Robust Toolkit Research Articles

ChemInform Abstract: Cation Exchange: A Versatile Tool for Nanomaterials Synthesis

AbstractReview: 82 refs.

A geoinformatic approach to the collection of archaeological survey data

This article explores the integration of GIS technology with archaeological survey, focusing primarily on two case studies from central Anatolia, the Göksu Archaeological Project and the Avkat Archaeological Project. The methodology employed allows for expediency and accuracy in data recording, which enables refined analyses of anthropogenic and environmental phenomena. The approaches outlined in this article allowed the investigators to move from field observation to publication quality results within a single field day, usually within a four-hour window from initial field observation. The techniques described in the article are some of the geoinformatic applications that classical archaeology is implementing increasingly to develop a robust archaeoinformatic tool kit.

Key principles for developing industrially relevant strategic technology management toolkits

When considering the potential uptake and utilization of technology management tools by industry, it must be recognized that companies face the difficult challenges of selecting, adopting and integrating individual tools into a toolkit that must be implemented within their current organizational processes and systems. This situation is compounded by the lack of sound advice on integrating well-founded individual tools into a robust toolkit that has the necessary degree of flexibility such that they can be tailored for application to specific problems faced by individual organizations. As an initial stepping stone to offering a toolkit with empirically proven utility, this paper provides a conceptual foundation to the development of toolkits by outlining an underlying philosophical position based on observations from multiple research and commercial collaborations with industry. This stance is underpinned by a set of operationalized principles that can offer guidance to organizations when deciding upon the appropriate form, functions and features that should be embodied by any potential tool/toolkit. For example, a key objective of any tool is to aid decision-making and a core set of powerful, flexible, scaleable and modular tools should be sufficient to allow users to generate, explore, shape and implement possible solutions across a wide array of strategic issues. From our philosophical stance, the preferred mode of engagement is facilitated workshops with a participatory process that enables multiple perspectives and structures the conversation through visual representations in order to manage the cognitive load in the collaborative environment. The generic form of the tools should be configurable for the given context and utilized in a lightweight manner based on the premise of ‘start small and iterate fast’.

Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps.

The complex interplay of proteins and other molecules, often in the form of large transitory assemblies, are critical to cellular function. Today, X-ray crystallography and electron cryo-microscopy (cryo-EM) are routinely used to image these macromolecular complexes, though often at limited resolutions. Despite the rapidly growing number of macromolecular structures, few tools exist for modeling and annotating structures in the range of 3-10 Å resolution. To address this need, we have developed a number of utilities specifically targeting subnanometer resolution density maps. As part of the 2010 Cryo-EM Modeling Challenge, we demonstrated two of our latest de novo modeling tools, Pathwalking and Gorgon, as well as a tool for secondary structure identification (SSEHunter) and a new rigid-body/flexible fitting tool in Gorgon. In total, we submitted 30 structural models from ten different subnanometer resolution data sets in four of the six challenge categories. Each of our utlities produced accurate structural models and annotations across the various density maps. In the end, the utilities that we present here offer users a robust toolkit for analyzing and modeling protein structure in macromolecular assemblies at non-atomic resolutions.

Microsatellite loci for dreissenid mussels (Mollusca: Bivalvia: Dreissenidae) and relatives: markers for assessing exotic and native populations

We developed and tested 14 new polymorphic microsatellite loci for dreissenid mussels, including the two species that have invaded many freshwater habitats in Eurasia and North America, where they cause serious industrial fouling damage and ecological alterations. These new loci will aid our understanding of their genetic patterns in invasive populations as well as throughout their native Ponto-Caspian distributions. Eight new loci for the zebra mussel Dreissena polymorpha polymorpha and six for the quagga mussel D. rostriformis bugensis were compared with new results from six previously published loci to generate a robust molecular toolkit for dreissenid mussels and their relatives. Taxa tested include D. p. polymorpha, D. r. bugensis, D. r. grimmi, D. presbensis, the 'living fossil'Congeria kusceri, and the dark false mussel Mytilopsis leucophaeata (the latter also is invasive). Overall, most of the 24 zebra mussel (N = 583) and 13 quagga mussel (N = 269) population samples conformed to Hardy-Weinberg equilibrium expectations for the new loci following sequential Bonferroni correction. The 11 loci (eight new, three previously published) evaluated for D. p. polymorpha averaged 35.1 alleles and 0.72 mean observed heterozygosity per locus, and 25.3 and 0.75 for the nine loci (six new, three previously published) developed for D. r. bugensis. All but three of these loci successfully amplified the other species of Dreissena, and all but one also amplified Congeria and Mytilopsis. All species and populations tested were significantly divergent using the microsatellite data, with neighbour-joining trees reflecting their evolutionary relationships; our results reveal broad utility for resolving their biogeographic, evolutionary, population and ecological patterns.

A robust and efficient Lagrangian constraint toolkit for the simulation of 1D structures

This paper introduces an easy and efficient way to constrain a one-dimensional deformable model with Lagrangian constraints, allowing most needed interaction and combinations of 1D parts for the assembly of complex 3D structures like a bridge, a pearl necklace, cable beams and a bow. These examples illustrate non-trivial interactions, e.g. sliding, that can not be easily addressed by previous methods. All constraint formulations we propose are compatible with linear and displacement-based integration schemes. For an optimal integration numerical process, we discuss efficient reordering of the constraint and motion equations. This provides linear-time and robust simulation of complex structures.

Carrots versus sticks: Rewarding commuters for avoiding the rush-hour—a study of willingness to participate

This paper deals with the potential participation in a reward scheme to avoid peak hour driving. Using rewards in the context of congestion is novel compared to the attention received by road pricing. Psychological research emphasizes the importance of incentives such as rewards in promoting long term behavior changes. In the Netherlands, reward schemes have been tested as part of the ‘Spitsmijden’ project. This study analyses participation based on a survey of non-participants. Ordered Logit (OL) and mixed ordered logit discrete choice models were specified. The results show that participation is linked to working time flexibility, constraints in the household and the workplace and especially to personal motivations. These results provide critical insights in the formulation of a more coherent and flexible policy on transportation demand management and the development of a more robust tool kit for the inducement of large-scale behavioral changes.

SU-GG-T-369: Development and Application of a Robust Toolkit, Tomo-XML-DOM, for Helical Tomotherapy System

Purpose: To develop and implement a robust toolkit for analyzing XML files for patients treated on the Hi‐ART II helical tomotherapy system and to use the developed tool to facilitate post patient treatment analysis for research or administrative purposes. Method and Materials: The input file to the program is the patient Extensible Markup Language (XML) file. We used XMLDOM and JavaScript for file access and manipulation and Hyper Text Markup Language for graphical user interface. The XMLDOM is the Document Object Model for XML and defines a standard set of objects used in accessing and manipulating XML. JavaScript embedded in the HTML codes is used to create an instance of the XML parser for file manipulation. An XML parser enables us to load the XML file into computer memory. The toolkit has been designed to work on IE, Firefox and Mozilla. Results: The GUI options enable us to describe all the files in the archived patient folder stored in the form of unique identifiers (UID). This is a time efficient process considering the large number of files involved. We can also display data related to patient diagnosis and prescription, radiotherapy planning and delivery. With data manipulation, we can perform simple quality assurance checks such as track and match delivered to prescribed dose or apply different computational algorithms for verification purposes. The latter was illustrated by performing a second check on the calculated ROI volumes. Green's theorem was applied on each contour data to approximate the surface area and then multiply by the slice thickness to obtain the slice volume. Our results agreed to within 1% of the TPS calculated volumes. Conclusion: A robust toolkit for analyzing patient XML files treated on tomotherapy system has been developed and tested. It facilitates research and patient post analysis following radiotherapy on this system.

Low-Temperature Nanoparticle-Directed Solid-State Synthesis of Ternary and Quaternary Transition Metal Oxides

Ternary and quaternary transition metal oxides, which offer a wide variety of important physical properties, are traditionally synthesized using high-temperature reactions that often require several days of heating. A new nanoparticle-directed approach for the rapid low-temperature synthesis of nanocrystalline bulk-scale ternary and quaternary transition metal oxides has been developed. Readily available metal oxide nanoparticles can serve as a robust toolkit of highly reactive reagents, which can be mixed in solution in known ratios to form nanomodulated precursors and rapidly transformed, at relatively low temperatures, into more complex oxides. This approach is initially demonstrated for pyrochlore-type Y2Ti2O7 and Eu2Ti2O7 using XRD, DSC, and TEM to monitor the reaction. A nanocomposite of Y2O3 and TiO2 nanoparticles transforms into nanocrystalline Y2Ti2O7 within 2 h of heating to 700 °C, and Eu2Ti2O7 forms within 2 h of heating a nanocomposite of Eu2O3 and TiO2 nanoparticles to 800 °C. NiTiO3, CoTiO3...

A Robust Toolkit for Functional Profiling of the Yeast Genome

Study of mutant phenotypes is a fundamental method for understanding gene function. The construction of a near-complete collection of yeast knockouts (YKO) and the unique molecular barcodes (or TAGs) that identify each strain has enabled quantitative functional profiling of Saccharomyces cerevisiae. By using these TAGs and the SGA reporter, MFA1pr-HIS3, which facilitates conversion of heterozygous diploid YKO strains into haploid mutants, we have developed a set of highly efficient microarray-based techniques, collectively referred as dSLAM ( diploid-based synthetic lethality analysis on microarrays), to probe genome-wide gene-chemical and gene-gene interactions. Direct comparison revealed that these techniques are more robust than existing methods in functional profiling of the yeast genome. Widespread application of these tools will elucidate a comprehensive yeast genetic network.

A Robust Toolkit for Functional Profiling of the Yeast Genome

A Robust Toolkit for Functional Profiling of the Yeast Genome