John Barrett

Bio: John Barrett is an academic researcher from Cork Institute of Technology. The author has contributed to research in topics: Integrated circuit packaging & Wireless sensor network. The author has an hindex of 8, co-authored 44 publications receiving 329 citations.

Development of a DNA Microarray to Detect Antimicrobial Resistance Genes Identified in the National Center for Biotechnology Information Database

Abstract: To understand the mechanisms and epidemiology of antimicrobial resistance (AR), the genetic elements responsible must be identified. Due to the myriad of possible genes, a high-density genotyping technique is needed for initial screening. To achieve this, AR genes in the National Center for Biotechnology Information GenBank database were identified by their annotations and compiled into a nonredundant list of 775 genes. A DNA microarray was constructed of 70mer oligonucelotide probes designed to detect these genes encoding resistances to aminoglycosides, beta-lactams, chloramphenicols, glycopeptides, heavy metals, lincosamides, macrolides, metronidazoles, polyketides, quaternary ammonium compounds, streptogramins, sulfonamides, tetracyclines, and trimethoprims as well as resistance transfer genes. The microarray was validated with two fully sequenced control strains of Salmonella enterica: Typhimurium LT2 (sensitive) and Typhi CT18 (multidrug resistance [MDR]). All resistance genes encoded on the MDR plasmid, pHCM1, harbored by CT18 were detected in that strain, whereas no resistance genes were detected in LT2. The microarray was also tested with a variety of bacteria, including MDR Salmonella enterica serovars, Escherichia coli, Campylobacter spp., Enterococcus spp., methicillin-resistant Staphylococcus aureus, Listeria spp., and Clostridium difficile. The results presented here demonstrate that a microarray can be designed to detect virtually all AR genes found in the National Center for Biotechnology Information database, thus reducing the subsequent assays necessary to identify specific resistance gene alleles.

Development of an embedded wireless sensing system for the monitoring of concrete

Abstract: The application of the electromechanical impedance (EMI) method to monitor the condition of structures is an actively researched area. This article extends the method to allow it to be incorporated into a wireless sensing device, which is embedded into freshly poured concrete to monitor initial curing and subsequent structural health. The results show that the hydrating concrete has an effect on the sensing system and that it is sensitive enough to monitor the strength development of concrete. Initial results also show that the embedded EMI method is sensitive to the removal of formwork. The response of the system to compressive testing is also investigated, and the initial results show a good correlation with previously published reports on compressive testing of concrete. Finally, the ability of the system to be incorporated into a previously developed wireless-sensing platform is investigated. The AD5933 impedance chip offers this possibility, and its response is investigated and compared with the resp...

Microsystem packaging: lessons from conventional low cost IC packaging

Abstract: This paper describes some of the issues associated with the packaging of microsystems and how packaging can influence their reliability and performance. The importance of early consideration in the design cycle of packaging, and the environment in which the microsystem will be placed, is stressed. It illustrates how the IC packaging industry has striven to overcome the problems of residual stress, stress minimization, hermeticity, and improved thermal performance in their packages and how this can be applied to microsystem packaging. Packaging problems specific to microsystems are identified.

Introduction to United States Department of Agriculture VetNet: status of Salmonella and Campylobacter databases from 2004 through 2005.

Abstract: In 2003 the United States Department of Agriculture established USDA VetNet. It was modeled after PulseNet USA, the national molecular subtyping network for foodborne disease surveillance. The obje...

Methods of analysing thermomechanical stress in plastic packages for integrated circuits

Abstract: Thermomechanical stresses are built up in the plastic packages during the manufacture of an integrated device and also throughout the working life of the device, arising due to a mismatch between the coefficients of thermal expansion of the package materials. Excessive levels of thermomechanically induced stresses may lead to cracking in the packages, which could in turn lead to failure of the device. It is important, therefore, to be able to predict and measure thermomechanical stresses in order to improve package reliability. This paper describes the use of finite-element techniques and strain gauges to determine package stress levels. The effect of delaminations at the interfaces of the package materials is discussed also, and the scanning acoustic microscope is introduced as a complimentary tool to identify stress-related defects in plastic packages.

The Design and Analysis of Experiments

Abstract: THE DESIGN AND ANALYSIS OF EXPERIMENTS. By Oscar Kempthorne. New York, John Wiley and Sons, Inc., 1952. 631 pp. $8.50. This book by a teacher of statistics (as well as a consultant for \"experimenters\") is a comprehensive study of the philosophical background for the statistical design of experiment. It is necessary to have some facility with algebraic notation and manipulation to be able to use the volume intelligently. The problems are presented from the theoretical point of view, without such practical examples as would be helpful for those not acquainted with mathematics. The mathematical justification for the techniques is given. As a somewhat advanced treatment of the design and analysis of experiments, this volume will be interesting and helpful for many who approach statistics theoretically as well as practically. With emphasis on the \"why,\" and with description given broadly, the author relates the subject matter to the general theory of statistics and to the general problem of experimental inference. MARGARET J. ROBERTSON

Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet.

Abstract: Standardized rapid pulsed-field gel electrophoresis (PFGE) protocols for the subtyping of Escherichia coli O157:H7, Salmonella serotypes, and Shigella species are described. These protocols are used by laboratories in PulseNet, a network of state and local health departments, and other public health laboratories that perform real-time PFGE subtyping of these bacterial foodborne pathogens for surveillance and outbreak investigations. Development and standardization of these protocols consisted of a thorough optimization of reagents and reaction conditions to ensure that the protocols yielded consistent results and high-quality PFGE pattern data in all the PulseNet participating laboratories. These rapid PFGE protocols are based on the original 3–4-day standardized procedure developed at Centers for Disease Control and Prevention that was validated in 1996 and 1997 by eight independent laboratories. By using these rapid standardized PFGE protocols, PulseNet laboratories are able to subtype foodborne pathoge...

Stiction in surface micromachining

Abstract: Due to the smoothness of the surfaces in surface micromachining, large adhesion forces between fabricated structures and the substrate are encountered. Four major adhesion mechanisms have been analysed: capillary forces, hydrogen bridging, electrostatic forces and van der Waals forces. Once contact is made adhesion forces can be stronger than the restoring elastic forces and even short, thick beams will continue to stick to the substrate. Contact, resulting from drying liquid after release etching, has been successfully reduced. In order to make a fail-safe device stiction during its operational life-time should be anticipated. Electrostatic forces and acceleration forces caused by shocks encountered by the device can be large enough to bring structures into contact with the substrate. In order to avoid in-use stiction adhesion forces should therefore be minimized. This is possible by coating the device with weakly adhesive materials, by using bumps and side-wall spacers and by increasing the surface roughness at the interface. Capillary condensation should also be taken into account as this can lead to large increases in the contact area of roughened surfaces.

Micro-stereolithography of polymeric and ceramic microstructures

Abstract: Micro-stereolithography (μSL) is a novel micro-manufacturing process which builds the truly 3D microstructures by solidifying the liquid monomer in a layer by layer fashion. In this work, an advanced μSL apparatus is designed and developed which includes an Ar + laser, the beam delivery system, computer-controlled precision x–y–z stages and CAD design tool, and in situ process monitoring systems. The 1.2 μm resolution of μSL fabrication has been achieved with this apparatus. The microtubes with high aspect ratio of 16 and real 3D microchannels and microcones are fabricated on silicon substrate. For the first time, μSL of ceramic microgears has been successfully demonstrated.

PulseNet USA: a five-year update.

Abstract: PulseNet USA is the molecular surveillance network for foodborne infections in the United States. Since its inception in 1996, it has been instrumental in detection, investigation and control of numerous outbreaks caused by Shiga toxin-producing Escherichia coli O157:[H7] (STEC O157), Salmonella enterica, Listeria monocytogenes, Shigella spp., and Campylobacter. This paper describes the current status of the network, including the methodologies used and its future possibilities. The currently preferred subtyping method in the network is pulsed-field gel electrophoresis (PFGE), a proven highly discriminatory molecular subtyping method. New simpler sequencebased subtyping methods are under development and validation to complement and eventually replace PFGE. PulseNet is essentially a cluster detection network, but the data in the system will now also be used in attribution analyses of sporadic infections. The PulseNet platform will also be used as a primary tool in preparedness and response to acts of food bioterrorism.