Holevo-Ordering and the Continuous-Time Limit for Open Floquet Dynamics

Gough, John, (2004) 'Holevo-Ordering and the Continuous-Time Limit for Open Floquet Dynamics', Letters in Mathematical Physcis 67(3) pp.207-221 RAE2008

Columnar-to-disk structural transition in nanoscale (SiO2)(N) clusters

Bromley, S. T., Flikkema, E. (2005) 'Columnar-to-disk structural transition in nanoscale (SiO2)(N) clusters'. Physical Review Letters 95 (18), article no: 185505 RAE2008

open source spirituality: turning the world upside down

Sermon preached at Boston University School of Theology during Wednesday Chapel on October 24, 2007

Scholarship, Libraries, and Open Access Archiving Initiative

The resolution passed by the BU University Council approving an initiative to establish an archive of the research and scholarship produced by the faculty of the University.

OPEN DOORS AND OPEN MINDS: WHAT FACULTY AUTHORS CAN DO TO ENSURE OPEN ACCESS TO THEIR WORK THROUGH THEIR INSTITUTION

The Internet has brought unparalleled opportunities for expanding availability of research by bringing down economic and physical barriers to sharing. The digitally networked environment promises to democratize access, carry knowledge beyond traditional research niches, accelerate discovery, encourage new and interdisciplinary approaches to ever more complex research challenges, and enable new computational research strategies. However, despite these opportunities for increasing access to knowledge, the prices of scholarly journals have risen sharply over the past two decades, often forcing libraries to cancel subscriptions. Today even the wealthiest institutions cannot afford to sustain all of the journals needed by their faculties and students. To take advantage of the opportunities created by the Internet and to further their mission of creating, preserving, and disseminating knowledge, many academic institutions are taking steps to capture the benefits of more open research sharing. Colleges and universities have built digital repositories to preserve and distribute faculty scholarly articles and other research outputs. Many individual authors have taken steps to retain the rights they need, under copyright law, to allow their work to be made freely available on the Internet and in their institutionâ s repository. And, faculties at some institutions have adopted resolutions endorsing more open access to scholarly articles. Most recently, on February 12, 2008, the Faculty of Arts and Sciences (FAS) at Harvard University took a landmark step. The faculty voted to adopt a policy requiring that faculty authors send an electronic copy of their scholarly articles to the universityâ s digital repository and that faculty authors automatically grant copyright permission to the university to archive and to distribute these articles unless a faculty member has waived the policy for a particular article. Essentially, the faculty voted to make open access to the results of their published journal articles the default policy for the Faculty of Arts and Sciences of Harvard University. As of March 2008, a proposal is also under consideration in the University of California system by which faculty authors would commit routinely to grant copyright permission to the university to make copies of the facultyâ s scholarly work openly accessible over the Internet. Inspired by the example set by the Harvard faculty, this White Paper is addressed to the faculty and administrators of academic institutions who support equitable access to scholarly research and knowledge, and who believe that the institution can play an important role as steward of the scholarly literature produced by its faculty. This paper discusses both the motivation and the process for establishing a binding institutional policy that automatically grants a copyright license from each faculty member to permit deposit of his or her peer-reviewed scholarly articles in institutional repositories, from which the works become available for others to read and cite.

3'-UTR SIRF: A database for identifying clusters of short interspersed repeats in 3' untranslated regions

BACKGROUND:Short (~5 nucleotides) interspersed repeats regulate several aspects of post-transcriptional gene expression. Previously we developed an algorithm (REPFIND) that assigns P-values to all repeated motifs in a given nucleic acid sequence and reliably identifies clusters of short CAC-containing motifs required for mRNA localization in Xenopus oocytes.DESCRIPTION:In order to facilitate the identification of genes possessing clusters of repeats that regulate post-transcriptional aspects of gene expression in mammalian genes, we used REPFIND to create a database of all repeated motifs in the 3' untranslated regions (UTR) of genes from the Mammalian Gene Collection (MGC). The MGC database includes seven vertebrate species: human, cow, rat, mouse and three non-mammalian vertebrate species. A web-based application was developed to search this database of repeated motifs to generate species-specific lists of genes containing specific classes of repeats in their 3'-UTRs. This computational tool is called 3'-UTR SIRF (Short Interspersed Repeat Finder), and it reveals that hundreds of human genes contain an abundance of short CAC-rich and CAG-rich repeats in their 3'-UTRs that are similar to those found in mRNAs localized to the neurites of neurons. We tested four candidate mRNAs for localization in rat hippocampal neurons by in situ hybridization. Our results show that two candidate CAC-rich (Syntaxin 1B and Tubulin beta4) and two candidate CAG-rich (Sec61alpha and Syntaxin 1A) mRNAs are localized to distal neurites, whereas two control mRNAs lacking repeated motifs in their 3'-UTR remain primarily in the cell body.CONCLUSION:Computational data generated with 3'-UTR SIRF indicate that hundreds of mammalian genes have an abundance of short CA-containing motifs that may direct mRNA localization in neurons. In situ hybridization shows that four candidate mRNAs are localized to distal neurites of cultured hippocampal neurons. These data suggest that short CA-containing motifs may be part of a widely utilized genetic code that regulates mRNA localization in vertebrate cells. The use of 3'-UTR SIRF to search for new classes of motifs that regulate other aspects of gene expression should yield important information in future studies addressing cis-regulatory information located in 3'-UTRs.

Services to support BU Authors with Open Access Issues

A working paper written for Boston University Libraries to foster discussion about how to provide better support for BU faculty authors.

Discovering Clusters in Motion Time-Series Data

A new approach is proposed for clustering time-series data. The approach can be used to discover groupings of similar object motions that were observed in a video collection. A finite mixture of hidden Markov models (HMMs) is fitted to the motion data using the expectation-maximization (EM) framework. Previous approaches for HMM-based clustering employ a k-means formulation, where each sequence is assigned to only a single HMM. In contrast, the formulation presented in this paper allows each sequence to belong to more than a single HMM with some probability, and the hard decision about the sequence class membership can be deferred until a later time when such a decision is required. Experiments with simulated data demonstrate the benefit of using this EM-based approach when there is more "overlap" in the processes generating the data. Experiments with real data show the promising potential of HMM-based motion clustering in a number of applications.

Open Issues on TCP for Mobile Computing

We discuss the design principles of TCP within the context of heterogeneous wired/wireless networks and mobile networking. We identify three shortcomings in TCP's behavior: (i) the protocol's error detection mechanism, which does not distinguish different types of errors and thus does not suffice for heterogeneous wired/wireless environments, (ii) the error recovery, which is not responsive to the distinctive characteristics of wireless networks such as transient or burst errors due to handoffs and fading channels, and (iii) the protocol strategy, which does not control the tradeoff between performance measures such as goodput and energy consumption, and often entails a wasteful effort of retransmission and energy expenditure. We discuss a solution-framework based on selected research proposals and the associated evaluation criteria for the suggested modifications. We highlight an important angle that did not attract the required attention so far: the need for new performance metrics, appropriate for evaluating the impact of protocol strategies on battery-powered devices.

Searching the Sky with CONFIGR-STARS

SyNAPSE program of the Defense Advanced Projects Research Agency (HRL Laboratories LLC, subcontract #801881-BS under DARPA prime contract HR0011-09-C-0001); CELEST, a National Science Foundation Science of Learning Center (SBE-0354378)

Metacomputing on clusters augmented with reconfigurable hardware

Accepted Version

Nano-urchin: The formation and structure of high-density spherical clusters of vanadium oxide nanotubes

We report the observation of urchin-like nanostructures consisting of high-density spherical nanotube radial arrays of vanadium oxide nanocomposite, successfully synthesized by a simple chemical route using an ethanolic solution of vanadium tri-isopropoxide and alkyl amine hexadecylamine for 7 days at 180oC. The results show that the growth process of the NanoUrchin occurs in stages, starting with a radial self-organized arrangement of lamina followed by the rolling of the lamina into nanotubes. The longest nanotubes are measured to be several micrometers in length with diameters of ~120 nm and hollow centers typically measured to be ~75 nm. The NanoUrchin have an estimated density of nanotubes of ~40 sr-1. The tube walls comprise layers of vanadium oxide with the organic surfactant intercalated between atomic layers. The interlayer distance is measured to be 2.9 ± 0.1 nm and electron diffraction identified the vanadate phase in the VOx nanocomposite as orthorhombic V2O5. These nanostructures may be used as three-dimensional composite materials and as supports for other materials.

Reactivity of sub 1 nm supported clusters: (TiO2)(n) clusters supported on rutile TiO2 (110)

Metal oxide clusters of sub-nm dimensions dispersed on a metal oxide support are an important class of catalytic materials for a number of key chemical reactions, showing enhanced reactivity over the corresponding bulk oxide. In this paper we present the results of a density functional theory study of small sub-nm TiO2 clusters, Ti2O4, Ti3O6 and Ti4O8 supported on the rutile (110) surface. We find that all three clusters adsorb strongly with adsorption energies ranging from -3 eV to -4.5 eV. The more stable adsorption structures show a larger number of new Ti-O bonds formed between the cluster and the surface. These new bonds increase the coordination of cluster Ti and O as well as surface oxygen, so that each has more neighbours. The electronic structure shows that the top of the valence band is made up of cluster derived states, while the conduction band is made up of Ti 3d states from the surface, resulting in a reduction of the effective band gap and spatial separation of electrons and holes after photon absorption, which shows their potential utility in photocatalysis. To examine reactivity, we study the formation of oxygen vacancies in the cluster-support system. The most stable oxygen vacancy sites on the cluster show formation energies that are significantly lower than in bulk TiO2, demonstrating the usefulness of this composite system for redox catalysis.

Characterisation of the microbiota of traditional fermented beverages and screening these and other populations for novel antimicrobial producers and gene clusters

To screen for novel ribosomally synthesised antimicrobials, in-silico genome mining was performed on all publically available fully sequenced bacterial genomes. 49 novel type 1 lantibiotic clusters were identified from a number of species, genera and phyla not usually associated with lantibiotic production, and indicates high prevalence. A crucial step towards the commercialisation of fermented beverages is the characterisation of the microbial content. To achieve this goal, we applied next-generation sequencing techniques to analyse the bacterial and yeast populations of the organic, symbiotically-fermented beverages kefir, water kefir and kombucha. A number of minor components were revealed, many of which had not previously been associated with these beverages. The dominant microorganism in each of the water kefir grains and fermentates was Zymomonas, an ethanol-producing bacterium that had not previously been detected on such a scale. These studies represent the most accurate description of these populations to date, and should aid in future starter design and in determining which species are responsible for specific attributes of the beverages. Finally, high-throughput robotics was applied to screen for the presence of antimicrobial producers associated with these beverages. This revealed a low frequency of bacteriocin production amongst the bacterial isolates, with only lactococcins A, B and LcnN of lactococcin M being identified. However, a proteinaceous antimicrobial produced by the yeast Dekkera bruxellensis, isolated from kombucha, was found to be active against Lactobacillus bulgaricus. This peptide was patially purified.

Subterfuge-safe trust management for delegation of permissions in open environments

Open environments involve distributed entities interacting with each other in an open manner. Many distributed entities are unknown to each other but need to collaborate and share resources in a secure fashion. Usually resource owners alone decide who is trusted to access their resources. Since resource owners in open environments do not have a complete picture of all trusted entities, trust management frameworks are used to ensure that only authorized entities will access requested resources. Every trust management system has limitations, and the limitations can be exploited by malicious entities. One vulnerability is due to the lack of globally unique interpretation for permission specifications. This limitation means that a malicious entity which receives a permission in one domain may misuse the permission in another domain via some deceptive but apparently authorized route; this malicious behaviour is called subterfuge. This thesis develops a secure approach, Subterfuge Safe Trust Management (SSTM), that prevents subterfuge by malicious entities. SSTM employs the Subterfuge Safe Authorization Language (SSAL) which uses the idea of a local permission with a globally unique interpretation (localPermission) to resolve the misinterpretation of permissions. We model and implement SSAL with an ontology-based approach, SSALO, which provides a generic representation for knowledge related to the SSAL-based security policy. SSALO enables integration of heterogeneous security policies which is useful for secure cooperation among principals in open environments where each principal may have a different security policy with different implementation. The other advantage of an ontology-based approach is the Open World Assumption, whereby reasoning over an existing security policy is easily extended to include further security policies that might be discovered in an open distributed environment. We add two extra SSAL rules to support dynamic coalition formation and secure cooperation among coalitions. Secure federation of cloud computing platforms and secure federation of XMPP servers are presented as case studies of SSTM. The results show that SSTM provides robust accountability for the use of permissions in federation. It is also shown that SSAL is a suitable policy language to express the subterfuge-safe policy statements due to its well-defined semantics, ease of use, and integrability.