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At least 379 records · Page 21

Evidence for the existence and ecological relevance of fast-cycling mineral-associated organic matter

Longstanding theories and models classify mineral-associated organic matter as the large ( ~ 60%) but slow-cycling and persistent portion of soil organic matter. Strong physico-chemical interactions and diffusion limitations restrict the turnover of mineral-associated organic matter, allowing carbon and nitrogen bound therein to persist in soil for as long as centuries to millennia. However, mineral-associated organic matter is a chemically and functionally diverse pool with a substantial portion cycling at relatively fast (i.e., minutes to years) timescales. Despite a growing body of evidence for the heterogenous and multi-pool nature of mineral-associated organic matter, we lack consensus on how to conceptualize and directly quantify fast-cycling mineral-associated organic matter and its ecological significance. We demonstrate that the dynamic qualities of fast-cycling mineral-associated organic matter vary based on 1) the chemistry of the mineral particles and organic matter, 2) the complex set of interactions between organic matter and the mineral matrix, and 3) the presence and strength of destabilizing forces that lead to decomposition or loss of mineral-associated organic matter (i.e., plant-microbe interactions, agricultural intensification, and climate change). Finally, we discuss potential implications and research opportunities for how we measure, manage, and model the dynamic subfraction of this otherwise persistent pool of soil organic matter.

Biological and medical sciences↗

Improved accuracy and robustness of electron density profiles from JET’s X-mode frequency-modulated continuous-wave reflectometers

JET’s frequency-modulated continuous wave (FMCW) reflectometers have been operating well with the current design since 2005, and density profiles have been automatically calculated intershot since then. However, the calculated profiles had long suffered from several shortcomings: poor agreement with other diagnostics, sometimes inappropriately moving radially by several centimeters, elevated levels of radial jitter, and persistent wriggles (strong unphysical oscillations). Here, in this research, several techniques are applied to the reflectometry data analysis, and the shortcomings are significantly improved. Starting with improving the equilibrium reconstruction that estimates the background magnetic field, adding a ripple correction in the reconstructed magnetic field profile, and adding new inner-wall reflection positions estimated through ray-tracing, these changes not only improve the agreement of reconstructed profiles to other diagnostics but also solve density profile wriggles that were present during band transitions. Other smaller but also persistent wriggles were also suppressed by applying a localized correction to the measured beat frequency where persistent oscillations are present. Finally, the burst analysis method, as introduced by Varela et al., has been implemented to extract the beat frequency from stacked spectrograms. Due to the strong suppression of spurious reflections, the radial jitter that sometimes would span several centimeters has been strongly reduced. The stacking of spectrograms has also been shown to be very useful for stacking recurring events, like small gas puff modulations, and extracting transport coefficients that would otherwise be below the noise level.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A Practical Solver for Scalar Data Topological Simplification

This paper presents a practical approach for the optimization of topological simplification, a central pre-processing step for the analysis and visualization of scalar data. Given an input scalar field f and a set of “signal” persistence pairs to maintain, our approaches produces an output field g that is close to f and which optimizes (i) the cancellation of “non-signal” pairs, while (ii) preserving the “signal” pairs. In contrast to pre-existing simplification algorithms, our approach is not restricted to persistence pairs involving extrema and can thus address a larger class of topological features, in particular saddle pairs in three-dimensional scalar data. Our approach leverages recent generic persistence optimization frameworks and extends them with tailored accelerations specific to the problem of topological simplification. Extensive experiments report substantial accelerations over these frameworks, thereby making topological simplification optimization practical for real-life datasets. Our approach enables a direct visualization and analysis of the topologically simplified data, e.g., via isosurfaces of simplified topology (fewer components and handles). We apply our approach to the extraction of prominent filament structures in three-dimensional data. Specifically, we show that our pre-simplification of the data leads to practical improvements over standard topological techniques for removing filament loops. Here, we also show how our approach can be used to repair genus defects in surface processing. Finally, we provide a C++ implementation for reproducibility purposes.

97 MATHEMATICS AND COMPUTING↗

Self-Admitted Technical Debt in Scientific Software: Prioritization, Sentiment, and Propagation Across Artifacts

Self-admitted technical debt (SATD) impairs scientific software (SSW), yet its prioritization, sentiment, persistence, and propagation remains underexplored. Understanding how SSW developers express, and address SATD is crucial for improving SSW maintenance, and tooling. This study investigates how SATD types and artifacts in SSW are prioritized, how sentiment relates to urgency, SATD removal and resolution rates, and the extent to which SATD propagates across artifacts. We analyzed nine SSW repositories using a SATD classification model and a semantic embedding-based prioritization heuristic. SATD was examined across multiple artifacts, with sentiment assessed via a fine-tuned transformer. Propagation was traced, priority scores compared to static analysis, and removal and resolution rates quantified. SATD in comments, commits, and pull requests receive higher priority than SATD in issues, with negative sentiment amplifying urgency. Resolution and removal rates lag behind open-source software (OSS) averages. Most SATD remains confined to the originating artifact, but longer propagation chains are rare and correlate with higher priority, highlighting persistent and high impact debt. Prioritization is influenced by artifact type and sentiment, while low removal and resolution rates signal persistent debt. Cross-artifact propagation marks high priority, unresolved SATD, providing empirical guidance for targeted monitoring, review prioritization, and tool supported maintenance in SSW.

Melin, Eric [Boise State University]↗

Host population dynamics influence Leptospira spp. transmission patterns among Rattus norvegicus in Boston, Massachusetts, US

Leptospirosis (caused by pathogenic bacteria in the genus Leptospira ) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, or a urine-contaminated environment, which then can serve as an infection source for additional rats and other mammals, including humans. The brown rat, Rattus norvegicus , is an important reservoir of Leptospira spp. in urban settings. We investigated the presence of Leptospira spp. among brown rats in Boston, Massachusetts and hypothesized that rat population dynamics in this urban setting influence the transportation, persistence, and diversity of Leptospira spp. We analyzed DNA from 328 rat kidney samples collected from 17 sites in Boston over a seven-year period (2016–2022); 59 rats representing 12 of 17 sites were positive for Leptospira spp. We used 21 neutral microsatellite loci to genotype 311 rats and utilized the resulting data to investigate genetic connectivity among sampling sites. We generated whole genome sequences for 28 Leptospira spp. isolates obtained from frozen and fresh tissue from some of the 59 positive rat kidneys. When isolates were not obtained, we attempted genomic DNA capture and enrichment, which yielded 14 additional Leptospira spp. genomes from rats. We also generated an enriched Leptospira spp. genome from a 2018 human case in Boston. We found evidence of high genetic structure among rat populations that is likely influenced by major roads and/or other dispersal barriers, resulting in distinct rat population groups within the city; at certain sites these groups persisted for multiple years. We identified multiple distinct phylogenetic clades of L. interrogans among rats that were tightly linked to distinct rat populations. This pattern suggests L. interrogans persists in local rat populations and its transportation is influenced by rat population dynamics. Finally, our genomic analyses of the Leptospira spp. detected in the 2018 human leptospirosis case in Boston suggests a link to rats as the source. These findings will be useful for guiding rat control and human leptospirosis mitigation efforts in this and other similar urban settings.

Stone, Nathan E.↗

Modeling Radiation-Induced Epithelial Cell Injury in Murine Three-Dimensional Esophageal Organoids

Esophageal squamous cell carcinoma (ESCC) is a deadly consequence of radiation exposure to the esophagus. ESCC arises from esophageal epithelial cells that undergo malignant transformation and features a perturbed squamous cell differentiation program. Understanding the dose- and radiation quality-dependence of the esophageal epithelium response to radiation may provide insights into the ability of radiation to promote ESCC. We have explored factors that may play a role in esophageal epithelial radiosensitivity and their potential relationship to ESCC risk. We have utilized a murine three-dimensional (3D) organoid model that recapitulates the morphology and functions of the stratified squamous epithelium of the esophagus to study persistent dose- and radiation quality-dependent changes. Interestingly, although high-linear energy transfer (LET) Fe ion exposure induced a more intense and persistent alteration of squamous differentiation and 53BP1 DNA damage foci levels as compared to Cs, the MAPK/SAPK stress pathway signaling showed similar altered levels for most phospho-proteins with both radiation qualities. In addition, the lower dose of high-LET exposure also revealed nearly the same degree of morphological changes, even though only ~36% of the cells were predicted to be hit at the lower 0.1 Gy dose, suggesting that a bystander effect may be induced. Although p38 and ERK/MAPK revealed the highest levels following high-LET exposure, the findings reveal that even a low dose (0.1 Gy) of both radiation qualities can elicit a persistent stress signaling response that may critically impact the differentiation gradient of the esophageal epithelium, providing novel insights into the pathogenesis of radiation-induced esophageal injury and early stage esophageal carcinogenesis.

3D organoid culture↗

Diverse organic carbon dynamics captured by radiocarbon analysis of distinct compound classes in a grassland soil

Soil organic carbon (SOC) is a large, dynamic reservoir composed of a complex mixture of plant- and microbe-derived compounds with a wide distribution of cycling timescales and mechanisms. The distinct residence times of individual carbon components within this reservoir depend on a combination of factors, including compound reactivity, mineral association, and climate conditions. To better constrain SOC dynamics, bulk radiocarbon measurements are commonly used to trace biosphere inputs into soils and to estimate timescales of SOC cycling. However, understanding the mechanisms driving the persistence of organic compounds in bulk soil requires analyses of SOC pools that can be linked to plant sources and microbial transformation processes. Here, we adapt approaches, previously developed for marine sediments, to isolate organic compound classes from soils for radiocarbon ( 14 C) analysis. We apply these methods to a soil profile from an annual grassland in Hopland, California (USA), to assess changes in SOC persistence with depth (down to 1 m). We measured the radiocarbon values of water-extractable organic carbon (WEOC), total lipid extracts (TLEs), total hydrolyzable amino acids (AAs), and an acid-insoluble (AI) fraction from bulk and physically separated size fractions (< 2 mm, 2 mm–63 µm, and < 63 µm). Our results show that Δ 14 C values of bulk soil, size fractions, and extracted compound classes became more depleted with depth, and individual SOC components have distinct age–depth distributions that suggest distinguishable cycling rates. We found that AAs and TLEs cycle faster than the bulk soils and the AI fraction. The AI was the most 14 C-depleted fraction, indicating that it is the most chemically inert in this soil. Our approach enables the isolation and measurement of SOC fractions that separate functionally distinct SOC pools that can cycle relatively quickly (e.g., plant and microbial residues) from more passive or inert SOC pools (associated with minerals or petrogenic) from bulk soils and soil physical fractions. With the effort to move beyond SOC bulk analysis, we find that compound class 14 C analysis can improve our understanding of SOC cycling and disentangle the physical and chemical factors driving OC cycling rates and persistence.

58 GEOSCIENCES↗

Orientations of central peaks in lunar craters - Implications for regional structural trends

Impact craters are dominant features on the lunar surface and all fresh craters with diameters greater than 35 km possess central peaks. Approximately half of these central peaks (54%) have either linear or arcuate geometry and display some preferential orientation. These orientations were measured for 200 lunar craters of Pre-Nectarian to Copernican age. A pervasive regional north-south trend is identified for central peak orientation, with secondary trends at + or - 20-30 deg from this axis. No evidence for regional east-west trends is found. These orientations are shown to persist in craters formed through the last 4 billion years of lunar history. A lack of coincidence between impact direction, as determined from ejecta asymmetries and peak orientation, argues for structural control by the target as a source of the linear peak morphology. This is supported by the regional and temporal persistence of preferred peak orientations. It is proposed that linear central peak orientations in lunar craters reflect a pervasive regional structural system which developed early in lunar history and has persisted through geologic time.

Hale, W.↗

Medium-range numerical forecasts of atmospheric angular momentum

Forecasts of zonal wind fields produced by the medium-range forecast (MRF) model of the National Meteorological Center are used to create predictions of the atmosphere's angular momentum at lead times of 1-10 days. Based on momentum forecasts archived for the period December 1985-November 1986, it is found that, on average, the MRF exhibits positive skill relative to persistence-based forecasts at all lead times. Over the entire one-year study period, the improvement over persistence exceeds 20 percent for 2-6 day forecasts and remains as large as 10 percent even for 10-day forecasts. On the other hand, skill scores for the MRF momentum predictions vary considerably from month to month, and for a sizable fraction of the study period, the MRF is less skillful than persistence.

Rosen, Richard D.↗

A nonlinear optimization approach for disturbance rejection in flexible space structures

In this paper the design of an active control law for the rejection of persistent disturbances in large space structures is presented. The control system design approach is based on a deterministic model of the disturbances, with a model-based-compensator (MBC) structure, optimizing the magnitude of the disturbance that the structure can tolerate without violating certain predetermined constraints. In addition to closed-loop stability, the explicit treatment of state, control and control rate constraints, such as structural displacement, control actuator effort, and compensator time guarantees that the final design will exhibit desired performance characteristics. The technique is applied for the vibration damping of a simple two bay truss structure which is subjected to persistent disturbances, such as shuttle docking. Preliminary results indicate that the proposed control system can reject considerable persistent disturbances by utilizing most of the available control, while limiting the structural displacements to within desired tolerances. Further work, however, for incorporating additional design criteria, such as compensator robustness to be traded-off against performance specifications, is warranted.

Parlos, Alexander G.↗

Aerospace devices for magnetic replicas

Retained persistent magnetic field has been studied and improved in the superconductor YBa2Cu3O7 (Y123). During the study, trapped magnetic field, B(t), has been increased by over a factor of 10(exp 5). Methods used to improve magnetic field trapping were principally: (1) the adoption of the Melt Texturing process to increase grain size; (2) the addition of excess Y to disperse deposits of Y2BaCuO5 (Y211) and again increase grain size; (3) irradiation with high energy particles including 1H+, 3He++, 4He++, and fission fragments; and (4) utilizing temperatures below 77 K has also been quantified as a way to increase trapped field. In addition, in our study of B(t), we have found laws governing creep, activation, temperature dependence, creep vs. current flow, etc. In the range 20 K less than or equal to T less than or equal to 65 K, and for B less than 10 Tesla, a simple empirical relationship was found: B(trap) (T2) = B(trap) (T1) ((Tc - T2)/(Tc - T1))squared where Tc is the critical temperature. The highest experimental trapped field was B(trap) = 3.96 Tesla, at 65 K. We believe this to be the highest persistent field ever produced, by any method. A two component model of the persistent currents has been developed. This accurately reproduces the data, using as parameters only the magnitude of a constant surface current, J(s), and a constant volume current J(v). The model successfully predicts B(t) (xyz) for the case of maximum trapped field, for all samples observed. It has also been extended to describe the unsaturated case either zero field cooled, or field cooled. Loss of strap with time has been studied for the critical state (Bt,max), and non critical state (Bt less than Bt,max), for times from a few minutes to a few months, for unirradiated material, for irradiation by 1H+, 3He++, 4He++, high z projectiles, and neutrons, and for all materials used in the overall study. We conclude that: (1) multi Tesla trapped fields are attained; (2) fields over 10 T are achievable; (3) creep is not a large problem; (4) application is feasible to motors, generators, magnets for particle beam optics, separators, levitating bearings, energy storage, shielding, and transportation.

Weinstein, Roy↗

The use of stellite scatterometer winds to drive a primitive equation model of the Indian Ocean: The impact of bandlike sampling

The aim of this study is to evaluate the impact of the bandlike sampling of spaceborne scatterometers on the ability of scatterometer winds to successfully force the mean flow and seasonal cycle of an ocean model in the context of equatorial and tropical dynamics. The equatorial ocean is simulated with a four-layer, primitive equation, reduced gravity model of the Indian Ocean. The variable wind stress used in this study is derived from one year (1988) of 6-hour analyses of the 10-m wind vector over the Indian Ocean performed at the European Centre for Medium-Range Weather Forecasts (ECMWF). It is applied as a forcing at every grid point of the model to drive a reference circulation. Scatterometer winds are simulated from ECMWF winds, using the nominal configurations and orbital parameters of the European Remote Sensing 1 (ERS-1) and NASA Scatterometer (NSCAT) missions. The model is forced in real time under swaths with the raw scatterometer winds of ERS-1 and NSCAT, with a persistence condition (i.e., the wind is kept constsnt until the next passage of the satellite provides a new value). The circulation obtained for each of the scatterometer experiments is compared with the reference circulation. The seasonal circulation of the Indian Ocean with NSCAT winds is very similar to the reference. The perturbations introduced by the bandlike sampling and the persistance condition have an impact similar to that of a small uncorrelated noise added to the reference forcing. The persistence condition for ERS-1 does not give results which are as good as those obtained for NSCAT.

Barnier, Bernard↗

Restoring and Maintaining Bone in Osteopenic Female Rat Skeleton: Changes in Bone Mass and Structure - Part 1

This experiment contains the crucial data for the lose, restore, and maintain (LRM) concept, a practical approach for reversing existing osteoporosis. The LRM concept uses anabolic agents to restore bone mass and architecture (+ phase) and then switches to an agent with the established ability to maintain bone mass, to keep the new bone (+/- phase). The purpose of this study was to learn whether switching to an agent known chiefly for its ability to maintain existing bone mass preserves new bone induced by PGE2, in osteopenic,estrogen-depleted rats. The current study had three phases, the bone loss (-), restore (+), and maintain (+/-) phases. We ovariectomized (OX) or sham ovariectomized (sham-OX) 5.5 month-old female rats (- phase). The OX rats were treated 5 months postovariectomy with 1-6 mg PGE2, per kg/day for 75 days to restore lost cancellous bone mass (+ phase), and then PGE2, treatment was stopped and treatment began with 1 or 5 micro-g/kg of risedronate, a bisphosphonate, twice a week for 60 days (+/- phase). During the loss (-) phase, the cancellous bone volume of the proximal tibial metaphysis in the OX rat fell to 19% of initial and 30% of age-matched control levels. During the restore (+) phase, the cancellous bone volume in OX rats doubled. When PGE2 treatment was stopped, however, and no special maintenance efforts were made during the maintain (+/-) phase, the PGE2-induced cancellous bone disappeared. In contrast, the PGE2-induced cancellous bone persisted when the PGE2 treatment was followed by either a 1 or 5 micro-g treatment of risedronate per kg given twice a week for 60 days during the maintain (+/-) phase. The tibial shaft demonstrated very little cortical bone loss during the loss (-) phase in OX rats. The tibial shaft cortical bone fell some 8%. During the restore (+) phase, new cortical bone in OX rats increased by 22%. When PGE2 treatment was stopped and nothing was given during the maintain (+/-) phase, however, all but the PGE2-induced subperiosteal bone disappeared. In contrast, when PGE2 treatment was stopped and 1 micro-g risedronate per kg twice a week for 60 days was administered during the maintenance (+/-) phase, the PGE2-induced subperiosteal bone and some of the subendocortical bone and marrow trabeculae persisted. When 5 micro-g risedronate per kg was given twice a week, all the PGE2-induced bone persisted. The study shows that most of the new cancellous and cortical bone induced by PGE2, can be maintained for at least 60 days after discontinuing PGE2 by administering enough of the resorption inhibitor, risedronate. The lower dose of risedronate was not adequate to save most of the PGE2-induced endocortical bone.

Tang, Li Ya↗

Properties of the Second Outburst of the Bursting Pulsar (GRO J1744-28) as Observed with BASTE

One year after its discovery, the Bursting Pulsar (GRO J1744-28) went into outburst again, displaying the hard X-ray bursts and pulsations that make this source unique. We report on BATSE (Burst and Transient Source Experiment) observations of both the persistent and burst emission for this second outburst and draw comparisons with the first. The second outburst was smaller than the first in both duration and peak luminosity. The persistent flux, burst peak flux, and burst fluence were all reduced in amplitude by a factor of approximately 1.7. Despite these differences, the two outbursts were very similar with respect to the burst occurrence rate, the durations and spectra of bursts, the absence of spectral evolution during bursts, and the evolution of the ratio alpha of average persistent to burst luminosity. Although no spectral evolution was found within individual bursts, we find evidence for a small (20%) variation of the spectral temperature during the course of the second outburst.

Woods, Peter M.↗

TOO Observations Soft Gamma Repeaters

The goal of the project was to study the X-ray properties of the persistent and burst emission of Soft Gamma Repeaters (SGRs) during periods of burst activity. We monitored this activity with BATSE on the Compton Gamma-Ray Observatory, and made X-ray observations with the Rossi X-ray Timing Explorer (RXTE). SGR1806-20 became active in October 1996. We made observations with the PCA on the RXTE in November 1996. In the RXTE data we detected several hundred brief SGR events, which occurred in clear bunches, and persistent emission. From a Fouder analysis of the persistent emission (excluding time intervals with bursts) we found a period of 7.47 s. These pulsations are also present in RXTE data taken several weeks later (PI Dr. T. Strohmayer), which were combined with our data. Comparison with ASCA data taken in 1993 and 1995 shows that the period, which reflects the spin of a neutron star, increases on a time scale of 1500 years. These results show that SGR1 806-20 is a neutron star with a superstrong magnetic field (about 1"15) Gauss), thereby establishing, for the first time, the existence of magnetars.

vanParadijs, J.↗

Evidence for a Sudden Magnetic Field Reconfiguration in SGR 1900+14

We report on the detection of large flux changes in the persistent X-ray flux of SGR 1900+14 during its burst active episode in 1998. Most notably, we find a factor of approximately 700 increase in the non-burst X-ray flux following the August 27th flare that decayed in time as a power-law. Throughout the decay of this flux enhancement, our measurements indicate that the pulse fraction remains constant. This indicates a global flux enhancement as a consequence of the August 27th flare rather than localized heating. While the persistent flux has since recovered to the pre-outburst level, the pulse profile has not. The pulse shape changed to a near sinusoidal profile within the tail of the August 27th flare (in gamma-rays) and this effect has persisted for more than 1.5 years (in X-rays). The results presented here suggest the magnetic field of the neutron star in SGR 1900+14 was significantly altered (perhaps globally) during the giant flare of August 27.

Woods, Peter M.↗

Evidence for a Sudden Magnetic Field Reconfiguration in Soft Gamma Repeater 1900+14

We report the detection of large flux changes in the persistent X-ray flux of soft gamma repeater (SGR) 1900 + 14 during its burst active episode in 1998. Most notably, we find a factor of approx. 700 increase in the nonburst X-ray flux following the August 27 flare, which decayed in time as a power law. Our measurements indicate that the pulse fraction remains constant throughout this decay. This suggests a global flux enhancement as a consequence of the August 27 flare rather than localized heating. While the persistent flux has since recovered to the preoutburst level, the pulse profile has not. The pulse shape changed to a near sinusoidal profile within the tail of the August 27 flare (in gamma-rays), and this effect has persisted for more than 1.5 years (in X-rays). The results presented here suggest that the magnetic field of the neutron star in SGR 1900 + 14 was significantly altered (perhaps globally) during the giant flare of August 27.

Woods, Peter M.↗

Body Weight Gain during Altered Gravity: Spaceflight, Centrifugation and Transitions

Gravity is a force that influences all living systems, and is often disregarded in the study of environment on growth and development. To assess the effect of gravity exposure on growth, immature rats (130-200 g) were evaluated during chronic altered gravity exposure and during transition between gravity fields. The effects of 14 days of spaceflight on body weight gain were evaluated (n=12) and compared to controls. Spaceflight did not affect weight gain. In 6 rats, the transition from spaceflight to 1 G showed a significant (p less than 0.05) post flight weight loss over 48 hr of 13 g compared to controls. Over subsequent days this loss was compensated for with no difference noted after 5 days. Exposure to hypergravity, 2 G for 16 days, was evaluated in groups of n=6 (Control; On Center Control (OCC); Centrifuged). With centrifugation or OCC there was a reduction in body weight within 24 hr. The OCC regained control weights within 13 days. The weight difference, 26 +/- 1 g, persisted with 2 G with no subsequent difference in weight gain over days 3-16 compared to controls; 3.7 +/- 0.1 versus 3.9 +/- 0.1 g/day respectively. Transition from centrifugation to 1 G resulted in a weight increase within 48 hours. Over 16 days the rate of gain was increased 3.1 +/- 0.1 g/day for centrifuge compared to 2.1 +/- 0.1 g/day for controls between Day 3 to 16. However, differences from control were still noted on Day 16. Transition from one gravity field to another causes acute changes in body weight. Transition to microgravity or 1 G, following the acute changes, results in adjustments to attain a normal weight. In hypergravity the acute reduction in body weight persist, but weight gain is normal. Transitioning from hypergravity to 1G results in an increased weight gain to compensate for the persistent reduction during exposure.

Wade, Charles E.↗