Fluorescence Assay for Polymerase Arrival Rates

To engineer complex synthetic biological systems will require modular design, assembly, and characterization strategies. The RNA polymerase arrival rate (PAR) is defined to be the rate that RNA polymerases arrive at a specified location on the DNA. Designing and characterizing biological modules in terms of RNA polymerase arrival rates provides for many advantages in the construction and modeling of biological systems. PARMESAN is an in vitro method for measuring polymerase arrival rates using pyrrolo-dC, a fluorescent DNA base that can substitute for cytosine. Pyrrolo-dC shows a detectable fluorescence difference when in single-stranded versus double-stranded DNA. During transcription, RNA polymerase separates the two strands of DNA, leading to a change in the fluorescence of pyrrolo-dC. By incorporating pyrrolo-dC at specific locations in the DNA, fluorescence changes can be taken as a direct measurement of the polymerase arrival rate.

The random barrier-crossing problem

This paper addresses the time-variant reliability analysis of structures with random resistance or random system parameters. It deals with the problem of a random load process crossing a random barrier level. The implications of approximating the arrival rate of the first overload by an ensemble-crossing rate are studied. The error involved in this so-called ""ensemble-crossing rate"" approximation is described in terms of load process and barrier distribution parameters, and in terms of the number of load cycles. Existing results are reviewed, and significant improvements involving load process bandwidth, mean-crossing frequency and time are presented. The paper shows that the ensemble-crossing rate approximation can be accurate enough for problems where load process variance is large in comparison to barrier variance, but especially when the number of load cycles is small. This includes important practical applications like random vibration due to impact loadings and earthquake loading. Two application examples are presented, one involving earthquake loading and one involving a frame structure subject to wind and snow loadings. (C) 2007 Elsevier Ltd. All rights reserved.

Optimal information transmission in organizations: Search and congestion

We propose a stylized model of a problem-solving organization whoseinternal communication structure is given by a fixed network. Problemsarrive randomly anywhere in this network and must find their way to theirrespective specialized solvers by relying on local information alone.The organization handles multiple problems simultaneously. For this reason,the process may be subject to congestion. We provide a characterization ofthe threshold of collapse of the network and of the stock of foatingproblems (or average delay) that prevails below that threshold. We buildupon this characterization to address a design problem: the determinationof what kind of network architecture optimizes performance for any givenproblem arrival rate. We conclude that, for low arrival rates, the optimalnetwork is very polarized (i.e. star-like or centralized ), whereas it islargely homogenous (or decentralized ) for high arrival rates. We also showthat, if an auxiliary assumption holds, the transition between these twoopposite structures is sharp and they are the only ones to ever qualify asoptimal.

Non-stationary job search when jobs are not forever: A structural estimation

This paper considers a job search model where the environment is notstationary along the unemployment spell and where jobs do not lastforever. Under this circumstance, reservation wages can be lower thanwithout separations, as in a stationary environment, but they can alsobe initially higher because of the non-stationarity of the model. Moreover,the time-dependence of reservation wages is stronger than with noseparations. The model is estimated structurally using Spanish data forthe period 1985-1996. The main finding is that, although the decrease inreservation wages is the main determinant of the change in the exit ratefrom unemployment for the first four months, later on the only effect comesfrom the job offer arrival rate, given that acceptance probabilities areroughly equal to one.

Static Pricing for a Network Service Provider

This article studies the static pricing problem of a network service provider who has a fixed capacity and faces different types of customers (classes). Each type of customers can have its own capacity constraint but it is assumed that all classes have the same resource requirement. The provider must decide a static price for each class. The customer types are characterized by their arrival process, with a price-dependant arrival rate, and the random time they remain in the system. Many real-life situations could fit in this framework, for example an Internet provider or a call center, but originally this problem was thought for a company that sells phone-cards and needs to set the price-per-minute for each destination. Our goal is to characterize the optimal static prices in order to maximize the provider's revenue. We note that the model here presented, with some slight modifications and additional assumptions can be used in those cases when the objective is to maximize social welfare.

X-ray photoelectron spectroscopy analysis of zirconium nitride-like films prepared on Si(100) substrates by ion beam assisted deposition

Thin zirconium nitride films were prepared on Si(l 00) substrates at room temperature by ion beam assisted deposition with a 2 keV nitrogen ion beam. Arrival rate ratios ARR(N/Zr) used were 0.19, 0.39, 0.92, and 1.86. The chemical composition and bonding structure of the films were analyzed with X-ray photoelectron spectroscopy (XPS). Deconvolution results for Zr 3d, Zr 3p(3/2), N 1s, O 1s, and C 1s XPS spectra indicated self-consistently the presence of metal Zr-0, nitride ZrN, oxide ZrO2, oxymnide Zr2N2O, and carbide ZrC phases, and the amounts of these compounds were influenced by ARR(N/Zr). The chemical composition ratio N/Zr in the film increased with increasing ARR(N/Zr) until ARR(N/Zr) reached 0.92, reflecting the high reactivity of nitrogen in the ion beam, and stayed almost constant for ARR(N/Zr) >= 1, the excess nitrogen being rejected from the growing film. A considerable incorporation of contaminant oxygen and carbon into the depositing film was attributed to the getter effect of zirconium. (C) 2007 Elsevier B.V. All rights reserved.

MODELING AND PROTOCOL DESIGN FOR EMERGING WIRELESS SYSTEMS

Mobile Mesh Network based In-Transit Visibility (MMN-ITV) system facilitates global real-time tracking capability for the logistics system. In-transit containers form a multi-hop mesh network to forward the tracking information to the nearby sinks, which further deliver the information to the remote control center via satellite. The fundamental challenge to the MMN-ITV system is the energy constraint of the battery-operated containers. Coupled with the unique mobility pattern, cross-MMN behavior, and the large-spanned area, it is necessary to investigate the energy-efficient communication of the MMN-ITV system thoroughly. First of all, this dissertation models the energy-efficient routing under the unique pattern of the cross-MMN behavior. A new modeling approach, pseudo-dynamic modeling approach, is proposed to measure the energy-efficiency of the routing methods in the presence of the cross-MMN behavior. With this approach, it could be identified that the shortest-path routing and the load-balanced routing is energy-efficient in mobile networks and static networks respectively. For the MMN-ITV system with both mobile and static MMNs, an energy-efficient routing method, energy-threshold routing, is proposed to achieve the best tradeoff between them. Secondly, due to the cross-MMN behavior, neighbor discovery is executed frequently to help the new containers join the MMN, hence, consumes similar amount of energy as that of the data communication. By exploiting the unique pattern of the cross-MMN behavior, this dissertation proposes energy-efficient neighbor discovery wakeup schedules to save up to 60% of the energy for neighbor discovery. Vehicular Ad Hoc Networks (VANETs)-based inter-vehicle communications is by now growingly believed to enhance traffic safety and transportation management with low cost. The end-to-end delay is critical for the time-sensitive safety applications in VANETs, and can be a decisive performance metric for VANETs. This dissertation presents a complete analytical model to evaluate the end-to-end delay against the transmission range and the packet arrival rate. This model illustrates a significant end-to-end delay increase from non-saturated networks to saturated networks. It hence suggests that the distributed power control and admission control protocols for VANETs should aim at improving the real-time capacity (the maximum packet generation rate without causing saturation), instead of the delay itself. Based on the above model, it could be determined that adopting uniform transmission range for every vehicle may hinder the delay performance improvement, since it does not allow the coexistence of the short path length and the low interference. Clusters are proposed to configure non-uniform transmission range for the vehicles. Analysis and simulation confirm that such configuration can enhance the real-time capacity. In addition, it provides an improved trade off between the end-to-end delay and the network capacity. A distributed clustering protocol with minimum message overhead is proposed, which achieves low convergence time.

Approximate processing of massive continuous quantile queries over high-speed data streams

Quantile computation has many applications including data mining and financial data analysis. It has been shown that an is an element of-approximate summary can be maintained so that, given a quantile query d (phi, is an element of), the data item at rank [phi N] may be approximately obtained within the rank error precision is an element of N over all N data items in a data stream or in a sliding window. However, scalable online processing of massive continuous quantile queries with different phi and is an element of poses a new challenge because the summary is continuously updated with new arrivals of data items. In this paper, first we aim to dramatically reduce the number of distinct query results by grouping a set of different queries into a cluster so that they can be processed virtually as a single query while the precision requirements from users can be retained. Second, we aim to minimize the total query processing costs. Efficient algorithms are developed to minimize the total number of times for reprocessing clusters and to produce the minimum number of clusters, respectively. The techniques are extended to maintain near-optimal clustering when queries are registered and removed in an arbitrary fashion against whole data streams or sliding windows. In addition to theoretical analysis, our performance study indicates that the proposed techniques are indeed scalable with respect to the number of input queries as well as the number of items and the item arrival rate in a data stream.

Temporal correlations of local network losses

We introduce a continuum model describing data losses in a single node of a packet-switched network (like the Internet) which preserves the discrete nature of the data loss process. By construction, the model has critical behavior with a sharp transition from exponentially small to finite losses with increasing data arrival rate. We show that such a model exhibits strong fluctuations in the loss rate at the critical point and non-Markovian power-law correlations in time, in spite of the Markovian character of the data arrival process. The continuum model allows for rather general incoming data packet distributions and can be naturally generalized to consider the buffer server idleness statistics.

Random walks in local dynamics of network losses

We suggest a model for data losses in a single node (memory buffer) of a packet-switched network (like the Internet) which reduces to one-dimensional discrete random walks with unusual boundary conditions. By construction, the model has critical behavior with a sharp transition from exponentially small to finite losses with increasing data arrival rate. We show that for a finite-capacity buffer at the critical point the loss rate exhibits strong fluctuations and non-Markovian power-law correlations in time, in spite of the Markovian character of the data arrival process.

Single-Server Queueing System with Markov-Modulated Arrivals and Service Times

Key words: Markov-modulated queues, waiting time, heavy traffic.

Methods of modelling people using discrete-event simulation

Discrete-event simulation (DES) is a developed technology used to model manufacturing and service systems. However, although the importance of modelling people in a DES has been recognised, there is little guidance on how this can be achieved in practice. The results from a literature review were used in order to identify examples of the use of DES to model people. Each article was examined in order to determine the method used to model people within the simulation study. It was found that there are no common methods but a diverse range of approaches used to model human behaviour in DES. This paper provides an outline of the approaches used to model people in terms of their decision making, availability for work, task performance and arrival rate. The outcome brings together the current knowledge in this area and will be of interest to researchers considering developing a methodology for modelling people in DES and to practitioners engaged with a simulation project involving the model ling of people’s behaviour.

Accounting for the Multi-Period Impact of Service When Determining Employee Requirements for Labor Scheduling

Providing good customer service, inexpensively, is a problem commonly faced by managers of service operations. To tackle this problem, managers must do four tasks: forecast customer demand for the service; translate these forecasts into employee requirements; develop a labor schedule that provides appropriate numbers of employees at appropriate times; and control the delivery of the service in real-time. This paper focuses upon the translation of forecasts of customer demand into employee requirements. Specifically, it presents and evaluates two methods for determining desired staffing levels. One of these methods is a traditional approach to the task, while the other, by using modified customer arrival rates, offers a better means of accounting for the multi-period impact of customer service. To calculate the modified arrival rates, the latter method reduces (increases) the actual customer arrival rate for a period to account for customers who arrived in the period (in earlier periods) but have some of their service performed in subsequent periods (in the period). In an experiment simulating 13824 service delivery environments, the new method demonstrated its superiority by serving 2.74% more customers within the specified waiting time limit while using 7.57% fewer labor hours.

Microblogging Temporal Summarization: Filtering Important Twitter Updates for Breaking News

While news stories are an important traditional medium to broadcast and consume news, microblogging has recently emerged as a place where people can dis- cuss, disseminate, collect or report information about news. However, the massive information in the microblogosphere makes it hard for readers to keep up with these real-time updates. This is especially a problem when it comes to breaking news, where people are more eager to know “what is happening”. Therefore, this dis- sertation is intended as an exploratory effort to investigate computational methods to augment human effort when monitoring the development of breaking news on a given topic from a microblog stream by extractively summarizing the updates in a timely manner. More specifically, given an interest in a topic, either entered as a query or presented as an initial news report, a microblog temporal summarization system is proposed to filter microblog posts from a stream with three primary concerns: topical relevance, novelty, and salience. Considering the relatively high arrival rate of microblog streams, a cascade framework consisting of three stages is proposed to progressively reduce quantity of posts. For each step in the cascade, this dissertation studies methods that improve over current baselines. In the relevance filtering stage, query and document expansion techniques are applied to mitigate sparsity and vocabulary mismatch issues. The use of word embedding as a basis for filtering is also explored, using unsupervised and supervised modeling to characterize lexical and semantic similarity. In the novelty filtering stage, several statistical ways of characterizing novelty are investigated and ensemble learning techniques are used to integrate results from these diverse techniques. These results are compared with a baseline clustering approach using both standard and delay-discounted measures. In the salience filtering stage, because of the real-time prediction requirement a method of learning verb phrase usage from past relevant news reports is used in conjunction with some standard measures for characterizing writing quality. Following a Cranfield-like evaluation paradigm, this dissertation includes a se- ries of experiments to evaluate the proposed methods for each step, and for the end- to-end system. New microblog novelty and salience judgments are created, building on existing relevance judgments from the TREC Microblog track. The results point to future research directions at the intersection of social media, computational jour- nalism, information retrieval, automatic summarization, and machine learning.

Estimation of the Traffic Intensity in a Piecewise-stationary Mt/Gt/1 Queue with Probing

We use a probing strategy to estimate the time dependent traffic intensity in an Mt/Gt/1 queue, where the arrival rate and the general service-time distribution change from one time interval to another, and derive statistical properties of the proposed estimator. We present a method to detect a switch from a stationary interval to another using a sequence of probes to improve the estimation. At the end, we compare our results with two estimators proposed in the literature for the M/G/1 queue.