Software and methods for oligonucleotide and cDNA array data analysis.

Two HTML-based programs were developed to analyze and filter gene-expression data: 'Bullfrog' for Affymetrix oligonucleotide arrays and 'Spot' for custom cDNA arrays. The programs provide intuitive data-filtering tools through an easy-to-use interface. A background subtraction and normalization program for cDNA arrays was also built that provides an informative summary report with data-quality assessments. These programs are freeware to aid in the analysis of gene-expression results and facilitate the search for genes responsible for interesting biological processes and phenotypes

Extracellular ATP triggers proteolysis and cytosolic Ca²⁺ rise in Plasmodium berghei and Plasmodium yoelii malaria parasites.

BACKGROUND: Plasmodium has a complex cell biology and it is essential to dissect the cell-signalling pathways underlying its survival within the host. METHODS: Using the fluorescence resonance energy transfer (FRET) peptide substrate Abz-AIKFFARQ-EDDnp and Fluo4/AM, the effects of extracellular ATP on triggering proteolysis and Ca²⁺ signalling in Plasmodium berghei and Plasmodium yoelii malaria parasites were investigated. RESULTS: The protease activity was blocked in the presence of the purinergic receptor blockers suramin (50 μM) and PPADS (50 μM) or the extracellular and intracellular calcium chelators EGTA (5 mM) and BAPTA/AM (25, 100, 200 and 500 μM), respectively for P. yoelii and P. berghei. Addition of ATP (50, 70, 200 and 250 μM) to isolated parasites previously loaded with Fluo4/AM in a Ca²⁺-containing medium led to an increase in cytosolic calcium. This rise was blocked by pre-incubating the parasites with either purinergic antagonists PPADS (50 μM), TNP-ATP (50 μM) or the purinergic blockers KN-62 (10 μM) and Ip5I (10 μM). Incubating P. berghei infected cells with KN-62 (200 μM) resulted in a changed profile of merozoite surface protein 1 (MSP1) processing as revealed by western blot assays. Moreover incubating P. berghei for 17 h with KN-62 (10 μM) led to an increase in rings forms (82% ± 4, n = 11) and a decrease in trophozoite forms (18% ± 4, n = 11). CONCLUSIONS: The data clearly show that purinergic signalling modulates P. berghei protease(s) activity and that MSP1 is one target in this pathway

Ischemic preconditioning and acute recovery of performance in rugby union players

Ischemic preconditioning has been used as a training and/or pre-competition strategy; however its use for post-exercise recovery is still unclear. This study aimed to evaluate the impact of ischemic preconditioning on performance and recovery ratings following a simulated match in sub-elite rugby players. Following baseline measures, male players (n = 8) performed a 40 min, rugby-specific exercise protocol followed by an intervention: 21 min of ischemic preconditioning (3 × 5 min occlusion at 220 mmHg with 2 min reperfusion at 0 mmHg) or passive rest (control) on 2 separate days. An agility T-test, a single vertical countermovement jump and 30 s of continuous vertical jumps were performed at baseline (–24 h), immediately after exercise, and immediately after the intervention. The rugby-specific exercise protocol induced similar mean heartrates (158.3 ± 18.0 vs. 158.7 ± 16.0 bpm) and perceived exertion levels (8.2 ± 0.9 vs. 8.0 ± 1.0) for both trials with all recovery performance measures and rating of recovery (13.9 ± 1.4 vs. 13.6 ± 1.6) similar between ischemic preconditioning and control trials (best p = 0.385). We conclude that the use of ischemic preconditioning does not improve recovery acutely (~1 h) including specific variables related to rugby performance in amateur rugby union players

Genetic risk scores demonstrate the cumulative association of single nucleotide polymorphisms in gut microbiome-related genes with obesity phenotypes in preschool age children

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151317/1/ijpo12530_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151317/2/ijpo12530.pd

Navigability Analysis of Natural Terrains with Fuzzy Elevation Maps from Ground-based 3D Range Scans

Mobile robot navigation through natural terrains is a challenging issue with applications such as planetary exploration or search and rescue. This paper proposes navigability assessment of natural terrains scanned from ground-based 3D laser rangefinders. A continuous model of the terrain is obtained as a fuzzy elevation map (FEM). Based on this model, the proposed solution incorporates terrain navigability both in terms of uncertainties of the 3D input data and slope of the fuzzy surface. Moreover, the paper discusses the application of this method for local path planning. For this purpose, the Bug algorithm has been adapted to compute local paths on the navigable region of the FEM. The method has been applied to actual 3D point clouds on two different experimental sites.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. This work was partially supported by the Spanish CICYT project DPI 2011-22443 and the Andalusian project PE-2010 TEP-6101

Development and Dissemination of a New Multidisciplinary Undergraduate Curriculum in Digital Forensics

The Information Trust Institute (ITI) at the University of Illinois at Urbana-Champaign is developing an entirely new multidisciplinary undergraduate curriculum on the topic of digital forensics, and this paper presents the findings of the development process, including initial results and evaluation of a pilot offering of the coursework to students. The curriculum consists of a four-course sequence, including introductory and advanced lecture courses with parallel laboratory courses, followed by an advanced course. The content has been designed to reflect both the emerging national standards and the strong multidisciplinary character of the profession of digital forensics, and includes modules developed collaboratively by faculty experts in multiple fields of computer science, law, psychology, social sciences, and accountancy. A preliminary plan for the introductory course was presented to a workshop of digital forensics experts in May 2013 and received their strong approval. Pilot versions of the introductory and introductory lab courses were taught to a mixture of computer science and law students at the University of Illinois in the fall of 2013, and were very positively received by the students, who made it clear that they appreciated the multidisciplinary approach. The curriculum, which is designed to obviate the need for expensive labs or team-teaching by specialized faculty, will be made available to other colleges and universities in order to improve the content and quality of existing digital forensics programs, to inspire and greatly facilitate the creation of new programs, and, ultimately, to increase the number of educated practitioners. The developed resources can be used as the basis for future academic programs, distance learning, and multidisciplinary, multi-institutional programs that meet evolving digital forensics educational standards. Much of the material, including a virtual laboratory, will be provided on-line. Introductory course materials will be distributed to other institutions beginning in the summer of 2014; advanced course materials should be available for distribution in 2015. Related outreach activities have been undertaken and will be continued. Keywords: Digital forensics, Computer forensics, Curriculum development, Curriculum standards, Education standards, Training standards, Undergraduate education, Interdisciplinary studie

A Single Tri-Epitopic Antibody Virtually Recapitulates the Potency of a Combination of Three Monoclonal Antibodies in Neutralization of Botulinum Neurotoxin Serotype A.

The standard of treatment for botulism, equine antitoxin, is a foreign protein with associated safety issues and a short serum half-life which excludes its use as a prophylactic antitoxin and makes it a less-than-optimal therapeutic. Due to these limitations, a recombinant monoclonal antibody (mAb) product is preferable. It has been shown that combining three mAbs that bind non-overlapping epitopes leads to highly potent botulinum neurotoxin (BoNT) neutralization. Recently, a triple human antibody combination for BoNT/A has demonstrated potent toxin neutralization in mouse models with no serious adverse events when tested in a Phase I clinical trial. However, a triple antibody therapeutic poses unique development and manufacturing challenges. Thus, potentially to streamline development of BoNT antitoxins, we sought to achieve the potency of multiple mAb combinations in a single IgG-based molecule that has a long serum half-life. The design, production, and testing of a single tri-epitopic IgG1-based mAb (TeAb) containing the binding sites of each of the three parental BoNT/A mAbs yielded an antibody of nearly equal potency to the combination. The approach taken here could be applied to the design and creation of other multivalent antibodies that could be used for a variety of applications, including toxin elimination