Sheida Nabavi

Two-Dimensional Generalized Partial Response Equalizer for Bit-Patterned Media

The use of bit-patterned media is one of the approaches being investigated to extend magnetic recording densities to 1 Tbit/in2 and beyond. In patterned media, track pitch may be small causing adjacent tracks to have significant interference on the replay waveform from the main data track. To mitigate the effect of such inter-track interference (ITI), we propose the use of a two-dimensional (2D) generalized partial response (GPR) equalizer. We select both the equalizer and the partial response target using the minimum mean squared error (MMSE) criterion. However, we avoid the need for a 2D Viterbi algorithm by imposing a constraint on the 2D target that forces the adjacent track contributions (in the ideal case) to zero. Simulation results show that this 2D equalizer significantly improves the bit error rate (BER). In this work, the effect of a 2D GPR equalizer on the performance of a patterned media system in the presence of track misregistration (TMR) is also investigated. Based on the simulation results, the 2D equalization method appears to be more tolerant to TMR than the conventional GPR The main drawback of the proposed method is the need for simultaneously acquiring the signals from three adjacent tracks.

Modifying Viterbi Algorithm to Mitigate Intertrack Interference in Bit-Patterned Media

Bit-patterned media are currently being investigated to obtain magnetic recording densities of 1 Tbit/in2 and more. In bit-patterned media, the adjacent tracks may be as close as adjacent bits in a track resulting in significant intertrack interference (ITI). In this work, we propose a modified trellis for the Viterbi algorithm (VA) that can mitigate the effects of ITI. Simulation results show that the modified VA improves the bit error rate. Using a simple model for track misregistration (TMR), the performance of this modified VA in the presence of TMR is also investigated. Based on the simulation results, this modified VA also appears to be more tolerant to TMR than the conventional VA

Two-Dimensional Pulse Response and Media Noise Modeling for Bit-Patterned Media

In high density bit-patterned media (BPM), bits or magnetic islands are very close leading to significant inter-track interference (ITI) in addition to inter-symbol interference (ISI). Also, in BPM, major sources of media noise are the fluctuations in the location of the magnetic islands and fluctuations in the sizes of the magnetic islands. The location fluctuations can happen in both along-the-track and in cross-track directions. The size fluctuations affect both ISI and ITI. In order to obtain a more realistic channel model that includes the 2-D interference and the 2-D impact of media noise, we have developed a 2-D pulse response simulator for BPM. Utilizing the 2-D pulse response, we model the ITI and the media noise. Simulation results show that to achieve an acceptable bit error rate (BER), the location and size fluctuations should be smaller than 8% of the bit period at a density of 1.5 Tb/in2 .

Application of Image Processing to Characterize Patterning Noise in Self-Assembled Nano-Masks for Bit-Patterned Media

In bit-patterned media (BPM), media noise is expected to be dominated by fabrication imperfections and to manifest as island size and spacing fluctuations. Previous work has shown that media noise has a significant impact on the error rates of BPM channels. Thus, having a realistic model of media noise is essential to evaluate the performance of the BPM channels. In this work, we apply image processing techniques to a scanning electron microscope image of a candidate BPM nano-mask, produced by a self-assembly technique, to estimate likely size and location fluctuations of the islands. These statistics may also be useful to characterize the samples of candidate BPM masks. We assume that these observed fluctuations are representative of patterning noise that might result from such a mask. The results indicate that these fluctuations are correlated and can be modeled by Gaussian random processes. Using estimated characteristics of islands size and location fluctuations, we model the correlated media noise and investigate the performance of BPM channels in the presence of such correlated media noise.

Chromosome-breakage genomic instability and chromothripsis in breast cancer

BackgroundChromosomal breakage followed by faulty DNA repair leads to gene amplifications and deletions in cancers. However, the mere assessment of the extent of genomic changes, amplifications and deletions may reduce the complexity of genomic data observed by array comparative genomic hybridization (array CGH). We present here a novel approach to array CGH data analysis, which focuses on putative breakpoints responsible for rearrangements within the genome.ResultsWe performed array comparative genomic hybridization in 29 primary tumors from high risk patients with breast cancer. The specimens were flow sorted according to ploidy to increase tumor cell purity prior to array CGH. We describe the number of chromosomal breaks as well as the patterns of breaks on individual chromosomes in each tumor. There were differences in chromosomal breakage patterns between the 3 clinical subtypes of breast cancers, although the highest density of breaks occurred at chromosome 17 in all subtypes, suggesting a particular proclivity of this chromosome for breaks. We also observed chromothripsis affecting various chromosomes in 41% of high risk breast cancers.ConclusionsOur results provide a new insight into the genomic complexity of breast cancer. Genomic instability dependent on chromosomal breakage events is not stochastic, targeting some chromosomes clearly more than others. We report a much higher percentage of chromothripsis than described previously in other cancers and this suggests that massive genomic rearrangements occurring in a single catastrophic event may shape many breast cancer genomes.

Picket-Shift Codes for Bit-Patterned Media Recording With Insertion/Deletion Errors

We report the results of an investigation of bit-patterned media recording (BPMR) channels containing insertion/deletion errors that may be introduced because of the write synchronization problem. We first describe a simple channel model for insertion/deletion errors in BPM, as a result of write clock frequency offset. Based on this channel model, we propose a new error correction coding (ECC) scheme to correct insertion/deletion errors-picket shift. Simulation results show that picket shift performs significantly better than a no-ECC scheme in the presence of insertion/deletion errors.

An Analytical Approach for Performance Evaluation of Bit-Patterned Media Channels

In this work, a new analytical approach is used to evaluate the error performance of bit-patterned media (BPM) magnetic recording channels that employ one-dimensional (1D) and two-dimensional (2D) generalized partial response (GPR) equalizers to combat the significant inter-track interference (ITI) expected in BPM magnetic recording systems. The probability density function of ITI is obtained analytically and is used to estimate the bit error rate (BER) from the Viterbi detector. The proposed method takes into account most of the important factors affecting the BER such as ITI, un-equalized intersymbol interference (ISI), colored noise and the distance and the multiplicity of error events. In this work, it is shown that for 1D channels, modeling ITI and un-equalized ISI by Gaussian PDFs leads to inaccurate BERs and that the non-Gaussian distribution of the ITI and un-equalized ISI must be taken into account for more accurate BER estimates. This method provides fast and accurate estimates of BERs for moderate to high signal-to-noise ratios (SNRs). By using this analytical method, time-consuming numerical simulations for error performance evaluation can be avoided.

EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes

Motivation: A major goal of biomedical research is to identify molecular features associated with a biological or clinical class of interest. Differential expression analysis has long been used for this purpose; however, conventional methods perform poorly when applied to data with high within class heterogeneity. Results: To address this challenge, we developed EMDomics, a new method that uses the Earth mover’s distance to measure the overall difference between the distributions of a gene’s expression in two classes of samples and uses permutations to obtain q-values for each gene. We applied EMDomics to the challenging problem of identifying genes associated with drug resistance in ovarian cancer. We also used simulated data to evaluate the performance of EMDomics, in terms of sensitivity and specificity for identifying differentially expressed gene in classes with high within class heterogeneity. In both the simulated and real biological data, EMDomics outperformed competing approaches for the identification of differentially expressed genes, and EMDomics was significantly more powerful than conventional methods for the identification of drug resistance-associated gene sets. EMDomics represents a new approach for the identification of genes differentially expressed between heterogeneous classes and has utility in a wide range of complex biomedical conditions in which sample classes show within class heterogeneity. Availability and implementation: The R package is available at http://www.bioconductor.org/packages/release/bioc/html/EMDomics.html Contact: abeck2@bidmc.harvard.edu Supplementary information: supplementary data are available at Bioinformatics online.

Ultradense array CGH and discovery of micro-copy number alterations and gene fusions in the cancer genome.

The characterization of molecular alterations specific to cancer facilitates the discovery of predictive and prognostic biomarkers important to targeted therapeutics. Alterations critical to cancer therapeutics include copy number alterations (CNAs) such as gene amplifications and deletions as well as genomic rearrangements resulting in gene fusions. There are two genome-wide technologies used to detect CNAs: next generation sequencing (NGS) and dense microarray based comparative genomic hybridization, termed array CGH (aCGH). aCGH is a mature robust technology of lower cost and more accessible than NGS. This chapter describes the protocol steps and analysis required to obtain reliable aCGH results from clinical samples. Technical options and various necessary compromises related to the nature of clinical material are considered and the consequences of these choices for data analysis and interpretation are discussed. The chapter includes brief description of the data analysis, even though analysis is often performed by bioinformaticians. Todays cancer research requires collaboration of clinicians, molecular biologists, and mathematicians. Acquaintance with the basic principles related to the extraction of the data from arrays, its normalization and the algorithms available for analysis provides a baseline for mutual understanding and communication.

A Method for Simultaneous Position and Timing Error Detection for Bit-Patterned Media

This paper presents a method for simultaneously detecting the position and timing error in bit patterned media (BPM). Conventionally the position error is determined only in the servo area while the timing error is determined in the data area. However, the regular spatial arrangement of bits in BPM allows position information and timing information to be extracted from the data. The new method exploits interference between adjacent tracks by employing a read head wider than the track pitch. The new method also provides the capability of reading data from two tracks at the same time.