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++)     

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.     

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.     

Freestanding Alumina Membrane by Double-Layer Anodization

A novel method has been developed for fabricating full or partial freestanding anodic alumina. In our method a sacrificial metal layer is introduced between an Al film and a Si₃N₄ substrate. A freestanding alumina film at wafer scale is successfully achieved by anodizing the double metal layer, during which the alumina is spontaneously stripped off the Si₃N₄ substrate due to the anodic oxidation of the sacrificial layer. The barrier oxide of the alumina film is effectively removed either by H₃PO₄ dissolution or by CF₄ reactive ion etching. The freestanding alumina film is utilized as a contact mask to transfer its nanoporous pattern to a Si substrate. By patterning the sacrificial metal layer with contact lithography, a partial freestanding alumina film is successfully achieved on the silicon chip, producing a unique micro/nanofluidic channel. Compared with previous techniques, the method reported here is advantageous for its simplicity and flexibility     

Vehicle Localization Using Sensors Data Fusion Via Integration of Covariance Intersection and Interval Analysis

Achieving an innovative integrated sensor fusion architecture with a robust vehicle navigation and localization using an extended Kalman filter, interval analysis and covariance intersection that can overcome the uncertainty in the system model and sensor noise statistics. There are various approaches to the problem, but here the focus is on an approach which can guaranteed performance of sensor-based navigation. The guaranteed performance is quantified by explicit bounds of position estimate of a ground vehicle. Ground vehicles generally carry dead reckoning sensors such as wheel encoders and inertial sensors, to measure acceleration and angle rate, while obstacle detection and mapmaking is done with time-of-flight ultrasonic sensors. Most of these sensors give overlapping or complementary information and sometimes are redundant as well, which offers scope for exploiting data fusion. The purpose here is to achieve data fusion for ground vehicles with low-cost sensors by forming an intelligent sensor system. This is accomplished by combining the sensors' measurements and processing these measurements with data fusion algorithms. The algorithms are complementary in the sense that they compensate for each other's limitations, so that the resulting performance of the sensor system is better than its individual components.