Institutional Repositories, Policies, and Disruption

For many librarians, institutional repositories (IRs) promised significant change for academic libraries. We envisioned enlarging collection development scope to include locally produced scholarship and an expansion of library services to embrace scholarly publication and distribution. However, at the University of Rochester, as at many other institutions, this transformational technology was introduced in the conservative, controlled manner associated with stereotypical librarian culture, and so these expected changes never materialized. In this case study, we focus on the creation of our institutional repository (a potentially disruptive technology) and how its success was hampered by our organizational culture, manifested as a lengthy and complicated set of policies. In the following pages, we briefly describe our repository project, talk about our original policies, look at the ways those policies impeded our project, and discuss the disruption of those policies and the benefits in user uptake that resulted.

Nutrition or Detoxification: Why Bats Visit Mineral Licks of the Amazonian Rainforest

Many animals in the tropics of Africa, Asia and South America regularly visit so-called salt or mineral licks to consume clay or drink clay-saturated water. Whether this behavior is used to supplement diets with locally limited nutrients or to buffer the effects of toxic secondary plant compounds remains unclear. In the Amazonian rainforest, pregnant and lactating bats are frequently observed and captured at mineral licks. We measured the nitrogen isotope ratio in wing tissue of omnivorous short-tailed fruit bats, Carollia perspicillata, and in an obligate fruit-eating bat, Artibeus obscurus, captured at mineral licks and at control sites in the rainforest. Carollia perspicillata with a plant-dominated diet were more often captured at mineral licks than individuals with an insect-dominated diet, although insects were more mineral depleted than fruits. In contrast, nitrogen isotope ratios of A. obscurus did not differ between individuals captured at mineral lick versus control sites. We conclude that pregnant and lactating fruit-eating bats do not visit mineral licks principally for minerals, but instead to buffer the effects of secondary plant compounds that they ingest in large quantities during periods of high energy demand. These findings have potential implications for the role of mineral licks for mammals in general, including humans.

ACOUSTO-OPTIC IMAGING IN DIFFUSE MEDIA USING PULSED ULTRASOUND AND THE PHOTOREFRACTIVE EFFECT

Acousto-optic imaging (AOI) in optically diffuse media is a hybrid imaging modality in which a focused ultrasound beam is used to locally phase modulate light inside of turbid media. The modulated optical field carries with it information about the optical properties in the region where the light and sound interact. The motivation for the development of AOI systems is to measure optical properties at large depths within biological tissue with high spatial resolution. A photorefractive crystal (PRC) based interferometry system is developed for the detection of phase modulated light in AOI applications. Two-wave mixing in the PRC creates a reference beam that is wavefront matched to the modulated optical field collected from the specimen. The phase modulation is converted to an intensity modulation at the optical detector when these two fields interfere. The interferometer has a high optical etendue, making it well suited for AOI where the scattered light levels are typically low. A theoretical model for the detection of acoustically induced phase modulation in turbid media using PRC based interferometry is detailed. An AOI system, using a single element focused ultrasound transducer to pump the AO interaction and the PRC based detection system, is fabricated and tested on tissue mimicking phantoms. It is found that the system has sufficient sensitivity to detect broadband AO signals generated using pulsed ultrasound, allowing for AOI at low time averaged ultrasound output levels. The spatial resolution of the AO imaging system is studied as a function of the ultrasound pulse parameters. A theoretical model of light propagation in turbid media is used to explore the dependence of the AO response on the experimental geometry, light collection aperture, and target optical properties. Finally, a multimodal imaging system combining pulsed AOI and conventional B- mode ultrasound imaging is developed. B-mode ultrasound and AO images of targets embedded in both highly diffuse phantoms and biological tissue ex vivo are obtained, and millimeter resolution is demonstrated in three dimensions. The AO images are intrinsically co-registered with the B-mode ultrasound images. The results suggest that AOI can be used to supplement conventional B-mode ultrasound imaging with optical information.

Typability and Type Checking in the Second-Order Λ-Calculus Are Equivalent and Undecidable (Preliminary Draft)

We consider the problems of typability[1] and type checking[2] in the Girard/Reynolds second-order polymorphic typed λ-calculus, for which we use the short name "System F" and which we use in the "Curry style" where types are assigned to pure λ -terms. These problems have been considered and proven to be decidable or undecidable for various restrictions and extensions of System F and other related systems, and lower-bound complexity results for System F have been achieved, but they have remained "embarrassing open problems"[3] for System F itself. We first prove that type checking in System F is undecidable by a reduction from semi-unification. We then prove typability in System F is undecidable by a reduction from type checking. Since the reverse reduction is already known, this implies the two problems are equivalent. The second reduction uses a novel method of constructing λ-terms such that in all type derivations, specific bound variables must always be assigned a specific type. Using this technique, we can require that specific subterms must be typable using a specific, fixed type assignment in order for the entire term to be typable at all. Any desired type assignment may be simulated. We develop this method, which we call "constants for free", for both the λK and λI calculi.

A randomized solution to BGP divergence

The Border Gateway Protocol (BGP) is an interdomain routing protocol that allows each Autonomous System (AS) to define its own routing policies independently and use them to select the best routes. By means of policies, ASes are able to prevent some traffic from accessing their resources, or direct their traffic to a preferred route. However, this flexibility comes at the expense of a possibility of divergence behavior because of mutually conflicting policies. Since BGP is not guaranteed to converge even in the absence of network topology changes, it is not safe. In this paper, we propose a randomized approach to providing safety in BGP. The proposed algorithm dynamically detects policy conflicts, and tries to eliminate the conflict by changing the local preference of the paths involved. Both the detection and elimination of policy conflicts are performed locally, i.e. by using only local information. Randomization is introduced to prevent synchronous updates of the local preferences of the paths involved in the same conflict.

Application-Level Document Caching in the Internet

With the increasing demand for document transfer services such as the World Wide Web comes a need for better resource management to reduce the latency of documents in these systems. To address this need, we analyze the potential for document caching at the application level in document transfer services. We have collected traces of actual executions of Mosaic, reflecting over half a million user requests for WWW documents. Using those traces, we study the tradeoffs between caching at three levels in the system, and the potential for use of application-level information in the caching system. Our traces show that while a high hit rate in terms of URLs is achievable, a much lower hit rate is possible in terms of bytes, because most profitably-cached documents are small. We consider the performance of caching when applied at the level of individual user sessions, at the level of individual hosts, and at the level of a collection of hosts on a single LAN. We show that the performance gain achievable by caching at the session level (which is straightforward to implement) is nearly all of that achievable at the LAN level (where caching is more difficult to implement). However, when resource requirements are considered, LAN level caching becomes much more desirable, since it can achieve a given level of caching performance using a much smaller amount of cache space. Finally, we consider the use of organizational boundary information as an example of the potential for use of application-level information in caching. Our results suggest that distinguishing between documents produced locally and those produced remotely can provide useful leverage in designing caching policies, because of differences in the potential for sharing these two document types among multiple users.

Client-based Logging: A New Paradigm of Distributed Transaction Management

The proliferation of inexpensive workstations and networks has created a new era in distributed computing. At the same time, non-traditional applications such as computer-aided design (CAD), computer-aided software engineering (CASE), geographic-information systems (GIS), and office-information systems (OIS) have placed increased demands for high-performance transaction processing on database systems. The combination of these factors gives rise to significant challenges in the design of modern database systems. In this thesis, we propose novel techniques whose aim is to improve the performance and scalability of these new database systems. These techniques exploit client resources through client-based transaction management. Client-based transaction management is realized by providing logging facilities locally even when data is shared in a global environment. This thesis presents several recovery algorithms which utilize client disks for storing recovery related information (i.e., log records). Our algorithms work with both coarse and fine-granularity locking and they do not require the merging of client logs at any time. Moreover, our algorithms support fine-granularity locking with multiple clients permitted to concurrently update different portions of the same database page. The database state is recovered correctly when there is a complex crash as well as when the updates performed by different clients on a page are not present on the disk version of the page, even though some of the updating transactions have committed. This thesis also presents the implementation of the proposed algorithms in a memory-mapped storage manager as well as a detailed performance study of these algorithms using the OO1 database benchmark. The performance results show that client-based logging is superior to traditional server-based logging. This is because client-based logging is an effective way to reduce dependencies on server CPU and disk resources and, thus, prevents the server from becoming a performance bottleneck as quickly when the number of clients accessing the database increases.

Load Profiling in Distributed Real-Time Systems

Load balancing is often used to ensure that nodes in a distributed systems are equally loaded. In this paper, we show that for real-time systems, load balancing is not desirable. In particular, we propose a new load-profiling strategy that allows the nodes of a distributed system to be unequally loaded. Using load profiling, the system attempts to distribute the load amongst its nodes so as to maximize the chances of finding a node that would satisfy the computational needs of incoming real-time tasks. To that end, we describe and evaluate a distributed load-profiling protocol for dynamically scheduling time-constrained tasks in a loosely-coupled distributed environment. When a task is submitted to a node, the scheduling software tries to schedule the task locally so as to meet its deadline. If that is not feasible, it tries to locate another node where this could be done with a high probability of success, while attempting to maintain an overall load profile for the system. Nodes in the system inform each other about their state using a combination of multicasting and gossiping. The performance of the proposed protocol is evaluated via simulation, and is contrasted to other dynamic scheduling protocols for real-time distributed systems. Based on our findings, we argue that keeping a diverse availability profile and using passive bidding (through gossiping) are both advantageous to distributed scheduling for real-time systems.

Visible Volume: a Robust Measure for Protein Structure Characterization

We propose a new characterization of protein structure based on the natural tetrahedral geometry of the β carbon and a new geometric measure of structural similarity, called visible volume. In our model, the side-chains are replaced by an ideal tetrahedron, the orientation of which is fixed with respect to the backbone and corresponds to the preferred rotamer directions. Visible volume is a measure of the non-occluded empty space surrounding each residue position after the side-chains have been removed. It is a robust, parameter-free, locally-computed quantity that accounts for many of the spatial constraints that are of relevance to the corresponding position in the native structure. When computing visible volume, we ignore the nature of both the residue observed at each site and the ones surrounding it. We focus instead on the space that, together, these residues could occupy. By doing so, we are able to quantify a new kind of invariance beyond the apparent variations in protein families, namely, the conservation of the physical space available at structurally equivalent positions for side-chain packing. Corresponding positions in native structures are likely to be of interest in protein structure prediction, protein design, and homology modeling. Visible volume is related to the degree of exposure of a residue position and to the actual rotamers in native proteins. In this article, we discuss the properties of this new measure, namely, its robustness with respect to both crystallographic uncertainties and naturally occurring variations in atomic coordinates, and the remarkable fact that it is essentially independent of the choice of the parameters used in calculating it. We also show how visible volume can be used to align protein structures, to identify structurally equivalent positions that are conserved in a family of proteins, and to single out positions in a protein that are likely to be of biological interest. These properties qualify visible volume as a powerful tool in a variety of applications, from the detailed analysis of protein structure to homology modeling, protein structural alignment, and the definition of better scoring functions for threading purposes.

A Framework for Local Anonymity in the Internet

We describe and evaluate options for providing anonymous IP service, argue for the further investigation of local anonymity, and sketch a framework for the implementation of locally anonymous networks.

Estimating 3D Body Pose Using Uncalibrated Cameras

An approach for estimating 3D body pose from multiple, uncalibrated views is proposed. First, a mapping from image features to 2D body joint locations is computed using a statistical framework that yields a set of several body pose hypotheses. The concept of a "virtual camera" is introduced that makes this mapping invariant to translation, image-plane rotation, and scaling of the input. As a consequence, the calibration matrices (intrinsics) of the virtual cameras can be considered completely known, and their poses are known up to a single angular displacement parameter. Given pose hypotheses obtained in the multiple virtual camera views, the recovery of 3D body pose and camera relative orientations is formulated as a stochastic optimization problem. An Expectation-Maximization algorithm is derived that can obtain the locally most likely (self-consistent) combination of body pose hypotheses. Performance of the approach is evaluated with synthetic sequences as well as real video sequences of human motion.

An Information Theoretic Framework for Field Monitoring Using Autonomously Mobile Sensors

We consider a mobile sensor network monitoring a spatio-temporal field. Given limited cache sizes at the sensor nodes, the goal is to develop a distributed cache management algorithm to efficiently answer queries with a known probability distribution over the spatial dimension. First, we propose a novel distributed information theoretic approach in which the nodes locally update their caches based on full knowledge of the space-time distribution of the monitored phenomenon. At each time instant, local decisions are made at the mobile nodes concerning which samples to keep and whether or not a new sample should be acquired at the current location. These decisions account for minimizing an entropic utility function that captures the average amount of uncertainty in queries given the probability distribution of query locations. Second, we propose a different correlation-based technique, which only requires knowledge of the second-order statistics, thus relaxing the stringent constraint of having a priori knowledge of the query distribution, while significantly reducing the computational overhead. It is shown that the proposed approaches considerably improve the average field estimation error by maintaining efficient cache content. It is further shown that the correlation-based technique is robust to model mismatch in case of imperfect knowledge of the underlying generative correlation structure.

Service Provisioning in Mobile Networks Through Distributed Coordinated Resource Management

The pervasiveness of personal computing platforms offers an unprecedented opportunity to deploy large-scale services that are distributed over wide physical spaces. Two major challenges face the deployment of such services: the often resource-limited nature of these platforms, and the necessity of preserving the autonomy of the owner of these devices. These challenges preclude using centralized control and preclude considering services that are subject to performance guarantees. To that end, this thesis advances a number of new distributed resource management techniques that are shown to be effective in such settings, focusing on two application domains: distributed Field Monitoring Applications (FMAs), and Message Delivery Applications (MDAs). In the context of FMA, this thesis presents two techniques that are well-suited to the fairly limited storage and power resources of autonomously mobile sensor nodes. The first technique relies on amorphous placement of sensory data through the use of novel storage management and sample diffusion techniques. The second approach relies on an information-theoretic framework to optimize local resource management decisions. Both approaches are proactive in that they aim to provide nodes with a view of the monitored field that reflects the characteristics of queries over that field, enabling them to handle more queries locally, and thus reduce communication overheads. Then, this thesis recognizes node mobility as a resource to be leveraged, and in that respect proposes novel mobility coordination techniques for FMAs and MDAs. Assuming that node mobility is governed by a spatio-temporal schedule featuring some slack, this thesis presents novel algorithms of various computational complexities to orchestrate the use of this slack to improve the performance of supported applications. The findings in this thesis, which are supported by analysis and extensive simulations, highlight the importance of two general design principles for distributed systems. First, a-priori knowledge (e.g., about the target phenomena of FMAs and/or the workload of either FMAs or DMAs) could be used effectively for local resource management. Second, judicious leverage and coordination of node mobility could lead to significant performance gains for distributed applications deployed over resource-impoverished infrastructures.

An Invariant Representation for Matching Trajectories across Uncalibrated Video Streams

We introduce a view-point invariant representation of moving object trajectories that can be used in video database applications. It is assumed that trajectories lie on a surface that can be locally approximated with a plane. Raw trajectory data is first locally approximated with a cubic spline via least squares fitting. For each sampled point of the obtained curve, a projective invariant feature is computed using a small number of points in its neighborhood. The resulting sequence of invariant features computed along the entire trajectory forms the view invariant descriptor of the trajectory itself. Time parametrization has been exploited to compute cross ratios without ambiguity due to point ordering. Similarity between descriptors of different trajectories is measured with a distance that takes into account the statistical properties of the cross ratio, and its symmetry with respect to the point at infinity. In experiments, an overall correct classification rate of about 95% has been obtained on a dataset of 58 trajectories of players in soccer video, and an overall correct classification rate of about 80% has been obtained on matching partial segments of trajectories collected from two overlapping views of outdoor scenes with moving people and cars.

Amorphous Placement and Retrieval of Sensory Data in Sparse Mobile Ad-Hoc Networks

Abstract—Personal communication devices are increasingly being equipped with sensors that are able to passively collect information from their surroundings – information that could be stored in fairly small local caches. We envision a system in which users of such devices use their collective sensing, storage, and communication resources to query the state of (possibly remote) neighborhoods. The goal of such a system is to achieve the highest query success ratio using the least communication overhead (power). We show that the use of Data Centric Storage (DCS), or directed placement, is a viable approach for achieving this goal, but only when the underlying network is well connected. Alternatively, we propose, amorphous placement, in which sensory samples are cached locally and informed exchanges of cached samples is used to diffuse the sensory data throughout the whole network. In handling queries, the local cache is searched first for potential answers. If unsuccessful, the query is forwarded to one or more direct neighbors for answers. This technique leverages node mobility and caching capabilities to avoid the multi-hop communication overhead of directed placement. Using a simplified mobility model, we provide analytical lower and upper bounds on the ability of amorphous placement to achieve uniform field coverage in one and two dimensions. We show that combining informed shuffling of cached samples upon an encounter between two nodes, with the querying of direct neighbors could lead to significant performance improvements. For instance, under realistic mobility models, our simulation experiments show that amorphous placement achieves 10% to 40% better query answering ratio at a 25% to 35% savings in consumed power over directed placement.