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At least 127 records · Page 7

Effects of nitrogen enrichment on tree carbon allocation: A global synthesis

Aim: Increased atmospheric nitrogen deposition may have profound effects on tree carbon allocation dynamics. However, a comprehensive understanding of how nitro-gen (N) enrichment influences carbon (C) allocation across plant functional processes and tree organs in individual trees remains elusive. Location: Global forest ecosystems. Time period: 1990–2018. Major taxa studied: Trees. Methods: We compiled data from 75 N addition experiments and conducted a meta-analysis to evaluate the responses of C source (photosynthesis), sinks (growth and respiration) and storage (non-structural carbohydrate concentrations) in different tree organs (foliage, above-ground wood and roots) to N enrichment. Results: N enrichment significantly enhanced C supply via photosynthesis (+39.6%, n = 128). C allocation to growth (biomass increment/production) significantly in-creased in foliage (+15.9%, n = 68) and above-ground wood (+31.8%, n = 64; bole, branch, stem and/or twig) with increasing N availability, but not in roots, whereas allocation increased in roots via increasing fine root turnover rate (+22.6%, n = 11). N fertilization significantly increased C allocation to respiration in above-ground wood (+46.6%, n = 12) and roots (+5.5%, n = 57), but not in foliage. N addition decreased non-structural carbohydrate (NSC) concentrations in foliage (-5.4%, n = 16) and roots (-5.0%, n = 21), but increased NSC in above-ground wood (+6.1%, n = 22). In addition, N enrichment effects were strongly affected by moderator variables. Main conclusions: Our results demonstrate that N addition increased C allocation to growth and respiration more strongly than C allocation to NSC storage, and increased C allocation to above-ground parts more strongly than to below-ground parts. Our results are useful for better understanding the response of tree functional processes at organ level to N enrichment. The existing data also reveal that more long-term ex-perimental studies on mature trees in tropical and boreal forests are urgently needed to provide a basis for forecasting tree responses to N enrichment at the global scale.

Li, Weibin↗

Disrupted NOS2 metabolism drives myoblast response to wasting-associated cytokines

Highlights: • Amino acid metabolism is impacted in myoblasts treated with cancer cell conditioned media. • Inflammatory cytokines induce nitric oxide synthase 2 in myoblasts. • Elevated nitric oxide synthase 2 activity impairs myoblast proliferation and differentiation. Skeletal muscle wasting drives negative clinical outcomes and is associated with a spectrum of pathologies including cancer. Cancer cachexia is a multi-factorial syndrome that encompasses skeletal muscle wasting and remains understudied, despite being a frequent and serious co-morbidity. Deviation from the homeostatic balance between breakdown and regeneration leads to muscle wasting disorders, such as cancer cachexia. Muscle stem cells (MuSCs) are the cellular compartment responsible for muscle regeneration, which makes MuSCs an intriguing target in the context of wasting muscle. Molecular studies investigating MuSCs and skeletal muscle wasting largely focus on transcriptional changes, but our group and others propose that metabolic changes are another layer of cellular regulation underlying MuSC dysfunction in cancer cachexia. In the present study, we combined gene expression and non-targeted metabolomic profiling of myoblasts exposed to wasting conditions (cancer cell conditioned media, CC-CM) to derive a more complete picture of the myoblast response to wasting factors. After mapping these features to annotated pathways, we found that more than half of the mapped pathways were amino acid-related, linking global amino acid metabolic disruption to conditioned media-induced myoblast defects. Notably, arginine metabolism was a highly enriched pathway in combined metabolomic and transcriptomic data. Arginine catabolism generates nitric oxide (NO), an important signaling molecule known to have negative effects on mature muscle. We hypothesize that tumor-derived disruptions in Nitric Oxide Synthase (NOS)2-regulated arginine catabolism impair differentiation of MuSCs. The work presented here further investigates the effect of NOS2 overactivity on myoblast proliferation and differentiation. We show that NOS2 inhibition is sufficient to rescue wasting phenotypes associated with inflammatory cytokines. Ultimately, this work provides new insights into MuSC biology and opens up potential therapeutic avenues for addressing disrupted MuSC dynamics in cancer cachexia.

60 APPLIED LIFE SCIENCES↗

Data reduction in deterministic neutron transport calculations using machine learning

Neutron cross section matrices for fission and scattering data are required for each material, temperature, and enrichment level to calculate the neutron transport equation accurately. Here, this information can be a limiting factor when using the multigroup discrete ordinates (S N ) method when the number of energy groups is large. Machine Learning (ML) can be used to replace the need for the cross section matrices by reproducing the function that maps the scalar flux to the scattering and fission sources. Through the use of autoencoders and Deep Jointly-Informed Neural Networks (DJINN), the data storage requirements are reduced by 94% of the original data for a 618 group problem. This is accomplished while preserving the scalar flux, maintaining generality, and decreasing wall clock times.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Application of the Rossi-alpha method to simulations of HEU and organic scintillators

The International Criticality Safety Benchmark Evaluation Project (ICSBEP) Handbook contains thousands of high-quality benchmark measurements that include detailed descriptions of experiment designs and exhaustive accounting of uncertainties. These benchmarks are used extensively by the criticality safety and nuclear data communities. A subcritical benchmark involving bare, highly enriched uranium (HEU) has yet to be accepted to the handbook. The Measurement of Uranium Subcritical and Critical (MUSiC) was proposed to address this gap. MUSiC will be performed at the National Criticality Experiments Research Center (NCERC) and will leverage bare HEU hemisphere shells that can be assembled in a variety of configurations. The measurement has the following key benefits: it will be the first set of fast, subcritical measurements of HEU to be submitted to ICSBEP; ten configurations will be measured spanning from nearly no multiplication to critical (e.g., it is a measurement of similar systems with different re activities); measurements of an all-HEU system will be of value for nuclear data validation, providing results that assist in determining biases in both measurements and simulations. A variety of detector systems will be used including a Neutron Multiplicity Array Detector (NoMAD) system (similar to the MC-15), four small volume 0.635 cm (#8960;) × 7.59 cm 3He detectors (ideal for measuring prompt neutron decay constants due to their fast recovery speed), and an array of eight 5.08 cm (#8960;) × 5.08 cm EJ-309 organic scintillator detectors. The focus of this work is the simulation of the subcritical MUSiC configurations including the EJ-309 detectors and the application of the Rossi-α method. The EJ-309 organic scintillator detector array is a new detection system that will be deployed at NCERC. Organic scintillators are ideal for measurements of fast, subcritical systems due to their short time response on the order of nanoseconds.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

YAHFC: A Code Framework to Model Nuclear Reactions and Estimate Correlated Uncertainties

Reaction modeling is a key ingredient in designing experiments and interpreting their results, and is an essential component in the process of evaluating nuclear data and assembling nuclear data libraries used in nuclear technology applications. Typically, experimental data are available only for a handful of reaction channels and theory models are used to fill in the gaps. In addition, theory is often called upon as the arbitrator between discrepant data. Most importantly, theory and modeling are required for an accurate determination of uncertainties in the evaluated data and the correlations between the multiple channels. A fast, accurate, and flexible modeling capability has been developed at LLNL with the code system YAHFC (Yet Another Hauser-Feshbach Code). YAHFC is a Monte Carlo, Hauser-Feshbach code framework, making full use of dynamic memory allocation, derived types, and parallel computing. YAHFC can generate events to simulate experiments and is guiding experiments designed to measure inelastic neutron scattering from actinide targets. YAHFC is also being used to analyze decays from surrogate experiments, thereby enabling the inference of reaction cross sections inaccessible by direct measurement. Finally, by modeling nuclear reactions with constraints from experimental data, YAHFC can deliver complete nuclear data libraries, with evaluated uncertainties, using the modernized Generalized Nuclear Data Structure (GNDS).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Advancing Fissile Materials Production Modeling with Adaptive Computing Environment and Simulations (ACES)

The Department of Energy’s National Nuclear Security Administration (DOE/NNSA) provides advanced capabilities to simulate the uranium enrichment process to support international negotiations on the peaceful use of nuclear energy. Uranium isotope separation centrifuges connected in a cascade configuration can produce the low-enriched uranium needed for nuclear power. However, those same centrifuges connected in a different configuration can also produce highly enriched uranium for nuclear weapons. Having the capability to assess cascade operations and identify nefarious activities promotes the peaceful uses of nuclear energy while restricting nuclear weapons proliferation. DNN R&D's Nonproliferation Stewardship Program Adaptive Computing Environment and Simulations (ACES) project is creating a modern, sustainable ecosystem of physics-based models and data-analytics tools that enables analysts to model uranium enrichment systems, simulate operational scenarios, and apply various policy options to explore potential outcomes.

07 ISOTOPE AND RADIATION SOURCES↗

Scientific machine learning for closure models in multiscale problems: A review

Here, closure problems are omnipresent when simulating multiscale systems, where some quantities and processes cannot be fully prescribed despite their effects on the simulation's accuracy. Recently, scientific machine learning approaches have been proposed as a way to tackle the closure problem, combining traditional (physics-based) modeling with data-driven (machine-learned) techniques, typically through enriching differential equations with neural networks. This paper reviews the different reduced model forms, distinguished by the degree to which they include known physics, and the different objectives of a priori and a posteriori learning. The importance of adhering to physical laws (such as symmetries and conservation laws) in choosing the reduced model form and choosing the learning method is discussed. The effect of spatial and temporal discretization and recent trends toward discretization-invariant models are reviewed. In addition, we make the connections between closure problems and several other research disciplines: inverse problems, Mori-Zwanzig theory, and multi-fidelity methods. In conclusion, much progress has been made with scientific machine learning approaches for solving closure problems, but many challenges remain. In particular, the generalizability and interpretability of learned models is a major issue that needs to be addressed further.

97 MATHEMATICS AND COMPUTING↗

Mic-hackathon 2024: hackathon on machine learning for electron and scanning probe microscopy

Microscopy is one of the primary sources of information on materials structure and functionality at the nanometer and atomic scales. The data generated through microscopy is often contained in well-structured datasets, enriched with extensive metadata and sample histories, although not always with the same level of detail or storage format. The broad incorporation of data management plans by major funding agencies ensures the preservation and accessibility of this data. However, deriving insights from these rich datasets remains challenging due to the lack of established code ecosystems, standardized benchmarks, and integration strategies. Correspondingly, the efficiency of data usage is very low, and time expenditures at the analysis stage are enormous. In addition to post-acquisition data analysis, the emergence of application programming interfaces by major microscope manufacturers now creates opportunities for real-time ML-based data analytics to enable automated decision making, and particularly ML-agent controlled real-time microscope operation. Despite these opportunities, there is a significant gap in integrating the ML community with the broader microscopy community, limiting the value that these methods bring to physics and materials discovery and materials optimization. Hackathons address these challenges by fostering collaboration between ML experts and microscopy professionals, encouraging the development of innovative solutions that leverage ML for microscopy and preparing the workforce of the future both for microscopy-intensive domains areas, instrument manufacturers, and ML scientists interested in real world applications for fundamental research, materials optimization, and manufacturing. The hackathon generated benchmark datasets and digital twins of microscopes that further contribute to the development of the field and establish data analysis ecosystems. All the codes can be found at GitHub(https://github.com/KalininGroup/Mic-hackathon-2024-codes-publication/tree/1.0.0.1) and Zenodo (https://zenodo.org/records/15579940).

97 MATHEMATICS AND COMPUTING↗

Contributions of anoxic microsites to soil carbon protection across soil textures

Anoxic microsites, zones of oxygen depletion in otherwise oxic soils, may slow soil C turnover. However, the abundance of anoxic microsites and their contribution to soil C protection is yet undefined. In this study, we determine the contribution of anoxic microsites to soil C protection in soils of three distinct textures (clay loam, loam, sandy loam) across a range of soil moistures. We examined the influence of soil oxygen supply by increasing oxygen content in the incubation atmosphere (oxygen enrichment) and through disaggregation. We attributed increases in CO 2 efflux to the aeration of anoxic microsites. The contribution of anoxic microsites to soil C protection increased with decreasing clay content. Clay loam CO 2 efflux was relatively unaffected by aeration. Moderately moist, loam soils had CO 2 effluxes that did not increase with oxygen enrichment but increased by 375% upon disaggregation. Sandy loam soil CO 2 efflux increased by 50–75% with oxygen enrichment and 250% with disaggregation. Geochemical and microbial data reveal that anoxic microsite abundance also increased with decreasing clay content. The proportion of acid extractable Fe present as Fe(II) increased with decreasing clay content, and methanogens were more abundant in loam and sandy loam soils. Our results suggest that oxygen demand, rather than supply, can regulate anoxic microsite formation and that anoxic protection of soil C can be diminished through physical disruption of soil structure. Our findings further illustrate that anoxic microsites should be included in conceptual models of soil C protection to avoid soil C loss and improve predictions of soil C response to disturbance.

58 GEOSCIENCES↗

Peripheral blood hematology, plasma biochemistry, and the optimization of an in vitro immune-based assay in the brown watersnake ( Nerodia taxispilota )

Reptiles represent a phylogenetic lineage that provides a unique link between ectothermic anamniotes and endothermic amniotes. Compared to mammalian and avian species, our understanding of the reptilian immune system is greatly lacking. This gap in knowledge is largely due to an absence of established immune-based assays or specific reagents for these species. In the present study, brown watersnakes (Nerodia taxispilota) were live-captured in the wild, sexed, weighed, measured, bled via the caudal vein and released. At 24 hr post-collection, peripheral blood leukocytes were enriched and evaluated with an established mammalian in-vitro lymphocyte proliferation assay. Snake peripheral blood leukocyte enrichment yielded > 90% lymphocytes with viabilities averaging 81.5%. Baseline physiologic data for N. taxispilota, including hematology and total solids, leukocyte differentials, cell recovery and plasma biochemistry, were also collected. Cells cultured with Concanavalin A exhibited significantly increased proliferation at both 72 and 96 hr. Furthermore, these preliminary results show that enriched peripheral blood from wild-caught N. taxispilota provides a sufficient yield of leukocytes that can be cultured and functionally evaluated using a standard mammalian in-vitro immune-based assay.

59 BASIC BIOLOGICAL SCIENCES↗

Coarse Woody Debris Decomposition Assessment Tool: Model validation and application

Coarse woody debris (CWD) is a significant component of the forest biomass pool; hence a model is warranted to predict CWD decomposition and its role in forest carbon (C) and nutrient cycling under varying management and climatic conditions. A process-based model, CWDDAT (Coarse Woody Debris Decomposition Assessment Tool) was calibrated and validated using data from the FACE (Free Air Carbon Dioxide Enrichment) Wood Decomposition Experiment utilizing pine ( Pinus taeda ), aspen ( Populous tremuloides ) and birch ( Betula papyrifera ) on nine Experimental Forests (EF) covering a range of climate, hydrology, and soil conditions across the continental USA. The model predictions were evaluated against measured FACE log mass loss over 6 years. Four widely applied metrics of model performance demonstrated that the CWDDAT model can accurately predict CWD decomposition. The R 2 (squared Pearson’s correlation coefficient) between the simulation and measurement was 0.80 for the model calibration and 0.82 for the model validation ( P <0.01). The predicted mean mass loss from all logs was 5.4% lower than the measured mass loss and 1.4% lower than the calculated loss. The model was also used to assess the decomposition of mixed pine-hardwood CWD produced by Hurricane Hugo in 1989 on the Santee Experimental Forest in South Carolina, USA. The simulation reflected rapid CWD decomposition of the forest in this subtropical setting. The predicted dissolved organic carbon (DOC) derived from the CWD decomposition and incorporated into the mineral soil averaged 1.01 g C m -2 y -1 over the 30 years. The main agents for CWD mass loss were fungi (72.0%) and termites (24.5%), the remainder was attributed to a mix of other wood decomposers. These findings demonstrate the applicability of CWDDAT for large-scale assessments of CWD dynamics, and fine-scale considerations regarding the fate of CWD carbon.

54 ENVIRONMENTAL SCIENCES↗

Status of the n+ 234 U evaluation in the resolved resonance region (*), (**)

In natural uranium, the 234 U isotope represents only 0.0055%, however, this minor isotope can affect highly enriched uranium metal benchmark calculations. In fact, enriched uranium contains more 234 U than natural uranium as the result of the uranium enrichment process. Therefore, the n+ 234 U nuclear data evaluation is one of the milestones of the APPENDIX B within the Nuclear Criticality Safety Program (NCSP).

AMPX↗

Laser-Induced Spectrochemical Assay for Uranium Enrichment (LISA-UE)

Uranium hexafluoride (UF6) is the uranium compound typically involved in uranium enrichment process. As the first line of defense against nuclear proliferation, accurate determinations of the uranium enrichment ratio in UF6 are critical for materials verification, accounting and safeguards. Shipping gaseous UF6 samples off-site for analysis with mass spectrometry is cumbersome and costly, and results are not available for some time (months). In-field UF6 enrichment assay has the potential to substantially reduce the time, logistics and expense of sample handling. At present, COMPUCEA is the only accepted method for UF6 enrichment assay in the field. Laser-Induced Spectrochemical Assay for Uranium Enrichment (LISA-UE) is an all-optical (based on laser induced plasma emission) analytical technique intended for fieldable, accurate, precise and rapid UF6 enrichment assay. In its operation, laser induced plasma is created directly in the gaseous UF6 sample. Because different U isotopes emit at slightly different wavelengths, the isotopic information of the UF6 sample is inherently encoded in the atomic emission from the plasma. Isotopic emissions from 235U and 238U are measured simultaneously, which eliminate correlated noise from the laser induced plasma. Isotopic information of the UF6 sample can be extracted from the acquired spectrum with theoretical multi-variable non-linear spectral fitting. To date, advances made by the LISA-UE research team include optimization of the spectral window for direct gaseous UF6 enrichment assay with laser induced plasma, development of data reduction algorithms, and demonstrations of the LISA-UE technique with gaseous UF6 samples. In this presentation, the technical aspect of LISA-UE will be overviewed, the data reduction algorithm will be described, and performance of the technique will be discussed.

Chan, George↗

Towards a RAG-based summarization for the Electron Ion Collider

Abstract The complexity and sheer volume of information — encompassing documents, papers, data, and other resources — from large-scale experiments demand significant time and effort to navigate, making the task of accessing and utilizing these varied forms of information daunting, particularly for new collaborators and early-career scientists.To tackle this issue, a Retrieval Augmented Generation (RAG)-based Summarization AI for EIC (RAGS4EIC) is under development. This AI-Agent not only condenses information but also effectively references relevant responses, offering substantial advantages for collaborators. Our project involves a two-step approach: first, querying a comprehensive vector database containing all pertinent experiment information; second, utilizing a Large Language Model (LLM) to generate concise summaries enriched with citations based on user queries and retrieved data. We describe the evaluation methods that use RAG assessments (RAGAs) scoring mechanisms to assess the effectiveness of responses. Furthermore, we describe the concept of prompt template based instruction-tuning which provides flexibility and accuracy in summarization. Importantly, the implementation relies on LangChain [1], which serves as the foundation of our entire workflow. This integration ensures efficiency and scalability, facilitating smooth deployment and accessibility for various user groups within the Electron Ion Collider (EIC) community. This innovative AI-driven framework not only simplifies the understanding of vast datasets but also encourages collaborative participation, thereby empowering researchers. As a demonstration, a web application has been developed to explain each stage of the RAG Agent development in detail. The application can be accessed athttps://rags4eic-ai4eic.streamlit.app.[A tagged version of the source code can be found inhttps://github.com/ai4eic/EIC-RAG-Project/releases/tag/AI4EIC2023_PROCEEDING.]

Instruments & Instrumentation↗

Dataset_for_Conserved_macromolecular_architecture_of_Poplar_secondary_cell_walls_revealed_by_ssNMR_and_atomistic_modeling

This dataset contains solid-state 13C NMR data and atomistic molecular dynamics simulation files supporting the study of nanoscale secondary cell wall architecture across 13 genetically diverse Populus trichocarpa genotypes grown under uniform greenhouse conditions in 13C-enriched CO2 atmospheres (~89% 13C enrichment).The dataset contains two collections of solid-state 13C NMR data. (1) 200 MHz data (Bruker Avance III HD, 4 mm HX probe, 10 kHz MAS): raw Bruker TopSpin experiment folders and DMFIT-exported ascii spectra for selective and non-selective 1D 13C-13C spin diffusion experiments (3000 ms mixing) used to quantify inter-polymer spatial proximities, and short-mixing (1 ms) reference spectra used for polymeric abundance quantification by spectral deconvolution. (2) 600 MHz data (Bruker Avance III, 1.6 mm PhoenixNMR HXY probe, 30 kHz MAS): raw Bruker TopSpin experiment folders containing 2D CORD, 2D CP-INADEQUATE, and 13C/1H relaxation (T1, T1rho) experiments for all 13 genotypes, with processed Excel workbooks per experiment type. Molecular dynamics simulation code, coordinate files, and analysis scripts (NAMD/CHARMM/Python) for six atomistic cell wall models are included. Summarized ssNMR data are compiled into a single excel file and subjected to statistical analysis. Multivariate analysis code (PCA, Pearson correlation) and summary data are provided as excel worksheets and Jupyter notebooks (Python 3).

09 BIOMASS FUELS↗

Comparison of gamma-ray spectral analysis methods for thick-walled UF 6 cylinders

Three data analysis methods were compared for gamma ray spectra collected by planar and coaxial high-purity germanium detectors (HPGe) on thick-walled uranium hexafluoride cylinders. The cylinder contents range from natural to low-enriched uranium (4.95% 235 U). Each spectrum was analyzed with the traditional 185.7 keV enrichment meter method, a 185.7/1001 keV ratio method, and the Fixed Energy Response Function Analysis with Multiple Efficiency (FRAM) software that utilizes low- and high-energy gamma rays and X-rays. When results for all cylinders were compared, the enrichment meter method and the 185.7/1001 keV peak ratio method consistently provided the most accurate data for all detector types. The error on the enrichment calculations analyzed with FRAM did not meet the international target value whereas those calculated with the enrichment meter and ratio method did. Enrichments calculated by FRAM were found to skew to higher values on natural uranium and to lower values on low-enriched uranium. FRAM calculated the least-precise enrichments; replicate analyses of single cylinders resulted in 235 U values that varied by as much as 19%. FRAM does have the significant advantages in that it does not require the use of calibration cylinders, infinite thickness criteria are not necessary, and it can be applied to any HPGe detector. Finally, if calibration cylinders are available, the enrichment meter and 185.7/1001 peak ratio are the recommended methods as they are the most accurate and precise.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Sulfur Species in Zinc-Rich Condylar Zones of a Rat Temporomandibular Joint

We performed synchrotron-based micro-X-ray absorption near-edge spectroscopy (µ-XANES) coupled with micro-X-ray fluorescence (µ-XRF) for the identification of elements that included biometal zinc (Zn) and nonmetal sulfur (S) (and its species) in the condylar zones of a rat temporomandibular joint (TMJ). Zone-specific spatial localization of biometal Zn and nonmetal S from a materials viewpoint when correlated with hypoxia inducible factor-1α (HIF-1α) (a surrogate for tissue oxygenation) can provide insights into Zn-specific redox pathways at the vulnerable subchondral interface. Histologic localization of Zn, HIF-1α, and sulfur-rich proteoglycans (PGs) were mapped using an optical microscope. The µ-XRF maps coupled with site-specific micro-X-ray diffraction (µ-XRD) patterns were used to underline Zn-incorporated biological apatite in the subchondral bone and the bone of a rat TMJ condyle. Results demonstrated an association between Zn, PG, and HIF-1α histologic maps with µ-XRF, µ-XANES, and µ-XRD data and provided insights into plausible biological S species in Zn-enriched zones of a rat TMJ condyle. Spatially localized Zn and S underscore their roles in cell and tissue functions in a zone-specific manner. Elemental Zn with organic and inorganic S species at the cartilage-bone interface and the biomineral phase of Zn-enriched biological apatite from subchondral bone to condylar bone were ascertained using µ-XRF-XANES and µ-XRF-XRD. The coupled µ-XRF-XANES in situ complemented with µ-XRF-XRD in situ and immunohistochemistry provided valuable biological insights into zone-specific biological pathways in rat TMJ condyles. Based on these data, we present a workflow to reliably map and correlate S species within Zn-enriched regions of cartilage, bone, and their interface. We suggest the use of this correlative and complementary microspectroscopic spatial information for zone-specific localization of biometal Zn and nonmetal S to gain insights into plausible microanatomy-specific oxidative stress in the TMJ.

apatites↗