Data management and analysis for high-throughput DNA sequencingprojects

The rapid advances in molecular biology have begun to shift many of the bottlenecks in genome research from the laboratory to the data analysis facility. The pace at which this has occurred creates a situation in which software development always has to catch up with the flow of data. Since such large-scale processes were not anticipated, the analysis infrastructure has not been fully established. Furthermore, most systems that have been built were designed by the biologists who collected the data. More recently, computer scientists, mathematicians, and engineers have taken an interest in this problem. This has had a positive effect, since it has created a tight synergy between the informatics and the biology. Several principles affected the design of the system developed at TIGR. Each of the sample preparation, sequencing, and analysis steps had to be managed, scheduled, and tracked. This information had to be made readily available to those who needed it for carrying out their tasks. Different skill levels of the users had to be taken into account. The degree of human intervention at each step had to be evaluated and built into the design. A mixed processing environment of Macintosh and Unix platforms had to be integrated. Most importantly, the system had to save time, reduce error, and ensure uniformity of the analysis and quality of the results. In the authors' experience, the tools they have built work well because of their early decisions as to which systems to use for development. The authors settled on a robust relational database management system (Sybase) and a portable development environment (C, C++)     

Emotional and behavioral responses to aversive interpersonal behaviors.

In a conceptual replication of A. Biglan et al (see record 1989-39898-001), 288 Ss rated their emotional and behavioral responses to aggressive, distressed, and neutral behaviors. The stimulus behaviors occurred in the context of casual relationships and were portrayed by male and female actors. Consistent with Biglan et al, it was found that aggressive behaviors evoked angry emotions and negative behavioral responses; distressed behaviors evoked both angry and concerned emotions and supportive behavioral responses. However, in contrast to the original results, evidence was also found of negative (primarily avoidant) behavioral responses to distressed behavior. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Performance of advanced resuscitation skills by pediatric housestaff

OBJECTIVE: To describe pediatric housestaff resuscitation experience and their ability to perform key resuscitation skills. DESIGN: Cohort study of 63 pediatric residents in a university-based training program. PARTICIPANTS AND METHODS: Investigators observed, scored, and timed resident performance on 4 key resuscitation skills. Cognitive ability was tested with 4 written scenarios. Housestaff provided self-reports of the number of months since their last American Heart Association Pediatric Advanced Life Support course, number of mock and actual codes attended, number of times skills were performed, and self-confidence with respect to resuscitation. RESULTS: A total of 45 pediatric residents (71%) participated. Median cognitive score was 5 (range, 1-5). Of all residents, 44 (97%) successfully bag mask-ventilated the mannequin; 24 (53%) and 36 (80%) used the correct bag and mask size, respectively. Thirty-nine residents (87%) placed a tube in the mannequin trachea, 12 (27%) checked that suction was working prior to intubation, and 30 (67%) chose the correct endotracheal tube size. Forty residents (89%) discharged the defibrillator, and 25 (56%) and 32 (71%) correctly chose asynchronous mode and infant paddles, respectively. Thirty-eight residents (84%) inserted an intraosseous line; 35 (78%) had correct placement. Median times for successful skill completion were 83 seconds for bag mask ventilation, 136 seconds for intubation, 149 seconds for defibrillation, and 68 seconds for intraosseous line placement. CONCLUSION: Pediatric housestaff previously trained in pediatric advanced life support were generally able to reach the end point of 4 key resuscitation skills but less frequently performed the specific subcomponents of each skill. This poor performance and the prolonged time to skill completion suggest the need for greater attention to detail during training.     

Assessing the Assessments: Case Study of an Emergency Action Plan for the Control of Water Hyacinth in Lake Victoria

This study evaluates the impact assessment methodologies used by Uganda's Water Hyacinth Control Programme in Lake Victoria, a domestic project with transboundary implications. The Control Programme sought to reduce infestations of water hyacinth (Eichhornia crassipes), an aquatic weed native to South America, through the use of integrated chemical, mechanical and biological methods. The environmental impact assessment for the project was conducted by Aquatics Unlimited, with support from the United States Agency for International Development. Although the case study involves a domestic impact assessment, it raised transboundary concerns. One of the major outcomes of the assessment was recognition of the need for informed involvement of the other riparian countries, Kenya and Tanzania, in the assessment process to ensure a regional effort among all three East African Community Partner States to control water hyacinth and other invasive weeds in Lake Victoria.     

Predictors of outcome in LAAM, buprenorphine, and methadone treatment for opioid dependence.

This study examined (1) predictors of treatment outcome for opioid-dependent participants in a single-site controlled trial comparing methadone, buprenorphine, and LAAM treatments and (2) the extent to which various subpopulations of patients may have more successful outcomes with each medication. The relationships between patient demographics, drug use history, and psychological status and outcome measures of treatment retention, opiate use, and cocaine use were assessed. We believe this study to be the first to demonstrate that predictors of treatment success appear to be largely similar in LAAM, buprenorphine, and methadone treatment for opioid dependence. We did not find any factors that would strongly guide selection of one medication over others. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Octave-tunable miniature RF resonators

The development and testing of a miniaturized, high-Q, broadly tunable resonator is described. An exemplary device, with a center frequency that is continuously tunable from 1.2 to 2.6GHz, was tested in detail. Experimental results demonstrated a resonator Q of up to 380, and typical insertion loss of -1.9dB for a 25MHz 3-dB bandwidth. These resonators have been used to stabilize a broadly-tunable oscillator with phase noise of -132dBc/Hz at 100-kHz offset, with a center frequency tunable from 1.2-2.6GHz, and a tuning speed of 1GHz/ms.     

Screen‐printed biosensor for allergens

Allergen levels in indoor environments, leading to many diseases, eg asthma, rhinitis and conjunctivitis, affect a large and increasing fraction of the population. A quite effective and inexpensive method of a rough but very rapid overall assessment of total allergen level in the environment has been developed. The method involved estimation of protein in allergen extracts by screen‐printed electrodes using two different techniques. The biosensor comprised a rhodinised carbon working electrode, a silver/silver chloride reference electrode and a carbon counter electrode. In the first method the enzyme protease reacted with allergen protein to release amino acid, which produced hydrogen peroxide in the presence of amino acid oxidase. This was detected amperometrically. The second method used potassium bromide as electrolyte and the electrode was subjected to dual potential. Bromine, released due to electrolysis at higher potential, was consumed by the allergen protein at lower potential. In the first method, a unique technique was used to microencapsulate the enzyme protease and immobilise it on the surface of the electrode by in‐situ polymerisation to avoid contact with the amino acid oxidase. A total of seven allergens were tested and the results gave a good correlation with the standard protein measurement method. Environmental specimens from indoors, schools and workplaces can be evaluated for the aeroallergens produced by dust mites, animal hairs, cockroach debris, pollens, etc as a means of determining the exposure risk. Copyright © 2005 Society of Chemical Industry     

Gigabit pulse position bistability in semiconductor lasers

The paper briefly reviews the major forms of optical bistability in active optical devices compatible for use in gigabit optical communication systems, and reports an entirely new optical bistability for the first time. Unlike previous devices, the two bistable states of the optical device are each a series of picosecond optical pulses at 1 GHz or greater repetition rates, and are distinguished by a half period temporal shift between their temporal positions in relation to a clock pulse. The bistable device is based on a gain switched semiconductor laser. Theoretical studies suggest 100-ps switching speeds might be achieved, and experimental results are reported indicating optically triggered switching times of 500 ps.