fibrosis in Group B and Group C rats when compared to Group A rats. The treatment of WeiJia in Group C rats could reduce the fibrosis condition significantly compared to Group B rats. The effect could be observed after three weeks of treatment and was more obvious after eight weeks of treatment. Serum HA, CIV, ALT, AST and γ-GT levels after eight weeks of treatment for Group C rats were 58±22 μg/L (P 0.05) respectively, similar to normal control group (Group A), but significantly different from CCl 4 induced liver injury control group (Group B). An increase in PCNA and decrease in α-SMA expression level was also observed. Conclusion: WeiJia could improve liver function and reduce liver fibrosis which might be through the inhibition of stellate cell activity. © 2006 The WJG Press. All rights reserved.published_or_final_versio

The effect of cigarette price increase on the cigarette consumption in Taiwan: evidence from the National Health Interview Surveys on cigarette consumption

BACKGROUND: This study uses cigarette price elasticity to evaluate the effect of a new excise tax increase on cigarette consumption and to investigate responses from various types of smokers. METHODS: Our sample consisted of current smokers between 17 and 69 years old interviewed during an annual face-to-face survey conducted by Taiwan National Health Research Institutes between 2000 to 2003. We used Ordinary Least Squares (OLS) procedure to estimate double logarithmic function of cigarette demand and cigarette price elasticity. RESULTS: In 2002, after Taiwan had enacted the new tax scheme, cigarette price elasticity in Taiwan was found to be -0.5274. The new tax scheme brought about an average annual 13.27 packs/person (10.5%) reduction in cigarette consumption. Using the cigarette price elasticity estimate from -0.309 in 2003, we calculated that if the Health and Welfare Tax were increased by another NT$ 3 per pack and cigarette producers shifted this increase to the consumers, cigarette consumption would be reduced by 2.47 packs/person (2.2%). The value of the estimated cigarette price elasticity is smaller than one, meaning that the tax will not only reduce cigarette consumption but it will also generate additional tax revenues. Male smokers who had no income or who smoked light cigarettes were found to be more responsive to changes in cigarette price. CONCLUSIONS: An additional tax added to the cost of cigarettes would bring about a reduction in cigarette consumption and increased tax revenues. It would also help reduce incidents smoking-related illnesses. The additional tax revenues generated by the tax increase could be used to offset the current financial deficiency of Taiwan's National Health Insurance program and provide better public services

Analysis of airborne particulate matter (pm₂.₅) over Hong Kong using remote sensing and GIS

2011-2012 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe