Genome sequence assembly: algorithms and issues

Ultimately, genome sequencing seeks to provide an organism's complete DNA sequence. Automation of DNA sequencing allowed scientists to decode entire genomes and gave birth to genomics, the analytic and comparative study of genomes. Although genomes can include billions of nucleotides, the chemical reactions researchers use to decode the DNA are accurate for only about 600 to 700 nucleotides at a time. The DNA reads that sequencing produces must then be assembled into a complete picture of the genome. Errors and certain DNA characteristics complicate assembly. Resolving these problems entails an additional and costly finishing phase that involves extensive human intervention. Assembly programs can dramatically reduce this cost by taking into account additional information obtained during finishing. The paper considers how algorithms that can assemble millions of DNA fragments into gene sequences underlie the current revolution in biotechnology, helping researchers build the growing database of complete genomes     

The Homothorax homeoprotein activates the nuclear localization of another homeoprotein, extradenticle, and suppresses eye development in Drosophila

The Extradenticle (Exd) protein in Drosophila acts as a cofactor to homeotic proteins. Its nuclear localization is regulated. We report the cloning of the Drosophila homothorax (hth) gene, a homolog of the mouse Meis1 proto-oncogene that has a homeobox related to that of exd. Comparison with Meis1 finds two regions of high homology: a novel MH domain and the homeodomain. In imaginal discs, hth expression coincides with nuclear Exd. hth and exd also have virtually identical, mutant clonal phenotypes in adults. These results suggest that hth and exd function in the same pathway. We show that hth acts upstream of exd and is required and sufficient for Exd protein nuclear localization. We also show that hth and exd are both negative regulators of eye development; their mutant clones caused ectopic eye formation. Targeted expression of hth, but not of exd, in the eye disc abolished eye development completely. We suggest that hth acts with exd to delimit the eye field and prevent inappropriate eye development.     

Log-based middleware server recovery with transaction support

Providing enterprises with reliable and available Web-based application programs is a challenge. Applications are traditionally spread over multiple nodes, from user (client), to middle tier servers, to back end transaction systems, e.g. databases. It has proven very difficult to ensure that these applications persist across system crashes so that “exactly once” execution is produced, always important and sometimes essential, e.g., in the financial area. Our system provides a framework for exactly once execution of multi-tier Web applications, built on a commercially available Web infrastructure. Its capabilities include low logging overhead, recovery isolation (independence), and consistency between mid-tier and transactional back end. Good application performance is enabled via persistent shared state in the middle tier while providing for private session state as well. Our extensive experiments confirm both the desired properties and the good performance.     

Managing information for concurrent engineering: Challenges and barriers

An ongoing research project with a large international manufacturing company has uncovered many critical issues for the development and introduction of systems that supportconcurrent engineering. Several of these issues can be solved through careful interface design, while others require significant technical and organizational changes. To reduce training costs and support a broad spectrum of users, computer system developers must create a single system image, giving the users the impression that they are accessing a single database through a consistent and easy to use interface. This interface, and the tools it contains, may be used to support concurrent engineering activities even when a company is geographically distributed over a large area. The complexity of the firm's products and processes and the need for rapid access to relevant performance information make it essential that developers identify suitable frameworks for organizing database queries.Design hierarchies, representations of the structure and function of the firm's products and processes, have proven to be powerful tools for effective query management, and for efficient navigation through the database. The database interface must also produce integrated displays of data drawn from a number of sources in response to prestructured queries. Beyond these interface design issues, there are a number of technical and organizational barriers to the implementation of large-scale engineering systems. In particular, the existence of many incompatible databases in different parts of an organization makes the introduction of a new, uniform system very difficult. Organizational issues also play a major role in achieving, or hindering, the implementation of new computer systems. This paper describes some of the technical innovations, and the motivations behind them, from one particular engineering design system. It also discusses the reactions of engineers and management, and explains why management may oppose innovation even when engineers enthusiastically support it.     

Minimum water requirements for suppression of room fires

In many areas, it is essential that no water be wasted in fighting fire. How much water is needed to extinguish typical room fires? This is the question the authors sought to answer in the experiments reported here.     

Surgical management of pressure ulcers

Surgical management of pressure ulcers ranges from office or bedside debridement to formal debridement in the operating room for the more extensive necrosis. Closure of these wounds may be by advancement flap closure for the simple ulcers and by local muscle or myocutaneous flap closure for the more complex ulcers and defects. Some pressure ulcers recur following previous surgery or following conservative treatment. The simple recurrences can be managed by the use of simple techniques while the surgical options for the management of the more difficult recurrent ulcers are limited involving more complex surgery like sensate flaps, expanded flaps, free tissue transfers and fillet flaps.     

Best-case results for nearest-neighbor learning

Proposes a theoretical model for analysis of classification methods, in which the teacher knows the classification algorithm and chooses examples in the best way possible. The authors apply this model using the nearest-neighbor learning algorithm, and develop upper and lower bounds on sample complexity for several different concept classes. For some concept classes, the sample complexity turns out to be exponential even using this best-case model, which implies that the concept class is inherently difficult for the NN algorithm. The authors identify several geometric properties that make learning certain concepts relatively easy. Finally the authors discuss the relation of their work to helpful teacher models, its application to decision tree learning algorithms, and some of its implications for experimental work     

A Nearest Hyperrectangle Learning Method

This paper presents a theory of learning called nested generalized exemplar (NGE) theory, in which learning is accomplished by storing objects in Euclidean n-space, En, as hyperrectangles. The hyperrectangles may be nested inside one another to arbitrary depth. In contrast to generalization processes that replace symbolic formulae by more general formulae, the NGE algorithm modifies hyperrectangles by growing and reshaping them in a well-defined fashion. The axes of these hyperrectangles are defined by the variables measured for each example. Each variable can have any range on the real line; thus the theory is not restricted to symbolic or binary values.This paper describes some advantages and disadvantages of NGE theory, positions it as a form of exemplarbased learning, and compares it to other inductive learning theories. An implementation has been tested in three different domains, for which results are presented below: prediction of breast cancer, classification of iris flowers, and prediction of survival times for heart attack patients. The results in these domains support the claim that NGE theory can be used to create compact representations with excellent predictive accuracy.