Optimal Haplotype Assembly from High-Throughput Mate-Pair Reads

Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide polymorphisms (SNPs). A haplotype of an individual is the pair of sequences of SNPs on the two homologous chromosomes. In this paper, we study the problem of inferring haplotypes of individuals from mate-pair reads of their genome. We give a simple formula for the coverage needed for haplotype assembly, under a generative model. The analysis here leverages connections of this problem with decoding convolutional codes.Comment: 10 pages, 4 figures, Submitted to ISIT 201

Ocular Surface Squamous Neoplasia in Xeroderma Pigmentosum

Xeroderma pigmentosum (XP) is a rare genetic disorder associated with multiple oculocutaneous and neurological manifestations. It occurs due to deficiency of the enzymes responsible for repairing ultraviolet radiation-induced DNA damage. Persistence of un-repaired DNA results in somatic mutations, leading to neoplasia of the skin and ocular surface. As this condition is rare, only isolated case reports of XP with ocular surface squamous neoplasia (OSSN) are found in literature

Roles of Retinoic Acid and Cyp26 Inhibitors in Ovarian Follicle Development

The ovaries are the female reproductive organs that are located on either side of the uterus. They contain eggs and secrete hormones that are critical for female reproduction. Each follicle consists of an egg at the center, surrounded by multiple layers of somatic cells. These eggs undergo various stages of development wherein the follicular structure matures as a whole; the hormones and growth factors secreted by the somatic cells are essential for the maturation of the egg while the signaling molecules produced by the egg are crucial for somatic cell proliferation and follicle maturation and development. Thus, mammalian ovarian follicle formation and development involves the establishment of the initial follicle pool, follicle growth, proper maturation of eggs, and timely production and release of hormones and the mature eggs. This process is essential for propagation of the species as well as for development and homeostasis of the female reproductive system[1]. Abnormalities in the regulation and development of ovarian follicles such as inadequate maturation of the follicle due to inadequate cell-cell interactions and signaling between the somatic cells and the egg can lead to infertility and ovarian diseases, for instance Premature Ovarian Failure (POF), Polycystic Ovary Syndrome (PCOS) and ovarian cancer. These diseases lead to a loss of fertility due to the formation of immature or unhealthy follicles and/or oocyte development. Both intraovarian and extraovarian factors play a role in regulating the development of follicles. However, factors involved in follicular growth and survival are not well defined. Recently, studies have suggested that the potent morphogen retinoic acid (RA) plays a role in the development of a healthy ovary[1, 2]. However, the underlying mechanism is not understood. Germ cells in the fetal ovary undergo sex-specific entry into meiosis, the initiation of which is thought to be mediated by selective exposure of fetal ovarian germ cells to retinoic acid[2]. Nevertheless, the timing and regulation of meiosis vary amongst the sexes. It was determined that high levels of RA were necessary for initiation of meiosis in the ovary and the testes; however, while RA is required for germ cell development in the embryonic ovary, it is required during the juvenile and adult stages of testicular functioning[3, 4]. Cyp26b1, a member of the Cyp450 family of enzymes degrades retinoic acid in the ovary and the testes thereby limiting gonadal development [1, 3, 5]. However, information about the role of RA and Cyp26b1 in the gonads is limited. It is therefore necessary to further elucidate the roles of both RA and Cyp26b1 in ovarian and follicle development. The purpose of this study is to examine the roles of Cyp26b1 and RA in mouse ovarian follicle development. This will be done by performing in vitro follicle culture and ovary culture with treatments including retinoic acid, the Cyp26 inhibitor R115866 and the RA metabolism inhibitor Liarozole and monitoring their effects on follicular and ovary growth. We expect the findings from this study to contribute significantly to infertility treatments and disease prevention, as being able to successfully grow follicles invitro could help the large population of women whose difficulty with conceiving is due to an immature and underdeveloped follicle pool

Active Vibration Control of Structures using an Impedance Matching Control Technique

Active vibration control of structures has gained a lot of interest in recent years. This paper presents an active vibration control methodology of a structure using piezoelectric actuators. The proposed methodology is useful in practical applications where the system to be controlled is difficult to model due to the presence of complex boundary conditions. The impedance matching control technique uses a power flow approach wherein the controller is designed such that the power flow into the structure is minimized. The system transfer function is obtained from the experimental collocated actuator/sensor pair data using Eigen Realisation Algorithm (ERA). The controller is designed for the system transfer function according to impedance matching theory. The above approach is targeted towards the vibration control of wind tunnel stings, which suffer from flow-induced vibration. A wind tunnel sting model is designed and fabricated for this study. The real time implementation of the impedance matching controller has been carried out using dSPACE® Digital Signal Processor (DSP) card. The results are encouraging and demonstrate the feasibility of applying this technique in the wind tunne

Anionic clay-like behaviour of alpha-nickel hydroxide: chromate sorption studies

While the sorption capacity of alpha-nickel hydroxide for the chromate ion is comparable with that of hydrotalcite-like anionic clays, the control samples of beta- and beta(bc)(bc: badly crystalline)-nickel hydroxide show negligible sorption. This provides direct evidence for the clay-like nature of alpha-nickel hydroxide. (C) 2002 Elsevier Science B.V. All rights reserved