Comparison of the modelled thyroxine binding site in TBG with the experimentally determined site in transthyretin

The structure of cleaved thyroxine-binding globulin (TBG) hasbeen modelled on the crystal structure of cleaved 1-antitrypsin(a member of the serine proteinase inhibitor, serpin, superfamily)based on the high sequence homology exhibited by the two proteins.Particular attention was paid to the identification and modelledcharacteristics of the thyroxine binding site. The primary aimof the study was to compare the site qualitatively with thecrystallographically determined binding site of transthyretin,the other major transporter of thyroxine, in an attempt to explainthe higher binding affinity of the site compared with the knownthyrox ine binding site in transthyretin (10¹⁰ versus 10⁸ M^–1).The proposed binding site shares some similar characteristicswith the transthyretin binding site but also includes a clusterof aromatic residues which are entirely absent in transthyretin.It is proposed that this might account for the substantial differencein binding affinities.     

Fundamental Optical Absorption Edge of Sputter-Deposited Zirconia and Yttria

Zirconia and yttria films were sputter deposited onto unheated fused silica substrates using a metal target and rare gas-oxygen discharges. Double-beam spectrophotometry was used to measure the transmission and reflection as a function of incident photon energy, E , from which the absorption coefficient, α( E ), was calculated. An indirect interband transition at E _i= 4.70 eV and two direct interband transitions at E _g1= 5.17 eV and E _g2= 5.93 eV occur in monoclinic zirconia. Two direct interband transitions at E _g1= 5.07 eV and E _g2= 5.73 eV occur in cubic yttria. The absorption edge structure is modified when unusual phases, such as tetragonal zirconia, and zirconia and yttria with no longrange crystallographic order, are present.     

Activated gas plasma surface treatment of polymers for adhesive bonding

Polyethylene, polypropylene, poly(vinyl fluoride) (Tedlar), polystyrene, nylon 6, poly(ethylene terephthalate) (Mylar), polycarbonate, cellulose acetate butyrate, and a poly(oxymethylene) copolymer were treated with activated helium and with activated oxygen. Mechanical strengths of adhesive-bonded specimens prepared from treated and from untreated coupons were compared. Polyethylene (PE) and polypropylene (PP) showed the greatest increases in bond strength. Oxygen and helium were both effective with polyethylene, but polypropylene showed no improvement when treated with activated helium. The results with excited helium parallel the effects of ionizing radiation on these two polymers, as does the appearance of unsaturation bands in the infrared (965 cm^?1 in PE, and 887 and 910 cm^?1 in PP). Active nitrogen produced excellent bond strength with polyethylene but not with polypropylene. Of the remaining polymers examined, Tedlar, polystyrene, and nylon 6 showed the greatest improvement in bondability after treatment, and Mylar showed moderate improvement. Polycarbonate, cellulose acetate butyrate, and the poly(oxymethylene) copolymer gave approximately two-fold increases in lap-shear bond strength. In several cases, significant differences in response to time of treatment and type of excited gas were found.     

Micro-computed tomography scanning approaches to quantify,parameterize and visualize bioturbation activity in clogged streambeds: A proof of concept

Fine particle clogging and faunal bioturbation are two key processes co-occurring in the hyporheic zone that potentially affect hyporheic exchange through modifications in the sediment structure of streambeds. Clogging results from excessive fine sediment infiltration and deposition in rivers, and it is known to decrease matrix porosity and potentially reduce permeability. Faunal bioturbation activity may compensate for the negative effect of clogging by reworking the sediment, increasing porosity, and preventing further infiltration of fines. Although both processes of clogging and bioturbation have received significant attention in the literature separately, their combined effects on streambed sediment structure are not well understood, mostly due to the lack of a standard methodology for their assessment. Here, we illustrate a novel methodology using X-ray computed tomography (CT), as proof of concept, to investigate how, together, clogging and bioturbation affect streambed porosity in a controlled flow-through flume. By visualising gallery formations of an upward conveyor macroinvertebrate; Lumbriculus variegatus as a model species, we quantified bioturbation activity in a clogged streambed, focusing on orientation, depth, and volume at downwelling and upwelling areas of the flume. Gallery creation increased the porosity of the streambed sediment, suggesting a potential improvement in permeability and a possible offset of clogging effects. We illustrate the promising use of X-ray CT as a tool to assess bioturbation in clogged streambeds, and the potential role of bioturbation activity supporting hyporheic exchange processes in streambeds, warranting further studies to understand the extent of bioturbation impacts in natural systems.     

Exploring the costs of technical debt management – a case study

Technical debt is a metaphor for delayed software maintenance tasks. Incurring technical debt may bring short-term benefits to a project, but such benefits are often achieved at the cost of extra work in future, analogous to paying interest on the debt. Currently technical debt is managed implicitly, if at all. However, on large systems, it is too easy to lose track of delayed tasks or to misunderstand their impact. Therefore, we have proposed a new approach to managing technical debt, which we believe to be helpful for software managers to make informed decisions. In this study we explored the costs of the new approach by tracking the technical debt management activities in an on-going software project. The results from the study provided insights into the impact of technical debt management on software projects. In particular, we found that there is a significant start-up cost when beginning to track and monitor technical debt, but the cost of ongoing management soon declines to very reasonable levels.     

A coherence maximisation process for solving normative inconsistencies

Norms can be used in multi-agent systems for defining patterns of behaviour in terms of permissions, prohibitions and obligations that are addressed to agents playing a specific role. Agents may play different roles during their execution and they may even play different roles simultaneously. As a consequence, agents may be affected by inconsistent norms; e.g., an agent may be simultaneously obliged and forbidden to reach a given state of affairs. Dealing with this type of inconsistency is one of the main challenges of normative reasoning. Existing approaches tackle this problem by using a static and predefined order that determines which norm should prevail in the case where two norms are inconsistent. One main drawback of these proposals is that they allow only pairwise comparison of norms; it is not clear how agents may use the predefined order to select a subset of norms to abide by from a set of norms containing multiple inconsistencies. Furthermore, in dynamic and non-deterministic environments it can be difficult or even impossible to specify an order that resolves inconsistencies satisfactorily in all potential situations. In response to these two problems, we propose a mechanism with which an agent can dynamically compute a preference order over subsets of its competing norms by considering the coherence of its cognitive and normative elements. Our approach allows flexible resolution of normative inconsistencies, tailored to the current circumstances of the agent. Moreover, our solution can be used to determine norm prevalence among a set of norms containing multiple inconsistencies.     

Crafting the Compelling User Experience

This article provides an introduction to the usage of software engineering approaches and tools for the design of user experience (UE). This approach was developed for three main reasons: (a) to provide UE design teams a rigorous, methodical, encompassing method that can be applied throughout the entire product development cycle; (b) to provide designers a way to work with abstract concepts to establish the conceptual design of the system before progressing to the realization of the design to the appropriate platform; and (c) to communicate the intended design to the implementation team in a manner that is concise, complete, and familiar. The approach is the application of Unified Modeling Language concepts to describe users and the UE design rather than the technical architecture. It is believed that designing the UE design separately from the technical architecture will help ensure teams deliver a usable and delightful UE. The methods in this article have been applied to a handful of real-world projects in the last year and a half. Thus far, the application of software engineering approaches and tools have been found to be very powerful aids that have enabled the creation of highly useful Web experiences as well as software applications.

Our intent is to address the full gamut of issues involved in creating a total user experience (UE)-from discovery of users needs through high-level and low-level design, ensuring fidelity during development, and deployment, with a full assessment of how well the design meets users' needs. We believe that through a concerted use of such a rigorous approach we can greatly improve not only the UE of products we create, but also the experience of designing and developing them. We are not the only team taking this direction in UE design. It has become clear to many in our field that a more rigorous, thorough, and accurate approach to UE design is not only possible-it is necessary, for many of the same reasons that software engineers long ago embraced such practices. As we are evolving our approaches in other phases, this article focuses on the discovery and design phase activities.     

Quagga mussels (Dreissena bugensis) as biomonitors of metal contamination: A case study in the upper St. Lawrence River

In this study, the utility of quagga mussels (Dreissena bugensis) as biomonitors was investigated by measuring total concentrations of three trace metals, cadmium, copper, and zinc, in soft tissues. Quagga mussels were sampled from five sites along the upper St. Lawrence River, including one industrially influenced site, from 1999 through 2007. Mussels were collected from near-shore areas, divided into 5 size classes based on maximum shell length, and tissues were pooled for analysis of each size group. Two-way analysis of variance and a posteriori range tests were used to test for differences among sites along a distance gradient from the outflow of Lake Ontario and to examine inter-annual variability within and among sites. Cadmium concentrations were higher nearer the outflow of the lake. Copper concentrations varied among sites and years, but were generally highest near the industrial site. Zinc concentrations were relatively uniform, possibly reflecting internal regulation. Animal size measured as shell length was not an important factor in this section of the river, but warrants further consideration in a wider range of ecosystems and contaminant exposure levels. In general, concentrations of the three metals were not high compared to reports in the published literature for dreissenid mussels in contaminated environments. However, few studies have utilized quagga mussels rather than zebra mussels. The two species may differ in bioaccumulation patterns and may not be interchangeable as biomonitors. Further studies of bioaccumulation of contaminants by quagga mussels in a wider range of contaminant exposures would be useful particularly as quagga mussels displace zebra mussels in the Laurentian Great Lakes and the St. Lawrence River.