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At least 793 records · Page 44

Galba: genome annotation with miniprot and AUGUSTUS

The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes. Various gene annotation tools have been developed but each has its limitations. Here, we introduce GALBA, a fully automated pipeline that utilizes miniprot, a rapid protein-to-genome aligner, in combination with AUGUSTUS to predict genes with high accuracy. Accuracy results indicate that GALBA is particularly strong in the annotation of large vertebrate genomes. We also present use cases in insects, vertebrates, and a land plant. GALBA is fully open source and available as a docker image for easy execution with Singularity in high-performance computing environments. Our pipeline addresses the critical need for accurate gene annotation in newly sequenced genomes, and we believe that GALBA will greatly facilitate genome annotation for diverse organisms.

59 BASIC BIOLOGICAL SCIENCES↗

Final Report: Process Intensification of Hydrogen Production through Sorption-Enhanced Gasification of Biomass

The University of Utah, in partnership with Idaho National Laboratory (INL), evaluated Sorption-Enhanced Gasification (SEG) as a transformative pathway for producing hydrogen with the potential for negative CO 2 emissions. SEG integrates gasification, water-gas shift, and in-situ carbon capture within a dual fluidized bed reactor to enable efficient clean hydrogen production. Key challenges related to biomass variability and process complexity were addressed through feedstock engineering, reaction optimization, and process validation. A co-pelletized biomass–limestone feedstock was developed to simplify feeding and introduction of makeup limestone. Kinetic and sorbent studies identified optimal operating conditions and confirmed the suitability of low-cost limestone, while catalysts were developed to reduce tar formation. Reactor modeling and techno-economic analysis indicated that SEG can achieve competitive hydrogen production costs, particularly when combined with carbon incentives, supporting its potential for scale-up and carbon-negative operation.

08 HYDROGEN↗

Phosphoglucoisomerase Is an Important Regulatory Enzyme in Partitioning Carbon out of the Calvin-Benson Cycle

Phosphoglucoisomerase (PGI) isomerizes fructose 6-phosphate (F6P) and glucose 6-phosphate (G6P) in starch and sucrose biosynthesis. Both plastidic and cytosolic isoforms are found in plant leaves. Using recombinant enzymes and isolated chloroplasts, we have characterized the plastidic and cytosolic isoforms of PGI. We have found that the Arabidopsis plastidic PGI K m for G6P is three-fold greater compared to that for F6P and that erythrose 4-phosphate is a key regulator of PGI activity. Additionally, the K m of spinach plastidic PGI can be dynamically regulated in the dark compared to the light and increases by 200% in the dark. We also found that targeting Arabidopsis cytosolic PGI into plastids of Nicotiana tabacum disrupts starch accumulation and degradation. Our results, in combination with the observation that plastidic PGI is not in equilibrium, indicates that PGI is an important regulatory enzyme that restricts flow and acts as a one-way valve preventing backflow of G6P into the Calvin-Benson cycle. We propose the PGI may be manipulated to improve flow of carbon to desired targets of biotechnology.

54 ENVIRONMENTAL SCIENCES↗

Failure in Confined Brazilian Tests on Sandstone

Strength of rocks in the confined tension region, where the minimum principal stress is tensile, has only infrequently been measured and is not well understood. Quasi-static confined Brazilian tests under a range of confining stresses (2.76 to 27.58 MPa) where used to determine the strength of sandstone in the confined tension region. The test results indicate that the strength in the confined tension region was a strong function of the intermediate principal stress: increasing the intermediate principal stress significantly increased the strength of the sandstone. The strength data were well fit by the Mogi–Coulomb criterion, which accounts for the intermediate principal stress. Unconfined Brazilian strength data were not well fit to the Mogi–Coulomb criterion derived from the confined Brazilian test data, consistent with a transition from tensile to shear processes dominating failure with increasing confining pressure. Observations of post-failure fracture surfaces reveal more indication of shear processes with increasing confining pressure. Numerical simulations from combined finite-discrete element method are compared to the experimental results and reflect similar conditions for failure compared to the experimental tests in the confined tension region.

42 ENGINEERING↗

Carbon Nanotube Supported Amorphous MoS 2 via Microwave Heating Synthesis for Enhanced Performance of Hydrogen Evolution Reaction

Amorphous molybdenum disulfide (MoS 2 ) is a promising electrochemical catalyst for hydrogen evolution reaction (HER) due to more active sites exposed on the surface compared to its crystalline counterpart. In this study, a novel fast three-minute one-pot method is proposed to prepare the single-wall carbon nanotube- (SWCNT-) supported amorphous MoS 2 via a microwave heating process. Compared to traditional hydro- or solvent thermal methods to prepare MoS 2 which usually consume more than 10 hours, it is more promising for fast production. An overpotential at 10 mA/cm 2 of amorphous MoS 2 @SWCNT is 178 mV, which is 99 mV and 22 mV lower than crystalline MoS 2 @SWCNT and pure amorphous MoS 2 , respectively. After running 1000 cycles of polarization, ~2% increase in overpotential is observed, indicating its good stability. The enhanced performance results from the beneficial combination of the SWCNT substrate and the amorphous microstructures. The introduction of SWCNT increases catalyst conductivity and prevents MoS 2 aggregation. The amorphous microstructures of MoS 2 prepared by a microwave heating method lead to more Mo edges or active sites exposed.

Tang, Wei↗

Aerodynamic Loads on Tails at High Angles of Attack and Sideslip

Results are presented for the loads and moments acting on the individual tail surfaces of a body-tail combination over a wide range of angles of attack and sideslip. The effects of forebody length and panel-panel interference on the characteristics are included. It is shown that large nonlinear variations in these loads and moments, which occur at some combinations of angle of attack and sideslip, cannot be predicted by low-angle theory. A relatively simple, but general, theoretical method for calculating these load and moment characteristics is described, and the results from this method are found to be in good agreement with experiment provided the initial positions of the forebody vortices are known. It is shown that a simple application of slender-body theory can be used to predict the side loads due to sideslip that are contributed by a vertical tail on a wide variety of wing-body-tail combinations at low angles of attack. For several configurations, changes are indicated which reduced the vertical-tail loads per unit yawing moment of each complete configuration at large angles of attack. Some results are presented on the effect of high angle of attack on the induced-flow field and tail loads due to a wing at supersonic speed.

SLENDER BODY↗

Optimal flash rate and duty cycle for flashing visual indicators.

This experiment examined the ability of observers to determine, as quickly as possible, whether a visual indicator was steadily on or flashing. Six flash rates (periods) were combined factorially with three duty cycles (on-off ratios) to define 18 ?types' of intermittent signals. Experimental sessions were divided into six runs of 100 trials, each run utilizing one of the six flash rates. On any given trial in a run, the probability of a steady signal occurring was 0.5 and the probability of a flashing signal occurring was 0.5. A different duty cycle was employed daily for each experimental session. In all, 400 trials were devoted to each of the flash rates at each duty cycle. Accuracy and latency of response were the dependent variables of interest. The results show that the observers view the light for an interval of time appropriate to the expected flash rate and duty cycle; whether they judge the light to be steady or intermittent depends upon whether the light is extinguished during the predetermined waiting period. Adoption of this temporal criterion delays responding in comparison to those tasks involving responses to light onset. The decision or response criteria held by the observers are also sensitive to the parameters of the flashing light: observers become increasingly willing to call a flashing light ?steady' as flash duration increases.

Markowitz, J.↗

Effects of flight instrumentation errors on the estimation of aircraft stability and control derivatives

An error analysis program based on an output error estimation method was used to evaluate the effects of sensor and instrumentation errors on the estimation of aircraft stability and control derivatives. A Monte Carlo analysis was performed using simulated flight data for a high performance military aircraft, a large commercial transport, and a small general aviation aircraft for typical cruise flight conditions. The effects of varying the input sequence and combinations of the sensor and instrumentation errors were investigated. The results indicate that both the parameter accuracy and the corresponding measurement trajectory fit error can be significantly affected. Of the error sources considered, instrumentation lags and control measurement errors were found to be most significant.

Bryant, W. H.↗

Effect of water and ice on strength and fracture toughness of intermittently bonded boron-epoxy composites

The effects of water and ice on the strength and fracture toughness of boron-epoxy composites with polyurethane intermittent bonding have been investigated. Neither simple soaking in water nor soaking followed by freezing and thawing have marked effects on the strength of the fully-coated composites, but they have disastrous effects on the uncoated composites. Toughness is affected only marginally, with some small reductions in the fully-coated samples, and with essentially no effect on the uncoated composites. An analysis is presented which explains adequately the experimental strength and toughness results obtained, and which is based on an argument that water absorption reduces the interfacial shear strength only of the uncoated areas and not those regions coated by the polyurethane varnish. The results indicate that the advantages of appropriate intermittent bonding (i.e., high strength combined with high toughness) are retained in wet conditions so that such composites may be favorably used in such adverse environmental conditions.

Atkins, A. G.↗

Physical-chemical examination of the N2O3-SO3-H2O system

It was found that when (NO)HSO4 is added to absolute H2SO4, specific conductivity rises sharply, possibly due to an increase in mutual interionic effects and viscosity as the (NO)HSO4 concentration rises. The addition of SO3 to the solution yielded a precipitate; a combination of analysis, IR spectroscopy and X-ray diffraction techniques indicated that this precipitate was (NO)HS2O7.

Linstroem, C.↗

Tungsten fiber reinforced FeCrAlY - A first generation composite turbine blade material

General and composite turbine blade material requirements are examined to identify a specific tungsten fiber reinforced superalloy (TFRS) having, in addition to strength, the desired combination of other material properties needed in turbine blades. Experimental data indicated that a thoriated tungsten fiber reinforced FeCrAlY matrix composite should have the stress-rupture, creep, tensile, fatigue, and impact strengths required for turbine blades operating from 1250 to 1370 K. Fabrication and design concepts are developed to demonstrate the feasibility of fabricating a hollow TFRS turbine blade at reasonable cost.

Petrasek, D. W.↗

Dual throat engine design for a SSTO launch vehicle

A propulsion system analysis of a dual fuel, dual throat engine for launch vehicle application was conducted. Basic dual throat engine characterization data are presented to allow vehicle optimization studies to be conducted. A preliminary baseline engine system was defined. Dual throat engine performance, envelope, and weight parametric data were generated over the parametric range of thrust from 890 to 8896 KN (200K to 2M lb-force), chamber pressure from 6.89 million to 34.5 million N/sq m (1000 to 5000 psia) thrust ratio from 1.2 to 5, and a range of mixture ratios for the two tripropellant combinations: LO2/RP-1 + LH2 and LO2/LCH4 + LH2. The results of the study indicate that the dual fuel dual throat engine is a viable single stage to orbit candidate.

Obrien, C. J.↗

Flight evaluation of the STOL flare and landing during night operations

Simulated instrument approaches were made to Category 1 minimums followed by a visual landing on a 100 x 1700 ft STOL runway. Data were obtained for variations in the aircraft's flare response characteristics and control techniques and for different combinations of aircraft and runway lighting and a visual approach slope indication. With the complete aircraft and runway lighting and visual guidance no degradation in flying qualities or landing performance was observed compared to daylight operations. elimination of the touchdown zone floodlights or the aircraft landing lights led to somewhat greater pilot workload; however, the landing could still be accomplished successfully. Loss of both touchdown zone and aircraft landing lights led to a high workload situation and only a marginally adequate to inadequate landing capability.

Franklin, J. A.↗

Mapping irrigated lands in Western Kansas from Landsat

A description is presented of a multidate visual interpretation technique for identifying and mapping irrigated lands in Western Kansas based on gray tone interpretation of Landsat imagery. The technique provides detailed maps of irrigated lands that can be updated yearly (from 1972 onwards) and used as the basis for calculations of water use and its temporal trends. A review of remote sensing work on irrigated lands indicates that three different types of study have evolved, involving various combinations of desired final data and the means of arriving at it. Attention is given to crop characteristics, the development of an interpretation technique, the interpretation procedure, the computer assisted output, and aspects of verification and accuracy. It is pointed out that the considered technique is likely to be applicable to similar situations of a semi-arid area dominated by a small number of crops.

Williams, T. H. L.↗

The atmospheres of Io and other satellites

Voyager measurements of gaseous SO2 in a hot spot region and of ions of sulfur, oxygen, and SO2(+) in the plasma torus, combined with the groundbased measurements of SO2 frost on the surface, indicate that SO2 is perhaps the dominant constituent of Io's atmosphere. Indeed the ionosphere of Io can be sustained by a pure SO2 atmosphere in thermal equilibrium with the surface. Upper limits on common volatiles H2O, CO2, NH3, and CH4 and exceedingly small, although S2 and Ar may still be present. Photochemistry of SO2 could lead to O2 as the major gas on the night side. Reasonable processes for loss to the torus include thermal escape, sputtering, and sweep-up of ions. The symmetry of the sodium cloud between eastern and western elongation is difficult to reconcile with any substantial, diurnally varying atmosphere. Europa, Ganymede, and Callisto may have oxygen atmospheres resulting from photolysis of water vapor. A pressure of approximately 10 to the -6th microbar is predicted, consistent with the Voyager upper limit for Ganymede. A much higher pressure might be present if the water vapor pressure is increased by a low albedo (Callisto) or sputtering (Europa).

Kumar, S.↗

A mesoscale numerical forecast of an intense convective snowburst along the East Coast

Mesoscale numerical forecasts utilizing the Mesoscale Atmospheric Simulation System (MASS) are documented for a convective snowburst in the Washington, D.C.-Baltimore, Maryland, region on March 8, 1984 that was associated with secondary cyclogenesis along the East Coast. The forecasts are presented to demonstrate the ability of a mesoscale model to simulate dynamical interactions and diabatic process for a wintertime convective event that was inadequately predicted by local forecasters and to note some of the possible benefits of using mesoscale models for day-to-day forecasting. The results from this and other recent mesoscale modeling studies indicate that three-hourly output of key model fields, when combined with other data sources, can be a valuable aid to forecasters concerned with predicting weather events that are mesoscale in character.

Kocin, P. J.↗

The origin of the infrared luminosity in Centaurus A

The origin of the infrared luminosity in Centaurus A is studied using new tracking and data acquisition techniques which yield diffraction-limited profiles at both 50 and 100 microns. Ninety percent of the 100 micron flux is found to originate in a source which extends 5 kpc along the optical dust lane that bisects the galaxy; the remaining 10 percent comes from an unresolved source coincident with the active radio nucleus. The extended 100 micron emission profile is fully consistent with a uniform disk of thermally radiating particles; when combined with results of previous studies at shorter wavelengths, these measurements indicate that nearly all of the infrared luminosity is produced by thermally emitting grains which are heated by massive young stars distributed throughout the optically thick dust lane.

Joy, Marshall↗

Effects of scopolamine and dextroamphetamine on human performance

The effects of two drugs used to prevent symptoms of motion sickness in the operational environment were examined in this study of human performance as measured by computer-based tests of cognitive and psychomotor skills. Each subject was exposed repetitively to five tests: symbol-digit substitution, simple reaction time, pattern recognition, digit span memory, and pattern memory. Although there have been previous reports of decreases in human performance in similar testing with higher dosages of scopolamine or dextroamphetamine, no significant decrements were observed with the operational-level combined dose used in this study (0.4 mg oral scopolamine and 5.0 mg oral dextroamphetamine.) The controversy over the use of combination drug therapy in this environnment is discussed along with the indications for further research based on the findings.

Schmedtje, John F., Jr.↗