In-depth analysis of the J.A.C.K. model

The Texas Transportation Commission (“the Commission”) is responsible for planning and making policies for the location, construction, and maintenance of a comprehensive system of highways and public roads in Texas. In order for the Commission to carry out its legislative mandate, the Texas Constitution requires that most revenue generated by motor vehicle registration fees and motor fuel taxes be used for constructing and maintaining public roadways and other designated purposes. The Texas Department of Transportation (TxDOT) assists the Commission in executing state transportation policy. It is the responsibility of the legislature to appropriate money for TxDOT’s operation and maintenance expenses. All money authorized to be appropriated for TxDOT’s operations must come from the State Highway Fund (also known as Fund 6, Fund 006, or Fund 0006). The Commission can then use the balance in the fund to fulfill its responsibilities. However, the value of the revenue received in Fund 6 is not keeping pace with growing demand for transportation infrastructure in Texas. Additionally, diversion of revenue to nontransportation uses now exceeds $600 million per year. As shown in Figure 1.1, revenues and expenditures of the State Highway Fund per vehicle mile traveled (VMT) in Texas have remained almost flat since 1993. In the meantime, construction cost inflation has gone up more than 100%, effectively halving the value of expenditure.

Evaluation of TxDOT’s J.A.C.K. model for revenue and expenditure projections

This research report documents work conducted by the Center for Transportation (CTR) at The University of Texas at Austin in analyzing the Joint Analysis using the Combined Knowledge (J.A.C.K.) program. This program was developed by the Texas Department of Transportation (TxDOT) to make projections of revenues and expenditures. This research effort was to span from September 2008 to August 2009, but the bulk of the work was completed and presented by December 2008. J.A.C.K. was subsequently renamed TRENDS, but for consistency with the scope of work, the original name is used throughout this report.

Pyktree : a K-tree implementation in Python

In this paper we present pyktree, an implementation of the K-tree algorithm in the Python programming language. The K-tree algorithm provides highly balanced search trees for vector quantization that scales up to very large data sets. Pyktree is highly modular and well suited for rapid-prototyping of novel distance measures and centroid representations. It is easy to install and provides a python package for library use as well as command line tools.

PCR bias Toward the wild-type k-ras and p53 sequences: Implications for PCR detection of mutations and cancer diagnosis

PCR-based cancer diagnosis requires detection of rare mutations in k- ras, p53 or other genes. The assumption has been that mutant and wild-type sequences amplify with near equal efficiency, so that they are eventually present in proportions representative of the starting material. Work on factor IX suggests that this assumption is invalid for one case of near- sequence identity. To test the generality of this phenomenon and its relevance to cancer diagnosis, primers distant from point mutations in p53 and k-ras were used to amplify wild-type and mutant sequences from these genes. A substantial bias against PCR amplification of mutants was observed for two regions of the p53 gene and one region of k-ras. For k-ras and p53, bias was observed when the wild-type and mutant sequences were amplified separately or when mixed in equal proportions before PCR. Bias was present with proofreading and non-proofreading polymerase. Mutant and wild-type segments of the factor V, cystic fibrosis transmembrane conductance regulator and prothrombin genes were amplified and did not exhibit PCR bias. Therefore, the assumption of equal PCR efficiency for point mutant and wild-type sequences is invalid in several systems. Quantitative or diagnostic PCR will require validation for each locus, and enrichment strategies may be needed to optimize detection of mutants.

Are the ‘cave’ minerals archerite (K,NH4)H2PO4 and biphosphammite (K,NH4)H2PO4 identical? A molecular structural study

The molecular structure of the mineral archerite ((K,NH4)H2PO4) has been determined and compared with that of biphosphammite ((NH4,K)H2PO4). Raman spectroscopy and infrared spectroscopy has been used to characterise these ‘cave’ minerals. Both minerals originated from the Murra-el-elevyn Cave, Eucla, Western Australia. The mineral is formed by the reaction of the chemicals in bat guano with calcite substrates. Raman and infrared bands are assigned to H2PO4-, OH and NH stretching vibrations. The Raman band at 981 cm-1 is assigned to the HOP stretching vibration. Bands in the 1200 to 1800 cm-1 region are associated with NH4+ bending modes. The molecular structure of the two minerals appear to be very similar, and it is therefore concluded that the two minerals are identical.

Measurement of total body water (TBW) and total energy expenditure (TEE) using stable isotopes

Understanding the relationship between diet, physical activity and health in humans requires accurate measurement of body composition and daily energy expenditure. Stable isotopes provide a means of measuring total body water and daily energy expenditure under free-living conditions. While the use of isotope ratio mass spectrometry (IRMS) for the analysis of 2H (Deuterium) and 18O (Oxygen-18) is well established in the field of human energy metabolism research, numerous questions remain regarding the factors which influence analytical and measurement error using this methodology. This thesis was comprised of four studies with the following emphases. The aim of Study 1 was to determine the analytical and measurement error of the IRMS with regard to sample handling under certain conditions. Study 2 involved the comparison of TEE (Total daily energy expenditure) using two commonly employed equations. Further, saliva and urine samples, collected at different times, were used to determine if clinically significant differences would occur. Study 3 was undertaken to determine the appropriate collection times for TBW estimates and derived body composition values. Finally, Study 4, a single case study to investigate if TEE measures are affected when the human condition changes due to altered exercise and water intake. The aim of Study 1 was to validate laboratory approaches to measure isotopic enrichment to ensure accurate (to international standards), precise (reproducibility of three replicate samples) and linear (isotope ratio was constant over the expected concentration range) results. This established the machine variability for the IRMS equipment in use at Queensland University for both TBW and TEE. Using either 0.4mL or 0.5mL sample volumes for both oxygen-18 and deuterium were statistically acceptable (p>0.05) and showed a within analytical variance of 5.8 Delta VSOW units for deuterium, 0.41 Delta VSOW units for oxygen-18. This variance was used as “within analytical noise” to determine sample deviations. It was also found that there was no influence of equilibration time on oxygen-18 or deuterium values when comparing the minimum (oxygen-18: 24hr; deuterium: 3 days) and maximum (oxygen-18: and deuterium: 14 days) equilibration times. With regard to preparation using the vacuum line, any order of preparation is suitable as the TEE values fall within 8% of each other regardless of preparation order. An 8% variation is acceptable for the TEE values due to biological and technical errors (Schoeller, 1988). However, for the automated line, deuterium must be assessed first followed by oxygen-18 as the automated machine line does not evacuate tubes but merely refills them with an injection of gas for a predetermined time. Any fractionation (which may occur for both isotopes), would cause a slight elevation in the values and hence a lower TEE. The purpose of the second and third study was to investigate the use of IRMS to measure the TEE and TBW of and to validate the current IRMS practices in use with regard to sample collection times of urine and saliva, the use of two TEE equations from different research centers and the body composition values derived from these TEE and TBW values. Following the collection of a fasting baseline urine and saliva sample, 10 people (8 women, 2 men) were dosed with a doubly labeled water does comprised of 1.25g 10% oxygen-18 and 0.1 g 100% deuterium/kg body weight. The samples were collected hourly for 12 hrs on the first day and then morning, midday, and evening samples were collected for the next 14 days. The samples were analyzed using an isotope ratio mass spectrometer. For the TBW, time to equilibration was determined using three commonly employed data analysis approaches. Isotopic equilibration was reached in 90% of the sample by hour 6, and in 100% of the sample by hour 7. With regard to the TBW estimations, the optimal time for urine collection was found to be between hours 4 and 10 as to where there was no significant difference between values. In contrast, statistically significant differences in TBW estimations were found between hours 1-3 and from 11-12 when compared with hours 4-10. Most of the individuals in this study were in equilibrium after 7 hours. The TEE equations of Prof Dale Scholler (Chicago, USA, IAEA) and Prof K.Westerterp were compared with that of Prof. Andrew Coward (Dunn Nutrition Centre). When comparing values derived from samples collected in the morning and evening there was no effect of time or equation on resulting TEE values. The fourth study was a pilot study (n=1) to test the variability in TEE as a result of manipulations in fluid consumption and level of physical activity; the magnitude of change which may be expected in a sedentary adult. Physical activity levels were manipulated by increasing the number of steps per day to mimic the increases that may result when a sedentary individual commences an activity program. The study was comprised of three sub-studies completed on the same individual over a period of 8 months. There were no significant changes in TBW across all studies, even though the elimination rates changed with the supplemented water intake and additional physical activity. The extra activity may not have sufficiently strenuous enough and the water intake high enough to cause a significant change in the TBW and hence the CO2 production and TEE values. The TEE values measured show good agreement based on the estimated values calculated on an RMR of 1455 kcal/day, a DIT of 10% of TEE and activity based on measured steps. The covariance values tracked when plotting the residuals were found to be representative of “well-behaved” data and are indicative of the analytical accuracy. The ratio and product plots were found to reflect the water turnover and CO2 production and thus could, with further investigation, be employed to identify the changes in physical activity.

Platinum/graphene nanosheet/SiC contacts and their application for hydrogen gas sensing

Pt/graphene nanosheet/SiC based devices are fabricated and characterized and their performances toward hydrogen gas are investigated. The graphene nanosheets are synthesized via the reduction of spray-coated graphite oxide deposited onto SiC substrates. Raman and X-ray photoelectron spectroscopies indicate incomplete reduction of the graphite oxide, resulting in partially oxidized graphene nanosheet layers of less than 10 nm thickness. The effects of interfaces on the nonlinear behavior of the Pt/graphene and graphene/SiC junctions are investigated. Current-voltage measurements of the sensors toward 1% hydrogen in synthetic air gas mixture at various temperatures ranging up to 100. ° C are performed. From the dynamic response, a voltage shift of ∼100 mV is recorded for 1% hydrogen at a constant current bias of 1 mA at 100. °C. © 2010 American Chemical Society.

Stochastic models and simulation of ion channel dynamics

The behaviour of ion channels within cardiac and neuronal cells is intrinsically stochastic in nature. When the number of channels is small this stochastic noise is large and can have an impact on the dynamics of the system which is potentially an issue when modelling small neurons and drug block in cardiac cells. While exact methods correctly capture the stochastic dynamics of a system they are computationally expensive, restricting their inclusion into tissue level models and so approximations to exact methods are often used instead. The other issue in modelling ion channel dynamics is that the transition rates are voltage dependent, adding a level of complexity as the channel dynamics are coupled to the membrane potential. By assuming that such transition rates are constant over each time step, it is possible to derive a stochastic differential equation (SDE), in the same manner as for biochemical reaction networks, that describes the stochastic dynamics of ion channels. While such a model is more computationally efficient than exact methods we show that there are analytical problems with the resulting SDE as well as issues in using current numerical schemes to solve such an equation. We therefore make two contributions: develop a different model to describe the stochastic ion channel dynamics that analytically behaves in the correct manner and also discuss numerical methods that preserve the analytical properties of the model.

The role of soil characteristics on temperature sensitivity of soil organic matter

The uncertainty associated with how projected climate change will affect global C cycling could have a large impact on predictions of soil C stocks. The purpose of our study was to determine how various soil decomposition and chemistry characteristics relate to soil organic matter (SOM) temperature sensitivity. We accomplished this objective using long-term soil incubations at three temperatures (15, 25, and 35°C) and pyrolysis molecular beam mass spectrometry (py-MBMS) on 12 soils from 6 sites along a mean annual temperature (MAT) gradient (2–25.6°C). The Q10 values calculated from the CO2 respired during a long-term incubation using the Q10-q method showed decomposition of the more resistant fraction to be more temperature sensitive with a Q10-q of 1.95 ± 0.08 for the labile fraction and a Q10-q of 3.33 ± 0.04 for the more resistant fraction. We compared the fit of soil respiration data using a two-pool model (active and slow) with first-order kinetics with a three-pool model and found that the two and three-pool models statistically fit the data equally well. The three-pool model changed the size and rate constant for the more resistant pool. The size of the active pool in these soils, calculated using the two-pool model, increased with incubation temperature and ranged from 0.1 to 14.0% of initial soil organic C. Sites with an intermediate MAT and lowest C/N ratio had the largest active pool. Pyrolysis molecular beam mass spectrometry showed declines in carbohydrates with conversion from grassland to wheat cultivation and a greater amount of protected carbohydrates in allophanic soils which may have lead to differences found between the total amount of CO2 respired, the size of the active pool, and the Q10-q values of the soils.

The undirected feedback vertex set problem has a Poly(k) Kernel

Resolving a noted open problem, we show that the Undirected Feedback Vertex Set problem, parameterized by the size of the solution set of vertices, is in the parameterized complexity class Poly(k), that is, polynomial-time pre-processing is sufficient to reduce an initial problem instance (G, k) to a decision-equivalent simplified instance (G', k') where k' � k, and the number of vertices of G' is bounded by a polynomial function of k. Our main result shows an O(k11) kernelization bound.

Vibrational spectroscopic analysis of taranakite (K,NH4)Al3(PO4)3(OH) •9(H2O) from the Jenolan Caves, Australia

Many phosphate containing minerals are found in the Jenolan Caves. Such minerals are formed by the reaction of bat guano and clays from the caves. Among these cave minerals is the mineral taranakite (K,NH4)Al3(PO4)3(OH)•9(H2O) which has been identified by X-ray diffraction. Jenolan Caves taranakite has been characterised by Raman spectroscopy. Raman and infrared bands are assigned to H2PO4-, OH and NH stretching vibrations. By using a combination of XRD and Raman spectroscopy, the existence of taranakite in the caves has been proven.

Deformation behaviours of coarse-grained and nanocrystalline Mg-5wt% Al alloys

Magnesium alloys have been of growing interest to various engineering applications, such as the automobile, aerospace, communication and computer industries due to their low density, high specific strength, good machineability and availability as compared with other structural materials. However, most Mg alloys suffer from poor plasticity due to their Hexagonal Close Packed structure. Grain refinement has been proved to be an effective method to enhance the strength and alter the ductility of the materials. Several methods have been proposed to produce materials with nanocrystalline grain structures. So far, most of the research work on nanocrystalline materials has been carried out on Face-Centered Cubic and Body-Centered Cubic metals. However, there has been little investigation of nanocrystalline Mg alloys. In this study, bulk coarse-grained and nanocrystalline Mg alloys were fabricated by a mechanical alloying method. The mixed powder of Mg chips and Al powder was mechanically milled under argon atmosphere for different durations of 0 hours (MA0), 10 hours (MA10), 20 hours (MA20), 30 hours (MA30) and 40 hours (MA40), followed by compaction and sintering. Then the sintered billets were hot-extruded into metallic rods with a 7 mm diameter. The obtained Mg alloys have a nominal composition of Mg–5wt% Al, with grain sizes ranging from 13 μm down to 50 nm, depending on the milling durations. The microstructure characterization and evolution after deformation were carried out by means of Optical microscopy, X-Ray Diffraction, Scanning Electron Microscopy, Transmission Electron Microscopy, Scanning Probe Microscopy and Neutron Diffraction techniques. Nanoindentaion, compression and micro-compression tests on micro-pillars were used to study the size effects on the mechanical behaviour of the Mg alloys. Two kinds of size effects on the mechanical behaviours and deformation mechanisms were investigated: grain size effect and sample size effect. The nanoindentation tests were composed of constant strain rate, constant loading rate and indentation creep tests. The normally reported indentation size effect in single crystal and coarse-grained crystals was observed in both the coarse-grained and nanocrystalline Mg alloys. Since the indentation size effect is correlated to the Geometrically Necessary Dislocations under the indenter to accommodate the plastic deformation, the good agreement between the experimental results and the Indentation Size Effect model indicated that, in the current nanocrystalline MA20 and MA30, the dislocation plasticity was still the dominant deformation mechanism. Significant hardness enhancement with decreasing grain size, down to 58 nm, was found in the nanocrystalline Mg alloys. Further reduction of grain size would lead to a drop in the hardness values. The failure of grain refinement strengthening with the relatively high strain rate sensitivity of nanocrystalline Mg alloys suggested a change in the deformation mechanism. Indentation creep tests showed that the stress exponent was dependent on the loading rate during the loading section of the indentation, which was related to the dislocation structures before the creep starts. The influence of grain size on the mechanical behaviour and strength of extruded coarse-grained and nanocrystalline Mg alloys were investigated using uniaxial compression tests. The macroscopic response of the Mg alloys transited from strain hardening to strain softening behaviour, with grain size reduced from 13 ìm to 50 nm. The strain hardening was related to the twinning induced hardening and dislocation hardening effect, while the strain softening was attributed to the localized deformation in the nanocrystalline grains. The tension–compression yield asymmetry was noticed in the nanocrystalline region, demonstrating the twinning effect in the ultra-fine-grained and nanocrystalline region. The relationship k tensions < k compression failed in the nanocrystalline Mg alloys; this was attributed to the twofold effect of grain size on twinning. The nanocrystalline Mg alloys were found to exhibit increased strain rate sensitivity with decreasing grain size, with strain rate ranging from 0.0001/s to 0.01/s. Strain rate sensitivity of coarse-grained MA0 was increased by more than 10 times in MA40. The Hall-Petch relationship broke down at a critical grain size in the nanocrystalline region. The breakdown of the Hall-Petch relationship and the increased strain rate sensitivity were due to the localized dislocation activities (generalization and annihilation at grain boundaries) and the more significant contribution from grain boundary mediated mechanisms. In the micro-compression tests, the sample size effects on the mechanical behaviours were studied on MA0, MA20 and MA40 micro-pillars. In contrast to the bulk samples under compression, the stress-strain curves of MA0 and MA20 micro-pillars were characterized with a number of discrete strain burst events separated by nearly elastic strain segments. Unlike MA0 and MA20, the stress-strain curves of MA40 micro-pillars were smooth, without obvious strain bursts. The deformation mechanisms of the MA0 and MA20 micro-pillars under micro-compression tests were considered to be initially dominated by deformation twinning, followed by dislocation mechanisms. For MA40 pillars, the deformation mechanisms were believed to be localized dislocation activities and grain boundary related mechanisms. The strain hardening behaviours of the micro-pillars suggested that the grain boundaries in the nanocrystalline micro-pillars would reduce the source (nucleation sources for twins/dislocations) starvation hardening effect. The power law relationship of the yield strength on pillar dimensions in MA0, MA20 supported the fact that the twinning mechanism was correlated to the pre-existing defects, which can promote the nucleation of the twins. Then, we provided a latitudinal comparison of the results and conclusions derived from the different techniques used for testing the coarse-grained and nanocrystalline Mg alloy; this helps to better understand the deformation mechanisms of the Mg alloys as a whole. At the end, we summarized the thesis and highlighted the conclusions, contributions, innovations and outcomes of the research. Finally, it outlined recommendations for future work.

Hydrogen gas sensing performance of a Pt/graphene/SiC device

In this work, we present the development of a Pt/graphene/SiC device for hydrogen gas sensing. A single layer of graphene was deposited on 6H-SiC via chemical vapor deposition. The presence of graphene C-C bonds was observed via X-ray photoelectron spectroscopy analysis. Current-voltage characteristics of the device were measured at the presence of hydrogen at different temperatures, from 25°C to 170°C. The dynamic response of the device was recorded towards hydrogen gas at an optimum temperature of 130°C. A voltage shift of 191 mV was recorded towards 1% hydrogen at −1 mA constant current.

Classifying the user intent of web queries using k-means clustering

Purpose: Web search engines are frequently used by people to locate information on the Internet. However, not all queries have an informational goal. Instead of information, some people may be looking for specific web sites or may wish to conduct transactions with web services. This paper aims to focus on automatically classifying the different user intents behind web queries. Design/methodology/approach: For the research reported in this paper, 130,000 web search engine queries are categorized as informational, navigational, or transactional using a k-means clustering approach based on a variety of query traits. Findings: The research findings show that more than 75 percent of web queries (clustered into eight classifications) are informational in nature, with about 12 percent each for navigational and transactional. Results also show that web queries fall into eight clusters, six primarily informational, and one each of primarily transactional and navigational. Research limitations/implications: This study provides an important contribution to web search literature because it provides information about the goals of searchers and a method for automatically classifying the intents of the user queries. Automatic classification of user intent can lead to improved web search engines by tailoring results to specific user needs. Practical implications: The paper discusses how web search engines can use automatically classified user queries to provide more targeted and relevant results in web searching by implementing a real time classification method as presented in this research. Originality/value: This research investigates a new application of a method for automatically classifying the intent of user queries. There has been limited research to date on automatically classifying the user intent of web queries, even though the pay-off for web search engines can be quite beneficial. © Emerald Group Publishing Limited.

Stepping stones : student journal : year K

"ORIGO Stepping Stones gives mathematics teachers the best of both worlds by delivering lessons and teacher guides on a digital platform blended with the more traditional printed student journals." -- Publisher website