Examination of the Ion Beam Response of III-V Semiconductor Substrates.

This work examines the response of the III-V materials to ion beam irradiation in a series of four experimental studies and describes the observed results in terms of the fundamental materials processes and properties that control ion-induced change in those compounds. Two studies investigate the use of Ga+ focused ion beam (FIB) irradiation of III-V substrate materials to create nanostructures. In the first, the creation of FIB induced group III nanodots on GaAs, InP, InAs, and AlAs is studied. The analysis of those results in terms of basic material properties and a simple nanodot growth model represents the first unified investigation of the fundamental processes that drive the nanodot forming behavior of the III-V compounds. The second nanostructure formation study reports the discovery and characterization of unique spike-like InAs nanostructures, termed “nanospikes,” which may be useful for nanoscale electronic or thermoelectric applications. A novel method for controlling nanospike formation using InAs/InP heterostructures and film pre-patterning is developed, and the electrical properties of these ion erosion created nanostructures are characterized by in-situ TEM nanoprobe testing in a first-of-its-kind examination. The two remaining studies examine methods for using ion beam modification of III-V substrates to accommodate lattice-mismatched film growth with improved film properties. The first examines the effects of film growth on a wide range of different FIB created 3-D substrate patterns, and finds that 3-D surface features and patterns significantly alter film morphology and that growth on or near FIB irradiated regions does not improve film threading defect density. The second substrate modification study examines broad beam ion pre-implantation of GaAs wafers before InGaAs film growth, and is the first reported study of III-V substrate pre-implantation. Ar+ pre-implantation was found to enhance the formation of threading defects in InGaAs films and so improve their roughness and degree of relaxation. This effect, combined with a threading dislocation filtering structure, is anticipated to produce high quality buffers for lattice-mismatched film growth.Ph.D.Materials Science and EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/91437/1/kgrosskl_1.pd

Focused ion beam creation and templating of InAs and InAs/InP nanospikes

Ion beam irradiation has been examined as a method for creating nanoscale semiconductor pillar and cone structures, but has the drawback of inaccurate nanostructure placement. We report on a method for creating and templating nanoscale InAs spikes by focused ion beam (FIB) irradiation of both homoepitaxial InAs films and heteroepitaxial InAs on InP substrates. These 'nanospikes' are created as In droplets, formed due to FIB irradiation, act as etch masks for the underlying InAs. By pre-patterning the InAs to influence In droplet movement, nanospike locations on homoepitaxial InAs may be controlled with limited accuracy. Creating nanospikes using an InAs/InP heterostructure provides an additional measure of control over where the spikes form because nanospikes will not form on exposed regions of InP. This effect may be exploited to accurately control nanospike placement by pre-patterning an InAs/InP heterostructure to control the location of the InAs/InP interface. Using this heterostructure templating method it is possible to accurately place nanospikes into regular arrays that may be useful for a variety of applications.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90790/1/0957-4484_22_35_355302.pd

Mechanisms of nanodot formation under focused ion beam irradiation in compound semiconductors

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/98704/1/JApplPhys_109_014319.pd

Electrical transport in ion beam created InAs nanospikes

Ion beam irradiation has previously been demonstrated as a method for creating nanowire-like semiconductor nanostructures, but no previous studies have reported on the electrical properties of those structures. In this work we describe the creation and in situ transmission electron microscopy electrical characterization of nanoscale InAs spike structures on both InAs and InP substrates fabricated using a focused ion beam erosion method. Those InAs ‘nanospikes’ are found to possess internal structures with varying amounts of ion damaged and single crystalline material. Nanospike electrical behavior is analyzed with respect to model electronic structures and is similar to cases of barrier limited conduction in nanowires. The different electrical responses of each nanospike are found to be the result of variation in their structure, with the conductivity of InAs nanospikes formed on InAs substrates found to increase with the degree of nanospike core crystallinity. The conductivity of InAs nanospikes formed on InP substrates does not show a dependence on core crystallinity, and may be controlled by the other internal barriers to conduction inherent in that system.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/98603/1/0957-4484_23_31_315301.pd

Protective effects of antiâ C5a peptide antibodies in experimental sepsis

We evaluated antibodies to different peptide regions of rat C5a in the sepsis model of cecal ligation and puncture (CLP) for their protective effects in rats. Rabbit polyclonal antibodies were developed to the following peptide regions of rat C5a: aminoâ terminal region (A), residues 1â 16; middle region (M), residues 17â 36; and the carboxylâ terminal region (C), residues 58â 77. With rat neutrophils, the chemotactic activity of rat C5a was significantly inhibited by antibodies with the following rank order: antiâ C > antiâ M â « antiâ A. In vivo, antibodies to the M and C (but not A) regions of C5a were protective in experimental sepsis, as determined by survival over a 10â day period, in a doseâ dependent manner. The relative protective efficacies of antiâ C5a preparations (in descending order of efficacy) were antiâ C â ¥ antiâ M â « antiâ A. In CLP rats, a delay in infusion of antibodies, which were injected at 6 or 12 h after CLP, still resulted in significant improvement in survival rates. These in vivo and in vitro data suggest that there are optimal targets on C5a for blockade during sepsis and that delayed infusion of antiâ C5a antibody until after onset of clinical evidence of sepsis still provides protective effects.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154417/1/fsb2fj000653fje-sup-0001.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154417/2/fsb2fj000653fje.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154417/3/fsb2fj000653fje-sup-0002.pd

FungalRV: adhesin prediction and immunoinformatics portal for human fungal pathogens

<p>Abstract</p> <p>Background</p> <p>The availability of sequence data of human pathogenic fungi generates opportunities to develop Bioinformatics tools and resources for vaccine development towards benefitting at-risk patients.</p> <p>Description</p> <p>We have developed a fungal adhesin predictor and an immunoinformatics database with predicted adhesins. Based on literature search and domain analysis, we prepared a positive dataset comprising adhesin protein sequences from human fungal pathogens <it>Candida albicans, Candida glabrata, Aspergillus fumigatus, Coccidioides immitis, Coccidioides posadasii, Histoplasma capsulatum, Blastomyces dermatitidis, Pneumocystis carinii, Pneumocystis jirovecii and Paracoccidioides brasiliensis</it>. The negative dataset consisted of proteins with high probability to function intracellularly. We have used 3945 compositional properties including frequencies of mono, doublet, triplet, and multiplets of amino acids and hydrophobic properties as input features of protein sequences to Support Vector Machine. Best classifiers were identified through an exhaustive search of 588 parameters and meeting the criteria of best Mathews Correlation Coefficient and lowest coefficient of variation among the 3 fold cross validation datasets. The "FungalRV adhesin predictor" was built on three models whose average Mathews Correlation Coefficient was in the range 0.89-0.90 and its coefficient of variation across three fold cross validation datasets in the range 1.2% - 2.74% at threshold score of 0. We obtained an overall MCC value of 0.8702 considering all 8 pathogens, namely, <it>C. albicans, C. glabrata, A. fumigatus, B. dermatitidis, C. immitis, C. posadasii, H. capsulatum </it>and <it>P. brasiliensis </it>thus showing high sensitivity and specificity at a threshold of 0.511. In case of <it>P. brasiliensis </it>the algorithm achieved a sensitivity of 66.67%. A total of 307 fungal adhesins and adhesin like proteins were predicted from the entire proteomes of eight human pathogenic fungal species. The immunoinformatics analysis data on these proteins were organized for easy user interface analysis. A Web interface was developed for analysis by users. The predicted adhesin sequences were processed through 18 immunoinformatics algorithms and these data have been organized into MySQL backend. A user friendly interface has been developed for experimental researchers for retrieving information from the database.</p> <p>Conclusion</p> <p>FungalRV webserver facilitating the discovery process for novel human pathogenic fungal adhesin vaccine has been developed.</p

Applying the ALARA concept to the evaluation of vesicoureteric reflux

The voiding cystourethrogram (VCUG) is a widely used study to define lower urinary tract anatomy and to diagnose vesicoureteric reflux (VUR) in children. We examine the technical advances in the VCUG and other examinations for reflux that have reduced radiation exposure of children, and we give recommendations for the use of imaging studies in four groups of children: (1) children with urinary tract infection, (2) siblings of patients with VUR, (3) infants with antenatal hydronephrosis (ANH), and (4) children with a solitary functioning kidney. By performing examinations with little to no radiation, carefully selecting only the children who need imaging studies and judiciously timing follow-up examinations, we can reduce the radiation exposure of children being studied for reflux