Applying weighted network measures to microarray distance matrices

In recent work we presented a new approach to the analysis of weighted networks, by providing a straightforward generalization of any network measure defined on unweighted networks. This approach is based on the translation of a weighted network into an ensemble of edges, and is particularly suited to the analysis of fully connected weighted networks. Here we apply our method to several such networks including distance matrices, and show that the clustering coefficient, constructed by using the ensemble approach, provides meaningful insights into the systems studied. In the particular case of two data sets from microarray experiments the clustering coefficient identifies a number of biologically significant genes, outperforming existing identification approaches.Comment: Accepted for publication in J. Phys.

Regulatory networks and connected components of the neutral space

The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory systems is neutrality - typically a large number of alternative network structures give rise to the necessary dynamics. Here we study the discretized regulatory dynamics of the yeast cell cycle [Li et al., PNAS, 2004] and the set of networks capable of reproducing it, which we call functional. Among these, the empirical yeast wildtype network is close to optimal with respect to sparse wiring. Under point mutations, which establish or delete single interactions, the neutral space of functional networks is fragmented into 4.7 * 10^8 components. One of the smaller ones contains the wildtype network. On average, functional networks reachable from the wildtype by mutations are sparser, have higher noise resilience and fewer fixed point attractors as compared with networks outside of this wildtype component.Comment: 6 pages, 5 figure

Developing and Implementing Strategies to Address “Freddie Freeroader”

Although the majority Kentucky’s citizens pay their fair share of motor vehicle registration taxes, there are indications that a number of citizens evade motor vehicle property and usage tax through a variety of means. Some individuals license their cars in states that have no, or very low, property taxes on motor vehicles; others abuse the use of temporary tags, or simply fail to renew the registration on their vehicles. As a result, Kentucky is losing income that would be used to repair the state’s roadways and fund local services such as schools, libraries, health departments, and police and fire services. Despite the efforts of the Kentucky Department of Revenue and Kentucky State Police, collections from vehicle usage tax and property tax evaders have never reached their potential. This is primarily due to the limited resources available to these agencies and past technological challenges that prevented the ready identification of tax evaders. The objective of this research was to study new investigative techniques and technologies that are now available, and which could help to improve and streamline the Department of Revenue’s collection efforts. There are more tools available now to compliance staff within the Department of Revenue that will facilitate efforts to identify and verify a person’s residence. However, a more concerted effort is necessary to increase the collection of vehicle property and usage taxes. These tools have made the process more efficient, but additional resource commitments must be made in order to ensure that tax evaders — once identified — ultimately pay their taxes, penalties and interest

Evaluation of Thermal Imaging Technology for Commercial Vehicle Screening

Brake and tire violations are common problems identified through commercial vehicle inspections. Identifying and correcting these types of problems before a crash occurs can produce significant safety benefits. Thermal imaging technology can be used by commercial vehicle enforcement to screen vehicles as they approach a weigh station to determine if they may have flat tires and inoperable brakes. The vehicles do not have to be stopped at a weigh station to be screened. Kentucky currently has three stations outfitted with thermal imaging technology. The objectives of this study were to evaluate the benefits of using the thermal imaging cameras to identify brake and tire problems and to develop recommendations for how enforcement personnel can receive the most benefits from this technology. The data presented in this report include: 1) a summary of previous research, 2) evaluations of the technology, 3) on-site data collection at a Kentucky weigh station, 4) an interview with one of Kentucky’s primary users of the technology, and 5) an analysis of Kentucky inspection data, specifically, brake and tire violations and vehicle out-of-service (OOS) rates. A Federal Motor Carrier Safety Administration (FMCSA) evaluation concluded that the OOS rate for vehicles pinpointed via thermal imaging camera systems was 59 percent, whereas the OOS rate for conventional inspection was only 19 percent. Facilities with a thermal imaging system recorded a higher percentage of tire and brake violations per inspection as well as a higher vehicle out-of-service (VOOS) rate than facilities without a thermal imaging camera. However, the effectiveness of thermal imaging technology was significantly influenced by whether law enforcement embraced it as well as by inspectors’ proficiency operating the systems. This study recommends that enforcement staff who can access thermal imaging technology receive periodic training on its operation, then graduate to a practicum that lets them use the technology under expert supervision. Promotional materials that highlight the value of thermal imaging technologies should be distributed to all Kentucky enforcement personnel. In addition, methods and enforcement mechanisms should be identified so that personnel can be held accountable for using the technology

Dynamics of gene expression and the regulatory inference problem

From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding of transcription factor molecules to regulatory DNA. Here, we construct stochastic models of gene expression dynamics and test them on experimental time-series data of messenger-RNA concentrations. The models are used to infer biophysical parameters of gene transcription, including the statistics of transcription factor-DNA binding and the target genes controlled by a given transcription factor.Comment: revised version to appear in Europhys. Lett., new titl

Parametric study of modelling structural timber in fire with different software packages

In a bid to accurately model structural behaviour of timber buildings in fire, a number of obstacles have been identified which must be fully understood before advanced computer modelling can accurately be used to represent physical behaviour. This paper discusses the obstacles, with suggestions on how to mitigate them, incorporating the challenges of using general purpose finite element software. The paper examines modelling with ANSYS, SAFIR and ABAQUS and the individual and collective challenges related to thermal analyses of timber structures in fire conditions. It considers the effects various model parameters (thermal and structural) may have on physical interpretation of experimental data in comparison with the accuracy of numerical solutions. In detail, the study looks at the effects of 1D and 2D heat transfer analyses, finite element mesh sizes, time steps and different thermal property approaches on thermal models of timber members in fires. It further recommends how best to model these structures using the different finite element software packages

Treatment of tumours with the combination of WR-2721 and cis-dichlorodiammineplatinum (II) or cyclophosphamide.

The ability of WR-2721 [S-2(3-aminopropylamino)ethyl-phosporothioic acid] to selectively protect the host against the toxic effects of multiple doses of cis-dichlorodiammineplatinum [cis-Pt] or cyclophosphamide [CY] has been studied in mice and rats bearing 3 different tumours. Selective protection against cis-Pt induced nephrotoxicity has been demonstrated under all conditions studied, with the extent of protection being inversely related to the size of the cis-Pt dose. For example, pre-treatment with 200 mg/kg of WR-2721 30 min before each weekly dose of 2 mg/kg of cis-Pt allows the administration of this cytotoxic agent for 3 times longer before nephrotoxic injury. In none of these studies was there tumour protection. The same pattern was observed with CY, but quantitation of the extent of marrow protection was not possible for the multiple treatment studies, due to the longer latent period between induced and observed death with this drug. We conclude, therefore, that for both of these drugs, selective protection of the kidney and marrow is not only maintained under conditions of multiple treatment, but actually enhanced due to the need for smaller doses of cytotoxic agents in these protocols

Some properties of nilpotent groups

Property S, a finiteness property which can hold in infinite groups, was introduced by Stallings and others and shown to hold in free groups. In [2] it was shown to hold in nilpotent groups as a consequence of a technical result of Mal'cev. In that paper this technical result was dubbed property R. Hence, more generally, any property R group satisfies property S. In [7] it was shown that property R implies the following (labeled there weak property R) for a group G: If G₀ is any subgroup in G and G₀* is any homomorphic image of G₀, then the set of torsion elements in G₀* forms a locally finite subgroup. It was left as an open question in [7] whether weak property R is equivalent to property R. In this paper we give an explicit counterexample thereby proving that weak property R is strictly weaker than property R

Survey of generalized pregroups and a question of Reinhold Baer

There has been recent interest in Stallings’ Pregroups. (See [2] and [12].) This paper gives a survey of generalized pregroups. We also answer a question of Reinhold Baer [1] on pregroups and answer a generalization of this question for generalized pregroups