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