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At least 541 records · Page 30

Deconvolute individual genomes from metagenome sequences through short read clustering

Metagenome assembly from short next-generation sequencing data is a challenging process due to its large scale and computational complexity. Clustering short reads by species before assembly offers a unique opportunity for parallel downstream assembly of genomes with individualized optimization. However, current read clustering methods suffer either false negative (under-clustering) or false positive (over-clustering) problems. Here we extended our previous read clustering software, SpaRC, by exploiting statistics derived from multiple samples in a dataset to reduce the under-clustering problem. Using synthetic and real-world datasets we demonstrated that this method has the potential to cluster almost all of the short reads from genomes with sufficient sequencing coverage. The improved read clustering in turn leads to improved downstream genome assembly quality.

59 BASIC BIOLOGICAL SCIENCES↗

World Ocean Circulation Experiment

The oceans are an equal partner with the atmosphere in the global climate system. The World Ocean Circulation Experiment is presently being implemented to improve ocean models that are useful for climate prediction both by encouraging more model development but more importantly by providing quality data sets that can be used to force or to validate such models. WOCE is the first oceanographic experiment that plans to generate and to use multiparameter global ocean data sets. In order for WOCE to succeed, oceanographers must establish and learn to use more effective methods of assembling, quality controlling, manipulating and distributing oceanographic data.

Clarke, R. Allyn↗

Construction and Commissioning of Gas Electron Multiplier (GEM) Detectors in Advanced Assembly Design for Low-Energy Applications at High Rates and Analysis of GEM Data From the Muse Experiment at PSI

The search beyond the Standard Model explores dark matter and a potential fifth force. DarkLight@ARIEL investigates the dark photon as a mediator between ordinary and dark matter. The experiment aims to measure the process e?Ta ? e?TaX ? e?Ta(e?e+), by detecting a charged lepton pair in the final state. The spectrometers will be instrumented with Gas Electron Multiplier (GEM) detectors with minimal material budget for tracking. A novel GEM construction technique is employed for fabricating 25 cm x 40 cm GEM detectors, where all layers are mechanically stretched and assembled within a double frame. The dissertation outlines physics motivation, methods, experimental setup, and the role of GEM detectors in DarkLight. A comprehensive discussion on GEM detectors, focusing on the "NS2" technique, including design, parts, assembly, testing, and performance evaluation will be discussed. The proton has garnered attention due to discrepancies in measuring its charge radius using muonic hydrogen and electron-based methods. The 2010 muonic hydrogen measurement of the proton charge radius Rp = 0.84184(67) fm, showed a significant 7? discrepancy compared to the previously known value of Rp = 0.8775(51) fm, giving rise to the proton radius puzzle. Through simultaneous measurements of e ? p and ? ? p elastic scattering, MUSE facilitates a precise and direct comparison of the proton radius. The physics background of the proton radius puzzle, measurement techniques, the approach adopted by the MUSE experiment, its significance and the experimental setup will be discussed. Furthermore, the role of GEM detectors, along with an in-depth analysis of their data and efficiency will be discussed and evaluated.

Mohammed Prem Nazeer, Sahara↗

Make the Most Out of Genome Announcements with KBase

Genomics is a dynamic field driven by new technology, massive growth in data, and changes in how scientists share knowledge. This brings new challenges for researchers looking to maximize the impact of their science and ensure the longevity of their data. These changes are especially relevant for the practice of publishing genome announcements. Genome announcements are meant to share and promote newly sequenced organisms with the larger scientific community. A few decades ago, genome announcements were highly anticipated hallmarks of novel science. But, what was once a publishing coup is now an every day event. It is harder and harder to keep abreast of all the genomes that have been sequenced and promote your own new genomes to get the attention and recognition of your research community. Fortunately, KBase can help construct genomes from your sequencing data, generate reports for your announcement, and promote your data to your research community.

59 BASIC BIOLOGICAL SCIENCES↗

A survey of the state of the art and focused research in range systems, task 2

Many communication, control, and information processing subsystems are modeled by linear systems incorporating tapped delay lines (TDL). Such optimized subsystems result in full precision multiplications in the TDL. In order to reduce complexity and cost in a microprocessor implementation, these multiplications can be replaced by single-shift instructions which are equivalent to powers of two multiplications. Since, in general, the obvious operation of rounding the infinite precision TDL coefficients to the nearest powers of two usually yield quite poor system performance, the optimum powers of two coefficient solution was considered. Detailed explanations on the use of branch-and-bound algorithms for finding the optimum powers of two solutions are given. Specific demonstration of this methodology to the design of a linear data equalizer and its implementation in assembly language on a 8080 microprocessor with a 12 bit A/D converter are reported. This simple microprocessor implementation with optimized TDL coefficients achieves a system performance comparable to the optimum linear equalization with full precision multiplications for an input data rate of 300 baud. The philosophy demonstrated in this implementation is dully applicable to many other microprocessor controlled information processing systems.

Yao, K.↗

Use of CCSDS Packets Over SpaceWire to Control Hardware

For the Lunar Reconnaissance Orbiter, the Command and Data Handling subsystem consisted of several electronic hardware assemblies that were connected with SpaceWire serial links. Electronic hardware would be commanded/controlled and telemetry data was obtained using the SpaceWire links. Prior art focused on parallel data buses and other types of serial buses, which were not compatible with the SpaceWire and the core flight executive (CFE) software bus. This innovation applies to anything that utilizes both SpaceWire networks and the CFE software. The CCSDS (Consultative Committee for Space Data Systems) packet contains predetermined values in its payload fields that electronic hardware attached at the terminus of the SpaceWire node would decode, interpret, and execute. The hardware s interpretation of the packet data would enable the hardware to change its state/configuration (command) or generate status (telemetry). The primary purpose is to provide an interface that is compatible with the hardware and the CFE software bus. By specifying the format of the CCSDS packet, it is possible to specify how the resulting hardware is to be built (in terms of digital logic) that results in a hardware design that can be controlled by the CFE software bus in the final application

Haddad, Omar↗

JPL pyro shock test approaches and results

This paper presents the overall approach at JPL in performing spacecraft pyrotechnic shock qualification testing. Initially, the assembly shock requirements are developed early in the program based on previous spacecraft test experience and data. Pyrotechnic device development testing firings and spacecraft Development Test Model (DTM) pyro firings are then conducted to verify the adequacy of the assembly shock requirements and to determine the subsystem test firing and the subsequent system level test firing requirements. The electro-dynamic shaker, through shock synthesis techniques, is utilized to qualify the shock sensitive flight equipment with margins applied. Actual pyrotechnic device firings on spacecraft equipment or science instruments are performed when the influence of the pyros is localized and can be ignored at the system level. Full spacecraft system level shock tests, which include multiple firings of certain critical pyro devices, are conducted to verify the spacecraft design structural integrity and functions as well as to qualify hardware items which have not been previously qualified. These tests also provide a source of data from which assembly level requirements can be evaluated and compared. For example, during the Galileo program, the results demonstrated that good agreement between predicted and measured shock environments and adequate qualification of the flight spacecraft was achieved.

Chang, Kurng Y.↗

Assessment of Secondary Pitot Probe Locations on a Small UAS

Urban Air Mobility (UAM) and Advanced Air Mobility (AAM) have been at the forefront of many aeronautical discussions because of the potential revolutionary improvement to urban transportation. In this study, a representative Research Aircraft for eVTOL Enabling techNologies, Sub-scale Wind Tunnel Flight Test (RAVEN SWFT) nosecone was placed inside the NASA Langley Research Center’s 12-Foot Low-Speed Wind Tunnel with a pitot-static assembly installed. The study aimed to determine a suitable location and orientation of the pitot-static assembly on the nose of the vehicle, which consists of two airspeed sensors: one for the flight controller and one for data collection. The dynamic pressure was varied from 0.5 to 5psf for each test point. Additionally, three different offset distances from the center boom and three different angles for the flight controller pitot tube were tested. The data from both of the pitot tube assemblies were compared to the wind tunnel and the Aeroprobe pitot tube. The results show the flight controller pitot tube performs better when it is placed further away from the nosecone, regardless of the angle. The results also show that the angle does not affect the accuracy of the pitot tube when the vehicle yaws or pitches regardless of the mounting angle and location. The study provides useful insights for the design of the airspeed measurement systems on small Uncrewed Aerial Systems (sUAS), which can be applied to other UAM and AAM applications.

AAM↗

UnigeneFinder: An Automated Pipeline for Gene Calling From Transcriptome Assemblies Without a Reference Genome

ABSTRACT For most species, transcriptome data are much more readily available than genome data. Without a reference genome, gene calling is cumbersome and inaccurate because of the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared with existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high‐quality reference genomes. These features, coupled with the pipeline’s cross‐platform implementation, focus on automation, and an accessible, user‐friendly interface, make UnigeneFinder a useful tool for many downstream sequence‐based analyses in nonmodel organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high‐performance computing (HPC) systems and personal computers, further reducing barriers to use.

Xue, Bo [Plant Resilience Institute Michigan State↗

Shuttle S-band high gain switched beam breadboard antennas

The final fabrication and assembly of the S-band five-element, eight-beam breadboard antennas developed for the Space Shuttle program are described. Data summary sheets from component and final assembly testing are presented.

Mullaney, J. J.↗

Aircraft noise prediction program validation

A modular computer program (ANOPP) for predicting aircraft flyover and sideline noise was developed. A high quality flyover noise data base for aircraft that are representative of the U.S. commercial fleet was assembled. The accuracy of ANOPP with respect to the data base was determined. The data for source and propagation effects were analyzed and suggestions for improvements to the prediction methodology are given.

Shivashankara, B. N.↗

Progress toward a circulation atlas for application to coastal water siting problems

Circulation data needed to resolve coastal siting problems are assembled from historical hydrographic and remote sensing studies in the form of a Circulation Atlas. Empirical data are used instead of numerical model simulations to achieve fine resolution and include fronts and convergence zones. Eulerian and Langrangian data are collected, transformed, and combined into trajectory maps and current vector maps as a function of tidal phase and wind vector. Initial Atlas development is centered on the Elizabeth River, Hampton Roads, Virgina.

Munday, J. C., Jr.↗

Pilot land data system

The full realization of the potential of satellite remote sensing would require the utilization of information systems which are currently not available. However, technological advances make it now possible to design a data system for meeting the land scientists' most critical information needs. A working group has been assembled to examine the need for a Pilot Data System (PLDS). The pilot program is to establish a limited-scale, distributed information system to explore approaches to satisfy the needs of the land science research community. Aspects and objectives considered by the working group are discussed, taking into account science scenarios, required functions, the characteristics of a land data system, and questions of pilot land data system development.

Estes, J. E.↗

Bearing defect signature analysis using advanced nonlinear signal analysis in a controlled environment

Utilizing high-frequency data from a highly instrumented rotor assembly, seeded bearing defect signatures are characterized using both conventional linear approaches, such as power spectral density analysis, and recently developed nonlinear techniques such as bicoherence analysis. Traditional low-frequency (less than 20 kHz) analysis and high-frequency envelope analysis of both accelerometer and acoustic emission data are used to recover characteristic bearing distress information buried deeply in acquired data. The successful coupling of newly developed nonlinear signal analysis with recovered wideband envelope data from accelerometers and acoustic emission sensors is the innovative focus of this research.

Zoladz, T.↗

NOAA-20 VIIRS Thermal Emissive Bands On-Orbit Performance

The VIIRS (Visible Infrared Imaging Radiometer Suite) instrument onboard the NOAA-20 satellite (launched on November 18, 2017) started to collect Earth-view data after its nadir door opened on December 13, 2017. Seven of the VIIRS bands, I4-5 and M12-16 are thermal emissive bands (TEBs), covering a spectral range from 3.6 to 12.5 meters. They began collecting valid data after the cold focal plane assembly (CFPA) cooled down to its nominal operating temperature on January 6, 2018. This paper will present the performance of each TEB, including calibration coefficients, noise equivalent differential temperature (NEdT), on-orbit calibration coefficient estimates from scheduled onboard blackbody warm-up and cool-down (WUCD) data, as well as related telemetry temperatures. Several methods are tested and compared in the WUCD data analysis for estimating the calibration coefficients. Based on the preliminary results, the NEdT of each band is well below the design specification and very close to that of the VIIRS onboard the Suomi National Polar-orbiting Partnership (SNPP) satellite. The detector gains appear stable for bands on the short- and mid-wave infrared CFPA, whereas the detector gains have larger than expected degradation for bands on the long-wave infrared CFPA during the early mission. All TEB-related telemetry temperatures are stable. The on-orbit performance of NOAA-20 VIIRS TEB is compared with VIIRS onboard the SNPP.

Thermal Emissive Bands (TEB)↗

ANALYSIS OF THE MSL/MEDLI ENTRY DATA WITH COUPLED CFD AND MATERIAL RESPONSE.

The Mars Science Laboratory (MSL) was protected during its atmospheric entry by an instrumented heat-shield using NASA's Phenolic Impregnated Carbon Ablator (PICA) material. PICA is a lightweight carbon fiber/polymeric resin material that offers out-standing performances for protecting probes during planetary entry. The Mars Entry Descent and Landing Instrument (MEDLI) suite on MSL offers unique in-flight validation data for models of material response and atmospheric entry. MEDLI recorded, among other things, time-resolved in-depth temperature data of PICA using thermocouple sensors assembled in the MEDLI Integrated Sensor Plugs (MISP). The objective of this work is to showcase and analyze the coupling between the material response and the aerothermal environment. As shown in Figure 1, the workflow is divided into the following steps. First, the aerothermal properties are computed in the Data Parallel Line Relaxation (DPLR) code [3] and used with the Nonequilibrium air radiation (NEQAIR) program [8] to compute radiative heating. Second, the thermal response inside the material is computed in the Porous material Analysis Toolbox based on Open-FOAM (PATO) using a fixed blowing correction parameter. Third, the pyrolysis gases computed in PATO are used as inputs to a blowing boundary condition within DPLR. Fourth, the new environment properties from DPLR are used in NEQAIR to provide an updated solution, then both the updated aerothermal environment and radiative heating are used in PATO without blowing correction. The third and fourth steps are then repeated until convergence in surface temperature is obtained. Convergence in the radiative heating is generally achieved before surface temperature, at which point the radiative heating is no longer updated. Char mass loss rates are forced to zero to produce a non-receding surface condition. For early time points in the trajectory, where flow around the MSL aeroshell is rarefied, the Direct Simulation Monte Carlo (DSMC) code, SPARTA, is used to compute the aerothermal environment. Iteration between PATO and SPARTA is not performed due to the computational cost of DSMC simulations. Preliminary results of the coupling between PATO and DPLR for the MSL heatshield atmospheric entry model are presented in Figures 2-4 at 65 seconds after entry interface. Figure 2 shows the surface temperature results from an uncoupled simulation in PATO with the blowing correction parameter applied (left) along with the coupled surface temperature after iteration (right). Figure 3 shows the surface temperature along the centerline from windward to leeward for easier comparison. Figure 4 shows the coupled and uncoupled pyrolysis gas blowing rate. Mars 2020 used a similar heatshield consisting of PICA for thermal protection during entry, descent, and landing. In preparation for Mars 2020 post-flight analysis, the predictive material response capability is benchmarked against flight data from MEDLI. This work represents an important milestone toward the development of validated predictive capabilities for designing thermal protection systems for planetary probes.

Mars Science Laboratory↗

Lick Observatory charge-coupled-device data acquisition system

The Lick Observatory CCD data acquisition system is described, with some observational results to illustrate the system capability. The electronics for the CCD are subdivided into those attached to the dewar, a 'smart' controller near the dewar, and a computer connected by serial link to the smart controller. Software for the controller is in assembler code, while the software for data acquisition and on-line analysis is written in C and uses the UNIX operating system. The computers and controllers are programmed to recognize and operate several different types of CCD. Three separate instruments that use the CCDs are described briefly, together with examples of the data they produce.

Robinson, L. B.↗