Stony Brook University

About: Stony Brook University is a education organization based out in Stony Brook, New York, United States. It is known for research contribution in the topics: Population & Poison control. The organization has 32534 authors who have published 68218 publications receiving 3035131 citations. The organization is also known as: State University of New York at Stony Brook & SUNY Stony Brook.

Address obfuscation: an efficient approach to combat a board range of memory error exploits

Abstract: Attacks which exploit memory programming errors (such as buffer overflows) are one of today's most serious security threats. These attacks require an attacker to have an in-depth understanding of the internal details of a victim program, including the locations of critical data and/or code. Program obfuscation is a general technique for securing programs by making it difficult for attackers to acquire such a detailed understanding. This paper develops a systematic study of a particular kind of obfuscation called address obfuscation that randomizes the location of victim program data and code. We discuss different implementation strategies to randomize the absolute locations of data and code, as well as relative distances between data locations. We then present our implementation that transforms object files and executables at link-time and load-time. It requires no changes to the OS kernel or compilers, and can be applied to individual applications without affecting the rest of the system. It can be implemented with low runtime overheads. Address obfuscation can reduce the probability of successful attacks to be as low as a small fraction of a percent for most memory-error related attacks. Moreover, the randomization ensures that an attack that succeeds against one victim will likely not succeed against another victim, or even for a second time against the same victim. Each failed attempt will typically crash the victim program, thereby making it easy to detect attack attempts. These aspects make it particularly effective against large-scale attacks such as Code Red, since each infection attempt requires significantly more resources, thereby slowing down the propagation rate of such attacks.

Predicting extinction risks under climate change: coupling stochastic population models with dynamic bioclimatic habitat models.

Abstract: Species responses to climate change may be influenced by changes in available habitat, as well as population processes, species interactions and interactions between demographic and landscape dynamics. Current methods for assessing these responses fail to provide an integrated view of these influences because they deal with habitat change or population dynamics, but rarely both. In this study, we linked a time series of habitat suitability models with spatially explicit stochastic population models to explore factors that influence the viability of plant species populations under stable and changing climate scenarios in South African fynbos, a global biodiversity hot spot. Results indicate that complex interactions between life history, disturbance regime and distribution pattern mediate species extinction risks under climate change. Our novel mechanistic approach allows more complete and direct appraisal of future biotic responses than do static bioclimatic habitat modelling approaches, and will ultimately support development of more effective conservation strategies to mitigate biodiversity losses due to climate change.

A human functional protein interaction network and its application to cancer data analysis

Abstract: One challenge facing biologists is to tease out useful information from massive data sets for further analysis. A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system. We have constructed a protein functional interaction network by extending curated pathways with non-curated sources of information, including protein-protein interactions, gene coexpression, protein domain interaction, Gene Ontology (GO) annotations and text-mined protein interactions, which cover close to 50% of the human proteome. By applying this network to two glioblastoma multiforme (GBM) data sets and projecting cancer candidate genes onto the network, we found that the majority of GBM candidate genes form a cluster and are closer than expected by chance, and the majority of GBM samples have sequence-altered genes in two network modules, one mainly comprising genes whose products are localized in the cytoplasm and plasma membrane, and another comprising gene products in the nucleus. Both modules are highly enriched in known oncogenes, tumor suppressors and genes involved in signal transduction. Similar network patterns were also found in breast, colorectal and pancreatic cancers. We have built a highly reliable functional interaction network upon expert-curated pathways and applied this network to the analysis of two genome-wide GBM and several other cancer data sets. The network patterns revealed from our results suggest common mechanisms in the cancer biology. Our system should provide a foundation for a network or pathway-based analysis platform for cancer and other diseases.

Genetic control of programmed cell death in the Caenorhabditis elegans hermaphrodite germline.

Abstract: Development of the nematode Caenorhabditis elegans is highly reproducible and the fate of every somatic cell has been reported. We describe here a previously uncharacterized cell fate in C. elegans: we show that germ cells, which in hermaphrodites can differentiate into sperm and oocytes, also undergo apoptotic cell death. In adult hermaphrodites, over 300 germ cells die, using the same apoptotic execution machinery (ced-3, ced-4 and ced-9) as the previously described 131 somatic cell deaths. However, this machinery is activated by a distinct pathway, as loss of egl-1 function, which inhibits somatic cell death, does not affect germ cell apoptosis. Germ cell death requires ras/MAPK pathway activation and is used to maintain germline homeostasis. We suggest that apoptosis eliminates excess germ cells that acted as nurse cells to provide cytoplasmic components to maturing oocytes.

Ad hoc on-demand multipath distance vector routing

Abstract: We develop an on-demand, multipath distance vector routing protocol for mobile ad hoc networks. Specifically, we propose multipath extensions to a well-studied single path routing protocol known as ad hoc on-demand distance vector (AODV). The resulting protocol is referred to as ad hoc on-demand multipath distance vector (AOMDV). The protocol guarantees loop freedom and disjointness of alternate paths. Performance comparison of AOMDV with AODV using ns-2 simulations shows that AOMDV is able to effectively cope with mobility-induced route failures. In particular, it reduces the packet loss by up to 40% and achieves a remarkable improvement in the end-to-end delay (often more than a factor of two). AOMDV also reduces routing overhead by about 30% by reducing the frequency of route discovery operations. Copyright © 2006 John Wiley & Sons, Ltd.