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.

Pilot-scale evaluation of sulfite-activated ferrate for water reuse applications

Ferrate is a promising, “green” (i.e., iron-based) pre-oxidation technology in water treatment, but there has been limited research on its potential benefits in a water reuse (wastewater recycling) paradigm. Recent studies have shown ferrate treatment processes can be improved by activation, the addition of reductants (i.e., sulfite) to the reaction. Prior bench scale experimentation suggests sulfite-activated ferrate may be a feasible option for water reuse applications; however, extent questions need to be addressed. This study evaluated the viability of sulfite-activated ferrate in water reuse treatment through continuous-flow experiments using synthetic and field-collected secondary wastewater effluents. The effluents were processed through the piloting system which included various physicochemical processes such as ferrate pre-oxidation, coagulation, clarification, and dual-media filtration. In each trial, the system was run continuously for eight hours with data collected via grab samples and online instrumentation with real-time resolution. Results demonstrate that reuse systems using activated ferrate pre-oxidation can produce effluents with water quality meeting most regulatory requirements without major impacts on downstream physicochemical processes. When compared to traditional ferrate pre-oxidation, activation showed several improvements such as lower byproduct yields. Operationally, activated ferrate does increase the development of headloss across the dual-media filter. In general, sulfite-activated ferrate is viable in a water reuse setting, resulting in several improved water quality outcomes. Results from this work create a pathway for adaptation at scale

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

Full-scale fire tests of post-tensioned timber beams

This paper describes a series of full-scale furnace tests on loaded post tensioned LVL beams. Each beam was designed to exhibit a specific failure mechanism when exposed to the standard ISO834 fire. In addition to the beams a number of steel anchorage protection schemes were also investigated. These included wrapping the ends in kaowool, using intumescent paint, covering the anchorage with fire rated plasterboard and covering the anchorage with timber (LVL). The results of the full-scale tests cover temperature distributions through the timber members during the tests, the temperatures reached within the cavity and those of the tendons suspended within the cavity, the relaxation of the tendons during the test, the failure mechanisms experienced, and a summary of the anchorage protection details and their effectiveness. Recommendations for the design of both post-tensioned timber beams and associated anchorages are also provided

Sulfite activation changes character of ferrate resultant particles

The activation of ferrate with sulfite increases oxidative transformation of recalcitrant organic compounds; however, it also changes the characteristics of the iron particulates that result from the ferrate reduction. In this study, particles resulting from ferrate reduction both with and without sulfite were compared in a laboratory matrix simulating water treatment conditions at the bench-scale. Characteristics examined included magnetization, morphology, size, and surface charge. The activation of ferrate with sulfite changed the characteristics of resultant particles in several important ways. Activated ferrate resultant particles were less magnetic, more polydisperse including a higher fraction of nanoparticles, and exhibited a less-crystalline morphology compared to particles resulting from ferrate self-decay. Surface charges between the two particle types were similar, and negative. The relatively rapid formation of Fe(III) from Fe(VI) activation leads to particles of different character, likely though a greater supply of precursory low molecular weight iron hydroxo-species. Particles resulting from activated ferrate used as a preoxidant will impact downstream processes in important ways, such as gravimetric or magnetic separations and contaminant adsorption. Ferrate activation presents a possible trade-off between improved oxidation and impeded downstream physicochemical processes, and formation and fate of formed particles warrants consideration

Elucidation of Directionality for Co-Expressed Genes: Predicting Intra-Operon Termination Sites

We present a novel framework for inferring regulatory and sequence-level information from gene co-expression networks. The key idea of our methodology is the systematic integration of network inference and network topological analysis approaches for uncovering biological insights. We determine the gene co-expression network of Bacillus subtilis using Affymetrix GeneChip time series data and show how the inferred network topology can be linked to sequence-level information hard-wired in the organism's genome. We propose a systematic way for determining the correlation threshold at which two genes are assessed to be co-expressed by using the clustering coefficient and we expand the scope of the gene co-expression network by proposing the slope ratio metric as a means for incorporating directionality on the edges. We show through specific examples for B. subtilis that by incorporating expression level information in addition to the temporal expression patterns, we can uncover sequence-level biological insights. In particular, we are able to identify a number of cases where (i) the co-expressed genes are part of a single transcriptional unit or operon and (ii) the inferred directionality arises due to the presence of intra-operon transcription termination sites.Comment: 7 pages, 8 figures, accepted in Bioinformatic

Abatement of circumneutral mine drainage by Co-treatment with secondary municipal wastewater

Acid mine drainage is a persistent and problematic source of water pollution. Co-treatment with municipal wastewater at existing wastewater treatment plants has several advantages; however, potential impacts on plant physicochemical and biological processes have not been well explored. The primary purpose of this bench-scale study was to examine the impact of co-treatment by combining a mild acid mine drainage at various ratios with municipal wastewater, followed by sludge settling and supernatant comparative analysis using a variety of effluent water quality parameters. These measurements were combined with carbonate system and adsorption isotherm modeling to elucidate the mechanisms underlying the experimental results. Acid mine drainage addition decreased municipal wastewater effluent PO43− concentrations below 0.2 mg/L with greater than 97% removal, demonstrating co-treatment as an alternative solution for municipal wastewater nutrient removal. Biochemical oxygen demand remained similar to controls with \u3c10% variation after co-treatment. Coagulation from metals in acid mine drainage was incomplete due to PO43− adsorption, confirmed by comparing experimental results with Langmuir isotherm behavior. Sweep flocculation was the dominating particle aggregation mechanism, and co-treatment led to improved particle clarification outcomes. Improved clarification led to up to 50% Fe removal. Final pH had little variation with all conditions having pH \u3e 6.0. Carbonate system modeling adequately explains pH effects, and can also be applied to varying acid mine drainage matrices. The impact of acid mine drainage addition on the municipal wastewater microbial community was also investigated which provided evidence of microbial adaptation. This study demonstrates post-aeration co-treatment enables mitigation of mild acid mine drainage without adversely affecting wastewater treatment plant processes. Reported results also frame required future studies to address extant questions prior to full-scale adaptation

Potential Implications of Acid Mine Drainage and Wastewater Cotreatment on Solids Handling: A Review

Acid mine drainage (AMD) is a persistent and extensive source of water pollution and ecological degradation. Cotreating munici- pal wastewater (MWW) with AMD using existing infrastructure at conventional wastewater treatment plants (WWTPs) may serve as a potential option for AMD abatement. However, commonly elevated iron and aluminum concentrations and low pH of AMD could negatively impact various processes at a WWTP. The focus of this mini review was on determining how cotreating MWW with AMD could impact the solids handling processes at a WWTP. While no studies have explored the solids that could be generated during cotreatment in a WWTP, numerous articles separately discuss the solids generated during AMD or MWW treatment. Reviewing this literature revealed that iron and aluminum, common metals in AMD, are already present in MWW sludge and typically benefit most solids handling processes. The addition of AMD would elevate iron and aluminum concentration but would likely result in improved sludge dewatering, removal of odor-causing compounds during processing, and a decreased bioavailability of trace metals and water-soluble P in land applications. This review concludes that cotreating MWW with moderate to low volumes (\u3c50%) of AMD at WWTPs will have minimal impact on, and likely improve, solids handling processes

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

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