Rhodium Pyrazolate Complexes as Potential CVD Precursors

Reaction of 3,5-(CF3)(2)PzLi with [Rh(mu-Cl)(eta(2)-C2H4)(2)](2) or [Rh(mu-Cl)(PMe3)(2)](2) in Et2O gave the dinuclear complexes [Rh(eta(2)-C2H4)(2)(mu-3,5-(CF3)(2)-Pz)](2) (1) and [Rh-2(mu-Cl)(mu-3,5-(CF3)(2)-Pz) (PMe3)(4)] (2) respectively (3,5-(CF3)(2)Pz = bis-trifluoromethyl pyrazolate). Reaction of PMe3 with [Rh(COD)(mu-3,5-(CF3)(2)-Pz)](2) in toluene gave [Rh(3,5-(CF3)(2)-Pz)(PMe3)(3)] (3). Reaction of 1 and 3 in toluene (1 : 4) gave moderate yields of the dinuclear complex [Rh(PMe3)(2)(mu-3,5-(CF3)(2)-Pz)](2) (4). Reaction of 3,5-(CF3)(2)PzLi with [Rh(PMe3)(4)]Cl in Et2O gave the ionic complex [Rh(PMe3)(4)][3,5-(CF3)(2)-Pz] (5). Two of the complexes, 1 and 3, were studied for use as CVD precursors. Polycrystalline thin films of rhodium (fcc-Rh) and metastable-amorphous films of rhodium phosphide (Rh2P) were grown from 1 and 3 respectively at 170 and 130 degrees C, 0.3 mmHg in a hot wall reactor using Ar as the carrier gas (5 cc min(-1)). Thin films of amorphous rhodium and rhodium phosphide (Rh2P) were grown from 1 and 3 at 170 and 130 degrees C respectively at 0.3 mmHg in a hot wall reactor using H-2 as the carrier gas (7 cc min(-1)).Welch Foundation F-816Petroleum Research Fund 47014-ACSNSF 0741973Chemistr

A Workflow for Global Sensitivity Analysis of PBPK Models

Physiologically based pharmacokinetic (PBPK) models have a potentially significant role in the development of a reliable predictive toxicity testing strategy. The structure of PBPK models are ideal frameworks into which disparate in vitro and in vivo data can be integrated and utilized to translate information generated, using alternative to animal measures of toxicity and human biological monitoring data, into plausible corresponding exposures. However, these models invariably include the description of well known non-linear biological processes such as, enzyme saturation and interactions between parameters such as, organ mass and body mass. Therefore, an appropriate sensitivity analysis (SA) technique is required which can quantify the influences associated with individual parameters, interactions between parameters and any non-linear processes. In this report we have defined the elements of a workflow for SA of PBPK models that is computationally feasible, accounts for interactions between parameters, and can be displayed in the form of a bar chart and cumulative sum line (Lowry plot), which we believe is intuitive and appropriate for toxicologists, risk assessors, and regulators

VariVis: a visualisation toolkit for variation databases

<p>Abstract</p> <p>Background</p> <p>With the completion of the Human Genome Project and recent advancements in mutation detection technologies, the volume of data available on genetic variations has risen considerably. These data are stored in online variation databases and provide important clues to the cause of diseases and potential side effects or resistance to drugs. However, the data presentation techniques employed by most of these databases make them difficult to use and understand.</p> <p>Results</p> <p>Here we present a visualisation toolkit that can be employed by online variation databases to generate graphical models of gene sequence with corresponding variations and their consequences. The VariVis software package can run on any web server capable of executing Perl CGI scripts and can interface with numerous Database Management Systems and "flat-file" data files. VariVis produces two easily understandable graphical depictions of any gene sequence and matches these with variant data. While developed with the goal of improving the utility of human variation databases, the VariVis package can be used in any variation database to enhance utilisation of, and access to, critical information.</p

Measuring and Correcting Wind-Induced Pointing Errors of the Green Bank Telescope Using an Optical Quadrant Detector

Wind-induced pointing errors are a serious concern for large-aperture high-frequency radio telescopes. In this paper, we describe the implementation of an optical quadrant detector instrument that can detect and provide a correction signal for wind-induced pointing errors on the 100m diameter Green Bank Telescope (GBT). The instrument was calibrated using a combination of astronomical measurements and metrology. We find that the main wind-induced pointing errors on time scales of minutes are caused by the feedarm being blown along the direction of the wind vector. We also find that wind-induced structural excitation is virtually non-existent. We have implemented offline software to apply pointing corrections to the data from imaging instruments such as the MUSTANG 3.3 mm bolometer array, which can recover ~70% of sensitivity lost due to wind-induced pointing errors. We have also performed preliminary tests that show great promise for correcting these pointing errors in real-time using the telescope's subreflector servo system in combination with the quadrant detector signal.Comment: 17 pages, 11 figures; accepted for publication in PAS

A(1)ATVar: A Relational Database of Human SERPINA1 Gene Variants Leading to alpha(1)-Antitrypsin Deficiency and Application of the VariVis Software

We have developed a relational database of human SERPINA1 gene mutations, leading to a,antitrypsin (AAT) deficiency, called A(1)ATVar, which can be accessed over the World Wide Web at www.goldenhelix.org/A1ATVar. Extensive information has been extracted from the literature and converted into a searchable database, including genotype information, clinical phenotype, allelic frequencies for the commonest AAT variant alleles, methods of detection, and references. Mutation summaries are automatically displayed and user-generated queries can be formulated based on fields in the database. A separate module, linked to the FINDbase database for frequencies of inherited disorders allows the user to access allele frequency information for the three most frequent AAT alleles, namely PiM, PiS, and PiZ. The available experimental protocols to detect AAT variant alleles at the protein and DNA levels have been archived in a searchable format. A visualization tool, called VariVis, has been implemented to combine A(1)ATVar variant information with SERPINA1 sequence and annotation data. A direct data submission tool allows registered users to submit data on novel AAT variant alleles as well as experimental protocols to explore SERPINA1 genetic heterogeneity, via a password-protected interface. Database access is free of charge and there are no registration requirements for querying the data. The A(1)ATVar database is the only integrated database on the Internet offering summarized information on AAT allelic variants and could be useful not only for clinical diagnosis and research on AAT deficiency and the SERPINA1 gene, but could also serve as an example for an all-in-one solution for locus-specific database (LSDB) development and curation. Hum Mutat 30, 308-313, 2009

Stops making sense: translational trade-offs and stop codon reassignment

Background Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codons in the genetic code. Although genetic codes are highly constrained, stop codon number appears to be their most volatile feature. Results In the human genome, codons readily mutable to stops are underrepresented in coding sequences. We construct a simple mathematical model based on the relative likelihoods of premature termination and readthrough. When readthrough occurs, the resultant protein has a tail of amino acid residues incorrectly added to the C-terminus. Our results depend strongly on the number of stop codons in the genetic code. When the code has more stop codons, premature termination is relatively more likely, particularly for longer genes. When the code has fewer stop codons, the length of the tail added by readthrough will, on average, be longer, and thus more deleterious. Comparative analysis of taxa with a range of stop codon numbers suggests that genomes whose code includes more stop codons have shorter coding sequences. Conclusions We suggest that the differing trade-offs presented by alternative genetic codes may result in differences in genome structure. More speculatively, multiple stop codons may mitigate readthrough, counteracting the disadvantage of a higher rate of nonsense mutation. This could help explain the puzzling overrepresentation of stop codons in the canonical genetic code and most variants

The Development of the INFEWS-ER: A Virtual Resource Center for Transdisciplinary Graduate Student Training at the Nexus of Food, Energy, and Water

Problems at the nexus of Food, Energy and Water Systems (FEWS) are among the most complex challenges we face. Spanning simple to complex temporal, geographic, social, and political framings, the questions raised at this nexus require multidisciplinary if not transdisciplinary approaches. Answers to these questions must draw from engineering, the physical and biological sciences, and the social sciences. Practical solutions depend upon a wide community of stakeholders, including industry, policymakers, and the general public. Yet there are many obstacles to working in a transdisciplinary environment: unfamiliar concepts, specialized terminology, and countless “blind” spots. Graduate education occurs in disciplinary ‘silos’, often with little regard for the unintended consequences of our research. Existing pedagogicalmodels do not usually train students to understand neighboring disciplines, thus limiting student learning to narrow areas of expertise, and obstructing their potential for transdisciplinary discourse over their careers. Our goal is a virtual resource center—the INFEWS-ER—that provides educational opportunities to supplement graduate students, especially in their development of transdisciplinary competences. Addressing the grand challenges at the heart of the FEWS nexus will depend upon such competence. Students and scholars from diverse disciplines are working together to develop the INFEWS-ER. To date, we have sponsored both a workshop and a symposium to identify priorities to design the initial curriculum. We have also conducted surveys of the larger community of FEWS researchers. Our work confirms a widespread interest in transdisciplinary training and helps to identify core themes and promising pedagogical approaches. Our curriculum now centers upon several “Cohort Challenges,” supported by various “Toolbox Modules” organized around key themes (e.g., communicating science). We plan to initiate the first cohort of students in October of 2018. Students who successfully complete their Cohort Challenges will be certified as the FEW Graduate Scholars. In this paper, we describe the development of this curriculum. We begin with the need for training in transdisciplinary research. We then describe the workshop and symposium, as well as our survey results. We conclude with an outline of the curriculum, including the current Cohort Challenges and Toolbox Modules

On the possibility of magneto-structural correlations: detailed studies of di-nickel carboxylate complexes

A series of water-bridged dinickel complexes of the general formula [Ni&lt;sub&gt;2&lt;/sub&gt;(μ&lt;sub&gt;2&lt;/sub&gt;-OH&lt;sub&gt;2&lt;/sub&gt;)(μ2- O&lt;sub&gt;2&lt;/sub&gt;C&lt;sup&gt;t&lt;/sup&gt;Bu)&lt;sub&gt;2&lt;/sub&gt;(O&lt;sub&gt;2&lt;/sub&gt;C&lt;sup&gt;t&lt;/sup&gt;Bu)2(L)(L0)] (L = HO&lt;sub&gt;2&lt;/sub&gt;C&lt;sup&gt;t&lt;/sup&gt;Bu, L0 = HO&lt;sub&gt;2&lt;/sub&gt;C&lt;sup&gt;t&lt;/sup&gt;Bu (1), pyridine (2), 3-methylpyridine (4); L = L0 = pyridine (3), 3-methylpyridine (5)) has been synthesized and structurally characterized by X-ray crystallography. The magnetic properties have been probed by magnetometry and EPR spectroscopy, and detailed measurements show that the axial zero-field splitting, D, of the nickel(ii) ions is on the same order as the isotropic exchange interaction, J, between the nickel sites. The isotropic exchange interaction can be related to the angle between the nickel centers and the bridging water molecule, while the magnitude of D can be related to the coordination sphere at the nickel sites