Calibration of the ER-2 meteorological measurement system

The Meteorological Measurement System (MMS) on the high altitude ER-2 aircraft was developed specifically for atmospheric research. The MMS provides accurate measurements of pressure, temperature, wind vector, position (longitude, latitude, altitude), pitch, roll, heading, angle of attack, angle of sideslip, true airspeed, aircraft eastward velocity, northward velocity, vertical acceleration, and time, at a sample rate of 5/s. MMS data products are presented in the form of either 5 or 1 Hz time series. The 1 Hz data stream, generally used by ER-2 investigators, is obtained from the 5 Hz data stream by filtering and desampling. The method of measurement of the meteorological parameters is given and the results of their analyses are discussed

Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation

Background: Manual curation of experimental data from the biomedical literature is an expensive and time-consuming endeavor. Nevertheless, most biological knowledge bases still rely heavily on manual curation for data extraction and entry. Text mining software that can semi- or fully automate information retrieval from the literature would thus provide a significant boost to manual curation efforts. Results: We employ the Textpresso category-based information retrieval and extraction system http://www.textpresso.org webcite, developed by WormBase to explore how Textpresso might improve the efficiency with which we manually curate C. elegans proteins to the Gene Ontology's Cellular Component Ontology. Using a training set of sentences that describe results of localization experiments in the published literature, we generated three new curation task-specific categories (Cellular Components, Assay Terms, and Verbs) containing words and phrases associated with reports of experimentally determined subcellular localization. We compared the results of manual curation to that of Textpresso queries that searched the full text of articles for sentences containing terms from each of the three new categories plus the name of a previously uncurated C. elegans protein, and found that Textpresso searches identified curatable papers with recall and precision rates of 79.1% and 61.8%, respectively (F-score of 69.5%), when compared to manual curation. Within those documents, Textpresso identified relevant sentences with recall and precision rates of 30.3% and 80.1% (F-score of 44.0%). From returned sentences, curators were able to make 66.2% of all possible experimentally supported GO Cellular Component annotations with 97.3% precision (F-score of 78.8%). Measuring the relative efficiencies of Textpresso-based versus manual curation we find that Textpresso has the potential to increase curation efficiency by at least 8-fold, and perhaps as much as 15-fold, given differences in individual curatorial speed. Conclusion: Textpresso is an effective tool for improving the efficiency of manual, experimentally based curation. Incorporating a Textpresso-based Cellular Component curation pipeline at WormBase has allowed us to transition from strictly manual curation of this data type to a more efficient pipeline of computer-assisted validation. Continued development of curation task-specific Textpresso categories will provide an invaluable resource for genomics databases that rely heavily on manual curation

The meteorological measurement system on the NASA ER-2 aircraft

A Meteorological Measurement System (MMS) was designed for the high-altitude ER-2 aircraft (NASA 706). Through dedicated instrumentation installed on the aircraft and repeated calibrations, the MMS provides accurate in situ measurements of free-stream pressure, temperature, and the wind vector. The MMS has participated in two major high-altitude scientific expeditions, the Stratosphere-Troposphere Exchange Project (STEP) based in northern Australia and the Airborne Antarctic Ozone Experiment (AAOE) based in southern Chile. Key MMS subsystems are described. The MMS consists of a dedicated inertial navigation system (INS), a randome differential pressure system, a data acquisition system, and air data instrumentation. The MMS incorporates a high-resolution INS (Litton LIN-72RH model), which is specially configured and is updated at 25 Hz. The differential pressure system, consisting of two sets of pressure ports and transducers, is installed in the ER-2 radome to provide sensitive measurements of the airflow angles (angle of attack and angle of sideslip). The data acquisition system was designed to meet aircraft requirements of compactness and light weight (2 cu ft 50 lb) and for MMS requirements to sample, control, process, and store 45 parameters (some redundant) at a sampling rate up to 10 Hz. The MMS data are stored both in a tape recorder (20 MB) and a hermatically-sealed winchester hard disc (10 MB). Special and redundant instrumentation for temperature and pressure measurements were also installed on the aircraft

The NASA-ER2 meteorological measurement system: Instrumentaion, calibration and intercomparison results

The NASA ER-2 aircraft is used as a platform for high altitude atmospheric missions. The Meteorological Measurement System (MMS) was designed specifically for atmospheric research to provide accurate, fast response, in situ measurements of pressure, temperature, and the three dimensional wind vector. The MMS consists of three subsystems: an air motion sensing system to measure the velocity of the air with respect to the aircraft, a high resolution Inertial Navigation System (INS) to measure the velocity of the aircraft with respect to the Earth, and a Data Acquisition System, to sample, process and record the measured quantities. Details of each of these systems are given. The location of the MMS instrumentation is illustrated. The calibration of the MMS is discussed and results on an intercomparison of MMS measurements, Vaisala radiosonde observation and radar tracking data are given. An illustration of the MMS measurement of vertical wind is given

Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase

Biological knowledgebases rely on expert biocuration of the research literature to maintain up-to-date collections of data organized in machine-readable form. To enter information into knowledgebases, curators need to follow three steps: (i) identify papers containing relevant data, a process called triaging; (ii) recognize named entities; and (iii) extract and curate data in accordance with the underlying data models. WormBase (WB), the authoritative repository for research data on Caenorhabditis elegans and other nematodes, uses text mining (TM) to semi-automate its curation pipeline. In addition, WB engages its community, via an Author First Pass (AFP) system, to help recognize entities and classify data types in their recently published papers. In this paper, we present a new WB AFP system that combines TM and AFP into a single application to enhance community curation. The system employs string-searching algorithms and statistical methods (e.g. support vector machines (SVMs)) to extract biological entities and classify data types, and it presents the results to authors in a web form where they validate the extracted information, rather than enter it de novo as the previous form required. With this new system, we lessen the burden for authors, while at the same time receive valuable feedback on the performance of our TM tools. The new user interface also links out to specific structured data submission forms, e.g. for phenotype or expression pattern data, giving the authors the opportunity to contribute a more detailed curation that can be incorporated into WB with minimal curator review. Our approach is generalizable and could be applied to additional knowledgebases that would like to engage their user community in assisting with the curation. In the five months succeeding the launch of the new system, the response rate has been comparable with that of the previous AFP version, but the quality and quantity of the data received has greatly improved

Faces and Eyes in Human Lateral Prefrontal Cortex

Much of the work on face-selective neural activity has focused on posterior, ventral areas of the human and non-human primate brain. However, electrophysiological and fMRI studies have identified face responses in the prefrontal cortex. Here we used fMRI to characterize these responses in the human prefrontal cortex compared with face selectivity in posterior ventral region. We examined a region at the junction of the right inferior frontal sulcus and the precentral sulcus (right inferior frontal junction or rIFJ) that responds more to faces than to several other object categories. We find that the rIFJ and the right fusiform face area (rFFA) are broadly similar in their responses to whole faces, headless bodies, tools, and scenes. Strikingly, however, while the rFFA preferentially responds to the whole face, the rIFJ response to faces appears to be driven primarily by the eyes. This dissociation provides clues to the functional role of the rIFJ face response. We speculate on this role with reference to emotion perception, gaze perception, and to behavioral relevance more generally

Temperature and horizontal wind measurements on the ER-2 aircraft during the 1987 airborne Antarctic ozone experiment

The NASA ER-2 aircraft is equipped with special instrumentation to provide accurate in situ measurement of the atmospheric state variables during flight. The Meteorological Measurement System (MMS) on the ER-2 aircraft is described. Since the meteorological parameters (temperature, pressure, and wind vector) are extensively used by other ER-2 experimenters for data processing and interpretation, the accuracy and resolution of each of these parameters are assessed and discussed. During the 1987 Airborne Antarctic Ozone Experiment (AAOE) mission, the ER-2 aircraft was stationed at Punta Arenas, Chile (53 S, 72 W), and successfully flew over Antarctica on 12 occasions between August 17 and September 22, 1987. On each of the 12 flights, the ER-2 aircraft flight plan was to take off at approximately the same local time, fly southward at a near constant potential temperature surface, descend and ascend at the southernmost terminus at about 72 S over Antarctica and return northward at either the same or a different constant potential temperature surface. The measurements of the MMS experiment during the AAOE mission are presented. MMS data are organized to provide a composite view of the polar atmosphere, which is characterized by frigid temperatures and high zonal winds. Altitudinal variations of the temperature measurement (during takeoff/landing at Punta Arenas and during descent/ascent at the southern terminus) and latitudinal variations of the zonal wind (on near constant potential temperature surfaces) are emphasized and discussed

Applications of the ER-2 meteorological measurement system

The NASA ER-2 aircraft is used as a platform for high altitude atmospheric missions. The Meteorological Measurement System (MMS) was developed specifically for atmospheric research to provide accurate high resolution measurements of pressure, temperature, and the 3-D wind vector with a sampling rate of 5/s. The MMS consist of three subsystems: (1) an air motion sensing system to measure the velocity of the air with respect to the aircraft; (2) a high resolution inertial navigation system (INS) to measure the velocity of the aircraft with respect to the earth; and (3) a data acquisition system to sample, process, and record the measurement quantities. MMS data have been used extensively by ER-2 investigators in elucidating the polar ozone chemistry. Herein, applications on atmospheric dynamics are emphasized. Large scale (polar vortex, potential vorticity, model atmosphere), mesoscale (gravity waves, mountain waves) and microscale (heat fluxes) atmospheric phenomena are investigated and discussed