Integrated genomic classification of melanocytic tumors of the central nervous system using mutation analysis, copy number alterations and DNA methylation profiling.

PubMed

Griewank, Klaus; Koelsche, Christian; van de Nes, Johannes A P; Schrimpf, Daniel; Gessi, Marco; Möller, Inga; Sucker, Antje; Scolyer, Richard A; Buckland, Michael E; Murali, Rajmohan; Pietsch, Torsten; von Deimling, Andreas; Schadendorf, Dirk

2018-06-11

In the central nervous system, distinguishing primary leptomeningeal melanocytic tumors from melanoma metastases and predicting their biological behavior solely using histopathologic criteria can be challenging. We aimed to assess the diagnostic and prognostic value of integrated molecular analysis. Targeted next-generation-sequencing, array-based genome-wide methylation analysis and BAP1 immunohistochemistry was performed on the largest cohort of central nervous system melanocytic tumors analyzed to date, incl. 47 primary tumors of the central nervous system, 16 uveal melanomas. 13 cutaneous melanoma metastasis and 2 blue nevus-like melanomas. Gene mutation, DNA-methylation and copy-number profiles were correlated with clinicopathological features. Combining mutation, copy-number and DNA-methylation profiles clearly distinguished cutaneous melanoma metastases from other melanocytic tumors. Primary leptomeningeal melanocytic tumors, uveal melanomas and blue nevus-like melanoma showed common DNA-methylation, copy-number alteration and gene mutation signatures. Notably, tumors demonstrating chromosome 3 monosomy and BAP1 alterations formed a homogeneous subset within this group. Integrated molecular profiling aids in distinguishing primary from metastatic melanocytic tumors of the central nervous system. Primary leptomeningeal melanocytic tumors, uveal melanoma and blue nevus-like melanoma share molecular similarity with chromosome 3 and BAP1 alterations markers of poor prognosis. Copyright ©2018, American Association for Cancer Research.

A Profile Examination System for Physician Extenders and a Method for Curricular Prescription. Final Report.

ERIC Educational Resources Information Center

Smull, Ned W.; And Others

The basic purposes of the Profile Examination for Physician Extenders (PEPE) project included: (1) development of a computerized test item bank from which Profile Examinations could be generated, (2) review and analysis of curricula for the allied health groups, and (3) assessment of the reliability and validity of the Profile Examinations. The…

STS-1 operational flight profile. Volume 5: Descent, cycle 3. Appendix C: Monte Carlo dispersion analysis

NASA Technical Reports Server (NTRS)

1980-01-01

The results of three nonlinear the Monte Carlo dispersion analyses for the Space Transportation System 1 Flight (STS-1) Orbiter Descent Operational Flight Profile, Cycle 3 are presented. Fifty randomly selected simulation for the end of mission (EOM) descent, the abort once around (AOA) descent targeted line are steep target line, and the AOA descent targeted to the shallow target line are analyzed. These analyses compare the flight environment with system and operational constraints on the flight environment and in some cases use simplified system models as an aid in assessing the STS-1 descent flight profile. In addition, descent flight envelops are provided as a data base for use by system specialists to determine the flight readiness for STS-1. The results of these dispersion analyses supersede results of the dispersion analysis previously documented.

A Typology of Child School Behavior: Investigation Using Latent Profile Analysis and Cluster Analysis

ERIC Educational Resources Information Center

Mindrila, Diana L.

2016-01-01

To describe and facilitate the identification of child school behavior patterns, we developed a typology of child school behavior (ages 6-11 years) using the norming data (N = 2,338) for the second edition of the Behavior Assessment System for Children Teacher Rating-Child form). Latent profile analysis was conducted with the entire data set,…

How Linguistic Frames Affect Motivational Profiles and the Roles of Quantitative versus Qualitative Research Strategies

ERIC Educational Resources Information Center

Yeager, Joseph; Sommer, Linda

2005-01-01

The combined tools of psycholinguistics and systems analysis have produced advances in motivational profiling resulting in numerous applications to behavioral engineering. Knowing the way people frame their motive offers leverage in causing behavior change ranging from persuasive marketing campaigns, forensic profiling, individual psychotherapy,…

Mission Assurance Analysis of Theater Ballistic Missile Defense Systems

DTIC Science & Technology

2011-09-01

7  Figure 2. MOSAIC Management Paradigm ( Alberts et. al., 2008) .................................. 14  Figure 3. Basic...Success Profiles ( Alberts , et. al., 2008) ................................................... 16  Figure 4. Success Profile with Uncertainty Range... Alberts , et. al., 2008) ....................... 16  Figure 5. Success Profile with Event Sensitivity ( Alberts , et. al., 2008) .......................... 17

Identifying Students with Learning Disabilities: Composite Profile Analysis Using the Cognitive Assessment System

ERIC Educational Resources Information Center

Huang, Leesa V.; Bardos, Achilles N.; D'Amato, Rik Carl

2010-01-01

The detection of cognitive patterns in children with learning disabilities (LD) has been a priority in the identification process. Subtest profile analysis from traditional cognitive assessment has drawn sharp criticism for inaccurate identification and weak connections to educational planning. Therefore, the purpose of this study is to use a new…

Stratospheric NO and NO2 profiles at sunset from analysis of high-resolution balloon-borne infrared solar absorption spectra obtained at 33 deg N and calculations with a time-dependent photochemical model

NASA Technical Reports Server (NTRS)

Rinsland, C. P.; Boughner, R. E.; Larsen, J. C.; Goldman, A.; Murcray, F. J.; Murcray, D. G.

1984-01-01

Simultaneous stratospheric vertical profiles of NO and NO2 at sunset were derived from an analysis of infrared solar absorption spectra recorded from a float altitude of 33 km with an interferometer system during a balloon flight. A nonlinear least squares procedure was used to analyze the spectral data in regions of absorption by NO and NO2 lines. Normalized factors, determined from calculations of time dependent altitude profiles with a detailed photochemical model, were included in the onion peeling analysis to correct for the rapid diurnal changes in NO and NO2 concentrations with time near sunset. The CO2 profile was also derived from the analysis and is reported.

GLS-Finder: An Automated Data-Mining System for Fast Profiling Glucosinolates and its Application in Brassica Vegetables

USDA-ARS?s Scientific Manuscript database

A rapid computer-aided program for profiling glucosinolates, “GLS-Finder", was developed. GLS-Finder is a Matlab script based expert system that is capable for qualitative and semi-quantitative analysis of glucosinolates in samples using data generated by ultra-high performance liquid chromatograph...

Internal validation of the DNAscan/ANDE™ Rapid DNA Analysis™ platform and its associated PowerPlex® 16 high content DNA biochip cassette for use as an expert system with reference buccal swabs.

PubMed

Moreno, Lilliana I; Brown, Alice L; Callaghan, Thomas F

2017-07-01

Rapid DNA platforms are fully integrated systems capable of producing and analyzing short tandem repeat (STR) profiles from reference sample buccal swabs in less than two hours. The technology requires minimal user interaction and experience making it possible for high quality profiles to be generated outside an accredited laboratory. The automated production of point of collection reference STR profiles could eliminate the time delay for shipment and analysis of arrestee samples at centralized laboratories. Furthermore, point of collection analysis would allow searching against profiles from unsolved crimes during the normal booking process once the infrastructure to immediately search the Combined DNA Index System (CODIS) database from the booking station is established. The DNAscan/ANDE™ Rapid DNA Analysis™ System developed by Network Biosystems was evaluated for robustness and reliability in the production of high quality reference STR profiles for database enrollment and searching applications. A total of 193 reference samples were assessed for concordance of the CODIS 13 loci. Studies to evaluate contamination, reproducibility, precision, stutter, peak height ratio, noise and sensitivity were also performed. The system proved to be robust, consistent and dependable. Results indicated an overall success rate of 75% for the 13 CODIS core loci and more importantly no incorrect calls were identified. The DNAscan/ANDE™ could be confidently used without human interaction in both laboratory and non-laboratory settings to generate reference profiles. Published by Elsevier B.V.

Scalability Analysis of Gleipnir: A Memory Tracing and Profiling Tool, on Titan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Janjusic, Tommy; Kartsaklis, Christos; Wang, Dali

2013-01-01

Application performance is hindered by a variety of factors but most notably driven by the well know CPU-memory speed gap (also known as the memory wall). Understanding application s memory behavior is key if we are trying to optimize performance. Understanding application performance properties is facilitated with various performance profiling tools. The scope of profiling tools varies in complexity, ease of deployment, profiling performance, and the detail of profiled information. Specifically, using profiling tools for performance analysis is a common task when optimizing and understanding scientific applications on complex and large scale systems such as Cray s XK7. This papermore » describes the performance characteristics of using Gleipnir, a memory tracing tool, on the Titan Cray XK7 system when instrumenting large applications such as the Community Earth System Model. Gleipnir is a memory tracing tool built as a plug-in tool for the Valgrind instrumentation framework. The goal of Gleipnir is to provide fine-grained trace information. The generated traces are a stream of executed memory transactions mapped to internal structures per process, thread, function, and finally the data structure or variable. Our focus was to expose tool performance characteristics when using Gleipnir with a combination of an external tools such as a cache simulator, Gl CSim, to characterize the tool s overall performance. In this paper we describe our experience with deploying Gleipnir on the Titan Cray XK7 system, report on the tool s ease-of-use, and analyze run-time performance characteristics under various workloads. While all performance aspects are important we mainly focus on I/O characteristics analysis due to the emphasis on the tools output which are trace-files. Moreover, the tool is dependent on the run-time system to provide the necessary infrastructure to expose low level system detail; therefore, we also discuss any theoretical benefits that can be achieved if such modules were present.« less

MPEG-7-based description infrastructure for an audiovisual content analysis and retrieval system

NASA Astrophysics Data System (ADS)

Bailer, Werner; Schallauer, Peter; Hausenblas, Michael; Thallinger, Georg

2005-01-01

We present a case study of establishing a description infrastructure for an audiovisual content-analysis and retrieval system. The description infrastructure consists of an internal metadata model and access tool for using it. Based on an analysis of requirements, we have selected, out of a set of candidates, MPEG-7 as the basis of our metadata model. The openness and generality of MPEG-7 allow using it in broad range of applications, but increase complexity and hinder interoperability. Profiling has been proposed as a solution, with the focus on selecting and constraining description tools. Semantic constraints are currently only described in textual form. Conformance in terms of semantics can thus not be evaluated automatically and mappings between different profiles can only be defined manually. As a solution, we propose an approach to formalize the semantic constraints of an MPEG-7 profile using a formal vocabulary expressed in OWL, which allows automated processing of semantic constraints. We have defined the Detailed Audiovisual Profile as the profile to be used in our metadata model and we show how some of the semantic constraints of this profile can be formulated using ontologies. To work practically with the metadata model, we have implemented a MPEG-7 library and a client/server document access infrastructure.

Refining the Classification of Children with Selective Mutism: A Latent Profile Analysis

ERIC Educational Resources Information Center

Cohan, Sharon L.; Chavira, Denise A.; Shipon-Blum, Elisa; Hitchcock, Carla; Roesch, Scott C.; Stein, Murray B.

2008-01-01

The goal of this study was to develop an empirically derived classification system for selective mutism (SM) using parent-report measures of social anxiety, behavior problems, and communication delays. The sample consisted of parents of 130 children (ages 5-12) with SM. Results from latent profile analysis supported a 3-class solution made up of…

Beach Profile Analysis System (BPAS). Volume VII. BPAS User’s Guide: Analysis Module ELVDIS.

DTIC Science & Technology

1982-06-01

changes, common bonds are established relative to the landward and seaward extent of the surveys on each profile line. The computed area under each pro...Cyber 176 or equivalent computer. Such features include the 10-character, 60- bit word size, the FORTRAN- callable sort routine (interfacing with the NOS

Online Learning Flight Control for Intelligent Flight Control Systems (IFCS)

NASA Technical Reports Server (NTRS)

Niewoehner, Kevin R.; Carter, John (Technical Monitor)

2001-01-01

The research accomplishments for the cooperative agreement 'Online Learning Flight Control for Intelligent Flight Control Systems (IFCS)' include the following: (1) previous IFC program data collection and analysis; (2) IFC program support site (configured IFC systems support network, configured Tornado/VxWorks OS development system, made Configuration and Documentation Management Systems Internet accessible); (3) Airborne Research Test Systems (ARTS) II Hardware (developed hardware requirements specification, developing environmental testing requirements, hardware design, and hardware design development); (4) ARTS II software development laboratory unit (procurement of lab style hardware, configured lab style hardware, and designed interface module equivalent to ARTS II faceplate); (5) program support documentation (developed software development plan, configuration management plan, and software verification and validation plan); (6) LWR algorithm analysis (performed timing and profiling on algorithm); (7) pre-trained neural network analysis; (8) Dynamic Cell Structures (DCS) Neural Network Analysis (performing timing and profiling on algorithm); and (9) conducted technical interchange and quarterly meetings to define IFC research goals.

Measurement of bow tie profiles in CT scanners using a real-time dosimeter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whiting, Bruce R., E-mail: whitingbrucer@gmail.com; Evans, Joshua D.; Williamson, Jeffrey F.

2014-10-15

Purpose: Several areas of computed tomography (CT) research require knowledge about the intensity profile of the x-ray fan beam that is introduced by a bow tie filter. This information is considered proprietary by CT manufacturers, so noninvasive measurement methods are required. One method using real-time dosimeters has been proposed in the literature. A commercially available dosimeter was used to apply that method, and analysis techniques were developed to extract fan beam profiles from measurements. Methods: A real-time ion chamber was placed near the periphery of an empty CT gantry and the dose rate versus time waveform was recorded as themore » x-ray source rotated about the isocenter. In contrast to previously proposed analysis methods that assumed a pointlike detector, the finite-size ion chamber received varying amounts of coverage by the collimated x-ray beam during rotation, precluding a simple relationship between the source intensity as a function of fan beam angle and measured intensity. A two-parameter model for measurement intensity was developed that included both effective collimation width and source-to-detector distance, which then was iteratively solved to minimize the error between duplicate measurements at corresponding fan beam angles, allowing determination of the fan beam profile from measured dose-rate waveforms. Measurements were performed on five different scanner systems while varying parameters such as collimation, kVp, and bow tie filters. On one system, direct measurements of the bow tie profile were collected for comparison with the real-time dosimeter technique. Results: The data analysis method for a finite-size detector was found to produce a fan beam profile estimate with a relative error between duplicate measurement intensities of <5%. It was robust over a wide range of collimation widths (e.g., 1–40 mm), producing fan beam profiles that agreed with a relative error of 1%–5%. Comparison with a direct measurement technique on one system produced agreement with a relative error of 2%–6%. Fan beam profiles were found to differ for different filter types on a given system and between different vendors. Conclusions: A commercially available real-time dosimeter probe was found to be a convenient and accurate instrument for measuring fan beam profiles. An analysis method was developed that could handle a wide range of collimation widths by explicitly considering the finite width of the ion chamber. Relative errors in the profiles were found to be less than 5%. Measurements of five different clinical scanners demonstrate the variation in bow tie designs, indicating that generic bow tie models will not be adequate for CT system research.« less

Small-Signal Analysis of Autonomous Hybrid Distributed Generation Systems in Presence of Ultracapacitor and Tie-Line Operation

NASA Astrophysics Data System (ADS)

Ray, Prakash K.; Mohanty, Soumya R.; Kishor, Nand

2010-07-01

This paper presents small-signal analysis of isolated as well as interconnected autonomous hybrid distributed generation system for sudden variation in load demand, wind speed and solar radiation. The hybrid systems comprise of different renewable energy resources such as wind, photovoltaic (PV) fuel cell (FC) and diesel engine generator (DEG) along with the energy storage devices such as flywheel energy storage system (FESS) and battery energy storage system (BESS). Further ultracapacitors (UC) as an alternative energy storage element and interconnection of hybrid systems through tie-line is incorporated into the system for improved performance. A comparative assessment of deviation of frequency profile for different hybrid systems in the presence of different storage system combinations is carried out graphically as well as in terms of the performance index (PI), ie integral square error (ISE). Both qualitative and quantitative analysis reflects the improvements of the deviation in frequency profiles in the presence of the ultracapacitors (UC) as compared to other energy storage elements.

A review of the remote sensing of lower tropospheric thermodynamic profiles and its indispensable role for the understanding and the simulation of water and energy cycles: REMOTE SENSING OF THERMODYNAMIC PROFILES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wulfmeyer, Volker; Hardesty, R. Michael; Turner, David D.

A review of remote sensing technology for lower tropospheric thermodynamic (TD) profiling is presented with focus on high accuracy and high temporal-vertical resolution. The contributions of these instruments to the understanding of the Earth system are assessed with respect to radiative transfer, land surface-atmosphere feedback, convection initiation, and data assimilation. We demonstrate that for progress in weather and climate research, TD profilers are essential. These observational systems must resolve gradients of humidity and temperature in the stable or unstable atmospheric surface layer close to the ground, in the mixed layer, in the interfacial layer—usually characterized by an inversion—and the lowermore » troposphere. A thorough analysis of the current observing systems is performed revealing significant gaps that must be addressed to fulfill existing needs. We analyze whether current and future passive and active remote sensing systems can close these gaps. A methodological analysis and demonstration of measurement capabilities with respect to bias and precision is executed both for passive and active remote sensing including passive infrared and microwave spectroscopy, the global navigation satellite system, as well as water vapor and temperature Raman lidar and water vapor differential absorption lidar. Whereas passive remote sensing systems are already mature with respect to operational applications, active remote sensing systems require further engineering to become operational in networks. However, active remote sensing systems provide a smaller bias as well as higher temporal and vertical resolutions. For a suitable mesoscale network design, TD profiler system developments should be intensified and dedicated observing system simulation experiments should be performed.« less

Differential identification of Candida species and other yeasts by analysis of (/sup 35/S)methionine-labeled polypeptide profiles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shen, H.D.; Choo, K.B.; Tsai, W.C.

1988-12-01

This paper describes a scheme for differential identification of Candida species and other yeasts based on autoradiographic analysis of protein profiles of (/sup 35/S)methionine-labeled cellular proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Using ATCC strains as references, protein profile analysis showed that different Candida and other yeast species produced distinctively different patterns. Good agreement in results obtained with this approach and with other conventional systems was observed. Being accurate and reproducible, this approach provides a basis for the development of an alternative method for the identification of yeasts isolated from clinical specimens.

STS-1 operational flight profile. Volume 6: Abort analysis

NASA Technical Reports Server (NTRS)

1980-01-01

The abort analysis for the cycle 3 Operational Flight Profile (OFP) for the Space Transportation System 1 Flight (STS-1) is defined, superseding the abort analysis previously presented. Included are the flight description, abort analysis summary, flight design groundrules and constraints, initialization information, general abort description and results, abort solid rocket booster and external tank separation and disposal results, abort monitoring displays and discussion on both ground and onboard trajectory monitoring, abort initialization load summary for the onboard computer, list of the key abort powered flight dispersion analysis.

High-Resolution Metabolic Phenotyping of Genetically and Environmentally Diverse Potato Tuber Systems. Identification of Phenocopies

PubMed Central

Roessner, Ute; Willmitzer, Lothar; Fernie, Alisdair R.

2001-01-01

We conducted a comprehensive metabolic phenotyping of potato (Solanum tuberosum L. cv Desiree) tuber tissue that had been modified either by transgenesis or exposure to different environmental conditions using a recently developed gas chromatography-mass spectrometry profiling protocol. Applying this technique, we were able to identify and quantify the major constituent metabolites of the potato tuber within a single chromatographic run. The plant systems that we selected to profile were tuber discs incubated in varying concentrations of fructose, sucrose, and mannitol and transgenic plants impaired in their starch biosynthesis. The resultant profiles were then compared, first at the level of individual metabolites and then using the statistical tools hierarchical cluster analysis and principal component analysis. These tools allowed us to assign clusters to the individual plant systems and to determine relative distances between these clusters; furthermore, analyzing the loadings of these analyses enabled identification of the most important metabolites in the definition of these clusters. The metabolic profiles of the sugar-fed discs were dramatically different from the wild-type steady-state values. When these profiles were compared with one another and also with those we assessed in previous studies, however, we were able to evaluate potential phenocopies. These comparisons highlight the importance of such an approach in the functional and qualitative assessment of diverse systems to gain insights into important mediators of metabolism. PMID:11706160

The Propulsive Small Expendable Deployer System (ProSEDS)

NASA Technical Reports Server (NTRS)

Lorenzini, Enrico C.; Cosmo, Mario L.; Estes, Robert D.; Sanmartin, Juan; Pelaez, Jesus; Ruiz, Manuel

2003-01-01

This Final Report covers the following main topics: 1) Brief Description of ProSEDS; 2) Mission Analysis; 3) Dynamics Reference Mission; 4) Dynamics Stability; 5) Deployment Control; 6) Updated System Performance; 7) Updated Mission Analysis; 8) Updated Dynamics Reference Mission; 9) Updated Deployment Control Profiles and Simulations; 10) Updated Reference Mission; 11) Evaluation of Power Delivered by the Tether; 12) Deployment Control Profile Ref. #78 and Simulations; 13) Kalman Filters for Mission Estimation; 14) Analysis/Estimation of Deployment Flight Data; 15) Comparison of ED Tethers and Electrical Thrusters; 16) Dynamics Analysis for Mission Starting at a Lower Altitude; 17) Deployment Performance at a Lower Altitude; 18) Satellite Orbit after a Tether Cut; 19) Deployment with Shorter Dyneema Tether Length; 20) Interactive Software for ED Tethers.

Optimal design of reflectometer density profile measurements using a radar systems approach (invited) (abstract)

NASA Astrophysics Data System (ADS)

Doyle, E. J.; Kim, K. W.; Peebles, W. A.; Rhodes, T. L.

1997-01-01

Reflectometry is an attractive and versatile diagnostic technique that can address a wide range of measurement needs on fusion devices. However, progress in the area of profile measurement has been hampered by the lack of a well-understood basis for the optimum design and implementation of such systems. Such a design basis is provided by the realization that reflectometer systems utilized for density profile measurements are in fact specialized forms of radar systems. In this article five criteria are introduced by which reflectometer systems can be systematically designed for optimal performance: range resolution, spatial sampling, turbulence immunity, bandwidth optimization, and the need for adaptive data processing. Many of these criteria are familiar from radar systems analysis, and are applicable to reflectometry after allowance is made for differences stemming from the nature of the plasma target. These criteria are utilized to critically evaluate current reflectometer density profile techniques and indicate improvements that can impact current and next step devices, such as ITER.

Size-exclusion chromatography system for macromolecular interaction analysis

DOEpatents

Stevens, Fred J.

1988-01-01

A low pressure, microcomputer controlled system employing high performance liquid chromatography (HPLC) allows for precise analysis of the interaction of two reversibly associating macromolecules such as proteins. Since a macromolecular complex migrates faster than its components during size-exclusion chromatography, the difference between the elution profile of a mixture of two macromolecules and the summation of the elution profiles of the two components provides a quantifiable indication of the degree of molecular interaction. This delta profile is used to qualitatively reveal the presence or absence of significant interaction or to rank the relative degree of interaction in comparing samples and, in combination with a computer simulation, is further used to quantify the magnitude of the interaction in an arrangement wherein a microcomputer is coupled to analytical instrumentation in a novel manner.

Validation Test Report for the Improved Synthetic Ocean Profile (ISOP) System, Part I: Synthetic Profile Methods and Algorithm

DTIC Science & Technology

2013-03-15

methods as those used for constructing the Generalized Digital Environmental Model ( GDEM ) version 4 (Carnes, Helber, et al. 2010). The purpose of...in the EOF analysis, which is described in Sections 4.2. 1 and 5.2.3. The primary difference between the ISOP climatology and GDEM is that ISOP only...uses paired profiles of T and S whereas GDEM uses all T profiles available. Paired profiles of T and S are required for ISOP because the T and S co

Simultaneous Measurements of CO2 Concentration and Temperature profiles using 1.6 μm DIAL in the Lower-Atmosphere

NASA Astrophysics Data System (ADS)

Shibata, Y.; Nagasawa, C.; Abo, M.

2016-12-01

High-accurate vertical carbon dioxide (CO2) profiles are highly desirable in the inverse method to improve quantification and understanding of the global sink and source of CO2, and also global climate change. We have developed a ground based 1.6μm differential absorption lidar (DIAL) to achieve measurements of vertical CO2 profiles in the atmosphere. As the spectra of absorption lines of any molecules are influenced basically by the temperature and pressure in the atmosphere, it is important to measure them simultaneously so that the better accuracy of the DIAL measurement is realized. The barometric formula can derive atmospheric pressure of each altitude using atmospheric pressure of ground level at the lidar site. Comparison of atmospheric pressure prlofiles calculated from this equation and those obtained from radiosonde observations at Tateno, Japan are consisted within 0.2 % below 3 km altitude. So, we have developed a 1.6 μm CO2 DIAL system for simultaneous measurements of the CO2 concentration and temperature profiles in the lower-atmosphere. Laser beams of three wavelengths around a CO2 absorption spectrum is transmitted alternately to the atmosphere. Moreover, the value of the retrieved CO2 concentration will be improved remarkably by processing the iteration assignment of CO2 concentration and temperature, which measured by these DIAL techniques. We have acheived vertical CO2 concentration and temperature profile from 0.5 to 2.0 km altitude by this DIAL system. In the next step, we will use this high accuracy CO2 concentration profile and back-trajectory analysis for the behavior analysis of the CO2 mass. This work was financially supported by the System Development Program for Advanced Measurement and Analysis of the Japan Science and Technology Agency.

Analysis of lipoprotein profiles of healthy cats by gel-permeation high-performance liquid chromatography

PubMed Central

MIZUTANI, Hisashi; SAKO, Toshinori; OKUDA, Hiroko; ARAI, Nobuaki; KURIYAMA, Koji; MORI, Akihiro; YOSHIMURA, Itaru; KOYAMA, Hidekazu

2016-01-01

Density gradient ultracentrifugation (DGUC) and gel electrophoresis are conventionally used to obtain lipoprotein profiles of animals. We recently applied high-performance liquid chromatography with a gel permeation column (GP-HPLC) and an on-line dual enzymatic system to dogs for lipoprotein profile analysis. We compared the GP-HPLC with DGUC as a method to obtain a feline lipoprotein profile. The lipoprotein profiles showed large and small peaks, which corresponded to high-density lipoprotein (HDL) and low-density lipoprotein (LDL), respectively, whereas very low-density lipoprotein (VLDL) and chylomicron (CM) were only marginally detected. This profile was very similar to that of dogs reported previously. Healthy cats also had a small amount of cholesterol-rich particles distinct from the normal LDL or HDL profile. There was no difference in lipoprotein profiles between the sexes, but males had a significantly larger LDL particle size (P=0.015). This study shows the feasibility of GP-HPLC for obtaining accurate lipoprotein profiles with small sample volumes and provides valuable reference data for healthy cats that should facilitate diagnoses. PMID:27170431

Optical bi-sensorial measurement system for production control of extruded profiles

NASA Astrophysics Data System (ADS)

Weckenmann, A.; Bernstein, J.

2008-09-01

Extruded profiles are semi-finished products (made out of steel, brass, aluminum, synthetics...) which are appointed for wide applications in manufacturing of technical products. As yet used optical sensors in process control working to the shading technology detect the object's shadow orthographically to the axis of illumination. As a consequence they record it unattached by the profiles coat in measurement range at any point of the measured profile with high precision. As a matter of fact, concave zones cannot be captured. Alternatively the measurement of concave zones can be arranged by light-section systems. These do not comply with the required accuracy, are comparatively slow and moreover affected by dislocations of the section of the profile. A measurement system including a light-section and a shading system combines the advantages of both optical systems. It is to serve with a reliable conception for the assembly of a bi-sensorial measurement system consisting of both systems as well as suitable methods of analysis for the in-line inspection of concave profiles. As a result it contains conclusions concerning requirements of the light source, the arrangement of this source and the cameras, obtainable precision and sampling rate as well as the essential synchronization of both systems. After designing an appropriate prototype, the selected light-section system and the shading system will be synchronized and aligned. Therefore, the metered geometrical data will be merged for the evaluation of form deviation. So, developed and adapted software supports and contains proposals to the uncertainty after successful tests. The system and a calibration method will be proved in production where robustness will be a most critical despite of heat, dust and vibrations. The target uncertainty of less than 0.1 mm at every section of the profiles coat has to be met.

Profiling the different needs and expectations of patients for population-based medicine: a case study using segmentation analysis

PubMed Central

2012-01-01

Background This study illustrates an evidence-based method for the segmentation analysis of patients that could greatly improve the approach to population-based medicine, by filling a gap in the empirical analysis of this topic. Segmentation facilitates individual patient care in the context of the culture, health status, and the health needs of the entire population to which that patient belongs. Because many health systems are engaged in developing better chronic care management initiatives, patient profiles are critical to understanding whether some patients can move toward effective self-management and can play a central role in determining their own care, which fosters a sense of responsibility for their own health. A review of the literature on patient segmentation provided the background for this research. Method First, we conducted a literature review on patient satisfaction and segmentation to build a survey. Then, we performed 3,461 surveys of outpatient services users. The key structures on which the subjects’ perception of outpatient services was based were extrapolated using principal component factor analysis with varimax rotation. After the factor analysis, segmentation was performed through cluster analysis to better analyze the influence of individual attitudes on the results. Results Four segments were identified through factor and cluster analysis: the “unpretentious,” the “informed and supported,” the “experts” and the “advanced” patients. Their policies and managerial implications are outlined. Conclusions With this research, we provide the following: – a method for profiling patients based on common patient satisfaction surveys that is easily replicable in all health systems and contexts; – a proposal for segments based on the results of a broad-based analysis conducted in the Italian National Health System (INHS). Segments represent profiles of patients requiring different strategies for delivering health services. Their knowledge and analysis might support an effort to build an effective population-based medicine approach. PMID:23256543

Miscible gravitational instability of initially stable horizontal interface in a porous medium: Non-monotonic density profiles

NASA Astrophysics Data System (ADS)

Kim, Min Chan

2014-11-01

To simulate a CO2 sequestration process, some researchers employed a water/propylene glycol (PPG) system which shows a non-monotonic density profile. Motivated by this fact, the stability of the diffusion layer of two miscible fluids saturated in a porous medium is analyzed. For a non-monotonic density profile system, linear stability equations are derived in a global domain, and then transformed into a system of ordinary differential equations in an infinite domain. Initial growth rate analysis is conducted without the quasi-steady state approximation (QSSA) and shows that initially the system is unconditionally stable for the least stable disturbance. For the time evolving case, the ordinary differential equations are solved applying the eigen-analysis and numerical shooting scheme with and without the QSSA. To support these theoretical results, direct numerical simulations are conducted using the Fourier spectral method. The results of theoretical linear stability analyses and numerical simulations validate one another. The present linear and nonlinear analyses show that the water/PPG system is more unstable than the CO2/brine one, and the flow characteristics of these two systems are quite different from each other.

Analysis of Mesh Distribution Systems Considering Load Models and Load Growth Impact with Loops on System Performance

NASA Astrophysics Data System (ADS)

Kumar Sharma, A.; Murty, V. V. S. N.

2014-12-01

The distribution system is the final link between bulk power system and consumer end. A distinctive load flow solution method is used for analysis of the load flow of radial and weakly meshed network based on Kirchhoff's Current Law (KCL) and KVL. This method has excellent convergence characteristics for both radial as well as weakly meshed structure and is based on bus injection to branch current and branch-current to bus-voltage matrix. The main contribution of the paper is: (i) an analysis has been carried out for a weekly mesh network considering number of loops addition and its impact on the losses, kW and kVAr requirements from a system, and voltage profile, (ii) different load models, realistic ZIP load model and load growth impact on losses, voltage profile, kVA and kVAr requirements, (iii) impact of addition of loops on losses, voltage profile, kVA and kVAr requirements from substation, and (iv) comparison of system performance with radial distribution system. Voltage stability is a major concern in planning and operation of power systems. This paper also includes identifying the closeness critical bus which is the most sensitive to the voltage collapse in radial distribution networks. Node having minimum value of voltage stability index is the most sensitive node. Voltage stability index values are computed for meshed network with number of loops added in the system. The results have been obtained for IEEE 33 and 69 bus test system. The results have also been obtained for radial distribution system for comparison.

Principal component analysis of TOF-SIMS spectra, images and depth profiles: an industrial perspective

NASA Astrophysics Data System (ADS)

Pacholski, Michaeleen L.

2004-06-01

Principal component analysis (PCA) has been successfully applied to time-of-flight secondary ion mass spectrometry (TOF-SIMS) spectra, images and depth profiles. Although SIMS spectral data sets can be small (in comparison to datasets typically discussed in literature from other analytical techniques such as gas or liquid chromatography), each spectrum has thousands of ions resulting in what can be a difficult comparison of samples. Analysis of industrially-derived samples means the identity of most surface species are unknown a priori and samples must be analyzed rapidly to satisfy customer demands. PCA enables rapid assessment of spectral differences (or lack there of) between samples and identification of chemically different areas on sample surfaces for images. Depth profile analysis helps define interfaces and identify low-level components in the system.

Road profile estimation of city roads using DTPS

NASA Astrophysics Data System (ADS)

Wang, Qi; McDaniel, J. Gregory; Sun, Nian X.; Wang, Ming L.

2013-04-01

This work presents a non-destructive and non-contact acoustic sensing approach for measuring road profile of road and bridge deck with vehicles running at normal speed without stopping traffic. This approach uses an instantaneous and real-time dynamic tire pressure sensor (DTPS) that can measure dynamic response of the tire-road interaction and increases the efficiency of currently used road profile measuring systems with vehicle body-mounted profilers and axle-mounted accelerometers. In this work, a prototype of real-time DTPS system has been developed and demonstrated on a testing van at speeds from 5 to 80 miles per hour (mph). A data analysis algorithm has been developed to remove axle dynamic motions from the measured DTPS data and to find the transfer function between dynamic tire pressure change and the road profile. Field test has been performed to estimate road profiles. The road profile resolution is approximately 5 to 10 cm in width and sensitivity is 0. 3 cm for the height road surface features at driving speeds of 5 to 80 mph.

Assimilation of Quality Controlled AIRS Temperature Profiles using the NCEP GFS

NASA Technical Reports Server (NTRS)

Susskind, Joel; Reale, Oreste; Iredell, Lena; Rosenberg, Robert

2013-01-01

We have previously conducted a number of data assimilation experiments using AIRS Version-5 quality controlled temperature profiles as a step toward finding an optimum balance of spatial coverage and sounding accuracy with regard to improving forecast skill. The data assimilation and forecast system we used was the Goddard Earth Observing System Model , Version-5 (GEOS-5) Data Assimilation System (DAS), which represents a combination of the NASA GEOS-5 forecast model with the National Centers for Environmental Prediction (NCEP) operational Grid Point Statistical Interpolation (GSI) global analysis scheme. All analyses and forecasts were run at a 0.5deg x 0.625deg spatial resolution. Data assimilation experiments were conducted in four different seasons, each in a different year. Three different sets of data assimilation experiments were run during each time period: Control; AIRS T(p); and AIRS Radiance. In the "Control" analysis, all the data used operationally by NCEP was assimilated, but no AIRS data was assimilated. Radiances from the Aqua AMSU-A instrument were also assimilated operationally by NCEP and are included in the "Control". The AIRS Radiance assimilation adds AIRS observed radiance observations for a select set of channels to the data set being assimilated, as done operationally by NCEP. In the AIRS T(p) assimilation, all information used in the Control was assimilated as well as Quality Controlled AIRS Version-5 temperature profiles, i.e., AIRS T(p) information was substituted for AIRS radiance information. The AIRS Version-5 temperature profiles were presented to the GSI analysis as rawinsonde profiles, assimilated down to a case-by-case appropriate pressure level p(sub best) determined using the Quality Control procedure. Version-5 also determines case-by-case, level-by-level error estimates of the temperature profiles, which were used as the uncertainty of each temperature measurement. These experiments using GEOS-5 have shown that forecasts resulting from analyses using the AIRS T(p) assimilation system were superior to those from the Radiance assimilation system, both with regard to global 7 day forecast skill and also the ability to predict storm tracks and intensity.

The Profile Envision and Splicing Tool (PRESTO): Developing an Atmospheric Wind Analysis Tool for Space Launch Vehicles Using Python

NASA Technical Reports Server (NTRS)

Orcutt, John M.; Barbre, Robert E., Jr.; Brenton, James C.; Decker, Ryan K.

2017-01-01

Launch vehicle programs require vertically complete atmospheric profiles. Many systems at the ER to make the necessary measurements, but all have different EVR, vertical coverage, and temporal coverage. MSFC Natural Environments Branch developed a tool to create a vertically complete profile from multiple inputs using Python. Forward work: Finish Formal Testing Acceptance Testing, End-to-End Testing. Formal Release

A spatiotemporal profile of visual system activation revealed by current source density analysis in the awake macaque.

PubMed

Schroeder, C E; Mehta, A D; Givre, S J

1998-01-01

We investigated the spatiotemporal activation pattern, produced by one visual stimulus, across cerebral cortical regions in awake monkeys. Laminar profiles of postsynaptic potentials and action potentials were indexed with current source density (CSD) and multiunit activity profiles respectively. Locally, we found contrasting activation profiles in dorsal and ventral stream areas. The former, like V1 and V2, exhibit a 'feedforward' profile, with excitation beginning at the depth of Lamina 4, followed by activation of the extragranular laminae. The latter often displayed a multilaminar/columnar profile, with initial responses distributed across the laminae and reflecting modulation rather than excitation; CSD components were accompanied by either no changes or by suppression of action potentials. System-wide, response latencies indicated a large dorsal/ventral stream latency advantage, which generalizes across a wide range of methods. This predicts a specific temporal ordering of dorsal and ventral stream components of visual analysis, as well as specific patterns of dorsal-ventral stream interaction. Our findings support a hierarchical model of cortical organization that combines serial and parallel elements. Critical in such a model is the recognition that processing within a location typically entails multiple temporal components or 'waves' of activity, driven by input conveyed over heterogeneous pathways from the retina.

Audiologist-patient communication profiles in hearing rehabilitation appointments.

PubMed

Meyer, Carly; Barr, Caitlin; Khan, Asaduzzaman; Hickson, Louise

2017-08-01

To profile the communication between audiologists and patients in initial appointments on a biomedical-psychosocial continuum; and explore the associations between these profiles and 1) characteristics of the appointment and 2) patients' decisions to pursue hearing aids. Sixty-three initial hearing assessment appointments were filmed and audiologist-patient communication was coded using the Roter Interaction Analysis System. A hierarchical cluster analysis was conducted to profile audiologist-patient communication, after which regression modelling and Chi-squared analyses were conducted. Two distinct audiologist-patient communication profiles were identified during both the history taking phase (46=biopsychosocial profile, 15=psychosocial profile) and diagnosis and management planning phase (45=expanded biomedical profile, 11=narrowly biomedical profile). Longer appointments were significantly more likely to be associated with an expanded biomedical interaction during the diagnosis and management planning phase. No significant associations were found between audiologist-patient communication profile and patients' decisions to pursue hearing aids. Initial audiology consultations appear to remain clinician-centred. Three quarters of appointments began with a biopsychosocial interaction; however, 80% ended with an expanded biomedical interaction. Findings suggest that audiologists could consider modifying their communication in initial appointments to more holistically address the needs of patients. Copyright © 2017 Elsevier B.V. All rights reserved.

Local ensemble transform Kalman filter for ionospheric data assimilation: Observation influence analysis during a geomagnetic storm event

NASA Astrophysics Data System (ADS)

Durazo, Juan A.; Kostelich, Eric J.; Mahalov, Alex

2017-09-01

We propose a targeted observation strategy, based on the influence matrix diagnostic, that optimally selects where additional observations may be placed to improve ionospheric forecasts. This strategy is applied in data assimilation observing system experiments, where synthetic electron density vertical profiles, which represent those of Constellation Observing System for Meteorology, Ionosphere, and Climate/Formosa satellite 3, are assimilated into the Thermosphere-Ionosphere-Electrodynamics General Circulation Model using the local ensemble transform Kalman filter during the 26 September 2011 geomagnetic storm. During each analysis step, the observation vector is augmented with five synthetic vertical profiles optimally placed to target electron density errors, using our targeted observation strategy. Forecast improvement due to assimilation of augmented vertical profiles is measured with the root-mean-square error (RMSE) of analyzed electron density, averaged over 600 km regions centered around the augmented vertical profile locations. Assimilating vertical profiles with targeted locations yields about 60%-80% reduction in electron density RMSE, compared to a 15% average reduction when assimilating randomly placed vertical profiles. Assimilating vertical profiles whose locations target the zonal component of neutral winds (Un) yields on average a 25% RMSE reduction in Un estimates, compared to a 2% average improvement obtained with randomly placed vertical profiles. These results demonstrate that our targeted strategy can improve data assimilation efforts during extreme events by detecting regions where additional observations would provide the largest benefit to the forecast.

Psychosocial and Cognitive Functioning of Children with Specific Profiles of Maltreatment

ERIC Educational Resources Information Center

Pears, Katherine C.; Kim, Hyoun K.; Fisher, Philip A.

2008-01-01

Objective: Up to 90% of child welfare system cases involve multiple types of maltreatment; however, studies have rarely incorporated multiple dimensions of maltreatment. The present study employed a latent profile analysis to identify naturally occurring subgroups of children who had experienced maltreatment. Methods: Reports of maltreatment…

Improving Markov Chain Models for Road Profiles Simulation via Definition of States

DTIC Science & Technology

2012-04-01

wavelet transform in pavement profile analysis," Vehicle System Dynamics: International Journal of Vehicle Mechanics and Mobility, vol. 47, no. 4...34Estimating Markov Transition Probabilities from Micro -Unit Data," Journal of the Royal Statistical Society. Series C (Applied Statistics), pp. 355-371

Laser-induced breakdown spectroscopy for specimen analysis

DOEpatents

Kumar, Akshaya; Yu-Yueh, Fang; Burgess, Shane C.; Singh, Jagdish P.

2006-08-15

The present invention is directed to an apparatus, a system and a method for detecting the presence or absence of trace elements in a biological sample using Laser-Induced Breakdown Spectroscopy. The trace elements are used to develop a signature profile which is analyzed directly or compared with the known profile of a standard. In one aspect of the invention, the apparatus, system and method are used to detect malignant cancer cells in vivo.

Inorganic material profiling using Arn+ cluster: Can we achieve high quality profiles?

NASA Astrophysics Data System (ADS)

Conard, T.; Fleischmann, C.; Havelund, R.; Franquet, A.; Poleunis, C.; Delcorte, A.; Vandervorst, W.

2018-06-01

Retrieving molecular information by sputtering of organic systems has been concretized in the last years due to the introduction of sputtering by large gas clusters which drastically eliminated the compound degradation during the analysis and has led to strong improvements in depth resolution. Rapidly however, a limitation was observed for heterogeneous systems where inorganic layers or structures needed to be profiled concurrently. As opposed to organic material, erosion of the inorganic layer appears very difficult and prone to many artefacts. To shed some light on these problems we investigated a simple system consisting of aluminum delta layer(s) buried in a silicon matrix in order to define the most favorable beam conditions for practical analysis. We show that counterintuitive to the small energy/atom used and unlike monoatomic ion sputtering, the information depth obtained with large cluster ions is typically very large (∼10 nm) and that this can be caused both by a large roughness development at early stages of the sputtering process and by a large mixing zone. As a consequence, a large deformation of the Al intensity profile is observed. Using sample rotation during profiling significantly improves the depth resolution while sample temperature has no significant effect. The determining parameter for high depth resolution still remains the total energy of the cluster instead of the energy per atom in the cluster.

A measurement system for vertical seawater profiles close to the air-sea interface

NASA Astrophysics Data System (ADS)

Sims, Richard P.; Schuster, Ute; Watson, Andrew J.; Yang, Ming Xi; Hopkins, Frances E.; Stephens, John; Bell, Thomas G.

2017-09-01

This paper describes a near-surface ocean profiler, which has been designed to precisely measure vertical gradients in the top 10 m of the ocean. Variations in the depth of seawater collection are minimized when using the profiler compared to conventional CTD/rosette deployments. The profiler consists of a remotely operated winch mounted on a tethered yet free-floating buoy, which is used to raise and lower a small frame housing sensors and inlet tubing. Seawater at the inlet depth is pumped back to the ship for analysis. The profiler can be used to make continuous vertical profiles or to target a series of discrete depths. The profiler has been successfully deployed during wind speeds up to 10 m s-1 and significant wave heights up to 2 m. We demonstrate the potential of the profiler by presenting measured vertical profiles of the trace gases carbon dioxide and dimethylsulfide. Trace gas measurements use an efficient microporous membrane equilibrator to minimize the system response time. The example profiles show vertical gradients in the upper 5 m for temperature, carbon dioxide and dimethylsulfide of 0.15 °C, 4 µatm and 0.4 nM respectively.

Detecting phase separation of freeze-dried binary amorphous systems using pair-wise distribution function and multivariate data analysis.

PubMed

Chieng, Norman; Trnka, Hjalte; Boetker, Johan; Pikal, Michael; Rantanen, Jukka; Grohganz, Holger

2013-09-15

The purpose of this study is to investigate the use of multivariate data analysis for powder X-ray diffraction-pair-wise distribution function (PXRD-PDF) data to detect phase separation in freeze-dried binary amorphous systems. Polymer-polymer and polymer-sugar binary systems at various ratios were freeze-dried. All samples were analyzed by PXRD, transformed to PDF and analyzed by principal component analysis (PCA). These results were validated by differential scanning calorimetry (DSC) through characterization of glass transition of the maximally freeze-concentrate solute (Tg'). Analysis of PXRD-PDF data using PCA provides a more clear 'miscible' or 'phase separated' interpretation through the distribution pattern of samples on a score plot presentation compared to residual plot method. In a phase separated system, samples were found to be evenly distributed around the theoretical PDF profile. For systems that were miscible, a clear deviation of samples away from the theoretical PDF profile was observed. Moreover, PCA analysis allows simultaneous analysis of replicate samples. Comparatively, the phase behavior analysis from PXRD-PDF-PCA method was in agreement with the DSC results. Overall, the combined PXRD-PDF-PCA approach improves the clarity of the PXRD-PDF results and can be used as an alternative explorative data analytical tool in detecting phase separation in freeze-dried binary amorphous systems. Copyright © 2013 Elsevier B.V. All rights reserved.

A review of the remote sensing of lower-tropospheric thermodynamic profiles and its indispensable role for the understanding and the simulation of water and energy cycles

DOE PAGES

Wulfmeyer, Volker; Hardesty, Mike; Turner, David D.; ...

2015-07-08

A review of remote sensing technology for lower-tropospheric thermodynamic (TD) profiling is presented with focus on high accuracy and high temporal-vertical resolution. The contributions of these instruments to the understanding of the Earth system are assessed with respect to radiative transfer, land-surface-atmosphere feedback, convection initiation, and data assimilation. We demonstrate that for progress in weather and climate research, TD profilers are essential. These observational systems must resolve gradients of humidity and temperature in the stable or unstable atmospheric surface layer close to the ground, in the mixed layer, in the interfacial layer – usually characterized by an inversion – andmore » the lower troposphere. A thorough analysis of the current observing systems is performed revealing significant gaps that must be addressed to fulfill existing needs. We analyze whether current and future passive and active remote sensing systems can close these gaps. A methodological analysis and demonstration of measurement capabilities with respect to bias and precision is executed both for passive and active remote sensing including passive infrared and microwave spectroscopy, the global positioning system as well as water-vapor and temperature Raman lidar and water-vapor differential absorption lidar. Whereas passive remote sensing systems are already mature with respect to operational applications, active remote sensing systems require further engineering to become operational in networks. However, active remote sensing systems provide a smaller bias as well as higher temporal and vertical resolutions. For a suitable mesoscale network design, TD profiler system developments should be intensified and dedicated observing system simulation experiments should be performed.« less

A review of the remote sensing of lower-tropospheric thermodynamic profiles and its indispensable role for the understanding and the simulation of water and energy cycles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wulfmeyer, Volker; Hardesty, Mike; Turner, David D.

A review of remote sensing technology for lower-tropospheric thermodynamic (TD) profiling is presented with focus on high accuracy and high temporal-vertical resolution. The contributions of these instruments to the understanding of the Earth system are assessed with respect to radiative transfer, land-surface-atmosphere feedback, convection initiation, and data assimilation. We demonstrate that for progress in weather and climate research, TD profilers are essential. These observational systems must resolve gradients of humidity and temperature in the stable or unstable atmospheric surface layer close to the ground, in the mixed layer, in the interfacial layer – usually characterized by an inversion – andmore » the lower troposphere. A thorough analysis of the current observing systems is performed revealing significant gaps that must be addressed to fulfill existing needs. We analyze whether current and future passive and active remote sensing systems can close these gaps. A methodological analysis and demonstration of measurement capabilities with respect to bias and precision is executed both for passive and active remote sensing including passive infrared and microwave spectroscopy, the global positioning system as well as water-vapor and temperature Raman lidar and water-vapor differential absorption lidar. Whereas passive remote sensing systems are already mature with respect to operational applications, active remote sensing systems require further engineering to become operational in networks. However, active remote sensing systems provide a smaller bias as well as higher temporal and vertical resolutions. For a suitable mesoscale network design, TD profiler system developments should be intensified and dedicated observing system simulation experiments should be performed.« less

Surface profiling interferometer

DOEpatents

Takacs, Peter Z.; Qian, Shi-Nan

1989-01-01

The design of a long-trace surface profiler for the non-contact measurement of surface profile, slope error and curvature on cylindrical synchrotron radiation (SR) mirrors. The optical system is based upon the concept of a pencil-beam interferometer with an inherent large depth-of-field. The key feature of the optical system is the zero-path-difference beam splitter, which separates the laser beam into two colinear, variable-separation probe beams. A linear array detector is used to record the interference fringe in the image, and analysis of the fringe location as a function of scan position allows one to reconstruct the surface profile. The optical head is mounted on an air bearing slide with the capability to measure long aspheric optics, typical of those encountered in SR applications. A novel feature of the optical system is the use of a transverse "outrigger" beam which provides information on the relative alignment of the scan axis to the cylinder optic symmetry axis.

Analysis of energy dispersive x-ray diffraction profiles for material identification, imaging and system control

NASA Astrophysics Data System (ADS)

Cook, Emily Jane

2008-12-01

This thesis presents the analysis of low angle X-ray scatter measurements taken with an energy dispersive system for substance identification, imaging and system control. Diffraction measurements were made on illicit drugs, which have pseudo- crystalline structures and thus produce diffraction patterns comprising a se ries of sharp peaks. Though the diffraction profiles of each drug are visually characteristic, automated detection systems require a substance identification algorithm, and multivariate analysis was selected as suitable. The software was trained with measured diffraction data from 60 samples covering 7 illicit drugs and 5 common cutting agents, collected with a range of statistical qual ities and used to predict the content of 7 unknown samples. In all cases the constituents were identified correctly and the contents predicted to within 15%. Soft tissues exhibit broad peaks in their diffraction patterns. Diffraction data were collected from formalin fixed breast tissue samples and used to gen erate images. Maximum contrast between healthy and suspicious regions was achieved using momentum transfer windows 1.04-1.10 and 1.84-1.90 nm_1. The resulting images had an average contrast of 24.6% and 38.9% compared to the corresponding transmission X-ray images (18.3%). The data was used to simulate the feedback for an adaptive imaging system and the ratio of the aforementioned momentum transfer regions found to be an excellent pa rameter. Investigation into the effects of formalin fixation on human breast tissue and animal tissue equivalents indicated that fixation in standard 10% buffered formalin does not alter the diffraction profiles of tissue in the mo mentum transfer regions examined, though 100% unbuffered formalin affects the profile of porcine muscle tissue (a substitute for glandular and tumourous tissue), though fat is unaffected.

Assimilation of Atmospheric InfraRed Sounder (AIRS) Profiles using WRF-Var

NASA Technical Reports Server (NTRS)

Zavodsky, Brad; Jedlovec, Gary J.; Lapenta, William

2008-01-01

The Weather Research and Forecasting (WRF) model contains a three-dimensional variational (3DVAR) assimilation system (WRF-Var), which allows a user to join data from multiple sources into one coherent analysis. WRF-Var combines observations with a background field traditionally generated using a previous model forecast through minimization of a cost function. In data sparse regions, remotely-sensed observations may be able to improve analyses and produce improved forecasts. One such source comes from the Atmospheric Infrared Sounder (AIRS), which together with the Advanced Microwave Sounding Unit (AMSU), represents one of the most advanced space-based atmospheric sounding systems. The combined AIRS/AMSU system provides radiance measurements used as input to a sophisticated retrieval scheme which has been shown to produce temperature profiles with an accuracy of 1 K over 1 km layers and humidity profiles with accuracy of 15% in 2 km layers in both clear and partly cloudy conditions. The retrieval algorithm also provides estimates of the accuracy of the retrieved values at each pressure level, allowing the user to select profiles based on the required error tolerances of the application. The purpose of this paper is to describe a procedure to optimally assimilate high-resolution AIRS profile data into a regional configuration of the Advanced Research WRF (ARW) version 2.2 using WRF-Var. The paper focuses on development of background error covariances for the regional domain and background field type using gen_be and an optimal methodology for ingesting AIRS temperature and moisture profiles as separate overland and overwater retrievals with different error characteristics in the WRF-Var. The AIRS thermodynamic profiles are obtained from the version 5.0 Earth Observing System (EOS) science team retrieval algorithm and contain information about the quality of each temperature layer. The quality indicators are used to select the highest quality temperature and moisture data for each profile location and pressure level. Analyses are run to produce quasi-real-time regional weather forecasts over the continental U.S. The preliminary assessment of the impact of the AIRS profiles will focus on intelligent use of the quality indicators, optimized tuning of the WRF-Var, and comparison of analysis soundings to radiosondes.

NATbox: a network analysis toolbox in R.

PubMed

Chavan, Shweta S; Bauer, Michael A; Scutari, Marco; Nagarajan, Radhakrishnan

2009-10-08

There has been recent interest in capturing the functional relationships (FRs) from high-throughput assays using suitable computational techniques. FRs elucidate the working of genes in concert as a system as opposed to independent entities hence may provide preliminary insights into biological pathways and signalling mechanisms. Bayesian structure learning (BSL) techniques and its extensions have been used successfully for modelling FRs from expression profiles. Such techniques are especially useful in discovering undocumented FRs, investigating non-canonical signalling mechanisms and cross-talk between pathways. The objective of the present study is to develop a graphical user interface (GUI), NATbox: Network Analysis Toolbox in the language R that houses a battery of BSL algorithms in conjunction with suitable statistical tools for modelling FRs in the form of acyclic networks from gene expression profiles and their subsequent analysis. NATbox is a menu-driven open-source GUI implemented in the R statistical language for modelling and analysis of FRs from gene expression profiles. It provides options to (i) impute missing observations in the given data (ii) model FRs and network structure from gene expression profiles using a battery of BSL algorithms and identify robust dependencies using a bootstrap procedure, (iii) present the FRs in the form of acyclic graphs for visualization and investigate its topological properties using network analysis metrics, (iv) retrieve FRs of interest from published literature. Subsequently, use these FRs as structural priors in BSL (v) enhance scalability of BSL across high-dimensional data by parallelizing the bootstrap routines. NATbox provides a menu-driven GUI for modelling and analysis of FRs from gene expression profiles. By incorporating readily available functions from existing R-packages, it minimizes redundancy and improves reproducibility, transparency and sustainability, characteristic of open-source environments. NATbox is especially suited for interdisciplinary researchers and biologists with minimal programming experience and would like to use systems biology approaches without delving into the algorithmic aspects. The GUI provides appropriate parameter recommendations for the various menu options including default parameter choices for the user. NATbox can also prove to be a useful demonstration and teaching tool in graduate and undergraduate course in systems biology. It has been tested successfully under Windows and Linux operating systems. The source code along with installation instructions and accompanying tutorial can be found at http://bioinformatics.ualr.edu/natboxWiki/index.php/Main_Page.

The viscosity and temperature dependence of 1H T1-NMRD of the Gd(H 2O) 83+ complex

NASA Astrophysics Data System (ADS)

Zhou, Xiangzhi; Westlund, Per-Olof

2005-11-01

Water proton T1-NMRD profiles of the Gd(H 2O) 83+ complex have been recorded at three temperatures and at four concentrations of glycerol. The analysis is performed using both the generalized Solomon-Bloembergen-Morgan (GSBM) theory [J. Magn. Reson. 167(2004), 147-160], and the stochastic Liouville approach (SLA). The GSBM approach uses a two processes dynamic model of the zero-field splitting (ZFS) correlation function whereas SLA uses a single process model. Both models reproduce the proton T1-NMRD profiles well. However, the model parameters extracted from the two analyses, yield different ESR X-band spectra which moreover do not reproduce the experimental ESR spectra. It is shown that the analyses of the proton T1-NMRD profiles recorded for a solution Gd(H 2O) 83+ ions are relatively insensitive to the slow modulation part of dynamic model of the ZFS interaction correlation function. The description of the electron spin system results in a very small static ZFS, while recent ESR lineshape analysis indicates that the contribution from the static ZFS is important. Analysis of proton T1-NMRD profiles of Gd(H 2O) 83+ complex do result in a description of the electron spin system but these microscopic parameters are uncertain unless they also are tested in a ESR-lineshape analysis.

PERTS: A Prototyping Environment for Real-Time Systems

NASA Technical Reports Server (NTRS)

Liu, Jane W. S.; Lin, Kwei-Jay; Liu, C. L.

1993-01-01

PERTS is a prototyping environment for real-time systems. It is being built incrementally and will contain basic building blocks of operating systems for time-critical applications, tools, and performance models for the analysis, evaluation and measurement of real-time systems and a simulation/emulation environment. It is designed to support the use and evaluation of new design approaches, experimentations with alternative system building blocks, and the analysis and performance profiling of prototype real-time systems.

Prototype demonstration of a geographic information system application for seasonal analysis of traffic data : development of seasonal factors and seasonal adjustment of roadways

DOT National Transportation Integrated Search

1999-08-15

The Traffic Survey Unit plans to establish a methodology in which it can assign each Portable Traffic Counter (PTC) station a seasonal group profile through a means of statistical and geographical analysis. An ArcView Geographic Information Systems a...

Beach Profile Analysis Systems (BPAS). Volume VI. BPAS User’s Guide: Analysis Module VOLCTR.

DTIC Science & Technology

1982-06-01

the two seawardmost points. Before computing volume changes, common bonds are established relative to the landward and seaward extent of the surveys on...bit word size, the FORTRAN- callable sort routine (interfacing with the NOS or NOSME operating system SORTMRG utility), and the utility subroutines and

Measurement of whole tire profile

NASA Astrophysics Data System (ADS)

Yang, Yongyue; Jiao, Wenguang

2010-08-01

In this paper, a precision measuring device is developed for obtaining characteristic curve of tire profile and its geometric parameters. It consists of a laser displacement measurement unit, a closed-loop precision two-dimensional coordinate table, a step motor control system and a fast data acquisition and analysis system. Based on the laser trigonometry, a data map of tire profile and coordinate values of all points can be obtained through corresponding data transformation. This device has a compact structure, a convenient control, a simple hardware circuit design and a high measurement precision. Experimental results indicate that measurement precision can meet the customer accuracy requirement of +/-0.02 mm.

A Tool for Model-Based Generation of Scenario-driven Electric Power Load Profiles

NASA Technical Reports Server (NTRS)

Rozek, Matthew L.; Donahue, Kenneth M.; Ingham, Michel D.; Kaderka, Justin D.

2015-01-01

Power consumption during all phases of spacecraft flight is of great interest to the aerospace community. As a result, significant analysis effort is exerted to understand the rates of electrical energy generation and consumption under many operational scenarios of the system. Previously, no standard tool existed for creating and maintaining a power equipment list (PEL) of spacecraft components that consume power, and no standard tool existed for generating power load profiles based on this PEL information during mission design phases. This paper presents the Scenario Power Load Analysis Tool (SPLAT) as a model-based systems engineering tool aiming to solve those problems. SPLAT is a plugin for MagicDraw (No Magic, Inc.) that aids in creating and maintaining a PEL, and also generates a power and temporal variable constraint set, in Maple language syntax, based on specified operational scenarios. The constraint set can be solved in Maple to show electric load profiles (i.e. power consumption from loads over time). SPLAT creates these load profiles from three modeled inputs: 1) a list of system components and their respective power modes, 2) a decomposition hierarchy of the system into these components, and 3) the specification of at least one scenario, which consists of temporal constraints on component power modes. In order to demonstrate how this information is represented in a system model, a notional example of a spacecraft planetary flyby is introduced. This example is also used to explain the overall functionality of SPLAT, and how this is used to generate electric power load profiles. Lastly, a cursory review of the usage of SPLAT on the Cold Atom Laboratory project is presented to show how the tool was used in an actual space hardware design application.

Safe and Efficient Support for Embeded Multi-Processors in ADA

NASA Astrophysics Data System (ADS)

Ruiz, Jose F.

2010-08-01

New software demands increasing processing power, and multi-processor platforms are spreading as the answer to achieve the required performance. Embedded real-time systems are also subject to this trend, but in the case of real-time mission-critical systems, the properties of reliability, predictability and analyzability are also paramount. The Ada 2005 language defined a subset of its tasking model, the Ravenscar profile, that provides the basis for the implementation of deterministic and time analyzable applications on top of a streamlined run-time system. This Ravenscar tasking profile, originally designed for single processors, has proven remarkably useful for modelling verifiable real-time single-processor systems. This paper proposes a simple extension to the Ravenscar profile to support multi-processor systems using a fully partitioned approach. The implementation of this scheme is simple, and it can be used to develop applications amenable to schedulability analysis.

The Strong Ring: A Basic Interest Model of Occupational Structure

ERIC Educational Resources Information Center

Armstrong, Patrick Ian; Smith, Thomas J.; Donnay, David A. C.; Rounds, James

2004-01-01

A classification system and spatial map of occupations were developed using the Basic Interest Scale profiles of 198 occupational incumbent samples (31,010 women; 32,421 men) from the Strong Interest Inventory. Profile shape was found to be similar for incumbents of both genders, allowing for an analysis of combined-gender samples. Using…

A Module for Assimilating Hyperspectral Infrared Retrieved Profiles into the Gridpoint Statistical Interpolation System for Unique Forecasting Applications

NASA Technical Reports Server (NTRS)

Berndt, Emily; Zavodsky, Bradley; Srikishen, Jayanthi; Blankenship, Clay

2015-01-01

Hyperspectral infrared sounder radiance data are assimilated into operational modeling systems however the process is computationally expensive and only approximately 1% of available data are assimilated due to data thinning as well as the fact that radiances are restricted to cloud-free fields of view. In contrast, the number of hyperspectral infrared profiles assimilated is much higher since the retrieved profiles can be assimilated in some partly cloudy scenes due to profile coupling other data, such as microwave or neural networks, as first guesses to the retrieval process. As the operational data assimilation community attempts to assimilate cloud-affected radiances, it is possible that the use of retrieved profiles might offer an alternative methodology that is less complex and more computationally efficient to solve this problem. The NASA Short-term Prediction Research and Transition (SPoRT) Center has assimilated hyperspectral infrared retrieved profiles into Weather Research and Forecasting Model (WRF) simulations using the Gridpoint Statistical Interpolation (GSI) System. Early research at SPoRT demonstrated improved initial conditions when assimilating Atmospheric Infrared Sounder (AIRS) thermodynamic profiles into WRF (using WRF-Var and assigning more appropriate error weighting to the profiles) to improve regional analysis and heavy precipitation forecasts. Successful early work has led to more recent research utilizing WRF and GSI for applications including the assimilation of AIRS profiles to improve WRF forecasts of atmospheric rivers and assimilation of AIRS, Cross-track Infrared and Microwave Sounding Suite (CrIMSS), and Infrared Atmospheric Sounding Interferometer (IASI) profiles to improve model representation of tropopause folds and associated non-convective wind events. Although more hyperspectral infrared retrieved profiles can be assimilated into model forecasts, one disadvantage is the retrieved profiles have traditionally been assigned the same error values as the rawinsonde observations when assimilated with GSI. Typically, satellitederived profile errors are larger and more difficult to quantify than traditional rawinsonde observations (especially in the boundary layer), so it is important to appropriately assign observation errors within GSI to eliminate potential spurious innovations and analysis increments that can sometimes arise when using retrieved profiles. The goal of this study is to describe modifications to the GSI source code to more appropriately assimilate hyperspectral infrared retrieved profiles and outline preliminary results that show the differences between a model simulation that assimilated the profiles as rawinsonde observations and one that assimilated the profiles in a module with the appropriate error values.

Design and characteristic analysis of shaping optics for optical trepanning

NASA Astrophysics Data System (ADS)

Zeng, D.; Latham, W. P.; Kar, A.

2005-08-01

Optical trepanning is a new laser drilling method using an annular beam. The annular beams allow numerous irradiance profiles to supply laser energy to the workpiece and thus provide more flexibility in affecting the hole quality than a traditional circular laser beam. The refractive axicon system has been designed to generating a collimated annular beam. In this article, calculations of intensity distributions produced by this refractive system are made by evaluating the Kirchhoff-Fresnel diffraction. It is shown that the refractive system is able to transform a Gaussian beam into a full Gaussian annular beam. The base angle of the axicon lens, input laser beam diameter and intensity profiles are found to be important factors for the axcion refractive system. Their effects on the annular beam profiles are analyzed based on the numerical solutions of the diffraction patterns.

Depth profiling analysis of solar wind helium collected in diamond-like carbon film from Genesis

DOE PAGES

Bajo, Ken-ichi; Olinger, Chad T.; Jurewicz, Amy J.G.; ...

2015-01-01

The distribution of solar-wind ions in Genesis mission collectors, as determined by depth profiling analysis, constrains the physics of ion solid interactions involving the solar wind. Thus, they provide an experimental basis for revealing ancient solar activities represented by solar-wind implants in natural samples. We measured the first depth profile of ⁴He in a collector; the shallow implantation (peaking at <20 nm) required us to use sputtered neutral mass spectrometry with post-photoionization by a strong field. The solar wind He fluence calculated using depth profiling is ~8.5 x 10¹⁴ cm⁻². The shape of the solar wind ⁴He depth profile ismore » consistent with TRIM simulations using the observed ⁴He velocity distribution during the Genesis mission. It is therefore likely that all solar-wind elements heavier than H are completely intact in this Genesis collector and, consequently, the solar particle energy distributions for each element can be calculated from their depth profiles. Ancient solar activities and space weathering of solar system objects could be quantitatively reproduced by solar particle implantation profiles.« less

Development of an Aircraft Approach and Departure Atmospheric Profile Generation Algorithm

NASA Technical Reports Server (NTRS)

Buck, Bill K.; Velotas, Steven G.; Rutishauser, David K. (Technical Monitor)

2004-01-01

In support of NASA Virtual Airspace Modeling and Simulation (VAMS) project, an effort was initiated to develop and test techniques for extracting meteorological data from landing and departing aircraft, and for building altitude based profiles for key meteorological parameters from these data. The generated atmospheric profiles will be used as inputs to NASA s Aircraft Vortex Spacing System (AVOLSS) Prediction Algorithm (APA) for benefits and trade analysis. A Wake Vortex Advisory System (WakeVAS) is being developed to apply weather and wake prediction and sensing technologies with procedures to reduce current wake separation criteria when safe and appropriate to increase airport operational efficiency. The purpose of this report is to document the initial theory and design of the Aircraft Approach Departure Atmospheric Profile Generation Algorithm.

Swarming behaviors in multi-agent systems with nonlinear dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Wenwu, E-mail: wenwuyu@gmail.com; School of Electrical and Computer Engineering, RMIT University, Melbourne VIC 3001; Chen, Guanrong

2013-12-15

The dynamic analysis of a continuous-time multi-agent swarm model with nonlinear profiles is investigated in this paper. It is shown that, under mild conditions, all agents in a swarm can reach cohesion within a finite time, where the upper bounds of the cohesion are derived in terms of the parameters of the swarm model. The results are then generalized by considering stochastic noise and switching between nonlinear profiles. Furthermore, swarm models with limited sensing range inducing changing communication topologies and unbounded repulsive interactions between agents are studied by switching system and nonsmooth analysis. Here, the sensing range of each agentmore » is limited and the possibility of collision among nearby agents is high. Finally, simulation results are presented to demonstrate the validity of the theoretical analysis.« less

Secretome profiles of immortalized dental follicle cells using iTRAQ-based proteomic analysis.

PubMed

Dou, Lei; Wu, Yan; Yan, Qifang; Wang, Jinhua; Zhang, Yan; Ji, Ping

2017-08-04

Secretomes produced by mesenchymal stromal cells (MSCs) were considered to be therapeutic potential. However, harvesting enough primary MSCs from tissue was time-consuming and costly, which impeded the application of MSCs secretomes. This study was to immortalize MSCs and compare the secretomes profile of immortalized and original MSCs. Human dental follicle cells (DFCs) were isolated and immortalized using pMPH86. The secretome profile of immortalized DFCs (iDFCs) was investigated and compared using iTRAQ labeling combined with mass spectrometry (MS) quantitative proteomics. The MS data was analyzed using ProteinPilotTM software, and then bioinformatic analysis of identified proteins was done. A total of 2092 secreted proteins were detected in conditioned media of iDFCs. Compared with primary DFCs, 253 differently expressed proteins were found in iDFCs secretome (142 up-regulated and 111 down-regulated). Intensive bioinformatic analysis revealed that the majority of secreted proteins were involved in cellular process, metabolic process, biological regulation, cellular component organization or biogenesis, immune system process, developmental process, response to stimulus and signaling. Proteomic profile of cell secretome wasn't largely affected after immortalization converted by this piggyBac immortalization system. The secretome of iDFCs may be a good candidate of primary DFCs for regenerative medicine.

Study on photochemical analysis system (VLES) for EUV lithography

NASA Astrophysics Data System (ADS)

Sekiguchi, A.; Kono, Y.; Kadoi, M.; Minami, Y.; Kozawa, T.; Tagawa, S.; Gustafson, D.; Blackborow, P.

2007-03-01

A system for photo-chemical analysis of EUV lithography processes has been developed. This system has consists of 3 units: (1) an exposure that uses the Z-Pinch (Energetiq Tech.) EUV Light source (DPP) to carry out a flood exposure, (2) a measurement system RDA (Litho Tech Japan) for the development rate of photo-resists, and (3) a simulation unit that utilizes PROLITH (KLA-Tencor) to calculate the resist profiles and process latitude using the measured development rate data. With this system, preliminary evaluation of the performance of EUV lithography can be performed without any lithography tool (Stepper and Scanner system) that is capable of imaging and alignment. Profiles for 32 nm line and space pattern are simulated for the EUV resist (Posi-2 resist by TOK) by using VLES that hat has sensitivity at the 13.5nm wavelength. The simulation successfully predicts the resist behavior. Thus it is confirmed that the system enables efficient evaluation of the performance of EUV lithography processes.

The design and analysis of channel transmission communication system of XCTD profiler

NASA Astrophysics Data System (ADS)

Zheng, Yu; Wang, Xiao-Rui; Jin, Xiang-Yu; Song, Guo-Min; Shang, Ying-Sheng; Li, Hong-Zhi

2016-10-01

In this paper, a channel transmission communication system of expendable conductivity-temperature-depth is established in accordance to the operation characteristics of the transmission line to more accurately assess the characteristics of deep-sea abandoned profiler channel. The wrapping inductance is eliminated to maximum extent through the wrapping pattern of the underwater spool and the overwater spool and the calculation of the wrapping diameter. The feasibility of the proposed channel transmission communication system is verified through theoretical analysis and practical measurement of the transmission signal error rate in the amplitude shift keying (ASK) modulation. The proposed design provides a new research method for the channel assessment of complex abandoned measuring instrument and an important experiment evidence for the rapid development of the deep-sea abandoned measuring instrument.

The design and analysis of channel transmission communication system of XCTD profiler.

PubMed

Zheng, Yu; Wang, Xiao-Rui; Jin, Xiang-Yu; Song, Guo-Min; Shang, Ying-Sheng; Li, Hong-Zhi

2016-10-01

In this paper, a channel transmission communication system of expendable conductivity-temperature-depth is established in accordance to the operation characteristics of the transmission line to more accurately assess the characteristics of deep-sea abandoned profiler channel. The wrapping inductance is eliminated to maximum extent through the wrapping pattern of the underwater spool and the overwater spool and the calculation of the wrapping diameter. The feasibility of the proposed channel transmission communication system is verified through theoretical analysis and practical measurement of the transmission signal error rate in the amplitude shift keying (ASK) modulation. The proposed design provides a new research method for the channel assessment of complex abandoned measuring instrument and an important experiment evidence for the rapid development of the deep-sea abandoned measuring instrument.

High-throughput STR analysis for DNA database using direct PCR.

PubMed

Sim, Jeong Eun; Park, Su Jeong; Lee, Han Chul; Kim, Se-Yong; Kim, Jong Yeol; Lee, Seung Hwan

2013-07-01

Since the Korean criminal DNA database was launched in 2010, we have focused on establishing an automated DNA database profiling system that analyzes short tandem repeat loci in a high-throughput and cost-effective manner. We established a DNA database profiling system without DNA purification using a direct PCR buffer system. The quality of direct PCR procedures was compared with that of conventional PCR system under their respective optimized conditions. The results revealed not only perfect concordance but also an excellent PCR success rate, good electropherogram quality, and an optimal intra/inter-loci peak height ratio. In particular, the proportion of DNA extraction required due to direct PCR failure could be minimized to <3%. In conclusion, the newly developed direct PCR system can be adopted for automated DNA database profiling systems to replace or supplement conventional PCR system in a time- and cost-saving manner. © 2013 American Academy of Forensic Sciences Published 2013. This article is a U.S. Government work and is in the public domain in the U.S.A.

Development of Long-Pulse Heating and Current Drive Actuators and Operational Techniques Compatible with a High-Z Divertor and First Wall

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Guiding

Accurate measurement of the edge electron density profile is essential to optimizing antenna coupling and assessment of impurity contamination in studying long-pulse plasma heating and current drive in fusion devices. Measurement of the edge density profile has been demonstrated on the US fusion devices such as C-Mod, DIII-D, and TFTR amongst many devices, and has been used for RF loading and impurity modeling calculations for many years. University of Science and Technology of China (USTC) has recently installed a density profile reflectometer system on the EAST fusion device at the Institute of Plasma Physics, Chinese Academy of Sciences in Chinamore » based on the University of California Los Angeles (UCLA)-designed reflectometer system on the DIII-D fusion device at General Atomics Company in San Diego, California. UCLA has been working with USTC to optimize the existing microwave antenna, waveguide system, microwave electronics, and data analysis to produce reliable edge density profiles. During the past budget year, progress has been made in all three major areas: effort to achieve reliable system operations under various EAST operational conditions, effort to optimize system performance, and effort to provide quality density profiles into EAST’s database routinely.« less

Effects of Pump Pulsation on Hydrodynamic Properties and Dissolution Profiles in Flow-Through Dissolution Systems (USP 4).

PubMed

Yoshida, Hiroyuki; Kuwana, Akemi; Shibata, Hiroko; Izutsu, Ken-Ichi; Goda, Yukihiro

2016-06-01

To clarify the effects of pump pulsation and flow-through cell (FTC) dissolution system settings on the hydrodynamic properties and dissolution profiles of model formulations. Two FTC systems with different cell temperature control mechanisms were used. Particle image velocimetry (PIV) was used to analyze the hydrodynamic properties of test solutions in the flow-through dissolution test cell. Two pulsation pumps (semi-sine, full-sine) and a non-pulsatile pump were used to study the effects of varied flows on the dissolution profiles of United States Pharmacopeia standard tablets. PIV analysis showed periodic changes in the aligned upward fluid flow throughout the dissolution cell that was designed to reduce the temperature gradient during pump pulsation (0.5 s/pulse). The maximum instantaneous flow from the semi-sine pump was higher than that of the full-sine pump under all conditions. The flow from the semi-sine wave pump showed faster dissolution of salicylic acid and prednisone tablets than those from other pumps. The semi-sine wave pump flow showed similar dissolution profiles in the two FTC systems. Variations in instantaneous fluid flow caused by pump pulsation that meets the requirements of pharmacopoeias are a factor that affects the dissolution profiles of tablets in FTC systems.

Application of kernel principal component analysis and computational machine learning to exploration of metabolites strongly associated with diet.

PubMed

Shiokawa, Yuka; Date, Yasuhiro; Kikuchi, Jun

2018-02-21

Computer-based technological innovation provides advancements in sophisticated and diverse analytical instruments, enabling massive amounts of data collection with relative ease. This is accompanied by a fast-growing demand for technological progress in data mining methods for analysis of big data derived from chemical and biological systems. From this perspective, use of a general "linear" multivariate analysis alone limits interpretations due to "non-linear" variations in metabolic data from living organisms. Here we describe a kernel principal component analysis (KPCA)-incorporated analytical approach for extracting useful information from metabolic profiling data. To overcome the limitation of important variable (metabolite) determinations, we incorporated a random forest conditional variable importance measure into our KPCA-based analytical approach to demonstrate the relative importance of metabolites. Using a market basket analysis, hippurate, the most important variable detected in the importance measure, was associated with high levels of some vitamins and minerals present in foods eaten the previous day, suggesting a relationship between increased hippurate and intake of a wide variety of vegetables and fruits. Therefore, the KPCA-incorporated analytical approach described herein enabled us to capture input-output responses, and should be useful not only for metabolic profiling but also for profiling in other areas of biological and environmental systems.

The Israel DNA database--the establishment of a rapid, semi-automated analysis system.

PubMed

Zamir, Ashira; Dell'Ariccia-Carmon, Aviva; Zaken, Neomi; Oz, Carla

2012-03-01

The Israel Police DNA database, also known as IPDIS (Israel Police DNA Index System), has been operating since February 2007. During that time more than 135,000 reference samples have been uploaded and more than 2000 hits reported. We have developed an effective semi-automated system that includes two automated punchers, three liquid handler robots and four genetic analyzers. An inhouse LIMS program enables full tracking of every sample through the entire process of registration, pre-PCR handling, analysis of profiles, uploading to the database, hit reports and ultimately storage. The LIMS is also responsible for the future tracking of samples and their profiles to be expunged from the database according to the Israeli DNA legislation. The database is administered by an in-house developed software program, where reference and evidentiary profiles are uploaded, stored, searched and matched. The DNA database has proven to be an effective investigative tool which has gained the confidence of the Israeli public and on which the Israel National Police force has grown to rely. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Dislocation structure in textured zirconium tensile-deformed along rolling and transverse directions determined by X-ray diffraction line profile analysis

NASA Astrophysics Data System (ADS)

Fan, Zhijian; Jóni, Bertalan; Xie, Lei; Ribárik, Gábor; Ungár, Tamás

2018-04-01

Specimens of cold-rolled zirconium were tensile-deformed along the rolling (RD) and the transverse (TD) directions. The stress-strain curves revealed a strong texture dependence. High resolution X-ray line profile analysis was used to determine the prevailing active slip-systems in the specimens with different textures. The reflections in the X-ray diffraction patterns were separated into two groups. One group corresponds to the major and the other group to the random texture component, respectively. The dislocation densities, the subgrain size and the prevailing active slip-systems were evaluated by using the convolutional multiple whole profile (CMWP) procedure. These microstructure parameters were evaluated separately in the two groups of reflections corresponding to the two different texture components. Significant differences were found in both, the evolution of dislocation densities and the development of the fractions of and type slip systems in the RD and TD specimens during tensile deformation. The differences between the RD and TD stress-strain curves are discussed in terms of the differences of the microstructure evolution.

Cancer systems biology in the genome sequencing era: part 1, dissecting and modeling of tumor clones and their networks.

PubMed

Wang, Edwin; Zou, Jinfeng; Zaman, Naif; Beitel, Lenore K; Trifiro, Mark; Paliouras, Miltiadis

2013-08-01

Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has been viewed as a whole entity in cancer functional studies. With the advances of genome sequencing and computational analysis, we are able to quantify and computationally dissect clones from tumors, and then conduct clone-based analysis. Emerging technologies such as single-cell genome sequencing and RNA-Seq could profile tumor clones. Thus, we should reconsider how to conduct cancer systems biology studies in the genome sequencing era. We will outline new directions for conducting cancer systems biology by considering that genome sequencing technology can be used for dissecting, quantifying and genetically characterizing clones from tumors. Topics discussed in Part 1 of this review include computationally quantifying of tumor subpopulations; clone-based network modeling, cancer hallmark-based networks and their high-order rewiring principles and the principles of cell survival networks of fast-growing clones. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

Mesoscale kinematics derived from X-band Doppler radar observations of convective versus stratiform precipitation and comparison with GPS radiosonde profiles

NASA Astrophysics Data System (ADS)

Deshpande, Sachin M.; Dhangar, N.; Das, S. K.; Kalapureddy, M. C. R.; Chakravarty, K.; Sonbawne, S.; Konwar, M.

2015-11-01

Single Doppler analysis techniques known as velocity azimuth display (VAD) and volume velocity processing (VVP) are used to analyze kinematics of mesoscale flow such as horizontal wind and divergence using X-band Doppler weather radar observations, for selected cases of convective, stratiform, and shallow cloud systems near tropical Indian sites Pune (18.58°N, 73.92°E, above sea level (asl) 560 m) and Mandhardev (18.51°N, 73.85°E, asl 1297 m). The vertical profiles of horizontal wind estimated from radar VVP/VAD methods agree well with GPS radiosonde profiles, with the low-level jet at about 1.5 km during monsoon season well depicted in both. The vertical structure and temporal variability of divergence and reflectivity profiles are indicative of the dynamical and microphysical characteristics of shallow convective, deep convective, and stratiform cloud systems. In shallow convective systems, vertical development of reflectivity profiles is limited below 5 km. In deep convective systems, reflectivity values as large as 55 dBZ were observed above freezing level. The stratiform system shows the presence of a reflectivity bright band (~35 dBZ) near the melting level. The diagnosed vertical profiles of divergence in convective and stratiform systems are distinct. In shallow convective conditions, convergence was seen below 4 km with divergence above. Low-level convergence and upper level divergence are observed in deep convective profiles, while stratiform precipitation has midlevel convergence present between lower level and upper level divergence. The divergence profiles in stratiform precipitation exhibit intense shallow layers of "melting convergence" at 0°C level, near 4.5 km altitude, with a steep gradient on the both sides of the peak. The level of nondivergence in stratiform situations is lower than that in convective situations. These observed vertical structures of divergence are largely indicative of latent heating profiles in the atmosphere, an important ingredient of monsoon dynamics.

Computer simulation of schlieren images of rotationally symmetric plasma systems: a simple method.

PubMed

Noll, R; Haas, C R; Weikl, B; Herziger, G

1986-03-01

Schlieren techniques are commonly used methods for quantitative analysis of cylindrical or spherical index of refraction profiles. Many schlieren objects, however, are characterized by more complex geometries, so we have investigated the more general case of noncylindrical, rotationally symmetric distributions of index of refraction n(r,z). Assuming straight ray paths in the schlieren object we have calculated 2-D beam deviation profiles. It is shown that experimental schlieren images of the noncylindrical plasma generated by a plasma focus device can be simulated with these deviation profiles. The computer simulation allows a quantitative analysis of these schlieren images, which yields, for example, the plasma parameters, electron density, and electron density gradients.

Rapid Identification of Laboratory Contamination with Mycobacterium tuberculosis Using Variable Number Tandem Repeat Analysis

PubMed Central

Gascoyne-Binzi, Deborah M.; Barlow, Rachael E. L.; Frothingham, Richard; Robinson, Grant; Collyns, Timothy A.; Gelletlie, Ruth; Hawkey, Peter M.

2001-01-01

Compared with solid media, broth-based mycobacterial culture systems have increased sensitivity but also have higher false-positive rates due to cross-contamination. Systematic strain typing is rarely undertaken because the techniques are technically demanding and the data are difficult to organize. Variable number tandem repeat (VNTR) analysis by PCR is rapid and reproducible. The digital profile is easily manipulated in a database. We undertook a retrospective study of Mycobacterium tuberculosis isolates collected over an 18-month period following the introduction of the BACTEC MGIT 960 system. VNTR allele profiles were determined with early positive broth cultures and entered into a database with the specimen processing date and other specimen data. We found 36 distinct VNTR profiles in cultures from 144 patients. Three common VNTR profiles accounted for 45% of true-positive cases. By combining VNTR results with specimen data, we identified nine cross-contamination incidents, six of which were previously unsuspected. These nine incidents resulted in 34 false-positive cultures for 29 patients. False-positive cultures were identified for three patients who had previously been culture positive for tuberculosis and were receiving treatment. Identification of cross-contamination incidents requires careful documentation of specimen data and good communication between clinical and laboratory staff. Automated broth culture systems should be supplemented with molecular analysis to identify cross-contamination events. VNTR analysis is reproducible and provides timely results when applied to early positive broth cultures. This method should ensure that patients are not placed on unnecessary tuberculosis therapy or that cases are not falsely identified as treatment failures. In addition, areas where existing procedures may be improved can be identified. PMID:11136751

Failure mode analysis for lime/limestone FGD system. Volume III. Plant profiles. Part 1 of 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kenney, S.M.; Rosenberg, H.S.; Nilsson, L.I.O.

1984-08-01

This volume contains plant profiles for: Petersburg 3; Hawthorn 3, 4; La Cygne 1; Jeffry 1, 2; Lawrence 4, 5; Green River 1-3; Cane Run 4, 5; Mill Creek 1, 3; Paddy's Run 6; Clay Boswell 4; Milton R. Young 2; Pleasants 1, 2; and Colstrip 1, 2. (DLC)

In vivo Assessment and Potential Diagnosis of Xenobiotics that Perturb the Thyroid Pathway: Proteomic Analysis of Xenopus laevis Brain Tissue following Exposure to Model T4 Inhibitors

EPA Science Inventory

As part of a multi-endpoint systems approach to develop comprehensive methods for assessing endocrine stressors in vertebrates, differential protein profiling was used to investigate expression profiles in the brain of an amphibian model (Xenopus laevis) following in vivo exposur...

A dynamical study of Galactic globular clusters under different relaxation conditions

NASA Astrophysics Data System (ADS)

Zocchi, A.; Bertin, G.; Varri, A. L.

2012-03-01

Aims: We perform a systematic combined photometric and kinematic analysis of a sample of globular clusters under different relaxation conditions, based on their core relaxation time (as listed in available catalogs), by means of two well-known families of spherical stellar dynamical models. Systems characterized by shorter relaxation time scales are expected to be better described by isotropic King models, while less relaxed systems might be interpreted by means of non-truncated, radially-biased anisotropic f(ν) models, originally designed to represent stellar systems produced by a violent relaxation formation process and applied here for the first time to the study of globular clusters. Methods: The comparison between dynamical models and observations is performed by fitting simultaneously surface brightness and velocity dispersion profiles. For each globular cluster, the best-fit model in each family is identified, along with a full error analysis on the relevant parameters. Detailed structural properties and mass-to-light ratios are also explicitly derived. Results: We find that King models usually offer a good representation of the observed photometric profiles, but often lead to less satisfactory fits to the kinematic profiles, independently of the relaxation condition of the systems. For some less relaxed clusters, f(ν) models provide a good description of both observed profiles. Some derived structural characteristics, such as the total mass or the half-mass radius, turn out to be significantly model-dependent. The analysis confirms that, to answer some important dynamical questions that bear on the formation and evolution of globular clusters, it would be highly desirable to acquire larger numbers of accurate kinematic data-points, well distributed over the cluster field. Appendices are available in electronic form at http://www.aanda.org

Data base management system analysis and performance testing with respect to NASA requirements

NASA Technical Reports Server (NTRS)

Martin, E. A.; Sylto, R. V.; Gough, T. L.; Huston, H. A.; Morone, J. J.

1981-01-01

Several candidate Data Base Management Systems (DBM's) that could support the NASA End-to-End Data System's Integrated Data Base Management System (IDBMS) Project, later rescoped and renamed the Packet Management System (PMS) were evaluated. The candidate DBMS systems which had to run on the Digital Equipment Corporation VAX 11/780 computer system were ORACLE, SEED and RIM. Oracle and RIM are both based on the relational data base model while SEED employs a CODASYL network approach. A single data base application which managed stratospheric temperature profiles was studied. The primary reasons for using this application were an insufficient volume of available PMS-like data, a mandate to use actual rather than simulated data, and the abundance of available temperature profile data.

Analytical Solution to the Pneumatic Transient Rod System at ACRR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fehr, Brandon Michael

2016-01-08

The ACRR pulse is pneumatically driven by nitrogen in a system of pipes, valves and hoses up to the connection of the pneumatic system and mechanical linkages of the transient rod (TR). The main components of the TR pneumatic system are the regulator, accumulator, solenoid valve and piston-cylinder assembly. The purpose of this analysis is to analyze the flow of nitrogen through the TR pneumatic system in order to develop a motion profile of the piston during the pulse and be able to predict the pressure distributions inside both the cylinder and accumulators. The predicted pressure distributions will be validatedmore » against pressure transducer data, while the motion profile will be compared to proximity switch data. By predicting the motion of the piston, pulse timing will be determined and provided to the engineers/operators for verification. The motion profile will provide an acceleration distribution to be used in Razorback to more accurately predict reactivity insertion into the system.« less

THz optical design considerations and optimization for medical imaging applications

NASA Astrophysics Data System (ADS)

Sung, Shijun; Garritano, James; Bajwa, Neha; Nowroozi, Bryan; Llombart, Nuria; Grundfest, Warren; Taylor, Zachary D.

2014-09-01

THz imaging system design will play an important role making possible imaging of targets with arbitrary properties and geometries. This study discusses design consideration and imaging performance optimization techniques in THz quasioptical imaging system optics. Analysis of field and polarization distortion by off-axis parabolic (OAP) mirrors in THz imaging optics shows how distortions are carried in a series of mirrors while guiding the THz beam. While distortions of the beam profile by individual mirrors are not significant, these effects are compounded by a series of mirrors in antisymmetric orientation. It is shown that symmetric orientation of the OAP mirror effectively cancels this distortion to recover the original beam profile. Additionally, symmetric orientation can correct for some geometrical off-focusing due to misalignment. We also demonstrate an alternative method to test for overall system optics alignment by investigating the imaging performance of the tilted target plane. Asymmetric signal profile as a function of the target plane's tilt angle indicates when one or more imaging components are misaligned, giving a preferred tilt direction. Such analysis can offer additional insight into often elusive source device misalignment at an integrated system. Imaging plane tilting characteristics are representative of a 3-D modulation transfer function of the imaging system. A symmetric tilted plane is preferred to optimize imaging performance.

Improved Impact of Atmospheric Infrared Sounder (AIRS) Radiance Assimilation in Numerical Weather Prediction

NASA Technical Reports Server (NTRS)

Zavodsky, Bradley; Chou, Shih-Hung; Jedlovec, Gary

2012-01-01

Improvements to global and regional numerical weather prediction (NWP) have been demonstrated through assimilation of data from NASA s Atmospheric Infrared Sounder (AIRS). Current operational data assimilation systems use AIRS radiances, but impact on regional forecasts has been much smaller than for global forecasts. Retrieved profiles from AIRS contain much of the information that is contained in the radiances and may be able to reveal reasons for this reduced impact. Assimilating AIRS retrieved profiles in an identical analysis configuration to the radiances, tracking the quantity and quality of the assimilated data in each technique, and examining analysis increments and forecast impact from each data type can yield clues as to the reasons for the reduced impact. By doing this with regional scale models individual synoptic features (and the impact of AIRS on these features) can be more easily tracked. This project examines the assimilation of hyperspectral sounder data used in operational numerical weather prediction by comparing operational techniques used for AIRS radiances and research techniques used for AIRS retrieved profiles. Parallel versions of a configuration of the Weather Research and Forecasting (WRF) model with Gridpoint Statistical Interpolation (GSI) that mimics the analysis methodology, domain, and observational datasets for the regional North American Mesoscale (NAM) model run at the National Centers for Environmental Prediction (NCEP)/Environmental Modeling Center (EMC) are run to examine the impact of each type of AIRS data set. The first configuration will assimilate the AIRS radiance data along with other conventional and satellite data using techniques implemented within the operational system; the second configuration will assimilate AIRS retrieved profiles instead of AIRS radiances in the same manner. Preliminary results of this study will be presented and focus on the analysis impact of the radiances and profiles for selected cases.

Differentiation of Volatile Profiles from Stockpiled Almonds at Varying Relative Humidity Levels Using Benchtop and Portable GC-MS.

PubMed

Beck, John J; Willett, Denis S; Gee, Wai S; Mahoney, Noreen E; Higbee, Bradley S

2016-12-14

Contamination by aflatoxin, a toxic metabolite produced by Aspergillus fungi ubiquitous in California almond and pistachio orchards, results in millions of dollars of lost product annually. Current detection of aflatoxin relies on destructive, expensive, and time-intensive laboratory-based methods. To explore an alternative method for the detection of general fungal growth, volatile emission profiles of almonds at varying humidities were sampled using both static SPME and dynamic needle-trap SPE followed by benchtop and portable GC-MS analysis. Despite the portable SPE/GC-MS system detecting fewer volatiles than the benchtop system, both systems resolved humidity treatments and identified potential fungal biomarkers at extremely low water activity levels. This ability to resolve humidity levels suggests that volatile profiles from germinating fungal spores could be used to create an early warning, nondestructive, portable detection system of fungal growth.

Comparison of three officinal species of Callicarpa based on a biochemome profiling strategy with UHPLC-IT-MS and chemometrics analysis.

PubMed

Chen, Meng-Lu; Chang, Wen-Qi; Zhou, Jian-Liang; Yin, Ying-Hao; Xia, Wen-Rui; Liu, Jian-Qun; Liu, Li-Fang; Xin, Gui-Zhong

2017-10-25

Traditional Chinese medicine (TCM) materials with closely related species are frequently fungible in clinical use. Therefore, holistic comparison of the composition in bioactive compounds is essential to evaluate whether they are equivalent in efficacy. Taking three officinal species of Callicarpa as a case, we proposed and validated a standardized strategy for the discrimination of closely related TCM materials, which focused on the extraction, profiling and multivariate statistical analysis of their biochemome. Firstly, serial liquid-liquid extractions were utilized to prepare different batches of Callicarpa biochemome, and the preparation yields were utilized for the normalization of sampling quantity prior to UHPLC-IT-MS analysis. Secondly, 34 compounds, including 19 phenylethanoid glycosides, 10 flavonoids and 5 terpenoids, were identified based on an untargeted UHPLC-IT-MS method. Thirdly, method validation of linearity, precision and stability showed that the UHPLC-IT-MS system was qualified (R 2 >0.995, RSD<15%) for subsequent biochemome profiling. After PCA and PLS-DA analysis, 30 marker compounds were screened and demonstrated to be of good predictability using genetic algorithm optimized support vector machines. Finally, a heatmap visualization was employed for clarifying the distribution of marker compounds, which could be helpful to determine whether the three Callicarpa species are, in fact, equivalent substitutes. This study provides a standardized biochemome profiling strategy for systemic comparison analysis of closely related TCM materials, which shows promising perspectives in tracking the supply chain of pharmaceutical suppliers. Copyright © 2017 Elsevier B.V. All rights reserved.

Towards a typology of business process management professionals: identifying patterns of competences through latent semantic analysis

NASA Astrophysics Data System (ADS)

Müller, Oliver; Schmiedel, Theresa; Gorbacheva, Elena; vom Brocke, Jan

2016-01-01

While researchers have analysed the organisational competences that are required for successful Business Process Management (BPM) initiatives, individual BPM competences have not yet been studied in detail. In this study, latent semantic analysis is used to examine a collection of 1507 BPM-related job advertisements in order to develop a typology of BPM professionals. This empirical analysis reveals distinct ideal types and profiles of BPM professionals on several levels of abstraction. A closer look at these ideal types and profiles confirms that BPM is a boundary-spanning field that requires interdisciplinary sets of competence that range from technical competences to business and systems competences. Based on the study's findings, it is posited that individual and organisational alignment with the identified ideal types and profiles is likely to result in high employability and organisational BPM success.

Plant MetGenMAP: an integrative analysis system for plant systems biology

USDA-ARS?s Scientific Manuscript database

We have developed a web-based system, Plant MetGenMAP, which can identify significantly altered biochemical pathways and highly affected biological processes, predict functional roles of pathway genes, and potential pathway-related regulatory motifs from transcript and metabolite profile datasets. P...

Bioresearch module design definition and space shuttle vehicle integration study. Volume 2: Appendices

NASA Technical Reports Server (NTRS)

Lang, A. L., Jr.

1971-01-01

Data presented in the appendices covers: (1) summary description of baseline power system; (2) revised thermal profile analysis; (3) design analysis of television monitor; (4) bioresearch module ground station support evaluation; (5) variable spin control analysis; and (6) bioresearch modules and work flow.

An Accelerated Analytical Process for the Development of STR Profiles for Casework Samples.

PubMed

Laurin, Nancy; Frégeau, Chantal J

2015-07-01

Significant efforts are being devoted to the development of methods enabling rapid generation of short tandem repeat (STR) profiles in order to reduce turnaround times for the delivery of human identification results from biological evidence. Some of the proposed solutions are still costly and low throughput. This study describes the optimization of an analytical process enabling the generation of complete STR profiles (single-source or mixed profiles) for human identification in approximately 5 h. This accelerated process uses currently available reagents and standard laboratory equipment. It includes a 30-min lysis step, a 27-min DNA extraction using the Promega Maxwell(®) 16 System, DNA quantification in <1 h using the Qiagen Investigator(®) Quantiplex HYres kit, fast amplification (<26 min) of the loci included in AmpFℓSTR(®) Identifiler(®), and analysis of the profiles on the 3500-series Genetic Analyzer. This combination of fast individual steps produces high-quality profiling results and offers a cost-effective alternative approach to rapid DNA analysis. © 2015 American Academy of Forensic Sciences.

Space Station on-orbit solar array loads during assembly

NASA Astrophysics Data System (ADS)

Ghofranian, S.; Fujii, E.; Larson, C. R.

This paper is concerned with the closed-loop dynamic analysis of on-orbit maneuvers when the Space Shuttle is fully mated to the Space Station Freedom. A flexible model of the Space Station in the form of component modes is attached to a rigid orbiter and on-orbit maneuvers are performed using the Shuttle Primary Reaction Control System jets. The traditional approach for this type of problems is to perform an open-loop analysis to determine the attitude control system jet profiles based on rigid vehicles and apply the resulting profile to a flexible Space Station. In this study a closed-loop Structure/Control model was developed in the Dynamic Analysis and Design System (DADS) program and the solar array loads were determined for single axis maneuvers with various delay times between jet firings. It is shown that the Digital Auto Pilot jet selection is affected by Space Station flexibility. It is also shown that for obtaining solar array loads the effect of high frequency modes cannot be ignored.

Doppler Imaging with FUSE: The Partially Eclipsing Binary VW Cep

NASA Technical Reports Server (NTRS)

Sonneborn, George (Technical Monitor); Brickhouse, Nancy

2003-01-01

This report covers the FUSE Guest Observer program. This project involves the study of emission line profiles for the partially eclipsing, rapidly rotating binary system VW Cep. Active regions on the surface of the star(s) produce observable line shifts as the stars move with respect to the observer. By studying the time-dependence of the line profile changes and centroid shifts, one can determine the location of the activity. FUSE spectra were obtained by the P.I. 27 Sept 2002 and data reduction is in progress. Since we are interested in line profile analysis, we are now investigating the wavelength scale calibration in some detail. We have also obtained and are analyzing Chandra data in order to compare the X-ray velocities with the FUV velocities. A complementary project comparing X-ray and Far UltraViolet (FUV) emission for the similar system 44i Boo is also underway. Postdoctoral fellow Ronnie Hoogerwerf has joined the investigation team and will perform the data analysis, once the calibration is optimized.

Strong Updraft Feature Associated with Hurricane Earl During Landfall

NASA Technical Reports Server (NTRS)

Roberts, Barry C.; Knupp, Kevin R.

2004-01-01

On 2-3 September 1998 hurricane Earl made landfall along the Gulf of Mexico coast, east of Panama City, FL. The University of Alabama in Huntsville Mobile Integrated Profiling System (MIPS) was located at the airport in Tallahassee, FL and made measurements of Earl with a 915 MHz Doppler wind profiler as the system moved across the Florida panhandle. As the center of Earl approached MIPS, a particularly strong updraft feature, having a magnitude of approx. 15 m/s within the lowest 3.0 km above ground level was associated with a rain band. An analysis of the changes hurricane Earl underwent as it made landfall are presented. Measurements used include surface thermodynamic and pressure observations, lightning data, National Weather Service Doppler Weather Surveillance Radar (WSR-88D) data, and Geostationary Earth Orbiting Satellite (GOES) data. Then an analysis focusing on the boundary layer properties and the updraft feature's depth, intensity and duration as measured by the MIPS 915 MHz Doppler wind profiler are presented.

Spatial distribution of marine crenarchaeota group I in the vicinity of deep-sea hydrothermal systems.

PubMed

Takai, Ken; Oida, Hanako; Suzuki, Yohey; Hirayama, Hisako; Nakagawa, Satoshi; Nunoura, Takuro; Inagaki, Fumio; Nealson, Kenneth H; Horikoshi, Koki

2004-04-01

Distribution profiles of marine crenarchaeota group I in the vicinity of deep-sea hydrothermal systems were mapped with culture-independent molecular techniques. Planktonic samples were obtained from the waters surrounding two geographically and geologically distinct hydrothermal systems, and the abundance of marine crenarchaeota group I was examined by 16S ribosomal DNA clone analysis, quantitative PCR, and whole-cell fluorescence in situ hybridization. A much higher proportion of marine crenarchaeota group I within the microbial community was detected in deep-sea hydrothermal environments than in normal deep and surface seawaters. The highest proportion was always obtained from the ambient seawater adjacent to hydrothermal emissions and chimneys but not from the hydrothermal plumes. These profiles were markedly different from the profiles of epsilon-Proteobacteria, which are abundant in the low temperatures of deep-sea hydrothermal environments.

Morphometric synaptology of a whole neuron profile using a semiautomatic interactive computer system.

PubMed

Saito, K; Niki, K

1983-07-01

We propose a new method of dealing with morphometric synaptology that processes all synapses and boutons around the HRP marked neuron on a large composite electron micrograph, rather than a qualitative or a piecemeal quantitative study of a particular synapse and/or bouton that is not positioned on the surface of the neuron. This approach requires the development of both neuroanatomical procedures, by which a specific whole neuronal profile is identified, and valuable specialized tools, which support the collection and analysis of a great volume of morphometric data from composite electron micrographs, in order to reduce the burden of the morphologist. The present report is also concerned with the total and reliable semi-automatic interactive computer system for gathering and analyzing morphometric data that has been under development in our laboratory. A morphologist performs the pattern recognition portion by using a large-sized tablet digitizer and a menu-sheet command, and the system registers the various morphometric values of many different neurons and performs statistical analysis. Some examples of morphometric measurements and analysis show the usefulness and efficiency of the proposed system and method.

Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons.

PubMed

Kim, Eun Hye; Lee, Hwan Young; Yang, In Seok; Jung, Sang-Eun; Yang, Woo Ick; Shin, Kyoung-Jin

2016-05-01

The next-generation sequencing (NGS) method has been utilized to analyze short tandem repeat (STR) markers, which are routinely used for human identification purposes in the forensic field. Some researchers have demonstrated the successful application of the NGS system to STR typing, suggesting that NGS technology may be an alternative or additional method to overcome limitations of capillary electrophoresis (CE)-based STR profiling. However, there has been no available multiplex PCR system that is optimized for NGS analysis of forensic STR markers. Thus, we constructed a multiplex PCR system for the NGS analysis of 18 markers (13CODIS STRs, D2S1338, D19S433, Penta D, Penta E and amelogenin) by designing amplicons in the size range of 77-210 base pairs. Then, PCR products were generated from two single-sources, mixed samples and artificially degraded DNA samples using a multiplex PCR system, and were prepared for sequencing on the MiSeq system through construction of a subsequent barcoded library. By performing NGS and analyzing the data, we confirmed that the resultant STR genotypes were consistent with those of CE-based typing. Moreover, sequence variations were detected in targeted STR regions. Through the use of small-sized amplicons, the developed multiplex PCR system enables researchers to obtain successful STR profiles even from artificially degraded DNA as well as STR loci which are analyzed with large-sized amplicons in the CE-based commercial kits. In addition, successful profiles can be obtained from mixtures up to a 1:19 ratio. Consequently, the developed multiplex PCR system, which produces small size amplicons, can be successfully applied to STR NGS analysis of forensic casework samples such as mixtures and degraded DNA samples. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Analysis of tracheid development in suppressed-growth Ponderosa Pine using the FPL ring profiler

Treesearch

C. Tim Scott; David W. Vahey

2012-01-01

The Ring Profiler was developed to examine the cross-sectional morphology of wood tracheids in a 12.5-mm core sample. The instrument integrates a specially designed staging apparatus with an optical imaging system to obtain high-contrast, high-resolution images containing about 200-500 tracheids. These images are further enhanced and analyzed to extract tracheid cross-...

Integrated analysis of copy number alteration and RNA expression profiles of cancer using a high-resolution whole-genome oligonucleotide array.

PubMed

Jung, Seung-Hyun; Shin, Seung-Hun; Yim, Seon-Hee; Choi, Hye-Sun; Lee, Sug-Hyung; Chung, Yeun-Jun

2009-07-31

Recently, microarray-based comparative genomic hybridization (array-CGH) has emerged as a very efficient technology with higher resolution for the genome-wide identification of copy number alterations (CNA). Although CNAs are thought to affect gene expression, there is no platform currently available for the integrated CNA-expression analysis. To achieve high-resolution copy number analysis integrated with expression profiles, we established human 30k oligoarray-based genome-wide copy number analysis system and explored the applicability of this system for integrated genome and transcriptome analysis using MDA-MB-231 cell line. We compared the CNAs detected by the oligoarray with those detected by the 3k BAC array for validation. The oligoarray identified the single copy difference more accurately and sensitively than the BAC array. Seventeen CNAs detected by both platforms in MDA-MB-231 such as gains of 5p15.33-13.1, 8q11.22-8q21.13, 17p11.2, and losses of 1p32.3, 8p23.3-8p11.21, and 9p21 were consistently identified in previous studies on breast cancer. There were 122 other small CNAs (mean size 1.79 mb) that were detected by oligoarray only, not by BAC-array. We performed genomic qPCR targeting 7 CNA regions, detected by oligoarray only, and one non-CNA region to validate the oligoarray CNA detection. All qPCR results were consistent with the oligoarray-CGH results. When we explored the possibility of combined interpretation of both DNA copy number and RNA expression profiles, mean DNA copy number and RNA expression levels showed a significant correlation. In conclusion, this 30k oligoarray-CGH system can be a reasonable choice for analyzing whole genome CNAs and RNA expression profiles at a lower cost.

Methods, applications and concepts of metabolite profiling: primary metabolism.

PubMed

Steinhauser, Dirk; Kopka, Joachim

2007-01-01

In the 1990s the concept of a comprehensive analysis of the metabolic complement in biological systems, termed metabolomics or alternately metabonomics, was established as the last of four cornerstones for phenotypic studies in the post-genomic era. With genomic, transcriptomic, and proteomic technologies in place and metabolomic phenotyping under rapid development all necessary tools appear to be available today for a fully functional assessment of biological phenomena at all major system levels of life. This chapter attempts to describe and discuss crucial steps of establishing and maintaining a gas chromatography/electron impact ionization/ mass spectrometry (GC-EI-MS)-based metabolite profiling platform. GC-EI-MS can be perceived as the first and exemplary profiling technology aimed at simultaneous and non-biased analysis of primary metabolites from biological samples. The potential and constraints of this profiling technology are among the best understood. Most problems are solved as well as pitfalls identified. Thus GC-EI-MS serves as an ideal example for students and scientists who intend to enter the field of metabolomics. This chapter will be biased towards GC-EI-MS analyses but aims at discussing general topics, such as experimental design, metabolite identification, quantification and data mining.

Crack surface roughness in three-dimensional random fuse networks

NASA Astrophysics Data System (ADS)

Nukala, Phani Kumar V. V.; Zapperi, Stefano; Šimunović, Srđan

2006-08-01

Using large system sizes with extensive statistical sampling, we analyze the scaling properties of crack roughness and damage profiles in the three-dimensional random fuse model. The analysis of damage profiles indicates that damage accumulates in a diffusive manner up to the peak load, and localization sets in abruptly at the peak load, starting from a uniform damage landscape. The global crack width scales as Wtilde L0.5 and is consistent with the scaling of localization length ξ˜L0.5 used in the data collapse of damage profiles in the postpeak regime. This consistency between the global crack roughness exponent and the postpeak damage profile localization length supports the idea that the postpeak damage profile is predominantly due to the localization produced by the catastrophic failure, which at the same time results in the formation of the final crack. Finally, the crack width distributions can be collapsed for different system sizes and follow a log-normal distribution.

Benefit of the Use of GCxGC/MS Profiles for 1D GC/MS Data Treatment Illustrated by the Analysis of Pyrolysis Products from East Asian Handmade Papers

NASA Astrophysics Data System (ADS)

Han, Bin; Lob, Silvia; Sablier, Michel

2018-06-01

In this study, we report the use of pyrolysis-GCxGC/MS profiles for an optimized treatment of data issued from pyrolysis-GC/MS combined with the automatic deconvolution software Automated Mass Spectral Deconvolution and Identification System (AMDIS). The method was illustrated by the characterization of marker compounds of East Asian handmade papers through the examination of pyrolysis-GCxGC/MS data to get information which was used for manually identifying low concentrated and co-eluting compounds in 1D GC/MS data. The results showed that the merits of a higher separation power for co-eluting compounds and a better sensitivity for low concentration compounds offered by a GCxGC system can be used effectively for AMDIS 1D GC/MS data treatment: (i) the compound distribution in pyrolysis-GCxGC/MS profiles can be used as "peak finder" for manual check of low concentration and co-eluting compound identification in 1D GC/MS data, and (ii) pyrolysis-GCxGC/MS profiles can provide better quality mass spectra with observed higher match factors in the AMDIS automatic match process. The combination of 2D profile with AMDIS was shown to contribute efficiently to a better characterization of compound profiles in the chromatograms obtained by 1D analysis in focusing on the mass spectral identification. [Figure not available: see fulltext.

Development and evaluation of mechanized equipment for installation of the recessed reflective marker (RRM) delineation system. Task A, Design & feasibility analysis

DOT National Transportation Integrated Search

1978-06-01

A plow-resistant recessed reflective marker (RRM) delineation system having a linear tapered profile and which uses a reflector base/reflector unit is proposed. A single-operator mechanized vehicle to install the RRM delineation system is described. ...

Design and performance investigation of a highly accurate apodized fiber Bragg grating-based strain sensor in single and quasi-distributed systems.

PubMed

Ali, Taha A; Shehata, Mohamed I; Mohamed, Nazmi A

2015-06-01

In this work, fiber Bragg grating (FBG) strain sensors in single and quasi-distributed systems are investigated, seeking high-accuracy measurement. Since FBG-based strain sensors of small lengths are preferred in medical applications, and that causes the full width at half-maximum (FWHM) to be larger, a new apodization profile is introduced for the first time, to the best of our knowledge, with a remarkable FWHM at small sensor lengths compared to the Gaussian and Nuttall profiles, in addition to a higher mainlobe slope at these lengths. A careful selection of apodization profiles with detailed investigation is performed-using sidelobe analysis and the FWHM, which are primary judgment factors especially in a quasi-distributed configuration. A comparison between the elite selection of apodization profiles (extracted from related literature) and the proposed new profile is carried out covering the reflectivity peak, FWHM, and sidelobe analysis. The optimization process concludes that the proposed new profile with a chosen small length (L) of 10 mm and Δn_ac of 1.4×10^-4 is the optimum choice for single stage and quasi-distributed strain-sensor networks, even better than the Gaussian profile at small sensor lengths. The proposed profile achieves the smallest FWHM of 15 GHz (suitable for UDWDM), and the highest mainlobe slope of 130 dB/nm. For the quasi-distributed scenario, a noteworthy high isolation of 6.953 dB is achieved while applying a high strain value of 1500 μstrain (με) for a five-stage strain-sensing network. Further investigation was undertaken, proving that consistency in choosing the apodization profile in the quasi-distributed network is mandatory. A test was made of the inclusion of a uniform apodized sensor among other apodized sensors with the proposed profile in an FBG strain-sensor network.

Understanding Drug Release Data through Thermodynamic Analysis.

PubMed

Freire, Marjorie Caroline Liberato Cavalcanti; Alexandrino, Francisco; Marcelino, Henrique Rodrigues; Picciani, Paulo Henrique de Souza; Silva, Kattya Gyselle de Holanda E; Genre, Julieta; Oliveira, Anselmo Gomes de; Egito, Eryvaldo Sócrates Tabosa do

2017-06-13

Understanding the factors that can modify the drug release profile of a drug from a Drug-Delivery-System (DDS) is a mandatory step to determine the effectiveness of new therapies. The aim of this study was to assess the Amphotericin-B (AmB) kinetic release profiles from polymeric systems with different compositions and geometries and to correlate these profiles with the thermodynamic parameters through mathematical modeling. Film casting and electrospinning techniques were used to compare behavior of films and fibers, respectively. Release profiles from the DDSs were performed, and the mathematical modeling of the data was carried out. Activation energy, enthalpy, entropy and Gibbs free energy of the drug release process were determined. AmB release profiles showed that the relationship to overcome the enthalpic barrier was PVA-fiber > PVA-film > PLA-fiber > PLA-film. Drug release kinetics from the fibers and the films were better fitted on the Peppas-Sahlin and Higuchi models, respectively. The thermodynamic parameters corroborate these findings, revealing that the AmB release from the evaluated systems was an endothermic and non-spontaneous process. Thermodynamic parameters can be used to explain the drug kinetic release profiles. Such an approach is of utmost importance for DDS containing insoluble compounds, such as AmB, which is associated with an erratic bioavailability.

Understanding Drug Release Data through Thermodynamic Analysis

PubMed Central

Freire, Marjorie Caroline Liberato Cavalcanti; Alexandrino, Francisco; Marcelino, Henrique Rodrigues; Picciani, Paulo Henrique de Souza; Silva, Kattya Gyselle de Holanda e; Genre, Julieta; de Oliveira, Anselmo Gomes; do Egito, Eryvaldo Sócrates Tabosa

2017-01-01

Understanding the factors that can modify the drug release profile of a drug from a Drug-Delivery-System (DDS) is a mandatory step to determine the effectiveness of new therapies. The aim of this study was to assess the Amphotericin-B (AmB) kinetic release profiles from polymeric systems with different compositions and geometries and to correlate these profiles with the thermodynamic parameters through mathematical modeling. Film casting and electrospinning techniques were used to compare behavior of films and fibers, respectively. Release profiles from the DDSs were performed, and the mathematical modeling of the data was carried out. Activation energy, enthalpy, entropy and Gibbs free energy of the drug release process were determined. AmB release profiles showed that the relationship to overcome the enthalpic barrier was PVA-fiber > PVA-film > PLA-fiber > PLA-film. Drug release kinetics from the fibers and the films were better fitted on the Peppas–Sahlin and Higuchi models, respectively. The thermodynamic parameters corroborate these findings, revealing that the AmB release from the evaluated systems was an endothermic and non-spontaneous process. Thermodynamic parameters can be used to explain the drug kinetic release profiles. Such an approach is of utmost importance for DDS containing insoluble compounds, such as AmB, which is associated with an erratic bioavailability. PMID:28773009

Classification of speech and language profiles in 4-year old children with cerebral palsy: A prospective preliminary study

PubMed Central

Hustad, Katherine C.; Gorton, Kristin; Lee, Jimin

2010-01-01

Purpose Little is known about the speech and language abilities of children with cerebral palsy (CP) and there is currently no system for classifying speech and language profiles. Such a system would have epidemiological value and would have the potential to advance the development of interventions that improve outcomes. In this study, we propose and test a preliminary speech and language classification system by quantifying how well speech and language data differentiate among children classified into different hypothesized profile groups. Method Speech and language assessment data were collected in a laboratory setting from 34 children with CP (18 males; 16 females) who were a mean age of 54 months (SD 1.8 months). Measures of interest were vowel area, speech rate, language comprehension scores, and speech intelligibility ratings. Results Canonical discriminant function analysis showed that three functions accounted for 100% of the variance among profile groups, with speech variables accounting for 93% of the variance. Classification agreement varied from 74% to 97% using four different classification paradigms. Conclusions Results provide preliminary support for the classification of speech and language abilities of children with CP into four initial profile groups. Further research is necessary to validate the full classification system. PMID:20643795

Atmospheric Boundary Layer Wind Data During the Period January 1, 1998 Through January 31, 1999 at the Dallas-Fort Worth Airport. Volume 1; Quality Assessment

NASA Technical Reports Server (NTRS)

Zak, J. Allen; Rodgers, William G., Jr.

2000-01-01

The quality of the Aircraft Vortex Spacing System (AVOSS) is critically dependent on representative wind profiles in the atmospheric boundary layer. These winds observed from a number of sensor systems around the Dallas-Fort Worth airport were combined into single vertical wind profiles by an algorithm developed and implemented by MIT Lincoln Laboratory. This process, called the AVOSS Winds Analysis System (AWAS), is used by AVOSS for wake corridor predictions. During times when AWAS solutions were available, the quality of the resultant wind profiles and variance was judged from a series of plots combining all sensor observations and AWAS profiles during the period 1200 to 0400 UTC daily. First, input data was evaluated for continuity and consistency from criteria established. Next, the degree of agreement among all wind sensor systems was noted and cases of disagreement identified. Finally, the resultant AWAS solution was compared to the quality-assessed input data. When profiles differed by a specified amount from valid sensor consensus winds, times and altitudes were flagged. Volume one documents the process and quality of input sensor data. Volume two documents the data processing/sorting process and provides the resultant flagged files.

Vector wind profile gust model

NASA Technical Reports Server (NTRS)

Adelfang, S. I.

1979-01-01

Work towards establishing a vector wind profile gust model for the Space Transportation System flight operations and trade studies is reported. To date, all the statistical and computational techniques required were established and partially implemented. An analysis of wind profile gust at Cape Kennedy within the theoretical framework is presented. The variability of theoretical and observed gust magnitude with filter type, altitude, and season is described. Various examples are presented which illustrate agreement between theoretical and observed gust percentiles. The preliminary analysis of the gust data indicates a strong variability with altitude, season, and wavelength regime. An extension of the analyses to include conditional distributions of gust magnitude given gust length, distributions of gust modulus, and phase differences between gust components has begun.

Coupled Analysis of an Inlet and Fan for a Quiet Supersonic Aircraft

NASA Technical Reports Server (NTRS)

Chima, Rodrick V.; Conners, Timothy R.; Wayman, Thomas R.

2009-01-01

A computational analysis of a Gulfstream isentropic external compression supersonic inlet coupled to a Rolls-Royce fan was completed. The inlet was designed for a small, low sonic boom supersonic vehicle with a design cruise condition of M = 1.6 at 45,000 feet. The inlet design included an annular bypass duct that routed flow subsonically around an engine-mounted gearbox and diverted flow with high shock losses away from the fan tip. Two Reynolds-averaged Navier-Stokes codes were used for the analysis: an axisymmetric code called AVCS for the inlet and a 3-D code called SWIFT for the fan. The codes were coupled at a mixing plane boundary using a separate code for data exchange. The codes were used to determine the performance of the inlet/fan system at the design point and to predict the performance and operability of the system over the flight profile. At the design point the core inlet had a recovery of 96 percent, and the fan operated near its peak efficiency and pressure ratio. A large hub radial distortion generated in the inlet was not eliminated by the fan and could pose a challenge for subsequent booster stages. The system operated stably at all points along the flight profile. Reduced stall margin was seen at low altitude and Mach number where flow separated on the interior lips of the cowl and bypass ducts. The coupled analysis gave consistent solutions at all points on the flight profile that would be difficult or impossible to predict by analysis of isolated components.

Coupled Analysis of an Inlet and Fan for a Quiet Supersonic Jet

NASA Technical Reports Server (NTRS)

Chima, Rodrick V.; Conners, Timothy R.; Wayman, Thomas R.

2010-01-01

A computational analysis of a Gulfstream isentropic external compression supersonic inlet coupled to a Rolls-Royce fan has been completed. The inlet was designed for a small, low sonic boom supersonic vehicle with a design cruise condition of M = 1.6 at 45,000 ft. The inlet design included an annular bypass duct that routed flow subsonically around an engine-mounted gearbox and diverted flow with high shock losses away from the fan tip. Two Reynolds-averaged Navier-Stokes codes were used for the analysis: an axisymmetric code called AVCS for the inlet and a three dimensional (3-D) code called SWIFT for the fan. The codes were coupled at a mixing plane boundary using a separate code for data exchange. The codes were used to determine the performance of the inlet/fan system at the design point and to predict the performance and operability of the system over the flight profile. At the design point the core inlet had a recovery of 96 percent, and the fan operated near its peak efficiency and pressure ratio. A large hub radial distortion generated in the inlet was not eliminated by the fan and could pose a challenge for subsequent booster stages. The system operated stably at all points along the flight profile. Reduced stall margin was seen at low altitude and Mach number where flow separated on the interior lips of the cowl and bypass ducts. The coupled analysis gave consistent solutions at all points on the flight profile that would be difficult or impossible to predict by analysis of isolated components.

The contribution of antiphospholipid antibodies to organ damage in systemic lupus erythematosus.

PubMed

Taraborelli, M; Leuenberger, L; Lazzaroni, M G; Martinazzi, N; Zhang, W; Franceschini, F; Salmon, J; Tincani, A; Erkan, D

2016-10-01

The objective of this study was to assess the contribution of clinically significant antiphospholipid antibodies (aPL) to organ damage in systemic lupus erythematosus (SLE). Patients with disease duration of less than 10 years and at least 5 years of follow-up were identified from two SLE registries. A clinically significant antiphospholipid antibody (aPL) profile was defined as: positive lupus anticoagulant, anticardiolipin IgG/M ≥ 40 G phospholipid units (GPL)/M phospholipid units (MPL), and/or anti-β2-glycoprotein-I IgG/M ≥ 99th percentile on two or more occasions, at least 12 weeks apart. Organ damage was assessed by the Systemic Lupus International Collaborating Clinics Damage Index (SDI). Univariate and multivariate analysis compared SLE patients with and without SDI increase during a 15-year follow-up. Among 262 SLE patients, 33% had a clinically significant aPL profile, which was associated with an increased risk of organ damage accrual during a 5-year follow-up in univariate analysis, and during a 15-year follow-up in the multivariate analysis adjusting for age, gender, race, disease duration at registry entry, and time. In the multivariate analysis, older age at diagnosis and male gender were also associated with SDI increase at each time point. A clinically significant aPL profile is associated with an increased risk of organ damage accrual during a 15-year follow-up in SLE patients. © The Author(s) 2016.

A comparative analysis of user preference-based and existing knowledge management systems attributes in the aerospace industry

NASA Astrophysics Data System (ADS)

Varghese, Nishad G.

Knowledge management (KM) exists in various forms throughout organizations. Process documentation, training courses, and experience sharing are examples of KM activities performed daily. The goal of KM systems (KMS) is to provide a tool set which serves to standardize the creation, sharing, and acquisition of business critical information. Existing literature provides numerous examples of targeted evaluations of KMS, focusing on specific system attributes. This research serves to bridge the targeted evaluations with an industry-specific, holistic approach. The user preferences of aerospace employees in engineering and engineering-related fields were compared to profiles of existing aerospace KMS based on three attribute categories: technical features, system administration, and user experience. The results indicated there is a statistically significant difference between aerospace user preferences and existing profiles in the user experience attribute category, but no statistically significant difference in the technical features and system administration attribute categories. Additional analysis indicated in-house developed systems exhibit higher technical features and user experience ratings than commercial-off-the-self (COTS) systems.

Systemic bioinformatics analysis of skeletal muscle gene expression profiles of sepsis

PubMed Central

Yang, Fang; Wang, Yumei

2018-01-01

Sepsis is a type of systemic inflammatory response syndrome with high morbidity and mortality. Skeletal muscle dysfunction is one of the major complications of sepsis that may also influence the outcome of sepsis. The aim of the present study was to explore and identify potential mechanisms and therapeutic targets of sepsis. Systemic bioinformatics analysis of skeletal muscle gene expression profiles from the Gene Expression Omnibus was performed. Differentially expressed genes (DEGs) in samples from patients with sepsis and control samples were screened out using the limma package. Differential co-expression and coregulation (DCE and DCR, respectively) analysis was performed based on the Differential Co-expression Analysis package to identify differences in gene co-expression and coregulation patterns between the control and sepsis groups. Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways of DEGs were identified using the Database for Annotation, Visualization and Integrated Discovery, and inflammatory, cancer and skeletal muscle development-associated biological processes and pathways were identified. DCE and DCR analysis revealed several potential therapeutic targets for sepsis, including genes and transcription factors. The results of the present study may provide a basis for the development of novel therapeutic targets and treatment methods for sepsis. PMID:29805480

Surface characterization and testing II; Proceedings of the Meeting, San Diego, CA, Aug. 10, 11, 1989

NASA Technical Reports Server (NTRS)

Greivenkamp, John E. (Editor); Young, Matt (Editor)

1989-01-01

Various papers on surface characterization and testing are presented. Individual topics addressed include: simple Hartmann test data interpretation, optimum configuration of the Offner null corrector, system for phase-shifting interferometry in the presence of vibration, fringe variation and visibility in speckle-shearing interferometry, functional integral representation of rough surfaces, calibration of surface heights in an interferometric optical profiler, image formation in common path differential profilometers, SEM of optical surfaces, measuring surface profiles with scanning tunneling microscopes, surface profile measurements of curved parts, high-resolution optical profiler, scanning heterodyne interferometer with immunity from microphonics, real-time crystal axis measurements of semiconductor materials, radial metrology with a panoramic annular lens, surface analysis for the characterization of defects in thin-film processes, Spacelab Optical Viewport glass assembly optical test program for the Starlab mission, scanning differential intensity and phase system for optical metrology.

Handling of computational in vitro/in vivo correlation problems by Microsoft Excel: IV. Generalized matrix analysis of linear compartment systems.

PubMed

Langenbucher, Frieder

2005-01-01

A linear system comprising n compartments is completely defined by the rate constants between any of the compartments and the initial condition in which compartment(s) the drug is present at the beginning. The generalized solution is the time profiles of drug amount in each compartment, described by polyexponential equations. Based on standard matrix operations, an Excel worksheet computes the rate constants and the coefficients, finally the full time profiles for a specified range of time values.

Universal Profile of the Vortex Condensate in Two-Dimensional Turbulence

NASA Astrophysics Data System (ADS)

Laurie, Jason; Boffetta, Guido; Falkovich, Gregory; Kolokolov, Igor; Lebedev, Vladimir

2014-12-01

An inverse turbulent cascade in a restricted two-dimensional periodic domain creates a condensate—a pair of coherent system-size vortices. We perform extensive numerical simulations of this system and carry out theoretical analysis based on momentum and energy exchanges between the turbulence and the vortices. We show that the vortices have a universal internal structure independent of the type of small-scale dissipation, small-scale forcing, and boundary conditions. The theory predicts not only the vortex inner region profile, but also the amplitude, which both perfectly agree with the numerical data.

Metabolite profiling on wheat grain to enable a distinction of samples from organic and conventional farming systems.

PubMed

Bonte, Anja; Neuweger, Heiko; Goesmann, Alexander; Thonar, Cécile; Mäder, Paul; Langenkämper, Georg; Niehaus, Karsten

2014-10-01

Identification of biomarkers capable of distinguishing organic and conventional products would be highly welcome to improve the strength of food quality assurance. Metabolite profiling was used for biomarker search in organic and conventional wheat grain (Triticum aestivum L.) of 11 different old and new bread wheat cultivars grown in the DOK system comparison trial. Metabolites were extracted using methanol and analysed by gas chromatography-mass spectrometry. Altogether 48 metabolites and 245 non-identified metabolites (TAGs) were detected in the cultivar Runal. Principal component analysis showed a sample clustering according to farming systems and significant differences in peak areas between the farming systems for 10 Runal metabolites. Results obtained from all 11 cultivars indicated a greater influence of the cultivar than the farming system on metabolite concentrations. Nevertheless, a t-test on data of all cultivars still detected 5 metabolites and 11 TAGs with significant differences between the farming systems. Based on individual cultivars, metabolite profiling showed promising results for the categorization of organic and conventional wheat. Further investigations are necessary with wheat from more growing seasons and locations before definite conclusions can be drawn concerning the feasibility to evolve a combined set of biomarkers for organically grown wheat using metabolite profiles. © 2014 Society of Chemical Industry.

Nitric oxide assisted C60 secondary ion mass spectrometry for molecular depth profiling of polyelectrolyte multilayers.

PubMed

Zappalà, G; Motta, V; Tuccitto, N; Vitale, S; Torrisi, A; Licciardello, A

2015-12-15

Secondary ion mass spectrometry (SIMS) with polyatomic primary ions provides a successful tool for molecular depth profiling of polymer systems, relevant in many technological applications. Widespread C60 sources, however, cause in some polymers extensive damage with loss of molecular information along depth. We study a method, based on the use of a radical scavenger, for inhibiting ion-beam-induced reactions causing sample damage. Layered polystyrene sulfonate and polyacrylic acid based polyelectrolyte films, behaving differently towards C60 beam-induced damage, were selected and prepared as model systems. They were depth profiled by means of time-of-flight (TOF)-SIMS in dual beam mode, using fullerene ions for sputtering. Nitric oxide was introduced into the analysis chamber as a radical scavenger. The effect of sample cooling combined with NO-dosing on the quality of depth profiles was explored. NO-dosing during C60-SIMS depth profiling of >1 micrometer-thick multilayered polyelectrolytes allows detection, along depth, of characteristic fragments from systems otherwise damaged by C60 bombardment, and increases sputtering yield by more than one order of magnitude. By contrast, NO has little influence on those layers that are well profiled with C60 alone. Such leveling effect, more pronounced at low temperature, leads to a dramatic improvement of profile quality, with a clear definition of interfaces. NO-dosing provides a tool for extending the applicability, in SIMS depth profiling, of the widely spread fullerene ion sources. In view of the acceptable erosion rates on inorganics, obtainable with C60, the method could be of relevance also in connection with the 3D-imaging of hybrid polymer/inorganic systems. Copyright © 2015 John Wiley & Sons, Ltd.

Assessing the Organizational Social Context (OSC) of child welfare systems: implications for research and practice.

PubMed

Glisson, Charles; Green, Philip; Williams, Nathaniel J

2012-09-01

The study: (1) provides the first assessment of the a priori measurement model and psychometric properties of the Organizational Social Context (OSC) measurement system in a US nationwide probability sample of child welfare systems; (2) illustrates the use of the OSC in constructing norm-based organizational culture and climate profiles for child welfare systems; and (3) estimates the association of child welfare system-level organizational culture and climate profiles with individual caseworker-level job satisfaction and organizational commitment. The study applies confirmatory factor analysis (CFA) and hierarchical linear models (HLM) analysis to a US nationwide sample of 1,740 caseworkers from 81 child welfare systems participating in the second National Survey of Child and Adolescent Wellbeing (NSCAW II). The participating child welfare systems were selected using a national probability procedure reflecting the number of children served by child welfare systems nationwide. The a priori OSC measurement model is confirmed in this nationwide sample of child welfare systems. In addition, caseworker responses to the OSC scales generate acceptable to high scale reliabilities, moderate to high within-system agreement, and significant between-system differences. Caseworkers in the child welfare systems with the best organizational culture and climate profiles report higher levels of job satisfaction and organizational commitment. Organizational climates characterized by high engagement and functionality, and organizational cultures characterized by low rigidity are associated with the most positive work attitudes. The OSC is the first valid and reliable measure of organizational culture and climate with US national norms for child welfare systems. The OSC provides a useful measure of Organizational Social Context for child welfare service improvement and implementation research efforts which include a focus on child welfare system culture and climate. Copyright © 2012 Elsevier Ltd. All rights reserved.

Pilot Task Profiles, Human Factors, And Image Realism

NASA Astrophysics Data System (ADS)

McCormick, Dennis

1982-06-01

Computer Image Generation (CIG) visual systems provide real time scenes for state-of-the-art flight training simulators. The visual system reauires a greater understanding of training tasks, human factors, and the concept of image realism to produce an effective and efficient training scene than is required by other types of visual systems. Image realism must be defined in terms of pilot visual information reauirements. Human factors analysis of training and perception is necessary to determine the pilot's information requirements. System analysis then determines how the CIG and display device can best provide essential information to the pilot. This analysis procedure ensures optimum training effectiveness and system performance.

Two different approaches to the affective profiles model: median splits (variable-oriented) and cluster analysis (person-oriented).

PubMed

Garcia, Danilo; MacDonald, Shane; Archer, Trevor

2015-01-01

Background. The notion of the affective system as being composed of two dimensions led Archer and colleagues to the development of the affective profiles model. The model consists of four different profiles based on combinations of individuals' experience of high/low positive and negative affect: self-fulfilling, low affective, high affective, and self-destructive. During the past 10 years, an increasing number of studies have used this person-centered model as the backdrop for the investigation of between and within individual differences in ill-being and well-being. The most common approach to this profiling is by dividing individuals' scores of self-reported affect using the median of the population as reference for high/low splits. However, scores just-above and just-below the median might become high and low by arbitrariness, not by reality. Thus, it is plausible to criticize the validity of this variable-oriented approach. Our aim was to compare the median splits approach with a person-oriented approach, namely, cluster analysis. Method. The participants (N = 2, 225) were recruited through Amazons' Mechanical Turk and asked to self-report affect using the Positive Affect Negative Affect Schedule. We compared the profiles' homogeneity and Silhouette coefficients to discern differences in homogeneity and heterogeneity between approaches. We also conducted exact cell-wise analyses matching the profiles from both approaches and matching profiles and gender to investigate profiling agreement with respect to affectivity levels and affectivity and gender. All analyses were conducted using the ROPstat software. Results. The cluster approach (weighted average of cluster homogeneity coefficients = 0.62, Silhouette coefficients = 0.68) generated profiles with greater homogeneity and more distinctive from each other compared to the median splits approach (weighted average of cluster homogeneity coefficients = 0.75, Silhouette coefficients = 0.59). Most of the participants (n = 1,736, 78.0%) were allocated to the same profile (Rand Index = .83), however, 489 (21.98%) were allocated to different profiles depending on the approach. Both approaches allocated females and males similarly in three of the four profiles. Only the cluster analysis approach classified men significantly more often than chance to a self-fulfilling profile (type) and females less often than chance to this very same profile (antitype). Conclusions. Although the question whether one approach is more appropriate than the other is still without answer, the cluster method allocated individuals to profiles that are more in accordance with the conceptual basis of the model and also to expected gender differences. More importantly, regardless of the approach, our findings suggest that the model mirrors a complex and dynamic adaptive system.

High Tech for Milady's Makeup

NASA Technical Reports Server (NTRS)

1985-01-01

"Elizabeth," a computerized beauty analysis system marketed by Elizabeth Arden, is based upon an ARAC data base search of technologies measuring skin profiles. * "Elizabeth" is no longer commercially available.

Parts on Demand: Evaluation of Approaches to Achieve Flexible Manufacturing Systems for Navy Parts on Demand. Volume 2. Appendices

DTIC Science & Technology

1984-02-01

of Cost Analysis Worksheets * POD Program-Economic Analysis & Methodology - Economic Evaluation Procedures for POD Investment Program - System...Approval Considerations - POD Investment Program - Potential Improvement Areas for POD - Example Cost Categories and Determinants Appendix E Long Range R&D...Funding Profiles * Investment Strategy for Integrated Circuits Diminishing Sources of Supply - Problem Scope - Approach - Alternatives - Proposed

Phenotype profiling and multivariate statistical analysis of Spur-pruning type Grapevine in National Clonal Germplasm Repository (NCGR, Davis)

USDA-ARS?s Scientific Manuscript database

Most Korean vineyards employed spur-pruning type modified-T trellis system. This produce system is suitable to spur-pruning type cultivars. But most European table grape is not adaptable to this produce system because their fruitfulness is sufficient to cane-pruning type system. Total 20 of fruit ch...

Internet-based profiler system as integrative framework to support translational research

PubMed Central

Kim, Robert; Demichelis, Francesca; Tang, Jeffery; Riva, Alberto; Shen, Ronglai; Gibbs, Doug F; Mahavishno, Vasudeva; Chinnaiyan, Arul M; Rubin, Mark A

2005-01-01

Background Translational research requires taking basic science observations and developing them into clinically useful tests and therapeutics. We have developed a process to develop molecular biomarkers for diagnosis and prognosis by integrating tissue microarray (TMA) technology and an internet-database tool, Profiler. TMA technology allows investigators to study hundreds of patient samples on a single glass slide resulting in the conservation of tissue and the reduction in inter-experimental variability. The Profiler system allows investigator to reliably track, store, and evaluate TMA experiments. Here within we describe the process that has evolved through an empirical basis over the past 5 years at two academic institutions. Results The generic design of this system makes it compatible with multiple organ system (e.g., prostate, breast, lung, renal, and hematopoietic system,). Studies and folders are restricted to authorized users as required. Over the past 5 years, investigators at 2 academic institutions have scanned 656 TMA experiments and collected 63,311 digital images of these tissue samples. 68 pathologists from 12 major user groups have accessed the system. Two groups directly link clinical data from over 500 patients for immediate access and the remaining groups choose to maintain clinical and pathology data on separate systems. Profiler currently has 170 K data points such as staining intensity, tumor grade, and nuclear size. Due to the relational database structure, analysis can be easily performed on single or multiple TMA experimental results. The TMA module of Profiler can maintain images acquired from multiple systems. Conclusion We have developed a robust process to develop molecular biomarkers using TMA technology and an internet-based database system to track all steps of this process. This system is extendable to other types of molecular data as separate modules and is freely available to academic institutions for licensing. PMID:16364175

Internet-based Profiler system as integrative framework to support translational research.

PubMed

Kim, Robert; Demichelis, Francesca; Tang, Jeffery; Riva, Alberto; Shen, Ronglai; Gibbs, Doug F; Mahavishno, Vasudeva; Chinnaiyan, Arul M; Rubin, Mark A

2005-12-19

Translational research requires taking basic science observations and developing them into clinically useful tests and therapeutics. We have developed a process to develop molecular biomarkers for diagnosis and prognosis by integrating tissue microarray (TMA) technology and an internet-database tool, Profiler. TMA technology allows investigators to study hundreds of patient samples on a single glass slide resulting in the conservation of tissue and the reduction in inter-experimental variability. The Profiler system allows investigator to reliably track, store, and evaluate TMA experiments. Here within we describe the process that has evolved through an empirical basis over the past 5 years at two academic institutions. The generic design of this system makes it compatible with multiple organ system (e.g., prostate, breast, lung, renal, and hematopoietic system,). Studies and folders are restricted to authorized users as required. Over the past 5 years, investigators at 2 academic institutions have scanned 656 TMA experiments and collected 63,311 digital images of these tissue samples. 68 pathologists from 12 major user groups have accessed the system. Two groups directly link clinical data from over 500 patients for immediate access and the remaining groups choose to maintain clinical and pathology data on separate systems. Profiler currently has 170 K data points such as staining intensity, tumor grade, and nuclear size. Due to the relational database structure, analysis can be easily performed on single or multiple TMA experimental results. The TMA module of Profiler can maintain images acquired from multiple systems. We have developed a robust process to develop molecular biomarkers using TMA technology and an internet-based database system to track all steps of this process. This system is extendable to other types of molecular data as separate modules and is freely available to academic institutions for licensing.

The High Accuracy Measurement of CO2 Mixing Ratio Profiles Using Ground Based 1.6 μm CO2-DIAL with Temperature Measurement Techniques in the Lower-Atmosphere

NASA Astrophysics Data System (ADS)

Abo, M.; Shibata, Y.; Nagasawa, C.

2017-12-01

We have developed a ground based direct detection three-wavelength 1.6 μm differential absorption lidar (DIAL) to achieve measurements of vertical CO2 concentration and temperature profiles in the atmosphere. As the spectra of absorption lines of any molecules are influenced basically by the temperature and pressure in the atmosphere, it is important to measure them simultaneously so that the better accuracy of the DIAL measurement is realized. Conventionally, we have obtained the vertical profile of absorption cross sections using the atmospheric temperature profile by the objective analysis and the atmospheric pressure profile calculated by the pressure height equation. Comparison of atmospheric pressure profiles calculated from this equation and those obtained from radiosonde observations at Tateno, Japan is consistent within 0.2 % below 3 km altitude. But the temperature dependency of the CO2 density is 0.25 %/°C near the surface. Moreover, the CO2 concentration is often evaluated by the mixing ratio. Because the air density is related by the ideal gas law, the mixing ratio is also related by the atmospheric temperature. Therefore, the temperature affects not only accuracy of CO2 concentration but the CO2 mixing ratio. In this paper, some experimental results of the simultaneous measurement of atmospheric temperature profiles and CO2 mixing ratio profiles are reported from 0.4 to 2.5 km altitude using the three-wavelength 1.6 μm DIAL system. Temperature profiles of CO2 DIAL measurement were sometimes different from those of objective analysis below 1.5 km altitude. These differences are considered to be due to regionality at the lidar site. The temperature difference of 5.0 °C corresponds to a CO2 mixing ratio difference of 8.0 ppm at 500 m altitude. This cannot be ignored in estimates of regional sources and sinks of CO2. This three-wavelength CO2 DIAL technique can estimate accurately temporal behavior of CO2 mixing ratio profiles in the lower atmosphere. This work was financially supported by the System Development Program for Advanced Measurement and Analysis of the Japan Science and Technology Agency.

Global metabolic profiling procedures for urine using UPLC-MS.

PubMed

Want, Elizabeth J; Wilson, Ian D; Gika, Helen; Theodoridis, Georgios; Plumb, Robert S; Shockcor, John; Holmes, Elaine; Nicholson, Jeremy K

2010-06-01

The production of 'global' metabolite profiles involves measuring low molecular-weight metabolites (<1 kDa) in complex biofluids/tissues to study perturbations in response to physiological challenges, toxic insults or disease processes. Information-rich analytical platforms, such as mass spectrometry (MS), are needed. Here we describe the application of ultra-performance liquid chromatography-MS (UPLC-MS) to urinary metabolite profiling, including sample preparation, stability/storage and the selection of chromatographic conditions that balance metabolome coverage, chromatographic resolution and throughput. We discuss quality control and metabolite identification, as well as provide details of multivariate data analysis approaches for analyzing such MS data. Using this protocol, the analysis of a sample set in 96-well plate format, would take ca. 30 h, including 1 h for system setup, 1-2 h for sample preparation, 24 h for UPLC-MS analysis and 1-2 h for initial data processing. The use of UPLC-MS for metabolic profiling in this way is not faster than the conventional HPLC-based methods but, because of improved chromatographic performance, provides superior metabolome coverage.

The Propulsive Small Expendable Deployer System (ProSEDS)

NASA Technical Reports Server (NTRS)

Lorenzini, Enrico C.

2002-01-01

This Annual Report covers the following main topics: 1) Updated Reference Mission. The reference ProSEDS (Propulsive Small Expendable Deployer System) mission is evaluated for an updated launch date in the Summer of 2002 and for the new 80-s current operating cycle. Simulations are run for nominal solar activity condition at the time of launch and for extreme conditions of dynamic forcing. Simulations include the dynamics of the system, the electrodynamics of the bare tether, the neutral atmosphere and the thermal response of the tether. 2) Evaluation of power delivered by the tether system. The power delivered by the tethered system during the battery charging mode is computed under the assumption of minimum solar activity for the new launch date. 3) Updated Deployment Control Profiles and Simulations. A number of new deployment profiles were derived based on the latest results of the deployment ground tests. The flight profile is then derived based on the friction characteristics obtained from the deployment tests of the F-1 tether. 4) Analysis/estimation of deployment flight data. A process was developed to estimate the deployment trajectory of the endmass with respect to the Delta and the final libration amplitude from the data of the deployer turn counters. This software was tested successfully during the ProSEDS mission simulation at MSFC (Marshall Space Flight Center) EDAC (Environments Data Analysis Center).

Management of reliability and maintainability; a disciplined approach to fleet readiness

NASA Technical Reports Server (NTRS)

Willoughby, W. J., Jr.

1981-01-01

Material acquisition fundamentals were reviewed and include: mission profile definition, stress analysis, derating criteria, circuit reliability, failure modes, and worst case analysis. Military system reliability was examined with emphasis on the sparing of equipment. The Navy's organizational strategy for 1980 is presented.

A graph-based network-vulnerability analysis system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swiler, L.P.; Phillips, C.; Gaylor, T.

1998-05-03

This paper presents a graph based approach to network vulnerability analysis. The method is flexible, allowing analysis of attacks from both outside and inside the network. It can analyze risks to a specific network asset, or examine the universe of possible consequences following a successful attack. The analysis system requires as input a database of common attacks, broken into atomic steps, specific network configuration and topology information, and an attacker profile. The attack information is matched with the network configuration information and an attacker profile to create a superset attack graph. Nodes identify a stage of attack, for example themore » class of machines the attacker has accessed and the user privilege level he or she has compromised. The arcs in the attack graph represent attacks or stages of attacks. By assigning probabilities of success on the arcs or costs representing level of effort for the attacker, various graph algorithms such as shortest path algorithms can identify the attack paths with the highest probability of success.« less

A graph-based network-vulnerability analysis system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swiler, L.P.; Phillips, C.; Gaylor, T.

1998-01-01

This report presents a graph-based approach to network vulnerability analysis. The method is flexible, allowing analysis of attacks from both outside and inside the network. It can analyze risks to a specific network asset, or examine the universe of possible consequences following a successful attack. The analysis system requires as input a database of common attacks, broken into atomic steps, specific network configuration and topology information, and an attacker profile. The attack information is matched with the network configuration information and an attacker profile to create a superset attack graph. Nodes identify a stage of attack, for example the classmore » of machines the attacker has accessed and the user privilege level he or she has compromised. The arcs in the attack graph represent attacks or stages of attacks. By assigning probabilities of success on the arcs or costs representing level-of-effort for the attacker, various graph algorithms such as shortest-path algorithms can identify the attack paths with the highest probability of success.« less

[Analysis of Time-to-onset of Interstitial Lung Disease after the Administration of Small Molecule Molecularly-targeted Drugs].

PubMed

Komada, Fusao

2018-01-01

　The aim of this study was to investigate the time-to-onset of drug-induced interstitial lung disease (DILD) following the administration of small molecule molecularly-targeted drugs via the use of the spontaneous adverse reaction reporting system of the Japanese Adverse Drug Event Report database. DILD datasets for afatinib, alectinib, bortezomib, crizotinib, dasatinib, erlotinib, everolimus, gefitinib, imatinib, lapatinib, nilotinib, osimertinib, sorafenib, sunitinib, temsirolimus, and tofacitinib were used to calculate the median onset times of DILD and the Weibull distribution parameters, and to perform the hierarchical cluster analysis. The median onset times of DILD for afatinib, bortezomib, crizotinib, erlotinib, gefitinib, and nilotinib were within one month. The median onset times of DILD for dasatinib, everolimus, lapatinib, osimertinib, and temsirolimus ranged from 1 to 2 months. The median onset times of the DILD for alectinib, imatinib, and tofacitinib ranged from 2 to 3 months. The median onset times of the DILD for sunitinib and sorafenib ranged from 8 to 9 months. Weibull distributions for these drugs when using the cluster analysis showed that there were 4 clusters. Cluster 1 described a subgroup with early to later onset DILD and early failure type profiles or a random failure type profile. Cluster 2 exhibited early failure type profiles or a random failure type profile with early onset DILD. Cluster 3 exhibited a random failure type profile or wear out failure type profiles with later onset DILD. Cluster 4 exhibited an early failure type profile or a random failure type profile with the latest onset DILD.

Random Initialisation of the Spectral Variables: an Alternate Approach for Initiating Multivariate Curve Resolution Alternating Least Square (MCR-ALS) Analysis.

PubMed

Kumar, Keshav

2017-11-01

Multivariate curve resolution alternating least square (MCR-ALS) analysis is the most commonly used curve resolution technique. The MCR-ALS model is fitted using the alternate least square (ALS) algorithm that needs initialisation of either contribution profiles or spectral profiles of each of the factor. The contribution profiles can be initialised using the evolve factor analysis; however, in principle, this approach requires that data must belong to the sequential process. The initialisation of the spectral profiles are usually carried out using the pure variable approach such as SIMPLISMA algorithm, this approach demands that each factor must have the pure variables in the data sets. Despite these limitations, the existing approaches have been quite a successful for initiating the MCR-ALS analysis. However, the present work proposes an alternate approach for the initialisation of the spectral variables by generating the random variables in the limits spanned by the maxima and minima of each spectral variable of the data set. The proposed approach does not require that there must be pure variables for each component of the multicomponent system or the concentration direction must follow the sequential process. The proposed approach is successfully validated using the excitation-emission matrix fluorescence data sets acquired for certain fluorophores with significant spectral overlap. The calculated contribution and spectral profiles of these fluorophores are found to correlate well with the experimental results. In summary, the present work proposes an alternate way to initiate the MCR-ALS analysis.

The upgrade of the Thomson scattering system for measurement on the C-2/C-2U devices.

PubMed

Zhai, K; Schindler, T; Kinley, J; Deng, B; Thompson, M C

2016-11-01

The C-2/C-2U Thomson scattering system has been substantially upgraded during the latter phase of C-2/C-2U program. A Rayleigh channel has been added to each of the three polychromators of the C-2/C-2U Thomson scattering system. Onsite spectral calibration has been applied to avoid the issue of different channel responses at different spots on the photomultiplier tube surface. With the added Rayleigh channel, the absolute intensity response of the system is calibrated with Rayleigh scattering in argon gas from 0.1 to 4 Torr, where the Rayleigh scattering signal is comparable to the Thomson scattering signal at electron densities from 1 × 10 13 to 4 × 10 14 cm -3 . A new signal processing algorithm, using a maximum likelihood method and including detailed analysis of different noise contributions within the system, has been developed to obtain electron temperature and density profiles. The system setup, spectral and intensity calibration procedure and its outcome, data analysis, and the results of electron temperature/density profile measurements will be presented.

Characterization of the transcriptome profiles related to globin gene switching during in vitro erythroid maturation

PubMed Central

2012-01-01

Background The fetal and adult globin genes in the human β-globin cluster on chromosome 11 are sequentially expressed to achieve normal hemoglobin switching during human development. The pharmacological induction of fetal γ-globin (HBG) to replace abnormal adult sickle βS-globin is a successful strategy to treat sickle cell disease; however the molecular mechanism of γ-gene silencing after birth is not fully understood. Therefore, we performed global gene expression profiling using primary erythroid progenitors grown from human peripheral blood mononuclear cells to characterize gene expression patterns during the γ-globin to β-globin (γ/β) switch observed throughout in vitro erythroid differentiation. Results We confirmed erythroid maturation in our culture system using cell morphologic features defined by Giemsa staining and the γ/β-globin switch by reverse transcription-quantitative PCR (RT-qPCR) analysis. We observed maximal γ-globin expression at day 7 with a switch to a predominance of β-globin expression by day 28 and the γ/β-globin switch occurred around day 21. Expression patterns for transcription factors including GATA1, GATA2, KLF1 and NFE2 confirmed our system produced the expected pattern of expression based on the known function of these factors in globin gene regulation. Subsequent gene expression profiling was performed with RNA isolated from progenitors harvested at day 7, 14, 21, and 28 in culture. Three major gene profiles were generated by Principal Component Analysis (PCA). For profile-1 genes, where expression decreased from day 7 to day 28, we identified 2,102 genes down-regulated > 1.5-fold. Ingenuity pathway analysis (IPA) for profile-1 genes demonstrated involvement of the Cdc42, phospholipase C, NF-Kβ, Interleukin-4, and p38 mitogen activated protein kinase (MAPK) signaling pathways. Transcription factors known to be involved in γ-and β-globin regulation were identified. The same approach was used to generate profile-2 genes where expression was up-regulated over 28 days in culture. IPA for the 2,437 genes with > 1.5-fold induction identified the mitotic roles of polo-like kinase, aryl hydrocarbon receptor, cell cycle control, and ATM (Ataxia Telangiectasia Mutated Protein) signaling pathways; transcription factors identified included KLF1, GATA1 and NFE2 among others. Finally, profile-3 was generated from 1,579 genes with maximal expression at day 21, around the time of the γ/β-globin switch. IPA identified associations with cell cycle control, ATM, and aryl hydrocarbon receptor signaling pathways. Conclusions The transcriptome analysis completed with erythroid progenitors grown in vitro identified groups of genes with distinct expression profiles, which function in metabolic pathways associated with cell survival, hematopoiesis, blood cells activation, and inflammatory responses. This study represents the first report of a transcriptome analysis in human primary erythroid progenitors to identify transcription factors involved in hemoglobin switching. Our results also demonstrate that the in vitro liquid culture system is an excellent model to define mechanisms of global gene expression and the DNA-binding protein and signaling pathways involved in globin gene regulation. PMID:22537182

Multiple Interests of Users in Collaborative Tagging Systems

NASA Astrophysics Data System (ADS)

Au Yeung, Ching-Man; Gibbins, Nicholas; Shadbolt, Nigel

Performance of recommender systems depends on whether the user profiles contain accurate information about the interests of the users, and this in turn relies on whether enough information about their interests can be collected. Collaborative tagging systems allow users to use their own words to describe their favourite resources, resulting in some user-generated categorisation schemes commonly known as folksonomies. Folksonomies thus contain rich information about the interests of the users, which can be used to support various recommender systems. Our analysis of the folksonomy in Delicious reveals that the interests of a single user can be very diverse. Traditional methods for representing interests of users are usually not able to reflect such diversity. We propose a method to construct user profiles of multiple interests from folksonomies based on a network clustering technique. Our evaluation shows that the proposed method is able to generate user profiles which reflect the diversity of user interests and can be used as a basis of providing more focused recommendation to the users.

Study of component technologies for fuel cell on-site integrated energy system. Volume 2: Appendices

NASA Technical Reports Server (NTRS)

Lee, W. D.; Mathias, S.

1980-01-01

This data base catalogue was compiled in order to facilitate the analysis of various on site integrated energy system with fuel cell power plants. The catalogue is divided into two sections. The first characterizes individual components in terms of their performance profiles as a function of design parameters. The second characterizes total heating and cooling systems in terms of energy output as a function of input and control variables. The integrated fuel cell systems diagrams and the computer analysis of systems are included as well as the cash flows series for baseline systems.

Space radiator simulation system analysis

NASA Technical Reports Server (NTRS)

Black, W. Z.; Wulff, W.

1972-01-01

A transient heat transfer analysis was carried out on a space radiator heat rejection system exposed to an arbitrarily prescribed combination of aerodynamic heating, solar, albedo, and planetary radiation. A rigorous analysis was carried out for the radiation panel and tubes lying in one plane and an approximate analysis was used to extend the rigorous analysis to the case of a curved panel. The analysis permits the consideration of both gaseous and liquid coolant fluids, including liquid metals, under prescribed, time dependent inlet conditions. The analysis provided a method for predicting: (1) transient and steady-state, two dimensional temperature profiles, (2) local and total heat rejection rates, (3) coolant flow pressure in the flow channel, and (4) total system weight and protection layer thickness.

Application of modified profile analysis to function testing of the motion/no-motion issue in an aircraft ground-handling simulation. [statistical analysis procedure for man machine systems flight simulation

NASA Technical Reports Server (NTRS)

Parrish, R. V.; Mckissick, B. T.; Steinmetz, G. G.

1979-01-01

A recent modification of the methodology of profile analysis, which allows the testing for differences between two functions as a whole with a single test, rather than point by point with multiple tests is discussed. The modification is applied to the examination of the issue of motion/no motion conditions as shown by the lateral deviation curve as a function of engine cut speed of a piloted 737-100 simulator. The results of this application are presented along with those of more conventional statistical test procedures on the same simulator data.

Industry sector analysis: The profile of the market for water and wastewater pollution control systems (the Philippines). Export trade information

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miranda, A.L.

1990-11-01

The market survey covers the water and wastewater pollution control systems market in the Philippines. The analysis contains statistical and narrative information on projected market demand, end-users; receptivity of Philippine consumers to U.S. products; the competitive situation, and market access (tariffs, non-tariff barriers, standards, taxes, distribution channels). It also contains key contact information.

Heterogeneity of Systemic Oxidative Stress Profiles in COPD: A Potential Role of Gender.

PubMed

Maury, Jonathan; Gouzi, Farés; De Rigal, Philippe; Heraud, Nelly; Pincemail, Joël; Molinari, Nicolas; Pomiès, Pascal; Laoudj-Chenivesse, Dalila; Mercier, Jacques; Préfaut, Christian; Hayot, Maurice

2015-01-01

Oxidative stress (OS) plays a key role in the muscle impairment and exercise capacity of COPD patients. However, the literature reveals that systemic OS markers show great heterogeneity, which may hinder the prescription of effective antioxidant supplementation. This study therefore aimed to identify OS markers imbalance of COPD patients, relative to validated normal reference values, and to investigate the possibility of systemic OS profiles. We measured systemic enzymatic/nonenzymatic antioxidant and lipid peroxidation (LP) levels in 54 stable COPD patients referred for a rehabilitation program. The main systemic antioxidant deficits in these patients concerned vitamins and trace elements. Fully 89% of the COPD patients showed a systemic antioxidant imbalance which may have caused the elevated systemic LP levels in 69% of them. Interestingly, two patient profiles (clusters 3 and 4) had a more elevated increase in LP combined with increased copper and/or decreased vitamin C, GSH, and GPx. Further analysis revealed that the systemic LP level was higher in COPD women and associated with exercise capacity. Our present data therefore support future supplementations with antioxidant vitamins and trace elements to improve exercise capacity, but COPD patients will probably show different positive responses.

A graph-based system for network-vulnerability analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swiler, L.P.; Phillips, C.

1998-06-01

This paper presents a graph-based approach to network vulnerability analysis. The method is flexible, allowing analysis of attacks from both outside and inside the network. It can analyze risks to a specific network asset, or examine the universe of possible consequences following a successful attack. The graph-based tool can identify the set of attack paths that have a high probability of success (or a low effort cost) for the attacker. The system could be used to test the effectiveness of making configuration changes, implementing an intrusion detection system, etc. The analysis system requires as input a database of common attacks,more » broken into atomic steps, specific network configuration and topology information, and an attacker profile. The attack information is matched with the network configuration information and an attacker profile to create a superset attack graph. Nodes identify a stage of attack, for example the class of machines the attacker has accessed and the user privilege level he or she has compromised. The arcs in the attack graph represent attacks or stages of attacks. By assigning probabilities of success on the arcs or costs representing level-of-effort for the attacker, various graph algorithms such as shortest-path algorithms can identify the attack paths with the highest probability of success.« less

NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks.

PubMed

Theodosiou, Theodosios; Efstathiou, Georgios; Papanikolaou, Nikolas; Kyrpides, Nikos C; Bagos, Pantelis G; Iliopoulos, Ioannis; Pavlopoulos, Georgios A

2017-07-14

Nowadays, due to the technological advances of high-throughput techniques, Systems Biology has seen a tremendous growth of data generation. With network analysis, looking at biological systems at a higher level in order to better understand a system, its topology and the relationships between its components is of a great importance. Gene expression, signal transduction, protein/chemical interactions, biomedical literature co-occurrences, are few of the examples captured in biological network representations where nodes represent certain bioentities and edges represent the connections between them. Today, many tools for network visualization and analysis are available. Nevertheless, most of them are standalone applications that often (i) burden users with computing and calculation time depending on the network's size and (ii) focus on handling, editing and exploring a network interactively. While such functionality is of great importance, limited efforts have been made towards the comparison of the topological analysis of multiple networks. Network Analysis Provider (NAP) is a comprehensive web tool to automate network profiling and intra/inter-network topology comparison. It is designed to bridge the gap between network analysis, statistics, graph theory and partially visualization in a user-friendly way. It is freely available and aims to become a very appealing tool for the broader community. It hosts a great plethora of topological analysis methods such as node and edge rankings. Few of its powerful characteristics are: its ability to enable easy profile comparisons across multiple networks, find their intersection and provide users with simplified, high quality plots of any of the offered topological characteristics against any other within the same network. It is written in R and Shiny, it is based on the igraph library and it is able to handle medium-scale weighted/unweighted, directed/undirected and bipartite graphs. NAP is available at http://bioinformatics.med.uoc.gr/NAP .

Development of feature extraction analysis for a multi-functional optical profiling device applied to field engineering applications

NASA Astrophysics Data System (ADS)

Han, Xu; Xie, Guangping; Laflen, Brandon; Jia, Ming; Song, Guiju; Harding, Kevin G.

2015-05-01

In the real application environment of field engineering, a large variety of metrology tools are required by the technician to inspect part profile features. However, some of these tools are burdensome and only address a sole application or measurement. In other cases, standard tools lack the capability of accessing irregular profile features. Customers of field engineering want the next generation metrology devices to have the ability to replace the many current tools with one single device. This paper will describe a method based on the ring optical gage concept to the measurement of numerous kinds of profile features useful for the field technician. The ring optical system is composed of a collimated laser, a conical mirror and a CCD camera. To be useful for a wide range of applications, the ring optical system requires profile feature extraction algorithms and data manipulation directed toward real world applications in field operation. The paper will discuss such practical applications as measuring the non-ideal round hole with both off-centered and oblique axes. The algorithms needed to analyze other features such as measuring the width of gaps, radius of transition fillets, fall of step surfaces, and surface parallelism will also be discussed in this paper. With the assistance of image processing and geometric algorithms, these features can be extracted with a reasonable performance. Tailoring the feature extraction analysis to this specific gage offers the potential for a wider application base beyond simple inner diameter measurements. The paper will present experimental results that are compared with standard gages to prove the performance and feasibility of the analysis in real world field engineering. Potential accuracy improvement methods, a new dual ring design and future work will be discussed at the end of this paper.

An Interactive System For Fourier Analysis Of Artichoke Flower Shape.

NASA Astrophysics Data System (ADS)

Impedovo, Sebastiano; Fanelli, Anna M.; Ligouras, Panagiotis

1984-06-01

In this paper we present an interactive system which allows the Fourier analysis of the artichoke flower-head profile. The system consistsof a DEC pdp 11/34 computer with both a a track-following device and a Tektronix 4010/1 graphic and alpha numeric display on-line. Some experiments have been carried out taking into account some different parental types of artichoke flower-head samples. It is shown here that a narrow band of only eight harmonics is sufficient to classify different artichoke flower shapes.

Profiling of Arabidopsis secondary metabolites by capillary liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry.

PubMed

von Roepenack-Lahaye, Edda; Degenkolb, Thomas; Zerjeski, Michael; Franz, Mathias; Roth, Udo; Wessjohann, Ludger; Schmidt, Jürgen; Scheel, Dierk; Clemens, Stephan

2004-02-01

Large-scale metabolic profiling is expected to develop into an integral part of functional genomics and systems biology. The metabolome of a cell or an organism is chemically highly complex. Therefore, comprehensive biochemical phenotyping requires a multitude of analytical techniques. Here, we describe a profiling approach that combines separation by capillary liquid chromatography with the high resolution, high sensitivity, and high mass accuracy of quadrupole time-of-flight mass spectrometry. About 2000 different mass signals can be detected in extracts of Arabidopsis roots and leaves. Many of these originate from Arabidopsis secondary metabolites. Detection based on retention times and exact masses is robust and reproducible. The dynamic range is sufficient for the quantification of metabolites. Assessment of the reproducibility of the analysis showed that biological variability exceeds technical variability. Tools were optimized or established for the automatic data deconvolution and data processing. Subtle differences between samples can be detected as tested with the chalcone synthase deficient tt4 mutant. The accuracy of time-of-flight mass analysis allows to calculate elemental compositions and to tentatively identify metabolites. In-source fragmentation and tandem mass spectrometry can be used to gain structural information. This approach has the potential to significantly contribute to establishing the metabolome of Arabidopsis and other model systems. The principles of separation and mass analysis of this technique, together with its sensitivity and resolving power, greatly expand the range of metabolic profiling.

Field-based detection of biological samples for forensic analysis: Established techniques, novel tools, and future innovations.

PubMed

Morrison, Jack; Watts, Giles; Hobbs, Glyn; Dawnay, Nick

2018-04-01

Field based forensic tests commonly provide information on the presence and identity of biological stains and can also support the identification of species. Such information can support downstream processing of forensic samples and generate rapid intelligence. These approaches have traditionally used chemical and immunological techniques to elicit the result but some are known to suffer from a lack of specificity and sensitivity. The last 10 years has seen the development of field-based genetic profiling systems, with specific focus on moving the mainstay of forensic genetic analysis, namely STR profiling, out of the laboratory and into the hands of the non-laboratory user. In doing so it is now possible for enforcement officers to generate a crime scene DNA profile which can then be matched to a reference or database profile. The introduction of these novel genetic platforms also allows for further development of new molecular assays aimed at answering the more traditional questions relating to body fluid identity and species detection. The current drive for field-based molecular tools is in response to the needs of the criminal justice system and enforcement agencies, and promises a step-change in how forensic evidence is processed. However, the adoption of such systems by the law enforcement community does not represent a new strategy in the way forensic science has integrated previous novel approaches. Nor do they automatically represent a threat to the quality control and assurance practices that are central to the field. This review examines the historical need and subsequent research and developmental breakthroughs in field-based forensic analysis over the past two decades with particular focus on genetic methods Emerging technologies from a range of scientific fields that have potential applications in forensic analysis at the crime scene are identified and associated issues that arise from the shift from laboratory into operational field use are discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

Iodine-filter-based high spectral resolution lidar for atmospheric temperature measurements.

PubMed

Liu, Zhi-Shen; Bi, De-Cang; Song, Xiao-Quan; Xia, Jin-Bao; Li, Rong-Zhong; Wang, Zhang-Jun; She, Chiao-Yao

2009-09-15

This paper presents a method for measuring atmosphere temperature profile using a single iodine filter as frequency discriminator. This high spectral resolution lidar (HSRL) is a system reconfigured with the transmitter of a mobile Doppler wind lidar and with a receiving subsystem redesigned to pass the backscattering optical signal through the iodine cell twice to filter out the aerosol scattering signal and to allow analysis of the molecular scattering spectrum, thus measuring temperatures. We report what are believed to be the first results of vertical temperature profiling from the ground to 16 km altitude by this lidar system (power-aperture product=0.35 Wm(2)). Concurrent observations of an L band radiosonde were carried out on June 14 and August 3, 2008, in good agreement with HSRL temperature profiles.

Interstage Flammability Analysis Approach

NASA Technical Reports Server (NTRS)

Little, Jeffrey K.; Eppard, William M.

2011-01-01

The Interstage of the Ares I launch platform houses several key components which are on standby during First Stage operation: the Reaction Control System (ReCS), the Upper Stage (US) Thrust Vector Control (TVC) and the J-2X with the Main Propulsion System (MPS) propellant feed system. Therefore potentially dangerous leaks of propellants could develop. The Interstage leaks analysis addresses the concerns of localized mixing of hydrogen and oxygen gases to produce deflagration zones in the Interstage of the Ares I launch vehicle during First Stage operation. This report details the approach taken to accomplish the analysis. Specified leakage profiles and actual flammability results are not presented due to proprietary and security restrictions. The interior volume formed by the Interstage walls, bounding interfaces with the Upper and First Stages, and surrounding the J2-X engine was modeled using Loci-CHEM to assess the potential for flammable gas mixtures to develop during First Stage operations. The transient analysis included a derived flammability indicator based on mixture ratios to maintain achievable simulation times. Validation of results was based on a comparison to Interstage pressure profiles outlined in prior NASA studies. The approach proved useful in the bounding of flammability risk in supporting program hazard reviews.

Hyphenation of Raman spectroscopy with gravimetric analysis to interrogate water-solid interactions in pharmaceutical systems.

PubMed

Gift, Alan D; Taylor, Lynne S

2007-01-04

A moisture sorption gravimetric analyzer has been combined with a Raman spectrometer to better understand the various modes of water-solid interactions relevant to pharmaceutical systems. A commercial automated moisture sorption balance was modified to allow non-contact monitoring of the sample properties by interfacing a Raman probe with the sample holder. This hybrid instrument allows for gravimetric and spectroscopic changes to be monitored simultaneously. The utility of this instrument was demonstrated by investigating different types of water-solid interactions including stoichiometric and non-stoichiometric hydrate formation, deliquescence, amorphous-crystalline transformation, and capillary condensation. In each of the model systems, sulfaguanidine, cromolyn sodium, ranitidine HCl, amorphous sucrose and silica gel, spectroscopic changes were observed during the time course of the moisture sorption profile. Analysis of spectroscopic data provided information about the origin of the observed changes in moisture content as a function of relative humidity. Furthermore, multivariate data analysis techniques were employed as a means of processing the spectroscopic data. Principle components analysis was found to be useful to aid in data processing, handling and interpretation of the spectral changes that occurred during the time course of the moisture sorption profile.

An Investigation into the Impact of School Context on Achievement: A Situational Analysis of Five Western Cape Schools in South Africa

ERIC Educational Resources Information Center

Mushayikwa, Emmanuel

2009-01-01

The purpose of this study was to generate a snapshot profile of the teaching and learning environment in each of five schools in Cape Town, South Africa. The generated profile would in turn facilitate the identification of critical, localized and systemic factors that might be targeted by a whole school intervention programme to improve the…

Analyzing the texture changes in the quantitative phase maps of adipocytes

NASA Astrophysics Data System (ADS)

Roitshtain, Darina; Sharabani-Yosef, Orna; Gefen, Amit; Shaked, Natan T.

2016-03-01

We present a new analysis tool for studying texture changes in the quantitative phase maps of live cells acquired by wide-field interferometry. The sensitivity of wide-field interferometry systems to small changes in refractive index enables visualizing cells and inner cell organelles without the using fluorescent dyes or other cell-invasive approaches, which may affect the measurement and require external labeling. Our label-free texture-analysis tool is based directly on the optical path delay profile of the sample and does not necessitate decoupling refractive index and thickness in the cell quantitative phase profile; thus, relevant parameters can be calculated using a single-frame acquisition. Our experimental system includes low-coherence wide-field interferometer, combined with simultaneous florescence microscopy system for validation. We used this system and analysis tool for studying lipid droplets formation in adipocytes. The latter demonstration is relevant for various cellular functions such as lipid metabolism, protein storage and degradation to viral replication. These processes are functionally linked to several physiological and pathological conditions, including obesity and metabolic diseases. Quantification of these biological phenomena based on the texture changes in the cell phase map has a potential as a new cellular diagnosis tool.

Metabolic routes along digestive system of licorice: multicomponent sequential metabolism method in rat.

PubMed

Zhang, Lei; Zhao, Haiyu; Liu, Yang; Dong, Honghuan; Lv, Beiran; Fang, Min; Zhao, Huihui

2016-06-01

This study was conducted to establish the multicomponent sequential metabolism (MSM) method based on comparative analysis along the digestive system following oral administration of licorice (Glycyrrhiza uralensis Fisch., leguminosae), a traditional Chinese medicine widely used for harmonizing other ingredients in a formulae. The licorice water extract (LWE) dissolved in Krebs-Ringer buffer solution (1 g/mL) was used to carry out the experiments and the comparative analysis was performed using HPLC and LC-MS/MS methods. In vitro incubation, in situ closed-loop and in vivo blood sampling were used to measure the LWE metabolic profile along the digestive system. The incubation experiment showed that the LWE was basically stable in digestive juice. A comparative analysis presented the metabolic profile of each prototype and its corresponding metabolites then. Liver was the major metabolic organ for LWE, and the metabolism by the intestinal flora and gut wall was also an important part of the process. The MSM method was practical and could be a potential method to describe the metabolic routes of multiple components before absorption into the systemic blood stream. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Helios: History and Anatomy of a Successful In-House Enterprise High-Throughput Screening and Profiling Data Analysis System.

PubMed

Gubler, Hanspeter; Clare, Nicholas; Galafassi, Laurent; Geissler, Uwe; Girod, Michel; Herr, Guy

2018-06-01

We describe the main characteristics of the Novartis Helios data analysis software system (Novartis, Basel, Switzerland) for plate-based screening and profiling assays, which was designed and built about 11 years ago. It has been in productive use for more than 10 years and is one of the important standard software applications running for a large user community at all Novartis Institutes for BioMedical Research sites globally. A high degree of automation is reached by embedding the data analysis capabilities into a software ecosystem that deals with the management of samples, plates, and result data files, including automated data loading. The application provides a series of analytical procedures, ranging from very simple to advanced, which can easily be assembled by users in very flexible ways. This also includes the automatic derivation of a large set of quality control (QC) characteristics at every step. Any of the raw, intermediate, and final results and QC-relevant quantities can be easily explored through linked visualizations. Links to global assay metadata management, data warehouses, and an electronic lab notebook system are in place. Automated transfer of relevant data to data warehouses and electronic lab notebook systems are also implemented.

Characterization of proacrosin/acrosin system after liquid storage and cryopreservation of turkey semen (Meleagris gallopavo).

PubMed

Słowińska, M; Liszewska, E; Dietrich, G J; Ciereszko, A

2012-09-15

This study was designed to identify the effect of liquid storage at 4 °C for 48 h and cryopreservation on the proacrosin/acrosin system of turkey spermatozoa. Anti-acrosin I antibodies were produced and used to demonstrate Western blot analysis profile of the proacrosin/acrosin system of sperm and seminal plasma and possible changes in the proacrosin/acrosin system of turkey sperm stored for 2.5, 24, and 48 h or cryopreserved. At the same time acrosin-like activity was examined by the measurement of amidase activity of sperm extracts, sperm suspension, and seminal plasma of turkey semen. A computer-assisted sperm analysis system was used to monitor the sperm motility characteristics of turkey sperm stored for 48 h or cryopreserved. Different profiles of the sperm proacrosin/acrosin system were observed regarding the presence or absence of inhibitors (p-nitrophenyl-p'-guanidine benzoate [NPGB] and Kazal family inhibitor) during the extraction process. When NPGB was present three main bands were observed with the molecular weight ranging from 66 to 35 kDa. Bands corresponding to acrosin I and II were not observed. In sperm extract without NPGB, three or four bands were observed with the molecular weight ranging from 41 to 30 kDa. The bands corresponding to acrosin I and II were observed. During liquid storage a decrease in sperm motility and an increase in sperm-extracted amidase activity were observed. After 24 and 48 h of storage, extracted amidase activity was higher than at 2.5 h by 24% and 31%, respectively. However, no changes in the Western blot analysis profiles of sperm extract and seminal plasma were visible during liquid storage. After cryopreservation a decrease in sperm motility and all sperm motility parameters were observed. In contrast to liquid storage, cryopreservation did not increase extracted amidase activity. However, changes in Western blot analysis profiles were visible in sperm extract and seminal plasma after cryopreservation. After freezing-thawing, additional bands appeared in sperm extract and seminal plasma. These bands were of different molecular weight regarding the presence or absence of NPGB. These data suggest that the mechanism of damage to the proacrosin/acrosin system is different for liquid storage and cryopreservation. Liquid storage seems to increase in the susceptibility of the proacrosin/acrosin system to be activated during extraction. Kazal inhibitors of turkey seminal plasma are involved in the control of proacrosin activation. The disturbances of the proacrosin/acrosin system of turkey spermatozoa can be related to a disturbance in the induction of the acrosome reaction. Our results may be important for a better understanding of the proacrosin/acrosin system of turkey spermatozoa and disturbance to this system during liquid storage and cryopreservation. Copyright © 2012 Elsevier Inc. All rights reserved.

What Friends Are For: Collaborative Intelligence Analysis and Search

DTIC Science & Technology

2014-06-01

14. SUBJECT TERMS Intelligence Community, information retrieval, recommender systems , search engines, social networks, user profiling, Lucene...improvements over existing search systems . The improvements are shown to be robust to high levels of human error and low similarity between users ...precision NOLH nearly orthogonal Latin hypercubes P@ precision at documents RS recommender systems TREC Text REtrieval Conference USM user

Effect of management (organic vs conventional) on volatile profiles of six plum cultivars (Prunus salicina Lindl.). A chemometric approach for varietal classification and determination of potential markers.

PubMed

Cuevas, F J; Moreno-Rojas, J M; Arroyo, F; Daza, A; Ruiz-Moreno, M J

2016-05-15

The volatile profiles of six plum cultivars ('Laetitia', 'Primetime', 'Sapphire', 'Showtime', 'Songold' and 'Souvenir') produced under two management systems (conventional and organic) and harvested in two consecutive years were obtained by HS-SPME-GC-MS. Twenty-five metabolites were determined, five of which (pentanal, (E)-2-heptenal, 1-octanol, eucalyptol and 2-pentylfuran) are reported for the first time in Prunus salicina Lindl. Hexanal stood out as a major volatile compound affected by the management system. In addition, partial least square discriminant analysis (PLS-DA) achieved an effective classification of genotypes based on their volatile profiles. A high classification accuracy model was obtained with a sensitivity of 97.9% and a specificity of 99.6%. Furthermore, the application of a dual criterion, based on a method of variable selection, VIP (variable importance in projection) and the results of a univariate analysis (ANOVA), allowed the identification of potential volatile markers in 'Primetime', 'Showtime' and 'Souvenir' genotypes (cultivars not characterised to date). Copyright © 2015 Elsevier Ltd. All rights reserved.

Estimating forest structural characteristics using the airborne LiDAR scanning system and a near-real time profiling laser system

NASA Astrophysics Data System (ADS)

Zhao, Kaiguang

LiDAR (Light Detection and Ranging) directly measures canopy vertical structures, and provides an effective remote sensing solution to accurate and spatially-explicit mapping of forest characteristics, such as canopy height and Leaf Area Index. However, many factors, such as large data volume and high costs for data acquisition, precludes the operational and practical use of most currently available LiDARs for frequent and large-scale mapping. At the same time, a growing need is arising for real-time remote sensing platforms, e.g., to provide timely information for urgent applications. This study aims to develop an airborne profiling LiDAR system, featured with on-the-fly data processing, for near real- or real-time forest inventory. The development of such a system involves implementing the on-board data processing and analysis as well as building useful regression-based models to relate LiDAR measurements with forest biophysical parameters. This work established a paradigm for an on-the-fly airborne profiling LiDAR system to inventory regional forest resources in real- or near real-time. The system was developed based on an existing portable airborne laser system (PALS) that has been previously assembled at NASA by Dr. Ross Nelson. Key issues in automating PALS as an on-the-fly system were addressed, including the design of an archetype for the system workflow, the development of efficient and robust algorithms for automatic data processing and analysis, the development of effective regression models to predict forest biophysical parameters from LiDAR measurements, and the implementation of an integrated software package to incorporate all the above development. This work exploited the untouched potential of airborne laser profilers for real-time forest inventory, and therefore, documented an initial step toward developing airborne-laser-based, on-the-fly, real-time, forest inventory systems. Results from this work demonstrated the utility and effectiveness of airborne scanning or profiling laser systems for remotely measuring various forest structural attributes at a range of scales, i.e., from individual tree, plot, stand and up to regional levels. The system not only provides a regional assessment tool, one that can be used to repeatedly, remotely measure hundreds or thousands of square kilometers with little/no analyst interaction or interpretation, but also serves as a paradigm for future efforts in building more advanced airborne laser systems such as real-time laser scanners.

Illicit drug detection using energy dispersive x-ray diffraction

NASA Astrophysics Data System (ADS)

Cook, E. J.; Griffiths, J. A.; Koutalonis, M.; Gent, C.; Pani, S.; Horrocks, J. A.; George, L.; Hardwick, S.; Speller, R.

2009-05-01

Illicit drugs are imported into countries in myriad ways, including via the postal system and courier services. An automated system is required to detect drugs in parcels for which X-ray diffraction is a suitable technique as it is non-destructive, material specific and uses X-rays of sufficiently high energy to penetrate parcels containing a range of attenuating materials. A database has been constructed containing the measured powder diffraction profiles of several thousand materials likely to be found in parcels. These include drugs, cutting agents, packaging and other innocuous materials. A software model has been developed using these data to predict the diffraction profiles which would be obtained by X-ray diffraction systems with a range of suggested detector (high purity germanium, CZT and scintillation), source and collimation options. The aim of the model was to identify the most promising system geometries, which was done with the aid of multivariate analysis (MVA). The most promising systems were constructed and tested. The diffraction profiles of a range of materials have been measured and used to both validate the model and to identify the presence of drugs in sample packages.

Airborne Wind Profiling With the Data Acquisition and Processing System for a Pulsed 2-Micron Coherent Doppler Lidar System

NASA Technical Reports Server (NTRS)

Beyon, Jeffrey Y.; Koch, Grady J.; Kavaya, Michael J.

2012-01-01

A pulsed 2-micron coherent Doppler lidar system at NASA Langley Research Center in Virginia flew on the NASA's DC-8 aircraft during the NASA Genesis and Rapid Intensification Processes (GRIP) during the summer of 2010. The participation was part of the project Doppler Aerosol Wind Lidar (DAWN) Air. Selected results of airborne wind profiling are presented and compared with the dropsonde data for verification purposes. Panoramic presentations of different wind parameters over a nominal observation time span are also presented for selected GRIP data sets. The realtime data acquisition and analysis software that was employed during the GRIP campaign is introduced with its unique features.

Automated tumor analysis for molecular profiling in lung cancer

PubMed Central

Boyd, Clinton; James, Jacqueline A.; Loughrey, Maurice B.; Hougton, Joseph P.; Boyle, David P.; Kelly, Paul; Maxwell, Perry; McCleary, David; Diamond, James; McArt, Darragh G.; Tunstall, Jonathon; Bankhead, Peter; Salto-Tellez, Manuel

2015-01-01

The discovery and clinical application of molecular biomarkers in solid tumors, increasingly relies on nucleic acid extraction from FFPE tissue sections and subsequent molecular profiling. This in turn requires the pathological review of haematoxylin & eosin (H&E) stained slides, to ensure sample quality, tumor DNA sufficiency by visually estimating the percentage tumor nuclei and tumor annotation for manual macrodissection. In this study on NSCLC, we demonstrate considerable variation in tumor nuclei percentage between pathologists, potentially undermining the precision of NSCLC molecular evaluation and emphasising the need for quantitative tumor evaluation. We subsequently describe the development and validation of a system called TissueMark for automated tumor annotation and percentage tumor nuclei measurement in NSCLC using computerized image analysis. Evaluation of 245 NSCLC slides showed precise automated tumor annotation of cases using Tissuemark, strong concordance with manually drawn boundaries and identical EGFR mutational status, following manual macrodissection from the image analysis generated tumor boundaries. Automated analysis of cell counts for % tumor measurements by Tissuemark showed reduced variability and significant correlation (p < 0.001) with benchmark tumor cell counts. This study demonstrates a robust image analysis technology that can facilitate the automated quantitative analysis of tissue samples for molecular profiling in discovery and diagnostics. PMID:26317646

DOE Office of Scientific and Technical Information (OSTI.GOV)

Munganahalli, D.

Sedco Forex is a drilling contractor that operates approximately 80 rigs on land and offshore worldwide. The HSE management system developed by Sedco Forex is an effort to prevent accidents and minimize losses. An integral part of the HSE management system is establishing risk profiles and thereby minimizing risk and reducing loss exposures. Risk profiles are established based on accident reports, potential accident reports and other risk identification reports (RIR) like the Du Pont STOP system. A rig could fill in as many as 30 accident reports, 30 potential accident reports and 500 STOP cards each year. Statistics are importantmore » for an HSE management system, since they are indicators of success or failure of HSE systems. It is however difficult to establish risk profiles based on statistical information, unless tools are available at the rig site to aid with the analysis. Risk profiles are then used to identify important areas in the operation that may require specific attention to minimize the loss exposure. Programs to address the loss exposure can then be identified and implemented with either a local or corporate approach. In January 1995, Sedco Forex implemented a uniform HSE Database on all the rigs worldwide. In one year companywide, the HSE database would contain information on approximately 500 accident and potential accident reports, and 10,000 STOP cards. This paper demonstrates the salient features of the database and describes how it has helped in establishing key risk profiles. It also shows a recent example of how risk profiles have been established at the corporate level and used to identify the key contributing factors to hands and finger injuries. Based on this information, a campaign was launched to minimize the frequency of occurrence and associated loss attributed to hands and fingers accidents.« less

Autonomous Metabolomics for Rapid Metabolite Identification in Global Profiling

DOE PAGES

Benton, H. Paul; Ivanisevic, Julijana; Mahieu, Nathaniel G.; ...

2014-12-12

An autonomous metabolomic workflow combining mass spectrometry analysis with tandem mass spectrometry data acquisition was designed to allow for simultaneous data processing and metabolite characterization. Although previously tandem mass spectrometry data have been generated on the fly, the experiments described herein combine this technology with the bioinformatic resources of XCMS and METLIN. We can analyze large profiling datasets and simultaneously obtain structural identifications, as a result of this unique integration. Furthermore, validation of the workflow on bacterial samples allowed the profiling on the order of a thousand metabolite features with simultaneous tandem mass spectra data acquisition. The tandem mass spectrometrymore » data acquisition enabled automatic search and matching against the METLIN tandem mass spectrometry database, shortening the current workflow from days to hours. Overall, the autonomous approach to untargeted metabolomics provides an efficient means of metabolomic profiling, and will ultimately allow the more rapid integration of comparative analyses, metabolite identification, and data analysis at a systems biology level.« less

Existence of Inverted Profile in Chemically Responsive Molecular Pathways in the Zebrafish Liver

PubMed Central

Zhang, Xun; Li, Hu; Ma, Jing; Zhang, Louxin; Li, Baowen; Gong, Zhiyuan

2011-01-01

How a living organism maintains its healthy equilibrium in response to endless exposure of potentially harmful chemicals is an important question in current biology. By transcriptomic analysis of zebrafish livers treated by various chemicals, we defined hubs as molecular pathways that are frequently perturbed by chemicals and have high degree of functional connectivity to other pathways. Our network analysis revealed that these hubs were organized into two groups showing inverted functionality with each other. Intriguingly, the inverted activity profiles in these two groups of hubs were observed to associate only with toxicopathological states but not with physiological changes. Furthermore, these inverted profiles were also present in rat, mouse, and human under certain toxicopathological conditions. Thus, toxicopathological-associated anti-correlated profiles in hubs not only indicate their potential use in diagnosis but also development of systems-based therapeutics to modulate gene expression by chemical approach in order to rewire the deregulated activities of hubs back to normal physiology. PMID:22140468

Climatological Study to Determine the Impact of Icing on the Low Level Windshear Alert System. Volume I. Analysis.

DOT National Transportation Integrated Search

1989-09-01

The climatological study was performed to determine the impact of icing on the performance of Low Level Windshear Alert System (LLWAS). : This report presents the icing statistical profile in the form of data tables and histograms of 106 LLWAS sites....

How Confocal Is Confocal Raman Microspectroscopy on the Skin? Impact of Microscope Configuration and Sample Preparation on Penetration Depth Profiles.

PubMed

Lunter, Dominique Jasmin

2016-01-01

The aim of the study was to elucidate the effect of sample preparation and microscope configuration on the results of confocal Raman microspectroscopic evaluation of the penetration of a pharmaceutical active into the skin (depth profiling). Pig ear skin and a hydrophilic formulation containing procaine HCl were used as a model system. The formulation was either left on the skin during the measurement, or was wiped off or washed off prior to the analysis. The microscope configuration was varied with respect to objectives and pinholes used. Sample preparation and microscope configuration had a tremendous effect on the results of depth profiling. Regarding sample preparation, the best results could be observed when the formulation was washed off the skin prior to the analysis. Concerning microscope configuration, the use of a 40 × 0.6 numerical aperture (NA) objective in combination with a 25-µm pinhole or a 100 × 1.25 NA objective in combination with a 50-µm pinhole was found to be advantageous. Complete removal of the sample from the skin before the analysis was found to be crucial. A thorough analysis of the suitability of the chosen microscope configuration should be performed before acquiring concentration depth profiles. © 2016 S. Karger AG, Basel.

Evaluation of the LIA-ANA-Profile-17S for the detection of autoantibodies to nuclear antigens.

PubMed

Yi, Ahram; Lee, Chang-Hoon; Moon, Hee-Won; Kim, Hanah; Hur, Mina; Yun, Yeo-Min

2018-05-01

The diagnostic tests for autoimmune disease include screening for autoantibodies for nuclear antigens (ANA) and antibodies against extractable nuclear antigens (ENA). Using the line immunoassay (LIA) method, various kinds of ENA antibodies can be detected simultaneously. We evaluated the performance of the newly launched LIA-ANA-Profile-17S (Shenzhen YHLO Biotech, Shenzhen, China) as compared to a conventional LIA kit. Residual samples were collected from 200 patients who had been tested for ANA using indirect immunofluorescence. The LIA-ANA-Profile-17S was compared to the EuroLine ANA (Euroimmun, Oberlausitz, Germany) for the analysis of 17 different autoantibodies. The concordance rate and agreement between assays were determined. Samples showing discrepancies between the LIA-ANA-Profile-17S and EuroLine tests were further examined through additional analysis. The overall agreement was moderate (kappa = 0.759, 95% CI = 0.712-0.805). Agreement between assays ranged from weak to almost perfect, except for those tests targeting nucleosomes, histones, and PM-Scl. Of the 57 disparate results between LIA-ANA-Profile-17S and EuroLine, 38 (66.7%) samples tested positive under an additional assay, showing variable patterns between types of autoantibodies. The positive rate of each autoantibody between LIA-ANA-Profile-17S and EuroLine did not differ significantly, except for anti-nucleosome and anti-histone assays in samples from patients diagnosed with systemic lupus erythematosus (P = 0.004 and 0.001, respectively). Compared to those from the conventional EuroLine assay, the LIA-ANA-Profile-17S results showed variable agreement in samples showing different prevalence of each autoantibody. The most frequently detected antibodies showed almost perfect agreement. The LIA-ANA-Profile-17S could play a role in the diagnosis of systemic autoimmune disease in ANA-positive samples. Copyright © 2018 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Efficacy and safety of biologic therapies for systemic lupus erythematosus treatment: systematic review and meta-analysis.

PubMed

Borba, Helena Hiemisch Lobo; Wiens, Astrid; de Souza, Thais Teles; Correr, Cassyano Januário; Pontarolo, Roberto

2014-04-01

The objectives of this study were to evaluate the efficacy, safety, and tolerability of biologic drugs compared with placebo for systemic lupus erythematosus (SLE) treatment. A systematic review evaluating the efficacy and safety of biologic therapies compared with placebo in adult SLE patients treatment was performed. Data from studies performed before September 2013 were collected from several databases (MEDLINE, Cochrane Library, SCIELO, Scopus, and International Pharmaceutical Abstracts). Study eligibility criteria included randomized, double-blind, placebo-controlled trials; regarding treatment with biologic agents in SLE adult patients; and published in English, German, Portuguese, and Spanish. Extracted data were statistically analyzed in a meta-analysis using the Review Manager (RevMan) 5.1 software. Efficacy outcomes included the SELENA-SLEDAI (Safety of Estrogens in Lupus Erythematosus National Assessment version of the SLE Disease Activity Index) score, the SRI (Systemic Lupus Erythematosus Responder Index), normalization of low C3 (<90 mg/dL), anti-double-stranded DNA positive to negative, and no new BILAG (British Isles Lupus Assessment Group index) 1A or 2B flares. Data on safety profile included adverse events, serious and severe adverse events, death, malignancy, infections, and infusion reactions. We also evaluated withdrawals from treatment due to lack of efficacy or adverse events. Thirteen randomized placebo-controlled trials met the criteria for data extraction for systematic review. A meta-analysis regarding the efficacy and safety of belimumab compared with placebo involving four of these trials was undertaken and the remainder contributed to a meta-analysis of the safety of biologic agents. In addition, two trials allowed the performance of a meta-analysis regarding the efficacy and safety of rituximab compared with placebo. Belimumab was more effective than placebo in most evaluated outcomes. No significant differences in the safety and tolerability data were observed between the belimumab and placebo groups. No differences were observed between the rituximab and placebo groups for the efficacy outcomes or safety parameters. Extracted data from the 13 studies were pooled, allowing assessment of the safety of biologic drugs. The meta-analysis revealed a satisfactory safety profile of these agents when used for SLE treatment, as there were no significant differences between the two evaluated groups (biologic agents and placebo) for all outcomes analyzed. Belimumab exhibited a satisfactory profile regarding efficacy, safety, and tolerability. Rituximab showed no superiority over placebo in terms of efficacy, despite its suitable safety profile. Biologic agents exhibited a good safety profile for SLE treatment, indicating that these agents are promising therapies and should be further investigated.

Phenotypic mapping of metabolic profiles using self-organizing maps of high-dimensional mass spectrometry data.

PubMed

Goodwin, Cody R; Sherrod, Stacy D; Marasco, Christina C; Bachmann, Brian O; Schramm-Sapyta, Nicole; Wikswo, John P; McLean, John A

2014-07-01

A metabolic system is composed of inherently interconnected metabolic precursors, intermediates, and products. The analysis of untargeted metabolomics data has conventionally been performed through the use of comparative statistics or multivariate statistical analysis-based approaches; however, each falls short in representing the related nature of metabolic perturbations. Herein, we describe a complementary method for the analysis of large metabolite inventories using a data-driven approach based upon a self-organizing map algorithm. This workflow allows for the unsupervised clustering, and subsequent prioritization of, correlated features through Gestalt comparisons of metabolic heat maps. We describe this methodology in detail, including a comparison to conventional metabolomics approaches, and demonstrate the application of this method to the analysis of the metabolic repercussions of prolonged cocaine exposure in rat sera profiles.

Capacity of milk composition to identify the feeding system used to feed dairy cows.

PubMed

Vicente, Fernando; Santiago, Carme; Jiménez-Calderón, José D; Martínez-Fernández, Adela

2017-08-01

This Research Paper addresses the hypothesis that is possible to identify the type of feed used for dairy cows by means of the analysis of milk composition and the fatty acid profile of milk fat. Sixteen dairy farms were monitored during 1 year with quarterly visits between summer 2014 and spring 2015. Rations varied throughout the year due to annual dynamic change of forage production, forage rotation, variation of nutrient requirements according to physiological state of the animal, etc. The ingredients of the rations were analysed by cluster identifying five feeding systems based on the main ingredient of the diet: grazing, maize silage, grass silage, dry forage and concentrate. Milk composition could explain up to 91·3% of the total variability among feeding systems, while fatty acid profile could explain only up to 61·2% of total variability. However, when the sum of types of fatty acids and their ratios are taken, up to 93·5% of total variability could be explained. The maize silage system had the greatest milk yield, protein, solid non-fat and urea proportions, as well as the highest proportion of saturated fatty acid and lowest concentration of trans11 18 : 1, cis9 18 : 1 and 18 : 3 n3. Principal component analysis distinguishes the maize silage system from other feeding systems, both from milk composition and milk fatty acid profile. Concentrate system overlapped partially with the grazing, grass silage and dry forage systems. The latter systems had the highest concentrations of cis9 18 : 1, trans11 18 : 1 and 18 : 3, but there was no clear differentiation among them.

Profiles of mental health care professionals based on work role performance.

PubMed

Markon, Marie-Pierre; Bamvita, Jean-Marie; Chiocchio, François; Fleury, Marie-Josée

2017-12-01

The worldwide burden of mental disorders is considerable, and on the rise, putting pressure on health care systems. Current reforms aim to improve the efficiency of mental health care systems by increasing service integration in communities and strengthening primary mental health care. In this context, mental health care professionals (MHPs) are increasingly required to work on interdisciplinary teams in a variety of settings. Little is known, however, about the profiles of MHPs in relation to their perceived work role performance. MHPs in Quebec (N = 315) from four local service networks completed a self-administered questionnaire eliciting information on individual and team characteristics, as well as team processes and states. Profiles of MHPs were created using a two-step cluster analysis. Five profiles were generated. MHPs belonging to profiles labelled senior medical outpatient specialized care MHPs and senior psychosocial outpatient specialized care MHPs perceived themselves as more performing than MHPs in other profiles. The profile labelled low-collaborators was significantly less performing than all other groups. Two other profiles were identified, positioned between the aforementioned groups in terms of the perceived performance of MHPs: the junior primary care MHPs and the diversified specialized care MHPs. Seniority within the team, delivering specialized type of care, and positive team processes were all features associated with profiles where perceived work performance was high. Overall, this study supports the case for initiatives aimed at improving stability and interdisciplinary collaboration in health teams, especially in primary care.

Serum Metabolic Profiling of Oocyst-Induced Toxoplasma gondii Acute and Chronic Infections in Mice Using Mass-Spectrometry

PubMed Central

Zhou, Chun-Xue; Cong, Wei; Chen, Xiao-Qing; He, Shen-Yi; Elsheikha, Hany M.; Zhu, Xing-Quan

2018-01-01

Toxoplasma gondii is an obligate intracellular parasite causing severe diseases in immunocompromised individuals and congenitally infected neonates, such as encephalitis and chorioretinitis. This study aimed to determine whether serum metabolic profiling can (i) identify metabolites associated with oocyst-induced T. gondii infection and (ii) detect systemic metabolic differences between T. gondii-infected mice and controls. We performed the first global metabolomics analysis of mice serum challenged with 100 sporulated T. gondii Pru oocysts (Genotype II). Sera from acutely infected mice (11 days post-infection, dpi), chronically infected mice (33 dpi) and control mice were collected and analyzed using LC-MS/MS platform. Following False Discovery Rate filtering, we identified 3871 and 2825 ions in ESI+ or ESI− mode, respectively. Principal Component Analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) identified metabolomic profiles that clearly differentiated T. gondii-infected and -uninfected serum samples. Acute infection significantly influenced the serum metabolome. Our results identified common and uniquely perturbed metabolites and pathways. Acutely infected mice showed perturbations in metabolites associated with glycerophospholipid metabolism, biosynthesis of amino acid, and tyrosine metabolism. These findings demonstrated that acute T. gondii infection induces a global perturbation of mice serum metabolome, providing new insights into the mechanisms underlying systemic metabolic changes during early stage of T. gondii infection. PMID:29354104

EAST kinetic equilibrium reconstruction combining with Polarimeter-Interferometer internal measurement constraints

NASA Astrophysics Data System (ADS)

Lian, H.; Liu, H. Q.; Li, K.; Zou, Z. Y.; Qian, J. P.; Wu, M. Q.; Li, G. Q.; Zeng, L.; Zang, Q.; Lv, B.; Jie, Y. X.; EAST Team

2017-12-01

Plasma equilibrium reconstruction plays an important role in the tokamak plasma research. With a high temporal and spatial resolution, the POlarimeter-INTerferometer (POINT) system on EAST has provided effective measurements for 102s H-mode operation. Based on internal Faraday rotation measurements provided by the POINT system, the equilibrium reconstruction with a more accurate core current profile constraint has been demonstrated successfully on EAST. Combining other experimental diagnostics and external magnetic fields measurement, the kinetic equilibrium has also been reconstructed on EAST. Take the pressure and edge current information from kinetic EFIT into the equilibrium reconstruction with Faraday rotation constraint, the new equilibrium reconstruction not only provides a more accurate internal current profile but also contains edge current and pressure information. One time slice result using new kinetic equilibrium reconstruction with POINT data constraints is demonstrated in this paper and the result shows there is a reversed shear of q profile and the pressure profile is also contained. The new improved equilibrium reconstruction is greatly helpful to the future theoretical analysis.

Activated sludge pilot plant: comparison between experimental and predicted concentration profiles using three different modelling approaches.

PubMed

Le Moullec, Y; Potier, O; Gentric, C; Leclerc, J P

2011-05-01

This paper presents an experimental and numerical study of an activated sludge channel pilot plant. Concentration profiles of oxygen, COD, NO(3) and NH(4) have been measured for several operating conditions. These profiles have been compared to the simulated ones with three different modelling approaches, namely a systemic approach, CFD and compartmental modelling. For these three approaches, the kinetics model was the ASM-1 model (Henze et al., 2001). The three approaches allowed a reasonable simulation of all the concentration profiles except for ammonium for which the simulations results were far from the experimental ones. The analysis of the results showed that the role of the kinetics model is of primary importance for the prediction of activated sludge reactors performance. The fact that existing kinetics parameters in the literature have been determined by parametric optimisation using a systemic model limits the reliability of the prediction of local concentrations and of the local design of activated sludge reactors. Copyright © 2011 Elsevier Ltd. All rights reserved.

Next Generation Sequencing Technology and Genomewide Data Analysis: Perspectives for Retinal Research

PubMed Central

Chaitankar, Vijender; Karakülah, Gökhan; Ratnapriya, Rinki; Giuste, Felipe O.; Brooks, Matthew J.; Swaroop, Anand

2016-01-01

The advent of high throughput next generation sequencing (NGS) has accelerated the pace of discovery of disease-associated genetic variants and genomewide profiling of expressed sequences and epigenetic marks, thereby permitting systems-based analyses of ocular development and disease. Rapid evolution of NGS and associated methodologies presents significant challenges in acquisition, management, and analysis of large data sets and for extracting biologically or clinically relevant information. Here we illustrate the basic design of commonly used NGS-based methods, specifically whole exome sequencing, transcriptome, and epigenome profiling, and provide recommendations for data analyses. We briefly discuss systems biology approaches for integrating multiple data sets to elucidate gene regulatory or disease networks. While we provide examples from the retina, the NGS guidelines reviewed here are applicable to other tissues/cell types as well. PMID:27297499

Geometric analysis of maxillary first premolar prepared by two nickel-titanium rotary instruments.

PubMed

Al-Sudani, Dina; Almalki, Majed; Al-Shahrani, Saad; Ahlquist, Michael

2014-03-01

The present study was conducted with the aim of evaluating and comparing the shaping ability of two Nickel-titanium rotary instruments, with two disparate design features, on root canal geometry of extracted human maxillary first premolars using microcomputed tomography. Twenty four bifurcated maxillary first premolars were divided into two groups and embedded in a rubber-based impression material. Both groups were submitted to micro-computed tomography before and after canal preparation (buccal and palatal) with either ProFile Vortex or Revo-S rotary instruments. Images were reconstructed and cross-sections corresponding to a distance 1, 2, 3, 4, 5, 6, and 7 mm from the anatomical apex were selected for canal transportation analysis. Volume changes were also measured. The degree and direction of canal transportation were non-significant for both instruments. Statistically significant differences were observed only between levels in the buccal canal in both groups. There was no significant difference between the two rotary systems in regards to the volume of dentin removed. Our findings showed that ProFile Vortex and Revo-S instruments respected the original root canal anatomy and behaved similarly. ProFile Vortex rotary systems produced with innovative process were concluded to shape the upper maxillary premolar by leading minimal canal transportation, similar to Revo-S, rotary systems produced from traditional process.

Worldwide Topology of the Scientific Subject Profile: A Macro Approach in the Country Level

PubMed Central

Moya-Anegón, Félix; Herrero-Solana, Víctor

2013-01-01

Background Models for the production of knowledge and systems of innovation and science are key elements for characterizing a country in view of its scientific thematic profile. With regard to scientific output and publication in journals of international visibility, the countries of the world may be classified into three main groups according to their thematic bias. Methodology/Principal Findings This paper aims to classify the countries of the world in several broad groups, described in terms of behavioural models that attempt to sum up the characteristics of their systems of knowledge and innovation. We perceive three clusters in our analysis: 1) the biomedical cluster, 2) the basic science & engineering cluster, and 3) the agricultural cluster. The countries are conceptually associated with the clusters via Principal Component Analysis (PCA), and a Multidimensional Scaling (MDS) map with all the countries is presented. Conclusions/Significance As we have seen, insofar as scientific output and publication in journals of international visibility is concerned, the countries of the world may be classified into three main groups according to their thematic profile. These groups can be described in terms of behavioral models that attempt to sum up the characteristics of their systems of knowledge and innovation. PMID:24349467

Asymmetric simple exclusion process with position-dependent hopping rates: Phase diagram from boundary-layer analysis.

PubMed

Mukherji, Sutapa

2018-03-01

In this paper, we study a one-dimensional totally asymmetric simple exclusion process with position-dependent hopping rates. Under open boundary conditions, this system exhibits boundary-induced phase transitions in the steady state. Similarly to totally asymmetric simple exclusion processes with uniform hopping, the phase diagram consists of low-density, high-density, and maximal-current phases. In various phases, the shape of the average particle density profile across the lattice including its boundary-layer parts changes significantly. Using the tools of boundary-layer analysis, we obtain explicit solutions for the density profile in different phases. A detailed analysis of these solutions under different boundary conditions helps us obtain the equations for various phase boundaries. Next, we show how the shape of the entire density profile including the location of the boundary layers can be predicted from the fixed points of the differential equation describing the boundary layers. We discuss this in detail through several examples of density profiles in various phases. The maximal-current phase appears to be an especially interesting phase where the boundary layer flows to a bifurcation point on the fixed-point diagram.

microMS: A Python Platform for Image-Guided Mass Spectrometry Profiling

NASA Astrophysics Data System (ADS)

Comi, Troy J.; Neumann, Elizabeth K.; Do, Thanh D.; Sweedler, Jonathan V.

2017-09-01

Image-guided mass spectrometry (MS) profiling provides a facile framework for analyzing samples ranging from single cells to tissue sections. The fundamental workflow utilizes a whole-slide microscopy image to select targets of interest, determine their spatial locations, and subsequently perform MS analysis at those locations. Improving upon prior reported methodology, a software package was developed for working with microscopy images. microMS, for microscopy-guided mass spectrometry, allows the user to select and profile diverse samples using a variety of target patterns and mass analyzers. Written in Python, the program provides an intuitive graphical user interface to simplify image-guided MS for novice users. The class hierarchy of instrument interactions permits integration of new MS systems while retaining the feature-rich image analysis framework. microMS is a versatile platform for performing targeted profiling experiments using a series of mass spectrometers. The flexibility in mass analyzers greatly simplifies serial analyses of the same targets by different instruments. The current capabilities of microMS are presented, and its application for off-line analysis of single cells on three distinct instruments is demonstrated. The software has been made freely available for research purposes. [Figure not available: see fulltext.

microMS: A Python Platform for Image-Guided Mass Spectrometry Profiling.

PubMed

Comi, Troy J; Neumann, Elizabeth K; Do, Thanh D; Sweedler, Jonathan V

2017-09-01

Image-guided mass spectrometry (MS) profiling provides a facile framework for analyzing samples ranging from single cells to tissue sections. The fundamental workflow utilizes a whole-slide microscopy image to select targets of interest, determine their spatial locations, and subsequently perform MS analysis at those locations. Improving upon prior reported methodology, a software package was developed for working with microscopy images. microMS, for microscopy-guided mass spectrometry, allows the user to select and profile diverse samples using a variety of target patterns and mass analyzers. Written in Python, the program provides an intuitive graphical user interface to simplify image-guided MS for novice users. The class hierarchy of instrument interactions permits integration of new MS systems while retaining the feature-rich image analysis framework. microMS is a versatile platform for performing targeted profiling experiments using a series of mass spectrometers. The flexibility in mass analyzers greatly simplifies serial analyses of the same targets by different instruments. The current capabilities of microMS are presented, and its application for off-line analysis of single cells on three distinct instruments is demonstrated. The software has been made freely available for research purposes. Graphical Abstract ᅟ.

Speed Profiles for Improvement of Maritime Emission Estimation.

PubMed

Yau, Pui Shan; Lee, Shun-Cheng; Ho, Kin Fai

2012-12-01

Maritime emissions play an important role in anthropogenic emissions, particularly for cities with busy ports such as Hong Kong. Ship emissions are strongly dependent on vessel speed, and thus accurate vessel speed is essential for maritime emission studies. In this study, we determined minute-by-minute high-resolution speed profiles of container ships on four major routes in Hong Kong waters using Automatic Identification System (AIS). The activity-based ship emissions of NO(x), CO, HC, CO(2), SO(2), and PM(10) were estimated using derived vessel speed profiles, and results were compared with those using the speed limits of control zones. Estimation using speed limits resulted in up to twofold overestimation of ship emissions. Compared with emissions estimated using the speed limits of control zones, emissions estimated using vessel speed profiles could provide results with up to 88% higher accuracy. Uncertainty analysis and sensitivity analysis of the model demonstrated the significance of improvement of vessel speed resolution. From spatial analysis, it is revealed that SO(2) and PM(10) emissions during maneuvering within 1 nautical mile from port were the highest. They contributed 7%-22% of SO(2) emissions and 8%-17% of PM(10) emissions of the entire voyage in Hong Kong.

Asymmetric simple exclusion process with position-dependent hopping rates: Phase diagram from boundary-layer analysis

NASA Astrophysics Data System (ADS)

Mukherji, Sutapa

2018-03-01

In this paper, we study a one-dimensional totally asymmetric simple exclusion process with position-dependent hopping rates. Under open boundary conditions, this system exhibits boundary-induced phase transitions in the steady state. Similarly to totally asymmetric simple exclusion processes with uniform hopping, the phase diagram consists of low-density, high-density, and maximal-current phases. In various phases, the shape of the average particle density profile across the lattice including its boundary-layer parts changes significantly. Using the tools of boundary-layer analysis, we obtain explicit solutions for the density profile in different phases. A detailed analysis of these solutions under different boundary conditions helps us obtain the equations for various phase boundaries. Next, we show how the shape of the entire density profile including the location of the boundary layers can be predicted from the fixed points of the differential equation describing the boundary layers. We discuss this in detail through several examples of density profiles in various phases. The maximal-current phase appears to be an especially interesting phase where the boundary layer flows to a bifurcation point on the fixed-point diagram.

Chemotaxonomic Study of Citrus, Poncirus and Fortunella Genotypes Based on Peel Oil Volatile Compounds - Deciphering the Genetic Origin of Mangshanyegan (Citrus nobilis Lauriro)

PubMed Central

Liu, Cuihua; Jiang, Dong; Cheng, Yunjiang; Deng, Xiuxin; Chen, Feng; Fang, Liu; Ma, Zhaocheng; Xu, Juan

2013-01-01

Volatile profiles yielded from gas chromatography-mass spectrometry (GC-MS) analysis provide abundant information not only for metabolism-related research, but also for chemotaxonomy. To study the chemotaxonomy of Mangshanyegan, its volatile profiles of fruit and leaf and those of 29 other genotypes of Citrus, Poncirus, and Fortunella were subjected to phylogenetic analyses. Results showed that 145 identified (including 64 tentatively identified) and 15 unidentified volatile compounds were detected from their peel oils. The phylogenetic analysis of peel oils based on hierarchical cluster analysis (HCA) demonstrated a good agreement with the Swingle taxonomy system, in which the three genera of Citrus, Poncirus, and Fortunella were almost completely separated. As to Citrus, HCA indicated that Citrophorum, Cephalocitrus, and Sinocitrus fell into three subgroups, respectively. Also, it revealed that Mangshanyegan contain volatile compounds similar to those from pummelo, though it is genetically believed to be a mandarin. These results were further supported by the principal component analysis of the peel oils and the HCA results of volatile profiles of leaves in the study. PMID:23516475

Evaluation of vertical profiles to design continuous descent approach procedure

NASA Astrophysics Data System (ADS)

Pradeep, Priyank

The current research focuses on predictability, variability and operational feasibility aspect of Continuous Descent Approach (CDA), which is among the key concepts of the Next Generation Air Transportation System (NextGen). The idle-thrust CDA is a fuel economical, noise and emission abatement procedure, but requires increased separation to accommodate for variability and uncertainties in vertical and speed profiles of arriving aircraft. Although a considerable amount of researches have been devoted to the estimation of potential benefits of the CDA, only few have attempted to explain the predictability, variability and operational feasibility aspect of CDA. The analytical equations derived using flight dynamics and Base of Aircraft and Data (BADA) Total Energy Model (TEM) in this research gives insight into dependency of vertical profile of CDA on various factors like wind speed and gradient, weight, aircraft type and configuration, thrust settings, atmospheric factors (deviation from ISA (DISA), pressure and density of the air) and descent speed profile. Application of the derived equations to idle-thrust CDA gives an insight into sensitivity of its vertical profile to multiple factors. This suggests fixed geometric flight path angle (FPA) CDA has higher degree of predictability and lesser variability at the cost of non-idle and low thrust engine settings. However, with optimized design this impact can be overall minimized. The CDA simulations were performed using Future ATM Concept Evaluation Tool (FACET) based on radar-track and aircraft type data (BADA) of the real air-traffic to some of the busiest airports in the USA (ATL, SFO and New York Metroplex (JFK, EWR and LGA)). The statistical analysis of the vertical profiles of CDA shows 1) mean geometric FPAs derived from various simulated vertical profiles are consistently shallower than 3° glideslope angle and 2) high level of variability in vertical profiles of idle-thrust CDA even in absence of uncertainties in external factors. Analysis from operational feasibility perspective suggests that two key features of the performance based Flight Management System (FMS) i.e. required time of arrival (RTA) and geometric descent path would help in reduction of unpredictability associated with arrival time and vertical profile of aircraft guided by the FMS coupled with auto-pilot (AP) and auto-throttle (AT). The statistical analysis of the vertical profiles of CDA also suggests that for procedure design window type, 'AT or above' and 'AT or below' altitude and FPA constraints are more realistic and useful compared to obsolete 'AT' type altitude constraint.

Improved density profile measurements in the C-2U advanced beam-driven Field-Reversed Configuration (FRC) plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beall, M., E-mail: mbeall@trialphaenergy.com; Deng, B. H.; Gota, H.

2016-11-15

In the prior C-2 experiment, electron density was measured using a two-color 6-chord CO{sub 2}/HeNe interferometer. Analysis shows that high-frequency common mode phase noise can be reduced by a factor of 3 by constructing a reference chord. In the system upgrade from C-2 to C-2U a 4-chord far-infrared laser interferometer was developed, which demonstrated superior sensitivity (1 × 10{sup 16} m{sup −2} at >1 MHz bandwidth) and solved the under spatial sampling issue of the C-2 interferometer system. Improved density-profile measurement results are presented in this paper, including evidence of fast-ion modified density profile and stabilization of the n =more » 1 plasma wobble mode.« less

Improved upper winds models for several astronomical observatories.

PubMed

Roberts, Lewis C; Bradford, L William

2011-01-17

An understanding of wind speed and direction as a function of height are critical to the proper modeling of atmospheric turbulence. We have used radiosonde data from launch sites near significant astronomical observatories and created averaged profiles of wind speed and direction and have also computed Richardson number profiles. Using data from the last 30 years, we confirm a 1977 Greenwood wind profile, and extend it to include parameters that show seasonal variations and differences in location. The added information from our models is useful for the design of adaptive optics systems and other imaging systems. Our analysis of the Richardson number suggests that persistent turbulent layers may be inferred when low values are present in our long term averaged data. Knowledge of the presence of these layers may help with planning for adaptive optics and laser communications.

First results of the SOL reflectometer on Alcator C-Mod.

PubMed

Lau, C; Hanson, G; Lin, Y; Wilgen, J; Wukitch, S; Labombard, B; Wallace, G

2012-10-01

A swept-frequency X-mode reflectometer has been built on Alcator C-Mod to measure the scrape-off layer (SOL) density profiles adjacent to the lower hybrid launcher. The reflectometer system operates between 100 and 146 GHz at sweep rates from 10 μs to 1 ms and covers a density range of ∼10(16)-10(20) m(-3) at B(0) = 5-5.4 T. This paper discusses the analysis of reflectometer density profiles and presents first experimental results of SOL density profile modifications due to the application of lower hybrid range-of-frequencies power to L-mode discharges. Comparison between density profiles measured by the X-mode reflectometer and scanning Langmuir probes is also shown.

NASA Hispanic Heritage Month Employee Profile- Gustavo Martinez - Marshall Space Flight Center

NASA Image and Video Library

2016-10-19

In observance of National Hispanic Heritage Month, Gustavo Martinez, a propulsion engineer at NASA’s Marshall Space Flight Center, is featured in this video profile. Martinez, a first-generation American of Mexican descent, earned his bachelors and masters in mechanical engineering from the University of Texas at El Paso. He works in the Liquid Engine System Branch of Marshall’s Propulsion Systems Department, supporting RS-25 engine systems analysis and test preparations for NASA’s Space Launch System. National Hispanic Heritage Month honors the cultures and contributions of Americans whose ancestors originated from Spain, Mexico, the Caribbean and Central and South America. The observation started in 1968 as Hispanic Heritage Week under President Lyndon Johnson and was expanded into law by President Ronald Reagan in 1988.

MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways

PubMed Central

Koumakis, Lefteris; Kartsaki, Evgenia; Chatzimina, Maria; Zervakis, Michalis; Vassou, Despoina; Marias, Kostas; Moustakis, Vassilis; Potamias, George

2016-01-01

Pathway analysis methodologies couple traditional gene expression analysis with knowledge encoded in established molecular pathway networks, offering a promising approach towards the biological interpretation of phenotype differentiating genes. Early pathway analysis methodologies, named as gene set analysis (GSA), view pathways just as plain lists of genes without taking into account either the underlying pathway network topology or the involved gene regulatory relations. These approaches, even if they achieve computational efficiency and simplicity, consider pathways that involve the same genes as equivalent in terms of their gene enrichment characteristics. Most recent pathway analysis approaches take into account the underlying gene regulatory relations by examining their consistency with gene expression profiles and computing a score for each profile. Even with this approach, assessing and scoring single-relations limits the ability to reveal key gene regulation mechanisms hidden in longer pathway sub-paths. We introduce MinePath, a pathway analysis methodology that addresses and overcomes the aforementioned problems. MinePath facilitates the decomposition of pathways into their constituent sub-paths. Decomposition leads to the transformation of single-relations to complex regulation sub-paths. Regulation sub-paths are then matched with gene expression sample profiles in order to evaluate their functional status and to assess phenotype differential power. Assessment of differential power supports the identification of the most discriminant profiles. In addition, MinePath assess the significance of the pathways as a whole, ranking them by their p-values. Comparison results with state-of-the-art pathway analysis systems are indicative for the soundness and reliability of the MinePath approach. In contrast with many pathway analysis tools, MinePath is a web-based system (www.minepath.org) offering dynamic and rich pathway visualization functionality, with the unique characteristic to color regulatory relations between genes and reveal their phenotype inclination. This unique characteristic makes MinePath a valuable tool for in silico molecular biology experimentation as it serves the biomedical researchers’ exploratory needs to reveal and interpret the regulatory mechanisms that underlie and putatively govern the expression of target phenotypes. PMID:27832067

MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways.

PubMed

Koumakis, Lefteris; Kanterakis, Alexandros; Kartsaki, Evgenia; Chatzimina, Maria; Zervakis, Michalis; Tsiknakis, Manolis; Vassou, Despoina; Kafetzopoulos, Dimitris; Marias, Kostas; Moustakis, Vassilis; Potamias, George

2016-11-01

Pathway analysis methodologies couple traditional gene expression analysis with knowledge encoded in established molecular pathway networks, offering a promising approach towards the biological interpretation of phenotype differentiating genes. Early pathway analysis methodologies, named as gene set analysis (GSA), view pathways just as plain lists of genes without taking into account either the underlying pathway network topology or the involved gene regulatory relations. These approaches, even if they achieve computational efficiency and simplicity, consider pathways that involve the same genes as equivalent in terms of their gene enrichment characteristics. Most recent pathway analysis approaches take into account the underlying gene regulatory relations by examining their consistency with gene expression profiles and computing a score for each profile. Even with this approach, assessing and scoring single-relations limits the ability to reveal key gene regulation mechanisms hidden in longer pathway sub-paths. We introduce MinePath, a pathway analysis methodology that addresses and overcomes the aforementioned problems. MinePath facilitates the decomposition of pathways into their constituent sub-paths. Decomposition leads to the transformation of single-relations to complex regulation sub-paths. Regulation sub-paths are then matched with gene expression sample profiles in order to evaluate their functional status and to assess phenotype differential power. Assessment of differential power supports the identification of the most discriminant profiles. In addition, MinePath assess the significance of the pathways as a whole, ranking them by their p-values. Comparison results with state-of-the-art pathway analysis systems are indicative for the soundness and reliability of the MinePath approach. In contrast with many pathway analysis tools, MinePath is a web-based system (www.minepath.org) offering dynamic and rich pathway visualization functionality, with the unique characteristic to color regulatory relations between genes and reveal their phenotype inclination. This unique characteristic makes MinePath a valuable tool for in silico molecular biology experimentation as it serves the biomedical researchers' exploratory needs to reveal and interpret the regulatory mechanisms that underlie and putatively govern the expression of target phenotypes.

The upgrade of the Thomson scattering system for measurement on the C-2/C-2U devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhai, K.; Schindler, T.; Kinley, J.

The C-2/C-2U Thomson scattering system has been substantially upgraded during the latter phase of C-2/C-2U program. A Rayleigh channel has been added to each of the three polychromators of the C-2/C-2U Thomson scattering system. Onsite spectral calibration has been applied to avoid the issue of different channel responses at different spots on the photomultiplier tube surface. With the added Rayleigh channel, the absolute intensity response of the system is calibrated with Rayleigh scattering in argon gas from 0.1 to 4 Torr, where the Rayleigh scattering signal is comparable to the Thomson scattering signal at electron densities from 1 × 10{supmore » 13} to 4 × 10{sup 14} cm{sup −3}. A new signal processing algorithm, using a maximum likelihood method and including detailed analysis of different noise contributions within the system, has been developed to obtain electron temperature and density profiles. The system setup, spectral and intensity calibration procedure and its outcome, data analysis, and the results of electron temperature/density profile measurements will be presented.« less

DNA and RNA profiling of excavated human remains with varying postmortem intervals.

PubMed

van den Berge, M; Wiskerke, D; Gerretsen, R R R; Tabak, J; Sijen, T

2016-11-01

When postmortem intervals (PMIs) increase such as with longer burial times, human remains suffer increasingly from the taphonomic effects of decomposition processes such as autolysis and putrefaction. In this study, various DNA analysis techniques and a messenger RNA (mRNA) profiling method were applied to examine for trends in nucleic acid degradation and the postmortem interval. The DNA analysis techniques include highly sensitive DNA quantitation (with and without degradation index), standard and low template STR profiling, insertion and null alleles (INNUL) of retrotransposable elements typing and mitochondrial DNA profiling. The used mRNA profiling system targets genes with tissue specific expression for seven human organs as reported by Lindenbergh et al. (Int J Legal Med 127:891-900, 27) and has been applied to forensic evidentiary traces but not to excavated tissues. The techniques were applied to a total of 81 brain, lung, liver, skeletal muscle, heart, kidney and skin samples obtained from 19 excavated graves with burial times ranging from 4 to 42 years. Results show that brain and heart are the organs in which both DNA and RNA remain remarkably stable, notwithstanding long PMIs. The other organ tissues either show poor overall profiling results or vary for DNA and RNA profiling success, with sometimes DNA and other times RNA profiling being more successful. No straightforward relations were observed between nucleic acid profiling results and the PMI. This study shows that not only DNA but also RNA molecules can be remarkably stable and used for profiling of long-buried human remains, which corroborate forensic applications. The insight that the brain and heart tissues tend to provide the best profiling results may change sampling policies in identification cases of degrading cadavers.

Beach Profile Analysis System (BPAS). Volume III. BPAS User’s Guide: Analysis Module SURVY1.

DTIC Science & Technology

1982-06-01

extrapolated using the two seawardmost points. Before computing volume changes, common bonds are established relative to the landward and seawsrd extent...Cyber 176 or equivalent computer. Such features include the 10- character, 60-bit word size, the FORTRAN- callable sort routine (interfacing with the NOS

Beach Profile Analysis System (BPAS). Volume IV. BPAS User’s Guide: Analysis Module SURVY2.

DTIC Science & Technology

1982-06-01

feet NSL), the shoreline position can be extrapolated using the two sawardmost points. Before computing volume changes, comon bonds are established...computer. Such features include the 10- character, 60-bit word size, the FORTRAN- callable sort routine (interfacing with the NOS or NOS/BE operating

A risk-based approach to management of leachables utilizing statistical analysis of extractables.

PubMed

Stults, Cheryl L M; Mikl, Jaromir; Whelehan, Oliver; Morrical, Bradley; Duffield, William; Nagao, Lee M

2015-04-01

To incorporate quality by design concepts into the management of leachables, an emphasis is often put on understanding the extractable profile for the materials of construction for manufacturing disposables, container-closure, or delivery systems. Component manufacturing processes may also impact the extractable profile. An approach was developed to (1) identify critical components that may be sources of leachables, (2) enable an understanding of manufacturing process factors that affect extractable profiles, (3) determine if quantitative models can be developed that predict the effect of those key factors, and (4) evaluate the practical impact of the key factors on the product. A risk evaluation for an inhalation product identified injection molding as a key process. Designed experiments were performed to evaluate the impact of molding process parameters on the extractable profile from an ABS inhaler component. Statistical analysis of the resulting GC chromatographic profiles identified processing factors that were correlated with peak levels in the extractable profiles. The combination of statistically significant molding process parameters was different for different types of extractable compounds. ANOVA models were used to obtain optimal process settings and predict extractable levels for a selected number of compounds. The proposed paradigm may be applied to evaluate the impact of material composition and processing parameters on extractable profiles and utilized to manage product leachables early in the development process and throughout the product lifecycle.

An analysis of a charring ablator with thermal nonequilibrium, chemical kinetics, and mass transfer

NASA Technical Reports Server (NTRS)

Clark, R. K.

1973-01-01

The differential equations governing the transient response of a one-dimensional ablative thermal protection system are presented for thermal nonequilibrium between the pyrolysis gases and the char layer and with finite rate chemical reactions occurring. The system consists of three layers (the char layer, the uncharred layer, and an optical insulation layer) with concentrated heat sinks at the back surface and between the second and third layers. The equations are solved numerically by using a modified implicit finite difference scheme to obtain solutions for the thickness of the charred and uncharred layers, surface recession and pyrolysis rates, solid temperatures, porosity profiles, and profiles of pyrolysis-gas temperature, pressure, composition, and flow rate. Good agreement is obtained between numerical results and exact solutions for a number of simplified cases. The complete numerical analysis is used to obtain solutions for an ablative system subjected to a constant heating environment. Effects of thermal, chemical, and mass transfer processes are shown.

Enhanced semantic interoperability by profiling health informatics standards.

PubMed

López, Diego M; Blobel, Bernd

2009-01-01

Several standards applied to the healthcare domain support semantic interoperability. These standards are far from being completely adopted in health information system development, however. The objective of this paper is to provide a method and suggest the necessary tooling for reusing standard health information models, by that way supporting the development of semantically interoperable systems and components. The approach is based on the definition of UML Profiles. UML profiling is a formal modeling mechanism to specialize reference meta-models in such a way that it is possible to adapt those meta-models to specific platforms or domains. A health information model can be considered as such a meta-model. The first step of the introduced method identifies the standard health information models and tasks in the software development process in which healthcare information models can be reused. Then, the selected information model is formalized as a UML Profile. That Profile is finally applied to system models, annotating them with the semantics of the information model. The approach is supported on Eclipse-based UML modeling tools. The method is integrated into a comprehensive framework for health information systems development, and the feasibility of the approach is demonstrated in the analysis, design, and implementation of a public health surveillance system, reusing HL7 RIM and DIMs specifications. The paper describes a method and the necessary tooling for reusing standard healthcare information models. UML offers several advantages such as tooling support, graphical notation, exchangeability, extensibility, semi-automatic code generation, etc. The approach presented is also applicable for harmonizing different standard specifications.

A combined boundary-profile and automated data-reduction and analysis system. [meteorological balloon-calculator system

NASA Technical Reports Server (NTRS)

Deloach, R.; Morris, A. L.; Mcbeth, R. B.

1976-01-01

A portable boundary-layer meteorological data-acquisition and analysis system is described which employs a small tethered balloon and a programmable calculator. The system is capable of measuring pressure, wet- and dry-bulb temperature, wind speed, and temperature fluctuations as a function of height and time. Other quantities, which can be calculated in terms of these, can also be made available in real time. All quantities, measured and calculated, can be printed, plotted, and stored on magnetic tape in the field during the data-acquisition phase of an experiment.

Hall Thruster Technology for NASA Science Missions

NASA Technical Reports Server (NTRS)

Manzella, David; Oh, David; Aadland, Randall

2005-01-01

The performance of a prototype Hall thruster designed for Discovery-class NASA science mission applications was evaluated at input powers ranging from 0.2 to 2.9 kilowatts. These data were used to construct a throttle profile for a projected Hall thruster system based on this prototype thruster. The suitability of such a Hall thruster system to perform robotic exploration missions was evaluated through the analysis of a near Earth asteroid sample return mission. This analysis demonstrated that a propulsion system based on the prototype Hall thruster offers mission benefits compared to a propulsion system based on an existing ion thruster.

Gene expression analysis predicts insect venom anaphylaxis in indolent systemic mastocytosis.

PubMed

Niedoszytko, M; Bruinenberg, M; van Doormaal, J J; de Monchy, J G R; Nedoszytko, B; Koppelman, G H; Nawijn, M C; Wijmenga, C; Jassem, E; Elberink, J N G Oude

2011-05-01

Anaphylaxis to insect venom (Hymenoptera) is most severe in patients with mastocytosis and may even lead to death. However, not all patients with mastocytosis suffer from anaphylaxis. The aim of the study was to analyze differences in gene expression between patients with indolent systemic mastocytosis (ISM) and a history of insect venom anaphylaxis (IVA) compared to those patients without a history of anaphylaxis, and to determine the predictive use of gene expression profiling. Whole-genome gene expression analysis was performed in peripheral blood cells. Twenty-two adults with ISM were included: 12 with a history of IVA and 10 without a history of anaphylaxis of any kind. Significant differences in single gene expression corrected for multiple testing were found for 104 transcripts (P < 0.05). Gene ontology analysis revealed that the differentially expressed genes were involved in pathways responsible for the development of cancer and focal and cell adhesion suggesting that the expression of genes related to the differentiation state of cells is higher in patients with a history of anaphylaxis. Based on the gene expression profiles, a naïve Bayes prediction model was built identifying patients with IVA. In ISM, gene expression profiles are different between patients with a history of IVA and those without. These findings might reflect a more pronounced mast cells dysfunction in patients without a history of anaphylaxis. Gene expression profiling might be a useful tool to predict the risk of anaphylaxis on insect venom in patients with ISM. Prospective studies are needed to substantiate any conclusions. © 2010 John Wiley & Sons A/S.

LIDAR Developments at Clermont-Ferrand—France for Atmospheric Observation

PubMed Central

Fréville, Patrick; Montoux, Nadège; Baray, Jean-Luc; Chauvigné, Aurélien; Réveret, François; Hervo, Maxime; Dionisi, Davide; Payen, Guillaume; Sellegri, Karine

2015-01-01

We present a Rayleigh-Mie-Raman LIDAR system in operation at Clermont-Ferrand (France) since 2008. The system provides continuous vertical tropospheric profiles of aerosols, cirrus optical properties and water vapour mixing ratio. Located in proximity to the high altitude Puy de Dôme station, labelled as the GAW global station PUY since August 2014, it is a useful tool to describe the boundary layer dynamics and hence interpret in situ measurements. This LIDAR has been upgraded with specific hardware/software developments and laboratory calibrations in order to improve the quality of the profiles, calibrate the depolarization ratio, and increase the automation of operation. As a result, we provide a climatological water vapour profile analysis for the 2009–2013 period, showing an annual cycle with a winter minimum and a summer maximum, consistent with in-situ observations at the PUY station. An overview of a preliminary climatology of cirrus clouds frequency shows that in 2014, more than 30% of days present cirrus events. Finally, the backscatter coefficient profile observed on 27 September 2014 shows the capacity of the system to detect cirrus clouds at 13 km altitude, in presence of aerosols below the 5 km altitude. PMID:25643059

A Comparison and Evaluation of Real-Time Software Systems Modeling Languages

NASA Technical Reports Server (NTRS)

Evensen, Kenneth D.; Weiss, Kathryn Anne

2010-01-01

A model-driven approach to real-time software systems development enables the conceptualization of software, fostering a more thorough understanding of its often complex architecture and behavior while promoting the documentation and analysis of concerns common to real-time embedded systems such as scheduling, resource allocation, and performance. Several modeling languages have been developed to assist in the model-driven software engineering effort for real-time systems, and these languages are beginning to gain traction with practitioners throughout the aerospace industry. This paper presents a survey of several real-time software system modeling languages, namely the Architectural Analysis and Design Language (AADL), the Unified Modeling Language (UML), Systems Modeling Language (SysML), the Modeling and Analysis of Real-Time Embedded Systems (MARTE) UML profile, and the AADL for UML profile. Each language has its advantages and disadvantages, and in order to adequately describe a real-time software system's architecture, a complementary use of multiple languages is almost certainly necessary. This paper aims to explore these languages in the context of understanding the value each brings to the model-driven software engineering effort and to determine if it is feasible and practical to combine aspects of the various modeling languages to achieve more complete coverage in architectural descriptions. To this end, each language is evaluated with respect to a set of criteria such as scope, formalisms, and architectural coverage. An example is used to help illustrate the capabilities of the various languages.

Convergence to a pulsating travelling wave for an epidemic reaction-diffusion system with non-diffusive susceptible population.

PubMed

Ducrot, Arnaud; Giletti, Thomas

2014-09-01

In this work we study the asymptotic behaviour of the Kermack-McKendrick reaction-diffusion system in a periodic environment with non-diffusive susceptible population. This problem was proposed by Kallen et al. as a model for the spatial spread for epidemics, where it can be reasonable to assume that the susceptible population is motionless. For arbitrary dimensional space we prove that large classes of solutions of such a system have an asymptotic spreading speed in large time, and that the infected population has some pulse-like asymptotic shape. The analysis of the one-dimensional problem is more developed, as we are able to uncover a much more accurate description of the profile of solutions. Indeed, we will see that, for some initially compactly supported infected population, the profile of the solution converges to some pulsating travelling wave with minimal speed, that is to some entire solution moving at a constant positive speed and whose profile's shape is periodic in time.

Real-time turbulence profiling with a pair of laser guide star Shack-Hartmann wavefront sensors for wide-field adaptive optics systems on large to extremely large telescopes.

PubMed

Gilles, L; Ellerbroek, B L

2010-11-01

Real-time turbulence profiling is necessary to tune tomographic wavefront reconstruction algorithms for wide-field adaptive optics (AO) systems on large to extremely large telescopes, and to perform a variety of image post-processing tasks involving point-spread function reconstruction. This paper describes a computationally efficient and accurate numerical technique inspired by the slope detection and ranging (SLODAR) method to perform this task in real time from properly selected Shack-Hartmann wavefront sensor measurements accumulated over a few hundred frames from a pair of laser guide stars, thus eliminating the need for an additional instrument. The algorithm is introduced, followed by a theoretical influence function analysis illustrating its impulse response to high-resolution turbulence profiles. Finally, its performance is assessed in the context of the Thirty Meter Telescope multi-conjugate adaptive optics system via end-to-end wave optics Monte Carlo simulations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, K.A.; Neuman, M.C.; Simmonds, D.D.

An effective method for detecting computer misuse is the automatic monitoring and analysis of on-line user activity. This activity is reflected in the system audit record, in the system vulnerability posture, and in other evidence found through active testing of the system. During the last several years we have implemented an automatic misuse detection system at Los Alamos. This is the Network Anomaly Detection and Intrusion Reporter (NADIR). We are currently expanding NADIR to include processing of the Cray UNICOS operating system. This new component is called the UNICOS Realtime NADIR, or UNICORN. UNICORN summarizes user activity and system configurationmore » in statistical profiles. It compares these profiles to expert rules that define security policy and improper or suspicious behavior. It reports suspicious behavior to security auditors and provides tools to aid in follow-up investigations. The first phase of UNICORN development is nearing completion, and will be operational in late 1994.« less

PHYLOGENETIC AFFILIATION OF WATER DISTRIBUTION SYSTEM BACTERIAL ISOLATES USING 16S RDNA SEQUENCE ANALYSIS

EPA Science Inventory

In a previously described study, only 15% of the bacterial strains isolated from a water distribution system (WDS) grown on R2A agar were identifiable using fatty acid methyl esthers (FAME) profiling. The lack of success was attributed to the use of fatty acid databases of bacter...

Determination of accurate vertical atmospheric profiles of extinction and turbulence

NASA Astrophysics Data System (ADS)

Hammel, Steve; Campbell, James; Hallenborg, Eric

2017-09-01

Our ability to generate an accurate vertical profile characterizing the atmosphere from the surface to a point above the boundary layer top is quite rudimentary. The region from a land or sea surface to an altitude of 3000 meters is dynamic and particularly important to the performance of many active optical systems. Accurate and agile instruments are necessary to provide measurements in various conditions, and models are needed to provide the framework and predictive capability necessary for system design and optimization. We introduce some of the path characterization instruments and describe the first work to calibrate and validate them. Along with a verification of measurement accuracy, the tests must also establish each instruments performance envelope. Measurement of these profiles in the field is a problem, and we will present a discussion of recent field test activity to address this issue. The Comprehensive Atmospheric Boundary Layer Extinction/Turbulence Resolution Analysis eXperiment (CABLE/TRAX) was conducted late June 2017. There were two distinct objectives for the experiment: 1) a comparison test of various scintillometers and transmissometers on a homogeneous horizontal path; 2) a vertical profile experiment. In this paper we discuss only the vertical profiling effort, and we describe the instruments that generated data for vertical profiles of absorption, scattering, and turbulence. These three profiles are the core requirements for an accurate assessment of laser beam propagation.

The total assessment profile, volume 1. [including societal impact cost effectiveness, and economic analysis

NASA Technical Reports Server (NTRS)

Leininger, G.; Jutila, S.; King, J.; Muraco, W.; Hansell, J.; Lindeen, J.; Franckowiak, E.; Flaschner, A.

1975-01-01

A methodology is described for the evaluation of societal impacts associated with the implementation of a new technology. Theoretical foundations for the methodology, called the total assessment profile, are established from both the economic and social science perspectives. The procedure provides for accountability of nonquantifiable factors and measures through the use of a comparative value matrix by assessing the impacts of the technology on the value system of the society.

Differential absorption lidars for remote sensing of atmospheric pressure and temperature profiles

NASA Technical Reports Server (NTRS)

Korb, C. Laurence; Schwemmer, Geary K.; Famiglietti, Joseph; Walden, Harvey; Prasad, Coorg

1995-01-01

A near infrared differential absorption lidar technique is developed using atmospheric oxygen as a tracer for high resolution vertical profiles of pressure and temperature with high accuracy. Solid-state tunable lasers and high-resolution spectrum analyzers are developed to carry out ground-based and airborne measurement demonstrations and results of the measurements presented. Numerical error analysis of high-altitude airborne and spaceborne experiments is carried out, and system concepts developed for their implementation.

Systematic profiling of Caenorhabditis elegans locomotive behaviors reveals additional components in G-protein Gαq signaling.

PubMed

Yu, Hui; Aleman-Meza, Boanerges; Gharib, Shahla; Labocha, Marta K; Cronin, Christopher J; Sternberg, Paul W; Zhong, Weiwei

2013-07-16

Genetic screens have been widely applied to uncover genetic mechanisms of movement disorders. However, most screens rely on human observations of qualitative differences. Here we demonstrate the application of an automatic imaging system to conduct a quantitative screen for genes regulating the locomotive behavior in Caenorhabditis elegans. Two hundred twenty-seven neuronal signaling genes with viable homozygous mutants were selected for this study. We tracked and recorded each animal for 4 min and analyzed over 4,400 animals of 239 genotypes to obtain a quantitative, 10-parameter behavioral profile for each genotype. We discovered 87 genes whose inactivation causes movement defects, including 50 genes that had never been associated with locomotive defects. Computational analysis of the high-content behavioral profiles predicted 370 genetic interactions among these genes. Network partition revealed several functional modules regulating locomotive behaviors, including sensory genes that detect environmental conditions, genes that function in multiple types of excitable cells, and genes in the signaling pathway of the G protein Gαq, a protein that is essential for animal life and behavior. We developed quantitative epistasis analysis methods to analyze the locomotive profiles and validated the prediction of the γ isoform of phospholipase C as a component in the Gαq pathway. These results provided a system-level understanding of how neuronal signaling genes coordinate locomotive behaviors. This study also demonstrated the power of quantitative approaches in genetic studies.

Representativeness analysis of CO_{2} profiles near a tall tower and from commercial airliner programs

NASA Astrophysics Data System (ADS)

Chen, Huilin; Katrynski, Krzysztof; Nedelec, Philippe; Machida, Toshinobu; Matsueda, Hidekazu; Sawa, Yousuke; Gerbig, Christoph

2010-05-01

Aircraft profiles for atmospheric trace gases have been collected using both rental aircraft and from commercial airliners. High-accuracy regular in situ CO2 measurements aboard rental aircraft over northeast Poland have been upgraded since August 2008. During each flight, two profiles are taken with a spatial separation of 20 kilometers. Until now, 74 profiles with continuous CO2 have been collected. Meanwhile, aircraft profiles for carbon monoxide (CO) have been made aboard commercial airliners within MOZAIC (Measurement of Ozone, water vapor, carbon monoxide and nitrogen oxides by AIrbus in-service airCraft) and for CO2 within CONTRAIL (Comprehensive Observation Network for TRace gases byAIrLiner) respectively. Starting from 2011, IAGOS-ERI (Integration of routine Aircraft measurements into a Global Observing System - European Research Infrastructure) will provide continuous CO2, CH4 and H2O measurements using instruments deployed aboard commercial airliners, with many profiles during take-off and landing over airports distributed all over the globe. These profiles contain not only vertical gradients but also regionally representative information. It is of importance to investigate how these profiles could be used for applications such as satellite validation and inverse modeling to retrieve surface-atmosphere exchange fluxes of greenhouse gases at regional to continental scales. Especially profiles from commercial airliners near major cities, which are potentially influenced by local fossil fuel emissions, need to be assessed with respect to their regional representativeness. We analyzed CO profiles over Frankfurt airport from the MOZAIC and CO2 profiles from CONTRAIL using STILT (the Stochastic Time Inverted Lagrangian Transport model) combined with a high resolution CO emission map in central Europe. Combining STILT footprints (maps of sensitivities to upstream surface fluxes) with high resolution emission inventories allows to attribute the contribution fossil fuel emissions to local vs. regional sources. In contrast, we analyzed CO2 profiles over northeast Poland in a similar way, where fossil fuel emissions are insignificant. The representativeness analysis provides information on under which circumstances such profiles can be used for potential applications, i.e. satellite validation and inverse modeling. The analysis suggests that a combined measurement of CO2 and CO significantly improves the usability of the regular profiles, where CO serves as the emission tracer.

Internal validation of the RapidHIT® ID system.

PubMed

Wiley, Rachel; Sage, Kelly; LaRue, Bobby; Budowle, Bruce

2017-11-01

Traditionally, forensic DNA analysis has required highly skilled forensic geneticists in a dedicated laboratory to generate short tandem repeat (STR) profiles. STR profiles are routinely used either to associate or exclude potential donors of forensic biological evidence. The typing of forensic reference samples has become more demanding, especially with the requirement in some jurisdictions to DNA profile arrestees. The Rapid DNA (RDNA) platform, the RapidHIT ® ID (IntegenX ® , Pleasanton, CA), is a fully automated system capable of processing reference samples in approximately 90min with minimal human intervention. Thus, the RapidHIT ID instrument can be deployed to non-laboratory environments (e.g., booking stations) and run by trained atypical personnel such as law enforcement. In order to implement the RapidHIT ID platform, validation studies are needed to define the performance and limitations of the system. Internal validation studies were undertaken with four early-production RapidHIT ID units. Reliable and concordant STR profiles were obtained from reference buccal swabs. Throughout the study, no contamination was observed. The overall first-pass success rate with an "expert-like system" was 72%, which is comparable to another current RDNA platform commercially available. The system's second-pass success rate (involving manual interpretation on first-pass inconclusive results) increased to 90%. Inhibitors (i.e., coffee, smoking tobacco, and chewing tobacco) did not appear to affect typing by the instrument system; however, substrate (i.e., swab type) did impact typing success. Additionally, one desirable feature not available with other Rapid systems is that in the event of a system failed run, a swab can be recovered and subsequently re-analyzed in a new sample cartridge. Therefore, rarely should additional sampling or swab consumption be necessary. The RapidHIT ID system is a robust and reliable tool capable of generating complete STR profiles within the forensic DNA typing laboratory or with proper training in decentralized environments by non-laboratory personnel. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of wind profile measurements from an instrumented aircraft

NASA Technical Reports Server (NTRS)

Paige, Terry S.; Murphy, Patrick J.

1990-01-01

The results of an experimental program to determine the capability of measuring wind profiles on support of STS operations with an instrumented aircraft are discussed. These results are a compilation of the flight experiments and the statistical data comparing the quality of the aircraft measurements with quasi-simultaneous and quasi-spatial overlapping Jimsphere measurements. An instrumented aircraft was chosen as a potential alternative to the Jimsphere/radar system for expediting the wind profile calculation by virtue of the ability of an aircraft to traverse the altitudes of interest in roughly 10 minutes. The two aircraft which participated in the study were F-104 and ER-2.

Post-conviction DNA testing: the UK's first ‘exoneration’ case?

PubMed Central

Johnson, Paul; Williams, Robin

2005-01-01

The routine incorporation of forensic DNA profiling into the criminal justice systems of the United Kingdom has been widely promoted as a device for improving the quality of investigative and prosecutorial processes. From its first uses in the 1980s, in cases of serious crime, to the now daily collection, analysis and comparison of genetic samples in the National DNA Database, DNA profiling has become a standard instrument of policing and a powerful evidential resource for prosecutors. However, the use of post-conviction DNA testing has, until recently, been uncommon in the United Kingdom. This paper explores the first case, in England, of the contribution of DNA profiling to a successful appeal against conviction by an imprisoned offender. Analysis of the details of this case is used to emphasise the ways in which novel forms of scientific evidence remain subject to traditional and heterogeneous tests of relevance and credibility. PMID:15112595

ECONOMIC ANALYSIS FOR THE GROUND WATER RULE ...

EPA Pesticide Factsheets

The Ground Water Rule Economic Analysis provides a description of the need for the rule, consideration of regulatory alternatives, baseline analysis including national ground water system profile and an estimate of pathogen and indicator occurrence (Chapter 4), a risk assessment and benefits analysis (Chapter 5), and a cost analysis ( Chapter 6). Chapters 4, 5 and 6, selected appendices and sections of other chapters will be peer reviewed. The objective of the Economic Analysis Document is to support the final Ground Water Rule.

Forensic genetic analysis of bone remain samples.

PubMed

Siriboonpiputtana, T; Rinthachai, T; Shotivaranon, J; Peonim, V; Rerkamnuaychoke, B

2018-03-01

DNA typing from degraded human remains is still challenging forensic DNA scientists not only in the prospective of DNA purification but also in the interpretation of established DNA profiles and data manipulation, especially in mass fatalities. In this report, we presented DNA typing protocol to investigate many skeletal remains in different degrees of decomposing. In addition, we established the grading system aiming for prior determination of the association between levels of decomposing and overall STR amplification efficacy. A total of 80 bone samples were subjected to DNA isolation using the modified DNA IQ™ System (Promega, USA) for bone extraction following with STR analysis using the AmpFLSTR Identifiler ® (Thermo Fisher Scientific, USA). In low destruction group, complete STR profiles were observed as 84.4% whereas partial profiles and non-amplified were found as 9.4% and 6.2%, respectively. Moreover, in medium destruction group, both complete and partial STR profiles were observed as 31.2% while 37.5% of this group was unable to amplify. Nevertheless, we could not purify DNA and were unable to generate STR profile in any sample from the high destroyed bone samples. Compact bones such as femur and humerus have high successful amplification rate superior than loose/spongy bones. Furthermore, costal cartilage could be a designate specimen for DNA isolation in a case of the body that was discovered approximately to 3 days after death which enabled to isolate high quality and quantity of DNA, reduce time and cost, and do not require special tools such as freezer mill. Copyright © 2018 Elsevier B.V. All rights reserved.

Impact of Atmospheric Infrared Sounder (AIRS) Thermodynamic Profiles on Regional Weather Forecasting

NASA Technical Reports Server (NTRS)

Chou, Shih-Hung; Zavodsky, Bradley T.; Jedlovee, Gary J.

2010-01-01

In data sparse regions, remotely-sensed observations can be used to improve analyses and lead to better forecasts. One such source comes from the Atmospheric Infrared Sounder (AIRS), which together with the Advanced Microwave Sounding Unit (AMSU), provides temperature and moisture profiles with accuracy comparable to that of radiosondes. The purpose of this paper is to describe a procedure to assimilate AIRS thermodynamic profile data into a regional configuration of the Advanced Research Weather Research and Forecasting (WRF-ARW) model using its three-dimension variational (3DVAR) analysis component (WRF-Var). Quality indicators are used to select only the highest quality temperature and moisture profiles for assimilation in both clear and partly cloudy regions. Separate error characteristics for land and water profiles are also used in the assimilation process. Assimilation results indicate that AIRS profiles produce an analysis closer to in situ observations than the background field. Forecasts from a 37-day case study period in the winter of 2007 show that AIRS profile data can lead to improvements in 6-h cumulative precipitation forecasts due to instability added in the forecast soundings by the AIRS profiles. Additionally, in a convective heavy rainfall event from February 2007, assimilation of AIRS profiles produces a more unstable boundary layer resulting in enhanced updrafts in the model. These updrafts produce a squall line and precipitation totals that more closely reflect ground-based observations than a no AIRS control forecast. The location of available high-quality AIRS profiles ahead of approaching storm systems is found to be of paramount importance to the amount of impact the observations will have on the resulting forecasts.

Metagenomic analysis of antibiotic resistance genes in coastal industrial mariculture systems.

PubMed

Wang, Jian-Hua; Lu, Jian; Zhang, Yu-Xuan; Wu, Jun; Luo, Yongming; Liu, Hao

2018-04-01

The overuse of antibiotics has posed a propagation of antibiotic resistance genes (ARGs) in aquaculture systems. This study firstly explored the ARGs profiles of the typical mariculture farms including conventional and recirculating systems using metagenomics approach. Fifty ARGs subtypes belonging to 21 ARGs types were identified, showing the wide-spectrum profiles of ARGs in the coastal industrial mariculture systems. ARGs with multiple antibiotics resistance have emerged in the mariculure systems. The co-occurrence pattern between ARGs and microbial taxa showed that Proteobacteria and Bacteroidetes were potential dominant hosts of ARGs in the industrial mariculture systems. Typical nitrifying bacteria such as Nitrospinae in mariculture systems also carried with some resistance genes. Relative abundance of ARGs in fish ponds and wastewater treatment units was relatively high. The investigation showed that industrial mariculture systems were important ARGs reservoirs in coastal area, indicating the critical role of recirculating systems in the terms of ARGs pollution control. Copyright © 2018 Elsevier Ltd. All rights reserved.

Clinical and investigative profile of biopsy-proven sarcoid uveitis in India.

PubMed

Ganesh, Sudha K; Agarwal, Manisha

2008-01-01

Retrospective analysis of the clinical features, investigative profile, response to treatment, and final visual outcome in histopathologically confirmed cases of sarcoid uveitis. Retrospective case series analysis was done of 15 eyes of 9 patients seen between July 1999 and August 2003 with biopsy-proven sarcoid uveitis. There were 3 were males and 6 females. The mean age at presentation was 44.1 years (range 11-62 years), The mean follow-up was 28.4 months. Six patients had bilateral ocular involvement and 3 had unilateral involvement. Five out of 9 patients had primarily ocular involvement. The most common presentation was intermediate uveitis and granulomatous anterior uveitis in 7 patients. Eight of 9 patients responded well to the medical treatment with systemic and periocular steroids. Ocular lesions can be the primary manifestation of systemic sarcoidosis. Sarcoid uveitis in the Asian Indian population often presents an intermediate uveitis with granulomatous anterior uveitis.

Peak expiratory flow profiles delivered by pump systems. Limitations due to wave action.

PubMed

Miller, M R; Jones, B; Xu, Y; Pedersen, O F; Quanjer, P H

2000-06-01

Pump systems are currently used to test the performance of both spirometers and peak expiratory flow (PEF) meters, but for certain flow profiles the input signal (i.e., requested profile) and the output profile can differ. We developed a mathematical model of wave action within a pump and compared the recorded flow profiles with both the input profiles and the output predicted by the model. Three American Thoracic Society (ATS) flow profiles and four artificial flow-versus-time profiles were delivered by a pump, first to a pneumotachograph (PT) on its own, then to the PT with a 32-cm upstream extension tube (which would favor wave action), and lastly with the PT in series with and immediately downstream to a mini-Wright peak flow meter. With the PT on its own, recorded flow for the seven profiles was 2.4 +/- 1.9% (mean +/- SD) higher than the pump's input flow, and similarly was 2.3 +/- 2.3% higher than the pump's output flow as predicted by the model. With the extension tube in place, the recorded flow was 6.6 +/- 6.4% higher than the input flow (range: 0.1 to 18.4%), but was only 1.2 +/- 2.5% higher than the output flow predicted by the model (range: -0.8 to 5.2%). With the mini-Wright meter in series, the flow recorded by the PT was on average 6.1 +/- 9.1% below the input flow (range: -23.8 to 2. 5%), but was only 0.6 +/- 3.3% above the pump's output flow predicted by the model (range: -5.5 to 3.9%). The mini-Wright meter's reading (corrected for its nonlinearity) was on average 1.3 +/- 3.6% below the model's predicted output flow (range: -9.0 to 1. 5%). The mini-Wright meter would be deemed outside ATS limits for accuracy for three of the seven profiles when compared with the pump's input PEF, but this would be true for only one profile when compared with the pump's output PEF as predicted by the model. Our study shows that the output flow from pump systems can differ from the input waveform depending on the operating configuration. This effect can be predicted with reasonable accuracy using a model based on nonsteady flow analysis that takes account of pressure wave reflections within pump systems.

The use of various X-ray fluorescence analysis modalities for the investigation of historical paintings: The case study on the Late Gothic panel painting

NASA Astrophysics Data System (ADS)

Bártová, H.; Trojek, T.; Čechák, T.; Šefců, R.; Chlumská, Š.

2017-10-01

The presence of heavy chemical elements in old pigments is possible to identify in historical paintings using X-ray fluorescence analysis (XRF). This is a non-destructive analytical method frequently used in examination of objects that require in situ analysis, where it is necessary to avoid damaging the object by taking samples. Different modalities are available, such as microanalysis, scanning selected areas, or depth profiling techniques. Surface scanning is particularly profitable since 2D element distribution maps are much more understandable than the results of individual analyses. Information on the layered structure of the painting can be also obtained by handheld portable systems. Results presented in our paper combine 2D element distribution maps obtained by scanning analysis, and depth profiling using conventional XRF. The latter is very suitable for objects of art, as it can be evaluated from data measured with portable XRF device. Depth profiling by conventional XRF is based on the differences in X-ray absorption in paint layers. The XRF technique was applied for analysis of panel paintings of the Master of the St George Altarpiece who was active in Prague in the 1470s and 1480s. The results were evaluated by taking micro-samples and performing a material analysis.

Profiles of criminal justice system involvement of mentally ill homeless adults.

PubMed

Roy, Laurence; Crocker, Anne G; Nicholls, Tonia L; Latimer, Eric; Gozdzik, Agnes; O'Campo, Patricia; Rae, Jennifer

2016-01-01

This study aims to examine the rates of self-reported contacts with the criminal justice system among homeless adults with mental illness, to identify the characteristics of participants who have had contacts with the criminal justice system, to report the dimensional structure of criminal justice system involvement in this sample, and to identify typologies of justice-involved participants. Self-report data on criminal justice system involvement of 2221 adults participating in a Canadian Housing First trial were analyzed using multiple correspondence and cluster analysis. Almost half of the participants had at least one contact with the criminal justice system in the 6months prior to study enrollment. Factors associated with justice involvement included age, gender, ethnic background, diagnosis, substance misuse, impulse control, compliance, victimization, service use, and duration of homelessness. A typology of criminal justice involvement was developed. Seven criminal justice system involvement profiles emerged; substance use and impulse control distinguished the clusters, whereas demographic and contextual variables did not. The large number of profiles indicates the need for a diverse and flexible range of interventions that could be integrated within or in addition to current support of housing services, including integrated substance use and mental health interventions, risk management strategies, and trauma-oriented services. Copyright © 2016 Elsevier Ltd. All rights reserved.

Autonomous microfluidic sample preparation system for protein profile-based detection of aerosolized bacterial cells and spores.

PubMed

Stachowiak, Jeanne C; Shugard, Erin E; Mosier, Bruce P; Renzi, Ronald F; Caton, Pamela F; Ferko, Scott M; Van de Vreugde, James L; Yee, Daniel D; Haroldsen, Brent L; VanderNoot, Victoria A

2007-08-01

For domestic and military security, an autonomous system capable of continuously monitoring for airborne biothreat agents is necessary. At present, no system meets the requirements for size, speed, sensitivity, and selectivity to warn against and lead to the prevention of infection in field settings. We present a fully automated system for the detection of aerosolized bacterial biothreat agents such as Bacillus subtilis (surrogate for Bacillus anthracis) based on protein profiling by chip gel electrophoresis coupled with a microfluidic sample preparation system. Protein profiling has previously been demonstrated to differentiate between bacterial organisms. With the goal of reducing response time, multiple microfluidic component modules, including aerosol collection via a commercially available collector, concentration, thermochemical lysis, size exclusion chromatography, fluorescent labeling, and chip gel electrophoresis were integrated together to create an autonomous collection/sample preparation/analysis system. The cycle time for sample preparation was approximately 5 min, while total cycle time, including chip gel electrophoresis, was approximately 10 min. Sensitivity of the coupled system for the detection of B. subtilis spores was 16 agent-containing particles per liter of air, based on samples that were prepared to simulate those collected by wetted cyclone aerosol collector of approximately 80% efficiency operating for 7 min.

EPICS-based control and data acquisition for the APS slope profiler (Conference Presentation)

NASA Astrophysics Data System (ADS)

Sullivan, Joseph; Assoufid, Lahsen; Qian, Jun; Jemian, Peter R.; Mooney, Tim; Rivers, Mark L.; Goetze, Kurt; Sluiter, Ronald L.; Lang, Keenan

2016-09-01

The motion control, data acquisition and analysis system for APS Slope Measuring Profiler was implemented using the Experimental Physics and Industrial Control System (EPICS). EPICS was designed as a framework with software tools and applications that provide a software infrastructure used in building distributed control systems to operate devices such as particle accelerators, large experiments and major telescopes. EPICS was chosen to implement the APS Slope Measuring Profiler because it is also applicable to single purpose systems. The control and data handling capability available in the EPICS framework provides the basic functionality needed for high precision X-ray mirror measurement. Those built in capabilities include hardware integration of high-performance motion control systems (3-axis gantry and tip-tilt stages), mirror measurement devices (autocollimator, laser spot camera) and temperature sensors. Scanning the mirror and taking measurements was accomplished with an EPICS feature (the sscan record) which synchronizes motor positioning with measurement triggers and data storage. Various mirror scanning modes were automatically configured using EPICS built-in scripting. EPICS tools also provide low-level image processing (areaDetector). Operation screens were created using EPICS-aware GUI screen development tools.

Data Acquisition and Processing System for Airborne Wind Profiling with a Pulsed, 2-Micron, Coherent-Detection, Doppler Lidar System

NASA Technical Reports Server (NTRS)

Beyon, J. Y.; Koch, G. J.; Kavaya, M. J.

2010-01-01

A data acquisition and signal processing system is being developed for a 2-micron airborne wind profiling coherent Doppler lidar system. This lidar, called the Doppler Aerosol Wind Lidar (DAWN), is based on a Ho:Tm:LuLiF laser transmitter and 15-cm diameter telescope. It is being packaged for flights onboard the NASA DC-8, with the first flights in the summer of 2010 in support of the NASA Genesis and Rapid Intensification Processes (GRIP) campaign for the study of hurricanes. The data acquisition and processing system is housed in a compact PCI chassis and consists of four components such as a digitizer, a digital signal processing (DSP) module, a video controller, and a serial port controller. The data acquisition and processing software (DAPS) is also being developed to control the system including real-time data analysis and display. The system detects an external 10 Hz trigger pulse and initiates the data acquisition and processing process, and displays selected wind profile parameters such as Doppler shift, power distribution, wind directions and velocities. Doppler shift created by aircraft motion is measured by an inertial navigation/GPS sensor and fed to the signal processing system for real-time removal of aircraft effects from wind measurements. A general overview of the system and the DAPS as well as the coherent Doppler lidar system is presented in this paper.

Degrees of difference among minority female juvenile offenders' psychological functioning, risk behavior engagement, and health status: a latent profile investigation.

PubMed

Guthrie, Barbara J; Cooper, Shauna M; Brown, Charity; Metzger, Isha

2012-02-01

Given the increase in the number of female youth who come in contact with the juvenile justice system, particularly those from ethnic minority backgrounds, concerns have been raised about the health status of this population. Using a latent profile analysis, we identified health profiles using indicators of psychological well-being, health risk behaviors, and health status. Participants included 153 minority adolescent females (M=15.13, SD=1.70) who were currently in a juvenile diversion program. Results indicated that a three-class solution fit the data optimally. Profiles included girls with low to moderate health risks (n=35; 22.9%), higher mental health symptoms (n=68; 44.4%), and a combination of multiple health risks (n=50; 32.7%). Additionally, demographic, contextual and offense-related variation existed across health profiles. Treatment and policy implications are discussed.

Reduced viscosity interpreted for fluid/gas mixtures

NASA Technical Reports Server (NTRS)

Lewis, D. H.

1981-01-01

Analysis predicts decrease in fluid viscosity by comparing pressure profile of fluid/gas mixture with that of power-law fluid. Fluid is taken to be viscous, non-Newtonian, and incompressible; the gas to be ideal; the flow to be inertia-free, isothermal, and one dimensional. Analysis assists in design of flow systems for petroleum, coal, polymers, and other materials.

Simultaneous measurement of multiple radiation-induced protein expression profiles using the Luminex(TM) system

NASA Technical Reports Server (NTRS)

Desai, N.; Wu, H.; George, K.; Gonda, S. R.; Cucinotta, F. A.; Cucniotta, F. A. (Principal Investigator)

2004-01-01

Space flight results in the exposure of astronauts to a mixed field of radiation composed of energetic particles of varying energies, and biological indicators of space radiation exposure provides a better understanding of the associated long-term health risks. Current methods of biodosimetry have employed the use of cytogenetic analysis for biodosimetry, and more recently the advent of technological progression has led to advanced research in the use of genomic and proteomic expression profiling to simultaneously assess biomarkers of radiation exposure. We describe here the technical advantages of the Luminex(TM) 100 system relative to traditional methods and its potential as a tool to simultaneously profile multiple proteins induced by ionizing radiation. The development of such a bioassay would provide more relevant post-translational dynamics of stress response and will impart important implications in the advancement of space and other radiation contact monitoring. c2004 COSPAR. Published by Elsevier Ltd. All rights reserved.

Clinical Correlations of Transcriptional Profile in Patients Infected with Avian Influenza H7N9 Virus.

PubMed

Guan, Wenda; Wu, Nicholas C; Lee, Horace H Y; Li, Yimin; Jiang, Wenxin; Shen, Lihan; Wu, Douglas C; Chen, Rongchang; Zhong, Nanshan; Wilson, Ian A; Peiris, Malik; Yang, Zifeng; Mok, Chris K P

2018-05-28

Avian influenza A (H7N9) viruses emerged in China in 2013 and caused zoonotic disease associated with a case-fatality ratio of over 30%. Transcriptional profiles in peripheral blood reflect host responses and can help to elucidate disease pathogenesis. We correlated serial blood transcriptomic profiles of patients with avian influenza A (H7N9) virus infection and determined the biological significances from the analysis. We found that specific gene expression profiles in the blood were strongly correlated with the PaO2/FiO2 ratio and viral load in the lower respiratory tract (LRT). Cell cycle and leukocyte-related immunity were activated at the acute stage of the infection while T cell functions and various metabolic processes were associated with the recovery phase of the illness. A transition from systemic innate to adaptive immunity was found. We developed a novel approach for transcriptomic analysis to identify key host responses that were strongly correlated with specific clinical and virologic parameters in patients with H7N9 infection.

An Optimized DNA Analysis Workflow for the Sampling, Extraction, and Concentration of DNA obtained from Archived Latent Fingerprints.

PubMed

Solomon, April D; Hytinen, Madison E; McClain, Aryn M; Miller, Marilyn T; Dawson Cruz, Tracey

2018-01-01

DNA profiles have been obtained from fingerprints, but there is limited knowledge regarding DNA analysis from archived latent fingerprints-touch DNA "sandwiched" between adhesive and paper. Thus, this study sought to comparatively analyze a variety of collection and analytical methods in an effort to seek an optimized workflow for this specific sample type. Untreated and treated archived latent fingerprints were utilized to compare different biological sampling techniques, swab diluents, DNA extraction systems, DNA concentration practices, and post-amplification purification methods. Archived latent fingerprints disassembled and sampled via direct cutting, followed by DNA extracted using the QIAamp® DNA Investigator Kit, and concentration with Centri-Sep™ columns increased the odds of obtaining an STR profile. Using the recommended DNA workflow, 9 of the 10 samples provided STR profiles, which included 7-100% of the expected STR alleles and two full profiles. Thus, with carefully selected procedures, archived latent fingerprints can be a viable DNA source for criminal investigations including cold/postconviction cases. © 2017 American Academy of Forensic Sciences.

Bathymetric surveys of Morse and Geist Reservoirs in central Indiana made with acoustic Doppler current profiler and global positioning system technology, 1996

USGS Publications Warehouse

Wilson, J.T.; Morlock, S.E.; Baker, N.T.

1997-01-01

Acoustic Doppler current profiler, global positioning system, and geographic information system technology were used to map the bathymetry of Morse and Geist Reservoirs, two artificial lakes used for public water supply in central Indiana. The project was a pilot study to evaluate the use of the technologies for bathymetric surveys. Bathymetric surveys were last conducted in 1978 on Morse Reservoir and in 1980 on Geist Reservoir; those surveys were done with conventional methods using networks of fathometer transects. The 1996 bathymetric surveys produced updated estimates of reservoir volumes that will serve as base-line data for future estimates of storage capacity and sedimentation rates.An acoustic Doppler current profiler and global positioning system receiver were used to collect water-depth and position data from April 1996 through October 1996. All water-depth and position data were imported to a geographic information system to create a data base. The geographic information system then was used to generate water-depth contour maps and to compute the volumes for each reservoir.The computed volume of Morse Reservoir was 22,820 acre-feet (7.44 billion gallons), with a surface area of 1,484 acres. The computed volume of Geist Reservoir was 19,280 acre-feet (6.29 billion gallons), with a surface area of 1,848 acres. The computed 1996 reservoir volumes are less than the design volumes and indicate that sedimentation has occurred in both reservoirs. Cross sections were constructed from the computer-generated surfaces for 1996 and compared to the fathometer profiles from the 1978 and 1980 surveys; analysis of these cross sections also indicates that some sedimentation has occurred in both reservoirs.The acoustic Doppler current profiler, global positioning system, and geographic information system technologies described in this report produced bathymetric maps and volume estimates more efficiently and with comparable or greater resolution than conventional bathymetry methods.

Characterization and application of automated in-vacuum PIXE/EBS system for direct analysis of chloride and sulfate ions attack in cementitious materials

NASA Astrophysics Data System (ADS)

Rihawy, M. S.; Alwazzeh, M.; Abbas, K.

2018-01-01

Ion beam analysis (IBA) techniques (Particle Induced X-ray Emission, PIXE and Elastic Backscattering Spectrometry, EBS), were applied to investigate chloride and sulfate ions diffusion into laboratory prepared mortar samples. Development and characterization of an automated in-vacuum macro PIXE/EBS system is thoroughly discussed. Depth profile information of both chloride and sulfate ions in laboratory prepared mortar samples, after immersion in sea water for nine months, was rapidly and easily obtained at fairly low cost and with standardless analysis, demonstrating the value of the application of IBA to elemental depth profiling in cementitious materials. Chloride and sulfate depth profiles were obtained for two sets of mortar samples, one prepared with different water/cement (W/C) ratios and the other with different sand/cement (S/C) ratios. Results showed higher diffusion rates of both chloride and sulfate ions when both ratios are increased. Additionally, the W/C ratio has a stronger influence in both sulfate and chloride penetration than the S/C ratio, and chloride ions penetrate faster than sulfates. Advantages and limitations of applying IBA techniques in this investigation are discussed. The comparison between PIXE and other X-ray based analytical techniques, namely X-ray fluorescence (XRF) and energy and wavelength dispersive X-rays (EDX/WDX), as well as other traditional wet chemical methods is reviewed, and industrial applications are discussed.

Evaluation of tropical Pacific observing systems using NCEP and GFDL ocean data assimilation systems

NASA Astrophysics Data System (ADS)

Xue, Yan; Wen, Caihong; Yang, Xiaosong; Behringer, David; Kumar, Arun; Vecchi, Gabriel; Rosati, Anthony; Gudgel, Rich

2017-08-01

The TAO/TRITON array is the cornerstone of the tropical Pacific and ENSO observing system. Motivated by the recent rapid decline of the TAO/TRITON array, the potential utility of TAO/TRITON was assessed for ENSO monitoring and prediction. The analysis focused on the period when observations from Argo floats were also available. We coordinated observing system experiments (OSEs) using the global ocean data assimilation system (GODAS) from the National Centers for Environmental Prediction and the ensemble coupled data assimilation (ECDA) from the Geophysical Fluid Dynamics Laboratory for the period 2004-2011. Four OSE simulations were conducted with inclusion of different subsets of in situ profiles: all profiles (XBT, moorings, Argo), all except the moorings, all except the Argo and no profiles. For evaluation of the OSE simulations, we examined the mean bias, standard deviation difference, root-mean-square difference (RMSD) and anomaly correlation against observations and objective analyses. Without assimilation of in situ observations, both GODAS and ECDA had large mean biases and RMSD in all variables. Assimilation of all in situ data significantly reduced mean biases and RMSD in all variables except zonal current at the equator. For GODAS, the mooring data is critical in constraining temperature in the eastern and northwestern tropical Pacific, while for ECDA both the mooring and Argo data is needed in constraining temperature in the western tropical Pacific. The Argo data is critical in constraining temperature in off-equatorial regions for both GODAS and ECDA. For constraining salinity, sea surface height and surface current analysis, the influence of Argo data was more pronounced. In addition, the salinity data from the TRITON buoys played an important role in constraining salinity in the western Pacific. GODAS was more sensitive to withholding Argo data in off-equatorial regions than ECDA because it relied on local observations to correct model biases and there were few XBT profiles in those regions. The results suggest that multiple ocean data assimilation systems should be used to assess sensitivity of ocean analyses to changes in the distribution of ocean observations to get more robust results that can guide the design of future tropical Pacific observing systems.

Geomorphic effectiveness of long profile shape and role of inherent geological controls, Ganga River Basin, India

NASA Astrophysics Data System (ADS)

Sonam, Sonam; Jain, Vikrant

2017-04-01

River long profile is one of the fundamental geomorphic parameters which provides a platform to study interaction of geological and geomorphic processes at different time scales. Long profile shape is governed by geological processes at 10 ^ 5 - 10 ^ 6 years' time scale and it controls the modern day (10 ^ 0 - 10 ^ 1 years' time scale) fluvial processes by controlling the spatial variability of channel slope. Identification of an appropriate model for river long profile may provide a tool to analyse the quantitative relationship between basin geology, profile shape and its geomorphic effectiveness. A systematic analysis of long profiles has been carried for the Himalayan tributaries of the Ganga River basin. Long profile shape and stream power distribution pattern is derived using SRTM DEM data (90 m spatial resolution). Peak discharge data from 34 stations is used for hydrological analysis. Lithological variability and major thrusts are marked along the river long profile. The best fit of long profile is analysed for power, logarithmic and exponential function. Second order exponential function provides the best representation of long profiles. The second order exponential equation is Z = K1*exp(-β1*L) + K2*exp(-β2*L), where Z is elevation of channel long profile, L is the length, K and β are coefficients of the exponential function. K1 and K2 are the proportion of elevation change of the long profile represented by β1 (fast) and β2 (slow) decay coefficients of the river long profile. Different values of coefficients express the variability in long profile shapes and is related with the litho-tectonic variability of the study area. Channel slope of long profile is estimated taking the derivative of exponential function. Stream power distribution pattern along long profile is estimated by superimposing the discharge and long profile slope. Sensitivity analysis of stream power distribution with decay coefficients of the second order exponential equation is evaluated for a range of coefficient values. Our analysis suggests that the amplitude of stream power peak value is dependent on K1, the proportion of elevation change coming under the fast decay exponent and the location of stream power peak is dependent of the long profile decay coefficient (β1). Different long profile shapes owing to litho-tectonic variability across the Himalayas are responsible for spatial variability of stream power distribution pattern. Most of the stream power peaks lie in the Higher Himalaya. In general, eastern rivers have higher stream power in hinterland area and low stream power in the alluvial plains. This is responsible for, 1) higher erosion rate and sediment supply in hinterland of eastern rivers, 2) the incised and stable nature of channels in the western alluvial plains and 3) aggrading channels with dynamic nature in the eastern alluvial plains. Our study shows that the spatial variability of litho-units defines the coefficients of long profile function which in turn controls the position and magnitude of stream power maxima and hence the geomorphic variability in a fluvial system.

Analysis of optical scheme for medium-range directed energy laser weapon system

NASA Astrophysics Data System (ADS)

Jabczyński, Jan K.; Kaśków, Mateusz; Gorajek, Łukasz; Kopczyński, Krzysztof

2017-10-01

The relations between range of operation and aperture of laser weapon system were investigated, taking into account diffraction and technical limitations as beam quality, accuracy of point tracking, technical quality of optical train, etc. As a result for the medium ranges of 1 - 2 km we restricted the analysis to apertures not wider than 150 mm and the optical system without adaptive optics. To choose the best laser beam shape, the minimization of aperture losses and thermooptical effects inside optics as well as the effective width of laser beam in far field should be taken into account. We have analyzed theoretically such a problem for the group of a few most interesting from that point of view profiles including for reference two limiting cases of Gaussian beam and `top hat' profile. We have found that the most promising is the SuperGaussian profile of index p = 2 for which the surfaces of beam shaper elements can be manufactured in the acceptable cost-effective way and beam quality does not decrease noticeably. Further, we have investigated the thermo-optic effects on the far field parameters of Gaussian and `top hat' beams to determine the influence of absorption in optical elements on beam quality degradation. The simplified formulae were derived for beam quality measures (parameter M2 and Strehl ratio) which enables to estimate the influence of absorption losses on degradation of beam quality.

Speed Profiles for Improvement of Maritime Emission Estimation

PubMed Central

Yau, Pui Shan; Lee, Shun-Cheng; Ho, Kin Fai

2012-01-01

Abstract Maritime emissions play an important role in anthropogenic emissions, particularly for cities with busy ports such as Hong Kong. Ship emissions are strongly dependent on vessel speed, and thus accurate vessel speed is essential for maritime emission studies. In this study, we determined minute-by-minute high-resolution speed profiles of container ships on four major routes in Hong Kong waters using Automatic Identification System (AIS). The activity-based ship emissions of NOx, CO, HC, CO2, SO2, and PM10 were estimated using derived vessel speed profiles, and results were compared with those using the speed limits of control zones. Estimation using speed limits resulted in up to twofold overestimation of ship emissions. Compared with emissions estimated using the speed limits of control zones, emissions estimated using vessel speed profiles could provide results with up to 88% higher accuracy. Uncertainty analysis and sensitivity analysis of the model demonstrated the significance of improvement of vessel speed resolution. From spatial analysis, it is revealed that SO2 and PM10 emissions during maneuvering within 1 nautical mile from port were the highest. They contributed 7%–22% of SO2 emissions and 8%–17% of PM10 emissions of the entire voyage in Hong Kong. PMID:23236250

Rayleigh-wave dispersive energy imaging and mode separating by high-resolution linear Radon transform

USGS Publications Warehouse

Luo, Y.; Xu, Y.; Liu, Q.; Xia, J.

2008-01-01

In recent years, multichannel analysis of surface waves (MASW) has been increasingly used for obtaining vertical shear-wave velocity profiles within near-surface materials. MASW uses a multichannel recording approach to capture the time-variant, full-seismic wavefield where dispersive surface waves can be used to estimate near-surface S-wave velocity. The technique consists of (1) acquisition of broadband, high-frequency ground roll using a multichannel recording system; (2) efficient and accurate algorithms that allow the extraction and analysis of 1D Rayleigh-wave dispersion curves; (3) stable and efficient inversion algorithms for estimating S-wave velocity profiles; and (4) construction of the 2D S-wave velocity field map.

A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model

PubMed Central

Martin, François-Pierre J; Dumas, Marc-Emmanuel; Wang, Yulan; Legido-Quigley, Cristina; Yap, Ivan K S; Tang, Huiru; Zirah, Séverine; Murphy, Gerard M; Cloarec, Olivier; Lindon, John C; Sprenger, Norbert; Fay, Laurent B; Kochhar, Sunil; van Bladeren, Peter; Holmes, Elaine; Nicholson, Jeremy K

2007-01-01

Symbiotic gut microorganisms (microbiome) interact closely with the mammalian host's metabolism and are important determinants of human health. Here, we decipher the complex metabolic effects of microbial manipulation, by comparing germfree mice colonized by a human baby flora (HBF) or a normal flora to conventional mice. We perform parallel microbiological profiling, metabolic profiling by 1H nuclear magnetic resonance of liver, plasma, urine and ileal flushes, and targeted profiling of bile acids by ultra performance liquid chromatography–mass spectrometry and short-chain fatty acids in cecum by GC-FID. Top-down multivariate analysis of metabolic profiles reveals a significant association of specific metabotypes with the resident microbiome. We derive a transgenomic graph model showing that HBF flora has a remarkably simple microbiome/metabolome correlation network, impacting directly on the host's ability to metabolize lipids: HBF mice present higher ileal concentrations of tauro-conjugated bile acids, reduced plasma levels of lipoproteins but higher hepatic triglyceride content associated with depletion of glutathione. These data indicate that the microbiome modulates absorption, storage and the energy harvest from the diet at the systems level. PMID:17515922

Segment density profiles of polyelectrolyte brushes determined by Fourier transform ellipsometry

NASA Astrophysics Data System (ADS)

Biesalski, Markus; Rühe, Jürgen; Johannsmann, Diethelm

1999-10-01

We describe a method for the explicit determination of the segment density profile φ(z) of surface-attached polymer brushes with multiple angle of incidence null-ellipsometry. Because the refractive index contrast between the brush layer and the solvent is weak, multiple reflections are of minor influence and the ellipsometric spectrum is closely related to the Fourier transform of the refractive index profile, thereby allowing for explicit inversion of the ellipsometric data. We chose surface-attached monolayers of polymethacrylic acid (PMAA), a weak polyelectrolyte, as a model system and determined the segment density profile of this system as a function of the pH value of the surrounding medium by the Fourier method. Complementary to the Fourier analysis, fits with error functions are given as well. The brushes were prepared on the bases of high refractive index prisms with the "grafting-from" technique. In water, the brushes swell by more than a factor of 30. The swelling increases with increasing pH because of a growing fraction of dissociated acidic groups leading to a larger electrostatic repulsion.

Validation and Verification of Operational Land Analysis Activities at the Air Force Weather Agency

NASA Technical Reports Server (NTRS)

Shaw, Michael; Kumar, Sujay V.; Peters-Lidard, Christa D.; Cetola, Jeffrey

2011-01-01

The NASA developed Land Information System (LIS) is the Air Force Weather Agency's (AFWA) operational Land Data Assimilation System (LDAS) combining real time precipitation observations and analyses, global forecast model data, vegetation, terrain, and soil parameters with the community Noah land surface model, along with other hydrology module options, to generate profile analyses of global soil moisture, soil temperature, and other important land surface characteristics. (1) A range of satellite data products and surface observations used to generate the land analysis products (2) Global, 1/4 deg spatial resolution (3) Model analysis generated at 3 hours

Predicting vertical phase segregation in polymer-fullerene bulk heterojunction solar cells by free energy analysis.

PubMed

Clark, Michael D; Jespersen, Michael L; Patel, Romesh J; Leever, Benjamin J

2013-06-12

Blends of poly(3-hexylthiophene) (P3HT) and C61-butyric acid methyl ester (PCBM) are widely used as a model system for bulk heterojunction active layers developed for solution-processable, flexible solar cells. In this work, vertical concentration profiles within the P3HT:PCBM active layer are predicted based on a thermodynamic analysis of the constituent materials and typical solvents. Surface energies of the active layer components and a common transport interlayer blend, poly(3,4-ethylenedioxythiophene) poly(styrenesulfonate) (PEDOT:PSS), are first extracted using contact angle measurements coupled with the acid-base model. From this data, intra- and interspecies interaction free energies are calculated, which reveal that the thermodynamically favored arrangement consists of a uniformly blended "bulk" structure capped with a P3HT-rich air interface and a slightly PCBM-rich buried interface. Although the "bulk" composition is solely determined by P3HT:PCBM ratio, composition near the buried interface is dependent on both the blend ratio and interaction free energy difference between solvated P3HT and PCBM deposition onto PEDOT:PSS. In contrast, the P3HT-rich overlayer is independent of processing conditions, allowing kinetic formation of a PCBM-rich sublayer during film casting due to limitations in long-range species diffusion. These thermodynamic calculations are experimentally validated by angle-resolved X-ray photoelectron spectroscopy (XPS) and low energy XPS depth profiling, which show that the actual composition profiles of the cast and annealed films closely match the predicted behavior. These experimentally derived profiles provide clear evidence that typical bulk heterojunction active layers are predominantly characterized by thermodynamically stable composition profiles. Furthermore, the predictive capabilities of the comprehensive free energy approach are demonstrated, which will enable investigation of structurally integrated devices and novel active layer systems including low band gap polymers, ternary systems, and small molecule blends.

Biogeochemical Typing of Paddy Field by a Data-Driven Approach Revealing Sub-Systems within a Complex Environment - A Pipeline to Filtrate, Organize and Frame Massive Dataset from Multi-Omics Analyses

PubMed Central

Ogawa, Diogo M. O.; Moriya, Shigeharu; Tsuboi, Yuuri; Date, Yasuhiro; Prieto-da-Silva, Álvaro R. B.; Rádis-Baptista, Gandhi; Yamane, Tetsuo; Kikuchi, Jun

2014-01-01

We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS) for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES); and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR) spectroscopy and proton nuclear magnetic resonance (1H-NMR) all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that the BGC typing is a successful technique for elucidating the sub-systems of organismal communities with associated chemical profiles in complex ecosystems. PMID:25330259

Biogeochemical typing of paddy field by a data-driven approach revealing sub-systems within a complex environment--a pipeline to filtrate, organize and frame massive dataset from multi-omics analyses.

PubMed

Ogawa, Diogo M O; Moriya, Shigeharu; Tsuboi, Yuuri; Date, Yasuhiro; Prieto-da-Silva, Álvaro R B; Rádis-Baptista, Gandhi; Yamane, Tetsuo; Kikuchi, Jun

2014-01-01

We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS) for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES); and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR) spectroscopy and proton nuclear magnetic resonance (1H-NMR) all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that the BGC typing is a successful technique for elucidating the sub-systems of organismal communities with associated chemical profiles in complex ecosystems.

Nocturnal pituitary hormone and renin profiles during chronic heat exposure.

PubMed

Saini, J; Brandenberger, G; Libert, J P; Follenius, M

1993-07-01

To establish the principal endocrine systems involved in the initial adaptation to chronic passive heat exposure, responses of the hydromineral and pituitary systems were compared. Nocturnal plasma profiles of growth hormone, prolactin, thyrotropin, and plasma renin activity were determined during a period of prolonged heat exposure designed to simulate a hot climate. Two groups of six male subjects (G1 and G2) were kept for 11 days in a climatically controlled apartment. The G1 group was exposed to 20 degrees C throughout the study, and the G2 group was exposed to 20 degrees C for 5 days and to 35 degrees C for the following 6 days. Blood was collected continuously during the 1st and 10th nights from 2300 to 0700 h and was sampled in 10-min aliquots for hormone analysis. Heat exposure increased the nocturnal mean core temperature (P < 0.02) and stimulated plasma renin activity (P < 0.01) but had little effect on the pituitary hormones except for a small increase in prolactin (P < 0.05). For the G1 group there was no change in hormone profiles. These results demonstrate that the principal initial endocrine system involved in acclimatization to passive heat exposure is the renin-angiotensin system, reflecting counteractive measures against salt and water losses. In contrast, 5 days of continuous heat exposure does not provoke metabolic changes, indicated by the small effect on pituitary hormone profiles.

Metabolite profiling of non-sterile rhizosphere soil.

PubMed

Pétriacq, Pierre; Williams, Alex; Cotton, Anne; McFarlane, Alexander E; Rolfe, Stephen A; Ton, Jurriaan

2017-10-01

Rhizosphere chemistry is the sum of root exudation chemicals, their breakdown products and the microbial products of soil-derived chemicals. To date, most studies about root exudation chemistry are based on sterile cultivation systems, which limits the discovery of microbial breakdown products that act as semiochemicals and shape microbial rhizosphere communities. Here, we present a method for untargeted metabolic profiling of non-sterile rhizosphere soil. We have developed an experimental growth system that enables the collection and analysis of rhizosphere chemicals from different plant species. High-throughput sequencing of 16SrRNA genes demonstrated that plants in the growth system support a microbial rhizosphere effect. To collect a range of (a)polar chemicals from the system, we developed extraction methods that do not cause detectable damage to root cells or soil-inhabiting microbes, thus preventing contamination with cellular metabolites. Untargeted metabolite profiling by UPLC-Q-TOF mass spectrometry, followed by uni- and multivariate statistical analyses, identified a wide range of secondary metabolites that are enriched in plant-containing soil, compared with control soil without roots. We show that the method is suitable for profiling the rhizosphere chemistry of Zea mays (maize) in agricultural soil, thereby demonstrating the applicability to different plant-soil combinations. Our study provides a robust method for the comprehensive metabolite profiling of non-sterile rhizosphere soil, which represents a technical advance towards the establishment of causal relationships between the chemistry and microbial composition of the rhizosphere. © 2017 The Authors The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

Short infusion of paclitaxel imbalances plasmatic lipid metabolism and correlates with cardiac markers of acute damage in patients with breast cancer.

PubMed

Panis, C; Binato, R; Correa, S; Victorino, V J; Dias-Alves, V; Herrera, A C S A; Cecchini, R; Simão, A N C; Barbosa, D S; Pizzatti, L; Abdelhay, E

2017-09-01

Although paclitaxel-based chemotherapy is widely used for treating breast cancer, paclitaxel therapy has been associated with several adverse effects. Such adverse effects have primarily been associated with long-term regimens, but some acute effects are being increasingly reported in the literature. In this context, the present study analyzed the systemic proteomic profiles of women diagnosed with breast cancer at the first cycle of short paclitaxel infusion (n = 30). Proteomic profiles thus obtained were compared with those of breast cancer patients without chemotherapy (n = 50), as well as with those of healthy controls (n = 40). Plasma samples were evaluated by label-free LC-MS to obtain systemic proteomic profiles. Putative dysregulated pathways were identified and validated by in silico analysis of proteomic profiles. Our results identified 188 proteins that were differentially expressed in patients who received a single short paclitaxel infusion when compared to patients who did not receive the infusion. Gene ontology analysis indicated that the cholesterol pathway may be dysregulated by paclitaxel in these patients. Validation analysis showed that paclitaxel treatment significantly reduced plasma high-density lipoprotein levels and increased plasma hydroperoxide levels when compared to breast cancer patients without chemotherapy. Furthermore, augmented C-reactive protein and creatine kinase fraction MB were found to be significantly higher in paclitaxel-treated patients in comparison with healthy controls. Taken together, these data suggest that a single dose of short paclitaxel infusion is sufficient to trigger significant alterations in lipid metabolism, which puts breast cancer patients at risk for increased incidence of cardiovascular disease.

Heterogeneity of (18)F-FDG PET combined with expression of EGFR may improve the prognostic stratification of advanced oropharyngeal carcinoma.

PubMed

Wang, Hung-Ming; Cheng, Nai-Ming; Lee, Li-Yu; Fang, Yu-Hua Dean; Chang, Joseph Tung-Chieh; Tsan, Din-Li; Ng, Shu-Hang; Liao, Chun-Ta; Yang, Lan-Yan; Yen, Tzu-Chen

2016-02-01

The Ang's risk profile (based on p16, smoking and cancer stage) is a well-known prognostic factor in oropharyngeal squamous cell carcinoma (OPSCC). Whether heterogeneity in (18)F-fluorodeoxyglucose (FDG) positron emission tomographic (PET) images and epidermal growth factor receptor (EGFR) expression could provide additional information on clinical outcomes in advanced-stage OPSCC was investigated. Patients with stage III-IV OPSCC who completed primary therapy were eligible. Zone-size nonuniformity (ZSNU) extracted from pretreatment FDG PET scans was used as an index of image heterogeneity. EGFR and p16 expression were examined by immunohistochemistry. Disease-specific survival (DSS) and overall survival (OS) served as outcome measures. Kaplan-Meier estimates and Cox proportional hazards regression models were used for survival analysis. A bootstrap resampling technique was applied to investigate the stability of outcomes. Finally, a recursive partitioning analysis (RPA)-based model was constructed. A total of 113 patients were included, of which 28 were p16-positive. Multivariate analysis identified the Ang's profile, EGFR and ZSNU as independent predictors of both DSS and OS. Using RPA, the three risk factors were used to devise a prognostic scoring system that successfully predicted DSS in both p16-positive and -negative cases. The c-statistic of the prognostic index for DSS was 0.81, a value which was significantly superior to both AJCC stage (0.60) and the Ang's risk profile (0.68). In patients showing an Ang's high-risk profile (N = 77), the use of our scoring system clearly identified three distinct prognostic subgroups. It was concluded that a novel index may improve the prognostic stratification of patients with advanced-stage OPSCC. © 2015 UICC.

Metabolomic analysis of urine with Nuclear Magnetic Resonance spectroscopy in patients with idiopathic sudden sensorineural hearing loss: A preliminary study.

PubMed

Carta, Filippo; Lussu, Milena; Bandino, Fabrizio; Noto, Antonio; Peppi, Marcello; Chuchueva, Natalia; Atzori, Luigi; Fanos, Vassilios; Puxeddu, Roberto

2017-08-01

Idiopathic sudden sensorineural hearing loss is a frequent emergency, with unknown aetiology and usually treated with empiric therapy. Steroids represent the only validated treatment but prognosis is unpredictable and the possibility to select the patients who will not respond to steroids could avoid unnecessary treatments. Metabolomic profiling of the biofluids target the analysis of the final product of genic expression and enzymatic activity, defining the biochemical phenotype of a whole biologic system. We studied the metabolomics of the urine of a cohort of patients with idiopathic sudden sensorineural hearing loss, correlating the metabolic profiles with the clinical outcomes. Metabolomic profiling of urine samples was performed by 1 H Nuclear Magnetic Resonance spectroscopy in combination with multivariate statistical approaches. 26 patients were included in the study: 5 healthy controls, 13 patients who did not recover after treatment at 6 months while the remaining 8 patients recovered from the hearing loss. The orthogonal partial least square-discriminant analysis score plot showed a significant separation between the two groups, responders and non-responders after steroid therapy, R 2 Y of 0.83, Q 2 of 0.38 and p value <0.05. The resulting metabolic profiles were characterized by higher levels of urinary B-Alanine, 3-hydroxybutyrate and Trimethylamine N-oxide, and lower levels of Citrate and Creatinine in patients with worst outcome. Idiopathic sudden sensorineural hearing loss is a specific disease with unclear systemic changes, but our data suggest that there are different types of this disorder or patients predisposed to effective action of steroids allowing the recover after treatment. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Vertical Navigation Control Laws and Logic for the Next Generation Air Transportation System

NASA Technical Reports Server (NTRS)

Hueschen, Richard M.; Khong, Thuan H.

2013-01-01

A vertical navigation (VNAV) outer-loop control system was developed to capture and track the vertical path segments of energy-efficient trajectories that are being developed for high-density operations in the evolving Next Generation Air Transportation System (NextGen). The VNAV control system has a speed-on-elevator control mode to pitch the aircraft for tracking a calibrated airspeed (CAS) or Mach number profile and a path control mode for tracking the VNAV altitude profile. Mode control logic was developed for engagement of either the speed or path control modes. The control system will level the aircraft to prevent it from flying through a constraint altitude. A stability analysis was performed that showed that the gain and phase margins of the VNAV control system significantly exceeded the design gain and phase margins. The system performance was assessed using a six-deg-of-freedom non-linear transport aircraft simulation and the performance is illustrated with time-history plots of recorded simulation data.

Evaluating the effect placement capacitor and distributed photovoltaic generation for power system losses minimization in radial distribution system

NASA Astrophysics Data System (ADS)

Rahman, Yuli Asmi; Manjang, Salama; Yusran, Ilham, Amil Ahmad

2018-03-01

Power loss minimization have many advantagess to the distribution system radial among others reduction of power flow in feeder lines, freeing stress on feeder loading, deterrence of power procurement from the grid and also the cost of loss compensating instruments. This paper, presents capacitor and photovoltaic (PV) placement as alternative means to decrease power system losses. The paper aims to evaluate the best alternative for decreasing power system losses and improving voltage profile in the radial distribution system. To achieve the objectives of paper, they are used three cases tested by Electric Transient and Analysis Program (ETAP) simulation. Firstly, it performs simulation of placement capacitor. Secondly, simulated placement of PV. Lastly, it runs simulation of placement capacitor and PV simultaneously. The simulations were validated using the IEEE 34-bus test system. As a result, they proved that the installation of capacitor and PV integration simultaneously leading to voltage profile correction and power losses minimization significantly.

Multivariate proteomic profiling identifies novel accessory proteins of coated vesicles

PubMed Central

Antrobus, Robin; Hirst, Jennifer; Bhumbra, Gary S.; Kozik, Patrycja; Jackson, Lauren P.; Sahlender, Daniela A.

2012-01-01

Despite recent advances in mass spectrometry, proteomic characterization of transport vesicles remains challenging. Here, we describe a multivariate proteomics approach to analyzing clathrin-coated vesicles (CCVs) from HeLa cells. siRNA knockdown of coat components and different fractionation protocols were used to obtain modified coated vesicle-enriched fractions, which were compared by stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative mass spectrometry. 10 datasets were combined through principal component analysis into a “profiling” cluster analysis. Overall, 136 CCV-associated proteins were predicted, including 36 new proteins. The method identified >93% of established CCV coat proteins and assigned >91% correctly to intracellular or endocytic CCVs. Furthermore, the profiling analysis extends to less well characterized types of coated vesicles, and we identify and characterize the first AP-4 accessory protein, which we have named tepsin. Finally, our data explain how sequestration of TACC3 in cytosolic clathrin cages causes the severe mitotic defects observed in auxilin-depleted cells. The profiling approach can be adapted to address related cell and systems biological questions. PMID:22472443

“Exosomics”—A Review of Biophysics, Biology and Biochemistry of Exosomes With a Focus on Human Breast Milk

PubMed Central

de la Torre Gomez, Carolina; Goreham, Renee V.; Bech Serra, Joan J.; Nann, Thomas; Kussmann, Martin

2018-01-01

Exosomes are biomolecular nanostructures released from cells. They carry specific biomolecular information and are mainly researched for their exquisite properties as a biomarker source and delivery system. We introduce exosomes in the context of other extracellular vesicles, describe their biophysical isolation and characterisation and discuss their biochemical profiling. Motivated by our interest in early-life nutrition and health, and corresponding studies enrolling lactating mothers and their infants, we zoom into exosomes derived from human breast milk. We argue that these should be more extensively studied at proteomic and micronutrient profiling level, because breast milk exosomes provide a more specific window into breast milk quality from an immunological (proteomics) and nutritional (micronutrient) perspective. Such enhanced breast milk exosome profiling would thereby complement and enrich the more classical whole breast milk analysis and is expected to deliver more functional insights than the rather descriptive analysis of human milk, or larger fractions thereof, such as milk fat globule membrane. We substantiate our arguments by a bioinformatic analysis of two published proteomic data sets of human breast milk exosomes. PMID:29636770

"Exosomics"-A Review of Biophysics, Biology and Biochemistry of Exosomes With a Focus on Human Breast Milk.

PubMed

de la Torre Gomez, Carolina; Goreham, Renee V; Bech Serra, Joan J; Nann, Thomas; Kussmann, Martin

2018-01-01

Exosomes are biomolecular nanostructures released from cells. They carry specific biomolecular information and are mainly researched for their exquisite properties as a biomarker source and delivery system. We introduce exosomes in the context of other extracellular vesicles, describe their biophysical isolation and characterisation and discuss their biochemical profiling. Motivated by our interest in early-life nutrition and health, and corresponding studies enrolling lactating mothers and their infants, we zoom into exosomes derived from human breast milk. We argue that these should be more extensively studied at proteomic and micronutrient profiling level, because breast milk exosomes provide a more specific window into breast milk quality from an immunological (proteomics) and nutritional (micronutrient) perspective. Such enhanced breast milk exosome profiling would thereby complement and enrich the more classical whole breast milk analysis and is expected to deliver more functional insights than the rather descriptive analysis of human milk, or larger fractions thereof, such as milk fat globule membrane. We substantiate our arguments by a bioinformatic analysis of two published proteomic data sets of human breast milk exosomes.

Evaluation of the Impact of AIRS Radiance and Profile Data Assimilation in Partly Cloudy Regions

NASA Technical Reports Server (NTRS)

Zavodsky, Bradley; Srikishen, Jayanthi; Jedlovec, Gary

2013-01-01

Improvements to global and regional numerical weather prediction have been demonstrated through assimilation of data from NASA s Atmospheric Infrared Sounder (AIRS). Current operational data assimilation systems use AIRS radiances, but impact on regional forecasts has been much smaller than for global forecasts. Retrieved profiles from AIRS contain much of the information that is contained in the radiances and may be able to reveal reasons for this reduced impact. Assimilating AIRS retrieved profiles in an identical analysis configuration to the radiances, tracking the quantity and quality of the assimilated data in each technique, and examining analysis increments and forecast impact from each data type can yield clues as to the reasons for the reduced impact. By doing this with regional scale models individual synoptic features (and the impact of AIRS on these features) can be more easily tracked. This project examines the assimilation of hyperspectral sounder data used in operational numerical weather prediction by comparing operational techniques used for AIRS radiances and research techniques used for AIRS retrieved profiles. Parallel versions of a configuration of the Weather Research and Forecasting (WRF) model with Gridpoint Statistical Interpolation (GSI) are run to examine the impact AIRS radiances and retrieved profiles. Statistical evaluation of a long-term series of forecast runs will be compared along with preliminary results of in-depth investigations for select case comparing the analysis increments in partly cloudy regions and short-term forecast impacts.

Evaluation of the Impact of Atmospheric Infrared Sounder (AIRS) Radiance and Profile Data Assimilation in Partly Cloudy Regions

NASA Technical Reports Server (NTRS)

Zavodsky, Bradley; Srikishen, Jayanthi; Jedlovec, Gary

2013-01-01

Improvements to global and regional numerical weather prediction have been demonstrated through assimilation of data from NASA s Atmospheric Infrared Sounder (AIRS). Current operational data assimilation systems use AIRS radiances, but impact on regional forecasts has been much smaller than for global forecasts. Retrieved profiles from AIRS contain much of the information that is contained in the radiances and may be able to reveal reasons for this reduced impact. Assimilating AIRS retrieved profiles in an identical analysis configuration to the radiances, tracking the quantity and quality of the assimilated data in each technique, and examining analysis increments and forecast impact from each data type can yield clues as to the reasons for the reduced impact. By doing this with regional scale models individual synoptic features (and the impact of AIRS on these features) can be more easily tracked. This project examines the assimilation of hyperspectral sounder data used in operational numerical weather prediction by comparing operational techniques used for AIRS radiances and research techniques used for AIRS retrieved profiles. Parallel versions of a configuration of the Weather Research and Forecasting (WRF) model with Gridpoint Statistical Interpolation (GSI) are run to examine the impact AIRS radiances and retrieved profiles. Statistical evaluation of 6 weeks of forecast runs will be compared along with preliminary results of in-depth investigations for select case comparing the analysis increments in partly cloudy regions and short-term forecast impacts.

Gathering Real World Evidence with Cluster Analysis for Clinical Decision Support.

PubMed

Xia, Eryu; Liu, Haifeng; Li, Jing; Mei, Jing; Li, Xuejun; Xu, Enliang; Li, Xiang; Hu, Gang; Xie, Guotong; Xu, Meilin

2017-01-01

Clinical decision support systems are information technology systems that assist clinical decision-making tasks, which have been shown to enhance clinical performance. Cluster analysis, which groups similar patients together, aims to separate patient cases into phenotypically heterogenous groups and defining therapeutically homogeneous patient subclasses. Useful as it is, the application of cluster analysis in clinical decision support systems is less reported. Here, we describe the usage of cluster analysis in clinical decision support systems, by first dividing patient cases into similar groups and then providing diagnosis or treatment suggestions based on the group profiles. This integration provides data for clinical decisions and compiles a wide range of clinical practices to inform the performance of individual clinicians. We also include an example usage of the system under the scenario of blood lipid management in type 2 diabetes. These efforts represent a step toward promoting patient-centered care and enabling precision medicine.

Automatic analysis of the micronucleus test in primary human lymphocytes using image analysis.

PubMed

Frieauff, W; Martus, H J; Suter, W; Elhajouji, A

2013-01-01

The in vitro micronucleus test (MNT) is a well-established test for early screening of new chemical entities in industrial toxicology. For assessing the clastogenic or aneugenic potential of a test compound, micronucleus induction in cells has been shown repeatedly to be a sensitive and a specific parameter. Various automated systems to replace the tedious and time-consuming visual slide analysis procedure as well as flow cytometric approaches have been discussed. The ROBIAS (Robotic Image Analysis System) for both automatic cytotoxicity assessment and micronucleus detection in human lymphocytes was developed at Novartis where the assay has been used to validate positive results obtained in the MNT in TK6 cells, which serves as the primary screening system for genotoxicity profiling in early drug development. In addition, the in vitro MNT has become an accepted alternative to support clinical studies and will be used for regulatory purposes as well. The comparison of visual with automatic analysis results showed a high degree of concordance for 25 independent experiments conducted for the profiling of 12 compounds. For concentration series of cyclophosphamide and carbendazim, a very good correlation between automatic and visual analysis by two examiners could be established, both for the relative division index used as cytotoxicity parameter, as well as for micronuclei scoring in mono- and binucleated cells. Generally, false-positive micronucleus decisions could be controlled by fast and simple relocation of the automatically detected patterns. The possibility to analyse 24 slides within 65h by automatic analysis over the weekend and the high reproducibility of the results make automatic image processing a powerful tool for the micronucleus analysis in primary human lymphocytes. The automated slide analysis for the MNT in human lymphocytes complements the portfolio of image analysis applications on ROBIAS which is supporting various assays at Novartis.

Influence of Alternative Engine Concepts on LCTR2 Sizing and Mission Profile

DTIC Science & Technology

2012-01-01

II), and engine performance was estimated with the Numerical Propulsion System Simulation ( NPSS ). Design trades for the ACE vs. VSPT are presented...Maximum Continuous Power MRP Maximum Rated Power (take-off power) NDARC NASA Design and Analysis of Rotorcraft NPSS Numerical Propulsion System...System Simulation ( NPSS ). Design trades for the ACE vs. VSPT are presented in terms of vehicle weight empty for variations in mission altitude and

PERTS: A Prototyping Environment for Real-Time Systems

NASA Technical Reports Server (NTRS)

Liu, Jane W. S.; Lin, Kwei-Jay; Liu, C. L.

1991-01-01

We discuss an ongoing project to build a Prototyping Environment for Real-Time Systems, called PERTS. PERTS is a unique prototyping environment in that it has (1) tools and performance models for the analysis and evaluation of real-time prototype systems, (2) building blocks for flexible real-time programs and the support system software, (3) basic building blocks of distributed and intelligent real time applications, and (4) an execution environment. PERTS will make the recent and future theoretical advances in real-time system design and engineering readily usable to practitioners. In particular, it will provide an environment for the use and evaluation of new design approaches, for experimentation with alternative system building blocks and for the analysis and performance profiling of prototype real-time systems.

Comparison of Mesospheric Winds From a High-Altitude Meteorological Analysis System and Meteor Radar Observations During the Boreal Winters of 2009-2010 and 2012-2013

NASA Technical Reports Server (NTRS)

McCormack, J.; Hoppel, K.; Kuhl, D.; de Wit, R.; Stober, G.; Espy, P.; Baker, N.; Brown, P.; Fritts, D.; Jacobi, C.;

Adaptive neuro-fuzzy inference system for temperature and humidity profile retrieval from microwave radiometer observations

NASA Astrophysics Data System (ADS)

Ramesh, K.; Kesarkar, A. P.; Bhate, J.; Venkat Ratnam, M.; Jayaraman, A.

2015-01-01

The retrieval of accurate profiles of temperature and water vapour is important for the study of atmospheric convection. Recent development in computational techniques motivated us to use adaptive techniques in the retrieval algorithms. In this work, we have used an adaptive neuro-fuzzy inference system (ANFIS) to retrieve profiles of temperature and humidity up to 10 km over the tropical station Gadanki (13.5° N, 79.2° E), India. ANFIS is trained by using observations of temperature and humidity measurements by co-located Meisei GPS radiosonde (henceforth referred to as radiosonde) and microwave brightness temperatures observed by radiometrics multichannel microwave radiometer MP3000 (MWR). ANFIS is trained by considering these observations during rainy and non-rainy days (ANFIS(RD + NRD)) and during non-rainy days only (ANFIS(NRD)). The comparison of ANFIS(RD + NRD) and ANFIS(NRD) profiles with independent radiosonde observations and profiles retrieved using multivariate linear regression (MVLR: RD + NRD and NRD) and artificial neural network (ANN) indicated that the errors in the ANFIS(RD + NRD) are less compared to other retrieval methods. The Pearson product movement correlation coefficient (r) between retrieved and observed profiles is more than 92% for temperature profiles for all techniques and more than 99% for the ANFIS(RD + NRD) technique Therefore this new techniques is relatively better for the retrieval of temperature profiles. The comparison of bias, mean absolute error (MAE), RMSE and symmetric mean absolute percentage error (SMAPE) of retrieved temperature and relative humidity (RH) profiles using ANN and ANFIS also indicated that profiles retrieved using ANFIS(RD + NRD) are significantly better compared to the ANN technique. The analysis of profiles concludes that retrieved profiles using ANFIS techniques have improved the temperature retrievals substantially; however, the retrieval of RH by all techniques considered in this paper (ANN, MVLR and ANFIS) has limited success.

A novel JEAnS analysis of the Fornax dwarf using evolutionary algorithms: mass follows light with signs of an off-centre merger

NASA Astrophysics Data System (ADS)

Diakogiannis, Foivos I.; Lewis, Geraint F.; Ibata, Rodrigo A.; Guglielmo, Magda; Kafle, Prajwal R.; Wilkinson, Mark I.; Power, Chris

2017-09-01

Dwarf galaxies, among the most dark matter dominated structures of our Universe, are excellent test-beds for dark matter theories. Unfortunately, mass modelling of these systems suffers from the well-documented mass-velocity anisotropy degeneracy. For the case of spherically symmetric systems, we describe a method for non-parametric modelling of the radial and tangential velocity moments. The method is a numerical velocity anisotropy 'inversion', with parametric mass models, where the radial velocity dispersion profile, σrr2, is modelled as a B-spline, and the optimization is a three-step process that consists of (I) an evolutionary modelling to determine the mass model form and the best B-spline basis to represent σrr2; (II) an optimization of the smoothing parameters and (III) a Markov chain Monte Carlo analysis to determine the physical parameters. The mass-anisotropy degeneracy is reduced into mass model inference, irrespective of kinematics. We test our method using synthetic data. Our algorithm constructs the best kinematic profile and discriminates between competing dark matter models. We apply our method to the Fornax dwarf spheroidal galaxy. Using a King brightness profile and testing various dark matter mass models, our model inference favours a simple mass-follows-light system. We find that the anisotropy profile of Fornax is tangential (β(r) < 0) and we estimate a total mass of M_{tot} = 1.613^{+0.050}_{-0.075} × 10^8 M_{⊙}, and a mass-to-light ratio of Υ_V = 8.93 ^{+0.32}_{-0.47} (M_{⊙}/L_{⊙}). The algorithm we present is a robust and computationally inexpensive method for non-parametric modelling of spherical clusters independent of the mass-anisotropy degeneracy.

Characterization of potential plasma biomarkers related to cognitive impairment by untargeted profiling of phospholipids using the HILIC-ESI-IT-TOF-MS system.

PubMed

Song, Shuang; Cheong, Ling-Zhi; Man, Qing-Qing; Pang, Shao-Jie; Li, Yue-Qi; Ren, Biao; Zhang, Jian

2018-05-01

Early diagnosis of neural changes causing cognitive impairment is critical for development of preventive therapies for dementia. Biomarkers currently characterized cannot be extensively applied due to the invasive sampling of cerebrospinal fluid. The other imaging approaches are either expensive or require a high technique. Phospholipids (PLs), which are basic constituents of neurons, might be a key variable in the pathogenesis of cognitive impairment. Changes in plasma PL provide the possibility for development of novel biomarkers with minimal invasion and high patient acceptance. In this work, a HILIC-ESI-IT-TOF-MS system was introduced for untargeted profiling of plasma PLs to investigate the relationship between changes of plasma PL profiles and cognitive impairment. A total of 272 types of PL molecular structures were characterized in human plasma and quantified through the internal standard method. Univariate analysis shows 29 PLs were significantly different between the control (n = 41) and the cognitive impairment (CI) group (n = 41). Multivariate analysis (PCA and OPLS-DA) was conducted based on these 29 potential PL biomarkers. Both univariate and multivariate analyses show abnormality of PL metabolism in the CI group, and the downregulation of ethanolamine plasmalogen (pPE) supply, especially those with PUFAs, in the circulation system should be strongly associated with neurodegeneration. A discriminative model was established with satisfied fit (R2) and prediction (Q2) abilities, and the classification test showed better recognition of the CI group than the control group indicating that this model of PL biomarkers could be used as indicators for screening of CI. Graphical abstract Characterization of potential plasma biomarkers related to cognitive impairment by untargeted profiling of phospholipids.

Online identification of the antioxidant constituents of traditional Chinese medicine formula Chaihu-Shu-Gan-San by LC-LTQ-Orbitrap mass spectrometry and microplate spectrophotometer.

PubMed

Su, Zhi-Heng; Zou, Guo-An; Preiss, Alfred; Zhang, Hong-Wu; Zou, Zhong-Mei

2010-11-02

Chaihu-Shu-Gan-San (CSGS), a traditional Chinese medicine (TCM) formula containing seven herbal medicines, has been used in treatment of gastritis, peptic ulcer, irritable bowel syndrome and depression clinically. However, the chemical constituents in CSGS had not been studied so far. To quickly identify the chemical constituents of CSGS and to understand the chemical profiles related to antioxidant activity of CSGS, liquid chromatography coupled with electrospray ionization hybrid linear trap quadrupole orbitrap (LC-LTQ-Orbitrap) mass spectrometry has been applied for online identification of chemical constituents in complex system, meanwhile, antioxidant profile of CSGS was investigated by the fraction collecting and microplate reading system. As a result, 33 chemical constituents in CSGS were identified. Among them, 13 components could be detected both in positive and in negative ion modes, 20 constituents were determined only in positive ion mode and 2 components were only detected in negative ion mode. Meanwhile, the potential antioxidant profile of CSGS was also characterized by combination of 96-well plate collection of elutes from HPLC analysis and microplate spectrophotometer, in which the scavenging activities of free radical produced by DPPH of each fraction could be directly investigated by the analysis of microplate reader. This study quickly screened the contribution of CSGS fractions to the antioxidant activity and online identified the corresponding active constituents. The results indicated that the combination of LC-MS(n) and 96-well plate assay system established in this paper would be a useful strategy for correlating the chemical profile of TCMs with their bioactivities without isolation and purification. Crown Copyright (c) 2010. Published by Elsevier B.V. All rights reserved.

MaizeCyc: Metabolic networks in maize

USDA-ARS?s Scientific Manuscript database

MaizeCyc is a catalog of known and predicted metabolic and transport pathways that enables plant researchers to graphically represent the metabolome of maize (Zea mays), thereby supporting integrated systems-biology analysis. Supported analyses include molecular and genetic/phenotypic profiling (e.g...

Pathway-Based Concentration Response Profiles from Toxicogenomics Data

EPA Science Inventory

Microarray analysis of gene expression of in vitro systems could be a powerful tool for assessing chemical hazard. Differentially expressed genes specific to cells, chemicals, and concentrations can be organized into molecular pathways that inform mode of action. An important par...

Cross-modal work helps OMC improve the safety of commercial transportation

DOT National Transportation Integrated Search

1997-01-01

This article describes the Commercial Vehicle Information System (CVIS), designed to deploy a national safety program for the U.S. commercial trucking fleet. CVIS is built around a safety analysis algorithm called SafeStat which constructs a profile ...

Perceived parental security profiles in African American adolescents involved in the juvenile justice system.

PubMed

Andretta, James R; Ramirez, Aaron M; Barnes, Michael E; Odom, Terri; Roberson-Adams, Shelia; Woodland, Malcolm H

2015-12-01

Many researchers have shown the importance of parent attachment in childhood and adolescence. The present study extends the attachment literature to African Americans involved in the juvenile justice system (N = 213), and provides an initial inquiry using person-oriented methods. The average age was 16.17 years (SD = 1.44), and the sample was predominantly male (71%). Results of a confirmatory factor analysis of Inventory of Parent and Peer Attachment-Short Form (IPPA-S) scores supported a 3-factor model: (a) Communication, (b) Trust, and (c) Alienation. Model-based clustering was applied to IPPA-S scores, and results pointed to 4 perceived parental security profiles: high security, moderately high security, moderately low security, and low security. In keeping with our hypotheses, IPPA-S profiles were associated with prosocial behaviors, depression, anxiety, and oppositional defiance. Contrary to hypotheses, IPPA-S profiles were not associated with perspective taking, emotional concern, or behaviors characteristic of a conduct disorder. Results also showed that gender, age, family member with whom the participant resides, charge severity, and offense history did not have an effect on IPPA-S clustering. Implications for therapeutic jurisprudence in African Americans involved with the juvenile justice system are provided. (c) 2015 APA, all rights reserved).

Extracting 3D Information from 1D and 2D Diagnostic Systems on the DIII-D Tokamak

NASA Astrophysics Data System (ADS)

Brookman, Michael

2017-10-01

The interpretation of tokamak data often hinges on assumptions of axisymetry and flux surface equilibria, neglecting 3D effects. This work discusses examples on the DIII-D tokamak where this assumption is an insufficient approximation, and explores the diagnostic information available to resolve 3D effects while preserving 1D profiles. Methods for extracting 3D data from the electron cyclotron emission radiometers, density profile reflectometer, and Thomson scattering system are discussed. Coordinating diagnostics around the tokamak shows the significance of 3D features, such as sawteeth[1] and resonant magnetic perturbations. A consequence of imposed 3D perturbations is a shift in major radius of measured profiles between diagnostics at different toroidal locations. Integrating different diagnostics requires a database containing information about their toroidal, poloidal, and radial locations. Through the data analysis framework OMFIT, it is possible to measure the magnitude of the apparent shifts from 3D effects and enforce consistency between diagnostics. Using the existing 1D and 2D diagnostic systems on DIII-D, this process allows the effects of the 3D perturbations on 1D profiles to be addressed. Supported by US DOE contracts DE-FC02-04ER54698, DE-FG03-97ER54415.

Implementations of the Navy Coupled Ocean Data Assimilation System at the Naval Oceanographic Office

DTIC Science & Technology

2010-06-01

Clim ( GDEM ) +−2std = 95.4% GDEM POE at Depth MODAS Synthetic Profile T,S with Sat SST Local OI of Nearby Valid Data Global3D Analysis Fig. 3. NCODA...observation (Obs), NCODA analysis (Anal), RNCOM nowcast (NCST) for today, RNCOM 24–hour forecast (FCST) from yesterday, GDEM climatology (Clim), and the

The perception of the relationship between environment and health according to data from Italian Behavioural Risk Factor Surveillance System (PASSI).

PubMed

Sampaolo, Letizia; Tommaso, Giulia; Gherardi, Bianca; Carrozzi, Giuliano; Freni Sterrantino, Anna; Ottone, Marta; Goldoni, Carlo Alberto; Bertozzi, Nicoletta; Scaringi, Meri; Bolognesi, Lara; Masocco, Maria; Salmaso, Stefania; Lauriola, Paolo

2017-01-01

"OBJECTIVES: to identify groups of people in relation to the perception of environmental risk and to assess the main characteristics using data collected in the environmental module of the surveillance network Italian Behavioral Risk Factor Surveillance System (PASSI). perceptive profiles were identified using a latent class analysis; later they were included as outcome in multinomial logistic regression models to assess the association between environmental risk perception and demographic, health, socio-economic and behavioural variables. the latent class analysis allowed to split the sample in "worried", "indifferent", and "positive" people. The multinomial logistic regression model showed that the "worried" profile typically includes people of Italian nationality, living in highly urbanized areas, with a high level of education, and with economic difficulties; they pay special attention to their own health and fitness, but they have a negative perception of their own psychophysical state. the application of advanced statistical analysis enable to appraise PASSI data in order to characterize the perception of environmental risk, making the planning of interventions related to risk communication possible. ".

Altered gene expression of the innate immune, neuroendocrine, and nuclear factor-kappa B (NF-κB) systems is associated with posttraumatic stress disorder in military personnel.

PubMed

Guardado, Pedro; Olivera, Anlys; Rusch, Heather L; Roy, Michael; Martin, Christiana; Lejbman, Natasha; Lee, Hwyunhwa; Gill, Jessica M

2016-03-01

Whole transcriptome analysis provides an unbiased examination of biological activity, and likely, unique insight into the mechanisms underlying posttraumatic stress disorder (PTSD) and comorbid depression and traumatic brain injury. This study compared gene-expression profiles in military personnel with PTSD (n=28) and matched controls without PTSD (n=27) using HG-U133 Plus 2.0 microarrays (Affymetrix), which contain 54,675 probe sets representing more than 38,500 genes. Analysis of expression profiles revealed 203 differentially expressed genes in PTSD, of which 72% were upregulated. Using Partek Genomics Suite 6.6, differentially expressed transcription clusters were filtered based on a selection criterion of ≥1.5 relative fold change at a false discovery rate of ≤5%. Ingenuity Pathway Analysis (Qiagen) of the differentially expressed genes indicated a dysregulation of genes associated with the innate immune, neuroendocrine, and NF-κB systems. These findings provide novel insights that may lead to new pharmaceutical agents for PTSD treatments and help mitigate mental and physical comorbidity risk. Copyright © 2016. Published by Elsevier Ltd.

Real-time Transmission and Distribution of NOAA Tail Doppler Radar Data and Other Data Products

NASA Astrophysics Data System (ADS)

Carswell, J.; Chang, P.; Robinson, D.; Gamache, J.; Hill, J.

2011-12-01

The NOAA WP-3D and G-IV aircraft have conducted and continue to conduct numerous research and operational measurement missions. However, typically only a fraction of the data collected aboard each flight is transmitted to the ground in near real-time utilizing low bandwidth satellite data links. The advancements in aircraft satellite phones have increased available bandwidth and reliability to a point where these systems can be utilized for near real-time data flow in support of decision making. A robust and flexible data delivery system has been developed by Remote Sensing Solutions with support from NOAA's National Environmental Satellite, Data and Information Service (NESDIS), Aircraft Operations Center (AOC) and Hurricane Forecast Improvement Project (HFIP). X-band Doppler/reflectivity measurements of tropical storms and cyclones collected from the NOAA WP-3D aircraft have been the most recent focus. Doppler measurements from volume backscatter precipitation profiles can provide critical observations of the horizontal winds as the precipitation advects with these winds. The data delivery system captures these profiles and send the radial Doppler profile observations to National Weather Service in near real-time over satellite communication data link. The design of this transmission system included features to enhance the reliability and robustness of the data flow from the P-3 aircraft to the end user. Routine real-time transmission, using this system, of the full resolution Tail Doppler Radar profile data to the ground and distribution to the NOAA's Hurricane Research Division for analysis and processing in support of initializing the operational HWRF model is planned. The end objective is to provide these Doppler profiles in a routine fashion to NWS and others in the forecasting community for operational utilization in support of hurricane forecasting and warning. Other data sources that are being collected and transmitted to the ground with this system for distribution in near real-time, include but are not limited to, the NOAA Lower Fuselage Radar reflectivity profiles, SFMR retrievals, flight level data, AXBT profiles and Imaging Wind and Rain Airborne Profiler data. The transmission and distribution of these data has a latency of only several seconds from initial acquisition on the aircraft to end users accessing the data through the Internet enabling end users to have a virtual seat on the aircraft and quick dissemination critical observations to the hurricane research, forecasting and modeling communities. In this presentation, the system capabilities and architecture will be described. Examples of the data products and data visualization tools (client applications) will be shown.

Multi-Component Profiling of Trace Volatiles in Blood by Gas Chromatography/Mass Spectrometry with Dynamic Headspace Extraction

PubMed Central

Kakuta, Shoji; Yamashita, Toshiyuki; Nishiumi, Shin; Yoshida, Masaru; Fukusaki, Eiichiro; Bamba, Takeshi

2015-01-01

A dynamic headspace extraction method (DHS) with high-pressure injection is described. This dynamic extraction method has superior sensitivity to solid phase micro extraction, SPME and is capable of extracting the entire gas phase by purging the headspace of a vial. Optimization of the DHS parameters resulted in a highly sensitive volatile profiling system with the ability to detect various volatile components including alcohols at nanogram levels. The average LOD for a standard volatile mixture was 0.50 ng mL−1, and the average LOD for alcohols was 0.66 ng mL−1. This method was used for the analysis of volatile components from biological samples and compared with acute and chronic inflammation models. The method permitted the identification of volatiles with the same profile pattern as in vitro oxidized lipid-derived volatiles. In addition, the concentration of alcohols and aldehydes from the acute inflammation model samples were significantly higher than that for the chronic inflammation model samples. The different profiles between these samples could also be identified by this method. Finally, it was possible to analyze alcohols and low-molecular-weight volatiles that are difficult to analyze by SPME in high sensitivity and to show volatile profiling based on multi-volatile simultaneous analysis. PMID:26819905

Multi-Component Profiling of Trace Volatiles in Blood by Gas Chromatography/Mass Spectrometry with Dynamic Headspace Extraction.

PubMed

Kakuta, Shoji; Yamashita, Toshiyuki; Nishiumi, Shin; Yoshida, Masaru; Fukusaki, Eiichiro; Bamba, Takeshi

2015-01-01

A dynamic headspace extraction method (DHS) with high-pressure injection is described. This dynamic extraction method has superior sensitivity to solid phase micro extraction, SPME and is capable of extracting the entire gas phase by purging the headspace of a vial. Optimization of the DHS parameters resulted in a highly sensitive volatile profiling system with the ability to detect various volatile components including alcohols at nanogram levels. The average LOD for a standard volatile mixture was 0.50 ng mL(-1), and the average LOD for alcohols was 0.66 ng mL(-1). This method was used for the analysis of volatile components from biological samples and compared with acute and chronic inflammation models. The method permitted the identification of volatiles with the same profile pattern as in vitro oxidized lipid-derived volatiles. In addition, the concentration of alcohols and aldehydes from the acute inflammation model samples were significantly higher than that for the chronic inflammation model samples. The different profiles between these samples could also be identified by this method. Finally, it was possible to analyze alcohols and low-molecular-weight volatiles that are difficult to analyze by SPME in high sensitivity and to show volatile profiling based on multi-volatile simultaneous analysis.

Measurements of CO2 Concentration and Wind Profiles with A Scanning 1.6μm DIAL

NASA Astrophysics Data System (ADS)

Abo, M.; Shibata, Y.; Nagasawa, C.; Nagai, T.; Sakai, T.; Tsukamoto, M.

2012-12-01

Horizontal carbon dioxide (CO2) distribution and wind profiles are important information for understanding of the regional sink and source of CO2. The differential absorption lidar (DIAL) and the Doppler lidar with the range resolution is expected to bring several advantages over passive measurements. We have developed a new scanning 1.6μm DIAL and incoherent Doppler lidar system to perform simultaniously measurements of CO2 concentration and wind speed profiles in the atmosphere. The 1.6μm DIAL and Doppler lidar system consists of the Optical Parametric Generator (OPG) transmitter that excited by the LD pumped Nd:YAG laser with high repetition rate (500 Hz). The receiving optics include the near-infrared photomultiplier tube with high quantum efficiency operating at the photon counting mode, a fiber Bragg grating (FBG) filter to detct Doppler shift, and a 25 cm telescope[1][2]. Laser beam is transmitted coaxially and motorized scanning mirror system can scan the laser beam and field of view 0-360deg horizontally and 0-52deg vertically. We report the results of vertical CO2 scanning measurenents and vertical wind profiles. The scanning elevation angles were from 12deg to 24deg with angular step of 4deg and CO2 concentration profiles were obtained up to 1 km altitude with 200 m altitude resolution. We also obtained vertical wind vector profiles by measuring line-of-sight wind profiles at two azimuth angles with a fixed elevation angle 52deg. Vertical wind vector profiles were obtained up to 5 km altitude with 1 km altitude rasolution. This work was financially supported by the System Development Program for Advanced Measurement and Analysis of the Japan Science and Technology Agency. References [1] L. B. Vann, et al., "Narrowband fiber-optic phase-shifted Fabry-Perot Bragg grating filters for atmospheric water vapor lidar measurements", Appl. Opt., 44, pp. 7371-7377 (2005). [2] Y. Shibata, et al., "1.5μm incoherent Doppler lidar using a FBG filter", Proceedings of 25th International Laser Radar Conference (ILRC25), pp. 338-340 (2010)

Improved operating scenarios of the DIII-D tokamak as a result of the addition of UNIX computer systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henline, P.A.

1995-12-31

The increased use of UNIX based computer systems for machine control, data handling and analysis has greatly enhanced the operating scenarios and operating efficiency of the DIII-D tokamak. This paper will describe some of these UNIX systems and their specific uses. These include the plasma control system, the electron cyclotron heating control system, the analysis of electron temperature and density measurements and the general data acquisition system (which is collecting over 130 Mbytes of data). The speed and total capability of these systems has dramatically affected the ability to operate DIII-D. The improved operating scenarios include better plasma shape controlmore » due to the more thorough MHD calculations done between shots and the new ability to see the time dependence of profile data as it relates across different spatial locations in the tokamak. Other analysis which engenders improved operating abilities will be described.« less

Improved operating scenarios of the DIII-D tokamak as a result of the addition of UNIX computer systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henline, P.A.

1995-10-01

The increased use of UNIX based computer systems for machine control, data handling and analysis has greatly enhanced the operating scenarios and operating efficiency of the DRI-D tokamak. This paper will describe some of these UNIX systems and their specific uses. These include the plasma control system, the electron cyclotron heating control system, the analysis of electron temperature and density measurements and the general data acquisition system (which is collecting over 130 Mbytes of data). The speed and total capability of these systems has dramatically affected the ability to operate DIII-D. The improved operating scenarios include better plasma shape controlmore » due to the more thorough MHD calculations done between shots and the new ability to see the time dependence of profile data as it relates across different spatial locations in the tokamak. Other analysis which engenders improved operating abilities will be described.« less

Biochemical Association of Metabolic Profile and Microbiome in Chronic Pressure Ulcer Wounds

PubMed Central

Ammons, Mary Cloud B.; Morrissey, Kathryn; Tripet, Brian P.; Van Leuven, James T.; Han, Anne; Lazarus, Gerald S.; Zenilman, Jonathan M.; Stewart, Philip S.; James, Garth A.; Copié, Valérie

2015-01-01

Chronic, non-healing wounds contribute significantly to the suffering of patients with co-morbidities in the clinical population with mild to severely compromised immune systems. Normal wound healing proceeds through a well-described process. However, in chronic wounds this process seems to become dysregulated at the transition between resolution of inflammation and re-epithelialization. Bioburden in the form of colonizing bacteria is a major contributor to the delayed headlining in chronic wounds such as pressure ulcers. However how the microbiome influences the wound metabolic landscape is unknown. Here, we have used a Systems Biology approach to determine the biochemical associations between the taxonomic and metabolomic profiles of wounds colonized by bacteria. Pressure ulcer biopsies were harvested from primary chronic wounds and bisected into top and bottom sections prior to analysis of microbiome by pyrosequencing and analysis of metabolome using 1H nuclear magnetic resonance (NMR) spectroscopy. Bacterial taxonomy revealed that wounds were colonized predominantly by three main phyla, but differed significantly at the genus level. While taxonomic profiles demonstrated significant variability between wounds, metabolic profiles shared significant similarity based on the depth of the wound biopsy. Biochemical association between taxonomy and metabolic landscape indicated significant wound-to-wound similarity in metabolite enrichment sets and metabolic pathway impacts, especially with regard to amino acid metabolism. To our knowledge, this is the first demonstration of a statistically robust correlation between bacterial colonization and metabolic landscape within the chronic wound environment. PMID:25978400

Toxicological Assessment and UV/TiO2-Based Induced Degradation Profile of Reactive Black 5 Dye

NASA Astrophysics Data System (ADS)

Bilal, Muhammad; Rasheed, Tahir; Iqbal, Hafiz M. N.; Hu, Hongbo; Wang, Wei; Zhang, Xuehong

2018-01-01

In this study, the toxicological and degradation profile of Reactive Black 5 (RB5) dye was evaluated using a UV/TiO2-based degradation system. Fourier transform infrared spectroscopy (FT-IR), thin layer chromatography (TLC), high-performance liquid chromatography (HPLC) and ultra-performance liquid chromatography coupled with mass spectrometry (UPLC-MS) techniques were used to evaluate the degradation level of RB5. The UV-Vis spectral analysis revealed the disappearance of peak intensity at 599 nm (λmax). The FT-IR spectrum of UV/TiO2 treated dye sample manifest appearance of new peaks mainly because of the degraded product and/or disappearance of some characteristics peaks which were present in the untreated spectrum. The HPLC profile verified the RB5 degradation subject to the formation of metabolites at different retention times. A stable color removal higher than 96% with COD removal in the range of 74-82.3% was noted at all evaluated dye concentrations. The tentative degradation pathway of RB5 is proposed following a careful analysis of the intermediates identified by UPLC-MS. Toxicity profile of untreated and degraded dye samples was monitored using three types of human cell lines via MTT assay and acute toxicity testing with Artemia salina. In conclusion, the UV/TiO2-based degradation system could be effectively employed for the remediation of textile wastewater comprising a high concentration of reactive dyes.

Appending High-Resolution Elevation Data to GPS Speed Traces for Vehicle Energy Modeling and Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wood, E.; Burton, E.; Duran, A.

Accurate and reliable global positioning system (GPS)-based vehicle use data are highly valuable for many transportation, analysis, and automotive considerations. Model-based design, real-world fuel economy analysis, and the growing field of autonomous and connected technologies (including predictive powertrain control and self-driving cars) all have a vested interest in high-fidelity estimation of powertrain loads and vehicle usage profiles. Unfortunately, road grade can be a difficult property to extract from GPS data with consistency. In this report, we present a methodology for appending high-resolution elevation data to GPS speed traces via a static digital elevation model. Anomalous data points in the digitalmore » elevation model are addressed during a filtration/smoothing routine, resulting in an elevation profile that can be used to calculate road grade. This process is evaluated against a large, commercially available height/slope dataset from the Navteq/Nokia/HERE Advanced Driver Assistance Systems product. Results will show good agreement with the Advanced Driver Assistance Systems data in the ability to estimate road grade between any two consecutive points in the contiguous United States.« less

Analyzing Power Supply and Demand on the ISS

NASA Technical Reports Server (NTRS)

Thomas, Justin; Pham, Tho; Halyard, Raymond; Conwell, Steve

2006-01-01

Station Power and Energy Evaluation Determiner (SPEED) is a Java application program for analyzing the supply and demand aspects of the electrical power system of the International Space Station (ISS). SPEED can be executed on any computer that supports version 1.4 or a subsequent version of the Java Runtime Environment. SPEED includes an analysis module, denoted the Simplified Battery Solar Array Model, which is a simplified engineering model of the ISS primary power system. This simplified model makes it possible to perform analyses quickly. SPEED also includes a user-friendly graphical-interface module, an input file system, a parameter-configuration module, an analysis-configuration-management subsystem, and an output subsystem. SPEED responds to input information on trajectory, shadowing, attitude, and pointing in either a state-of-charge mode or a power-availability mode. In the state-of-charge mode, SPEED calculates battery state-of-charge profiles, given a time-varying power-load profile. In the power-availability mode, SPEED determines the time-varying total available solar array and/or battery power output, given a minimum allowable battery state of charge.

The casualty profile from the Reading train crash, November 2004: proposals for improved major incident reporting and the application of trauma scoring systems.

PubMed

Howells, N R; Dunne, N; Reddy, S

2006-07-01

To report the casualty profile of the major incident at the Royal Berkshire Hospital, Reading, following the Ufton Nervet Train crash, November 2004. To make further proposals regarding major incident reporting and implementation of trauma-scoring systems. Retrospective analysis of emergency department and hospital notes. Calculation of index Injury Severity Score (ISS) and Trauma and Injury Severity Score (TRISS) in all patients. Of 61 casualties, the majority (74%) were seen in the minors area of our emergency department with a mixture of blunt impact and penetrating glass injuries. One died and 16 were admitted. 10% had an ISS >16. All surviving patients had a TRISS predicted probability of survival >90%. We propose mandatory major incident reporting within 6 months of a major incident to aid development of a national database. As previously proposed, this will aid education and facilitate future major incident planning. We further propose the widespread use of trauma scoring systems to facilitate comparative analysis between major incidents, perhaps extrapolating this to develop a major incident score.

Physiological typing of Pseudallescheria and Scedosporium strains using Taxa Profile, a semi-automated, 384-well microtitre system.

PubMed

Horré, R; Schaal, K P; Marklein, G; de Hoog, G S; Reiffert, S-M

2011-10-01

During the last few decades, Pseudallescheria and Scedosporium infections in humans are noted with increasing frequency. Multi-drug resistance commonly occurring in this species complex interferes with adequate therapy. Rapid and correct identification of clinical isolates is of paramount significance for optimal treatment in the early stages of infection, while strain typing is necessary for epidemiological purposes. In view of the development of physiological diagnostic parameters, 570 physiological reactions were evaluated using the Taxa Profile Micronaut system, a semi-automatic, computer-assisted, 384-well microtitre platform. Thirty two strains of the Pseudallescheria and Scedosporium complex were analysed after molecular verification of correct species attribution. Of the compounds tested, 254 proved to be polymorphic. Cluster analysis was performed with the Micronaut profile software, which is linked to the ntsypc® program. The systemic opportunist S. prolificans was unambiguously separated from the remaining species. Within the P. boydii/P. apiosperma complex differentiation was noted at the level of individual strains, but no unambiguous parameters for species recognition were revealed. © 2011 Blackwell Verlag GmbH.

Multicomponent Oxide Systems for Corrosion Protection.

DTIC Science & Technology

1980-11-15

hydroxides on film growth. New types of mixed oxide coatings deposited from nonaqueous solutions of organometallic compounds were developed. Titanium -aluminum...mixed oxide coatings, deposited from solutions of titanium alkoxides in isopropanol, served as a prototype system for much of this work. It was found...45 13. Coating Steps and Analysis... ...................... 50 14. Auger Depth Profiles of Titanium -Aluminum Mixed Oxide *Coatings Deposited

Teacher Education Curricula after the Bologna Process--A Comparative Analysis of Written Curricula in Finland and Estonia

ERIC Educational Resources Information Center

Jakku-Sihvonen, Ritva; Tissari, Varpu; Ots, Aivar; Uusiautti, Satu

2012-01-01

During the Bologna process, from 2003 to 2006, degree programmes, including teacher education curricula, were developed in line with the two-tier system--the European Credit Transfer and Accumulation System (ECTS) and modularization. The purpose of the present study is to contribute to the development of teacher education profiling measures by…

DNA Barcoding of the Mexican Sedative and Anxiolytic Plant Galphimia glauca

PubMed Central

Sharma, Ashutosh; Folch, Jorge Luis; Cardoso-Taketa, Alexandre; Lorence, Argelia; Villarreal, María Luisa

2015-01-01

Ethnopharmacology relevance Galphimiaglauca (Malpighiaceae) is a Mexican plant popularly used as a tranquilizer in the treatment of nervous system disorders, although it is also used to treat other common illnesses. Aim of the study The aim of this investigation is to find out if populations of Galphimiaglauca collected in different regions and ecosystems in Mexico actually belong to the same species by using the contemporary technique of DNA barcodes. Our previous metabolic profiling study demonstrates that different collections of this plant obtained from various geographical areas exhibited diverse chemical profiles in terms of the active compounds named Galphimines. We expected the DNA barcodes apart from indicating the different species of Galphimia would indicate the active populations. Materials and methods We employed matK, rpoC1 and rbcL DNA barcodes to indicate the different species. Furthermore to investigate the possible impact of the several different ecosystems where the seven populations were collected, thin layer chromatography was employed to create a partial chemical profile, which was then compared with the metabolic profiles obtained by 1H-NMR and multivariate data analysis. Results and conclusions This study showed that the seven populations here analyzed contain at least three different species of the genus Galphimia, although each individual population is homogeneous. Interestingly our TLC analysis clearly showed that the active populations displayed a distinctively unique chemical profile. This work also showed that the use of DNA barcodes combined with chemical profile analysis is an excellent approach to solve the problems of quality control in the development of Galphimia-based medicines, as well as for any breeding programs for this species. PMID:23010364

Evaluation and optimization of lidar temperature analysis algorithms using simulated data

NASA Technical Reports Server (NTRS)

Leblanc, Thierry; McDermid, I. Stuart; Hauchecorne, Alain; Keckhut, Philippe

1998-01-01

The middle atmosphere (20 to 90 km altitude) ha received increasing interest from the scientific community during the last decades, especially since such problems as polar ozone depletion and climatic change have become so important. Temperature profiles have been obtained in this region using a variety of satellite-, rocket-, and balloon-borne instruments as well as some ground-based systems. One of the more promising of these instruments, especially for long-term high resolution measurements, is the lidar. Measurements of laser radiation Rayleigh backscattered, or Raman scattered, by atmospheric air molecules can be used to determine the relative air density profile and subsequently the temperature profile if it is assumed that the atmosphere is in hydrostatic equilibrium and follows the ideal gas law. The high vertical and spatial resolution make the lidar a well adapted instrument for the study of many middle atmospheric processes and phenomena as well as for the evaluation and validation of temperature measurements from satellites, such as the Upper Atmosphere Research Satellite (UARS). In the Network for Detection of Stratospheric Change (NDSC) lidar is the core instrument for measuring middle atmosphere temperature profiles. Using the best lidar analysis algorithm possible is therefore of crucial importance. In this work, the JPL and CNRS/SA lidar analysis software were evaluated. The results of this evaluation allowed the programs to be corrected and optimized and new production software versions were produced. First, a brief description of the lidar technique and the method used to simulate lidar raw-data profiles from a given temperature profile is presented. Evaluation and optimization of the JPL and CNRS/SA algorithms are then discussed.

It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR.

PubMed

Lun, Aaron T L; Chen, Yunshun; Smyth, Gordon K

2016-01-01

RNA sequencing (RNA-seq) is widely used to profile transcriptional activity in biological systems. Here we present an analysis pipeline for differential expression analysis of RNA-seq experiments using the Rsubread and edgeR software packages. The basic pipeline includes read alignment and counting, filtering and normalization, modelling of biological variability and hypothesis testing. For hypothesis testing, we describe particularly the quasi-likelihood features of edgeR. Some more advanced downstream analysis steps are also covered, including complex comparisons, gene ontology enrichment analyses and gene set testing. The code required to run each step is described, along with an outline of the underlying theory. The chapter includes a case study in which the pipeline is used to study the expression profiles of mammary gland cells in virgin, pregnant and lactating mice.

Nondestructive measurement of an optical fiber refractive-index profile by a transmitted-light differential interference contact microscope.

PubMed

Liu, Zhongyao; Dong, Xiaoman; Chen, Qianghua; Yin, Chunyong; Xu, Yuxian; Zheng, Yingjun

2004-03-01

A novel transmitted-light differential interference contrast (DIC) system is used for nondestructive measurement of the refractive-index profile (RIP) of an optical fiber. By means of this system the phase of a measured light beam can be modulated with an analyzer, and the phase distribution of a fiber is obtained by calculation of the various interference patterns. The measurement theory and structure and some typical applications of this system are demonstrated. The results of measuring RIPs in graded-index fiber are presented. Both the experimental results and theoretical analysis show that the system takes the advantage of high index resolution and of sufficient measurement accuracy for measuring the refractive index of the optical fiber. The system has strong ability to overcome environmental disturbance because of its common-path design. Moreover, one can use the system to measure the RIP along the fiber axis and acquire an image of the three-dimensional RIP of the fiber.

Identifying drought response of semi-arid aeolian systems using near-surface luminescence profiles and changepoint analysis, Nebraska Sandhills.

NASA Astrophysics Data System (ADS)

Buckland, Catherine; Bailey, Richard; Thomas, David

2017-04-01

Two billion people living in drylands are affected by land degradation. Sediment erosion by wind and water removes fertile soil and destabilises landscapes. Vegetation disturbance is a key driver of dryland erosion caused by both natural and human forcings: drought, fire, land use, grazing pressure. A quantified understanding of vegetation cover sensitivities and resultant surface change to forcing factors is needed if the vegetation and landscape response to future climate change and human pressure are to be better predicted. Using quartz luminescence dating and statistical changepoint analysis (Killick & Eckley, 2014) this study demonstrates the ability to identify step-changes in depositional age of near-surface sediments. Lx/Tx luminescence profiles coupled with statistical analysis show the use of near-surface sediments in providing a high-resolution record of recent system response and aeolian system thresholds. This research determines how the environment has recorded and retained sedimentary evidence of drought response and land use disturbances over the last two hundred years across both individual landforms and the wider Nebraska Sandhills. Identifying surface deposition and comparing with records of climate, fire and land use changes allows us to assess the sensitivity and stability of the surface sediment to a range of forcing factors. Killick, R and Eckley, IA. (2014) "changepoint: An R Package for Changepoint Analysis." Journal of Statistical Software, (58) 1-19.

Further Examining Berry's Model: The Applicability of Latent Profile Analysis to Acculturation

ERIC Educational Resources Information Center

Fox, Rina S.; Merz, Erin L.; Solórzano, Martha T.; Roesch, Scott C.

2013-01-01

This study used latent profile analysis (LPA) to identify acculturation profiles. A three-profile solution fit the data best, and comparisons on demographic and psychosocial outcomes as a function of profile yielded expected results. The findings support using LPA as a parsimonious way to model acculturation without anticipating profiles in…

Structural, vibrational, thermal and optical studies of organic single crystal: Benzotriazolium p-toluene sulfonate (BTPTS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, R. Ramesh; Sathya, P.; Gopalakrishnan, R., E-mail: krgkrishnan@yahoo.com

Benzotriazolium p-toluene sulfonate (BTPTS) was grown by solution growth technique. The powder X-ray diffraction analysis was carried out to evaluate crystal system of the compound. LeBail Profile fitting analysis was performed to extract the individual peak intensities. FTIR spectrum analysis was recorded to study vibration frequencies of the prepared organic salt. Thermal studies were carried out using TG-DSC analysis. Optical absorption and energy band gap of the title compound was evaluated by UV-Vis spectral study.

Towards A Self Adaptive System for Social Wellness.

PubMed

Khattak, Asad Masood; Khan, Wajahat Ali; Pervez, Zeeshan; Iqbal, Farkhund; Lee, Sungyoung

2016-04-13

Advancements in science and technology have highlighted the importance of robust healthcare services, lifestyle services and personalized recommendations. For this purpose patient daily life activity recognition, profile information, and patient personal experience are required. In this research work we focus on the improvement in general health and life status of the elderly through the use of an innovative services to align dietary intake with daily life and health activity information. Dynamic provisioning of personalized healthcare and life-care services are based on the patient daily life activities recognized using smart phone. To achieve this, an ontology-based approach is proposed, where all the daily life activities and patient profile information are modeled in ontology. Then the semantic context is exploited with an inference mechanism that enables fine-grained situation analysis for personalized service recommendations. A generic system architecture is proposed that facilitates context information storage and exchange, profile information, and the newly recognized activities. The system exploits the patient's situation using semantic inference and provides recommendations for appropriate nutrition and activity related services. The proposed system is extensively evaluated for the claims and for its dynamic nature. The experimental results are very encouraging and have shown better accuracy than the existing system. The proposed system has also performed better in terms of the system support for a dynamic knowledge-base and the personalized recommendations.

Validation of a rapid DNA process with the RapidHIT® ID system using GlobalFiler® Express chemistry, a platform optimized for decentralized testing environments.

PubMed

Salceda, Susana; Barican, Arnaldo; Buscaino, Jacklyn; Goldman, Bruce; Klevenberg, Jim; Kuhn, Melissa; Lehto, Dennis; Lin, Frank; Nguyen, Phong; Park, Charles; Pearson, Francesca; Pittaro, Rick; Salodkar, Sayali; Schueren, Robert; Smith, Corey; Troup, Charles; Tsou, Dean; Vangbo, Mattias; Wunderle, Justus; King, David

2017-05-01

The RapidHIT ® ID is a fully automated sample-to-answer system for short tandem repeat (STR)-based human identification. The RapidHIT ID has been optimized for use in decentralized environments and processes presumed single source DNA samples, generating Combined DNA Index System (CODIS)-compatible DNA profiles in less than 90min. The system is easy to use, requiring less than one minute of hands-on time. Profiles are reviewed using centralized linking software, RapidLINK™ (IntegenX, Pleasanton, CA), a software tool designed to collate DNA profiles from single or multiple RapidHIT ID systems at different geographic locations. The RapidHIT ID has been designed to employ GlobalFiler ® Express and AmpFLSTR ® NGMSElect™, Thermo Fisher Scientific (Waltham, MA) STR chemistries. The Developmental Validation studies were performed using GlobalFiler ® Express with single source reference samples according to Scientific Working Group for DNA Analysis Methods guidelines. These results show that multiple RapidHIT ID systems networked with RapidLINK software form a highly reliable system for wide-scale deployment in locations such as police booking stations and border crossings enabling real-time testing of arrestees, potential human trafficking victims, and other instances where rapid turnaround is essential. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Spectral Line-Shape Model to Replace the Voigt Profile in Spectroscopic Databases

NASA Astrophysics Data System (ADS)

Lisak, Daniel; Ngo, Ngoc Hoa; Tran, Ha; Hartmann, Jean-Michel

2014-06-01

The standard description of molecular line shapes in spectral databases and radiative transfer codes is based on the Voigt profile. It is well known that its simplified assumptions of absorber free motion and independence of collisional parameters from absorber velocity lead to systematic errors in analysis of experimental spectra, and retrieval of gas concentration. We demonstrate1,2 that the partially correlated quadratic speed-dependent hardcollision profile3. (pCqSDHCP) is a good candidate to replace the Voigt profile in the next generations of spectroscopic databases. This profile takes into account the following physical effects: the Doppler broadening, the pressure broadening and shifting of the line, the velocity-changing collisions, the speed-dependence of pressure broadening and shifting, and correlations between velocity- and phase/state-changing collisions. The speed-dependence of pressure broadening and shifting is incorporated into the pCqSDNGP in the so-called quadratic approximation. The velocity-changing collisions lead to the Dicke narrowing effect; however in many cases correlations between velocityand phase/state-changing collisions may lead to effective reduction of observed Dicke narrowing. The hard-collision model of velocity-changing collisions is also known as the Nelkin-Ghatak model or Rautian model. Applicability of the pCqSDHCP for different molecular systems was tested on calculated and experimental spectra of such molecules as H2, O2, CO2, H2O in a wide span of pressures. For all considered systems, pCqSDHCP is able to describe molecular spectra at least an order of magnitude better than the Voigt profile with all fitted parameters being linear with pressure. In the most cases pCqSDHCP can reproduce the reference spectra down to 0.2% or better, which fulfills the requirements of the most demanding remote-sensing applications. An important advantage of pCqSDHCP is that a fast algorithm for its computation was developedab4,5 and allows for its calculation only a few times slower than the standard Voigt profile. Moreover, the pCqSDHCP reduces to many simpler models commonly used in experimental spectra analysis simply by setting some parameters to zero, and it can be easily extended to incorporate the line-mixing effect in the first-order approximation. The idea of using pCqSDHCP as a standard profile to go beyond the Voigt profile for description of H2O line shapes was recently supported by the IUPAC task group6 which also recommended to call this profile with fast computation algorithm the HTP profile (for Hartmann-Tran).

Analysis of the Radiated Field in an Electromagnetic Reverberation Chamber as an Upset-Inducing Stimulus for Digital Systems

NASA Technical Reports Server (NTRS)

Torres-Pomales, Wilfredo

2012-01-01

Preliminary data analysis for a physical fault injection experiment of a digital system exposed to High Intensity Radiated Fields (HIRF) in an electromagnetic reverberation chamber suggests a direct causal relation between the time profile of the field strength amplitude in the chamber and the severity of observed effects at the outputs of the radiated system. This report presents an analysis of the field strength modulation induced by the movement of the field stirrers in the reverberation chamber. The analysis is framed as a characterization of the discrete features of the field strength waveform responsible for the faults experienced by a radiated digital system. The results presented here will serve as a basis to refine the approach for a detailed analysis of HIRF-induced upsets observed during the radiation experiment. This work offers a novel perspective into the use of an electromagnetic reverberation chamber to generate upset-inducing stimuli for the study of fault effects in digital systems.

Strategic assessment of the Highway Performance Monitoring System

DOT National Transportation Integrated Search

1995-02-01

The appendix contains a series of border crossing profiles covering the major, and in some cases, minor crossings in the border frontier. The frontier itself is a definition created for the 6015 Study to aid in the analysis of trade and traffic flows...

Advanced density profile reflectometry; the state-of-the-art and measurement prospects for ITER

NASA Astrophysics Data System (ADS)

Doyle, E. J.

2006-10-01

Dramatic progress in millimeter-wave technology has allowed the realization of a key goal for ITER diagnostics, the routine measurement of the plasma density profile from millimeter-wave radar (reflectometry) measurements. In reflectometry, the measured round-trip group delay of a probe beam reflected from a plasma cutoff is used to infer the density distribution in the plasma. Reflectometer systems implemented by UCLA on a number of devices employ frequency-modulated continuous-wave (FM-CW), ultrawide-bandwidth, high-resolution radar systems. One such system on DIII-D has routinely demonstrated measurements of the density profile over a range of electron density of 0-6.4x10^19,m-3, with ˜25 μs time and ˜4 mm radial resolution, meeting key ITER requirements. This progress in performance was made possible by multiple advances in the areas of millimeter-wave technology, novel measurement techniques, and improved understanding, including: (i) fast sweep, solid-state, wide bandwidth sources and power amplifiers, (ii) dual polarization measurements to expand the density range, (iii) adaptive radar-based data analysis with parallel processing on a Unix cluster, (iv) high memory depth data acquisition, and (v) advances in full wave code modeling. The benefits of advanced system performance will be illustrated using measurements from a wide range of phenomena, including ELM and fast-ion driven mode dynamics, L-H transition studies and plasma-wall interaction. The measurement capabilities demonstrated by these systems provide a design basis for the development of the main ITER profile reflectometer system. This talk will explore the extent to which these reflectometer system designs, results and experience can be translated to ITER, and will identify what new studies and experimental tests are essential.

Multicomponent quantitative spectroscopic analysis without reference substances based on ICA modelling.

PubMed

Monakhova, Yulia B; Mushtakova, Svetlana P

2017-05-01

A fast and reliable spectroscopic method for multicomponent quantitative analysis of targeted compounds with overlapping signals in complex mixtures has been established. The innovative analytical approach is based on the preliminary chemometric extraction of qualitative and quantitative information from UV-vis and IR spectral profiles of a calibration system using independent component analysis (ICA). Using this quantitative model and ICA resolution results of spectral profiling of "unknown" model mixtures, the absolute analyte concentrations in multicomponent mixtures and authentic samples were then calculated without reference solutions. Good recoveries generally between 95% and 105% were obtained. The method can be applied to any spectroscopic data that obey the Beer-Lambert-Bouguer law. The proposed method was tested on analysis of vitamins and caffeine in energy drinks and aromatic hydrocarbons in motor fuel with 10% error. The results demonstrated that the proposed method is a promising tool for rapid simultaneous multicomponent analysis in the case of spectral overlap and the absence/inaccessibility of reference materials.

Metabolic Disturbances in Adult-Onset Still's Disease Evaluated Using Liquid Chromatography/Mass Spectrometry-Based Metabolomic Analysis.

PubMed

Chen, Der-Yuan; Chen, Yi-Ming; Chien, Han-Ju; Lin, Chi-Chen; Hsieh, Chia-Wei; Chen, Hsin-Hua; Hung, Wei-Ting; Lai, Chien-Chen

2016-01-01

Liquid chromatography/mass spectrometry (LC/MS)-based comprehensive analysis of metabolic profiles with metabolomics approach has potential diagnostic and predictive implications. However, no metabolomics data have been reported in adult-onset Still's disease (AOSD). This study investigated the metabolomic profiles in AOSD patients and examined their association with clinical characteristics and disease outcome. Serum metabolite profiles were determined on 32 AOSD patients and 30 healthy controls (HC) using ultra-performance liquid chromatography (UPLC)/MS analysis, and the differentially expressed metabolites were quantified using multiple reactions monitoring (MRM)/MS analysis in 44 patients and 42 HC. Pure standards were utilized to confirm the presence of the differentially expressed metabolites. Eighteen differentially expressed metabolites were identified in AOSD patents using LC/MS-based analysis, of which 13 metabolites were validated by MRM/MS analysis. Among them, serum levels of lysoPC(18:2), urocanic acid and indole were significantly lower, and L-phenylalanine levels were significantly higher in AOSD patients compared with HC. Moreover, serum levels of lysoPC(18:2), PhePhe, uridine, taurine, L-threonine, and (R)-3-Hydroxy-hexadecanoic acid were significantly correlated with disease activity scores (all p<0.05) in AOSD patients. A different clustering of metabolites was associated with a different disease outcome, with significantly lower levels of isovalerylsarcosine observed in patients with chronic articular pattern (median, 77.0AU/ml) compared with monocyclic (341.5AU/ml, p<0.01) or polycyclic systemic pattern (168.0AU/ml, p<0.05). Thirteen differentially expressed metabolites identified and validated in AOSD patients were shown to be involved in five metabolic pathways. Significant associations of metabolic profiles with disease activity and outcome of AOSD suggest their involvement in AOSD pathogenesis.

Design and verification by nonlinear simulation of a Mach/CAS control law for the NASA TCV B737 aircraft

NASA Technical Reports Server (NTRS)

Bruce, Kevin R.

1986-01-01

A Mach/CAS control system using an elevator was designed and developed for use on the NASA TCV B737 aircraft to support research in profile descent procedures and approach energy management. The system was designed using linear analysis techniques primarily. The results were confirmed and the system validated at additional flight conditions using a nonlinear 737 aircraft simulation. All design requirements were satisfied.

Comparative genome analysis in the integrated microbial genomes (IMG) system.

PubMed

Markowitz, Victor M; Kyrpides, Nikos C

2007-01-01

Comparative genome analysis is critical for the effective exploration of a rapidly growing number of complete and draft sequences for microbial genomes. The Integrated Microbial Genomes (IMG) system (img.jgi.doe.gov) has been developed as a community resource that provides support for comparative analysis of microbial genomes in an integrated context. IMG allows users to navigate the multidimensional microbial genome data space and focus their analysis on a subset of genes, genomes, and functions of interest. IMG provides graphical viewers, summaries, and occurrence profile tools for comparing genes, pathways, and functions (terms) across specific genomes. Genes can be further examined using gene neighborhoods and compared with sequence alignment tools.

Design of refractive laser beam shapers to generate complex irradiance profiles

NASA Astrophysics Data System (ADS)

Li, Meijie; Meuret, Youri; Duerr, Fabian; Vervaeke, Michael; Thienpont, Hugo

2014-05-01

A Gaussian laser beam is reshaped to have specific irradiance distributions in many applications in order to ensure optimal system performance. Refractive optics are commonly used for laser beam shaping. A refractive laser beam shaper is typically formed by either two plano-aspheric lenses or by one thick lens with two aspherical surfaces. Ray mapping is a general optical design technique to design refractive beam shapers based on geometric optics. This design technique in principle allows to generate any rotational-symmetric irradiance profile, yet in literature ray mapping is mainly developed to transform a Gaussian irradiance profile to a uniform profile. For more complex profiles especially with low intensity in the inner region, like a Dark Hollow Gaussian (DHG) irradiance profile, ray mapping technique is not directly applicable in practice. In order to these complex profiles, the numerical effort of calculating the aspherical surface points and fitting a surface with sufficient accuracy increases considerably. In this work we evaluate different sampling approaches and surface fitting methods. This allows us to propose and demonstrate a comprehensive numerical approach to efficiently design refractive laser beam shapers to generate rotational-symmetric collimated beams with a complex irradiance profile. Ray tracing analysis for several complex irradiance profiles demonstrates excellent performance of the designed lenses and the versatility of our design procedure.

Estimation and Psychometric Analysis of Component Profile Scores via Multivariate Generalizability Theory

ERIC Educational Resources Information Center

Grochowalski, Joseph H.

2015-01-01

Component Universe Score Profile analysis (CUSP) is introduced in this paper as a psychometric alternative to multivariate profile analysis. The theoretical foundations of CUSP analysis are reviewed, which include multivariate generalizability theory and constrained principal components analysis. Because CUSP is a combination of generalizability…

Systemic Metabolomic Changes in Blood Samples of Lung Cancer Patients Identified by Gas Chromatography Time-of-Flight Mass Spectrometry

PubMed Central

Miyamoto, Suzanne; Taylor, Sandra L.; Barupal, Dinesh K.; Taguchi, Ayumu; Wohlgemuth, Gert; Wikoff, William R.; Yoneda, Ken Y.; Gandara, David R.; Hanash, Samir M.; Kim, Kyoungmi; Fiehn, Oliver

2015-01-01

Lung cancer is a leading cause of cancer deaths worldwide. Metabolic alterations in tumor cells coupled with systemic indicators of the host response to tumor development have the potential to yield blood profiles with clinical utility for diagnosis and monitoring of treatment. We report results from two separate studies using gas chromatography time-of-flight mass spectrometry (GC-TOF MS) to profile metabolites in human blood samples that significantly differ from non-small cell lung cancer (NSCLC) adenocarcinoma and other lung cancer cases. Metabolomic analysis of blood samples from the two studies yielded a total of 437 metabolites, of which 148 were identified as known compounds and 289 identified as unknown compounds. Differential analysis identified 15 known metabolites in one study and 18 in a second study that were statistically different (p-values <0.05). Levels of maltose, palmitic acid, glycerol, ethanolamine, glutamic acid, and lactic acid were increased in cancer samples while amino acids tryptophan, lysine and histidine decreased. Many of the metabolites were found to be significantly different in both studies, suggesting that metabolomics appears to be robust enough to find systemic changes from lung cancer, thus showing the potential of this type of analysis for lung cancer detection. PMID:25859693

Evaluating the Invariance of Cognitive Profile Patterns Derived from Profile Analysis via Multidimensional Scaling (PAMS): A Bootstrapping Approach

ERIC Educational Resources Information Center

Kim, Se-Kang

2010-01-01

The aim of the current study is to validate the invariance of major profile patterns derived from multidimensional scaling (MDS) by bootstrapping. Profile Analysis via Multidimensional Scaling (PAMS) was employed to obtain profiles and bootstrapping was used to construct the sampling distributions of the profile coordinates and the empirical…

The UTRC wind energy conversion system performance analysis for horizontal axis wind turbines (WECSPER)

NASA Technical Reports Server (NTRS)

Egolf, T. A.; Landgrebe, A. J.

1981-01-01

The theory for the UTRC Energy Conversion System Performance Analysis (WECSPER) for the prediction of horizontal axis wind turbine performance is presented. Major features of the analysis are the ability to: (1) treat the wind turbine blades as lifting lines with a prescribed wake model; (2) solve for the wake-induced inflow and blade circulation using real nonlinear airfoil data; and (3) iterate internally to obtain a compatible wake transport velocity and blade loading solution. This analysis also provides an approximate treatment of wake distortions due to tower shadow or wind shear profiles. Finally, selected results of internal UTRC application of the analysis to existing wind turbines and correlation with limited test data are described.

Statistical inference methods for sparse biological time series data.

PubMed

Ndukum, Juliet; Fonseca, Luís L; Santos, Helena; Voit, Eberhard O; Datta, Susmita

2011-04-25

Comparing metabolic profiles under different biological perturbations has become a powerful approach to investigating the functioning of cells. The profiles can be taken as single snapshots of a system, but more information is gained if they are measured longitudinally over time. The results are short time series consisting of relatively sparse data that cannot be analyzed effectively with standard time series techniques, such as autocorrelation and frequency domain methods. In this work, we study longitudinal time series profiles of glucose consumption in the yeast Saccharomyces cerevisiae under different temperatures and preconditioning regimens, which we obtained with methods of in vivo nuclear magnetic resonance (NMR) spectroscopy. For the statistical analysis we first fit several nonlinear mixed effect regression models to the longitudinal profiles and then used an ANOVA likelihood ratio method in order to test for significant differences between the profiles. The proposed methods are capable of distinguishing metabolic time trends resulting from different treatments and associate significance levels to these differences. Among several nonlinear mixed-effects regression models tested, a three-parameter logistic function represents the data with highest accuracy. ANOVA and likelihood ratio tests suggest that there are significant differences between the glucose consumption rate profiles for cells that had been--or had not been--preconditioned by heat during growth. Furthermore, pair-wise t-tests reveal significant differences in the longitudinal profiles for glucose consumption rates between optimal conditions and heat stress, optimal and recovery conditions, and heat stress and recovery conditions (p-values <0.0001). We have developed a nonlinear mixed effects model that is appropriate for the analysis of sparse metabolic and physiological time profiles. The model permits sound statistical inference procedures, based on ANOVA likelihood ratio tests, for testing the significance of differences between short time course data under different biological perturbations.

Accuracy, reproducibility, and interpretation of fatty acid methyl ester profiles of model bacterial communities

USGS Publications Warehouse

Kidd, Haack S.; Garchow, H.; Odelson, D.A.; Forney, L.J.; Klug, M.J.

1994-01-01

We determined the accuracy and reproducibility of whole-community fatty acid methyl ester (FAME) analysis with two model bacterial communities differing in composition by using the Microbial ID, Inc. (MIDI), system. The biomass, taxonomic structure, and expected MIDI-FAME profiles under a variety of environmental conditions were known for these model communities a priori. Not all members of each community could be detected in the composite profile because of lack of fatty acid 'signatures' in some isolates or because of variations (approximately fivefold) in fatty acid yield across taxa. MIDI- FAME profiles of replicate subsamples of a given community were similar in terms of fatty acid yield per unit of community dry weight and relative proportions of specific fatty acids. Principal-components analysis (PCA) of MIDI-FAME profiles resulted in a clear separation of the two different communities and a clustering of replicates of each community from two separate experiments on the first PCA axis. The first PCA axis accounted for 57.1% of the variance in the data and was correlated with fatty acids that varied significantly between communities and reflected the underlying community taxonomic structure. On the basis of our data, community fatty acid profiles can be used to assess the relative similarities and differences of microbial communities that differ in taxonomic composition. However, detailed interpretation of community fatty acid profiles in terms of biomass or community taxonomic composition must be viewed with caution until our knowledge of the quantitative and qualitative distribution of fatty acids over a wide variety of taxa and the effects of growth conditions on fatty acid profiles is more extensive.

Refining the classification of children with selective mutism: a latent profile analysis.

PubMed

Cohan, Sharon L; Chavira, Denise A; Shipon-Blum, Elisa; Hitchcock, Carla; Roesch, Scott C; Stein, Murray B

2008-10-01

The goal of this study was to develop an empirically derived classification system for selective mutism (SM) using parent-report measures of social anxiety, behavior problems, and communication delays. The sample consisted of parents of 130 children (ages 5-12) with SM. Results from latent profile analysis supported a 3-class solution made up of an anxious-mildly oppositional group, an anxious-communication delayed group, and an exclusively anxious group. Follow-up tests indicated significant group differences on measures of SM symptom severity, externalizing problems, and expressive/receptive language abilities. These results suggest that, although social anxiety is typically a prominent feature of SM, children with the disorder are also likely to present with communication delays and/or mild behavior problems.

Precision analysis for standard deviation measurements of immobile single fluorescent molecule images.

PubMed

DeSantis, Michael C; DeCenzo, Shawn H; Li, Je-Luen; Wang, Y M

2010-03-29

Standard deviation measurements of intensity profiles of stationary single fluorescent molecules are useful for studying axial localization, molecular orientation, and a fluorescence imaging system's spatial resolution. Here we report on the analysis of the precision of standard deviation measurements of intensity profiles of single fluorescent molecules imaged using an EMCCD camera.We have developed an analytical expression for the standard deviation measurement error of a single image which is a function of the total number of detected photons, the background photon noise, and the camera pixel size. The theoretical results agree well with the experimental, simulation, and numerical integration results. Using this expression, we show that single-molecule standard deviation measurements offer nanometer precision for a large range of experimental parameters.

21 CFR 862.1163 - Cardiac allograft gene expression profiling test system.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Cardiac allograft gene expression profiling test... Chemistry Test Systems § 862.1163 Cardiac allograft gene expression profiling test system. (a) Identification. A cardiac allograft gene expression profiling test system is a device that measures the...

A new retrieval algorithm for tropospheric temperature, humidity and pressure profiling based on GNSS radio occultation data

NASA Astrophysics Data System (ADS)

Kirchengast, Gottfried; Li, Ying; Scherllin-Pirscher, Barbara; Schwärz, Marc; Schwarz, Jakob; Nielsen, Johannes K.

2017-04-01

The GNSS radio occultation (RO) technique is an important remote sensing technique for obtaining thermodynamic profiles of temperature, humidity, and pressure in the Earth's troposphere. However, due to refraction effects of both dry ambient air and water vapor in the troposphere, retrieval of accurate thermodynamic profiles at these lower altitudes is challenging and requires suitable background information in addition to the RO refractivity information. Here we introduce a new moist air retrieval algorithm aiming to improve the quality and robustness of retrieving temperature, humidity and pressure profiles in moist air tropospheric conditions. The new algorithm consists of four steps: (1) use of prescribed specific humidity and its uncertainty to retrieve temperature and its associated uncertainty; (2) use of prescribed temperature and its uncertainty to retrieve specific humidity and its associated uncertainty; (3) use of the previous results to estimate final temperature and specific humidity profiles through optimal estimation; (4) determination of air pressure and density profiles from the results obtained before. The new algorithm does not require elaborated matrix inversions which are otherwise widely used in 1D-Var retrieval algorithms, and it allows a transparent uncertainty propagation, whereby the uncertainties of prescribed variables are dynamically estimated accounting for their spatial and temporal variations. Estimated random uncertainties are calculated by constructing error covariance matrices from co-located ECMWF short-range forecast and corresponding analysis profiles. Systematic uncertainties are estimated by empirical modeling. The influence of regarding or disregarding vertical error correlations is quantified. The new scheme is implemented with static input uncertainty profiles in WEGC's current OPSv5.6 processing system and with full scope in WEGC's next-generation system, the Reference Occultation Processing System (rOPS). Results from both WEGC systems, current OPSv5.6 and next-generation rOPS, are shown and discussed, based on both insights from individual profiles and statistical ensembles, and compared to moist air retrieval results from the UCAR Boulder and ROM-SAF Copenhagen centers. The results show that the new algorithmic scheme improves the temperature, humidity and pressure retrieval performance, in particular also the robustness including for integrated uncertainty estimation for large-scale applications, over the previous algorithms. The new rOPS-implemented algorithm will therefore be used in the first large-scale reprocessing towards a tropospheric climate data record 2001-2016 by the rOPS, including its integrated uncertainty propagation.

The application of transcriptomic data in the authentication of beef derived from contrasting production systems.

PubMed

Sweeney, Torres; Lejeune, Alex; Moloney, Aidan P; Monahan, Frank J; Gettigan, Paul Mc; Downey, Gerard; Park, Stephen D E; Ryan, Marion T

2016-09-21

Differences between cattle production systems can influence the nutritional and sensory characteristics of beef, in particular its fatty acid (FA) composition. As beef products derived from pasture-based systems can demand a higher premium from consumers, there is a need to understand the biological characteristics of pasture produced meat and subsequently to develop methods of authentication for these products. Here, we describe an approach to authentication that focuses on differences in the transcriptomic profile of muscle from animals finished in different systems of production of practical relevance to the Irish beef industry. The objectives of this study were to identify a panel of differentially expressed (DE) genes/networks in the muscle of cattle raised outdoors on pasture compared to animals raised indoors on a concentrate based diet and to subsequently identify an optimum panel which can classify the meat based on a production system. A comparison of the muscle transcriptome of outdoor/pasture-fed and Indoor/concentrate-fed cattle resulted in the identification of 26 DE genes. Functional analysis of these genes identified two significant networks (1: Energy Production, Lipid Metabolism, Small Molecule Biochemistry; and 2: Lipid Metabolism, Molecular Transport, Small Molecule Biochemistry), both of which are involved in FA metabolism. The expression of selected up-regulated genes in the outdoor/pasture-fed animals correlated positively with the total n-3 FA content of the muscle. The pathway and network analysis of the DE genes indicate that peroxisome proliferator-activated receptor (PPAR) and FYN/AMPK could be implicit in the regulation of these alterations to the lipid profile. In terms of authentication, the expression profile of three DE genes (ALAD, EIF4EBP1 and NPNT) could almost completely separate the samples based on production system (95 % authentication for animals on pasture-based and 100 % for animals on concentrate- based diet) in this context. The majority of DE genes between muscle of the outdoor/pasture-fed and concentrate-fed cattle were related to lipid metabolism and in particular β-oxidation. In this experiment the combined expression profiles of ALAD, EIF4EBP1 and NPNT were optimal in classifying the muscle transcriptome based on production system. Given the overall lack of comparable studies and variable concordance with those that do exist, the use of transcriptomic data in authenticating production systems requires more exploration across a range of contexts and breeds.

Research on aspheric focusing lens processing and testing technology in the high-energy laser test system

NASA Astrophysics Data System (ADS)

Liu, Dan; Fu, Xiu-hua; Jia, Zong-he; Wang, Zhe; Dong, Huan

2014-08-01

In the high-energy laser test system, surface profile and finish of the optical element are put forward higher request. Taking a focusing aspherical zerodur lens with a diameter of 100mm as example, using CNC and classical machining method of combining surface profile and surface quality of the lens were investigated. Taking profilometer and high power microscope measurement results as a guide, by testing and simulation analysis, process parameters were improved constantly in the process of manufacturing. Mid and high frequency error were trimmed and improved so that the surface form gradually converged to the required accuracy. The experimental results show that the final accuracy of the surface is less than 0.5μm and the surface finish is □, which fulfils the accuracy requirement of aspherical focusing lens in optical system.

Correlation electron cyclotron emission diagnostic and improved calculation of turbulent temperature fluctuation levels on ASDEX Upgrade

NASA Astrophysics Data System (ADS)

Creely, A. J.; Freethy, S. J.; Burke, W. M.; Conway, G. D.; Leccacorvi, R.; Parkin, W. C.; Terry, D. R.; White, A. E.

2018-05-01

A newly upgraded correlation electron cyclotron emission (CECE) diagnostic has been installed on the ASDEX Upgrade tokamak and has begun to perform experimental measurements of electron temperature fluctuations. CECE diagnostics measure small amplitude electron temperature fluctuations by correlating closely spaced heterodyne radiometer channels. This upgrade expanded the system from six channels to thirty, allowing simultaneous measurement of fluctuation level radial profiles without repeat discharges, as well as opening up the possibility of measuring radial turbulent correlation lengths. Newly refined statistical techniques have been developed in order to accurately analyze the fluctuation data collected from the CECE system. This paper presents the hardware upgrades for this system and the analysis techniques used to interpret the raw data, as well as measurements of fluctuation spectra and fluctuation level radial profiles.

[Morbidity profile and hospital expenses with elderly patients in Paraná State, Brazil, 2008-2012].

PubMed

Kernkamp, Clarice da Luz; Costa, Cassia Kely Favoretto; Massuda, Ely Mitie; Silva, Eraldo Schunk; Yamaguchi, Mirian Ueda; Bernuci, Marcelo Picinin

2016-07-21

Growth in the elderly population has increased both the demand for health services and healthcare expenses, with relevant consequences for economic stability. The current study aimed to analyze the morbidity profile and hospital expenses with elderly patients in relation to socioeconomic and demographic conditions in Paraná State, Brazil, from 2008 to 2012, applying principal components analysis and groupings. Regions with higher and lower economic and human development showed high prevalence of hospitalizations and costs pertaining to the circulatory and respiratory systems and cardiac diseases for males and females. In regions with intermediary development, diseases of the nervous system in men and of the circulatory system in women had the highest morbidity and hospital expenses. Thus, measures for prevention and health promotion in this elderly population should be targeted to regional investigations.

Direct profiling of phytochemicals in tulip tissues and in vivo monitoring of the change of carbohydrate content in tulip bulbs by probe electrospray ionization mass spectrometry.

PubMed

Yu, Zhan; Chen, Lee Chuin; Suzuki, Hiroaki; Ariyada, Osamu; Erra-Balsells, Rosa; Nonami, Hiroshi; Hiraoka, Kenzo

2009-12-01

Probe electrospray ionization (PESI) is a recently developed ESI-based ionization technique which generates electrospray from the tip of a solid needle. In this study, we have applied PESI interfaced with a time of flight mass spectrometer (TOF-MS) for direct profiling of phytochemicals in a section of a tulip bulb in different regions, including basal plate, outer and inner rims of scale, flower bud and foliage leaves. Different parts of tulip petals and leaves have also been investigated. Carbohydrates, amino acids and other phytochemicals were detected. A series of in vivo PESI-MS experiments were carried out on the second outermost scales of four living tulip bulbs to monitoring the change of carbohydrate content during the first week of initial growth. The breakdown of carbohydrates was observed which was in accordance with previous reports achieved by other techniques. This study has indicated that PESI-MS can be used for rapid and direct analysis of phytochemicals in living biological systems with advantages of low sample consumption and little sample preparation. Therefore, PESI-MS can be a new choice for direct analysis/profiling of bioactive compounds or monitoring metabolic changes in living biological systems.

Integrated analysis of drug-induced gene expression profiles predicts novel hERG inhibitors.

PubMed

Babcock, Joseph J; Du, Fang; Xu, Kaiping; Wheelan, Sarah J; Li, Min

2013-01-01

Growing evidence suggests that drugs interact with diverse molecular targets mediating both therapeutic and toxic effects. Prediction of these complex interactions from chemical structures alone remains challenging, as compounds with different structures may possess similar toxicity profiles. In contrast, predictions based on systems-level measurements of drug effect may reveal pharmacologic similarities not evident from structure or known therapeutic indications. Here we utilized drug-induced transcriptional responses in the Connectivity Map (CMap) to discover such similarities among diverse antagonists of the human ether-à-go-go related (hERG) potassium channel, a common target of promiscuous inhibition by small molecules. Analysis of transcriptional profiles generated in three independent cell lines revealed clusters enriched for hERG inhibitors annotated using a database of experimental measurements (hERGcentral) and clinical indications. As a validation, we experimentally identified novel hERG inhibitors among the unannotated drugs in these enriched clusters, suggesting transcriptional responses may serve as predictive surrogates of cardiotoxicity complementing existing functional assays.

An Integrated Platform for Isolation, Processing, and Mass Spectrometry-based Proteomic Profiling of Rare Cells in Whole Blood*

PubMed Central

Li, Siyang; Plouffe, Brian D.; Belov, Arseniy M.; Ray, Somak; Wang, Xianzhe; Murthy, Shashi K.; Karger, Barry L.; Ivanov, Alexander R.

2015-01-01

Isolation and molecular characterization of rare cells (e.g. circulating tumor and stem cells) within biological fluids and tissues has significant potential in clinical diagnostics and personalized medicine. The present work describes an integrated platform of sample procurement, preparation, and analysis for deep proteomic profiling of rare cells in blood. Microfluidic magnetophoretic isolation of target cells spiked into 1 ml of blood at the level of 1000–2000 cells/ml, followed by focused acoustics-assisted sample preparation has been coupled with one-dimensional PLOT-LC-MS methodology. The resulting zeptomole detection sensitivity enabled identification of ∼4000 proteins with injection of the equivalent of only 100–200 cells per analysis. The characterization of rare cells in limited volumes of physiological fluids is shown by the isolation and quantitative proteomic profiling of first MCF-7 cells spiked into whole blood as a model system and then two CD133+ endothelial progenitor and hematopoietic cells in whole blood from volunteers. PMID:25755294

Integrated Analysis of Drug-Induced Gene Expression Profiles Predicts Novel hERG Inhibitors

PubMed Central

Babcock, Joseph J.; Du, Fang; Xu, Kaiping; Wheelan, Sarah J.; Li, Min

2013-01-01

Growing evidence suggests that drugs interact with diverse molecular targets mediating both therapeutic and toxic effects. Prediction of these complex interactions from chemical structures alone remains challenging, as compounds with different structures may possess similar toxicity profiles. In contrast, predictions based on systems-level measurements of drug effect may reveal pharmacologic similarities not evident from structure or known therapeutic indications. Here we utilized drug-induced transcriptional responses in the Connectivity Map (CMap) to discover such similarities among diverse antagonists of the human ether-à-go-go related (hERG) potassium channel, a common target of promiscuous inhibition by small molecules. Analysis of transcriptional profiles generated in three independent cell lines revealed clusters enriched for hERG inhibitors annotated using a database of experimental measurements (hERGcentral) and clinical indications. As a validation, we experimentally identified novel hERG inhibitors among the unannotated drugs in these enriched clusters, suggesting transcriptional responses may serve as predictive surrogates of cardiotoxicity complementing existing functional assays. PMID:23936032

International Space Station External Contamination Status

NASA Technical Reports Server (NTRS)

Mikatarian, Ron; Soares, Carlos

2000-01-01

PResentation slides examine external contamination requirements; International Space Station (ISS) external contamination sources; ISS external contamination sensitive surfaces; external contamination control; external contamination control for pre-launch verification; flight experiments and observations; the Space Shuttle Orbiter waste water dump, materials outgassing, active vacuum vents; example of molecular column density profile, modeling and analysis tools; sources of outgassing induced contamination analyzed to date, quiescent sources, observations on optical degradation due to induced external contamination in LEO; examples of typical contaminant and depth profiles; and status of the ISS system, material outgassing, thruster plumes, and optical degradation.

Detailed mechanism of benzene oxidation

NASA Technical Reports Server (NTRS)

Bittker, David A.

1987-01-01

A detailed quantitative mechanism for the oxidation of benzene in both argon and nitrogen diluted systems is presented. Computed ignition delay time for argon diluted mixtures are in satisfactory agreement with experimental results for a wide range of initial conditions. An experimental temperature versus time profile for a nitrogen diluted oxidation was accurately matched and several concentration profiles were matched qualitatively. Application of sensitivity analysis has given approximate rate constant expressions for the two dominant heat release reactions, the oxidation of C6H5 and C5H5 radicals by molecular oxygen.

Design optimization of a prescribed vibration system using conjoint value analysis

NASA Astrophysics Data System (ADS)

Malinga, Bongani; Buckner, Gregory D.

2016-12-01

This article details a novel design optimization strategy for a prescribed vibration system (PVS) used to mechanically filter solids from fluids in oil and gas drilling operations. A dynamic model of the PVS is developed, and the effects of disturbance torques are detailed. This model is used to predict the effects of design parameters on system performance and efficiency, as quantified by system attributes. Conjoint value analysis, a statistical technique commonly used in marketing science, is utilized to incorporate designer preferences. This approach effectively quantifies and optimizes preference-based trade-offs in the design process. The effects of designer preferences on system performance and efficiency are simulated. This novel optimization strategy yields improvements in all system attributes across all simulated vibration profiles, and is applicable to other industrial electromechanical systems.

Evaluation of a new filing system's ability to maintain canal morphology.

PubMed

Thompson, Matthew; Sidow, Stephanie J; Lindsey, Kimberly; Chuang, Augustine; McPherson, James C

2014-06-01

The manufacturer of the Hyflex CM endodontic files claims the files remain centered within the canal, and if unwound during treatment, they will regain their original shape after sterilization. The purpose of this study was to evaluate and compare the canal centering ability of the Hyflex CM and the ProFile ISO filing systems after repeated uses in simulated canals, followed by autoclaving. Sixty acrylic blocks with a canal curvature of 45° were stained with methylene blue, photographed, and divided into 2 groups, H (Hyflex CM) and P (ProFile ISO). The groups were further subdivided into 3 subgroups: H1, H2, H3; P1, P2, P3 (n = 10). Groups H1 and P1 were instrumented to 40 (.04) with the respective file system. Used files were autoclaved for 26 minutes at 126°C. After sterilization, the files were used to instrument groups H2 and P2. The same sterilization and instrumentation procedure was repeated for groups H3 and P3. Post-instrumentation digital images were taken and superimposed over the pre-instrumentation images. Changes in the location of the center of the canal at predetermined reference points were recorded and compared within subgroups and between filing systems. Statistical differences in intergroup and intragroup transportation measures were analyzed by using the Kruskal-Wallis analysis of variance of ranks with the Bonferroni post hoc test. There was a difference between Hyflex CM and ProFile ISO groups, although it was not statistically significant. Intragroup differences for both Hyflex CM and ProFile ISO groups were not significant (P < .05). The Hyflex CM and ProFile ISO files equally maintained the original canal's morphology after 2 sterilization cycles. Published by Elsevier Inc.

Unsupervised user similarity mining in GSM sensor networks.

PubMed

Shad, Shafqat Ali; Chen, Enhong

2013-01-01

Mobility data has attracted the researchers for the past few years because of its rich context and spatiotemporal nature, where this information can be used for potential applications like early warning system, route prediction, traffic management, advertisement, social networking, and community finding. All the mentioned applications are based on mobility profile building and user trend analysis, where mobility profile building is done through significant places extraction, user's actual movement prediction, and context awareness. However, significant places extraction and user's actual movement prediction for mobility profile building are a trivial task. In this paper, we present the user similarity mining-based methodology through user mobility profile building by using the semantic tagging information provided by user and basic GSM network architecture properties based on unsupervised clustering approach. As the mobility information is in low-level raw form, our proposed methodology successfully converts it to a high-level meaningful information by using the cell-Id location information rather than previously used location capturing methods like GPS, Infrared, and Wifi for profile mining and user similarity mining.

Using probabilistic theory to develop interpretation guidelines for Y-STR profiles.

PubMed

Taylor, Duncan; Bright, Jo-Anne; Buckleton, John

2016-03-01

Y-STR profiling makes up a small but important proportion of forensic DNA casework. Often Y-STR profiles are used when autosomal profiling has failed to yield an informative result. Consequently Y-STR profiles are often from the most challenging samples. In addition to these points, Y-STR loci are linked, meaning that evaluation of haplotype probabilities are either based on overly simplified counting methods or computationally costly genetic models, neither of which extend well to the evaluation of mixed Y-STR data. For all of these reasons Y-STR data analysis has not seen the same advances as autosomal STR data. We present here a probabilistic model for the interpretation of Y-STR data. Due to the fact that probabilistic systems for Y-STR data are still some way from reaching active casework, we also describe how data can be analysed in a continuous way to generate interpretational thresholds and guidelines. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

SU-F-T-179: Fast and Accurate Profile Acquisition for Proton Beam Using Multi-Ion Chamber Arrays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, X; Zou, J; Chen, T

2016-06-15

Purpose: Proton beam profile measurement is more time-consuming than photon beam. Due to the energy modulation during proton delivery, chambers have to move step-by-step instead of continuously. Multi-ion chamber arrays are appealing to this task since multiple measurements can be performed at once. However, their utilization suffers from sparse spatial resolution and potential intrinsic volume-averaging effect of the disk-shaped ion chambers. We proposed an approach to measure proton beam profiles accurately and efficiently. Methods: Mevion S250 proton system and IBA Matrixx ion chamber arrays were used in this study. Matrixx has interchamber distance of 7.62 mm, and chamber diameter ofmore » 4.5 mm. We measured the same beam profile by moving the Matrixx seven times with 1 mm each time along y axis. All 7 measurements were superimposed to get a “finer” profile with 1 mm spatial resolution. Coarser resolution profiles of 2 mm and 3 mm were also generated by using subsets of measurements. Those profiles were compared to the TPS calculated beam profile. Gamma analysis was performed for 2D dose maps to evaluate the difference to TPS dose plane. Results: Preliminary results showed a large discrepancy between the TPS calculated profile and the single measurement profile with 7.6 mm resolution. A good match could be achieved when the resolution reduced to 3 mm by adding one extra measurement. Gamma analysis for 2D dose map of a 10×10 field showed a passing rate (γ ≤ 1) of 90.6% using a 3% and 3mm criterion for single measurement, which increased to 92.3% for 2-measurement superimposition, and slightly further increased to 92.9% for 7-measurement superimposition. Conclusion: The results indicated that 2 measurements shifted by 3mm using Matrixx generated a smooth proton beam profile with good matching to Eclipse beam profile. We suggest using this 2-measurement approach in clinic for double scattering proton beam profile measurement.« less

Assimilation of NUCAPS Retrieved Profiles in GSI for Unique Forecasting Applications

NASA Technical Reports Server (NTRS)

Berndt, Emily Beth; Zavodsky, Bradley; Srikishen, Jayanthi; Blankenship, Clay

2015-01-01

Hyperspectral IR profiles can be assimilated in GSI as a separate observation other than radiosondes with only changes to tables in the fix directory. Assimilation of profiles does produce changes to analysis fields and evidenced by: Innovations larger than +/-2.0 K are present and represent where individual profiles impact the final temperature analysis.The updated temperature analysis is colder behind the cold front and warmer in the warm sector. The updated moisture analysis is modified more in the low levels and tends to be drier than the original model background Analysis of model output shows: Differences relative to 13-km RAP analyses are smaller when profiles are assimilated with NUCAPS errors. CAPE is under-forecasted when assimilating NUCAPS profiles, which could be problematic for severe weather forecasting Refining the assimilation technique to incorporate an error covariance matrix and creating a separate GSI module to assimilate satellite profiles may improve results.

Analysis and optimization of surface profile correcting mechanism of the pitch lap in large-aperture annular polishing

NASA Astrophysics Data System (ADS)

Zhang, Huifang; Yang, Minghong; Xu, Xueke; Wu, Lunzhe; Yang, Weiguang; Shao, Jianda

2017-10-01

The surface figure control of the conventional annular polishing system is realized ordinarily by the interaction between the conditioner and the lap. The surface profile of the pitch lap corrected by the marble conditioner has been measured and analyzed as a function of kinematics, loading conditions, and polishing time. The surface profile measuring equipment of the large lap based on laser alignment was developed with the accuracy of about 1μm. The conditioning mechanism of the conditioner is simply determined by the kinematics and fully fitting principle, but the unexpected surface profile deviation of the lap emerged frequently due to numerous influencing factors including the geometrical relationship, the pressure distribution at the conditioner/lap interface. Both factors are quantitatively evaluated and described, and have been combined to develop a spatial and temporal model to simulate the surface profile evolution of pitch lap. The simulations are consistent with the experiments. This study is an important step toward deterministic full-aperture annular polishing, providing a beneficial guidance for the surface profile correction of the pitch lap.

Diffusion profiling of tumor volumes using a histogram approach can predict proliferation and further microarchitectural features in medulloblastoma.

PubMed

Schob, Stefan; Beeskow, Anne; Dieckow, Julia; Meyer, Hans-Jonas; Krause, Matthias; Frydrychowicz, Clara; Hirsch, Franz-Wolfgang; Surov, Alexey

2018-05-31

Medulloblastomas are the most common central nervous system tumors in childhood. Treatment and prognosis strongly depend on histology and transcriptomic profiling. However, the proliferative potential also has prognostical value. Our study aimed to investigate correlations between histogram profiling of diffusion-weighted images and further microarchitectural features. Seven patients (age median 14.6 years, minimum 2 years, maximum 20 years; 5 male, 2 female) were included in this retrospective study. Using a Matlab-based analysis tool, histogram analysis of whole apparent diffusion coefficient (ADC) volumes was performed. ADC entropy revealed a strong inverse correlation with the expression of the proliferation marker Ki67 (r = - 0.962, p = 0.009) and with total nuclear area (r = - 0.888, p = 0.044). Furthermore, ADC percentiles, most of all ADCp90, showed significant correlations with Ki67 expression (r = 0.902, p = 0.036). Diffusion histogram profiling of medulloblastomas provides valuable in vivo information which potentially can be used for risk stratification and prognostication. First of all, entropy revealed to be the most promising imaging biomarker. However, further studies are warranted.

Regio- and stereospecific analysis of glycerolipids.

PubMed

Kuksis, Arnis; Itabashi, Yutaka

2005-06-01

In recent years researchers have recognized the potential value of comprehensive lipid profiling (lipidomics), which was invented and promoted by lipidologists who recognized the many valuable applications that grew out of the fields of DNA profiling (genomics) and protein profiling (proteonomics). Through lipid class-selective intrasource ionization and subsequent analysis of two-dimensional cross-peak intensities, the chemical identity and mass composition of individual molecular species of most lipid classes can now be determined in a chloroform extract. There remains, however, the necessity to distinguish the enantiomers and isobaric regioisomers resulting from enzymatic and chemical reactions, which conventional high performance liquid chromatography/mass spectrometry (HPLC/MS) has been slow to accommodate, and tandem MS unable to provide. While reversed-phase HPLC can separate regioisomers, normal-phase HPLC can resolve diastereomers, and chiral-phase HPLC can effect dramatic resolution of enantiomers, the full potential of the combined systems has seldom been exploited. The present chapter calls attention to both recent and earlier combinations of these methodologies with mass spectrometry, which allows the HPLC/ESI (electrospray ionization)-MS/MS separation and identification of enantiomeric diacylglycerols, triacylglycerols, and glycerophospholipids as well as their isobaric regioisomers. These developments permit further expansion of lipid profiling (lipidomics) and better understanding of lipid metabolism.

A fundamental approach to adhesion: Synthesis, surface analysis, thermodynamics and mechanics

NASA Technical Reports Server (NTRS)

Chen, W.; Wightman, J. P.

1979-01-01

Adherend surfaces and fractography were studied using electron spectroscopy for chemical analysis and scanning electron microscopy/energy dispersive analysis of X-rays. In addition, Auger Electron Spectroscopy with depth profiling capability was used. It is shown that contamination of adhesion systems plays an important role not only in determining initial bond strengths but also in the durability of adhesive bonds. It is concluded that the analytical techniques used to characterize and monitor such contamination.

Classification of Marital Relationships: An Empirical Approach.

ERIC Educational Resources Information Center

Snyder, Douglas K.; Smith, Gregory T.

1986-01-01

Derives an empirically based classification system of marital relationships, employing a multidimensional self-report measure of marital interaction. Spouses' profiles on the Marital Satisfaction Inventory for samples of clinic and nonclinic couples were subjected to cluster analysis, resulting in separate five-group typologies for husbands and…

Understanding developmental and adaptive cues in pine through metabolite profiling and co-expression network analysis

PubMed Central

Cañas, Rafael A.; Canales, Javier; Muñoz-Hernández, Carmen; Granados, Jose M.; Ávila, Concepción; García-Martín, María L.; Cánovas, Francisco M.

2015-01-01

Conifers include long-lived evergreen trees of great economic and ecological importance, including pines and spruces. During their long lives conifers must respond to seasonal environmental changes, adapt to unpredictable environmental stresses, and co-ordinate their adaptive adjustments with internal developmental programmes. To gain insights into these responses, we examined metabolite and transcriptomic profiles of needles from naturally growing 25-year-old maritime pine (Pinus pinaster L. Aiton) trees over a year. The effect of environmental parameters such as temperature and rain on needle development were studied. Our results show that seasonal changes in the metabolite profiles were mainly affected by the needles’ age and acclimation for winter, but changes in transcript profiles were mainly dependent on climatic factors. The relative abundance of most transcripts correlated well with temperature, particularly for genes involved in photosynthesis or winter acclimation. Gene network analysis revealed relationships between 14 co-expressed gene modules and development and adaptation to environmental stimuli. Novel Myb transcription factors were identified as candidate regulators during needle development. Our systems-based analysis provides integrated data of the seasonal regulation of maritime pine growth, opening new perspectives for understanding the complex regulatory mechanisms underlying conifers’ adaptive responses. Taken together, our results suggest that the environment regulates the transcriptome for fine tuning of the metabolome during development. PMID:25873654

Inpatient Profile of Patients with Major Depression in Portuguese National Health System Hospitals, in 2008 and 2013: Variation in a Time of Economic Crisis.

PubMed

Rodrigues, Daniel Francisco Santos; Nunes, Carla

2018-02-01

The economic crisis has placed Portugal in a situation of budgetary constraints with repercussions on mental health, since 2009. This study analyses the association between economic crisis and the inpatient profile of major depression in the working-age population in Portuguese National Health System hospitals. This was an observational, descriptive and cross-sectional study. An individual analysis of hospitalisation and an ecological analysis at district level, were performed before 2008 and during the crisis (2013). Data on the hospitalisation episodes, working-age population and psychiatric inpatient beds were analysed. An increase in hospitalisation rates for major depression were observed, and across country, high spatial variations were perceived: districts with lower rates of urbanisation and population density had higher hospitalisation rates for major depression. Hospitalisation rates were positively influenced by the available inpatient beds. The results for 2013 were more critical (higher hospitalisation rates, less beds). Further research is needed to understand all patterns, considering other individual and contextual information.

Applications of DNA-Based Liquid Biopsy for Central Nervous System Neoplasms.

PubMed

Wang, Joanna; Bettegowda, Chetan

2017-01-01

The management of central nervous system malignancies remains reliant on histopathological analysis and neuroimaging, despite their complex genetic profile. The intratumoral heterogeneity displayed by these tumors necessitates a more sophisticated method of tumor analysis and monitoring, with the ability to assess tumors over space and time. Circulating biomarkers, including circulating tumor cells, circulating tumor DNA, and extracellular vesicles, hold promise as a type of real-time liquid biopsy able to provide dynamic information not only regarding tumor burden to monitor disease progression and treatment response, but also regarding genetic profile to enable changes in management to match a constantly evolving tumor. In numerous cancer types, including glioma, they have demonstrated their clinical utility as a minimally invasive means for diagnosis, prognostication, and prediction. In addition, they can be used in the laboratory to probe mechanisms of acquired drug resistance and tumor invasion and dissemination. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

From genes to genomes: a new paradigm for studying fungal pathogenesis in Magnaporthe oryzae.

PubMed

Xu, Jin-Rong; Zhao, Xinhua; Dean, Ralph A

2007-01-01

Magnaporthe oryzae is the most destructive fungal pathogen of rice worldwide and because of its amenability to classical and molecular genetic manipulation, availability of a genome sequence, and other resources it has emerged as a leading model system to study host-pathogen interactions. This chapter reviews recent progress toward elucidation of the molecular basis of infection-related morphogenesis, host penetration, invasive growth, and host-pathogen interactions. Related information on genome analysis and genomic studies of plant infection processes is summarized under specific topics where appropriate. Particular emphasis is placed on the role of MAP kinase and cAMP signal transduction pathways and unique features in the genome such as repetitive sequences and expanded gene families. Emerging developments in functional genome analysis through large-scale insertional mutagenesis and gene expression profiling are detailed. The chapter concludes with new prospects in the area of systems biology, such as protein expression profiling, and highlighting remaining crucial information needed to fully appreciate host-pathogen interactions.

A Study on Water Surface Profiles of Rivers with Constriction

NASA Astrophysics Data System (ADS)

Qian, Chaochao; Yamada, Tadashi

2013-04-01

Water surface profile of rivers with constrictions is precious in both classic hydraulics and river management practice. This study was conducted to clarify the essences of the water surface profiles. 3 cases of experiments and 1D numerical calculations with different discharges were made in the study and analysis solutions of the non-linear basic equation of surface profile in varied flow without considering friction were derived. The manning's number was kept in the same in each case by using crosspiece roughness. We found a new type of water surface profile of varied flow from the results of 1D numerical calculation and that of experiments and named it as Mc curve because of its mild condition with constriction segment. This kind of curves appears as a nature phenomenon ubiquitously. The process of water surface forming is dynamic and bore occurs at the upper side of constriction during increasing discharge before the surface profile formed. As a theoretical work, 3 analysis solutions were derived included 2 physical-meaning solutions in the study by using Man-Machine system. One of the derived physical-meaning solutions was confirmed that it is validity by comparing to the results of 1D numerical calculation and that of experiments. The solution represents a flow profile from under critical condition at the upper side to super critical condition at the down side of constriction segment. The other derived physical-meaning solution represents a flow profile from super critical condition at the upper side to under critical condition at the down side of constriction segment. These two kinds of flow profiles exist in the nature but no theoretical solution can express the phenomenon. We find the depth distribution only concerned with unit width discharge distribution and critical depth under a constant discharge from the derived solutions. Therefor, the profile can be gained simply and precisely by using the theoretical solutions instead of numerical calculation even in practice.

3D Doppler Tomography of the X-Ray Binary System Cygnus X-1 from Spectral Observations in 2007 in the HeII λ 4686 Å Line

NASA Astrophysics Data System (ADS)

Agafonov, M. I.; Karitskaya, E. A.; Sharova, O. I.; Bochkarev, N. G.; Zharikov, S. V.; Butenko, G. Z.; Bondar', A. V.; Sidorov, M. Yu.

2018-02-01

The results of a 3D Doppler tomography analysis for the X-ray binary system Cyg X-1 in the HeII λ 4686 Å line are presented. Information about the motions of gaseous flows outside the orbital plane has been obtained for the first time. Line profiles obtained in June 2007 on the 2-m telescope of the Terskol Branch of the Institute of Astronomy (Russia) and on the 2.1-m telescope of the National Astronomical Observatory of Mexico were used. A detailed analysis of these spectral data is presented: the distribution of the data in time, distribution of orbital phases for the projections, comparison of the line profile shapes for the data from two observatories. The geometry of the total transfer function obtained in the reconstruction is considered. The possibility of applying the profiles obtained to realize 3D tomography is justified. The resolution of the constructed 3D tomogram in velocity space is 60 × 60 × 40 km/s for V x , V y , V z . Fifteen cross sections for 15 different V z values perpendicular to the orbital plane are presented. The intensity distributions corresponding to the velocities of gaseous structures in the binary system are obtained. The reconstruction was realized using the radio-astronomical approach, developed for solving problems in tomography with a limited number of projections.

Thermal analysis of the in-vessel components of the ITER plasma-position reflectometry.

PubMed

Quental, P B; Policarpo, H; Luís, R; Varela, P

2016-11-01

The ITER plasma position reflectometry system measures the edge electron density profile of the plasma, providing real-time supplementary contribution to the magnetic measurements of the plasma-wall distance. Some of the system components will be in direct sight of the plasma and therefore subject to plasma and stray radiation, which may cause excessive temperatures and stresses. In this work, thermal finite element analysis of the antenna and adjacent waveguides is conducted with ANSYS V17 (ANSYS® Academic Research, Release 17.0, 2016). Results allow the identification of critical temperature points, and solutions are proposed to improve the thermal behavior of the system.

Thermal analysis of the in-vessel components of the ITER plasma-position reflectometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quental, P. B., E-mail: pquental@ipfn.tecnico.ulisboa.pt; Policarpo, H.; Luís, R.

The ITER plasma position reflectometry system measures the edge electron density profile of the plasma, providing real-time supplementary contribution to the magnetic measurements of the plasma-wall distance. Some of the system components will be in direct sight of the plasma and therefore subject to plasma and stray radiation, which may cause excessive temperatures and stresses. In this work, thermal finite element analysis of the antenna and adjacent waveguides is conducted with ANSYS V17 (ANSYS® Academic Research, Release 17.0, 2016). Results allow the identification of critical temperature points, and solutions are proposed to improve the thermal behavior of the system.

Energy audit data for a resort island in the South China Sea.

PubMed

Basir Khan, M Reyasudin; Jidin, Razali; Pasupuleti, Jagadeesh

2016-03-01

The data consists of actual generation-side auditing including the distribution of loads, seasonal load profiles, and types of loads as well as an analysis of local development planning of a resort island in the South China Sea. The data has been used to propose an optimal combination of hybrid renewable energy systems that able to mitigate the diesel fuel dependency on the island. The resort island selected is Tioman, as it represents the typical energy requirements of many resort islands in the South China Sea. The data presented are related to the research article "Optimal Combination of Solar, Wind, Micro-Hydro and Diesel Systems based on Actual Seasonal Load Profiles for a Resort Island in the South China Sea" [1].

Analysis of Cloud-Based Database Systems

DTIC Science & Technology

2015-06-01

EU) citizens under the Patriot Act [3]. Unforeseen virtualization bugs have caused wide-reaching outages [4], leaving customers helpless to assist...collected from SQL Server Profiler traces. We analyze the trace results captured from our test bed both before and after increasing system resources...cloud test- bed . A. DATA COLLECTION, PARSING, AND ORGANIZATION Once we finished collecting the trace data, we knew we needed to have as close a

Metabolites Associated With Malnutrition in the Intensive Care Unit Are Also Associated With 28-Day Mortality.

PubMed

Mogensen, Kris M; Lasky-Su, Jessica; Rogers, Angela J; Baron, Rebecca M; Fredenburgh, Laura E; Rawn, James; Robinson, Malcolm K; Massarro, Anthony; Choi, Augustine M K; Christopher, Kenneth B

2017-02-01

We hypothesized that metabolic profiles would differ in critically ill patients with malnutrition relative to those without. We performed a prospective cohort study on 85 adult patients with systemic inflammatory response syndrome or sepsis admitted to a 20-bed medical intensive care unit (ICU) in Boston. We generated metabolomic profiles using gas and liquid chromatography and mass spectroscopy. We followed this by logistic regression and partial least squares discriminant analysis to identify individual metabolites that were significant. We then interrogated the entire metabolomics profile using metabolite set enrichment analysis and network model construction of chemical-protein target interactions to identify groups of metabolites and pathways that were differentiates in patients with and without malnutrition. Of the cohort, 38% were malnourished at admission to the ICU. Metabolomic profiles differed in critically ill patients with malnutrition relative to those without. Ten metabolites were significantly associated with malnutrition ( P < .05). A parsimonious model of 5 metabolites effectively differentiated patients with malnutrition (AUC = 0.76), including pyroglutamine and hypoxanthine. Using pathway enrichment analysis, we identified a critical role of glutathione and purine metabolism in predicting nutrition. Nutrition status was associated with 28-day mortality, even after adjustment for known phenotypic variables associated with ICU mortality. Importantly, 7 metabolites associated with nutrition status were also associated with 28-day mortality. Malnutrition is associated with differential metabolic profiles early in critical illness. Common to all of our metabolome analyses, glutathione and purine metabolism, which play principal roles in cellular redox regulation and accelerated tissue adenosine triphosphate degradation, respectively, were significantly altered with malnutrition.

40 CFR 141.532 - How does my system develop a disinfection profile and when must it begin?

Code of Federal Regulations, 2012 CFR

2012-07-01

... disinfection profile and when must it begin? 141.532 Section 141.532 Protection of Environment ENVIRONMENTAL... Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Disinfection Profile § 141.532 How does my system develop a disinfection profile and when must it begin? A disinfection profile consists of...

40 CFR 141.532 - How does my system develop a disinfection profile and when must it begin?

Code of Federal Regulations, 2011 CFR

2011-07-01

... disinfection profile and when must it begin? 141.532 Section 141.532 Protection of Environment ENVIRONMENTAL... Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Disinfection Profile § 141.532 How does my system develop a disinfection profile and when must it begin? A disinfection profile consists of...

40 CFR 141.532 - How does my system develop a disinfection profile and when must it begin?

Code of Federal Regulations, 2014 CFR

2014-07-01

... disinfection profile and when must it begin? 141.532 Section 141.532 Protection of Environment ENVIRONMENTAL... Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Disinfection Profile § 141.532 How does my system develop a disinfection profile and when must it begin? A disinfection profile consists of...

40 CFR 141.532 - How does my system develop a disinfection profile and when must it begin?

Code of Federal Regulations, 2013 CFR

2013-07-01

... disinfection profile and when must it begin? 141.532 Section 141.532 Protection of Environment ENVIRONMENTAL... Filtration and Disinfection-Systems Serving Fewer Than 10,000 People Disinfection Profile § 141.532 How does my system develop a disinfection profile and when must it begin? A disinfection profile consists of...

Data Mining of Determinants of Intrauterine Growth Retardation Revisited Using Novel Algorithms Generating Semantic Maps and Prototypical Discriminating Variable Profiles

PubMed Central

Buscema, Massimo; Grossi, Enzo; Montanini, Luisa; Street, Maria E.

2015-01-01

Objectives Intra-uterine growth retardation is often of unknown origin, and is of great interest as a “Fetal Origin of Adult Disease” has been now well recognized. We built a benchmark based upon a previously analysed data set related to Intrauterine Growth Retardation with 46 subjects described by 14 variables, related with the insulin-like growth factor system and pro-inflammatory cytokines, namely interleukin -6 and tumor necrosis factor -α. Design and Methods We used new algorithms for optimal information sorting based on the combination of two neural network algorithms: Auto-contractive Map and Activation and Competition System. Auto-Contractive Map spatializes the relationships among variables or records by constructing a suitable embedding space where ‘closeness’ among variables or records reflects accurately their associations. The Activation and Competition System algorithm instead works as a dynamic non linear associative memory on the weight matrices of other algorithms, and is able to produce a prototypical variable profile of a given target. Results Classical statistical analysis, proved to be unable to distinguish intrauterine growth retardation from appropriate-for-gestational age (AGA) subjects due to the high non-linearity of underlying functions. Auto-contractive map succeeded in clustering and differentiating completely the conditions under study, while Activation and Competition System allowed to develop the profile of variables which discriminated the two conditions under study better than any other previous form of attempt. In particular, Activation and Competition System showed that ppropriateness for gestational age was explained by IGF-2 relative gene expression, and by IGFBP-2 and TNF-α placental contents. IUGR instead was explained by IGF-I, IGFBP-1, IGFBP-2 and IL-6 gene expression in placenta. Conclusion This further analysis provided further insight into the placental key-players of fetal growth within the insulin-like growth factor and cytokine systems. Our previous published analysis could identify only which variables were predictive of fetal growth in general, and identified only some relationships. PMID:26158499

Effects of Organic and Conventional Crop Nutrition on Profiles of Polar Metabolites in Grain of Wheat.

PubMed

Shewry, Peter; Rakszegi, Marianna; Lovegrove, Alison; Amos, Dominic; Corol, Delia-Irina; Tawfike, Ahmed; Mikó, Péter; Ward, Jane L

2018-05-30

The profiles of polar metabolites were determined in wholemeal flours of grain from the Broadbalk wheat experiment and from plants grown under organic and low-input systems to study the effects of nutrition on composition. The Broadbalk samples showed increased amino acids, acetate, and choline and decreased fructose and succinate with increasing nitrogen fertilization. Samples receiving farm yard manure had similar grain nitrogen to those receiving 96 kg of N/ha but had higher contents of amino acids, sugars, and organic acids. A comparison of the profiles of grain from organic and low-input systems showed only partial separation, with clear effects of climate and agronomy. However, supervised multivariate analysis showed that the low-input samples had higher contents of many amino acids, raffinose, glucose, organic acids, and choline and lower sucrose, fructose, and glycine. Consequently, although differences between organic and conventional grain occur, these cannot be used to confirm sample identity.

Fatty acid profiles of benthic environment associated with artificial reefs in subtropical Hong Kong.

PubMed

Cheung, Siu Gin; Wai, Ho Yin; Shin, Paul K S

2010-02-01

Artificial reefs can enhance habitat heterogeneity, especially in seabed degraded by bottom-dredging and trawling. However, the trophodynamics of such reef systems are not well understood. This study provided baseline data on trophic relationships in the benthic environment associated with artificial reefs in late spring and mid summer of subtropical Hong Kong, using fatty acid profiles as an indicator. Data from sediments collected at the reef base, materials from sediment traps deployed on top and bottom of the reefs, total particulate matter from the water column and oyster tissues from reef surface were subjected to principal component analysis. Results showed variations of fatty acid profiles in the total particulate matter, upper sediment trap and oyster tissue samples collected in the two samplings, indicating seasonal, trophodynamic changes within the reef system. The wastes produced by fish aggregating at the reefs can also contribute a source of biodeposits to the nearby benthic environment. Copyright 2009 Elsevier Ltd. All rights reserved.

Shock drive capabilities of a 30-Joule laser at the matter in extreme conditions hutch of the Linac Coherent Light Source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, Shaughnessy Brennan; Hashim, Akel; Gleason, Arianna

In this paper, we measure the shock drive capabilities of a 30 J, nanosecond, 527 nm laser system at the matter in extreme conditions hutch of the Linac Coherent Light Source. Using a velocity interferometer system for any reflector, we ascertain the maximum instantaneous ablation pressure and characterize its dependence on a drive laser spot size, spatial profile, and temporal profile. We also examine the effects of these parameters on shock spatial and temporal uniformity. Our analysis shows the drive laser capable of generating instantaneous ablation pressures exceeding 160 GPa while maintaining a 1D shock profile. We find that slopemore » pulses provide higher instantaneous ablation pressures than plateau pulses. Our results show instantaneous ablation pressures comparable to those measured at the Omega Laser Facility in Rochester, NY under similar optical drive parameters. In conclusion, we analyze how optical laser ablation pressures are compare with known scaling relations, accounting for variable laser wavelengths.« less

Shock drive capabilities of a 30-Joule laser at the matter in extreme conditions hutch of the Linac Coherent Light Source

DOE PAGES

Brown, Shaughnessy Brennan; Hashim, Akel; Gleason, Arianna; ...

2017-10-23

In this paper, we measure the shock drive capabilities of a 30 J, nanosecond, 527 nm laser system at the matter in extreme conditions hutch of the Linac Coherent Light Source. Using a velocity interferometer system for any reflector, we ascertain the maximum instantaneous ablation pressure and characterize its dependence on a drive laser spot size, spatial profile, and temporal profile. We also examine the effects of these parameters on shock spatial and temporal uniformity. Our analysis shows the drive laser capable of generating instantaneous ablation pressures exceeding 160 GPa while maintaining a 1D shock profile. We find that slopemore » pulses provide higher instantaneous ablation pressures than plateau pulses. Our results show instantaneous ablation pressures comparable to those measured at the Omega Laser Facility in Rochester, NY under similar optical drive parameters. In conclusion, we analyze how optical laser ablation pressures are compare with known scaling relations, accounting for variable laser wavelengths.« less

Assigning protein functions by comparative genome analysis protein phylogenetic profiles

DOEpatents

Pellegrini, Matteo; Marcotte, Edward M.; Thompson, Michael J.; Eisenberg, David; Grothe, Robert; Yeates, Todd O.

2003-05-13

A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

Methods and tools for profiling and control of distributed systems

NASA Astrophysics Data System (ADS)

Sukharev, R.; Lukyanchikov, O.; Nikulchev, E.; Biryukov, D.; Ryadchikov, I.

2018-02-01

This article is devoted to the topic of profiling and control of distributed systems. Distributed systems have a complex architecture, applications are distributed among various computing nodes, and many network operations are performed. Therefore, today it is important to develop methods and tools for profiling distributed systems. The article analyzes and standardizes methods for profiling distributed systems that focus on simulation to conduct experiments and build a graph model of the system. The theory of queueing networks is used for simulation modeling of distributed systems, receiving and processing user requests. To automate the above method of profiling distributed systems the software application was developed with a modular structure and similar to a SCADA-system.

Profiling Fast Healthcare Interoperability Resources (FHIR) of Family Health History based on the Clinical Element Models.

PubMed

Lee, Jaehoon; Hulse, Nathan C; Wood, Grant M; Oniki, Thomas A; Huff, Stanley M

2016-01-01

In this study we developed a Fast Healthcare Interoperability Resources (FHIR) profile to support exchanging a full pedigree based family health history (FHH) information across multiple systems and applications used by clinicians, patients, and researchers. We used previously developed clinical element models (CEMs) that are capable of representing the FHH information, and derived essential data elements including attributes, constraints, and value sets. We analyzed gaps between the FHH CEM elements and existing FHIR resources. Based on the analysis, we developed a profile that consists of 1) FHIR resources for essential FHH data elements, 2) extensions for additional elements that were not covered by the resources, and 3) a structured definition to integrate patient and family member information in a FHIR message. We implemented the profile using an open-source based FHIR framework and validated it using patient-entered FHH data that was captured through a locally developed FHH tool.

An empirical analysis of the radio propagation characteristics in high-speed railway environment

NASA Astrophysics Data System (ADS)

Hu, Guoqing; Ma, Guangjin; Li, Chunlai; Xu, Yongchi; He, Jin; Yu, Ying; He, Yandong

2017-09-01

For a wireless mobile network, a profile of radio propagation characteristics is the key to study any wireless techniques, especially in High-Speed Railway (HSR) environment. Unfortunately, such a profile is not available so far, which leads manifold challenges to wireless study for HSR scenarios. In this paper, we focus on this topic, and try to obtain this profile in various kinds of HSR scenarios based on previous field tests in China. Our study reveals that the Line-Of-Sight (LOS) propagation path plays a predominant role in the HSR scenarios, which can suppress the shadow fading. Finally, we find out that each kind of small-scale fading effects has a unique profile on different wireless mobile systems for HSR scenarios. As a result, this study presents a theoretical guidance for studying any wireless techniques in HSR environment, e.g., cell handover for HSR.

Social Disadvantage, Severe Child Abuse, and Biological Profiles in Adulthood.

PubMed

Lee, Chioun; Coe, Christopher L; Ryff, Carol D

2017-09-01

Guided by the stress process model and the life course perspective, we hypothesize: (1) that childhood abuse is concentrated, in terms of type and intensity, among socially disadvantaged individuals, and (2) that experiencing serious abuse contributes to poor biological profiles in multiple body systems in adulthood. Data came from the Biomarker subsample of Midlife in the United States (2004-2006). We used latent class analysis to identify distinct profiles of childhood abuse, each reflecting a combination of type and severity. Results indicate that disadvantaged groups, women, and those from disadvantaged families are at greater risk of experiencing more severe and multiple types of abuse. Those with more severe and multifaceted childhood abuse show greater physiological dysregulation. Childhood abuse experiences partially accounted for the social status differences in physiological profiles. Our findings underscore that differential exposure to serious childhood stressors plays a significant role in gender and class inequalities in adult health.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Janjusic, Tommy; Kartsaklis, Christos

Application analysis is facilitated through a number of program profiling tools. The tools vary in their complexity, ease of deployment, design, and profiling detail. Specifically, understand- ing, analyzing, and optimizing is of particular importance for scientific applications where minor changes in code paths and data-structure layout can have profound effects. Understanding how intricate data-structures are accessed and how a given memory system responds is a complex task. In this paper we describe a trace profiling tool, Glprof, specifically aimed to lessen the burden of the programmer to pin-point heavily involved data-structures during an application's run-time, and understand data-structure run-time usage.more » Moreover, we showcase the tool's modularity using additional cache simulation components. We elaborate on the tool's design, and features. Finally we demonstrate the application of our tool in the context of Spec bench- marks using the Glprof profiler and two concurrently running cache simulators, PPC440 and AMD Interlagos.« less

Thermally developed peristaltic propulsion of magnetic solid particles in biorheological fluids

NASA Astrophysics Data System (ADS)

Bhatti, M. M.; Zeeshan, A.; Tripathi, D.; Ellahi, R.

2018-04-01

In this article, effects of heat and mass transfer on MHD peristaltic motion of solid particles in a dusty fluid are investigated. The effects of nonlinear thermal radiation and Hall current are also taken into account. The relevant flow analysis is modelled for fluid phase and dust phase in wave frame by means of Casson fluid model. Computation of solutions is presented for velocity profile, temperature profile and concentration profile. The effects of all the physical parameters such as particle volume fraction, Hartmann number, Hall Effect, Prandtl number, Eckert number, Schmidt number and Soret number are discussed mathematically and graphically. It is noted that the influence of magnetic field and particle volume fraction opposes the flow. Also, the impact of particle volume fraction is quite opposite on temperature and concentration profile. This model is applicable in smart drug delivery systems and bacteria movement in urine flow through the ureter.

Differential absorption lidar measurements of atmospheric temperature and pressure profiles

NASA Technical Reports Server (NTRS)

Korb, C. L.

1981-01-01

The theory and methodology of using differential absorption lidar techniques for the remote measurement of atmospheric pressure profiles, surface pressure, and temperature profiles from ground, air, and space-based platforms are presented. Pressure measurements are effected by means of high resolution measurement of absorption at the edges of the oxygen A band lines where absorption is pressure dependent due to collisional line broadening. Temperature is assessed using measurements of the absorption at the center of the oxygen A band line originating from a quantum state with high ground state energy. The population of the state is temperature dependent, allowing determination of the temperature through the Boltzmann term. The results of simulations of the techniques using Voigt profile and variational analysis are reported for ground-based, airborne, and Shuttle-based systems. Accuracies in the 0.5-1.0 K and 0.1-0.3% range are projected.

Grizzly Valley fault system, Sierra Valley, CA

USGS Publications Warehouse

Gold, Ryan; Stephenson, William; Odum, Jack; Briggs, Rich; Crone, Anthony; Angster, Steve

2012-01-01

The Grizzly Valley fault system (GVFS) strikes northwestward across Sierra Valley, California and is part of a network of active, dextral strike-slip faults in the northern Walker Lane (Figure 1). To investigate Quaternary motion across the GVFS, we analyzed high-resolution (0.25 m) airborne LiDAR data (Figure 2) in combination with six, high-resolution, P-wave, seismic-reflection profiles [Gold and others, 2012]. The 0.5- to 2.0-km-long seismic-reflection profiles were sited orthogonal to suspected tectonic lineaments identified from previous mapping and our analysis of airborne LiDAR data. To image the upper 400–700 m of subsurface stratigraphy of Sierra Valley (Figure 3), we used a 230-kg accelerated weight drop source. Geophone spacing ranged from 2 to 5 m and shots were co-located with the geophones. The profiles reveal a highly reflective, deformed basal marker that we interpret to be the top of Tertiary volcanic rocks, overlain by a 120- to 300-m-thick suite of subhorizontal reflectors we interpret as Plio-Pleistocene lacustrine deposits. Three profiles image the principle active trace of the GVFS, which is a steeply dipping fault zone that offsets the volcanic rocks and the basin fill (Figures 4 & 5).

HealthStyles: a new psychographic segmentation system for health care marketers.

PubMed

Endresen, K W; Wintz, J C

1988-01-01

HealthStyles is a new psychographic segmentation system specifically designed for the health care industry. This segmentation system goes beyond traditional geographic and demographic analysis and examines health-related consumer attitudes and behaviors. Four statistically distinct "styles" of consumer health care preferences have been identified. The profiles of the four groups have substantial marketing implications in terms of design and promotion of products and services. Each segment of consumers also has differing expectations of physician behavior.

[Forensic hematology genetics--paternity testing].

PubMed

Kratzer, A; Bär, W

1997-05-01

In Switzerland paternity investigations are carried out using DNA analysis only since 1991. DNA patterns are inherited and only with the exception of genetically identical twins they are different in everyone and therefore unique to an individual. Hence DNA-systems are an excellent tool to resolve paternity disputes. DNA polymorphisms used for paternity diagnosis are length polymorphisms of the highly polymorphic VNTR loci [variable number of tandem repeats]. The most frequently applied systems are the DNA single locus systems. In addition to the DNA single locus systems the application of PCR (PCR = polymerase chain reaction) based DNA systems has increased particularly in difficult deficiency cases or in cases where only small evidential samples or partially degraded DNA are available. Normally four independent DNA single probes are used to produce a DNA profile from the mother, the child and the alleged father. A child inherits half the DNA patterns from its mother and the other half from its true biological father. If an alleged father doesn't possess the paternal specific DNA pattern in his DNA profile he is excluded from the paternity. In case of non-exclusion the probability for paternity is calculated according to Essen-Möller. When applying four highly polymorphic DNA single locus systems the biostatistical evaluation leads always to W-values exceeding 99.8% [= required value for positive proof of paternity]. DNA analysis is currently the best available method to achieve such effective conclusions in paternity investigations.

Species identification of corynebacteria by cellular fatty acid analysis.

PubMed

Van den Velde, Sandra; Lagrou, Katrien; Desmet, Koen; Wauters, Georges; Verhaegen, Jan

2006-02-01

We evaluated the usefulness of cellular fatty acid analysis for the identification of corynebacteria. Therefore, 219 well-characterized strains belonging to 21 Corynebacterium species were analyzed with the Sherlock System of MIDI (Newark, DE). Most Corynebacterium species have a qualitative different fatty acid profile. Corynebacterium coyleae (subgroup 1), Corynebacterium riegelii, Corynebacterium simulans, and Corynebacterium imitans differ only quantitatively. Corynebacterium afermentans afermentans and C. coyleae (subgroup 2) have both a similar qualitative and quantitative profile. The commercially available database (CLIN 40, MIDI) identified only one third of the 219 strains correctly at the species level. We created a new database with these 219 strains. This new database was tested with 34 clinical isolates and could identify 29 strains correctly. Strains that remained unidentified were 2 Corynebacterium aurimucosum (not included in our database), 1 C. afermentans afermentans, and 2 Corynebacterium pseudodiphtheriticum. Cellular fatty acid analysis with a self-created database can be used for the identification and differentiation of corynebacteria.

Impact of AIRS Thermodynamic Profiles on Precipitation Forecasts for Atmospheric River Cases Affecting the Western United States

NASA Technical Reports Server (NTRS)

Zavodsky, Bradley T.; Jedlovec, Gary J.; Blakenship, Clay B.; Wick, Gary A.; Neiman, Paul J.

2013-01-01

This project is a collaborative activity between the NASA Short-term Prediction Research and Transition (SPoRT) Center and the NOAA Hydrometeorology Testbed (HMT) to evaluate a SPoRT Advanced Infrared Sounding Radiometer (AIRS: Aumann et al. 2003) enhanced moisture analysis product. We test the impact of assimilating AIRS temperature and humidity profiles above clouds and in partly cloudy regions, using the three-dimensional variational Gridpoint Statistical Interpolation (GSI) data assimilation (DA) system (Developmental Testbed Center 2012) to produce a new analysis. Forecasts of the Weather Research and Forecasting (WRF) model initialized from the new analysis are compared to control forecasts without the additional AIRS data. We focus on some cases where atmospheric rivers caused heavy precipitation on the US West Coast. We verify the forecasts by comparison with dropsondes and the Cooperative Institute for Research in the Atmosphere (CIRA) Blended Total Precipitable Water product.

Quantitative Analysis of Human Pluripotency and Neural Specification by In-Depth (Phospho)Proteomic Profiling.

PubMed

Singec, Ilyas; Crain, Andrew M; Hou, Junjie; Tobe, Brian T D; Talantova, Maria; Winquist, Alicia A; Doctor, Kutbuddin S; Choy, Jennifer; Huang, Xiayu; La Monaca, Esther; Horn, David M; Wolf, Dieter A; Lipton, Stuart A; Gutierrez, Gustavo J; Brill, Laurence M; Snyder, Evan Y

2016-09-13

Controlled differentiation of human embryonic stem cells (hESCs) can be utilized for precise analysis of cell type identities during early development. We established a highly efficient neural induction strategy and an improved analytical platform, and determined proteomic and phosphoproteomic profiles of hESCs and their specified multipotent neural stem cell derivatives (hNSCs). This quantitative dataset (nearly 13,000 proteins and 60,000 phosphorylation sites) provides unique molecular insights into pluripotency and neural lineage entry. Systems-level comparative analysis of proteins (e.g., transcription factors, epigenetic regulators, kinase families), phosphorylation sites, and numerous biological pathways allowed the identification of distinct signatures in pluripotent and multipotent cells. Furthermore, as predicted by the dataset, we functionally validated an autocrine/paracrine mechanism by demonstrating that the secreted protein midkine is a regulator of neural specification. This resource is freely available to the scientific community, including a searchable website, PluriProt. Published by Elsevier Inc.

Advances in Analysis of Human Milk Oligosaccharides123

PubMed Central

Ruhaak, L. Renee; Lebrilla, Carlito B.

2012-01-01

Oligosaccharides in human milk strongly influence the composition of the gut microflora of neonates. Because it is now clear that the microflora play important roles in the development of the infant immune system, human milk oligosaccharides (HMO) are studied frequently. Milk samples contain complex mixtures of HMO, usually comprising several isomeric structures that can be either linear or branched. Traditionally, HMO profiling was performed using HPLC with fluorescence or UV detection. By using porous graphitic carbon liquid chromatography MS, it is now possible to separate and identify most of the isomers, facilitating linkage-specific analysis. Matrix-assisted laser desorption ionization time-of-flight analysis allows fast profiling, but does not allow isomer separation. Novel MS fragmentation techniques have facilitated structural characterization of HMO that are present at lower concentrations. These techniques now facilitate more accurate studies of HMO consumption as well as Lewis blood group determinations. PMID:22585919

Identification of Neurodegenerative Factors Using Translatome-Regulatory Network Analysis

PubMed Central

Brichta, Lars; Shin, William; Jackson-Lewis, Vernice; Blesa, Javier; Yap, Ee-Lynn; Walker, Zachary; Zhang, Jack; Roussarie, Jean-Pierre; Alvarez, Mariano J.; Califano, Andrea; Przedborski, Serge; Greengard, Paul

2016-01-01

For degenerative disorders of the central nervous system, the major obstacle to therapeutic advancement has been the challenge of identifying the key molecular mechanisms underlying neuronal loss. We developed a combinatorial approach including translational profiling and brain regulatory network analysis to search for key determinants of neuronal survival or death. Following the generation of transgenic mice for cell type-specific profiling of midbrain dopaminergic neurons, we established and compared translatome libraries reflecting the molecular signature of these cells at baseline or under degenerative stress. Analysis of these libraries by interrogating a context-specific brain regulatory network led to the identification of a repertoire of intrinsic upstream regulators that drive the dopaminergic stress response. The altered activity of these regulators was not associated with changes in their expression levels. This strategy can be generalized for the elucidation of novel molecular determinants involved in the degeneration of other classes of neurons. PMID:26214373

Thermal analysis of Bridgman-Stockbarger growth. [mercury cadmium telluride single crystals

NASA Technical Reports Server (NTRS)

Knopf, F. W.

1979-01-01

A thermal analysis of a cylindrical HgCdTe sample in a Bridgman-Stockbarger crystal growth configuration was conducted with emphasis on the thermal profile, interface shape and position, and the thermal gradients at the liquid-solid interface. Alloys of HgTe and CdTe with compositions approximating 20 percent CdTe, 80 percent HgTe were used. This composition results in a bandgap suited for the detection of 10.6 micron CO2 radiation. The sensitivity of the sample thermal characteristics to important growth parameters, such as thermal diffusivities, thermal conductivities, furnace temperature profile, ampoule dimensions, and growth velocity was assessed. Numerical techniques and associated computational models necessary to analyze the heat transfer process within the sample and the Bridgman-Stockbarger boundary conditions were developed. This thermal analysis mode was programmed in FORTRAN V, and is currently operational on the MSFC Univac 1100 system.

Capillary nano-immunoassays: advancing quantitative proteomics analysis, biomarker assessment, and molecular diagnostics.

PubMed

Chen, Jin-Qiu; Wakefield, Lalage M; Goldstein, David J

2015-06-06

There is an emerging demand for the use of molecular profiling to facilitate biomarker identification and development, and to stratify patients for more efficient treatment decisions with reduced adverse effects. In the past decade, great strides have been made to advance genomic, transcriptomic and proteomic approaches to address these demands. While there has been much progress with these large scale approaches, profiling at the protein level still faces challenges due to limitations in clinical sample size, poor reproducibility, unreliable quantitation, and lack of assay robustness. A novel automated capillary nano-immunoassay (CNIA) technology has been developed. This technology offers precise and accurate measurement of proteins and their post-translational modifications using either charge-based or size-based separation formats. The system not only uses ultralow nanogram levels of protein but also allows multi-analyte analysis using a parallel single-analyte format for increased sensitivity and specificity. The high sensitivity and excellent reproducibility of this technology make it particularly powerful for analysis of clinical samples. Furthermore, the system can distinguish and detect specific protein post-translational modifications that conventional Western blot and other immunoassays cannot easily capture. This review will summarize and evaluate the latest progress to optimize the CNIA system for comprehensive, quantitative protein and signaling event characterization. It will also discuss how the technology has been successfully applied in both discovery research and clinical studies, for signaling pathway dissection, proteomic biomarker assessment, targeted treatment evaluation and quantitative proteomic analysis. Lastly, a comparison of this novel system with other conventional immuno-assay platforms is performed.

Genome-Wide Investigation and Expression Profiling of HD-Zip Transcription Factors in Foxtail Millet (Setaria italica L.).

PubMed

Chai, Wenbo; Si, Weina; Ji, Wei; Qin, Qianqian; Zhao, Manli; Jiang, Haiyang

2018-01-01

HD-Zip proteins represent the major transcription factors in higher plants, playing essential roles in plant development and stress responses. Foxtail millet is a crop to investigate the systems biology of millet and biofuel grasses and the HD-Zip gene family has not been studied in foxtail millet. For further investigation of the expression profile of the HD-Zip gene family in foxtail millet, a comprehensive genome-wide expression analysis was conducted in this study. We found 47 protein-encoding genes in foxtail millet using BLAST search tools; the putative proteins were classified into four subfamilies, namely, subfamilies I, II, III, and IV. Gene structure and motif analysis indicate that the genes in one subfamily were conserved. Promotor analysis showed that HD-Zip gene was involved in abiotic stress. Duplication analysis revealed that 8 (~17%) hdz genes were tandemly duplicated and 28 (58%) were segmentally duplicated; purifying duplication plays important roles in gene expansion. Microsynteny analysis revealed the maximum relationship in foxtail millet-sorghum and foxtail millet-rice. Expression profiling upon the abiotic stresses of drought and high salinity and the biotic stress of ABA revealed that some genes regulated responses to drought and salinity stresses via an ABA-dependent process, especially sihdz29 and sihdz45. Our study provides new insight into evolutionary and functional analyses of HD-Zip genes involved in environmental stress responses in foxtail millet.

The effects of plant extracts on microbial community structure in a rumen-simulating continuous-culture system as revealed by molecular profiling.

PubMed

Ferme, D; Banjac, M; Calsamiglia, S; Busquet, M; Kamel, C; Avgustin, G

2004-01-01

An in vitro study in dual-flow continuous-culture fermentors was conducted with two different concentrations of monensin, cinnamaldehyde or garlic extract added to 1:1 forage-to-concentrate diet in order to determine their effects on selected rumen bacterial populations. Samples were subjected to total DNA extraction, restriction analysis of PCR amplified parts of 16S rRNA genes (ARDRA) and subsequent analysis of the restriction profiles by lab-on-chip technology with the Agilent's Bioanalyser 2100. Eub338-BacPre primer pair was used to select for the bacteria from the genera Bacteroides, Porphyromonas and Prevotella, especially the latter representing the dominant Gram-negative bacterial population in the rumen. Preliminary results of HaeIII restriction analysis show that the effects of monensin, cinnamaldehyde and garlic extract on the BacPre targeted ruminal bacteria are somewhat different in regard to targeted populations and to the nature of the effect. Garlic extract was found to trigger the most intensive changes in the structure of the BacPre targeted population. Comparison of the in silico restriction analysis of BacPre sequences deposited in different DNA databanks and of the results of performed amplified ribosomal DNA restriction analysis showed differences between the predicted and obtained HaeIII restriction profiles, and suggested the presence of novel, still unknown Prevotella populations in studied samples.

Environmental/Thermal Barrier Coatings for Ceramic Matrix Composites: Thermal Tradeoff Studies

NASA Technical Reports Server (NTRS)

Murthy, Pappu L. M.; Brewer, David; Shah, Ashwin R.

2007-01-01

Recent interest in environmental/thermal barrier coatings (EBC/TBCs) has prompted research to develop life-prediction methodologies for the coating systems of advanced high-temperature ceramic matrix composites (CMCs). Heat-transfer analysis of EBC/TBCs for CMCs is an essential part of the effort. It helps establish the resulting thermal profile through the thickness of the CMC that is protected by the EBC/TBC system. This report documents the results of a one-dimensional analysis of an advanced high-temperature CMC system protected with an EBC/TBC system. The one-dimensional analysis was used for tradeoff studies involving parametric variation of the conductivity; the thickness of the EBC/TBCs, bond coat, and CMC substrate; and the cooling requirements. The insight gained from the results will be used to configure a viable EBC/TBC system for CMC liners that meet the desired hot surface, cold surface, and substrate temperature requirements.

Linguistic Alternatives to Quantitative Research Strategies. Part One: How Linguistic Mechanisms Advance Research Outcomes

ERIC Educational Resources Information Center

Yeager, Joseph; Sommer, Linda

2007-01-01

Combining psycholinguistic technologies and systems analysis created advances in motivational profiling and numerous new behavioral engineering applications. These advances leapfrog many mainstream statistical research methods, producing superior research results via cause-effect language mechanisms. Entire industries explore motives ranging from…

The Predictive Effects of Early Pregnancy Lipid Profiles and Fasting Glucose on the Risk of Gestational Diabetes Mellitus Stratified by Body Mass Index.

PubMed

Wang, Chen; Zhu, Weiwei; Wei, Yumei; Su, Rina; Feng, Hui; Lin, Li; Yang, Huixia

2016-01-01

This study aimed at evaluating the predictive effects of early pregnancy lipid profiles and fasting glucose on the risk of gestational diabetes mellitus (GDM) in patients stratified by prepregnancy body mass index (p-BMI) and to determine the optimal cut-off values of each indicator for different p-BMI ranges. A retrospective system cluster sampling survey was conducted in Beijing during 2013 and a total of 5,265 singleton pregnancies without prepregnancy diabetes were included. The information for each participant was collected individually using questionnaires and medical records. Logistic regression analysis and receiver operator characteristics analysis were used in the analysis. Outcomes showed that potential markers for the prediction of GDM include early pregnancy lipid profiles (cholesterol, triacylglycerols, low-density lipoprotein cholesterol/high-density lipoprotein cholesterol ratios [LDL-C/HDL-C], and triglyceride to high-density lipoprotein cholesterol ratios [TG/HDL-C]) and fasting glucose, of which fasting glucose level was the most accurate indicator. Furthermore, the predictive effects and cut-off values for these factors varied according to p-BMI. Thus, p-BMI should be a consideration for the risk assessment of pregnant patients for GDM development.

Cross Racial Identity Scale (CRIS) scores and profiles in African American adolescents involved with the juvenile justice system.

PubMed

Worrell, Frank C; Andretta, James R; Woodland, Malcolm H

2014-10-01

In this study, we examined the internal consistency and structural validity of Cross Racial Identity Scale (CRIS) scores in a sample of 477 African American adolescents who had been arrested in a city in the mid-Atlantic. Using cluster analysis, we also identified profiles of CRIS scores and compared adolescents with different profiles on Major Depressive Episode, Manic Episode, Generalized Anxiety Disorder, and Obsessive-Compulsive Disorder scores. Results indicated that CRIS subscale scores were reliable, and the 6-factor structure of the CRIS was supported. Five nigrescence profiles were identified: Miseducation-Pro-Black, Conflicted-Self-Hatred, Multiculturalist, Low Race Salience, and Conflicted-Anti-White. Individuals with Conflicted-Self-Hatred profiles reported significantly and meaningfully higher scores on the 4 syndromes than did their peers, and individuals with the Multiculturalist and Low Race Salience profiles reported the lowest scores. A greater percentage of individuals with Conflicted racial identity profiles had syndrome scores in the clinically significant range. The results of this study demonstrate that some of the nigrescence profiles found in college-age students generalize to adolescents. The implications of the findings for theory, research, and practice are discussed. PsycINFO Database Record (c) 2014 APA, all rights reserved.

A novel regenerative shock absorber with a speed doubling mechanism and its Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Zhang, Ran; Wang, Xu; Liu, Zhenwei

2018-03-01

A novel regenerative shock absorber has been designed and fabricated. The novelty of the presented work is the application of the double speed regenerative shock absorber that utilizes the rack and pinion mechanism to increase the magnet speed with respect to the coils for higher power output. The simulation models with parameters identified from finite element analysis and the experiments are developed. The proposed regenerative shock absorber is compared with the regenerative shock absorber without the rack and pinion mechanism, when they are integrated into the same quarter vehicle suspension system. The sinusoidal wave road profile displacement excitation and the random road profile displacement excitation with peak amplitude of 0.035 m are applied as the inputs in the frequency range of 0-25 Hz. It is found that with the sinusoidal and random road profile displacement input, the proposed innovative design can increase the output power by 4 times comparing to the baseline design. The proposed double speed regenerative shock absorber also presents to be more sensitive to the road profile irregularity than the single speed regenerative shock absorber as suggested by Monte Carlo simulation. Lastly the coil mass and amplification factor are studied for sensitivity analysis and performance optimization, which provides a general design method of the regenerative shock absorbers. It shows that for the system power output, the proposed design becomes more sensitive to either the coil mass or amplification factor depending on the amount of the coil mass. With the specifically selected combination of the coil mass and amplification factor, the optimized energy harvesting performance can be achieved.

Structural analysis of star-forming blue early-type galaxies. Merger-driven star formation in elliptical galaxies

NASA Astrophysics Data System (ADS)

George, Koshy

2017-02-01

Context. Star-forming blue early-type galaxies at low redshift can give insight to the stellar mass growth of L⋆ elliptical galaxies in the local Universe. Aims: We wish to understand the reason for star formation in these otherwise passively evolving red and dead stellar systems. The fuel for star formation can be acquired through recent accretion events such as mergers or flyby. The signatures of such events should be evident from a structural analysis of the galaxy image. Methods: We carried out structural analysis on SDSS r-band imaging data of 55 star-forming blue elliptical galaxies, derived the structural parameters, analysed the residuals from best-fit to surface brightness distribution, and constructed the galaxy scaling relations. Results: We found that star-forming blue early-type galaxies are bulge-dominated systems with axial ratio >0.5 and surface brightness profiles fitted by Sérsic profiles with index (n) mostly >2. Twenty-three galaxies are found to have n< 2; these could be hosting a disc component. The residual images of the 32 galaxy surface brightness profile fits show structural features indicative of recent interactions. The star-forming blue elliptical galaxies follow the Kormendy relation and show the characteristics of normal elliptical galaxies as far as structural analysis is concerned. There is a general trend for high-luminosity galaxies to display interaction signatures and high star formation rates. Conclusions: The star-forming population of blue early-type galaxies at low redshifts could be normal ellipticals that might have undergone a recent gas-rich minor merger event. The star formation in these galaxies will shut down once the recently acquired fuel is consumed, following which the galaxy will evolve to a normal early-type galaxy.

Non-invasive intraoperative optical coherence tomography of the resection cavity during surgery of intrinsic brain tumors

NASA Astrophysics Data System (ADS)

Giese, A.; Böhringer, H. J.; Leppert, J.; Kantelhardt, S. R.; Lankenau, E.; Koch, P.; Birngruber, R.; Hüttmann, G.

2006-02-01

Optical coherence tomography (OCT) is a non-invasive imaging technique with a micrometer resolution. It allows non-contact / non-invasive analysis of central nervous system tissues with a penetration depth of 1-3,5 mm reaching a spatial resolution of approximately 4-15 μm. We have adapted spectral-domain OCT (SD-OCT) and time-domain OCT (TD-OCT) for intraoperative detection of residual tumor during brain tumor surgery. Human brain tumor tissue and areas of the resection cavity were analyzed during the resection of gliomas using this new technology. The site of analysis was registered using a neuronavigation system and biopsies were taken and submitted to routine histology. We have used post image acquisition processing to compensate for movements of the brain and to realign A-scan images for calculation of a light attenuation factor. OCT imaging of normal cortex and white matter showed a typical light attenuation profile. Tumor tissue depending on the cellularity of the specimen showed a loss of the normal light attenuation profile resulting in altered light attenuation coefficients compared to normal brain. Based on this parameter and the microstructure of the tumor tissue, which was entirely absent in normal tissue, OCT analysis allowed the discrimination of normal brain tissue, invaded brain, solid tumor tissue, and necrosis. Following macroscopically complete resections OCT analysis of the resection cavity displayed the typical microstructure and light attenuation profile of tumor tissue in some specimens, which in routine histology contained microscopic residual tumor tissue. We have demonstrated that this technology may be applied to the intraoperative detection of residual tumor during resection of human gliomas.

Covariance of bacterioplankton composition and environmental variables in a temperate delta system

USGS Publications Warehouse

Stepanauskas, R.; Moran, M.A.; Bergamaschi, B.A.; Hollibaugh, J.T.

2003-01-01

We examined seasonal and spatial variation in bacterioplankton composition in the Sacramento-San Joaquin River Delta (CA) using terminal restriction fragment length polymorphism (T-RFLP) analysis. Cloned 16S rRNA genes from this system were used for putative identification of taxa dominating the T-RFLP profiles. Both cloning and T-RFLP analysis indicated that Actinobacteria, Verrucomicrobia, Cytophaga-Flavobacterium and Proteobacteria were the most abundant bacterioplankton groups in the Delta. Despite the broad variety of sampled habitats (deep water channels, lakes, marshes, agricultural drains, freshwater and brackish areas), and the spatial and temporal differences in hydrology, temperature and water chemistry among the sampling campaigns, T-RFLP electropherograms from all samples were similar, indicating that the same bacterioplankton phylotypes dominated in the various habitats of the Delta throughout the year. However, principal component analysis (PCA) and partial least-squares regression (PLS) of T-RFLP profiles revealed consistent grouping of samples on a seasonal, but not a spatial, basis. ??-Proteobacteria related to Ralstonia, Actinobacteria related to Microthrix, and ??-Proteobacteria identical to the environmental Clone LD12 had the highest relative abundance in summer/fall T-RFLP profiles and were associated with low river flow, high pH, and a number of optical and chemical characteristics of dissolved organic carbon (DOC) indicative of an increased proportion of phytoplankton-produced organic material as opposed to allochthonous, terrestrially derived organic material. On the other hand, Geobacter-related ??-Proteobacteria showed a relative increase in abundance in T-RFLP analysis during winter/spring, and probably were washed out from watershed soils or sediment. Various phylotypes associated with the same phylogenetic division, based on tentative identification of T-RFLP fragments, exhibited diverse seasonal patterns, suggesting that ecological roles of Delta bacterioplankton were partitioned at the genus or species level.

The FTS atomic spectrum tool (FAST) for rapid analysis of line spectra

NASA Astrophysics Data System (ADS)

Ruffoni, M. P.

2013-07-01

The FTS Atomic Spectrum Tool (FAST) is an interactive graphical program designed to simplify the analysis of atomic emission line spectra obtained from Fourier transform spectrometers. Calculated, predicted and/or known experimental line parameters are loaded alongside experimentally observed spectral line profiles for easy comparison between new experimental data and existing results. Many such line profiles, which could span numerous spectra, may be viewed simultaneously to help the user detect problems from line blending or self-absorption. Once the user has determined that their experimental line profile fits are good, a key feature of FAST is the ability to calculate atomic branching fractions, transition probabilities, and oscillator strengths-and their uncertainties-which is not provided by existing analysis packages. Program SummaryProgram title: FAST: The FTS Atomic Spectrum Tool Catalogue identifier: AEOW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEOW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 293058 No. of bytes in distributed program, including test data, etc.: 13809509 Distribution format: tar.gz Programming language: C++. Computer: Intel x86-based systems. Operating system: Linux/Unix/Windows. RAM: 8 MB minimum. About 50-200 MB for a typical analysis. Classification: 2.2, 2.3, 21.2. Nature of problem: Visualisation of atomic line spectra including the comparison of theoretical line parameters with experimental atomic line profiles. Accurate intensity calibration of experimental spectra, and the determination of observed relative line intensities that are needed for calculating atomic branching fractions and oscillator strengths. Solution method: FAST is centred around a graphical interface, where a user may view sets of experimental line profiles and compare them to calculated data (such as from the Kurucz database [1]), predicted line parameters, and/or previously known experimental results. With additional information on the spectral response of the spectrometer, obtained from a calibrated standard light source, FT spectra may be intensity calibrated. In turn, this permits the user to calculate atomic branching fractions and oscillator strengths, and their respective uncertainties. Running time: Open ended. Defined by the user. References: [1] R.L. Kurucz (2007). URL http://kurucz.harvard.edu/atoms/.

Integration of Ground-Based Solar FT-IR Absorption Spectroscopy and Open-Path Systems for Atmospheric Analysis

NASA Astrophysics Data System (ADS)

Steill, J. D.; Hager, J. S.; Compton, R. N.

2005-12-01

Air quality issues in the Knoxville and East Tennessee region are of great concern, particularly as regards the nearby Great Smoky Mountains National Park. Integration of a Bomem DA8 FT-IR spectrometer with rooftop sun-tracking optics and an open-path system provides a unique opportunity to analyze the local atmospheric chemical composition. Many trace atmospheric constituents are open to this analysis, such as O3, CO, CH4, and N2O. Boundary layer concentrations as well as total column abundances and vertical concentration profiles are derived. Vertical concentration profiles are determined by fitting solar absorbance lines with the SFIT2 algorithm. Improved fitting of solar spectra has been demonstrated by incorporating the tropospheric concentrations as determined by open-path measurements. In addition to providing a means to improve the analysis of solar spectra, the open-path data is useful for elucidation of diurnal trends in the trace gas concentrations. Anthropogenic influences are of special interest, and seasonal and daily trends in amounts of tropospheric pollutants such as ozone correlate with other sources such as the EPA. Although obviously limited by weather considerations, the technique is suited to the regional climate and a body of data of more than two years extent is available for analysis.

Untargeted Metabolomic Analysis of Rat Neuroblastoma Cells as a Model System to Study the Biochemical Effects of the Acute Administration of Methamphetamine.

PubMed

Maker, Garth L; Green, Tobias; Mullaney, Ian; Trengove, Robert D

2018-06-07

Methamphetamine is an illicit psychostimulant drug that is linked to a number of diseases of the nervous system. The downstream biochemical effects of its primary mechanisms are not well understood, and the objective of this study was to investigate whether untargeted metabolomic analysis of an in vitro model could generate data relevant to what is already known about this drug. Rat B50 neuroblastoma cells were treated with 1 mM methamphetamine for 48 h, and both intracellular and extracellular metabolites were profiled using gas chromatography⁻mass spectrometry. Principal component analysis of the data identified 35 metabolites that contributed most to the difference in metabolite profiles. Of these metabolites, the most notable changes were in amino acids, with significant increases observed in glutamate, aspartate and methionine, and decreases in phenylalanine and serine. The data demonstrated that glutamate release and, subsequently, excitotoxicity and oxidative stress were important in the response of the neuronal cell to methamphetamine. Following this, the cells appeared to engage amino acid-based mechanisms to reduce glutamate levels. The potential of untargeted metabolomic analysis has been highlighted, as it has generated biochemically relevant data and identified pathways significantly affected by methamphetamine. This combination of technologies has clear uses as a model for the study of neuronal toxicology.

Nonlinear Transient Thermal Analysis by the Force-Derivative Method

NASA Technical Reports Server (NTRS)

Balakrishnan, Narayani V.; Hou, Gene

1997-01-01

High-speed vehicles such as the Space Shuttle Orbiter must withstand severe aerodynamic heating during reentry through the atmosphere. The Shuttle skin and substructure are constructed primarily of aluminum, which must be protected during reentry with a thermal protection system (TPS) from being overheated beyond the allowable temperature limit, so that the structural integrity is maintained for subsequent flights. High-temperature reusable surface insulation (HRSI), a popular choice of passive insulation system, typically absorbs the incoming radiative or convective heat at its surface and then re-radiates most of it to the atmosphere while conducting the smallest amount possible to the structure by virtue of its low diffusivity. In order to ensure a successful thermal performance of the Shuttle under a prescribed reentry flight profile, a preflight reentry heating thermal analysis of the Shuttle must be done. The surface temperature profile, the transient response of the HRSI interior, and the structural temperatures are all required to evaluate the functioning of the HRSI. Transient temperature distributions which identify the regions of high temperature gradients, are also required to compute the thermal loads for a structural thermal stress analysis. Furthermore, a nonlinear analysis is necessary to account for the temperature-dependent thermal properties of the HRSI as well as to model radiation losses.

Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks.

PubMed

Pellacani, Davide; Bilenky, Misha; Kannan, Nagarajan; Heravi-Moussavi, Alireza; Knapp, David J H F; Gakkhar, Sitanshu; Moksa, Michelle; Carles, Annaick; Moore, Richard; Mungall, Andrew J; Marra, Marco A; Jones, Steven J M; Aparicio, Samuel; Hirst, Martin; Eaves, Connie J

2016-11-15

The normal adult human mammary gland is a continuous bilayered epithelial system. Bipotent and myoepithelial progenitors are prominent and unique components of the outer (basal) layer. The inner (luminal) layer includes both luminal-restricted progenitors and a phenotypically separable fraction that lacks progenitor activity. We now report an epigenomic comparison of these three subsets with one another, with their associated stromal cells, and with three immortalized, non-tumorigenic human mammary cell lines. Each genome-wide analysis contains profiles for six histone marks, methylated DNA, and RNA transcripts. Analysis of these datasets shows that each cell type has unique features, primarily within genomic regulatory regions, and that the cell lines group together. Analyses of the promoter and enhancer profiles place the luminal progenitors in between the basal cells and the non-progenitor luminal subset. Integrative analysis reveals networks of subset-specific transcription factors. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Feasibility analysis of cislunar flight using the Shuttle Orbiter

NASA Technical Reports Server (NTRS)

Haynes, Davy A.

1991-01-01

A first order orbital mechanics analysis was conducted to examine the possibility of utilizing the Space Shuttle Orbiter to perform payload delivery missions to lunar orbit. In the analysis, the earth orbit of departure was constrained to be that of Space Station Freedom. Furthermore, no enhancements of the Orbiter's thermal protection system were assumed. Therefore, earth orbit insertion maneuvers were constrained to be all propulsive. Only minimal constraints were placed on the lunar orbits and no consideration was given to possible landing sites for lunar surface payloads. The various phases and maneuvers of the mission are discussed for both a conventional (Apollo type) and an unconventional mission profile. The velocity impulses needed, and the propellant masses required are presented for all of the mission maneuvers. Maximum payload capabilities were determined for both of the mission profiles examined. In addition, other issues relating to the feasibility of such lunar shuttle missions are discussed. The results of the analysis indicate that the Shuttle Orbiter would be a poor vehicle for payload delivery missions to lunar orbit.

Parameterization of photon beam dosimetry for a linear accelerator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lebron, Sharon; Barraclough, Brendan; Lu, Bo

2016-02-15

Purpose: In radiation therapy, accurate data acquisition of photon beam dosimetric quantities is important for (1) beam modeling data input into a treatment planning system (TPS), (2) comparing measured and TPS modeled data, (3) the quality assurance process of a linear accelerator’s (Linac) beam characteristics, (4) the establishment of a standard data set for comparison with other data, etcetera. Parameterization of the photon beam dosimetry creates a data set that is portable and easy to implement for different applications such as those previously mentioned. The aim of this study is to develop methods to parameterize photon beam dosimetric quantities, includingmore » percentage depth doses (PDDs), profiles, and total scatter output factors (S{sub cp}). Methods: S{sub cp}, PDDs, and profiles for different field sizes, depths, and energies were measured for a Linac using a cylindrical 3D water scanning system. All data were smoothed for the analysis and profile data were also centered, symmetrized, and geometrically scaled. The S{sub cp} data were analyzed using an exponential function. The inverse square factor was removed from the PDD data before modeling and the data were subsequently analyzed using exponential functions. For profile modeling, one halfside of the profile was divided into three regions described by exponential, sigmoid, and Gaussian equations. All of the analytical functions are field size, energy, depth, and, in the case of profiles, scan direction specific. The model’s parameters were determined using the minimal amount of measured data necessary. The model’s accuracy was evaluated via the calculation of absolute differences between the measured (processed) and calculated data in low gradient regions and distance-to-agreement analysis in high gradient regions. Finally, the results of dosimetric quantities obtained by the fitted models for a different machine were also assessed. Results: All of the differences in the PDDs’ buildup and the profiles’ penumbra regions were less than 2 and 0.5 mm, respectively. The differences in the low gradient regions were 0.20% ± 0.20% (<1% for all) and 0.50% ± 0.35% (<1% for all) for PDDs and profiles, respectively. For S{sub cp} data, all of the absolute differences were less than 0.5%. Conclusions: This novel analytical model with minimum measurement requirements was proved to accurately calculate PDDs, profiles, and S{sub cp} for different field sizes, depths, and energies.« less

1.6μm DIAL System for Measurements of CO2 Concentration Profiles in the Atmosphere

NASA Astrophysics Data System (ADS)

Nagasawa, C.; Abo, M.; Shibata, Y.

2013-12-01

We have developed a direct detection 1.6 μm differential absorption lidar (DIAL) technique to perform range-resolved measurements of vertical CO2 concentration profiles in the atmosphere. Our 1.6 μm DIAL system has a 60 cm telescope for vertical measurement and a 25 cm scanning telescope for horizontal measurement. This 1.6 μm DIAL system is also available to measure CO2 concentration profiles for daytime by using narrow-band interference filters. The 1.6 μm DIAL measurement was achieved successfully the vertical CO2 profile up to 7 km altitude with an error less than 1.0 % by integration time of 30 minutes and vertical resolution of 300 - 600 m. The CO2 DIAL was also operated with the range-height indicator (RHI) mode, and the 2-D measurement provided inhomogeneity in the boundary layer. The vertical distribution of CO2 concentration from 2 km to 7 km altitude has been observed using two telescopes with different apertures. We hope to get the data of the CO2 concentration from lower altitude to 7 km at the same time. Since the change of signal intensity is larger near the ground, it is also important to the install the photon counter with the faster count rate to expand the dynamic range. The high speed counter and the telescope system make the dynamic range expand more than 10 times and the vertical distribution observation of CO2 concentration from 0.5 km to 7 km altitude is performed. This work was financially supported by the System Development Program for Advanced Measurement and Analysis of the Japan Science and Technology Agency. References Sakaizawa, D., C. Nagasawa, T. Nagai, M. Abo, Y. Shibata, H. Nagai, M. Nakazato, and T. Sakai, Development of a 1.6μm differential absorption lidar with a quasi-phase-matching optical parametric oscillator and photon-counting detector for the vertical CO2 profile, Applied Optics, Vol.48, No.4, pp. 748-757, 2009. Stephens, B. B. et al., Weak Northern and Strong Tropical Land Carbon Uptake from Vertical Profiles of Atmospheric CO2, Science 316, pp. 1732-1735, 2007.

River profile response to normal fault growth and linkage: an example from the Hellenic forearc of south-central Crete, Greece

NASA Astrophysics Data System (ADS)

Gallen, Sean F.; Wegmann, Karl W.

2017-02-01

Topography is a reflection of the tectonic and geodynamic processes that act to uplift the Earth's surface and the erosional processes that work to return it to base level. Numerous studies have shown that topography is a sensitive recorder of tectonic signals. A quasi-physical understanding of the relationship between river incision and rock uplift has made the analysis of fluvial topography a popular technique for deciphering relative, and some argue absolute, histories of rock uplift. Here we present results from a study of the fluvial topography from south-central Crete, demonstrating that river longitudinal profiles indeed record the relative history of uplift, but several other processes make it difficult to recover quantitative uplift histories. Prior research demonstrates that the south-central coastline of Crete is bound by a large ( ˜ 100 km long) E-W striking composite normal fault system. Marine terraces reveal that it is uplifting between 0.1 and 1.0 mm yr-1. These studies suggest that two normal fault systems, the offshore Ptolemy and onshore South-Central Crete faults, linked together in the recent geologic past (ca. 0.4-1 My BP). Fault mechanics predict that when adjacent faults link into a single fault the uplift rate in footwalls of the linkage zone will increase rapidly. We use this natural experiment to assess the response of river profiles to a temporal jump in uplift rate and to assess the applicability of the stream power incision model to this setting. Using river profile analysis we show that rivers in south-central Crete record the relative uplift history of fault growth and linkage as theory predicts that they should. Calibration of the commonly used stream power incision model shows that the slope exponent, n, is ˜ 0.5, contrary to most studies that find n ≥ 1. Analysis of fluvial knickpoints shows that migration distances are not proportional to upstream contributing drainage area, as predicted by the stream power incision model. Maps of the transformed stream distance variable, χ, indicate that drainage basin instability, drainage divide migration, and river capture events complicate river profile analysis in south-central Crete. Waterfalls are observed in southern Crete and appear to operate under less efficient and different incision mechanics than assumed by the stream power incision model. Drainage area exchange and waterfall formation are argued to obscure linkages between empirically derived metrics and quasi-physical descriptions of river incision, making it difficult to quantitatively interpret rock uplift histories from river profiles in this setting. Karst hydrology, break down of assumed drainage area discharge scaling, and chemical weathering might also contribute to the failure of the stream power incision model to adequately predict the behavior of the fluvial system in south-central Crete.

Circulating microRNAs as biomarkers of disease and typification of the atherothrombotic status in antiphospholipid syndrome

PubMed Central

Pérez-Sánchez, Carlos; Arias-de la Rosa, Iván; Aguirre, María Ángeles; Luque-Tévar, María; Ruiz-Limón, Patricia; Barbarroja, Nuria; Jiménez-Gómez, Yolanda; Ábalos-Aguilera, María Carmen; Collantes-Estévez, Eduardo; Segui, Pedro; Velasco, Francisco; Herranz, María Teresa; Lozano-Herrero, Jesús; Hernandez-Vidal, María Julia; Martínez, Constantino; González-Conejero, Rocío; Radin, Massimo; Sciascia, Savino; Cecchi, Irene; Cuadrado, María José; López-Pedrera, Chary

2018-01-01

We aimed to identify the plasma miRNA profile of antiphospholipid syndrome (APS) patients and to investigate the potential role of specific circulating miRNAs as non-invasive disease biomarkers. Ninety APS patients and 42 healthy donors were recruited. Profiling of miRNAs by PCR-array in plasma of APS patients identified a set of miRNAs differentially expressed and collectively involved in clinical features. Logistic regression and ROC analysis identified a signature of 10 miRNA ratios as biomarkers of disease. In addition, miRNA signature was related to fetal loss, atherosclerosis, and type of thrombosis, and correlated with parameters linked to inflammation, thrombosis, and autoimmunity. Hard clustering analysis differentiated 3 clusters representing different thrombotic risk profile groups. Significant differences between groups for several miRNA ratios were found. Moreover, miRNA signature remained stable over time, demonstrated by their analysis three months after the first sample collection. Parallel analysis in two additional cohorts of patients, including thrombosis without autoimmune disease, and systemic lupus erythematosus without antiphospholipid antibodies, each displayed specific miRNA profiles that were distinct from those of APS patients. In vitro, antiphospholipid antibodies of IgG isotype promoted deregulation in selected miRNAs and their potential atherothrombotic protein targets in monocytes and endothelial cells. Taken together, differentially expressed circulating miRNAs in APS patients, modulated at least partially by antiphospholipid antibodies of IgG isotype, might have the potential to serve as novel biomarkers of disease features and to typify patients’ atherothrombotic status, thus constituting a useful tool in the management of the disease. PMID:29545345

A cell-based systems biology assessment of human blood to monitor immune responses after influenza vaccination.

PubMed

Hoek, Kristen L; Samir, Parimal; Howard, Leigh M; Niu, Xinnan; Prasad, Nripesh; Galassie, Allison; Liu, Qi; Allos, Tara M; Floyd, Kyle A; Guo, Yan; Shyr, Yu; Levy, Shawn E; Joyce, Sebastian; Edwards, Kathryn M; Link, Andrew J

2015-01-01

Systems biology is an approach to comprehensively study complex interactions within a biological system. Most published systems vaccinology studies have utilized whole blood or peripheral blood mononuclear cells (PBMC) to monitor the immune response after vaccination. Because human blood is comprised of multiple hematopoietic cell types, the potential for masking responses of under-represented cell populations is increased when analyzing whole blood or PBMC. To investigate the contribution of individual cell types to the immune response after vaccination, we established a rapid and efficient method to purify human T and B cells, natural killer (NK) cells, myeloid dendritic cells (mDC), monocytes, and neutrophils from fresh venous blood. Purified cells were fractionated and processed in a single day. RNA-Seq and quantitative shotgun proteomics were performed to determine expression profiles for each cell type prior to and after inactivated seasonal influenza vaccination. Our results show that transcriptomic and proteomic profiles generated from purified immune cells differ significantly from PBMC. Differential expression analysis for each immune cell type also shows unique transcriptomic and proteomic expression profiles as well as changing biological networks at early time points after vaccination. This cell type-specific information provides a more comprehensive approach to monitor vaccine responses.

Supporting the Loewenstein occupational therapy cognitive assessment using distributed user interfaces.

PubMed

Tesoriero, Ricardo; Gallud Lazaro, Jose A; Altalhi, Abdulrahman H

2017-02-01

Improve the quantity and quality of information obtained from traditional Loewenstein Occupational Therapy Cognitive Assessment Battery systems to monitor the evolution of patients' rehabilitation process as well as to compare different rehabilitation therapies. The system replaces traditional artefacts with virtual versions of them to take advantage of cutting edge interaction technology. The system is defined as a Distributed User Interface (DUI) supported by a display ecosystem, including mobile devices as well as multi-touch surfaces. Due to the heterogeneity of the devices involved in the system, the software technology is based on a client-server architecture using the Web as the software platform. The system provides therapists with information that is not available (or it is very difficult to gather) using traditional technologies (i.e. response time measurements, object tracking, information storage and retrieval facilities, etc.). The use of DUIs allows therapists to gather information that is unavailable using traditional assessment methods as well as adapt the system to patients' profile to increase the range of patients that are able to take this assessment. Implications for Rehabilitation Using a Distributed User Interface environment to carry out LOTCAs improves the quality of the information gathered during the rehabilitation assessment. This system captures physical data regarding patient's interaction during the assessment to improve the rehabilitation process analysis. Allows professionals to adapt the assessment procedure to create different versions according to patients' profile. Improves the availability of patients' profile information to therapists to adapt the assessment procedure.

Ultra-narrow band diode lasers with arbitrary pulse shape modulation (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ryasnyanskiy, Aleksandr I.; Smirnov, Vadim; Mokhun, Oleksiy; Glebov, Alexei L.; Glebov, Leon B.

2017-03-01

Wideband emission spectra of laser diode bars (several nanometers) can be largely narrowed by the usage of thick volume Bragg gratings (VBGs) recorded in photo-thermo-refractive glass. Such narrowband systems, with GHz-wide emission spectra, found broad applications for Diode Pumped Alkali vapor Lasers, optically pumped rare gas metastable lasers, Spin Exchange Optical Pumping, atom cooling, etc. Although the majority of current applications of narrow line diode lasers require CW operation, there are a variety of fields where operation in a different pulse mode regime is necessary. Commercial electric pulse generators can provide arbitrary current pulse profiles (sinusoidal, rectangular, triangular and their combinations). The pulse duration and repetition rate however, have an influence on the laser diode temperature, and therefore, the emitting wavelength. Thus, a detailed analysis is needed to understand the correspondence between the optical pulse profiles from a diode laser and the current pulse profiles; how the pulse profile and duty cycle affects the laser performance (e.g. the wavelength stability, signal to noise ratio, power stability etc.). We present the results of detailed studies of the narrowband laser diode performance operating in different temporal regimes with arbitrary pulse profiles. The developed narrowband (16 pm) tunable laser systems at 795 nm are capable of operating in different pulse regimes while keeping the linewidth, wavelength, and signal-to-noise ratio (>20 dB) similar to the corresponding CW modules.

Sci-Fin: Visual Mining Spatial and Temporal Behavior Features from Social Media

PubMed Central

Pu, Jiansu; Teng, Zhiyao; Gong, Rui; Wen, Changjiang; Xu, Yang

2016-01-01

Check-in records are usually available in social services, which offer us the opportunity to capture and analyze users’ spatial and temporal behaviors. Mining such behavior features is essential to social analysis and business intelligence. However, the complexity and incompleteness of check-in records bring challenges to achieve such a task. Different from the previous work on social behavior analysis, in this paper, we present a visual analytics system, Social Check-in Fingerprinting (Sci-Fin), to facilitate the analysis and visualization of social check-in data. We focus on three major components of user check-in data: location, activity, and profile. Visual fingerprints for location, activity, and profile are designed to intuitively represent the high-dimensional attributes. To visually mine and demonstrate the behavior features, we integrate WorldMapper and Voronoi Treemap into our glyph-like designs. Such visual fingerprint designs offer us the opportunity to summarize the interesting features and patterns from different check-in locations, activities and users (groups). We demonstrate the effectiveness and usability of our system by conducting extensive case studies on real check-in data collected from a popular microblogging service. Interesting findings are reported and discussed at last. PMID:27999398

Sci-Fin: Visual Mining Spatial and Temporal Behavior Features from Social Media.

PubMed

Pu, Jiansu; Teng, Zhiyao; Gong, Rui; Wen, Changjiang; Xu, Yang

2016-12-20

Check-in records are usually available in social services, which offer us the opportunity to capture and analyze users' spatial and temporal behaviors. Mining such behavior features is essential to social analysis and business intelligence. However, the complexity and incompleteness of check-in records bring challenges to achieve such a task. Different from the previous work on social behavior analysis, in this paper, we present a visual analytics system, Social Check-in Fingerprinting (Sci-Fin), to facilitate the analysis and visualization of social check-in data. We focus on three major components of user check-in data: location, activity, and profile. Visual fingerprints for location, activity, and profile are designed to intuitively represent the high-dimensional attributes. To visually mine and demonstrate the behavior features, we integrate WorldMapper and Voronoi Treemap into our glyph-like designs. Such visual fingerprint designs offer us the opportunity to summarize the interesting features and patterns from different check-in locations, activities and users (groups). We demonstrate the effectiveness and usability of our system by conducting extensive case studies on real check-in data collected from a popular microblogging service. Interesting findings are reported and discussed at last.

Continuation of SAGE and MLS High-Resolution Ozone Profiles with the Suomi NPP OMPS Limb Profiler

NASA Astrophysics Data System (ADS)

Kramarova, N. A.; Bhartia, P. K.; Moy, L.; Chen, Z.; Frith, S. M.

2015-12-01

The Ozone Mapper and Profiler Suite (OMPS) Limb Profiler (LP) onboard the Suomi NPP satellite is design to measure ozone profiles with a high vertical resolution (~2 km) and dense spatial sampling (~1° latitude). The LP sensor represents a new generation of the US ozone profile instruments with the plan for a follow-up limb instrument onboard the Joint Polar Satellite System 2 (JPSS-2) in 2021. In this study we will examine the suitability of using LP profiles to continue the EOS climate ozone profile record from the SAGE and MLS datasets. First of all, we evaluate the accuracy in determining the LP tangent height by analyzing measured and calculated radiances. The accurate estimation of the tangent height is critical for limb observations. Several methods were explored to estimate the uncertainties in the LP tangent height registration, and the results will be briefly summarized in this presentation. Version 2 of LP data, released in May 2014, includes a static adjustment of ~1.5 km and a dynamic tangent height adjustment within each orbit. A recent analysis of Version 2 Level 1 radiances revealed a 100 m step in the tangent height that occurred on 26 April 2013, due to a switch to two star trackers in determining spacecraft position. In addition, a ~200 m shift in the tangent height along each orbit was detected. These uncertainties in tangent height registrations can affect the stability of the LP ozone record. Therefore, the second step in our study includes a validation of LP ozone profiles against correlative satellite ozone measurements (Aura MLS, ACE-FTS, OSIRIS, and SBUV) with the focus on time-dependent changes. We estimate relative drifts between OMPS LP and correlative ozone records to evaluate stability of the LP measurements. We also test the tangent height corrections found in the internal analysis of Version 2 measurements to determine their effect on the long-term stability of the LP ozone record.

Essential-oil composition of the needles collected from natural populations of Macedonian pine (Pinus peuce Griseb.) from the Scardo-Pindic mountain system.

PubMed

Nikolić, Biljana; Ristić, Mihailo; Bojović, Srdjan; Matevski, Vlado; Krivošej, Zoran; Marin, Petar D

2014-06-01

The needle-terpene profiles of two natural Pinus peuce populations from the Scardo-Pindic mountain system (Mt. Ošljak and Mt. Pelister) were analyzed. Among the 90 detected compounds, 87 were identified. The dominant constituents were α-pinene (45.5%), germacrene D (11.1%), β-pinene (10.8%), and camphene (10.3%). The following eight additional components were found to be present in medium-to-high amounts (0.5-10%): bornyl acetate (5.0%), β-phellandrene (3.4%), β-caryophyllene (2.9%), β-myrcene (0.9%), germacrene D-4-ol (0.9%), tricyclene (0.7%), (E)-hex-2-enal (0.7%), and bicyclogermacrene (0.6%). Although the general needle-terpene profiles of the populations from Mt. Ošljak and Mt. Pelister were found to be similar to those of the populations from Zeletin, Sjekirica, and Mokra Gora (Dinaric Alps), principle component analysis (PCA) of eight terpenes (α-pinene, β-myrcene, α-terpinolene, bornyl acetate, α-terpinyl acetate, β-caryophyllene, trans-β-farnesene, and germacrene D) in 139 tree samples suggested a divergence between the two population groups, i.e., the samples from the Scardo-Pindic mountain system and those from the Dinaric Alps. Genetic analysis of the β-pinene content demonstrated a partial divergence between the two geographical groups. The profiles of both population groups differed from those published for populations from the Balkan-Rhodope mountains system (literature results), which were characterized by high contents of bornyl acetate and citronellol (Greek populations) or δ-car-3-ene (Bulgarian populations). Copyright © 2014 Verlag Helvetica Chimica Acta AG, Zürich.

Wind and turbine characteristics needed for integration of wind turbine arrays into a utility system

NASA Technical Reports Server (NTRS)

Park, G. L.

1982-01-01

Wind data and wind turbine generator (WTG) performance characteristics are often available in a form inconvenient for use by utility planners and engineers. The steps used by utility planners are summarized and the type of wind and WTG data needed for integration of WTG arrays suggested. These included long term yearly velocity averages for preliminary site feasibility, hourly velocities on a 'wind season' basis for more detailed economic analysis and for reliability studies, worst-case velocity profiles for gusts, and various minute-to-hourly velocity profiles for estimating the effect of longer-term wind fluctuations on utility operations. wind turbine data needed includes electrical properties of the generator, startup and shutdown characteristics, protection characteristics, pitch control response and control strategy, and electro-mechanical model for stability analysis.

Optical Feedback Interferometry for Velocity Measurement of Parallel Liquid-Liquid Flows in a Microchannel

PubMed Central

Ramírez-Miquet, Evelio E.; Perchoux, Julien; Loubière, Karine; Tronche, Clément; Prat, Laurent; Sotolongo-Costa, Oscar

2016-01-01

Optical feedback interferometry (OFI) is a compact sensing technique with recent implementation for flow measurements in microchannels. We propose implementing OFI for the analysis at the microscale of multiphase flows starting with the case of parallel flows of two immiscible fluids. The velocity profiles in each phase were measured and the interface location estimated for several operating conditions. To the authors knowledge, this sensing technique is applied here for the first time to multiphase flows. Theoretical profiles issued from a model based on the Couette viscous flow approximation reproduce fairly well the experimental results. The sensing system and the analysis presented here provide a new tool for studying more complex interactions between immiscible fluids (such as liquid droplets flowing in a microchannel). PMID:27527178

Power System Trade Studies for the Lunar Surface Access Module

NASA Technical Reports Server (NTRS)

Kohout, Lisa, L.

2008-01-01

A Lunar Lander Preparatory Study (LLPS) was undertaken for NASA's Lunar Lander Pre-Project in 2006 to explore a wide breadth of conceptual lunar lander designs. Civil servant teams from nearly every NASA center responded with dozens of innovative designs that addressed one or more specific lander technical challenges. Although none of the conceptual lander designs sought to solve every technical design issue, each added significantly to the technical database available to the Lunar Lander Project Office as it began operations in 2007. As part of the LLPS, a first order analysis was performed to identify candidate power systems for the ascent and descent stages of the Lunar Surface Access Module (LSAM). A power profile by mission phase was established based on LSAM subsystem power requirements. Using this power profile, battery and fuel cell systems were modeled to determine overall mass and volume. Fuel cell systems were chosen for both the descent and ascent stages due to their low mass. While fuel cells looked promising based on these initial results, several areas have been identified for further investigation in subsequent studies, including the identification and incorporation of peak power requirements into the analysis, refinement of the fuel cell models to improve fidelity and incorporate ongoing technology developments, and broadening the study to include solar power.

An integrated one-step system to extract, analyze and annotate all relevant information from image-based cell screening of chemical libraries.

PubMed

Rabal, Obdulia; Link, Wolfgang; Serelde, Beatriz G; Bischoff, James R; Oyarzabal, Julen

2010-04-01

Here we report the development and validation of a complete solution to manage and analyze the data produced by image-based phenotypic screening campaigns of small-molecule libraries. In one step initial crude images are analyzed for multiple cytological features, statistical analysis is performed and molecules that produce the desired phenotypic profile are identified. A naïve Bayes classifier, integrating chemical and phenotypic spaces, is built and utilized during the process to assess those images initially classified as "fuzzy"-an automated iterative feedback tuning. Simultaneously, all this information is directly annotated in a relational database containing the chemical data. This novel fully automated method was validated by conducting a re-analysis of results from a high-content screening campaign involving 33 992 molecules used to identify inhibitors of the PI3K/Akt signaling pathway. Ninety-two percent of confirmed hits identified by the conventional multistep analysis method were identified using this integrated one-step system as well as 40 new hits, 14.9% of the total, originally false negatives. Ninety-six percent of true negatives were properly recognized too. A web-based access to the database, with customizable data retrieval and visualization tools, facilitates the posterior analysis of annotated cytological features which allows identification of additional phenotypic profiles; thus, further analysis of original crude images is not required.

Massively parallel sequencing of forensic STRs and SNPs using the Illumina® ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx™ Forensic Genomics System.

PubMed

Guo, Fei; Yu, Jiao; Zhang, Lu; Li, Jun

2017-11-01

The ForenSeq™ DNA Signature Prep Kit (ForenSeq Kit) is designed to detect more than 200 forensically relevant markers in a single reaction on the MiSeq FGx™ Forensic Genomics System (MiSeq FGx System), including Amelogenin, 27 autosomal short tandem repeats (A-STRs), 7 X chromosomal STRs (X-STRs), 24 Y chromosomal STRs (Y-STRs) and 94 identity-informative single nucleotide polymorphisms (iSNPs) with the option to contain 22 phenotypic-informative SNPs (pSNPs) and 56 ancestry-informative SNPs (aSNPs). In this study, we evaluated the MiSeq FGx System on three major parts: methodological optimization (DNA extraction, sample quantification, library normalization, diluted libraries concentration, and sample-to-cell arrangement), massively parallel sequencing (MPS) performance (depth of coverage, sequence coverage ratio, and allele coverage ratio), and ForenSeq Kit characteristics (repeatability and concordance, sensitivity, mixture, stability and case-type samples). Results showed that quantitative polymerase chain reaction (qPCR)-based sample quantification and library normalization and the appropriate number of pooled libraries and concentration of diluted libraries provided a greater level of MPS performance and repeatability. Repeatable and concordant genotypes were obtained by the ForenSeq Kit. Full profiles were obtained from ≥100pg input DNA for STRs and ≥200pg for SNPs. A sample with ≥5% minor contributors was considered as a mixture by imbalanced allele coverage ratio distribution, and full profiles from minor contributors were easily detected between 9:1 and 1:9 mixtures with known reference profiles. The ForenSeq Kit tolerated considerable concentrations of inhibitors like ≤200μM hematin and ≤50μg/ml humic acid, and >56% STR profiles and >88% SNP profiles were obtained from ≥200-bp degraded samples. Also, it was adapted to case-type samples. As a whole, the ForenSeq Kit is a well-performed, robust, reliable, reproducible and highly informative assay, and it can fully meet requirements for human identification. Further, sensitive QC indicator and automated sample comparison function in the ForenSeq™ Universal Analysis Software are quite helpful, so that we can concentrate on questionable genotypes and avoid tedious and time-consuming labor to maximum the time spent in data analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Velocity Plume Profiles for Hall Thrusters Using Laser Diagnostic

DTIC Science & Technology

2010-06-01

53 Collecting LIF Using Fiber Optics .............................................................................58 Vacuum ...54 Figure 40. Etalon Issue Through Vacuum Chamber Window [25]. ................................. 55 Figure 41. Collimator with Adapter in a...Methodology Facility Set-up Vacuum Chamber Testing took place within a vacuum chamber located at the AFIT Space Propulsion Analysis and System Simulation

Energy Management and the Infrastructure System.

ERIC Educational Resources Information Center

Blackburn, James M.

1998-01-01

Describes a state-of-the-art energy management program at Wake Forest University (North Carolina) designed to include all on-campus property, and explores the various aspects of cost/benefit analysis in its development. A campus profile, electrical and thermal energy analyses, and a summary table of utility budget data are included. (GR)

Analysis of hyperspectral scattering images using a moment method for apple firmness prediction

USDA-ARS?s Scientific Manuscript database

This article reports on using a moment method to extract features from the hyperspectral scattering profiles for apple fruit firmness prediction. Hyperspectral scattering images between 500 nm and 1000 nm were acquired online, using a hyperspectral scattering system, for ‘Golden Delicious’, ’Jonagol...

Spectral analysis of large-eddy advection in ET from eddy covariance towers and a large weighting lysimeter

USDA-ARS?s Scientific Manuscript database

Evapotranspiration was continuously measured by an array of eddy covariance systems and large weighting lysimeter in a cotton field in Bushland, Texas. The advective divergence from both horizontal and vertical directions were measured through profile measurements above canopy. All storage terms wer...

Profile of an Accident Flying Squad

PubMed Central

Little, Keith

1972-01-01

An analysis of 184 accident flying squad calls and of 280 patients injured in road accidents and treated by a flying squad based on an accident department inclusive from 1967 to 1971 has shown that such a service can provide an efficient system without disrupting the routine work of the hospital. PMID:5076258

Profile of an accident flying squad.

PubMed

Little, K

1972-09-30

An analysis of 184 accident flying squad calls and of 280 patients injured in road accidents and treated by a flying squad based on an accident department inclusive from 1967 to 1971 has shown that such a service can provide an efficient system without disrupting the routine work of the hospital.

Comparative Geostatistical Analysis of Flowmeter and Direct-Push Hydraulic Conductivity Profiles at the MADE Site

NASA Astrophysics Data System (ADS)

Bohling, G.; Liu, G.; Knobbe, S. J.; Reboulet, E. C.; Hyndman, D. W.; Dietrich, P.; Butler, J. J.

2010-12-01

Spatial variations in hydraulic conductivity (K) are a critical control on subsurface solute transport. Characterization of such variations at the resolution (cm to dm) required for transport investigations, however, has proven to be a formidable challenge. A new generation of direct-push (DP) tools has now been developed for the characterization of vertical K variations at this resolution. These tools, which can be run in high- (0.015-m) and low- (0.4 m) resolution modes, were recently applied to the extensively studied and highly heterogeneous MADE site. Results from a geostatistical analysis of 64 DP K profiles compare favorably with the flowmeter K data that have served as the primary basis for previous MADE studies. The global statistics of the low-resolution DP and flowmeter K data are in excellent agreement. The correlation structures for the high-resolution DP data show excellent agreement with those computed from the flowmeter data. However, the geometric mean DP K value for high-resolution profiling is roughly one order of magnitude lower than the geometric mean flowmeter K value, possibly as a result of the biases inherent in each approach compounded with differences in the areal distribution of flowmeter and DP profile locations. A DP profile through the MADE aquifer to a depth of 12 m can be completed as rapidly as 1.5-2 hours, a small fraction of the time required to obtain a single flowmeter profile when well drilling, installation, and development are considered. The results of this study demonstrate that DP profiling is a practically feasible approach for characterization of spatial variations in K at the resolution required for transport investigations in highly heterogeneous systems.

Performance analysis of sliding window filtering of two dimensional signals based on stream data processing systems

NASA Astrophysics Data System (ADS)

Kazanskiy, Nikolay; Protsenko, Vladimir; Serafimovich, Pavel

2016-03-01

This research article contains an experiment with implementation of image filtering task in Apache Storm and IBM InfoSphere Streams stream data processing systems. The aim of presented research is to show that new technologies could be effectively used for sliding window filtering of image sequences. The analysis of execution was focused on two parameters: throughput and memory consumption. Profiling was performed on CentOS operating systems running on two virtual machines for each system. The experiment results showed that IBM InfoSphere Streams has about 1.5 to 13.5 times lower memory footprint than Apache Storm, but could be about 2.0 to 2.5 slower on a real hardware.

Assessment of a three‐dimensional (3D) water scanning system for beam commissioning and measurements on a helical tomotherapy unit

PubMed Central

Ashenafi, Michael S.; McDonald, Daniel G.; Vanek, Kenneth N.

2015-01-01

Beam scanning data collected on the tomotherapy linear accelerator using the TomoScanner water scanning system is primarily used to verify the golden beam profiles included in all Helical TomoTherapy treatment planning systems (TOMO TPSs). The user is not allowed to modify the beam profiles/parameters for beam modeling within the TOMO TPSs. The authors report the first feasibility study using the Blue Phantom Helix (BPH) as an alternative to the TomoScanner (TS) system. This work establishes a benchmark dataset using BPH for target commissioning and quality assurance (QA), and quantifies systematic uncertainties between TS and BPH. Reproducibility of scanning with BPH was tested by three experienced physicists taking five sets of measurements over a six‐month period. BPH provides several enhancements over TS, including a 3D scanning arm, which is able to acquire necessary beam‐data with one tank setup, a universal chamber mount, and the OmniPro software, which allows online data collection and analysis. Discrepancies between BPH and TS were estimated by acquiring datasets with each tank. In addition, data measured with BPH and TS was compared to the golden TOMO TPS beam data. The total systematic uncertainty, defined as the combination of scanning system and beam modeling uncertainties, was determined through numerical analysis and tabulated. OmniPro was used for all analysis to eliminate uncertainty due to different data processing algorithms. The setup reproducibility of BPH remained within 0.5 mm/0.5%. Comparing BPH, TS, and Golden TPS for PDDs beyond maximum depth, the total systematic uncertainties were within 1.4 mm/2.1%. Between BPH and TPS golden data, maximum differences in the field width and penumbra of in‐plane profiles were within 0.8 and 1.1 mm, respectively. Furthermore, in cross‐plane profiles, the field width differences increased at depth greater than 10 cm up to 2.5 mm, and maximum penumbra uncertainties were 5.6 mm and 4.6 mm from TS scanning system and TPS modeling, respectively. Use of BPH reduced measurement time by 1–2 hrs per session. The BPH has been assessed as an efficient, reproducible, and accurate scanning system capable of providing a reliable benchmark beam data. With this data, a physicist can utilize the BPH in a clinical setting with an understanding of the scan discrepancy that may be encountered while validating the TPS or during routine machine QA. Without the flexibility of modifying the TPS and without a golden beam dataset from the vendor or a TPS model generated from data collected with the BPH, this represents the best solution for current clinical use of the BPH. PACS number: 87.56.Fc

Surface profile measurement by using the integrated Linnik WLSI and confocal microscope system

NASA Astrophysics Data System (ADS)

Wang, Wei-Chung; Shen, Ming-Hsing; Hwang, Chi-Hung; Yu, Yun-Ting; Wang, Tzu-Fong

2017-06-01

The white-light scanning interferometer (WLSI) and confocal microscope (CM) are the two major optical inspection systems for measuring three-dimensional (3D) surface profile (SP) of micro specimens. Nevertheless, in practical applications, WLSI is more suitable for measuring smooth and low-slope surfaces. On the other hand, CM is more suitable for measuring uneven-reflective and low-reflective surfaces. As for aspect of surface profiles to be measured, the characteristics of WLSI and CM are also different. WLSI is generally used in semiconductor industry while CM is more popular in printed circuit board industry. In this paper, a self-assembled multi-function optical system was integrated to perform Linnik white-light scanning interferometer (Linnik WLSI) and CM. A connecting part composed of tubes, lenses and interferometer was used to conjunct finite and infinite optical systems for Linnik WLSI and CM in the self-assembled optical system. By adopting the flexibility of tubes and lenses, switching to perform two different optical measurements can be easily achieved. Furthermore, based on the shape from focus method with energy of Laplacian filter, the CM was developed to enhance the on focal information of each pixel so that the CM can provide all-in-focus image for performing the 3D SP measurement and analysis simultaneously. As for Linnik WLSI, eleven-step phase shifting algorithm was used to analyze vertical scanning signals and determine the 3D SP.

Gluing for Raman lidar systems using the lamp mapping technique.

PubMed

Walker, Monique; Venable, Demetrius; Whiteman, David N

2014-12-20

In the context of combined analog and photon counting (PC) data acquisition in a Lidar system, glue coefficients are defined as constants used for converting an analog signal into a virtual PC signal. The coefficients are typically calculated using Lidar profile data taken under clear, nighttime conditions since, in the presence of clouds or high solar background, it is difficult to obtain accurate glue coefficients from Lidar backscattered data. Here we introduce a new method in which we use the lamp mapping technique (LMT) to determine glue coefficients in a manner that does not require atmospheric profiles to be acquired and permits accurate glue coefficients to be calculated when adequate Lidar profile data are not available. The LMT involves scanning a halogen lamp over the aperture of a Lidar receiver telescope such that the optical efficiency of the entire detection system is characterized. The studies shown here involve two Raman lidar systems; the first from Howard University and the second from NASA/Goddard Space Flight Center. The glue coefficients determined using the LMT and the Lidar backscattered method agreed within 1.2% for the water vapor channel and within 2.5% for the nitrogen channel for both Lidar systems. We believe this to be the first instance of the use of laboratory techniques for determining the glue coefficients for Lidar data analysis.

An adhered-particle analysis system based on concave points

NASA Astrophysics Data System (ADS)

Wang, Wencheng; Guan, Fengnian; Feng, Lin

2018-04-01

Particles adhered together will influence the image analysis in computer vision system. In this paper, a method based on concave point is designed. First, corner detection algorithm is adopted to obtain a rough estimation of potential concave points after image segmentation. Then, it computes the area ratio of the candidates to accurately localize the final separation points. Finally, it uses the separation points of each particle and the neighboring pixels to estimate the original particles before adhesion and provides estimated profile images. The experimental results have shown that this approach can provide good results that match the human visual cognitive mechanism.

The Propulsive Small Expendable Deployer System (ProSEDS)

NASA Technical Reports Server (NTRS)

Lorenzini, Enrico C.; Estes, Robert D.; Cosmo, Mario L.

2001-01-01

This is the Annual Report #2 entitled "The Propulsive Small Expendable Deployer System (ProSEDS)" prepared by the Smithsonian Astrophysical Observatory for NASA Marshall Space Flight Center. This report covers the period of activity from 1 August 2000 through 30 July 2001. The topics include: 1) Updated System Performance; 2) Mission Analysis; 3) Updated Dynamics Reference Mission; 4) Updated Deployment Control Profiles and Simulations; 5) Comparison of ED tethers and electrical thrusters; 6) Kalman filters for mission estimation; and 7) Delivery of interactive software for ED tethers.

Comparative Discussion on Psychophysiological Effect of Self-administered Facial Massage by Treatment Method

NASA Astrophysics Data System (ADS)

Nozawa, Akio; Takei, Yuya

The aim of study was to quantitatively evaluate the effects of self-administered facial massage, which was done by hand or facial roller. In this study, the psychophysiological effects of facial massage were evaluated. The central nerves system and the autonomic nervous system were administered to evaluate physiological system. The central nerves system was assessed by Electroencephalogram (EEG). The autonomic nervous system were assessed by peripheral skin temperature(PST) and heart rate variability (HRV) with spectral analysis. In the spectral analysis of HRV, the high-frequency components (HF) were evaluated. State-Trait Anxiety Inventory (STAI), Profile of Mood Status (POMS) and subjective sensory amount with Visual Analog Scale (VAS) were administered to evaluate psychological status. These results suggest that kept brain activity and had strong effects on stress alleviation.

Noninvasive Real-Time Assessment of Cell Viability in a Three-Dimensional Tissue.

PubMed

Mahfouzi, Seyed Hossein; Amoabediny, Ghassem; Doryab, Ali; Safiabadi-Tali, Seyed Hamid; Ghanei, Mostafa

2018-04-01

Maintaining cell viability within 3D tissue engineering scaffolds is an essential step toward a functional tissue or organ. Assessment of cell viability in 3D scaffolds is necessary to control and optimize tissue culture process. Monitoring systems based on respiration activity of cells (e.g., oxygen consumption) have been used in various cell cultures. In this research, an online monitoring system based on respiration activity was developed to monitor cell viability within acellular lung scaffolds. First, acellular lung scaffolds were recellularized with human umbilical cord vein endothelial cells, and then, cell viability was monitored during a 5-day period. The real-time monitoring system generated a cell growth profile representing invaluable information on cell viability and proliferative states during the culture period. The cell growth profile obtained by the monitoring system was consistent with 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide analysis and glucose consumption measurement. This system provided a means for noninvasive, real-time, and repetitive investigation of cell viability. Also, we showed the applicability of this monitoring system by introducing shaking as an operating parameter in a long-term culture.

The Non-linear Trajectory of Change in Play Profiles of Three Children in Psychodynamic Play Therapy.

PubMed

Halfon, Sibel; Çavdar, Alev; Orsucci, Franco; Schiepek, Gunter K; Andreassi, Silvia; Giuliani, Alessandro; de Felice, Giulio

2016-01-01

Aim: Even though there is substantial evidence that play based therapies produce significant change, the specific play processes in treatment remain unexamined. For that purpose, processes of change in long-term psychodynamic play therapy are assessed through a repeated systematic assessment of three children's "play profiles," which reflect patterns of organization among play variables that contribute to play activity in therapy, indicative of the children's coping strategies, and an expression of their internal world. The main aims of the study are to investigate the kinds of play profiles expressed in treatment, and to test whether there is emergence of new and more adaptive play profiles using dynamic systems theory as a methodological framework. Methods and Procedures: Each session from the long-term psychodynamic treatment (mean number of sessions = 55) of three 6-year-old good outcome cases presenting with Separation Anxiety were recorded, transcribed and coded using items from the Children's Play Therapy Instrument (CPTI), created to assess the play activity of children in psychotherapy, generating discrete and measurable units of play activity arranged along a continuum of four play profiles: "Adaptive," "Inhibited," "Impulsive," and "Disorganized." The play profiles were clustered through K -means Algorithm, generating seven discrete states characterizing the course of treatment and the transitions between these states were analyzed by Markov Transition Matrix, Recurrence Quantification Analysis (RQA) and odds ratios comparing the first and second halves of psychotherapy. Results: The Markov Transitions between the states scaled almost perfectly and also showed the ergodicity of the system, meaning that the child can reach any state or shift to another one in play. The RQA and odds ratios showed two trends of change, first concerning the decrease in the use of "less adaptive" strategies, second regarding the reduction of play interruptions. Conclusion: The results support that these children express different psychic states in play, which can be captured through the lens of play profiles, and begin to modify less dysfunctional profiles over the course of treatment. The methodology employed showed the productivity of treating psychodynamic play therapy as a complex system, taking advantage of non-linear methods to study psychotherapeutic play activity.

Energy audit data for a resort island in the South China Sea

PubMed Central

Basir Khan, M. Reyasudin; Jidin, Razali; Pasupuleti, Jagadeesh

2015-01-01

The data consists of actual generation-side auditing including the distribution of loads, seasonal load profiles, and types of loads as well as an analysis of local development planning of a resort island in the South China Sea. The data has been used to propose an optimal combination of hybrid renewable energy systems that able to mitigate the diesel fuel dependency on the island. The resort island selected is Tioman, as it represents the typical energy requirements of many resort islands in the South China Sea. The data presented are related to the research article “Optimal Combination of Solar, Wind, Micro-Hydro and Diesel Systems based on Actual Seasonal Load Profiles for a Resort Island in the South China Sea” [1]. PMID:26900590

Fast neutron-gamma discrimination on neutron emission profile measurement on JT-60U.

PubMed

Ishii, K; Shinohara, K; Ishikawa, M; Baba, M; Isobe, M; Okamoto, A; Kitajima, S; Sasao, M

2010-10-01

A digital signal processing (DSP) system is applied to stilbene scintillation detectors of the multichannel neutron emission profile monitor in JT-60U. Automatic analysis of the neutron-γ pulse shape discrimination is a key issue to diminish the processing time in the DSP system, and it has been applied using the two-dimensional (2D) map. Linear discriminant function is used to determine the dividing line between neutron events and γ-ray events on a 2D map. In order to verify the validity of the dividing line determination, the pulse shape discrimination quality is evaluated. As a result, the γ-ray contamination in most of the beam heating phase was negligible compared with the statistical error with 10 ms time resolution.

Fast neutron-gamma discrimination on neutron emission profile measurement on JT-60U

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ishii, K.; Okamoto, A.; Kitajima, S.

2010-10-15

A digital signal processing (DSP) system is applied to stilbene scintillation detectors of the multichannel neutron emission profile monitor in JT-60U. Automatic analysis of the neutron-{gamma} pulse shape discrimination is a key issue to diminish the processing time in the DSP system, and it has been applied using the two-dimensional (2D) map. Linear discriminant function is used to determine the dividing line between neutron events and {gamma}-ray events on a 2D map. In order to verify the validity of the dividing line determination, the pulse shape discrimination quality is evaluated. As a result, the {gamma}-ray contamination in most of themore » beam heating phase was negligible compared with the statistical error with 10 ms time resolution.« less

On the source of cross-grain lineations in the central Pacific gravity field

NASA Technical Reports Server (NTRS)

Mcadoo, David C.; Sandwell, David T.

1989-01-01

The source of cross-grain lineations in marine gravity field observed in central Pacific was investigated by comparing multiple collinear gravity profiles from Geosat data with coincident bathymetry profiles, in the Fourier transform domain. Bathymetric data were collected by multibeam sonar systems operating from two research vessels, one in June-August 1985, the other in February and March 1987. The results of this analysis indicate that the lineations are superficial features that appear to result from a combination of subsurface and surface loads supported by a thin (2 km to 5 km) lithosphere.

Molecular profiles to biology and pathways: a systems biology approach.

PubMed

Van Laere, Steven; Dirix, Luc; Vermeulen, Peter

2016-06-16

Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters.

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

PubMed Central

Abby, Sophie S.; Néron, Bertrand; Ménager, Hervé; Touchon, Marie; Rocha, Eduardo P. C.

2014-01-01

Motivation Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose. Results Macromolecular System Finder (MacSyFinder) provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway) including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems. Models are used to search for molecular systems in complete genomes or in unstructured data like metagenomes. The components of the systems are searched by sequence similarity using Hidden Markov model (HMM) protein profiles. The assignment of hits to a given system is decided based on compliance with the content and organization of the system model. A graphical interface, MacSyView, facilitates the analysis of the results by showing overviews of component content and genomic context. To exemplify the use of MacSyFinder we built models to detect and class CRISPR-Cas systems following a previously established classification. We show that MacSyFinder allows to easily define an accurate “Cas-finder” using publicly available protein profiles. Availability and Implementation MacSyFinder is a standalone application implemented in Python. It requires Python 2.7, Hmmer and makeblastdb (version 2.2.28 or higher). It is freely available with its source code under a GPLv3 license at https://github.com/gem-pasteur/macsyfinder. It is compatible with all platforms supporting Python and Hmmer/makeblastdb. The “Cas-finder” (models and HMM profiles) is distributed as a compressed tarball archive as Supporting Information. PMID:25330359

A pharmacological profile of the aldehyde receptor repertoire in rat olfactory epithelium

PubMed Central

Araneda, Ricardo C; Peterlin, Zita; Zhang, Xinmin; Chesler, Alex; Firestein, Stuart

2004-01-01

Several lines of evidence suggest that odorants are recognized through a combinatorial process in the olfactory system; a single odorant is recognized by multiple receptors and multiple odorants are recognized by the same receptor. However few details of how this might actually function for any particular odour set or receptor family are available. Approaching the problem from the ligands rather than the receptors, we used the response to a common odorant, octanal, as the basis for defining multiple receptor profiles. Octanal and other aldehydes induce large EOG responses in the rodent olfactory epithelium, suggesting that these compounds activate a large number of odour receptors (ORs). Here, we have determined and compared the pharmacological profile of different octanal receptors using Ca2+ imaging in isolated olfactory sensory neurones (OSNs). It is believed that each OSN expresses only one receptor, thus the response profile of each cell corresponds to the pharmacological profile of one particular receptor. We stimulated the cells with a panel of nine odorants, which included octanal, octanoic acid, octanol and cinnamaldehyde among others (all at 30μm). Cluster analysis revealed several distinct pharmacological profiles for cells that were all sensitive to octanal. Some receptors had a broad molecular range, while others were activated only by octanal. Comparison of the profiles with that of the one identified octanal receptor, OR-I7, indicated several differences. While OR-I7 is activated by low concentrations of octanal and blocked by citral, other receptors were less sensitive to octanal and not blocked by citral. A lower estimate for the maximal number of octanal receptors is between 33 and 55. This large number of receptors for octanal suggests that, although the peripheral olfactory system is endowed with high sensitivity, discrimination among different compounds probably requires further central processing. PMID:14724183

The Profile Envision and Splice Tool (PRESTO): Developing an Atmospheric Wind Analysis Tool for Space Launch Vehicles Using Python

NASA Technical Reports Server (NTRS)

Orcutt, John M.; Barbre, Robert E., Jr.; Brenton, James C.; Decker, Ryan K.

2017-01-01

Tropospheric winds are an important driver of the design and operation of space launch vehicles. Multiple types of weather balloons and Doppler Radar Wind Profiler (DRWP) systems exist at NASA's Kennedy Space Center (KSC), co-located on the United States Air Force's (USAF) Eastern Range (ER) at the Cape Canaveral Air Force Station (CCAFS), that are capable of measuring atmospheric winds. Meteorological data gathered by these instruments are being used in the design of NASA's Space Launch System (SLS) and other space launch vehicles, and will be used during the day-of-launch (DOL) of SLS to aid in loads and trajectory analyses. For the purpose of SLS day-of-launch needs, the balloons have the altitude coverage needed, but take over an hour to reach the maximum altitude and can drift far from the vehicle's path. The DRWPs have the spatial and temporal resolutions needed, but do not provide complete altitude coverage. Therefore, the Natural Environments Branch (EV44) at Marshall Space Flight Center (MSFC) developed the Profile Envision and Splice Tool (PRESTO) to combine balloon profiles and profiles from multiple DRWPs, filter the spliced profile to a common wavelength, and allow the operator to generate output files as well as to visualize the inputs and the spliced profile for SLS DOL operations. PRESTO was developed in Python taking advantage of NumPy and SciPy for the splicing procedure, matplotlib for the visualization, and Tkinter for the execution of the graphical user interface (GUI). This paper describes in detail the Python coding implementation for the splicing, filtering, and visualization methodology used in PRESTO.

Pneumoperitoneum deteriorates intratidal respiratory system mechanics: an observational study in lung-healthy patients.

PubMed

Wirth, Steffen; Biesemann, Andreas; Spaeth, Johannes; Schumann, Stefan

2017-02-01

Pneumoperitoneum during laparoscopic surgery leads to atelectasis and impairment of oxygenation. Positive end-expiratory pressure (PEEP) is supposed to counteract atelectasis. We hypothesized that the derecruiting effects of pneumoperitoneum would deteriorate the intratidal compliance profile in patients undergoing laparoscopic surgery. In 30 adult patients scheduled for surgery with pneumoperitoneum, respiratory variables were measured during mechanical ventilation. We calculated the dynamic compliance of the respiratory system (C RS ) and the intratidal volume-dependent C RS curve using the gliding-SLICE method. The C RS curve was then classified in terms of indicating intratidal recruitment/derecruitment (increasing profile) and overdistension (decreasing profile). During the surgical interventions, the PEEP level was maintained nearly constant at 7 cm H 2 O. Data are expressed as mean [confidence interval]. Baseline C RS was 60 [54-67] mL cm H 2 O -1 . Application of pneumoperitoneum decreased C RS to 40 [37-43] mL cm H 2 O -1 which partially recovered to 54 [50-59] mL cm H 2 O -1 (P < 0.001) after removal but remained below the value measured before pneumoperitoneum (P < 0.001). Baseline compliance profiles indicated intratidal recruitment/derecruitment in 48 % patients. After induction of pneumoperitoneum, intratidal recruitment/derecruitment was indicated in 93 % patients (P < 0.01), and after removal intratidal recruitment/derecruitment was indicated in 59 % patients. Compliance profiles showing overdistension were not observed. Analyses of the intratidal compliance profiles reveal that pneumoperitoneum during laparoscopic surgery causes intratidal recruitment/derecruitment which partly persists after its removal. The analysis of the intratidal volume-dependent C RS profiles could be used to guide intraoperative PEEP adjustments during elevated intraabdominal pressure.

Shotgun metabolomic approach based on mass spectrometry for hepatic mitochondria of mice under arsenic exposure.

PubMed

García-Sevillano, M A; García-Barrera, T; Navarro, F; Montero-Lobato, Z; Gómez-Ariza, J L

2015-04-01

Mass spectrometry (MS)-based toxicometabolomics requires analytical approaches for obtaining unbiased metabolic profiles. The present work explores the general application of direct infusion MS using a high mass resolution analyzer (a hybrid systems triple quadrupole-time-of-flight) and a complementary gas chromatography-MS analysis to mitochondria extracts from mouse hepatic cells, emphasizing on mitochondria isolation from hepatic cells with a commercial kit, sample treatment after cell lysis, comprehensive metabolomic analysis and pattern recognition from metabolic profiles. Finally, the metabolomic platform was successfully checked on a case-study based on the exposure experiment of mice Mus musculus to inorganic arsenic during 12 days. Endogenous metabolites alterations were recognized by partial least squares-discriminant analysis. Subsequently, metabolites were identified by combining MS/MS analysis and metabolomics databases. This work reports for the first time the effects of As-exposure on hepatic mitochondria metabolic pathways based on MS, and reveals disturbances in Krebs cycle, β-oxidation pathway, amino acids degradation and perturbations in creatine levels. This non-target analysis provides extensive metabolic information from mitochondrial organelle, which could be applied to toxicology, pharmacology and clinical studies.

Excimer laser system Profile-500

NASA Astrophysics Data System (ADS)

Atejev, V. V.; Bukreyev, V. S.; Vartapetov, Serge K.; Semenov, A. D.; Sugrobov, V. A.; Turin, V. S.; Fedorov, Sergei N.

1999-07-01

The description of ophthalmological excimer laser system 'PROFILE-500' for photorefractive and physiotherapeutic keratectomy is presented. Excimer Laser Systems 'PROFILE- 500' are optical system that use ArF excimer lasers to perform photorefractive keratectomy or LASIK; surgical procedures used to correct myopia, hyperopia and astigmatism.

Extractables analysis of single-use flexible plastic biocontainers.

PubMed

Marghitoiu, Liliana; Liu, Jian; Lee, Hans; Perez, Lourdes; Fujimori, Kiyoshi; Ronk, Michael; Hammond, Matthew R; Nunn, Heather; Lower, Asher; Rogers, Gary; Nashed-Samuel, Yasser

2015-01-01

Studies of the extractable profiles of bioprocessing components have become an integral part of drug development efforts to minimize possible compromise in process performance, decrease in drug product quality, and potential safety risk to patients due to the possibility of small molecules leaching out from the components. In this study, an effective extraction solvent system was developed to evaluate the organic extractable profiles of single-use bioprocess equipment, which has been gaining increasing popularity in the biopharmaceutical industry because of the many advantages over the traditional stainless steel-based bioreactors and other fluid mixing and storage vessels. The chosen extraction conditions were intended to represent aggressive conditions relative to the application of single-use bags in biopharmaceutical manufacture, in which aqueous based systems are largely utilized. Those extraction conditions, along with a non-targeted analytical strategy, allowed for the generation and identification of an array of extractable compounds; a total of 53 organic compounds were identified from four types of commercially available single-use bags, the majority of which are degradation products of polymer additives. The success of this overall extractables analysis strategy was reflected partially by the effectiveness in the extraction and identification of a compound that was later found to be highly detrimental to mammalian cell growth. The usage of single-use bioreactors has been increasing in biopharmaceutical industry because of the appealing advantages that it promises regarding to the cleaning, sterilization, operational flexibility, and so on, during manufacturing of biologics. However, compared to its conventional counterparts based mainly on stainless steel, single-use bioreactors are more susceptible to potential problems associated with compound leaching into the bioprocessing fluid. As a result, extractable profiling of the single-use system has become essential in the qualification of such systems for its use in drug manufacturing. The aim of this study is to evaluate the effectiveness of an extraction solvent system developed to study the extraction profile of single-use bioreactors in which aqueous-based systems are largely used. The results showed that with a non-targeted analytical approach, the extraction solvent allowed the generation and identification of an array of extractable compounds from four commercially available single-use bioreactors. Most of extractables are degradation products of polymer additives, among which was a compound that was later found to be highly detrimental to mammalian cell growth. © PDA, Inc. 2015.

Comparing helicopter-borne profiling radar with airborne laser scanner data for forest structure estimation.

NASA Astrophysics Data System (ADS)

Piermattei, Livia; Hollaus, Markus; Pfeifer, Norbert; Chen, Yuwei; Karjalainen, Mika; Hakala, Teemu; Hyyppä, Juha; Wagner, Wolfgang

2017-04-01

Forests are complex ecosystems that show substantial variation with respect to climate, management regime, stand history, disturbance, and needs of local communities. The dynamic processes of growth and disturbance are reflected in the structural components of forests that include the canopy vertical structure and geometry (e.g. size, height, and form), tree position and species diversity. Current remote-sensing systems to measure forest structural attributes include passive optical sensors and active sensors. The technological capabilities of active remote sensing like the ability to penetrate the vegetation and provide information about its vertical structure has promoted an extensive use of LiDAR (Light Detection And Ranging) and radar (RAdio Detection And Ranging) system over the last 20 years. LiDAR measurements from aircraft (airborne laser scanning, ALS) currently represents the primary data source for three-dimensional information on forest vertical structure. Contrary, despite the potential of radar remote sensing, their use is not yet established in forest monitoring. In order to better understand the interaction of pulsed radar with the forest canopy, and to increase the feasibility of this system, the Finnish Geospatial Research Institute has developed a helicopter-borne profiling radar system, called TomoRadar. TomoRadar is capable of recording a canopy-penetrating profile of forests. To georeference the radar measurements the system was equipped with a global navigation satellite system and an inertial measurement unit with a centimeter level accuracy of the flight trajectory. The TomoRadar operates at Ku-band, (wave lengths λ 1.5cm) with two separated parabolic antennas providing co- and cross-polarization modes. The purpose of this work is to investigate the capability of the TomoRadar system, for estimating the forest vertical profile, terrain topography and tree height. We analysed 600 m TomoRadar crosspolarized (i.e. horizontal - vertical) profile, acquired in October 2016 over a boreal test site in Evo, Finland. The intensity of the reflected backscatter energy was used to measure the height canopy distribution within an individual footprint. As the intensity of the backscatter energy from the ground is exceeding the intensity from vegetation, the estimation of canopy height and the forest structure were based on i) a threshold between canopy and ground and ii) a peak analysis of the backscattering profile. ALS data collected simultaneously was used to validate the TomoRadar results (i.e. canopy height) and to obtain elevation ground truth. The first results show a high agreement between ALS and TomoRadar derived canopy heights. The derived knowledge about the energy distribution within the canopy height profile leads to an increased understanding of the interactions between the radar signal and the forest canopy and will support optimization of future radar systems with respect to forest structure observation.

Gene Expression Profile Change and Associated Physiological and Pathological Effects in Mouse Liver Induced by Fasting and Refeeding

PubMed Central

Zhang, Fang; Xu, Xiang; Zhou, Ben; He, Zhishui; Zhai, Qiwei

2011-01-01

Food availability regulates basal metabolism and progression of many diseases, and liver plays an important role in these processes. The effects of food availability on digital gene expression profile, physiological and pathological functions in liver are yet to be further elucidated. In this study, we applied high-throughput sequencing technology to detect digital gene expression profile of mouse liver in fed, fasted and refed states. Totally 12162 genes were detected, and 2305 genes were significantly regulated by food availability. Biological process and pathway analysis showed that fasting mainly affected lipid and carboxylic acid metabolic processes in liver. Moreover, the genes regulated by fasting and refeeding in liver were mainly enriched in lipid metabolic process or fatty acid metabolism. Network analysis demonstrated that fasting mainly regulated Drug Metabolism, Small Molecule Biochemistry and Endocrine System Development and Function, and the networks including Lipid Metabolism, Small Molecule Biochemistry and Gene Expression were affected by refeeding. In addition, FunDo analysis showed that liver cancer and diabetes mellitus were most likely to be affected by food availability. This study provides the digital gene expression profile of mouse liver regulated by food availability, and demonstrates the main biological processes, pathways, gene networks and potential hepatic diseases regulated by fasting and refeeding. These results show that food availability mainly regulates hepatic lipid metabolism and is highly correlated with liver-related diseases including liver cancer and diabetes. PMID:22096593

Gene expression profile change and associated physiological and pathological effects in mouse liver induced by fasting and refeeding.

PubMed

Zhang, Fang; Xu, Xiang; Zhou, Ben; He, Zhishui; Zhai, Qiwei

2011-01-01

Food availability regulates basal metabolism and progression of many diseases, and liver plays an important role in these processes. The effects of food availability on digital gene expression profile, physiological and pathological functions in liver are yet to be further elucidated. In this study, we applied high-throughput sequencing technology to detect digital gene expression profile of mouse liver in fed, fasted and refed states. Totally 12162 genes were detected, and 2305 genes were significantly regulated by food availability. Biological process and pathway analysis showed that fasting mainly affected lipid and carboxylic acid metabolic processes in liver. Moreover, the genes regulated by fasting and refeeding in liver were mainly enriched in lipid metabolic process or fatty acid metabolism. Network analysis demonstrated that fasting mainly regulated Drug Metabolism, Small Molecule Biochemistry and Endocrine System Development and Function, and the networks including Lipid Metabolism, Small Molecule Biochemistry and Gene Expression were affected by refeeding. In addition, FunDo analysis showed that liver cancer and diabetes mellitus were most likely to be affected by food availability. This study provides the digital gene expression profile of mouse liver regulated by food availability, and demonstrates the main biological processes, pathways, gene networks and potential hepatic diseases regulated by fasting and refeeding. These results show that food availability mainly regulates hepatic lipid metabolism and is highly correlated with liver-related diseases including liver cancer and diabetes.

Assimilation of temperature and salinity profile data in the Norwegian Climate Prediction Model

NASA Astrophysics Data System (ADS)

Wang, Yiguo; Counillon, Francois; Bertino, Laurent; Bethke, Ingo; Keenlyside, Noel

2016-04-01

Assimilating temperature and salinity profile data is promising to constrain the ocean component of Earth system models for the purpose of seasonal-to-dedacal climate predictions. However, assimilating temperature and salinity profiles that are measured in standard depth coordinate (z-coordinate) into isopycnic coordinate ocean models that are discretised by water densities is challenging. Prior studies (Thacker and Esenkov, 2002; Xie and Zhu, 2010) suggested that converting observations to the model coordinate (i.e. innovations in isopycnic coordinate) performs better than interpolating model state to observation coordinate (i.e. innovations in z-coordinate). This problem is revisited here with the Norwegian Climate Prediction Model, which applies the ensemble Kalman filter (EnKF) into the ocean isopycnic model (MICOM) of the Norwegian Earth System Model. We perform Observing System Simulation Experiments (OSSEs) to compare two schemes (the EnKF-z and EnKF-ρ). In OSSEs, the truth is set to the EN4 objective analyses and observations are perturbations of the truth with white noises. Unlike in previous studies, it is found that EnKF-z outperforms EnKF-ρ for different observed vertical resolution, inhomogeneous sampling (e.g. upper 1000 meter observations only), or lack of salinity measurements. That is mostly because the operator converting observations into isopycnic coordinate is strongly non-linear. We also study the horizontal localisation radius at certain arbitrary grid points. Finally, we perform the EnKF-z with the chosen localisation radius in a realistic framework with NorCPM over a 5-year analysis period. The analysis is validated by different independent datasets.

Metrics for Analyzing Quantifiable Differentiation of Designs with Varying Integrity for Hardware Assurance

DTIC Science & Technology

2017-03-01

proposed. Expected profiles can incorporate a level of overdesign. Finally, the Design Integrity measuring techniques are applied to five Test Article ...Inserted into Test System Table 2 presents the results of the analysis applied to each of the test article designs. Each of the domains are...the lowest integrities. Based on the analysis, the DI metric shows measurable differentiation between all five Test Article Error Location Error

Flash Study Analysis and the Music Learning Pro-Files Project

ERIC Educational Resources Information Center

Cremata, Radio; Pignato, Joseph; Powell, Bryan; Smith, Gareth Dylan

2016-01-01

This paper introduces the Music Learning Profiles Project, and its methodological approach, flash study analysis. Flash study analysis is a method that draws heavily on extant qualitative approaches to education research, to develop broad understandings of music learning in diverse contexts. The Music Learning Profiles Project (MLPP) is an…

Analysis of BSRT Profiles in the LHC at Injection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fitterer, M.; Stancari, G.; Papadopoulou, S.

The beam synchrotron radiation telescope (BSRT) at the LHC allows to take profiles of the transverse beam distribution, which can provide useful additional insight in the evolution of the transverse beam distribution. A python class has been developed [1], which allows to read in the BSRT profiles, usually stored in binary format, run different analysis tools and generate plots of the statistical parameters and profiles as well as videos of the the profiles. The detailed analysis will be described in this note. The analysis is based on the data obtained at injection energy (450 GeV) during MD1217 [2] and MD1415more » [3] which will be also used as illustrative example. A similar approach is also taken with a MATLAB based analysis described in [4].« less

MiniSODAR(TradeMark) Evaluation

NASA Technical Reports Server (NTRS)

Short, David A.; Wheeler, Mark M.

2003-01-01

This report describes results of the AMU's Instrumentation and Measurement task for evaluation of the Doppler miniSODAR(TradeMark) System (DmSS). The DmSS is an acoustic wind profiler providing high resolution data to a height of approx. 410 ft. The Boeing Company installed a DmSS near Space Launch Complex 37 in mid-2002 as a substitute for a tall wind tower and plans to use DmSS data for the analysis and forecasting of winds during ground and launch operations. Peak wind speed data are of particular importance to Launch Weather Officers of the 45th Weather Squadron for evaluating user Launch Commit Criteria. The AMU performed a comparative analysis of wind data between the DmSS and nearby wind towers from August 2002 to July 2003. The DmSS vertical profile of average wind speed showed good agreement with the wind towers. However, the DMSS peak wind speeds were higher, on average, than the wind tower peak wind speeds by about 25%. A statistical model of an idealized Doppler profiler was developed and it predicted that average wind speeds would be well determined but peak wind speeds would be over-estimated due to an under-specification of vertical velocity variations in the atmosphere over the Profiler.

A New System to Monitor Data Analyses and Results of Physics Data Validation Between Pulses at DIII-D

NASA Astrophysics Data System (ADS)

Flanagan, S.; Schachter, J. M.; Schissel, D. P.

2001-10-01

A Data Analysis Monitoring (DAM) system has been developed to monitor between pulse physics analysis at the DIII-D National Fusion Facility. The system allows for rapid detection of discrepancies in diagnostic measurements or the results from physics analysis codes. This enables problems to be detected and possibly fixed between pulses as opposed to after the experimental run has concluded thus increasing the efficiency of experimental time. An example of a consistency check is comparing the stored energy from integrating the measured kinetic profiles to that calculated from magnetic measurements by EFIT. This new system also tracks the progress of MDSplus dispatching of software for data analysis and the loading of analyzed data into MDSplus. DAM uses a Java Servlet to receive messages, Clips to implement expert system logic, and displays its results to multiple web clients via HTML. If an error is detected by DAM, users can view more detailed information so that steps can be taken to eliminate the error for the next pulse. A demonstration of this system including a simulated DIII-D pulse cycle will be presented.

Profiles of family needs of children and youth with cerebral palsy.

PubMed

Almasri, N; Palisano, R J; Dunst, C; Chiarello, L A; O'Neil, M E; Polansky, M

2012-11-01

To identify profiles of family needs of families of children and youth with cerebral palsy (CP), and determine whether profile membership is related to child, family and service characteristics. Participants were mostly mothers (80%) of 579 children and youth with CP. A family member completed modified version of the Family Needs Survey and questionnaires about their child, family and services. Research assistants determined the Gross Motor Function Classification System levels. K-means cluster analysis identified profiles of needs. Cluster membership was analysed to examine differences in clusters based on selected characteristics. Four profiles of needs were identified: Low needs, Needs related to community and financial resources, Needs related to child health condition and High needs. Profile membership was differentiated based on child/youth gross motor function, adaptive behaviour, family relationships, family income, access and effort to co-ordinate services. Despite heterogeneity among individuals with CP and their families, four profiles of family needs were identified. In total, 51% of families had low needs suggesting that they are effectively managing their children's health conditions while 11% of families had high needs that may require high levels of services and supports. Service providers are encouraged to partner with families, provide anticipatory guidance and co-ordinate services. © 2011 Blackwell Publishing Ltd.

Effects of Histidine Supplementation on Global Serum and Urine 1H NMR-based Metabolomics and Serum Amino Acid Profiles in Obese Women from a Randomized Controlled Study.

PubMed

Du, Shanshan; Sun, Shuhong; Liu, Liyan; Zhang, Qiao; Guo, Fuchuan; Li, Chunlong; Feng, Rennan; Sun, Changhao

2017-06-02

The aim of current study was to investigate the metabolic changes associated with histidine supplementation in serum and urine metabolic signatures and serum amino acid (AA) profiles. Serum and urine 1 H NMR-based metabolomics and serum AA profiles were employed in 32 and 37 obese women with metabolic syndrome (MetS) intervened with placebo or histidine for 12 weeks. Multivariable statistical analysis were conducted to define characteristic metabolites. In serum 1 H NMR metabolic profiles, increases in histidine, glutamine, aspartate, glycine, choline, and trimethylamine-N-oxide (TMAO) were observed; meanwhile, decreases in cholesterol, triglycerides, fatty acids and unsaturated lipids, acetone, and α/β-glucose were exhibited after histidine supplement. In urine 1 H NMR metabolic profiles, citrate, creatinine/creatine, methylguanidine, and betaine + TMAO were higher, while hippurate was lower in histidine supplement group. In serum AA profiles, 10 AAs changed after histidine supplementation, including increased histidine, glycine, alanine, lysine, asparagine, and tyrosine and decreased leucine, isoleucine, ornithine, and citrulline. The study showed a systemic metabolic response in serum and urine metabolomics and AA profiles to histidine supplementation, showing significantly changed metabolism in AAs, lipid, and glucose in obese women with MetS.

Unsupervised User Similarity Mining in GSM Sensor Networks

PubMed Central

Shad, Shafqat Ali; Chen, Enhong

2013-01-01

Mobility data has attracted the researchers for the past few years because of its rich context and spatiotemporal nature, where this information can be used for potential applications like early warning system, route prediction, traffic management, advertisement, social networking, and community finding. All the mentioned applications are based on mobility profile building and user trend analysis, where mobility profile building is done through significant places extraction, user's actual movement prediction, and context awareness. However, significant places extraction and user's actual movement prediction for mobility profile building are a trivial task. In this paper, we present the user similarity mining-based methodology through user mobility profile building by using the semantic tagging information provided by user and basic GSM network architecture properties based on unsupervised clustering approach. As the mobility information is in low-level raw form, our proposed methodology successfully converts it to a high-level meaningful information by using the cell-Id location information rather than previously used location capturing methods like GPS, Infrared, and Wifi for profile mining and user similarity mining. PMID:23576905

COOL CORE CLUSTERS FROM COSMOLOGICAL SIMULATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rasia, E.; Borgani, S.; Murante, G.

2015-11-01

We present results obtained from a set of cosmological hydrodynamic simulations of galaxy clusters, aimed at comparing predictions with observational data on the diversity between cool-core (CC) and non-cool-core (NCC) clusters. Our simulations include the effects of stellar and active galactic nucleus (AGN) feedback and are based on an improved version of the smoothed particle hydrodynamics code GADGET-3, which ameliorates gas mixing and better captures gas-dynamical instabilities by including a suitable artificial thermal diffusion. In this Letter, we focus our analysis on the entropy profiles, the primary diagnostic we used to classify the degree of cool-coreness of clusters, and themore » iron profiles. In keeping with observations, our simulated clusters display a variety of behaviors in entropy profiles: they range from steadily decreasing profiles at small radii, characteristic of CC systems, to nearly flat core isentropic profiles, characteristic of NCC systems. Using observational criteria to distinguish between the two classes of objects, we find that they occur in similar proportions in both simulations and observations. Furthermore, we also find that simulated CC clusters have profiles of iron abundance that are steeper than those of NCC clusters, which is also in agreement with observational results. We show that the capability of our simulations to generate a realistic CC structure in the cluster population is due to AGN feedback and artificial thermal diffusion: their combined action allows us to naturally distribute the energy extracted from super-massive black holes and to compensate for the radiative losses of low-entropy gas with short cooling time residing in the cluster core.« less

Cool Core Clusters from Cosmological Simulations

NASA Astrophysics Data System (ADS)

Rasia, E.; Borgani, S.; Murante, G.; Planelles, S.; Beck, A. M.; Biffi, V.; Ragone-Figueroa, C.; Granato, G. L.; Steinborn, L. K.; Dolag, K.

2015-11-01

We present results obtained from a set of cosmological hydrodynamic simulations of galaxy clusters, aimed at comparing predictions with observational data on the diversity between cool-core (CC) and non-cool-core (NCC) clusters. Our simulations include the effects of stellar and active galactic nucleus (AGN) feedback and are based on an improved version of the smoothed particle hydrodynamics code GADGET-3, which ameliorates gas mixing and better captures gas-dynamical instabilities by including a suitable artificial thermal diffusion. In this Letter, we focus our analysis on the entropy profiles, the primary diagnostic we used to classify the degree of cool-coreness of clusters, and the iron profiles. In keeping with observations, our simulated clusters display a variety of behaviors in entropy profiles: they range from steadily decreasing profiles at small radii, characteristic of CC systems, to nearly flat core isentropic profiles, characteristic of NCC systems. Using observational criteria to distinguish between the two classes of objects, we find that they occur in similar proportions in both simulations and observations. Furthermore, we also find that simulated CC clusters have profiles of iron abundance that are steeper than those of NCC clusters, which is also in agreement with observational results. We show that the capability of our simulations to generate a realistic CC structure in the cluster population is due to AGN feedback and artificial thermal diffusion: their combined action allows us to naturally distribute the energy extracted from super-massive black holes and to compensate for the radiative losses of low-entropy gas with short cooling time residing in the cluster core.

Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

PubMed Central

Chiu, Isaac M; Barrett, Lee B; Williams, Erika K; Strochlic, David E; Lee, Seungkyu; Weyer, Andy D; Lou, Shan; Bryman, Gregory S; Roberson, David P; Ghasemlou, Nader; Piccoli, Cara; Ahat, Ezgi; Wang, Victor; Cobos, Enrique J; Stucky, Cheryl L; Ma, Qiufu; Liberles, Stephen D; Woolf, Clifford J

2014-01-01

The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4+SNS-Cre/TdTomato+, 2) IB4−SNS-Cre/TdTomato+, and 3) Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation. DOI: http://dx.doi.org/10.7554/eLife.04660.001 PMID:25525749

Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles* #

PubMed Central

Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-yu; Zhang, Xiao-mei; Song, Da-feng; Zhang, Chen

2016-01-01

Objective: In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. Methods: The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). Results: We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Conclusions: Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate. PMID:27487802

Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles.

PubMed

Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-Yu; Zhang, Xiao-Mei; Song, Da-Feng; Zhang, Chen

2016-08-01

In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate.

Numerical Analysis of Infiltration Into a Sand Profile Bounded by a Capillary Fringe

NASA Astrophysics Data System (ADS)

Curtis, Alan A.; Watson, Keith K.

1980-04-01

The rapid response sometimes observed in a tile drain system following surface ponding of water is discussed in terms of the air compressibility effect. An earlier numerical study describing water movement into a bounded profile with a lower boundary impermeable to the passage of both air and water is reviewed with particular reference to the validity of the time-dependent boundary condition transformation used in simulating the inhibiting effects of the air pressure increase on infiltration. The extension of the transformation approach to a profile bounded by a capillary fringe is then considered in detail, and the results of numerical analyses are presented for infiltration into two columns of a fine sand initially in hydraulic equilibrium from a prior gravity drainage regime. The shorter column develops a steady state flow condition at short times which is consistent with earlier experimental findings. In contrast, the pressure of the entrapped air in the longer column gradually increases as infiltration proceeds until the analysis is terminated when air escape through the lower boundary is imminent.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christoph, G.G; Jackson, K.A.; Neuman, M.C.

An effective method for detecting computer misuse is the automatic auditing and analysis of on-line user activity. This activity is reflected in the system audit record, by changes in the vulnerability posture of the system configuration, and in other evidence found through active testing of the system. In 1989 we started developing an automatic misuse detection system for the Integrated Computing Network (ICN) at Los Alamos National Laboratory. Since 1990 this system has been operational, monitoring a variety of network systems and services. We call it the Network Anomaly Detection and Intrusion Reporter, or NADIR. During the last year andmore » a half, we expanded NADIR to include processing of audit and activity records for the Cray UNICOS operating system. This new component is called the UNICOS Real-time NADIR, or UNICORN. UNICORN summarizes user activity and system configuration information in statistical profiles. In near real-time, it can compare current activity to historical profiles and test activity against expert rules that express our security policy and define improper or suspicious behavior. It reports suspicious behavior to security auditors and provides tools to aid in follow-up investigations. UNICORN is currently operational on four Crays in Los Alamos` main computing network, the ICN.« less

Development Status: Automation Advanced Development Space Station Freedom Electric Power System

NASA Technical Reports Server (NTRS)

Dolce, James L.; Kish, James A.; Mellor, Pamela A.

1990-01-01

Electric power system automation for Space Station Freedom is intended to operate in a loop. Data from the power system is used for diagnosis and security analysis to generate Operations Management System (OMS) requests, which are sent to an arbiter, which sends a plan to a commander generator connected to the electric power system. This viewgraph presentation profiles automation software for diagnosis, scheduling, and constraint interfaces, and simulation to support automation development. The automation development process is diagrammed, and the process of creating Ada and ART versions of the automation software is described.

Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish

PubMed Central

2010-01-01

Background Systematic research on fish immunogenetics is indispensable in understanding the origin and evolution of immune systems. This has long been a challenging task because of the limited number of deep sequencing technologies and genome backgrounds of non-model fish available. The newly developed Solexa/Illumina RNA-seq and Digital gene expression (DGE) are high-throughput sequencing approaches and are powerful tools for genomic studies at the transcriptome level. This study reports the transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus using RNA-seq and DGE in an attempt to gain insights into the immunogenetics of marine fish. Results RNA-seq analysis generated 169,950 non-redundant consensus sequences, among which 48,987 functional transcripts with complete or various length encoding regions were identified. More than 52% of these transcripts are possibly involved in approximately 219 known metabolic or signalling pathways, while 2,673 transcripts were associated with immune-relevant genes. In addition, approximately 8% of the transcripts appeared to be fish-specific genes that have never been described before. DGE analysis revealed that the host transcriptome profile of Vibrio harveyi-challenged L. japonicus is considerably altered, as indicated by the significant up- or down-regulation of 1,224 strong infection-responsive transcripts. Results indicated an overall conservation of the components and transcriptome alterations underlying innate and adaptive immunity in fish and other vertebrate models. Analysis suggested the acquisition of numerous fish-specific immune system components during early vertebrate evolution. Conclusion This study provided a global survey of host defence gene activities against bacterial challenge in a non-model marine fish. Results can contribute to the in-depth study of candidate genes in marine fish immunity, and help improve current understanding of host-pathogen interactions and evolutionary history of immunogenetics from fish to mammals. PMID:20707909

Estimating the Effects of Damping Treatments on the Vibration of Complex Structures

DTIC Science & Technology

2012-09-26

26 4.3 Literature review 26 4.3.1 CLD Theory 26 4.3.2 Temperature Profiling 28 4.4 Constrained Layer Damping Analysis 29 4.5 Results 35...Coordinate systems and length scales are noted. Constraining layer, viscoelastic layer and base layer pertain to the nomenclature used through CLD ...for vibrational damping 4.1 Introduction Constrained layer damping ( CLD ) treatment systems are widely used in complex structures to dissipate

HD 156324: A Tidally Locked Magnetic SB3 With an Orbitally Disrupted Centrifugal Magnetosphere

NASA Astrophysics Data System (ADS)

Shultz, M.; Rivinius, Th.; Wade, G. A.; Alecian, E.; Kochukhov, O.; BinaMIcS Collaboration

2018-01-01

Period analysis of radial velocity, equivalent width, and magnetic measurements of the SB3 system HD 156324 yield identical results in all cases, indicating the system is tidally locked with orbital and rotational periods of 1.58 d. Its Hα emission profile exhibits marked morphological departures from the usual pattern observed amongst magnetic B-type stars, which can plausibly be ascribed to tidal disruption of the gravitocentrifugal potential.

Assessment of Virginia's hybrid South Dakota road profiling system.

DOT National Transportation Integrated Search

1996-01-01

South Dakota Road Profiling (SDRP) systems have been widely sanctioned for use in assessing road roughness and rutting at highway speeds. Traditionally, these high-speed profiling systems have been built around ultrasonic height sensors. More recentl...

Nuclear magnetic relaxation by the dipolar EMOR mechanism: Multi-spin systems

NASA Astrophysics Data System (ADS)

Chang, Zhiwei; Halle, Bertil

2017-08-01

In aqueous systems with immobilized macromolecules, including biological tissues, the longitudinal spin relaxation of water protons is primarily induced by exchange-mediated orientational randomization (EMOR) of intra- and intermolecular magnetic dipole-dipole couplings. Starting from the stochastic Liouville equation, we have previously developed a rigorous EMOR relaxation theory for dipole-coupled two-spin and three-spin systems. Here, we extend the stochastic Liouville theory to four-spin systems and use these exact results as a guide for constructing an approximate multi-spin theory, valid for spin systems of arbitrary size. This so-called generalized stochastic Redfield equation (GSRE) theory includes the effects of longitudinal-transverse cross-mode relaxation, which gives rise to an inverted step in the relaxation dispersion profile, and coherent spin mode transfer among solid-like spins, which may be regarded as generalized spin diffusion. The GSRE theory is compared to an existing theory, based on the extended Solomon equations, which does not incorporate these phenomena. Relaxation dispersion profiles are computed from the GSRE theory for systems of up to 16 protons, taken from protein crystal structures. These profiles span the range from the motional narrowing limit, where the coherent mode transfer plays a major role, to the ultra-slow motion limit, where the zero-field rate is closely related to the strong-collision limit of the dipolar relaxation rate. Although a quantitative analysis of experimental data is beyond the scope of this work, it is clear from the magnitude of the predicted relaxation rate and the shape of the relaxation dispersion profile that the dipolar EMOR mechanism is the principal cause of water-1H low-field longitudinal relaxation in aqueous systems of immobilized macromolecules, including soft biological tissues. The relaxation theory developed here therefore provides a basis for molecular-level interpretation of endogenous soft-tissue image contrast obtained by the emerging low-field magnetic resonance imaging techniques.

C-Band Airport Surface Communications System Engineering-Initial High-Level Safety Risk Assessment and Mitigation

NASA Technical Reports Server (NTRS)

Zelkin, Natalie; Henriksen, Stephen

2011-01-01

This document is being provided as part of ITT's NASA Glenn Research Center Aerospace Communication Systems Technical Support (ACSTS) contract: "New ATM Requirements--Future Communications, C-Band and L-Band Communications Standard Development." ITT has completed a safety hazard analysis providing a preliminary safety assessment for the proposed C-band (5091- to 5150-MHz) airport surface communication system. The assessment was performed following the guidelines outlined in the Federal Aviation Administration Safety Risk Management Guidance for System Acquisitions document. The safety analysis did not identify any hazards with an unacceptable risk, though a number of hazards with a medium risk were documented. This effort represents an initial high-level safety hazard analysis and notes the triggers for risk reassessment. A detailed safety hazards analysis is recommended as a follow-on activity to assess particular components of the C-band communication system after the profile is finalized and system rollout timing is determined. A security risk assessment has been performed by NASA as a parallel activity. While safety analysis is concerned with a prevention of accidental errors and failures, the security threat analysis focuses on deliberate attacks. Both processes identify the events that affect operation of the system; and from a safety perspective the security threats may present safety risks.

Gene Expression Profiling of Peripheral Blood From Kidney Transplant Recipients for the Early Detection of Digestive System Cancer.

PubMed

Kusaka, M; Okamoto, M; Takenaka, M; Sasaki, H; Fukami, N; Kataoka, K; Ito, T; Kenmochi, T; Hoshinaga, K; Shiroki, R

2017-06-01

Kidney transplant recipients are at increased risk of developing cancer in comparison with the general population. To effectively manage post-transplantation malignancies, it is essential to proactively monitor patients. A long-term intensive screening program was associated with a reduced incidence of cancer after transplantation. This study evaluated the usefulness of the gene expression profiling of peripheral blood samples obtained from kidney transplant patients and adopted a screening test for detecting cancer of the digestive system (gastric, colon, pancreas, and biliary tract). Nineteen patients were included in this study and a total of 53 gene expression screening tests were performed. The gene expression profiles of blood-delivered total RNA and whole genome human gene expression profiles were obtained. We investigated the expression levels of 2665 genes associated with digestive cancers and counted the number of genes in which expression was altered. A hierarchical clustering analysis was also performed. The final prediction of the cancer possibility was determined according to an algorithm. The number of genes in which expression was altered was significantly increased in the kidney transplant recipients in comparison with the general population (1091 ± 63 vs 823 ± 94; P = .0024). The number of genes with altered expression decreased after the induction of mechanistic target of rapamycin (mTOR) inhibitor (1484 ± 227 vs 883 ± 154; P = .0439). No cases of possible digestive cancer were detected in this study period. The gene expression profiling of peripheral blood samples may be a useful and noninvasive diagnostic tool that allows for the early detection of cancer of the digestive system. Copyright © 2017 Elsevier Inc. All rights reserved.

Stress management at the worksite: reversal of symptoms profile and cardiovascular dysregulation.

PubMed

Lucini, Daniela; Riva, Silvano; Pizzinelli, Paolo; Pagani, Massimo

2007-02-01

Work stress may increase cardiovascular risk either indirectly, by inducing unhealthy life styles, or directly, by affecting the autonomic nervous system and arterial pressure. We hypothesized that, before any apparent sign of disease, work-related stress is already accompanied by alterations of RR variability profile and that a simple onsite stress management program based on cognitive restructuring and relaxation training could reduce the level of stress symptoms, revert stress-related autonomic nervous system dysregulation, and lower arterial pressure. We compared 91 white-collar workers, enrolled at a time of work downsizing (hence, in a stress condition), with 79 healthy control subjects. Psychological profiles were assessed by questionnaires and autonomic nervous system regulation by spectral analysis of RR variability. We also tested a simple onsite stress management program (cognitive restructuring and relaxation training) in a subgroup of workers compared with a sham subgroup (sham program). Workers presented an elevated level of stress-related symptoms and an altered variability profile as compared with control subjects (low-frequency component of RR variability was, respectively, 65.2+/-2 versus 55.3+/-2 normalized units; P<0.001; opposite changes were observed for the high-frequency component). These alterations were largely reverted (low-frequency component of RR variability from 63.6+/-3.9 to 49.3+/-3 normalized units; P<0.001) by the stress management program, which also slightly lowered systolic arterial pressure. No changes were observed in the sham program group. This noninvasive study indicates that work stress is associated with unpleasant symptoms and with an altered autonomic profile and suggests that a stress management program could be implemented at the worksite, with possible preventive advantages for hypertension.

Conceptual Analysis of System Average Water Stability

NASA Astrophysics Data System (ADS)

Zhang, H.

2016-12-01

Averaging over time and area, the precipitation in an ecosystem (SAP - system average precipitation) depends on the average surface temperature and relative humidity (RH) in the system if uniform convection is assumed. RH depends on the evapotranspiration of the system (SAE - system average evapotranspiration). There is a non-linear relationship between SAP and SAE. Studying this relationship can lead mechanistic understanding of the ecosystem health status and trend under different setups. If SAP is higher than SAE, the system will have a water runoff which flows out through rivers. If SAP is lower than SAE, irrigation is needed to maintain the vegetation status. This presentation will give a conceptual analysis of the stability in this relationship under different assumed areas, water or forest coverages, elevations and latitudes. This analysis shows that desert is a stable system. Water circulation in basins is also stabilized at a specific SAP based on the basin profile. It further shows that deforestation will reduce SAP, and can flip the system to an irrigation required status. If no irrigation is provided, the system will automatically reduce to its stable point - desert, which is extremely difficult to turn around.

Gene integrated set profile analysis: a context-based approach for inferring biological endpoints

PubMed Central

Kowalski, Jeanne; Dwivedi, Bhakti; Newman, Scott; Switchenko, Jeffery M.; Pauly, Rini; Gutman, David A.; Arora, Jyoti; Gandhi, Khanjan; Ainslie, Kylie; Doho, Gregory; Qin, Zhaohui; Moreno, Carlos S.; Rossi, Michael R.; Vertino, Paula M.; Lonial, Sagar; Bernal-Mizrachi, Leon; Boise, Lawrence H.

2016-01-01

The identification of genes with specific patterns of change (e.g. down-regulated and methylated) as phenotype drivers or samples with similar profiles for a given gene set as drivers of clinical outcome, requires the integration of several genomic data types for which an ‘integrate by intersection’ (IBI) approach is often applied. In this approach, results from separate analyses of each data type are intersected, which has the limitation of a smaller intersection with more data types. We introduce a new method, GISPA (Gene Integrated Set Profile Analysis) for integrated genomic analysis and its variation, SISPA (Sample Integrated Set Profile Analysis) for defining respective genes and samples with the context of similar, a priori specified molecular profiles. With GISPA, the user defines a molecular profile that is compared among several classes and obtains ranked gene sets that satisfy the profile as drivers of each class. With SISPA, the user defines a gene set that satisfies a profile and obtains sample groups of profile activity. Our results from applying GISPA to human multiple myeloma (MM) cell lines contained genes of known profiles and importance, along with several novel targets, and their further SISPA application to MM coMMpass trial data showed clinical relevance. PMID:26826710

Serum Biochemical Phenotypes in the Domestic Dog

PubMed Central

Chang, Yu-Mei; Hadox, Erin; Szladovits, Balazs; Garden, Oliver A.

2016-01-01

The serum or plasma biochemical profile is essential in the diagnosis and monitoring of systemic disease in veterinary medicine, but current reference intervals typically take no account of breed-specific differences. Breed-specific hematological phenotypes have been documented in the domestic dog, but little has been published on serum biochemical phenotypes in this species. Serum biochemical profiles of dogs in which all measurements fell within the existing reference intervals were retrieved from a large veterinary database. Serum biochemical profiles from 3045 dogs were retrieved, of which 1495 had an accompanying normal glucose concentration. Sixty pure breeds plus a mixed breed control group were represented by at least 10 individuals. All analytes, except for sodium, chloride and glucose, showed variation with age. Total protein, globulin, potassium, chloride, creatinine, cholesterol, total bilirubin, ALT, CK, amylase, and lipase varied between sexes. Neutering status significantly impacted all analytes except albumin, sodium, calcium, urea, and glucose. Principal component analysis of serum biochemical data revealed 36 pure breeds with distinctive phenotypes. Furthermore, comparative analysis identified 23 breeds with significant differences from the mixed breed group in all biochemical analytes except urea and glucose. Eighteen breeds were identified by both principal component and comparative analysis. Tentative reference intervals were generated for breeds with a distinctive phenotype identified by comparative analysis and represented by at least 120 individuals. This is the first large-scale analysis of breed-specific serum biochemical phenotypes in the domestic dog and highlights potential genetic components of biochemical traits in this species. PMID:26919479

Transcriptomic and metabolomic profiles of Chinese citrus fly, Bactrocera minax (Diptera: Tephritidae), along with pupal development provide insight into diapause program

PubMed Central

Fan, Huan; Xiong, Ke-Cai; Liu, Ying-Hong

2017-01-01

The Chinese citrus fly, Bactrocera minax (Enderlein), is a devastating citrus pest in Asia. This univoltine insect enters obligatory pupal diapause in each generation, while little is known about the course and the molecular mechanisms of diapause. In this study, the course of diapause was determined by measuring the respiratory rate throughout the pupal stage. In addition, the variation of transcriptomic and metabolomic profiles of pupae at five developmental stages (pre-, early-, middle-, late-, and post-diapause) were evaluated by next-generation sequencing technology and 1H nuclear magnetic resonance spectroscopy (NMR), respectively. A total of 4,808 genes were significantly altered in ten pairwise comparisons, representing major shifts in metabolism and signal transduction as well as endocrine system and digestive system. Gene expression profiles were validated by qRT-PCR analysis. In addition, 48 metabolites were identified and quantified by 1H NMR. Nine of which significantly contributed to the variation in the metabolomic profiles, especially proline and trehalose. Moreover, the samples collected within diapause maintenance (early-, middle-, and late-diapause) only exhibited marginal transcriptomic and metabolomic variation with each other. These findings greatly improve our understanding of B. minax diapause and lay the foundation for further pertinent studies. PMID:28704500

Metabolic Profiling of Adiponectin Levels in Adults: Mendelian Randomization Analysis.

PubMed

Borges, Maria Carolina; Barros, Aluísio J D; Ferreira, Diana L Santos; Casas, Juan Pablo; Horta, Bernardo Lessa; Kivimaki, Mika; Kumari, Meena; Menon, Usha; Gaunt, Tom R; Ben-Shlomo, Yoav; Freitas, Deise F; Oliveira, Isabel O; Gentry-Maharaj, Aleksandra; Fourkala, Evangelia; Lawlor, Debbie A; Hingorani, Aroon D

2017-12-01

Adiponectin, a circulating adipocyte-derived protein, has insulin-sensitizing, anti-inflammatory, antiatherogenic, and cardiomyocyte-protective properties in animal models. However, the systemic effects of adiponectin in humans are unknown. Our aims were to define the metabolic profile associated with higher blood adiponectin concentration and investigate whether variation in adiponectin concentration affects the systemic metabolic profile. We applied multivariable regression in ≤5909 adults and Mendelian randomization (using cis -acting genetic variants in the vicinity of the adiponectin gene as instrumental variables) for analyzing the causal effect of adiponectin in the metabolic profile of ≤37 545 adults. Participants were largely European from 6 longitudinal studies and 1 genome-wide association consortium. In the multivariable regression analyses, higher circulating adiponectin was associated with higher high-density lipoprotein lipids and lower very-low-density lipoprotein lipids, glucose levels, branched-chain amino acids, and inflammatory markers. However, these findings were not supported by Mendelian randomization analyses for most metabolites. Findings were consistent between sexes and after excluding high-risk groups (defined by age and occurrence of previous cardiovascular event) and 1 study with admixed population. Our findings indicate that blood adiponectin concentration is more likely to be an epiphenomenon in the context of metabolic disease than a key determinant. © 2017 The Authors.

A Direct Detection 1.6μm DIAL with Three Wavelengths for Measurements of Vertical CO2 Concentration and Temperature Profiles in the Atmosphere

NASA Astrophysics Data System (ADS)

Nagasawa, C.; Abo, M.; Shibata, Y.; Nagai, T.; Tsukamoto, M.

2012-12-01

We report the new 1.6 μm DIAL system that can measure the temperature profiles with the CO2 concentration profiles in the atmosphere because of improvement of measurement accuracy of the CO2 density and mixing ratio (ppm). We have developed a direct detection 1.6 μm differential absorption lidar (DIAL) technique to perform range-resolved measurements of vertical CO2 concentration profiles in the atmosphere [Sakaizawa et al. 2009]. Our 1.6 μm DIAL system consists of the Optical Parametric Generator (OPG) transmitter that excited by the LD pumped Nd:YAG laser with high repetition rate (500 Hz) and the receiving optics that included the near-infrared photomultiplier tube with high quantum efficiency operating at the photon counting mode and the telescope with larger aperture than that of the coherent detection method. Laser beams of three wavelengths around a CO2 absorption line is transmitted alternately to the atmosphere for measurements of CO2 concentration and temperature profiles. Moreover, a few retrieval algorithms of CO2-DIAL are also performed for improvement of measurement accuracy. The accurate vertical CO2 profiles in the troposphere are highly desirable in the inverse techniques to improve quantification and understanding of the global budget of CO2 and also global climate changes [Stephens et al. 2007]. In comparison with the ground-based monitoring network, CO2 measurements for vertical profiles in the troposphere have been limited to campaign-style aircraft and commercial airline observations with the limited spatial and temporal coverage. This work was financially supported by the System Development Program for Advanced Measurement and Analysis of the Japan Science and Technology Agency. References Sakaizawa, D., C. Nagasawa, T. Nagai, M. Abo, Y. Shibata, H. Nagai, M. Nakazato, and T. Sakai, Development of a 1.6μm differential absorption lidar with a quasi-phase-matching optical parametric oscillator and photon-counting detector for the vertical CO2 profile, Applied Optics, Vol.48, No.4, pp.748-757, 2009. Stephens, B. B. et al., Weak Northern and Strong Tropical Land Carbon Uptake from Vertical Profiles of Atmospheric CO2, Science 316, pp.1732-1735, 2007.

High-spatial-resolution passive microwave sounding systems

NASA Technical Reports Server (NTRS)

Staelin, D. H.; Rosenkranz, P. W.

1994-01-01

The principal contributions of this combined theoretical and experimental effort were to advance and demonstrate new and more accurate techniques for sounding atmospheric temperature, humidity, and precipitation profiles at millimeter wavelengths, and to improve the scientific basis for such soundings. Some of these techniques are being incorporated in both research and operational systems. Specific results include: (1) development of the MIT Microwave Temperature Sounder (MTS), a 118-GHz eight-channel imaging spectrometer plus a switched-frequency spectrometer near 53 GHz, for use on the NASA ER-2 high-altitude aircraft, (2) conduct of ER-2 MTS missions in multiple seasons and locations in combination with other instruments, mapping with unprecedented approximately 2-km lateral resolution atmospheric temperature and precipitation profiles, atmospheric transmittances (at both zenith and nadir), frontal systems, and hurricanes, (3) ground based 118-GHz 3-D spectral images of wavelike structure within clouds passing overhead, (4) development and analysis of approaches to ground- and space-based 5-mm wavelength sounding of the upper stratosphere and mesosphere, which supported the planning of improvements to operational weather satellites, (5) development of improved multidimensional and adaptive retrieval methods for atmospheric temperature and humidity profiles, (6) development of combined nonlinear and statistical retrieval techniques for 183-GHz humidity profile retrievals, (7) development of nonlinear statistical retrieval techniques for precipitation cell-top altitudes, and (8) numerical analyses of the impact of remote sensing data on the accuracy of numerical weather predictions; a 68-km gridded model was used to study the spectral properties of error growth.

Pattern Analysis and Decision Support for Cancer through Clinico-Genomic Profiles

NASA Astrophysics Data System (ADS)

Exarchos, Themis P.; Giannakeas, Nikolaos; Goletsis, Yorgos; Papaloukas, Costas; Fotiadis, Dimitrios I.

Advances in genome technology are playing a growing role in medicine and healthcare. With the development of new technologies and opportunities for large-scale analysis of the genome, genomic data have a clear impact on medicine. Cancer prognostics and therapeutics are among the first major test cases for genomic medicine, given that all types of cancer are related with genomic instability. In this paper we present a novel system for pattern analysis and decision support in cancer. The system integrates clinical data from electronic health records and genomic data. Pattern analysis and data mining methods are applied to these integrated data and the discovered knowledge is used for cancer decision support. Through this integration, conclusions can be drawn for early diagnosis, staging and cancer treatment.

Ft. McHenry tunnel study: Source profiles and mercury emissions from diesel and gasoline powered vehicles

NASA Astrophysics Data System (ADS)

Landis, Matthew S.; Lewis, Charles W.; Stevens, Robert K.; Keeler, Gerald J.; Dvonch, J. Timothy; Tremblay, Raphael T.

During the fall of 1998, the US Environmental Protection Agency and the Florida Department of Environmental Protection sponsored a 7-day study at the Ft. McHenry tunnel in Baltimore, MD with the objective of obtaining PM 2.5 vehicle source profiles for use in atmospheric mercury source apportionment studies. PM 2.5 emission profiles from gasoline and diesel powered vehicles were developed from analysis of trace elements, polycyclic aromatic hydrocarbons (PAH), and condensed aliphatic hydrocarbons. PM 2.5 samples were collected using commercially available sampling systems and were extracted and analyzed using conventional well-established methods. Both inorganic and organic profiles were sufficiently unique to mathematically discriminate the contributions from each source type using a chemical mass balance source apportionment approach. However, only the organic source profiles provided unique PAH tracers (e.g., fluoranthene, pyrene, and chrysene) for diesel combustion that could be used to identify source contributions generated using multivariate statistical receptor modeling approaches. In addition, the study found significant emission of gaseous elemental mercury (Hg 0), divalent reactive gaseous mercury (RGM), and particulate mercury (Hg(p)) from gasoline but not from diesel powered motor vehicles. Fuel analysis supported the tunnel measurement results showing that total mercury content in all grades of gasoline (284±108 ng L -1) was substantially higher than total mercury content in diesel fuel (62±37 ng L -1) collected contemporaneously at local Baltimore retailers.

Plasma Free Amino Acid Profiling of Five Types of Cancer Patients and Its Application for Early Detection

PubMed Central

Miyagi, Yohei; Higashiyama, Masahiko; Gochi, Akira; Akaike, Makoto; Ishikawa, Takashi; Miura, Takeshi; Saruki, Nobuhiro; Bando, Etsuro; Kimura, Hideki; Imamura, Fumio; Moriyama, Masatoshi; Ikeda, Ichiro; Chiba, Akihiko; Oshita, Fumihiro; Imaizumi, Akira; Yamamoto, Hiroshi; Miyano, Hiroshi; Horimoto, Katsuhisa; Tochikubo, Osamu; Mitsushima, Toru; Yamakado, Minoru; Okamoto, Naoyuki

2011-01-01

Background Recently, rapid advances have been made in metabolomics-based, easy-to-use early cancer detection methods using blood samples. Among metabolites, profiling of plasma free amino acids (PFAAs) is a promising approach because PFAAs link all organ systems and have important roles in metabolism. Furthermore, PFAA profiles are known to be influenced by specific diseases, including cancers. Therefore, the purpose of the present study was to determine the characteristics of the PFAA profiles in cancer patients and the possibility of using this information for early detection. Methods and Findings Plasma samples were collected from approximately 200 patients from multiple institutes, each diagnosed with one of the following five types of cancer: lung, gastric, colorectal, breast, or prostate cancer. Patients were compared to gender- and age- matched controls also used in this study. The PFAA levels were measured using high-performance liquid chromatography (HPLC)–electrospray ionization (ESI)–mass spectrometry (MS). Univariate analysis revealed significant differences in the PFAA profiles between the controls and the patients with any of the five types of cancer listed above, even those with asymptomatic early-stage disease. Furthermore, multivariate analysis clearly discriminated the cancer patients from the controls in terms of the area under the receiver-operator characteristics curve (AUC of ROC >0.75 for each cancer), regardless of cancer stage. Because this study was designed as case-control study, further investigations, including model construction and validation using cohorts with larger sample sizes, are necessary to determine the usefulness of PFAA profiling. Conclusions These findings suggest that PFAA profiling has great potential for improving cancer screening and diagnosis and understanding disease pathogenesis. PFAA profiles can also be used to determine various disease diagnoses from a single blood sample, which involves a relatively simple plasma assay and imposes a lower physical burden on subjects when compared to existing screening methods. PMID:21915291

A method to identify differential expression profiles of time-course gene data with Fourier transformation.

PubMed

Kim, Jaehee; Ogden, Robert Todd; Kim, Haseong

2013-10-18

Time course gene expression experiments are an increasingly popular method for exploring biological processes. Temporal gene expression profiles provide an important characterization of gene function, as biological systems are both developmental and dynamic. With such data it is possible to study gene expression changes over time and thereby to detect differential genes. Much of the early work on analyzing time series expression data relied on methods developed originally for static data and thus there is a need for improved methodology. Since time series expression is a temporal process, its unique features such as autocorrelation between successive points should be incorporated into the analysis. This work aims to identify genes that show different gene expression profiles across time. We propose a statistical procedure to discover gene groups with similar profiles using a nonparametric representation that accounts for the autocorrelation in the data. In particular, we first represent each profile in terms of a Fourier basis, and then we screen out genes that are not differentially expressed based on the Fourier coefficients. Finally, we cluster the remaining gene profiles using a model-based approach in the Fourier domain. We evaluate the screening results in terms of sensitivity, specificity, FDR and FNR, compare with the Gaussian process regression screening in a simulation study and illustrate the results by application to yeast cell-cycle microarray expression data with alpha-factor synchronization.The key elements of the proposed methodology: (i) representation of gene profiles in the Fourier domain; (ii) automatic screening of genes based on the Fourier coefficients and taking into account autocorrelation in the data, while controlling the false discovery rate (FDR); (iii) model-based clustering of the remaining gene profiles. Using this method, we identified a set of cell-cycle-regulated time-course yeast genes. The proposed method is general and can be potentially used to identify genes which have the same patterns or biological processes, and help facing the present and forthcoming challenges of data analysis in functional genomics.

SysBioCube: A Data Warehouse and Integrative Data Analysis Platform Facilitating Systems Biology Studies of Disorders of Military Relevance

DTIC Science & Technology

2013-12-18

include interactive gene and methylation profiles, interactive heatmaps, cytoscape network views, integrative genomics viewer ( IGV ), and protein-protein...single chart. The website also provides an option to include multiple genes. Integrative Genomics Viewer ( IGV )1, is a high-performance desktop tool for

Serum Metabolomic Profiling and Liver Transcriptomic Analysis Provide Mechanistic Evidence of Ozone (O3)- Induced Systemic Metabolic Impairment

EPA Science Inventory

Recently, air pollution has been linked to insulin resistance and obesity but the mechanisms remain to be elucidated. We have recently shown that acute O3 exposure induces glucose intolerance, hyperglycemia and increases in leptin and epinephrine in rats. Here, we hypothesized th...

Examination of Modeling Languages to Allow Quantitative Analysis for Model-Based Systems Engineering

DTIC Science & Technology

2014-06-01

x THIS PAGE INTENTIONALLY LEFT BLANK xi LIST OF ACRONYMS AND ABBREVIATIONS BOM Base Object Model BPMN Business Process Model & Notation DOD...SysML. There are many variants such as the Unified Profile for DODAF/MODAF (UPDM) and Business Process Model & Notation ( BPMN ) that have origins in

Examining IS Curriculum Profiles and the IS 2010 Model Curriculum Guidelines in AACSB-Accredited Schools

ERIC Educational Resources Information Center

Mills, Robert J.; Velasquez, Nicole Forsgren; Fadel, Kelly J.; Bell, Corbin C.

2012-01-01

The IS 2010 Model Curriculum Guidelines were developed to provide recommendations for standardized information systems curricula while simultaneously allowing for customization within individual programs. While some studies have examined program adherence to the IS 2010 Model Curriculum Guidelines, a more detailed analysis of IS curriculum…

The IEO Data Center Management System: Tools for quality control, analysis and access marine data

NASA Astrophysics Data System (ADS)

Casas, Antonia; Garcia, Maria Jesus; Nikouline, Andrei

2010-05-01

Since 1994 the Data Centre of the Spanish Oceanographic Institute develops system for archiving and quality control of oceanographic data. The work started in the frame of the European Marine Science & Technology Programme (MAST) when a consortium of several Mediterranean Data Centres began to work on the MEDATLAS project. Along the years, old software modules for MS DOS were rewritten, improved and migrated to Windows environment. Oceanographic data quality control includes now not only vertical profiles (mainly CTD and bottles observations) but also time series of currents and sea level observations. New powerful routines for analysis and for graphic visualization were added. Data presented originally in ASCII format were organized recently in an open source MySQL database. Nowadays, the IEO, as part of SeaDataNet Infrastructure, has designed and developed a new information system, consistent with the ISO 19115 and SeaDataNet standards, in order to manage the large and diverse marine data and information originated in Spain by different sources, and to interoperate with SeaDataNet. The system works with data stored in ASCII files (MEDATLAS, ODV) as well as data stored within the relational database. The components of the system are: 1.MEDATLAS Format and Quality Control - QCDAMAR: Quality Control of Marine Data. Main set of tools for working with data presented as text files. Includes extended quality control (searching for duplicated cruises and profiles, checking date, position, ship velocity, constant profiles, spikes, density inversion, sounding, acceptable data, impossible regional values,...) and input/output filters. - QCMareas: A set of procedures for the quality control of tide gauge data according to standard international Sea Level Observing System. These procedures include checking for unexpected anomalies in the time series, interpolation, filtering, computation of basic statistics and residuals. 2. DAMAR: A relational data base (MySql) designed to manage the wide variety of marine information as common vocabularies, Catalogues (CSR & EDIOS), Data and Metadata. 3.Other tools for analysis and data management - Import_DB: Script to import data and metadata from the Medatlas ASCII files into the database. - SelDamar/Selavi: interface with the database for local and web access. Allows selective retrievals applying the criteria introduced by the user, as geographical bounds, data responsible, cruises, platform, time periods, etc. Includes also statistical reference values calculation, plotting of original and mean profiles together with vertical interpolation. - ExtractDAMAR: Script to extract data when they are archived in ASCII files that meet the criteria upon an user request through SelDamar interface and export them in ODV format, making also a unit conversion.

Chip-LC-MS for label-free profiling of human serum.

PubMed

Horvatovich, Peter; Govorukhina, Natalia I; Reijmers, Theo H; van der Zee, Ate G J; Suits, Frank; Bischoff, Rainer

2007-12-01

The discovery of biomarkers in easily accessible body fluids such as serum is one of the most challenging topics in proteomics requiring highly efficient separation and detection methodologies. Here, we present the application of a microfluidics-based LC-MS system (chip-LC-MS) to the label-free profiling of immunodepleted, trypsin-digested serum in comparison to conventional capillary LC-MS (cap-LC-MS). Both systems proved to have a repeatability of approximately 20% RSD for peak area, all sample preparation steps included, while repeatability of the LC-MS part by itself was less than 10% RSD for the chip-LC-MS system. Importantly, the chip-LC-MS system had a two times higher resolution in the LC dimension and resulted in a lower average charge state of the tryptic peptide ions generated in the ESI interface when compared to cap-LC-MS while requiring approximately 30 times less (~5 pmol) sample. In order to characterize both systems for their capability to find discriminating peptides in trypsin-digested serum samples, five out of ten individually prepared, identical sera were spiked with horse heart cytochrome c. A comprehensive data processing methodology was applied including 2-D smoothing, resolution reduction, peak picking, time alignment, and matching of the individual peak lists to create an aligned peak matrix amenable for statistical analysis. Statistical analysis by supervised classification and variable selection showed that both LC-MS systems could discriminate the two sample groups. However, the chip-LC-MS system allowed to assign 55% of the overall signal to selected peaks against 32% for the cap-LC-MS system.

A statistical inference approach for the retrieval of the atmospheric ozone profile from simulated satellite measurements of solar backscattered ultraviolet radiation

NASA Technical Reports Server (NTRS)

Bonavito, N. L.; Gordon, C. L.; Inguva, R.; Serafino, G. N.; Barnes, R. A.

1994-01-01

NASA's Mission to Planet Earth (MTPE) will address important interdisciplinary and environmental issues such as global warming, ozone depletion, deforestation, acid rain, and the like with its long term satellite observations of the Earth and with its comprehensive Data and Information System. Extensive sets of satellite observations supporting MTPE will be provided by the Earth Observing System (EOS), while more specific process related observations will be provided by smaller Earth Probes. MTPE will use data from ground and airborne scientific investigations to supplement and validate the global observations obtained from satellite imagery, while the EOS satellites will support interdisciplinary research and model development. This is important for understanding the processes that control the global environment and for improving the prediction of events. In this paper we illustrate the potential for powerful artificial intelligence (AI) techniques when used in the analysis of the formidable problems that exist in the NASA Earth Science programs and of those to be encountered in the future MTPE and EOS programs. These techniques, based on the logical and probabilistic reasoning aspects of plausible inference, strongly emphasize the synergetic relation between data and information. As such, they are ideally suited for the analysis of the massive data streams to be provided by both MTPE and EOS. To demonstrate this, we address both the satellite imagery and model enhancement issues for the problem of ozone profile retrieval through a method based on plausible scientific inferencing. Since in the retrieval problem, the atmospheric ozone profile that is consistent with a given set of measured radiances may not be unique, an optimum statistical method is used to estimate a 'best' profile solution from the radiances and from additional a priori information.