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At least 145 records · Page 8

The Microbial Community and Functional Potential in the Midland Basin Reveal a Community Dominated by Both Thiosulfate and Sulfate-Reducing Microorganisms

The Permian Basin is the highest producing oil and gas reservoir in the United States. Hydrocarbon resources in this region are often accessed by unconventional extraction methods, including horizontal drilling and hydraulic fracturing. Despite the importance of the Permian Basin, there is no publicly available microbiological data from this region. We completed an analysis of Permian produced water samples to understand the dynamics present in hydraulically fractured wells in this region. We analyzed produced water samples taken from 10 wells in the Permian region of the Midland Basin using geochemical measurements, 16S rRNA gene sequencing, and metagenomic sequencing. Compared to other regions, we found that Permian Basin produced water was characterized by higher sulfate and lower total dissolved solids (TDS) concentrations, with a median of 1,110 mg/L and 107,000 mg/L. Additionally, geochemical measurements revealed the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. The occurrence of frac hits was supported by correlations between the microbiome and the geochemical parameters. Our 16S rRNA gene sequencing identified a produced water microbiome characterized by anaerobic, halophilic, and sulfur reducing taxa. Interestingly, sulfate and thiosulfate reducing taxa including Halanaerobium, Orenia, Marinobacter, and Desulfohalobium were the most prevalent microbiota in most wells. We further investigated the metabolic potential of microorganisms in the Permian Basin with metagenomic sequencing. We recovered 15 metagenome assembled genomes (MAGs) from seven different samples representing 6 unique well sites. These MAGs corroborated the high presence of sulfate and thiosulfate reducing genes across all wells, especially from key taxa including Halanaerobium and Orenia. The observed microbiome composition and metabolic capabilities in conjunction with the high sulfate concentrations demonstrate a high potential for hydrogen sulfide production in the Permian Basin. Additionally, evidence of frac hits suggests the possibility for the exchange of microbial cells and/or genetic information between wells. This exchange would increase the likelihood of hydrogen sulfide production and has implications for the oil and gas industry.

16S RNA↗

Python HITMIX

SAND2024-10158O Python HITMIX is a software package for computing hitting time moments of vertices in a graph. Hitting time moments can be used to rank the strengths of relationships between vertices in a graph. Examples are provided for computing and using hitting time moments on generic graphs and similarity graphs arising from the analysis of text documents in information retrieval applications. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Dunlavy, Daniel↗

The ETROC2 as the Final Version for CMS Endcap Timing Layer (ETL) Upgrade

The ETROC (Endcap Timing Readout Chip) is being developed for the LGAD-based CMS Endcap Timing Layer (ETL) at HL-LHC. The ETL on each side of the interaction region will be instrumented with a two-disk system of MIP-sensitive LGAD (Low Gain Avalanche Diodes) silicon devices, read out by ETROCs for precision timing measurement with down to ~30 ps timing resolution per track. The ETROC is designed to handle a 16 x 16 pixel cell matrix, with each pixel being 1.3 mm x 1.3 mm to match the LGAD sensor pixel size. The front-end design for preamplifier and discriminator has been specifically optimized for the reduced LGAD signals, with enough flexibilities to meet the ETL specific needs for time resolution, power budget and radiation profile. The ETROC chip is implemented in a commercial 65nm CMOS process. Each channel consists of a preamplifier, a discriminator, a TDC used for TOA (Time Of Arrival) and TOT (Time Over Threshold) measurements, and a memory for data storage and readout. An in-pixel auto threshold calibration is included, along with a self-testing pattern generator. The TOT is used for time-walk correction of the TOA measurement. The detailed hit information (TOA and TOT) from each cell will be read out from a local circular buffer after each Level-1 Accept (about 1 MHz). In addition, a charge injection circuit is implemented to allow for testing and calibration. For more detailed monitoring of the signal pulses, waveform sampling circuits are included for one pixel. The clock distribution is based on a 16x16 H-tree design with a shielding structure to alleviate potential interference. The global peripheral circuits include a PLL, a phase shifter, an I2C slave controller, a fast control block, a global readout, and a data driver along with an efuse and temperature sensor. The ETROC builds event data frames for each L1A selected event and is also capable of providing L1 trigger information for user-defined delayed hits. The main design challenge is how to extract precision timing information from the small LGAD signals in the presence of high irradiation fluence, while keeping the power consumption and digital activity low. The ETL design goal for the time resolution of 50 ps per hit is required to achieve a 35 ps arrival time measurement for a MIP particle, which has its track registered in two ETL disk layers. The LGAD contribution is known to be about 30 ps, this means that the jitter from the ETROC has to be kept below 40 ps. The ETROC2 is the first full size full functionality prototype design fully compatible with the final chip specifications for CMS ETL and now becomes the final version. The ETROC2 chips have been extensively tested. We will present here new testing results including the bump bonding yield improvement study, the time walk correction (TWC) generality study with one pixel TWC applying to all pixels, the final SEU testing using both heavy ion and proton beam, more beam test studies including different sensors, and readiness for the ETROC2 production for CMS ETL upgrade.

Liu, Tiehui [Fermilab] (ORCID:0009000765225605)↗

CLUE: A Fast Parallel Clustering Algorithm for High Granularity Calorimeters in High-Energy Physics

One of the challenges of high granularity calorimeters, such as that to be built to cover the endcap region in the CMS Phase-2 Upgrade for HL-LHC, is that the large number of channels causes a surge in the computing load when clustering numerous digitized energy deposits (hits) in the reconstruction stage. In this article, we propose a fast and fully parallelizable density-based clustering algorithm, optimized for high-occupancy scenarios, where the number of clusters is much larger than the average number of hits in a cluster. The algorithm uses a grid spatial index for fast querying of neighbors and its timing scales linearly with the number of hits within the range considered. We also show a comparison of the performance on CPU and GPU implementations, demonstrating the power of algorithmic parallelization in the coming era of heterogeneous computing in high-energy physics.

Rovere, Marco↗

A New Drug Discovery Platform: Application to DNA Polymerase Eta and Apurinic/Apyrimidinic Endonuclease 1

The ability to quickly discover reliable hits from screening and rapidly convert them into lead compounds, which can be verified in functional assays, is central to drug discovery. The expedited validation of novel targets and the identification of modulators to advance to preclinical studies can significantly increase drug development success. Our SaXPyTM (“SAR by X-ray Poses Quickly”) platform, which is applicable to any X-ray crystallography-enabled drug target, couples the established methods of protein X-ray crystallography and fragment-based drug discovery (FBDD) with advanced computational and medicinal chemistry to deliver small molecule modulators or targeted protein degradation ligands in a short timeframe. Our approach, especially for elusive or “undruggable” targets, allows for (i) hit generation; (ii) the mapping of protein–ligand interactions; (iii) the assessment of target ligandability; (iv) the discovery of novel and potential allosteric binding sites; and (v) hit-to-lead execution. These advances inform chemical tractability and downstream biology and generate novel intellectual property. We describe here the application of SaXPy in the discovery and development of DNA damage response inhibitors against DNA polymerase eta (Pol η or POLH) and apurinic/apyrimidinic endonuclease 1 (APE1 or APEX1). Notably, our SaXPy platform allowed us to solve the first crystal structures of these proteins bound to small molecules and to discover novel binding sites for each target.

59 BASIC BIOLOGICAL SCIENCES↗

Bayesian Inference of State-Level COVID-19 Basic Reproduction Numbers across the United States

Although many persons in the United States have acquired immunity to COVID-19, either through vaccination or infection with SARS-CoV-2, COVID-19 will pose an ongoing threat to non-immune persons so long as disease transmission continues. We can estimate when sustained disease transmission will end in a population by calculating the population-specific basic reproduction number ℛ0, the expected number of secondary cases generated by an infected person in the absence of any interventions. The value of ℛ0 relates to a herd immunity threshold (HIT), which is given by 1−1/ℛ0. When the immune fraction of a population exceeds this threshold, sustained disease transmission becomes exponentially unlikely (barring mutations allowing SARS-CoV-2 to escape immunity). Here, we report state-level ℛ0 estimates obtained using Bayesian inference. Maximum a posteriori estimates range from 7.1 for New Jersey to 2.3 for Wyoming, indicating that disease transmission varies considerably across states and that reaching herd immunity will be more difficult in some states than others. ℛ0 estimates were obtained from compartmental models via the next-generation matrix approach after each model was parameterized using regional daily confirmed case reports of COVID-19 from 21 January 2020 to 21 June 2020. Our ℛ0 estimates characterize the infectiousness of ancestral strains, but they can be used to determine HITs for a distinct, currently dominant circulating strain, such as SARS-CoV-2 variant Delta (lineage B.1.617.2), if the relative infectiousness of the strain can be ascertained. On the basis of Delta-adjusted HITs, vaccination data, and seroprevalence survey data, we found that no state had achieved herd immunity as of 20 September 2021.

60 APPLIED LIFE SCIENCES↗

Decision-related cortical potentials during an auditory signal detection task with cued observation intervals

Cortical-evoked potentials were recorded from human subjects performing an auditory detection task with confidence rating responses. Unlike earlier studies that used similar procedures, the observation interval during which the auditory signal could occur was clearly marked by a visual cue light. By precisely defining the observation interval and, hence, synchronizing all perceptual decisions to the evoked potential averaging epoch, it was possible to demonstrate that high-confidence false alarms are accompanied by late-positive P3 components equivalent to those for equally confident hits. Moreover the hit and false alarm evoked potentials were found to covary similarly with variations in confidence rating and to have similar amplitude distributions over the scalp. In a second experiment, it was demonstrated that correct rejections can be associated with a P3 component larger than that for hits. Thus it was possible to show, within the signal detection paradigm, how the two major factors of decision confidence and expectancy are reflected in the P3 component of the cortical-evoked potential.

Squires, K. C.↗

Toward a comprehensive theory for the sweeping of trapped radiation by inert orbiting matter

There is a need to calculate loss rates when trapped Van Allen radiation encounters inert orbiting material such as planetary rings and satellites. An analytic expression for the probability of a hit in a bounce encounter is available for all cases where the absorber is spherical and the particles are gyrotropically distributed on a cylindrical flux tube. The hit probability is a function of the particle's pitch angle, the size of the absorber, and the distance between flux tube and absorber, when distances are scaled to the gyroradius of a particle moving perpendicular to the magnetic field. Using this expression, hit probabilities have been computed in drift encounters for all regimes of particle energies and absorber sizes. This technique generalizes the approach to sweeping lifetimes, and is particularly suitable for attacking the inverse problem, where one is given a sweeping signature and wants to deduce the properties of the absorber(s).

Fillius, Walker↗

Toward a comprehensive theory for the sweeping of trapped radiation by inert orbiting matter

There is a need to calculate loss rates when trapped Van Allen radiation encounters inert orbiting material such as planetary rings and satellites. An analytic expression for the probability of a hit in a bounce encounter is available for all cases where the absorber is spherical and the particles are gyrotropically distributed on a cylindrical flux tube. The hit probability is a function of the particle's pitch angle, the size of the absorber, and the distance between the flux tube and the absorber when distances are scaled to the gyroradius of a particle moving perpendicular to the magnetic field. Using this expression, hit probabilities in drift encounters were computed for all regimes of particle energies and absorber sizes.

Fillius, Walker↗

Characterization of multiple-bit errors from single-ion tracks in integrated circuits

The spread of charge induced by an ion track in an integrated circuit and its subsequent collection at sensitive nodal junctions can cause multiple-bit errors. The authors have experimentally and analytically investigated this phenomenon using a 256-kb dynamic random-access memory (DRAM). The effects of different charge-transport mechanisms are illustrated, and two classes of ion-track multiple-bit error clusters are identified. It is demonstrated that ion tracks that hit a junction can affect the lateral spread of charge, depending on the nature of the pull-up load on the junction being hit. Ion tracks that do not hit a junction allow the nearly uninhibited lateral spread of charge.

Zoutendyk, J. A.↗

Effects of competition on video-task performance in monkeys (Macaca mulatta)

The effects of competition on performance of a video-formatted task were examined in a series of experiments. Two rhesus monkeys (Macaca mulatta) were trained to manipulate a joystick to shoot at moving targets on a computer screen. The task was made competitive by requiring both animals to shoot at the same target and by rewarding only the animal that hit the target first each trial. The competitive task produced a significant and robust speed-accuracy trade-off in performance. The monkeys hit the target in significantly less time on contested than on uncontested trials. However, they required significantly more shots to hit the target on contested trials in relation to uncontested trials. This effect was unchanged when various schedules of reinforcement were introduced in the uncontested trials. This supports the influence of competition qua competition on performance, a point further bolstered by other findings of behavioral contrast presented here.

Washburn, David A.↗

A trace-driven analysis of name and attribute caching in a distributed system

This paper presents the results of simulating file name and attribute caching on client machines in a distributed file system. The simulation used trace data gathered on a network of about 40 workstations. Caching was found to be advantageous: a cache on each client containing just 10 directories had a 91 percent hit rate on name look ups. Entry-based name caches (holding individual directory entries) had poorer performance for several reasons, resulting in a maximum hit rate of about 83 percent. File attribute caching obtained a 90 percent hit rate with a cache on each machine of the attributes for 30 files. The simulations show that maintaining cache consistency between machines is not a significant problem; only 1 in 400 name component look ups required invalidation of a remotely cached entry. Process migration to remote machines had little effect on caching. Caching was less successful in heavily shared and modified directories such as /tmp, but there weren't enough references to /tmp overall to affect the results significantly. We estimate that adding name and attribute caching to the Sprite operating system could reduce server load by 36 percent and the number of network packets by 30 percent.

Shirriff, Ken W.↗

Visible and Ultraviolet Detectors for High Earth Orbit and Lunar Observatories

The current status of detectors for the visible and UV for future large observatories in earth orbit and the moon is briefly reviewed. For the visible, CCDs have the highest quantum efficiency, but are subject to contamination of the data by cosmic ray hits. For the moon, the level of hits can be brought down to that at the earth's surface by shielding below about 20 meters of rock. For high earth orbits above the geomagnetic shield, CCDs might be able to be used by combining many short exposures and vetoing the cosmic ray hits, otherwise photoemissive detectors will be necessary. For the UV, photoemissive detectors will be necessary to reject the visible; to use CCDs would require the development of UV-efficient filters which reject the visible by many orders of magnitude. Development of higher count rate capability would be desirable for photoemissive detectors.

Woodgate, Bruce E.↗

Attitude Determination and Control Systems

In the year 1900, Galveston, Texas, was a bustling community of approximately 40,000 people. The former capital of the Republic of Texas remained a trade center for the state and was one of the largest cotton ports in the United States. On September 8 of that year, however, a powerful hurricane struck Galveston island, tearing the Weather Bureau wind gauge away as the winds exceeded 100 mph and bringing a storm surge that flooded the entire city. The worst natural disaster in United States history even today the hurricane caused the deaths of between 6000 and 8000 people. Critical in the events that led to such a terrible loss of life was the lack of precise knowledge of the strength of the storm before it hit. In 2008, Hurricane Ike, the third costliest hurricane ever to hit the United States coast, traveled through the Gulf of Mexico. Ike was gigantic, and the devastation in its path included the Turk and Caicos Islands, Haiti, and huge swaths of the coast of the Gulf of Mexico. Once again, Galveston, now a city of nearly 60,000, took the direct hit as Ike came ashore. Almost 200 people in the Caribbean and the United States lost their lives; a tragedy to be sure, but far less deadly than the 1900 storm. This time, people were prepared, having received excellent warning from the GOES satellite network. The Geostationary Operational Environmental Satellites have been a continuous monitor of the world's weather since 1975, and they have since been joined by other Earth-observing satellites. This weather surveillance to which so many now owe their lives is possible in part because of the ability to point accurately and steadily at the Earth below. The importance of accurately pointing spacecraft to our daily lives is pervasive, yet somehow escapes the notice of most people. But the example of the lives saved from Hurricane Ike as compared to the 1900 storm is something no one should ignore. In this section, we will summarize the processes and technologies used in designing and operating spacecraft pointing (i.e. attitude) systems.

Starin, Scott R.↗

The Analysis of the Patterns of Radiation-Induced DNA Damage Foci by a Stochastic Monte Carlo Model of DNA Double Strand Breaks Induction by Heavy Ions and Image Segmentation Software

To create a generalized mechanistic model of DNA damage in human cells that will generate analytical and image data corresponding to experimentally observed DNA damage foci and will help to improve the experimental foci yields by simulating spatial foci patterns and resolving problems with quantitative image analysis. Material and Methods: The analysis of patterns of RIFs (radiation-induced foci) produced by low- and high-LET (linear energy transfer) radiation was conducted by using a Monte Carlo model that combines the heavy ion track structure with characteristics of the human genome on the level of chromosomes. The foci patterns were also simulated in the maximum projection plane for flat nuclei. Some data analysis was done with the help of image segmentation software that identifies individual classes of RIFs and colocolized RIFs, which is of importance to some experimental assays that assign DNA damage a dual phosphorescent signal. Results: The model predicts the spatial and genomic distributions of DNA DSBs (double strand breaks) and associated RIFs in a human cell nucleus for a particular dose of either low- or high-LET radiation. We used the model to do analyses for different irradiation scenarios. In the beam-parallel-to-the-disk-of-a-flattened-nucleus scenario we found that the foci appeared to be merged due to their high density, while, in the perpendicular-beam scenario, the foci appeared as one bright spot per hit. The statistics and spatial distribution of regions of densely arranged foci, termed DNA foci chains, were predicted numerically using this model. Another analysis was done to evaluate the number of ion hits per nucleus, which were visible from streaks of closely located foci. In another analysis, our image segmentaiton software determined foci yields directly from images with single-class or colocolized foci. Conclusions: We showed that DSB clustering needs to be taken into account to determine the true DNA damage foci yield, which helps to determine the DSB yield. Using the model analysis, a researcher can refine the DSB yield per nucleus per particle. We showed that purely geometric artifacts, present in the experimental images, can be analytically resolved with the model, and that the quantization of track hits and DSB yields can be provided to the experimentalists who use enumeration of radiation-induced foci in immunofluorescence experiments using proteins that detect DNA damage. An automated image segmentaiton software can prove useful in a faster and more precise object counting for colocolized foci images.

Ponomarev, Artem↗

Global Positioning System (GPS) Precipitable Water in Forecasting Lightning at Spaceport Canaveral

Using meteorology data, focusing on precipitable water (PW), obtained during the 2000-2003 thunderstorm seasons in Central Florida, this paper will, one, assess the skill and accuracy measurements of the current Mazany forecasting tool and, two, provide additional forecasting tools that can be used in predicting lightning. Kennedy Space Center (KSC) and Cape Canaveral Air Force Station (CCAFS) are located in east Central Florida. KSC and CCAFS process and launch manned (NASA Space Shuttle) and unmanned (NASA and Air Force Expendable Launch Vehicles) space vehicles. One of the biggest cost impacts is unplanned launch scrubs due to inclement weather conditions such as thunderstorms. Each launch delay/scrub costs over a quarter million dollars, and the need to land the Shuttle at another landing site and return to KSC costs approximately $ 1M. Given the amount of time lost and costs incurred, the ability to accurately forecast (predict) when lightning will occur can result in significant cost and time savings. All lightning prediction models were developed using binary logistic regression. Lightning is the dependent variable and is binary. The independent variables are the Precipitable Water (PW) value for a given time of the day, the change in PW up to 12 hours, the electric field mill value, and the K-index value. In comparing the Mazany model results for the 1999 period B against actual observations for the 2000-2003 thunderstorm seasons, differences were found in the False Alarm Rate (FAR), Probability of Detection (POD) and Hit Rate (H). On average, the False Alarm Rate (FAR) increased by 58%, the Probability of Detection (POD) decreased by 31% and the Hit Rate decreased by 20%. In comparing the performance of the 6 hour forecast period to the performance of the 1.5 hour forecast period for the Mazany model, the FAR was lower by 15% and the Hit Rate was higher by 7%. However, the POD for the 6 hour forecast period was lower by 16% as compared to the POD of the 1.5 hour forecast period. Neither forecast period performed at the accuracy measures expected. A 2-Hr Forecasting Tool was developed to support a Phase I Lightning Advisory, which requires a 30-minute lead time for predicting lightning.

Kehrer, Kristen↗

Verification of Real-Time WSA-ENLIL+Cone Simulations of CME Arrival-Time at the CCMC from 2010 to 2016

The Wang-Sheeley-Arge (WSA)-ENLIL+Cone model is used extensively in space weather operations world-wide to model coronal mass ejection (CME) propagation. As such, it is important to assess its performance. We present validation results of the WSA-ENLIL+Cone model installed at the Community Coordinated Modeling Center (CCMC) and executed in real-time by the CCMC space weather team. CCMC uses the WSA-ENLIL+Cone model to predict CME arrivals at NASA missions throughout the inner heliosphere. In this work we compare model predicted CME arrival-times to in situ interplanetary coronal mass ejection leading edge measurements at Solar TErrestrial RElations Observatory-Ahead (STEREO-A), Solar TErrestrial RElations Observatory-Behind (STEREO-B), and Earth (Wind and ACE) for simulations completed between March 2010 and December 2016 (over 1,800 CMEs). We report hit, miss, false alarm, and correct rejection statistics for all three locations. For all predicted CME arrivals, the hit rate is 0.5, and the false alarm rate is 0.1. For the 273 events where the CME was predicted to arrive at Earth, STEREO-A, or STEREO-B, and was actually observed (hit event), the mean absolute arrival-time prediction error was 10.4 +/- 0.9 h, with a tendency to early prediction error of -4.0 h. We show the dependence of the arrival-time error on CME input parameters. We also explore the impact of the multi-spacecraft observations used to initialize the model CME inputs by comparing model verification results before and after the STEREO-B communication loss (since September 2014) and STEREO-A sidelobe operations (August 2014- December 2015). There is an increase of 1.7 h in the CME arrival time error during single, or limited two-viewpoint periods, compared to the three-spacecraft viewpoint period. This trend would apply to a future space weather mission at L5 or L4 as another coronagraph viewpoint to reduce CME arrival time errors compared to a single L1 viewpoint.

MHD / modeling / validation / forecasting / corona↗

Importance of Contrast-to-Noise Ratio Sensitivity Function in Nondestructive Evaluation

A reliable nondestructive evaluation (NDE) technique provides minimum 90% probability of detection (POD) with 95% confidence for detection of cracklike flaws of a specific size. This requirement comes from fracture control. Fracture control is a risk assessment and control approach for preventing structural failure of fracture critical hardware during its service life. One of the approaches of fracture control is damage tolerance safe life analysis, which assumes that NDE reliably detectable size flaw may exist in the hardware post nondestructive evaluation. Analysis and/or testing are performed to verify that the hardware will not fail during its service life despite existence of such a flaw. NDE methods are conventionally qualified by probability of detection (POD) demonstration testing to ensure reliable flaw detection. Here, a novel and alternative to POD flaw detection reliability approach that uses contrast-to-noise ratio (CNR) is given. The approach uses CNR sensitivity function (SF) and CNR. CNR SF is the minimum CNR needed for reliable flaw detection as a function of certain flaw indication characteristics. Primary difference between POD approaches and CNR flaw detection reliability approach is resolution of flaw detection system. POD approach does not account for the resolution of the system, while CNR approach accounts for the flaw detection resolution. Resolution is determined from the modulation transfer function (MTF) of the flaw detection system. CNR flaw detection reliability approach emphasizes quantitative assessment of “how well each flaw indication is detected”. Therefore, CNR approach is helpful in reducing number of flaws in the sample used in NDE procedure qualification, resulting in cost and time savings. CNR approach is also a case of multi-hit flaw detection analysis which has better flaw detectability size than conventional single-hit flaw detectability. Thus, CNR approach, where applicable, may be superior to conventional POD approach. The paper is an overview of development of CNR modeling, CNR SF modeling and measurement by the author. The paper gives key references to currently used NDE procedure POD qualification approaches including those specific to CNR and CNR SF development in multi-hit flaw detection in NDE. The paper covers core topics in nondestructive evaluation engineering.

Contrast-to-noise ratio↗