A Linear Time Algorithm for Computing Longest Paths in Cactus Graphs

ACM Computing Classification System (1998): G.2.2.

Dimension Reduction of the Explanatory Variables in Multiple Linear Regression

2002 Mathematics Subject Classification: 62J05, 62G35.

Optimization Problem in a Class of Linear System. Application to Multiple Drug Administration

2000 Mathematics Subject Classification: 62H15, 62P10.

Parameterized Link Functions in Generalized Linear Random Effect Models: a Case Study on Breast Cancer Treatment

In non-linear random effects some attention has been very recently devoted to the analysis ofsuitable transformation of the response variables separately (Taylor 1996) or not (Oberg and Davidian 2000) from the transformations of the covariates and, as far as we know, no investigation has been carried out on the choice of link function in such models. In our study we consider the use of a random effect model when a parameterized family of links (Aranda-Ordaz 1981, Prentice 1996, Pregibon 1980, Stukel 1988 and Czado 1997) is introduced. We point out the advantages and the drawbacks associated with the choice of this data-driven kind of modeling. Difficulties in the interpretation of regression parameters, and therefore in understanding the influence of covariates, as well as problems related to loss of efficiency of estimates and overfitting, are discussed. A case study on radiotherapy usage in breast cancer treatment is discussed.

On Principle Eigenvalue for Linear Second Order Elliptic Equations in Divergence Form

2002 Mathematics Subject Classification: 35J15, 35J25, 35B05, 35B50

The Asymptotic Behaviour of the First Eigenvalue of Linear Second-Order Elliptic Equations in Divergente Form

2000 Mathematics Subject Classification: 35J70, 35P15.

Linear Colligations and Dynamic System Corresponding to Operators in the Banach Space

2000 Mathematics Subject Classification: Primary 47A48, 93B28, 47A65; Secondary 34C94.

Multi-threaded parallel simulation of non-local non-linear problems in ultrashort laser pulse propagation in the presence of plasma

We describe a parallel multi-threaded approach for high performance modelling of wide class of phenomena in ultrafast nonlinear optics. Specific implementation has been performed using the highly parallel capabilities of a programmable graphics processor. © 2011 SPIE.

Recent advances in fundamentals and applications of random fiber lasers

Random fiber lasers blend together attractive features of traditional random lasers, such as low cost and simplicity of fabrication, with high-performance characteristics of conventional fiber lasers, such as good directionality and high efficiency. Low coherence of random lasers is important for speckle-free imaging applications. The random fiber laser with distributed feedback proposed in 2010 led to a quickly developing class of light sources that utilize inherent optical fiber disorder in the form of the Rayleigh scattering and distributed Raman gain. The random fiber laser is an interesting and practically important example of a photonic device based on exploitation of optical medium disorder. We provide an overview of recent advances in this field, including high-power and high-efficiency generation, spectral and statistical properties of random fiber lasers, nonlinear kinetic theory of such systems, and emerging applications in telecommunications and distributed sensing.

On the fundamentals of research and development (R&D) spillovers in competitive markets

Rivals may voluntarily share Research and Development (R&D) results even in the absence of any binding agreements or collusion. In a model where rival firms engage in non-cooperative independent R&D process, we used optimization and game theory analysis to study the equilibrium strategy of the firms. Our work showed that, while minimal spillover is always equilibrium, there may be another equilibrium where firms may reciprocally choose high, sometimes perfect, spillover rates. The incentive for sharing R&D output is based on firms' expectations of learning from their rivals' R&D progress in the future. This leads to strategic complementarities between the firms' choices of spillover rates and thus policy implication follows. ^ Public research agencies can contribute more to social welfare by providing research as public goods. In a non-cooperative public-private research relationship where parallel R&D is conducted, by making its R&D results accessible, the public research agency can stimulate private spillovers, even if there exists rivalry among the private firms who can benefit from such spillovers. ^

A retrospective-longitudinal examination of the relationship between apportionment of seat time in community-college algebra courses and student academic performance

During the past decade, there has been a dramatic increase by postsecondary institutions in providing academic programs and course offerings in a multitude of formats and venues (Biemiller, 2009; Kucsera & Zimmaro, 2010; Lang, 2009; Mangan, 2008). Strategies pertaining to reapportionment of course-delivery seat time have been a major facet of these institutional initiatives; most notably, within many open-door 2-year colleges. Often, these enrollment-management decisions are driven by the desire to increase market-share, optimize the usage of finite facility capacity, and contain costs, especially during these economically turbulent times. So, while enrollments have surged to the point where nearly one in three 18-to-24 year-old U.S. undergraduates are community college students (Pew Research Center, 2009), graduation rates, on average, still remain distressingly low (Complete College America, 2011). Among the learning-theory constructs related to seat-time reapportionment efforts is the cognitive phenomenon commonly referred to as the spacing effect, the degree to which learning is enhanced by a series of shorter, separated sessions as opposed to fewer, more massed episodes. This ex post facto study explored whether seat time in a postsecondary developmental-level algebra course is significantly related to: course success; course-enrollment persistence; and, longitudinally, the time to successfully complete a general-education-level mathematics course. Hierarchical logistic regression and discrete-time survival analysis were used to perform a multi-level, multivariable analysis of a student cohort (N = 3,284) enrolled at a large, multi-campus, urban community college. The subjects were retrospectively tracked over a 2-year longitudinal period. The study found that students in long seat-time classes tended to withdraw earlier and more often than did their peers in short seat-time classes (p < .05). Additionally, a model comprised of nine statistically significant covariates (all with p-values less than .01) was constructed. However, no longitudinal seat-time group differences were detected nor was there sufficient statistical evidence to conclude that seat time was predictive of developmental-level course success. A principal aim of this study was to demonstrate—to educational leaders, researchers, and institutional-research/business-intelligence professionals—the advantages and computational practicability of survival analysis, an underused but more powerful way to investigate changes in students over time.

Predicting Transcript Production Rates in Yeast With Sparse Linear Models

To provide biological insights into transcriptional regulation, a couple of groups have recently presented models relating the promoter DNA-bound transcription factors (TFs) to downstream gene’s mean transcript level or transcript production rates over time. However, transcript production is dynamic in response to changes of TF concentrations over time. Also, TFs are not the only factors binding to promoters; other DNA binding factors (DBFs) bind as well, especially nucleosomes, resulting in competition between DBFs for binding at same genomic location. Additionally, not only TFs, but also some other elements regulate transcription. Within core promoter, various regulatory elements influence RNAPII recruitment, PIC formation, RNAPII searching for TSS, and RNAPII initiating transcription. Moreover, it is proposed that downstream from TSS, nucleosomes resist RNAPII elongation.

Here, we provide a machine learning framework to predict transcript production rates from DNA sequences. We applied this framework in the S. cerevisiae yeast for two scenarios: a) to predict the dynamic transcript production rate during the cell cycle for native promoters; b) to predict the mean transcript production rate over time for synthetic promoters. As far as we know, our framework is the first successful attempt to have a model that can predict dynamic transcript production rates from DNA sequences only: with cell cycle data set, we got Pearson correlation coefficient Cp = 0.751 and coefficient of determination r2 = 0.564 on test set for predicting dynamic transcript production rate over time. Also, for DREAM6 Gene Promoter Expression Prediction challenge, our fitted model outperformed all participant teams, best of all teams, and a model combining best team’s k-mer based sequence features and another paper’s biologically mechanistic features, in terms of all scoring metrics.

Moreover, our framework shows its capability of identifying generalizable fea- tures by interpreting the highly predictive models, and thereby provide support for associated hypothesized mechanisms about transcriptional regulation. With the learned sparse linear models, we got results supporting the following biological insights: a) TFs govern the probability of RNAPII recruitment and initiation possibly through interactions with PIC components and transcription cofactors; b) the core promoter amplifies the transcript production probably by influencing PIC formation, RNAPII recruitment, DNA melting, RNAPII searching for and selecting TSS, releasing RNAPII from general transcription factors, and thereby initiation; c) there is strong transcriptional synergy between TFs and core promoter elements; d) the regulatory elements within core promoter region are more than TATA box and nucleosome free region, suggesting the existence of still unidentified TAF-dependent and cofactor-dependent core promoter elements in yeast S. cerevisiae; e) nucleosome occupancy is helpful for representing +1 and -1 nucleosomes’ regulatory roles on transcription.

The Use of Almost Linear Phase IIR filters In DFT Modulated Filter Banks for Communication Systems

This paper is on the use and performance of M-path polyphase Infinite Impulse Response (IIR) filters for channelisation, conventionally where Finite Impulse Response (FIR) filters are preferred. This paper specifically focuses on the Discrete Fourier Transform (DFT) modulated filter banks, which are known to be an efficient choice for channelisation in communication systems. In this paper, the low-pass prototype filter for the DFT filter bank has been implemented using an M-path polyphase IIR filter and we show that the spikes present at the stopband can be avoided by making use of the guardbands between narrowband channels. It will be shown that the channelisation performance will not be affected when polyphase IIR filters are employed instead of their counterparts derived from FIR prototype filters. Detailed complexity and performance analysis of the proposed use will be given in this article.

Computer-aided tool for the teaching of relational algebra in data base courses

This article describes the design and implementation of computer-aided tool called Relational Algebra Translator (RAT) in data base courses, for the teaching of relational algebra. There was a problem when introducing the relational algebra topic in the course EIF 211 Design and Implementation of Databases, which belongs to the career of Engineering in Information Systems of the National University of Costa Rica, because students attending this course were lacking profound mathematical knowledge, which led to a learning problem, being this an important subject to understand what the data bases search and request do RAT comes along to enhance the teaching-learning process.It introduces the architectural and design principles required for its implementation, such as: the language symbol table, the gramatical rules and the basic algorithms that RAT uses to translate from relational algebra to SQL language. This tool has been used for one periods and has demonstrated to be effective in the learning-teaching process.  This urged investigators to publish it in the web site: www.slinfo.una.ac.cr in order for this tool to be used in other university courses.