Rapid haplotype inference for nuclear families

Hapi is a new dynamic programming algorithm that ignores uninformative states and state transitions in order to efficiently compute minimum-recombinant and maximum likelihood haplotypes. When applied to a dataset containing 103 families, Hapi performs 3.8 and 320 times faster than state-of-the-art algorithms. Because Hapi infers both minimum-recombinant and maximum likelihood haplotypes and applies to related individuals, the haplotypes it infers are highly accurate over extended genomic distances.National Institutes of Health (U.S.) (NIH grant 5-T90-DK070069)National Institutes of Health (U.S.) (Grant 5-P01-NS055923)National Science Foundation (U.S.) (Graduate Research Fellowship

Evidentialism and Moral Encroachment

Moral encroachment holds that the epistemic justification of a belief can be affected by moral factors. If the belief might wrong a person or group more evidence is required to justify the belief. Moral encroachment thereby opposes evidentialism, and kindred views, which holds that epistemic justification is determined solely by factors pertaining to evidence and truth. In this essay I explain how beliefs such as ‘that woman is probably an administrative assistant’—based on the evidence that most women employees at the firm are administrative assistants—motivate moral encroachment. I then describe weaknesses of moral encroachment. Finally I explain how we can countenance the moral properties of such beliefs without endorsing moral encroachment, and I argue that the moral status of such beliefs cannot be evaluated independently from the understanding in which they are embedded

Characterizing and improving passive-active shufflers for assays of 208-Liter waste drums

A passive and active neutron shuffler for 208-L waste drums has been used to perform over 1500 active and 500 passive measurements on uranium and plutonium samples in 28 different matrices. The shuffler is now better characterized and improvements have been implemented or suggested. An improved correction for the effects of the matrix material was devised from flux-monitor responses. The most important cause of inaccuracies in assays is a localized instead of a uniform distribution of fissile material in a drum; a technique for deducing the distribution from the assay data and then applying a correction is suggested and will be developed further. A technique is given to detect excessive amounts of moderator that could make hundreds of grams of {sup 235}U assay as zero grams. Sensitivities (minimum detectable masses) for {sup 235}U with active assays and for {sup 240}Pu{sub eff} with passive assays are presented and the effects of moderators and absorbers on sensitivities noted

A Type System for Safe Region-Based Memory Management In Real-Time Java

The Real-Time Specification for Java (RTSJ) allows a program to create real-time threads with hard real-time constraints. Real-time threads use region-based memory management to avoid unbounded pauses caused by interference from the garbage collector. The RTSJ uses runtime checks to ensure that deleting a region does not create dangling references and that real-time threads do not access references to objects allocated in the garbage-collected heap. This paper presents a static type system that guarantees that these runtime checks will never fail for well-typed programs. Our type system therefore 1) provides an important safety guarantee for real-time programs and 2) makes it possible to eliminate the runtime checks and their associated overhead. Our system also makes several contributions over previous work on region types. For object-oriented programs, it combines the benefits of region types and ownership types in a unified type system framework. For multithreaded programs, it allows long-lived threads to share objects without using the heap and without memory leaks. For real-time programs, it ensures that real-time threads do not interfere with the garbage collector. Our experience indicates that our type system is sufficiently expressive and requires little programming overhead, and that eliminating the RTSJ runtime checks using a static type system can significantly decrease the execution time of real-time programs