ppxscal/embedding_network huggingface dataset:
Motif discovery in tissue-specific regulatory sequences using directed information
Authors: Arvind Rao, Alfred O. Hero,  III, David J. States, James Douglas Engel
Venue: EURASIP Journal on Bioinformatics and Systems Biology (2007)

Motif discovery for the identification of functional regulatory elements underlying gene expression is a challenging problem. Sequence inspection often leads to discovery of novel motifs (including transcription factor sites) with previously uncharacterized function in gene expression. Coupled with the complexity underlying tissue-specific gene expression, there are several motifs that are putatively responsible for expression in a certain cell type. This has important implications in understanding fundamental biological processes such as development and disease progression. In this work, we present an approach to the identification of motifs (not necessarily transcription factor sites) and examine its application to some questions in current bioinformatics research. These motifs are seen to discriminate tissue-specific gene promoter or regulatory regions from those that are not tissue-specific. There are two main contributions of this work. Firstly, we propose the use of directed information for such classification constrained motif discovery, and then use the selected features with a support vector machine (SVM) classifier to find the tissue specificity of any sequence of interest. Such analysis yields several novel interesting motifs that merit further experimental characterization. Furthermore, this approach leads to a principled framework for the prospective examination of any chosen motif to be discriminatory motif for a group of coexpressed/coregulated genes, thereby integrating sequence and expression perspectives. We hypothesize that the discovery of these motifs would enable the large-scale investigation for the tissue-specific regulatory role of any conserved sequence element identified from genome-wide studies.
A secure and low-energy logic style using charge recovery approach
Authors: Mehrdad Khatir, Amir Moradi, Alireza Ejlali, Mohammad T. Manzuri Shalmani, Mahmoud Salmasizadeh
Venue: Proceeding of the 13th international symposium on Low power electronics and design (2008)

The charge recovery logic families have been designed several years ago not in order to eliminate the side-channel leakage but to reduce the power consumption. However, in this article we present a new charge recovery logic style not only to gain high energy efficiency but also to achieve the resistance against side-channel attacks especially against differential power analysis attacks. Our approach is a modified version of a classical charge recovery logic style namely 2N-2N2P. Simulation results show a significant improvement in DPA-resistance level as well as in power consumption reduction in comparison with 2N-2N2P and other DPA-resistant logic styles.
Supporting vehicular mobility in urban multi-hop wireless networks
Authors: Anastasios Giannoulis, Marco Fiore, Edward W. Knightly
Venue: Proceeding of the 6th international conference on Mobile systems, applications, and services (2008)

Deployments of city-wide multi-hop 802.11 networks introduce challenges for maintaining client performance at vehicular speeds. We experimentally demonstrate that current network interfaces employ policies that result in long outage durations, even when clients are always in range of at least one access point. Consequently, we design and evaluate a family of client-driven handoff techniques that target vehicular mobility in multi-tier multi-hop wireless mesh networks. Our key technique is for clients to invoke an association change based on (i) joint use of channel quality measurements and AP quality scores that reflect long-term differences in AP performance and (ii) controlled measurement and hand-off time scales to balance the need for the instantaneously best association against performance penalties incurred from spurious handoffs due to channel fluctuations and marginally improved associations. We utilize a 4,000 user urban deployment to evaluate the performance of a broad class of hand-off policies.
Epoxide functionalized molecular resists for high resolution electron-beam lithography
Authors: Richard A. Lawson, Cheng-Tsung Lee, Wang Yueh, Laren Tolbert, Clifford L. Henderson
Venue: Microelectronic Engineering (2008)

Chemically amplified resists would be a preferred option to non-amplified resists such as PMMA or ZEP for electron-beam lithography because of their much higher sensitivity and therefore faster write times, but are resolution limited compared to non-amplified resists due to photoacid diffusion. A chemically amplified molecular resist based on epoxide polymerization (4-Ep) has been developed that simultaneously has resolution of 35nm half-pitch, sensitivity of 20@mC/cm^2, and line edge roughness (3@s) of 2.3nm. The resist combines the performance advantages of both a molecular and polymeric resist. The extensive cross-linking effectively limits photoacid diffusion during resist processing, thus allowing for high resolution.
Hardware in the loop with electro-hydraulic brake system
Authors: Aldo Sorniotti, Gianfrancesco Maria Repici
Venue: Proceedings of the 9th WSEAS International Conference on Systems (2005)

The paper describes the procedure our research group followed to prototype an Electro-Hydraulic Braking system (EHB). The first step consisted in developing a model of the system, by using the softwares AMESim® and Simulink®. Then the Pedal Force Emulator (PFE) was designed in detail and built. A Hardware-In-the-Loop (HIL) bench was used to test the prototype. The same procedure was followed for the hydraulic unit. The aim of the activity consisted in trying to adapt the standard components of a traditional braking system to develop a low cost EHB. Also failsafe valves to connect the driver to the wheel calipers in case of fault were used to create a reliable failsafe system in order to improve system reliability.
Behavioral VHDL-AMS model and experimental validation of a nuclear magnetic resonance sensor
Authors: S. Megherbi, J.-C. Ginefri, L. Darrasse, G. Raynaud, J.-F. P&#x00f4;ne
Venue: Microsystem Technologies (2005)

This paper describes the development for a model of a nuclear magnetic resonance spiral coil sensor using analog hardware description. Our procedure implies several steps with emphasis on model complexity reduction, identification of critical parameters and validation of experimental measurements. The proposed macro-model permits an extremely fast simulation while providing nearly finite element method accuracy. As a tool for coding the description of system level modeling we use analog hardware description language VHDL-AMS (Ashenden et al. in the system designer&#x2019;s guide to VHDL-AMS, Morgan Kauffmann, 2002). In order to obtain the behavioral computation results, SYSTEM VISION simulation environment from Mentor Graphics&#x00ae; was employed. In our proposed model, the different parts of the sensor and the different effects involved (electrical parameters, physical and magnetic coupling, loss effects) can be modeled within the same tool, together with the sensor environment: electrical command and detection circuit, time dependent magnetic field, and so on.
A Software Model Reuse Strategy for Brazilian Satellite Launcher
Authors: Luciana Akemi Burgareli, Selma S. S. Melnikoff, Mauricio G. V. Ferreira
Venue: Proceedings of the 19th Australian Conference on Software Engineering (2008)

The purpose of this work is to define a strategy for the generation of Platform Independent Model (PIM) for the Brazilian Satellite Launcher (BSL) software, based on the Model Driven Architecture (MDA) approach. To accomplish that, a generic software model is created, using design patterns, to represent a family of satellite launcher vehicles whose characteristics are similar. From this generic model, PIMs are generated for variations of launcher vehicles, based on MDA approach. This strategy can contribute to the development of the software for same-family satellite launcher vehicles, as it defines a systematic for activities related to software modeling, and also allows the increase of BSL software models reuse.
A learner-centred design of a location-aware learning reminder
Authors: Hokyoung Ryu, David Parsons
Venue: International Journal of Mobile Learning and Organisation (2008)

To ensure the success of future mobile learning environments, it is essential to develop affordable and effective applications that are well matched to the characteristics of the users' (particularly, learners) learning experiences. As an early exploration of this line of study, this paper evaluates a location-aware learning organiser that can help university students to manage their learning activities through mobile devices. Empirical testing of the learning organiser revealed considerable benefits for students in the university context, and demonstrated some potential opportunities for them to be more engaged in further mobile learning activities.
Robust De-anonymization of Large Sparse Datasets
Authors: Arvind Narayanan, Vitaly Shmatikov
Venue: Proceedings of the 2008 IEEE Symposium on Security and Privacy (2008)

We present a new class of statistical de-anonymization attacks against high-dimensional micro-data, such as individual preferences, recommendations, transaction records and so on. Our techniques are robust to perturbation in the data and tolerate some mistakes in the adversary's background knowledge. We apply our de-anonymization methodology to the Netflix Prize dataset, which contains anonymous movie ratings of 500,000 subscribers of Netflix,the world's largest online movie rental service. We demonstrate that an adversary who knows only a little bit about an individual subscriber can easily identify this subscriber's record in the dataset. Using the Internet Movie Database as the source of background knowledge, we successfully identified the Netflix records of known users, uncovering their apparent political preferences and other potentially sensitive information.
Know Your Audience
Authors: David Alan Grier
Venue: Computer (2008)

Embracing digital technology has had a profound impact on modern entertainment media.
H-SMIL-Net: A Hierarchical Petri Net Model for SMIL Documents
Authors: Samia Bouyakoub, Abdelkader Belkhir
Venue: Proceedings of the Tenth International Conference on Computer Modeling and Simulation (2008)

We propose in this paper a hierarchical and temporal extension of Petri Nets for the incremental authoring of SMIL multimedia documents. The complexity of these documents can lead authors, in some cases, to specify synchronization relations which could not be satisfied during the presentation of the document, what characterizes the occurrence of inconsistencies; a consistency checking mechanism is then necessary. This new model, named H-SMIL-Net (Hierarchical SMIL-Petri Net) proposes a technique for the incremental verification of temporal consistency. The originality of the solution resides in the modular aspect of the modelling, and the local approach of verification, what optimizes the verification time after each editing operation. This formal approach has been integrated in an incremental authoring tool for SMIL presentations.
Roomba MADNeT: a mobile ad-hoc delay tolerant network testbed
Authors: Joshua Reich, Vishal Misra, Dan Rubenstein
Venue: ACM SIGMOBILE Mobile Computing and Communications Review (2008)

We have built a mobile, ad-hoc, delay tolerant, network testbed (MADNeT). Our testbed is geared towards enabling the exploration of highly disconnected networks whose nodes must store and forward information (multi-hop paths are very unlikely), while allowing us to explore connected network scenarios as well. Using our MADNeT, we can emulate a wide range of mobile networking scenarios and execute real-world (albeit somewhat simplified) data collection missions. Our system is built from commercial off-the-shelf (COTS) hardware running a paired-down Linux OS, yielding a relatively inexpensive but fairly flexible mobile network testbed. We have implemented replication-based information diffusion protocols and a distributed opportunistic surveillance application on the testbed as proof-of-concept. Currently, we are refining our software tool-set and instrumenting our nodes to test both our protocols and application.
Robust filtering for gene expression time series data with variance constraints
Authors: Guoliang Wei, Zidong Wang, Huisheng Shu, Karl Fraser, Xiaohui Liu
Venue: International Journal of Computer Mathematics (2007)

In this paper, an uncertain discrete-time stochastic system is employed to represent a model for gene regulatory networks from time series data. A robust variance-constrained filtering problem is investigated for a gene expression model with stochastic disturbances and norm-bounded parameter uncertainties, where the stochastic perturbation is in the form of a scalar Gaussian white noise with constant variance and the parameter uncertainties enter both the system matrix and the output matrix. The purpose of the addressed robust filtering problem is to design a linear filter such that, for the admissible bounded uncertainties, the filtering error system is Schur stable and the individual error variance is less than a prespecified upper bound. By using the linear matrix inequality (LMI) technique, sufficient conditions are first derived for ensuring the desired filtering performance for the gene expression model. Then the filter gain is characterized in terms of the solution to a set of LMIs, which can easily be solved by using available software packages. A simulation example is exploited for a gene expression model in order to demonstrate the effectiveness of the proposed design procedures.
Distributed topology control of wireless networks
Authors: Vivek S. Borkar, D. Manjunath
Venue: Wireless Networks (2008)

We propose and analyaze a distributed control law that will maintain prescribed local properties of a wireless ad hoc network in the presence of node mobility, MAC layer power control and link fades. The control law uses a simple and intuitive power adaptation mechanism. We consider as an example the topology requirement of maintaining the out-degrees of each node at prescribed values and keeping the in-degree close to the out-degree. The topology objective is achieved by adapting the transmission power based only on local information. This power adaptation algorithm is analyzed using the o.d.e. approach to stochastic approximation. Simulation results verify the analysis and demonstrate its effectiveness. We also study the ability of the proposed objective to maintain connectivity. Although many heuristics are described in the literature to maintain local topological properties, the algorithm proposed in this paper is the first one that has proven convergence properties.
A review of research towards computer integrated demanufacturing for materials recovery
Authors: J. A. S. Williams
Venue: International Journal of Computer Integrated Manufacturing (2007)

The recovery of both toxic and non-toxic materials from billions of end-of-life electronics calls for efficient processes and exploration of opportunities for computer integrated demanufacturing for materials recovery. To date, recycling automation for selective disassembly has been limited by the proliferation of product designs, the difficulty of acquiring product feature and material content information, and the lack of integration of collection and demanufacturing processing. Product designs with standard modules and standard fasteners would improve the options for more automated disassembly. Making product structure and material composition information from a product design profile available will support planning models, Petri net algorithms and control models for demanufacturing, as well as integrated manufacturing and demanufacturing. Advances in imaging and materials identification techniques as well as more flexible technologies to separate materials may provide new opportunities for expert Petri net approaches for selective robotic disassembly. Linking end-of-life product service demand information will enhance scheduling for demand-driven demanufacturing. Nonetheless, the random arrival of so many different product sizes and design structures will require new approaches to designing reverse logistics networks and linking their activities. The present paper reviews the research to automate materials recovery planning and control, identifies challenges, and discusses directions for future research.
A Pragmatic GIS-Oriented Ontology for Location Based Services
Authors: Jun Shen, Aneesh Krishna, Shuai Yuan, Ke Cai, Yuemin Qin
Venue: Proceedings of the 19th Australian Conference on Software Engineering (2008)

With advances in automatic position sensing and wireless connectivity, location-based services (LBS) are rapidly developing, particularly in fields of geographic, tourism and logistic information systems. Currently, Web service has been viewed as one of most significant innovations in business industry, and designed on demand to provide spatial related information for LBS consumption. However, the traditional Web Service Description Language (WSDL) cannot meet those requirements, as WSDL is not able to support semantic content and information. In recent years, Ontology came up with an effective approach to enhance service description, automated discovery, dynamic composition, enactment, and other tasks such as managing and using service-based systems. In this paper, we propose geographic ontology based on Geography Markup Language (GML) and extend OWL-S profile to form geographic profile. Web service, which is advertised on the basis of our GeoProfile, contains geographic information inherently.
Enabling Interoperable Mobile Learning: Evaluation Results from the Use of SMILE PDA Learning Design Player
Authors: Demetrios Sampson, Panayiotis Zervas
Venue: Proceedings of the Fifth IEEE International Conference on Wireless, Mobile, and Ubiquitous Technology in Education (2008)

During the last years m-learning has attracted the attention of technology-enhanced learning community mainly as a side effect of the growth of the mobile communications industry. While the educational added-value of m-learning is under investigation, technological efforts are much needed to align m-learning technologies with the current state-of-the-art specifications in TeL. Within this context, in this paper, we present initial evaluation results from the use of the SMILE PDA Learning Design Player, an open source software implementation for executing IMS Learning Design activities via mobile devices.
Impact of new mouth opening on morphology and water quality of the Chilika Lagoon-a study based on Resourcesat-1 LISS-III and AWiFS and IRS-1D LISS-III data
Authors: A. S. Rajawat, M. Gupta, B. C. Acharya, S. Nayak
Venue: International Journal of Remote Sensing (2007)

The northeasterly long shore transport (littoral drift) along the east coast of India shifts the mouth of the lagoon northeastwards. It results in lengthening of the outer channel, reduced tidal flux, fall in salinity levels, weed infestation, decline in fishery resources, and overall loss of biodiversity and productivity. The Chilika Development Authority made an artificial mouth near the village of Sipakuda, which was opened on 23 September 2000. The present study focuses on applications of Resourcesat-1 LISS-III and AWiFS data to understand the impact of the new mouth opening on the morphology and water quality of the Chilika Lagoon. Digital image processing of multi-temporal Resourcesat-1 AWiFS, LISS-III, and IRS-1D LISS-III data was carried out. Changes were shown out for pre-and post-opening of the new mouth. The results indicate that the initial cut of 80 m has widened to approximately 676 m and, so far, the process has not attained stability. There has been northward erosion for approximately 376 m and southward erosion for approximately 143 m at the new mouth. The study shows that the strong ebbing tide current from the northwest is responsible for this erosion. The old mouth has been closed completely just three years after the opening of the new mouth. There has been an overall rise in salinity levels in the Chilika Lagoon, in particular during the pre-monsoon period following the opening of the new mouth. This indicates that the tidal flux in the lagoon has increased and the associated circulation is effective in mixing the water masses. After the opening of the new mouth, weeds have reduced by a 172-km2 area, in particular in the northeast part of the lagoon. AWiFS data is extremely useful in identifying changes in morphology and water quality under different tide conditions. Tidal conditions influence the signatures of turbidity, weed cover, shoals, and spits under development. The SWIR channel of AWiFS is found to be extremely useful for detecting aquatic vegetation. The study concludes that large transport of sediments at the new mouth opening, along with predominant erosion of the northern bank, suggests a northward migration of the new mouth in the near future.
On a conjecture by Plummer and Toft
Authors: Mirko Horňák, Stanislav Jendrol'
Venue: Journal of Graph Theory (1999)

The cyclic chromatic number &chi;c(G) of a 2-connected plane graph G is the minimum number of colors in an assigment of colors to the vertices of G such that, for every face-bounding cycle f of G, the vertices of f have different colors. Plummer and Toft proved that, for a 3-connected plane graph G, under the assumption &Delta;*(G) &ge; 42, where &Delta;*(G) is the size of a largest face of G, it holds that &chi;c(G) &le; &Delta;*(G) + 4. They conjectured that, if G is a 3-connected plane graph, then &chi;c>(G) &le; &Delta;*(G) + 2. In the article the conjecture is proved for &Delta;*(G) &ge; 24. &copy; 1999 John Wiley Sons, Inc. J Graph Theory 30: 177189, 1999
Self-identifying patterns for plane-based camera calibration
Authors: Mark Fiala, Chang Shu
Venue: Machine Vision and Applications (2008)

Determining camera calibration parameters is a time-consuming task despite the availability of calibration algorithms and software. A set of correspondences between points on the calibration target and the camera image(s) must be found, usually a manual or manually guided process. Most calibration tools assume that the correspondences are already found. We present a system which allows a camera to be calibrated merely by passing it in front of a panel of self-identifying patterns. This calibration scheme uses an array of fiducial markers which are detected with a high degree of confidence, each detected marker provides one or four correspondence points. Experiments were performed calibrating several cameras in a short period of time with no manual intervention. This marker-based calibration system was compared to one using the OpenCV chessboard grid finder which also finds correspondences automatically. We show how our new marker-based system more robustly finds the calibration pattern and how it provides more accurate intrinsic camera parameters.
FPTAS for optimizing polynomials over the mixed-integer points of polytopes in fixed dimension
Authors: Jes&#x00fa;s A. De Loera, Raymond Hemmecke, Matthias K&#x00f6;ppe, Robert Weismantel
Venue: Mathematical Programming: Series A and B (2008)

We show the existence of a fully polynomial-time approximation scheme (FPTAS) for the problem of maximizing a non-negative polynomial over mixed-integer sets in convex polytopes, when the number of variables is fixed. Moreover, using a weaker notion of approximation, we show the existence of a fully polynomial-time approximation scheme for the problem of maximizing or minimizing an arbitrary polynomial over mixed-integer sets in convex polytopes, when the number of variables is fixed.