On denoising and compression of DNA microarray images

We address the problems of noise and huge data sizes in microarray images. First, we propose a mixture model for describing the statistical and structural properties of microarray images. Then, based on the microarray image model, we present methods for denoising and for compressing microarray images. The denoising method is based on a variant of the translation-invariant wavelet transform. The compression method introduces the notion of approximate contexts (rather than traditional exact contexts) in modeling the symbol probabilities in a microarray image. This inexact context modeling approach is important in dealing with the noisy nature of microarray images. Using the proposed denoising and compression methods, we describe a near-lossless compression scheme suitable for microarray images. Results on both denoising and compression are included, which show the performance of the proposed methods. Further experiments using the results of the proposed near-lossless compression scheme in gene clustering using cell-cycle microarray data for S. cerevisiae showed a general improvement in the clustering performance, when compared with using the original data. This provides an indirect validation of the effectiveness of the proposed denoising method.     

形式化语言在UMTS开发中的应用

由于3G协议规范的复杂性，3GPP方法论指导方针中鼓励使用标准的形式化语言来进行UMTS产品的设计、开发与测试。文中概要性地描述了UMTS的体系结构和在规范描述中用到的一些形式化语言的基本概念和特点，探讨了这些形式化语言在UMTS开发中的应用。使用形式化语言开发UMTS可以简化和改进测试程序，实现新产品与新标准的同步推出。     

The influence of directional associations on directed forgetting and interference.

Two experiments examined how cross-list directional associations influenced list-method directed forgetting and the degree of interference observed on each list. Each List 1 item had a (a) bidirectionally related item on List 2 (chip ←→ potato), (b) forward association with an item on List 2 (chip → wood), (c) backward association from an item on List 2 (chip ← chisel), or (d) no relationship with List 2 items. The results revealed that associative relationships that eliminated retroactive interference in the baseline condition also eliminated the directed forgetting costs. In contrast, associative relationships did not affect List 2 recall in the forget group, which remained unchanged across experimental conditions. However, certain conditions reduced proactive interference in the remember group, thereby eliminating the benefits of directed forgetting. The directed forgetting costs and benefits were observed independently of each other. The authors propose that these effects emerged from a combination of item and context strengthening induced by different associative directions. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The Construction of Minimal DNA Expressions

We describe a formal language/notation for DNA molecules that may contain nicks and gaps. The elements of the language, DNA expressions, denote formal DNA molecules. Different DNA expressions may denote the same formal DNA molecule. We analyse the shortest DNA expressions denoting a given formal DNA molecule. We determine lower bounds on their lengths and explain how we construct these minimal DNA expressions.     

Generation and context memory.

Generation enhances memory for occurrence but may not enhance other aspects of memory. The present study further delineates the negative generation effect in context memory reported in N. W. Mulligan (2004). First, the negative generation effect occurred for perceptual attributes of the target item (its color and font) but not for extratarget aspects of context (location and background color). Second, nonvisual generation tasks with either semantic or nonsemantic generation rules (antonym and rhyme generation, respectively) produced the same pattern of results. In contrast, a visual (or data-driven) generation task (letter transposition) did not disrupt context memory for color. Third, generating nonwords produced no effect on item memory but persisted in producing a negative effect on context memory for target attributes, implying that (a) the negative generation effect in context memory is not mediated by semantic encoding, and (b) the negative effect on context memory can be dissociated from the positive effect on item memory. The results are interpreted in terms of the processing account of generation. The original, perceptual-conceptual version of this account is too narrow, but a modified processing account, based on a more generic visual versus nonvisual processing distinction, accommodates the results. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Reasoning, Integration, Inference Alteration, and Text Comprehension.

This paper reports how the study of formal logical reasoning provides insight into more everyday types of reasoning, such as that involved in language comprehension. Both of these types of cognition are thought to involve the use of mental models, and so it is reasonable to think that the cognitive operations needed for formal logical reasoning would be involved in everyday reasoning as well. We focused on three aspects of formal reasoning: (a) the integration of information into a common mental model, (b) the drawing of inferences, and (c) the coordination of alternative possibilities. We were able to show that the integration and inference components were related to narrative comprehension processes, but the coordination of alternative models was not. Thus, there is evidence for some overlap in the mental processes used in formal and everyday reasoning. This further justifies the study of formal logical reasoning as a window into certain types of everyday reasoning. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The Amygdala Modulates Hippocampus-Dependent Context Memory Formation and Stores Cue-Shock Associations.

Preexposing rats to the context facilitates subsequent contextual fear conditioning. This effect depends on the hippocampus (J. W. Rudy, R. M. Barrientos, & R. C. O'Reilly, 2002). The authors report that inactivating the basolateral region of the amygdala (BLA) by injecting muscimol, a GABAA agonist, before or after preexposure reduced this effect. In contrast, bilateral injections of anisomycin, a protein synthesis inhibitor, into BLA did not impair the consolidation of the context memory. However, when injected after fear conditioning, anisomycin impaired consolidation of both contextual and auditory-cue fear conditioning. Results are consistent with 2 ideas about the amygdala's contribution to memory: (a) It modulates memory formation in other regions of the brain, and (b) it is a storage site for cue-shock associations. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Stability of formal thought disorder and referential communication disturbances in schizophrenia.

This study examined the degree to which different types of communication disturbances in the speech of 48 schizophrenia patients and 28 controls were variable and state related versus stable and traitlike. Clinically rated formal thought disorder and 5 types of referential disturbance showed substantial stability within participants over time. The sixth type of referential disturbance, the vague reference, was not stable over time. Formal thought disorder was associated with the severity of core psychotic symptoms in patients, whereas referential disturbances showed little or no association with positive or negative symptom severity. Furthermore, changes in psychotic symptoms over time were accompanied by corresponding changes in formal thought disorder but not referential disturbances. These results support the idea that some types of referential disturbances are traitlike and may be reflective of vulnerability as well as manifest illness. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Generation and Memory for Contextual Detail.

Generation enhances item memory but may not enhance other aspects of memory. In 12 experiments, the author investigated the effect of generation on context memory, motivated in part by the hypothesis that generation produces a trade-off in encoding item and contextual information. Participants generated some study words (e.g., hot-___) and read others (e.g., hot-cold). Generation consistently enhanced item memory but did not enhance context memory. More specifically, generation disrupted context memory for the color of the target word but did not affect context memory for location, background color, and cue-word color. The specificity of the negative generation effect in context memory argues against a general item-context trade-off. A processing account of generation meets greater success. In addition, the results provide no evidence that generation enhances recollection of contextual details. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Experience with Applying Formal Methods to Protocol Specification and System Architecture

In the last three years or so we at Enterprise Platforms Group at Intel Corporation have been applying formal methods to various problems that arose during the process of defining platform architectures for Intel's processor families. In this paper we give an overview of some of the problems we have worked on, the results we have obtained, and the lessons we have learned. The last topic is addressed mainly from the perspective of platform architects.