6114653
Alignment of Optical Maps
An adjustable device that provides a secure anchor in a crevice or other irregularity. The anchor may be used to assist rock climbers, rescue groups, military personnel, construction workers, etc. The device is comprised of a spring loaded sleeve mounted on a first end of a threaded shaft and limited in its movement on the shaft by a pin and slot arrangement. The sleeve provides a means for adjusting the length of the device. A first locking means releasably secures the sleeve in a retracted position, and a second locking means secures the sleeve at the desired extended position. A lever assembly is provided at the second end of the device in such a manner that a force applied to an attachment point of the assembly will be translated along the longitudinal axis of the device.
172003
Reconstructing the Evolutionary History of Complex Human Gene Clusters
Clusters of genes that evolved from single progenitors via repeated segmental duplications present significant challenges to the generation of a truly complete human genome sequence. Such clusters can confound both accurate sequence assembly and downstream computational analysis, yet they represent a hotbed of functional innovation, making them of extreme interest. We have developed an algorithm for reconstructing the evolutionary history of gene clusters using only human genomic sequence data. This method allows the tempo of large-scale evolutionary events in human gene clusters to be estimated, which in turn will facilitate primate comparative sequencing studies that will aim to reconstruct their evolutionary history more fully.
12263549
Tree-guided Bayesian inference of population structures
MOTIVATION
Inferring population structures using genetic data sampled from a group of individuals is a challenging task. Many methods either consider a fixed population number or ignore the correlation between populations. As a result, they can lose sensitivity and specificity in detecting subtle stratifications. In addition, when a large number of genetic markers are used, many existing algorithms perform rather inefficiently.


RESULT
We propose a new Bayesian method to infer population structures using multiple unlinked single nucleotide polymorphisms (SNPs). Our approach explicitly considers the population correlation through a tree hierarchy, and treat the population number as a random variable. Using both simulated and real datasets of worldwide samples, we demonstrate that an incorporated tree can consistently improve the power in detecting subtle population stratifications. A tree-based model often involves a large number of unknown parameters, and the corresponding estimation procedure can be highly inefficient. We further implement a partition method to analytically integrate out all nuisance parameters in the tree. As a result, our method can analyze large SNP datasets with significantly improved convergence rate.


AVAILABILITY
http://www.stat.psu.edu/~yuzhang/tips.tar.
32462907
Alignment of Optical Maps
We introduce a new scoring method for calculation of alignments of optical maps. Missing cuts, false cuts, and sizing errors present in optical maps are addressed by our alignment score through calculation of corresponding likelihoods. The size error model is derived through the application of Central Limit Theorem and validated by residual plots collected from real data. Missing cuts and false cuts are modeled as Bernoulli and Poisson events, respectively, as suggested by previous studies. Likelihoods are used to derive an alignment score through calculation of likelihood ratios for a certain hypothesis test. This allows us to achieve maximal descriminative power for the alignment score. Our scoring method is naturally embedded within a well known DP framework for finding optimal alignments.
29942985
Poisson approximation for significance in genome-wide ChIP-chip tiling arrays
MOTIVATION
A genome-wide ChIP-chip tiling array study requires millions of simultaneous comparisons of hybridization for significance. Controlling the false positive rate in genome-wide tiling array studies is very important, because the number of computationally identified regions can easily go beyond the capability of experimental verification. No accurate and efficient method exists for evaluating statistical significance in tiling arrays. The Bonferroni method is overly conservative and the permutation test is time consuming for genome-wide studies.


RESULT
Motivated by the Poisson clumping heuristic, we propose an accurate and efficient method for evaluating statistical significance in genome-wide ChIP-chip tiling arrays. The method works accurately for any large number of multiple comparisons, and the computational cost for evaluating P-values does not increase with the total number of tests. Based on a moving window approach, we demonstrate how to combine results using various window sizes to increase the detection power while maintaining a specified type I error rate. We further introduce a new false discovery rate control that is more appropriate in measuring the false proportion of binding intervals in tiling array analysis. Our method is general and can be applied to many large-scale genomic and genetic studies.


AVAILABILITY
http://www.stat.psu.edu/~yuzhang/pass.tar
21795877
An Eulerian Path Approach to Global Multiple Alignment for DNA Sequences
With the rapid increase in the dataset of genome sequences, the multiple sequence alignment problem is increasingly important and frequently involves the alignment of a large number of sequences. Many heuristic algorithms have been proposed to improve the speed of computation and the quality of alignment. We introduce a novel approach that is fundamentally different from all currently available methods. Our motivation comes from the Eulerian method for fragment assembly in DNA sequencing that transforms all DNA fragments into a de Bruijn graph and then reduces sequence assembly to a Eulerian path problem. The paper focuses on global multiple alignment of DNA sequences, where entire sequences are aligned into one configuration. Our main result is an algorithm with almost linear computational speed with respect to the total size (number of letters) of sequences to be aligned. Five hundred simulated sequences (averaging 500 bases per sequence and as low as 70% pairwise identity) have been aligned within three minutes on a personal computer, and the quality of alignment is satisfactory. As a result, accurate and simultaneous alignment of thousands of long sequences within a reasonable amount of time becomes possible. Data from an Arabidopsis sequencing project is used to demonstrate the performance.
17912176
Anatomy-based face reconstruction for animation using multi-layer deformation
This paper presents a novel multi-layer deformation (MLD) method for reconstructing animatable, anatomy-based human facial models with minimal manual intervention. Our method is based on adapting a prototype model with the multi-layer anatomical structure to the acquired range data in an ''outside-in'' manner: deformation applied to the external skin layer is propagated along with the subsequent transformations to the muscles, with the final effect of warping the underlying skull. The prototype model has a known topology and incorporates a multi-layer structure hierarchy of physically based skin, muscles, and skull. In the MLD, a global alignment is first carried out to adapt the position, size, and orientation of the prototype model to align it with the scanned data based on measurements between a subset of specified anthropometric landmarks. In the skin layer adaptation, the generic skin mesh is represented as a dynamic deformable model which is subjected to internal force stemming from the elastic properties of the surface and external forces generated by input data points and features. A fully automated approach has been developed for adapting the underlying muscle layer which consists of three types of physically based facial muscle models. MLD deforms a set of automatically generated skull feature points according to the adapted external skin and muscle layers. The new positions of these feature points are then used to drive a volume morphing applied to the template skull model. We demonstrate our method by applying it to generate a wide range of different facial models on which various facial expressions are animated.
14143063
Forming Proactive Team Cooperation by Observations
Proactivity is the ability to take initiative by exhibiting goal-directed behavior. Agents with proactivity can respond to dynamic environment in a timely way. Hence the ability to anticipate the information needs of teammates and assist them proactively is highly desirable. This research is directed toward helping agents produce effective communication through observations. We show how agents can use observation to estimate the teammates' beliefs and proactively provide the information that the teammates need. We present two experiments that explore: 1) effectiveness of different aspects of observability; 2) scalability of using observability with respect to the number of agents in a team.
41646301
A Comparison of Broadcast Strategy in MIMO Relay Networks
In this paper, the sum rate issue of a multiple-input multiple-output (MIMO) relay broadcast channel is studied, where the fixed relay station is used to support multiuser transmission in a downlink channel. With appropriate design, the sum rate can be expressed as a function of the processing units at the base station (BS) and relay, and the power allocation can be converted to a standard convex problem. We compared the sum rate of MIMO relay broadcast channel (BC) using time division multiple access (TDMA) to the strongest user, dirty paper coding (DPC) and beamforming (BF) when multiple antennas are deployed at each terminal in the system and separate power constraints at the BS and relay. Then, the sum rate bounds for each strategy and the sum capacity (achieved by DPC) gain over TDMA and BF are given, correspondingly. Finally, numerical results are presented to prove our discussions. With these results, we can easily obtain how far away TDMA and BF are from being optimal in terms of sum rate, and direct the practical system design.
759478
A New Load Balancing Scheme for Distributed Multi-Agent Simulations
Disclosed is a heat sink clip assembly for releaseably attaching a heat sink to a DIP or similar electronic device package. The clip assembly includes a non-conductive attachment clip which extends between the leads on the underside of the DIP and means for latching the attachment clip to a heat sink disposed adjacent the opposite side of the electronic device package with the heat sink in intimate thermal contact with the electronic device package.
15016600
Addressing Collaborative Attacks and Defense in Ad Hoc Wireless Networks
Since ad hoc networks rely on nodes cooperation to establish communication, malicious nodes can compromise the entire network. If they collaborate the devastation is even worse. Collaborative attacks may cause more devastating impacts on wireless environments than single and uncoordinated groups of attacks, as they combine efforts of more than one attacker against the target victim. In this paper, we present the most important forms of attacks,discuss possible collaborations among attackers, show how machine learning techniques and signal processing techniques can be used to detect and defend against collaborative attacks in such environments, and discuss implementation issues.