Divided we stand: Parallel distributed stack memory management

We present an overview of the stack-based memory management techniques that we used in our non-deterministic and-parallel Prolog systems: &-Prolog and DASWAM. We believe that the problems associated with non-deterministic and-parallel systems are more general than those encountered in or-parallel and deterministic and-parallel systems, which can be seen as subsets of this more general case. We develop on the previously proposed "marker scheme", lifting some of the restrictions associated with the selection of goals while keeping (virtual) memory consumption down. We also review some of the other problems associated with the stack-based management scheme, such as handling of forward and backward execution, cut, and roll-backs.

Issues in implementing ACE: A stack copying based and-or parallel system

We discuss several issues involved in the implementation of ACE, a model capable of exploiting both And-parallelism and Or-parallelism in Prolog in a unified framework. The Orparallel model that ACE employs is based on the idea of stack-copying developed for Muse, while the model of independent And-parallelism is based on the distributed stack approach of &-Prolog. We discuss the organization of the workers, a number of sharing assumtions, techniques for work load detection, and issues relaed to which parts need to be copied when a flexible and-scheduling strategy is used.

Anterograde flow of cargo across the Golgi stack potentially mediated via bidirectional “percolating” COPI vesicles

How do secretory proteins and other cargo targeted to post-Golgi locations traverse the Golgi stack? We report immunoelectron microscopy experiments establishing that a Golgi-restricted SNARE, GOS 28, is present in the same population of COPI vesicles as anterograde cargo marked by vesicular stomatitis virus glycoprotein, but is excluded from the COPI vesicles containing retrograde-targeted cargo (marked by KDEL receptor). We also report that GOS 28 and its partnering t-SNARE heavy chain, syntaxin 5, reside together in every cisterna of the stack. Taken together, these data raise the possibility that the anterograde cargo-laden COPI vesicles, retained locally by means of tethers, are inherently capable of fusing with neighboring cisternae on either side. If so, quanta of exported proteins would transit the stack in GOS 28–COPI vesicles via a bidirectional random walk, entering at the cis face and leaving at the trans face and percolating up and down the stack in between. Percolating vesicles carrying both post-Golgi cargo and Golgi residents up and down the stack would reconcile disparate observations on Golgi transport in cells and in cell-free systems.

STACK: Sequence Tag Alignment and Consensus Knowledgebase

STACK is a tool for detection and visualisation of expressed transcript variation in the context of developmental and pathological states. The datasystem organises and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body index and is accessible via WWW at http://www.sanbi.ac.za/Dbases.html. STACK represents a broadly applicable resource, as it is the only reconstructed transcript database for which the tools for its generation are also broadly available (http://www.sanbi.ac.za/CODES).

Pliocene-Pleistocene stack of globally distributed benthic stable oxygen isotope records

We present a 5.3-Myr stack (the ''LR04'' stack) of benthic d18O records from 57 globally distributed sites aligned by an automated graphic correlation algorithm. This is the first benthic delta18O stack composed of more than three records to extend beyond 850 ka, and we use its improved signal quality to identify 24 new marine isotope stages in the early Pliocene. We also present a new LR04 age model for the Pliocene-Pleistocene derived from tuning the delta18O stack to a simple ice model based on 21 June insolation at 65 N. Stacked sedimentation rates provide additional age model constraints to prevent overtuning. Despite a conservative tuning strategy, the LR04 benthic stack exhibits significant coherency with insolation in the obliquity band throughout the entire 5.3 Myr and in the precession band for more than half of the record. The LR04 stack contains significantly more variance in benthic delta18O than previously published stacks of the late Pleistocene as the result of higher resolution records, a better alignment technique, and a greater percentage of records from the Atlantic. Finally, the relative phases of the stack's 41- and 23-kyr components suggest that the precession component of delta18O from 2.7-1.6 Ma is primarily a deep-water temperature signal and that the phase of d18O precession response changed suddenly at 1.6 Ma.