Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses

The Human Reference Genome serves as the foundation for modern genomic analyses. However, in its present form, it does not adequately represent the vast genetic diversity of the human population. In this study, we explored the consensus genome as a potential successor of the current reference genome and assessed its effect on the accuracy of RNA-seq read alignment. To find the best haploid genome representation, we constructed consensus genomes at the pan-human, superpopulation, and population levels, using variant information from The 1000 Genomes Project Consortium. Using personal haploid genomes as the ground truth, we compared mapping errors for real RNA-seq reads aligned to the consensus genomes versus the reference genome. For reads overlapping homozygous variants, we found that the mapping error decreased by a factor of approximately two to three when the reference was replaced with the pan-human consensus genome. We also found that using more population-specific consensuses resulted in little to no increase over using the pan-human consensus, suggesting a limit in the utility of incorporating a more specific genomic variation. Replacing the reference with consensus genomes impacts functional analyses, such as differential expressions of isoforms, genes, and splice junctions

Ethical Issues in AIDS Research

There is a need for carefully controlled and scientifically rigorous research studies of the acquired immunodeficiency syndrome (AIDS). The morbidity and mortality associated with AIDS patients and the public health concerns for control of this epidemic have distorted the usual process of research. The Institutional Review Board at Boston City Hospital is suggested as an appropriate mechanism for clarifying the distinctions between research and innovative therapies and for assuring the protection of this vulnerable population of research subjects. This article addresses ethical concerns relating to the time frame of research, drug and antibody testing, vaccine trials, and questions of justice in micro- or macro-allocation. The unique problems in AIDS research with informed consent and confidentiality are discussed. Finally, the need is outlined for careful balancing of individual welfare and rights and those of society

Thermal properties of highly birefringent optical fibres and preforms

Temperature cycling of highly birefringent optical fibers and preforms has been used to investigate the thermal properties of bow-tie and elliptically clad structures. The thermal hysteresis of the birefringence is shown to be a direct consequence of the thermal history of the fiber or preform and has been related to volume changes in the stress-producing borosilicate sections. Annealing increases the axial stress as well as the stress anisotropy and hence the birefringence. Increases of up to a factor of 2 in the birefringence on suitable thermal treatment indicate a new method for further improvement of high birefringence fibers. The implications of the results in the design, fabrication, and use of such fibers are discussed

Gap plasmon polariton structure for very efficient micro to nano scale interfacing

The seamless transition between micro-scale photonics and nano-scale plasmonics requires the mitigation between different waveguiding mechanisms as well as between few orders of magnitude in the field lateral size, down to a small fraction of a wavelength. By exploiting gap plasmon polariton waves both at the micro and nano scale, very high power transfer efficiency (>60%) can be achieved using an ultrashort (few microns) non adiabatic tapered gap plasmon waveguide. Same mechanism may be used to harvest impinging light waves and direct them into a nano hole or slit, to exhibit an anomalous transmission - without the conventional periodic structures. The special interplay of plasmonic and oscillating modes is analyzed.Comment: Submitted to PRL. Part of the work was presented at IPRA-2005 conference, paper JWA

Extreme Outages due to Polarization Mode Dispersion

We investigate the dependence of the bit-error-rate (BER) caused by amplifier noise in a linear optical fiber telecommunication system on the fiber birefringence. We show that the probability distribution function (PDF) of BER obtained by averaging over many realizations of birefringent disorder has an extended tail corresponding to anomalously large values of BER. We specifically discuss the dependence of the tail on such details of the pulse detection at the fiber output as "setting the clock" and filtering procedures.Comment: 3 pages, 1 figure, submitted to Optics Letter

Why not pay interest on member bank reserves?

Interest ; Bank loans

The merits of efficient taxation

Taxation

Monitoring long distance WDM communication lines using a high-loss loopback supervisory system

In this paper, we present experimental results for monitoring long distance WDM communication links using a line monitoring system suitable for legacy optically amplified long-haul undersea systems. This monitoring system is based on setting up a simple, passive, low cost high-loss optical loopback circuit at each repeater that provides a connection between the existing anti-directional undersea fibres, and can be used to define fault location. Fault location is achieved by transmitting a short pulse supervisory signal along with the WDM data signals where a portion of the overall signal is attenuated and returned to the transmit terminal by the loopback circuit. A special receiver is used at the terminal to extract the weakly returned supervisory signal where each supervisory signal is received at different times corresponding to different optical repeaters. Therefore, the degradation in any repeater appears on its corresponding supervisory signal level. We use a recirculating loop to simulate a 4600 km fibre link, on which a high-loss loopback supervisory system is implemented. Successful monitoring is accomplished through the production of an appropriate supervisory signal at the terminal that is detected and identified in a satisfactory time period after passing through up to 45 dB attenuation in the loopback circuit

Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses

The Human Reference Genome serves as the foundation for modern genomic analyses. However, in its present form, it does not adequately represent the vast genetic diversity of the human population. In this study, we explored the consensus genome as a potential successor of the current reference genome and assessed its effect on the accuracy of RNA-seq read alignment. In order to find the best haploid genome representation, we constructed consensus genomes at the pan-human, super-population, and population levels, utilizing variant information from the 1000 Genomes Project. Using personal haploid genomes as the ground truth, we compared mapping errors for real RNA-seq reads aligned to the consensus genomes versus the reference genome. For reads overlapping homozygous variants, we found that the mapping error decreased by a factor of ~2-3 when the reference was replaced with the pan-human consensus genome. We also found that using more population-specific consensuses resulted in little to no increase overusing the pan-human consensus, suggesting a limit in the utility of incorporating more specific genomic variation. Replacing reference with consensus genomes impacts functional analyses, such as differential expressions of isoforms, genes, and splice junctions

Development of new all-optical signal regeneration technique

All-optical signal regeneration have been the active research area since last decade due to evolution of nonlinear optical signal processing. Existing all-optical signal regeneration techniques are agitated in producing low Bit Error Rate (BER) of 10-10 at below than -10 dBm power received. In this paper, a new all-optical signal regeneration technique is developed by using phase sensitive amplification and designed optical phase locked signal mechanism. The developed all-optical signal regeneration technique is tested for different 10 Gb/s Differential Phase Shift Keying degraded signals. It is determined that the designed all-optical signal regeneration technique is able to provide signal regeneration with noise mitigation for degraded signals. It is analyzed that overall, for all degraded test signals, average BER of 10-13 is achieved at received power of -14 dBm. The designed technique will be helpful to enhance the performance of existing signal regeneration systems in the presence of severe noise by providing minimum BER at low received power