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Background: Rapid monitoring of biomass conversion processes using techniques such as near-infrared (NIR) spectroscopy can be substantially quicker and less labor-, resource-, and energy-intensive than conventional measurement techniques such as gas or liquid chromatography (GC or LC) due to the lack of solvents and preparation methods, as well as removing the need to transfer samples to an external lab for analytical evaluation. The purpose of this study was to determine the feasibility of rapid monitoring of a biomass conversion process using NIR spectroscopy combined with multivariate statistical modeling, and to examine the impact of (1) subsetting the samples in the original dataset by process location and (2) reducing the spectral range used in the calibration model on model performance., Results: We develop multivariate calibration models for the concentrations of soluble xylo-oligosaccharides (XOS), monomeric xylose, and total solids at multiple points in a biomass conversion process which produces and then purifies XOS compounds from sugar cane bagasse. A single model using samples from multiple locations in the process stream showed acceptable performance as measured by standard statistical measures. However, compared to the single model, we show that separate models built by segregating the calibration samples according to process location show improved performance. We also show that combining an understanding of the sample spectra with simple multivariate analysis tools can result in a calibration model with a substantially smaller spectral range that provides essentially equal performance to the full-range model., Conclusions: We demonstrate that real-time monitoring of soluble xylo-oligosaccharides (XOS), monomeric xylose, and total solids concentration at multiple points in a process stream using NIR spectroscopy coupled with multivariate statistics is feasible. Segregation of sample populations by process location improves model performance. Models using a reduced spectral range containing the most relevant spectral signatures show very similar performance to the full-range model, reinforcing the importance of performing robust exploratory data analysis before beginning multivariate modeling., (© 2024. The Author(s).)

Metabolite extraction is the critical first-step in metabolomics experiments, where it is generally regarded to inactivate and remove proteins. Here, arising from efforts to improve extraction conditions for polar metabolomics, we discover a proteomic landscape of over 1000 proteins within metabolite extracts. This is a ubiquitous feature across several common extraction and sample types. By combining post-resuspension stable isotope addition and enzyme inhibitors, we demonstrate in-extract metabolite interconversions due to residual transaminase activity. We extend these findings with untargeted metabolomics where we observe extensive protein-mediated metabolite changes, including in-extract formation of glutamate dipeptide and depletion of total glutathione. Finally, we present a simple extraction workflow that integrates 3 kDa filtration for protein removal as a superior method for polar metabolomics. In this work, we uncover a previously unrecognized, protein-mediated source of observer effects in metabolomics experiments with broad-reaching implications across all research fields using metabolomics and molecular metabolism., (© 2024. The Author(s).)

Background: Neurofibromin, coded by the NF1 tumor suppressor gene, is the main negative regulator of the RAS pathway and is frequently mutated in various cancers. Women with Neurofibromatosis Type I (NF1)-a tumor predisposition syndrome caused by a germline NF1 mutation-have an increased risk of developing aggressive breast cancer with poorer prognosis. The mechanism by which NF1 mutations lead to breast cancer tumorigenesis is not well understood. Therefore, the objective of this work was to identify stromal alterations before tumor formation that result in the increased risk and poorer outcome seen among NF1 patients with breast cancer., Approach: To accurately model the germline monoallelic NF1 mutations in NF1 patients, we utilized an Nf1- deficient rat model with accelerated mammary development before presenting with highly penetrant breast cancer., Results: We identified increased collagen content in Nf1 -deficient rat mammary glands before tumor formation that correlated with age of tumor onset. Additionally, gene expression analysis revealed that Nf1 -deficient mature adipocytes in the rat mammary gland have increased collagen expression and shifted to a fibroblast and preadipocyte expression profile. This alteration in lineage commitment was also observed with in vitro differentiation, however, flow cytometry analysis did not show a change in mammary adipose-derived mesenchymal stem cell abundance., Conclusion: Collectively, this study uncovered the previously undescribed role of Nf1 in mammary collagen deposition and regulating adipocyte differentiation. In addition to unraveling the mechanism of tumor formation, further investigation of adipocytes and collagen modifications in preneoplastic mammary glands will create a foundation for developing early detection strategies of breast cancer among NF1 patients., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Arumugam, Tovar, Essenburg, Dischinger, Beddows, Wolfrum, Madaj, Turner, Feenstra, Gallik, Cohen, Nichols, Sheridan, Esquibel, Mouneimne, Graveel and Steensma.)

Malignant peripheral nerve sheath tumors (MPNSTs) are chemotherapy resistant sarcomas that are a leading cause of death in neurofibromatosis type 1 (NF1). Although NF1-related MPNSTs derive from neural crest cell origin, they also exhibit intratumoral heterogeneity. TP53 mutations are associated with significantly decreased survival in MPNSTs, however the mechanisms underlying TP53-mediated therapy responses are unclear in the context of NF1-deficiency. We evaluated the role of two commonly altered genes, MET and TP53, in kinome reprograming and cellular differentiation in preclinical MPNST mouse models. We previously showed that MET amplification occurs early in human MPNST progression and that Trp53 loss abrogated MET-addiction resulting in MET inhibitor resistance. Here we demonstrate a novel mechanism of therapy resistance whereby p53 alters MET stability, localization, and downstream signaling leading to kinome reprogramming and lineage plasticity. Trp53 loss also resulted in a shift from RAS/ERK to AKT signaling and enhanced sensitivity to MEK and mTOR inhibition. In response to MET, MEK and mTOR inhibition, we observed broad and heterogeneous activation of key differentiation genes in Trp53-deficient lines suggesting Trp53 loss also impacts lineage plasticity in MPNSTs. These results demonstrate the mechanisms by which p53 loss alters MET dependency and therapy resistance in MPNSTS through kinome reprogramming and phenotypic flexibility., (© 2024. The Author(s).)

Tokamak operational regimes with small edge localized modes (ELMs) could be a solution to the problem of large transient heat loads in fusion reactors. A ballooning mode near the last closed flux surface governed by the pressure gradient and the magnetic shear there has been proposed for small ELMs. In this Letter, we experimentally investigate several stabilizing effects near the last closed flux surface and present linear ideal simulations that indeed develop ballooninglike fluctuations there and connect them with nonlinear resistive simulations. The dimensionless parameters of the small ELM regime in the region of interest are very similar to those in a reactor, making this regime the ideal exhaust scenario for a future device.

Autophagic dysregulation and lysosomal impairment have been implicated in the pathogenesis of Parkinson's disease, partly due to the identification of mutations in multiple genes involved in these pathways such as GBA, SNCA, ATP13a2 (also known as PARK9), TMEM175 and LRRK2. Mutations resulting in lysosomal dysfunction are proposed to contribute to Parkinson's disease by increasing α-synuclein levels, that in turn may promote aggregation of this protein. Here, we used two different genetic models-one heterozygous for a mutated form of the GBA protein (D409V), and the other heterozygous for an ATP13a2 loss-of-function mutation, to test whether these mutations exacerbate the spread of α-synuclein pathology following injection of α-synuclein preformed fibrils in the olfactory bulb of 12-week-old mice. Contrary to our hypothesis, we found that mice harboring GBA D409V +/- and ATP13a2 +/- mutations did not have exacerbated behavioral impairments or histopathology (α-synuclein, LAMP2, and Iba1) when compared to their wildtype littermates. This indicates that in the young mouse brain, neither the GBA D409V mutation or ATP13a2 loss-of-function mutation accelerate the spread of α-synuclein pathology. As a consequence, we postulate that these mutations increase Parkinson's disease risk only by acting in one of the initial, upstream events in the Parkinson's disease pathogenic process. Further, the mutations, and the molecular pathways they impact, appear to play a less important role once the pathogenic process has been triggered and therefore do not specifically influence α-synuclein pathology spread., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Hyperglycemia affects over 400 million individuals worldwide. The detrimental health effects are well studied at the tissue level, but the in vivo effects at the organelle level are poorly understood. To establish such an in vivo model, we used mice lacking TXNIP, a negative regulator of glucose uptake. Examining mitochondrial function in brown adipose tissue, we find that TXNIP KO mice have a lower content of polyunsaturated fatty acids (PUFAs) in their membrane lipids, which affects mitochondrial integrity and electron transport chain efficiency and ultimately results in lower mitochondrial heat output. This phenotype can be rescued by a ketogenic diet, confirming the usefulness of this model and highlighting one facet of early cellular damage caused by excess glucose influx., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.)

Analysis of formalin-fixed paraffin-embedded (FFPE) tissue by immunohistochemistry (IHC) is commonplace in clinical and research laboratories. However, reports suggest that IHC results can be compromised by biospecimen preanalytical factors. The National Cancer Institute's Biospecimen Preanalytical Variables Program conducted a systematic study to examine the potential effects of delay to fixation (DTF) and time in fixative (TIF) on IHC using 24 cancer biomarkers. Differences in IHC staining, relative to controls with a DTF of 1 hr, were observed in FFPE kidney tumor specimens after a DTF of ≥2 hr. Reductions in H-score and/or staining intensity were observed for c-MET, p53, PAX2, PAX8, pAKT, and survivin, whereas increases were observed for RCC1, EGFR, and CD10. Prolonged TIF of 72 hr resulted in significantly reduced H-scores of CD44 and c-Met in kidney tumor specimens, compared with controls with 12-hr TIF. An elevated probability of altered staining intensity due to DTF was observed for nine antigens, whereas for prolonged TIF an elevated probability was observed for one antigen. Results reported here and elsewhere across tumor types and antigens support limiting DTF to ≤1 hr when possible and fixing tissues in formalin for 12-24 hr to avoid confounding effects of these preanalytical factors on IHC.

Glycero- and sphingo-lipids are important in plasma membrane structure, caloric storage and signaling. An un-targeted lipidomics approach for a cohort of critically ill pediatric intensive care unit (PICU) patients undergoing multi-organ dysfunction syndrome (MODS) was compared to sedation controls. After IRB approval, patients meeting the criteria for MODS were screened, consented ( n = 24), and blood samples were collected from the PICU at HDVCH, Michigan; eight patients needed veno-arterial extracorporeal membrane oxygenation (VA ECMO). Sedation controls were presenting for routine sedation ( n = 4). Plasma lipid profiles were determined by nano-electrospray (nESI) direct infusion high resolution/accurate mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Biostatistics analysis was performed using R v 3.6.0. Sixty-one patient samples over three time points revealed a ceramide metabolite, hexosylceramide (Hex-Cer) was high across all time points (mean 1.63-3.19%; vs. controls 0.22%). Fourteen species statistically differentiated from sedation controls ( p -value ≤ 0.05); sphingomyelin (SM) [SM(d18:1/23:0), SM(d18:1/22:0), SM(d18:1/23:1), SM(d18:1/21:0), SM(d18:1/24:0)]; and glycerophosphotidylcholine (GPC) [GPC(36:01), GPC(18:00), GPC(O:34:02), GPC(18:02), GPC(38:05), GPC(O:34:03), GPC(16:00), GPC(40:05), GPC(O:36:03)]. Hex-Cer has been shown to be involved in viral infection and may be at play during acute illness. GPC(36:01) was elevated in all MODS patients at all time points and is associated with inflammation and brain injury.

Lipids are molecules involved in metabolism and inflammation. This study investigates the plasma lipidome for markers of severity and nutritional status in critically ill children. Children with multi-organ dysfunction syndrome (MODS) ( n = 24) are analyzed at three time-points and cross-referenced to sedation controls ( n = 4) for a total of N = 28. Eight of the patients with MODS, needed veno-arterial extracorporeal membrane oxygenation (VA ECMO) support to survive. Blood plasma lipid profiles are quantified by nano-electrospray (nESI), direct infusion high resolution/accurate mass spectrometry (MS), and tandem mass spectrometry (MS/MS), and compared to nutritional profiles and pediatric logistic organ dysfunction (PELOD) scores. Our results show that PELOD scores were not significantly different between MODS and ECMO cases across time-points ( p = 0.66). Lipid profiling provides stratification between sedation controls and all MODS patients for total lysophosphatidylserine (lysoPS) ( p -value = 0.004), total phosphatidylserine (PS) ( p -value = 0.015), and total ether-linked phosphatidylethanolamine (ether-PE) ( p -value = 0.03) after adjusting for sex and age. Nutrition intake over time did not correlate with changes in lipid profiles, as measured by caloric and protein intake. Lipid measurement in the intensive care environment shows dynamic changes over an 8-day pediatric intensive care unit (PICU) course, suggesting novel metabolic indicators for defining critically ill children.

Objective: Social-emotional processing is key to daily interactions and routines, yet a challenging construct to quantify. Measuring social and emotional processing in young children, children with language impairments, or non-verbal children, presents additional challenges. This study addresses a pressing need for tools to probe internal responses such as feelings, drives, and motivations that do not rely on intact language skills., Methods: In this study, we extend our recent success of inducing conditioned place preference (CPP) in children to demonstrate the success of using a social unconditioned stimulus in the CPP paradigm in both typically developing children (n = 36) and in children with a diagnosis of autism spectrum disorder (n = 14)., Results: This is the first study to demonstrate successful social conditioned place preference in the human population. Both typically developing children and children with autism spectrum disorder demonstrate significant social conditioned place preference by spending significantly more time in the room paired with social interaction following training., Conclusions: Significant heterogeneity of CPP scores in both groups of children indicates that social motivation is expressed along a continuum, and that the CPP paradigm may provide a more comprehensive characterization of social motivation beyond a diagnosis of an autism spectrum disorder for each child., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Hyposmia is evident in over 90% of Parkinson's disease (PD) patients. A characteristic of PD is intraneuronal deposits composed in part of α-synuclein fibrils. Based on the analysis of post-mortem PD patients, Braak and colleagues suggested that early in the disease α-synuclein pathology is present in the dorsal motor nucleus of the vagus, as well as the olfactory bulb and anterior olfactory nucleus, and then later affects other interconnected brain regions. Here, we bilaterally injected α-synuclein preformed fibrils into the olfactory bulbs of wild type male and female mice. Six months after injection, the anterior olfactory nucleus and piriform cortex displayed a high α-synuclein pathology load. We evaluated olfactory perceptual function by monitoring odor-evoked sniffing behavior in a plethysmograph at one-, three- and six-months after injection. No overt impairments in the ability to engage in sniffing were evident in any group, suggesting preservation of the ability to coordinate respiration. At all-time points, females injected with fibrils exhibited reduced odor detection sensitivity, which was observed with the semi-automated plethysmography apparatus, but not a buried pellet test. In future studies, this sensitive methodology for assessing olfactory detection deficits could be used to define how α-synuclein pathology affects other aspects of olfactory perception and to clarify the neuropathological underpinnings of these deficits.

Neurofibromatosis Type 1 (NF1)-related Malignant Peripheral Nerve Sheath Tumors (MPNST) are highly resistant sarcomas that account for significant mortality. The mechanisms of therapy resistance are not well-understood in MPNSTs, particularly with respect to kinase inhibition strategies. In this study, we aimed to quantify the impact of both the genomic context and targeted therapy on MPNST resistance using reverse phase phosphoproteome array (RPPA) analysis. We treated tumorgrafts from three genetically engineered mouse models using MET (capmatinib) and MEK (trametinib) inhibitors and doxorubicin, and assessed phosphosignaling at 4 h, 2 days, and 21 days. Baseline kinase signaling in our mouse models recapitulated an MET-addicted state (NF1-MET), P53 mutation (NF1-P53), and HGF overexpression (NF1). Following perturbation with the drug, we observed broad and redundant kinome adaptations that extended well beyond canonical RAS/ERK or PI3K/AKT/mTOR signaling. MET and MEK inhibition were both associated with an initial inflammatory response mediated by kinases in the JAK/STAT pathway and NFkB. Growth signaling predominated at the 2-day and 21-day time points as a result of broad RTK and intracellular kinase activation. Interestingly, AXL and NFkB were strongly activated at the 2-day and 21-day time points, and tightly correlated, regardless of the treatment type or genomic context. The degree of kinome adaptation observed in innately resistant tumors was significantly less than the surviving fractions of responsive tumors that exhibited a latency period before reinitiating growth. Lastly, doxorubicin resistance was associated with kinome adaptations that strongly favored growth and survival signaling. These observations confirm that MPNSTs are capable of profound signaling plasticity in the face of kinase inhibition or DNA damaging agent administration. It is possible that by targeting AXL or NFkB, therapy resistance can be mitigated.

Study Question: Can endometrial stromal stem/progenitor cell markers, SUSD2 and CD146/CD140b, enrich for human myometrial and fibroid stem/progenitor cells?, Summary Answer: SUSD2 enriches for myometrial and fibroid cells that have mesenchymal stem cell (MSC) characteristics and can also be induced to decidualise., What Is Known Already: Mesenchymal stem-like cells have been separately characterised in the endometrial stroma and myometrium and may contribute to diseases in their respective tissues., Study Design, Size, Duration: Normal myometrium, fibroids and endometrium were collected from hysterectomies with informed consent. Primary cells or tissues were used from at least three patient samples for each experiment., Participants/materials, Setting, Methods: Flow cytometry, immunohistochemistry and immunofluorescence were used to characterise tissues. In vitro colony formation in normoxic and hypoxic conditions, MSC lineage differentiation (osteogenic and adipogenic) and decidualisation were used to assess stem cell activity. Xenotransplantation into immunocompromised mice was used to determine in vivo stem-like activity. Endpoint measures included quantitative PCR, colony formation, trichrome, Oil Red O and alkaline phosphatase activity staining., Main Results and the Role of Chance: CD146+CD140b+ and/or SUSD2+ myometrial and fibroid cells were located in the perivascular region and formed more colonies in vitro compared to control cells and differentiated down adipogenic and osteogenic mesenchymal lineages in vitro. SUSD2+ myometrial cells had greater in vitro decidualisation potential, and SUSD2+ fibroid cells formed larger tumours in vivo compared to control cells., Large-Scale Data: N/A., Limitations, Reasons for Caution: Markers used in this study enrich for cells with stem/progenitor cell activity; however, they do not distinguish stem from progenitor cells. SUSD2+ myometrial cells express markers of decidualisation when treated in vitro, but in vivo assays are needed to fully demonstration their ability to decidualise., Wider Implications of the Findings: These results suggest a possible common MSC for the endometrial stroma and myometrium, which could be the tumour-initiating cell for uterine fibroids., Study Funding/competing Interest(s): These studies were supported by NIH grants to JMT (R01OD012206) and to ALP (F32HD081856). The authors certify that we have no conflicts of interest to disclose., (© The Author(s) 2020. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The publicly available NREL suite of laboratory analytical procedures (LAPs) provides researchers with the analytical tools to determine the composition of woody and herbaceous feedstocks. Feedstock characterization includes several steps: sample preparation, starch determination, moisture analysis, ashing, extraction, and hydrolysis. These steps provide information on specific compounds and classes of compounds such as ash, protein, moisture, extractives, sucrose, starch, glucan, xylan, galactan, arabinan, acetate and lignin. Here, we describe the use of these procedures to characterize sorghum [Sorghum bicolor (L.) Moench] with specific consideration of four main sorghum types: grain, forage, sweet, and biomass, which can vary significantly in composition. Special attention is paid to the extraction and the differentiation of glucose from starch and glucan from cellulose in the hybrids with significant amounts of nonstructural carbohydrates.

Uterine remodeling during pregnancy is a fundamental, dynamic process required for successful propagation of eutherian species. The uterus can increase in size up to 40-fold during pregnancy, which is largely attributed to expansion of the myometrium by hyperplasia and hypertrophy. After pregnancy, the uterus repairs the remodeled or "damaged" tissue during uterine involution (INV). Little is known about this repair process, particularly the role of mesenchymal stem/progenitor cells. The objective of this study was to identify and characterize putative mesenchymal stem/progenitor cells in the murine myometrium using a combination of label retention and mesenchymal stem cell (MSC) marker expression and a pregnancy and uterine INV model. Tet-off transgenic mice with the Cre-lox system were used to specifically label mesenchymal cells (ie, myometrial and endometrial stromal cells) within the uterus while avoiding other cell types (eg, epithelial, immune, and endothelial cells) to identify slowly dividing cells and assess their stem cell qualities. We identified myometrial label-retaining cells (LRCs) that persisted for at least 3 months, expressed CD146 and CD140b (MSC markers), and proliferated at a higher rate during uterine INV compared with nonlabeled cells. The LRCs did not appear to express either estrogen receptor alpha or progesterone receptor, nor did the number of LRCs change at different estrous stages or in response to exogenous estradiol or progesterone administration, suggesting that LRCs were not involved in normal estrous cycling. The results from this study provide important insight into putative stem/progenitor cells in the myometrium and their possible role in uterine physiology.

The thermal helium beam edge diagnostic has recently been upgraded at the ASDEX Upgrade (AUG) tokamak experiment. Line ratio spectroscopy on neutral helium is a valuable tool for simultaneous determination of the electron temperature and density of plasmas. The diagnostic now offers a temporal resolution of 900 kHz with a spatial resolution of up to 3 mm at 32 lines of sight (LOS) simultaneously. The LOS covers a radial region of 8.5 cm, starting at the limiter radius and reaching into the confined region beyond the separatrix. Two components are of particular importance for the aforementioned hardware improvements. The first is the optical head, which collects the light from the experiment. Equipped with an innovative clamping system for optical fiber ends, an arbitrary distribution pattern of LOS can be achieved to gain radial and poloidal profiles. The second major development is a new polychromator system that measures the intensity of the 587 nm, 667 nm, 706 nm, and 728 nm helium lines simultaneously for 32 channels with filter-photomultiplier tube arrays. Thus, the thermal helium beam diagnostic supplements the AUG edge diagnostics, offering fast and spatially highly resolved electron temperature and density profile measurements that cover the plasma edge and scrape-off layer region. Plasma fluctuations, edge localized modes, filaments, and other turbulent structures are resolved, allowing analysis of their frequency and localization or their propagation velocity.

Recurrence of Clostridium difficile infection (CDI) places a major burden on the healthcare system. Previous studies have suggested that specific C. difficile strains, or ribotypes, are associated with severe disease and/or recurrence. However, in some patients a new strain is detected in subsequent infections, complicating longitudinal studies focused on strain differences that may contribute to disease outcome. We examined ribotype composition over time in patients who did or did not develop recurrence to examine infection with multiple C. difficile ribotypes (mixed infection), during the course of infection. Using a retrospective patient cohort, we isolated and ribotyped a median of 36 C. difficile colonies from 61 patients (105 total samples) at initial infection, recurrence (a second case of CDI within 15-56 days of initial infection), and reinfection (a second case of CDI after 56 days of initial infection). We observed mixed infection in 78.6% of samples at initial infection in patients who went on to develop recurrence compared to 18.1% of patients who did not, and mixed infection remained associated with subsequent recurrence after adjusting for gender and prior antibiotic exposure (OR 3.5, 95% CI 1.3-9.4, P = .015). In patients who were sampled longitudinally (44 consecutive events in 32 patients), the dominant ribotype changed in 31.8% of consecutive samples and the newly dominant ribotype was not detected in prior samples from that patient. Our results suggest that mixed C. difficile infection is more prevalent than previously demonstrated and potentially a marker of susceptibility to recurrence., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Background: Biofuels derived from lignocellulosic plant material are an important component of current renewable energy strategies. Improvement efforts in biofuel feedstock crops have been primarily focused on increasing biomass yield with less consideration for tissue quality or composition. Four primary components found in the plant cell wall contribute to the overall quality of plant tissue and conversion characteristics, cellulose and hemicellulose polysaccharides are the primary targets for fuel conversion, while lignin and ash provide structure and defense. We explore the genetic architecture of tissue characteristics using a quantitative trait loci (QTL) mapping approach in Panicum hallii , a model lignocellulosic grass system. Diversity in the mapping population was generated by crossing xeric and mesic varietals, comparative to northern upland and southern lowland ecotypes in switchgrass. We use near-infrared spectroscopy with a primary analytical method to create a P. hallii specific calibration model to quickly quantify cell wall components., Results: Ash, lignin, glucan, and xylan comprise 68% of total dry biomass in P. hallii : comparable to other feedstocks. We identified 14 QTL and one epistatic interaction across these four cell wall traits and found almost half of the QTL to localize to a single linkage group., Conclusions: Panicum hallii serves as the genomic model for its close relative and emerging biofuel crop, switchgrass ( P. virgatum ). We used high throughput phenotyping to map genomic regions that impact natural variation in leaf tissue composition. Understanding the genetic architecture of tissue traits in a tractable model grass system will lead to a better understanding of cell wall structure as well as provide genomic resources for bioenergy crop breeding programs.

In magnetically confined fusion plasmas controlled gas injection is crucial for plasma fuelling as well as for various diagnostic applications such as active spectroscopy. We present a new, versatile system for the injection of collimated thermal gas beams into a vacuum chamber. This system consists of a gas pressure chamber, sealed by a custom made piezo valve towards a small capillary for gas injection. The setup can directly be placed inside of the vacuum chamber of fusion devices as it is small and immune against high magnetic fields. This enables gas injection close to the plasma periphery with high duty cycles and fast switch on/off times ≲ 0.5 ms. In this work, we present the design details of this new injection system and a systematic characterization of the beam properties as well as the gas flowrates which can be accomplished. The thin and relatively short capillary yields a small divergence of the injected beam with a half opening angle of 20°. The gas box is designed for pre-fill pressures of 10 mbar up to 100 bars and makes a flowrate accessible from 10 18 part/s up to 10 23 part/s. It hence is a versatile system for both diagnostic as well as fuelling applications. The implementation of this system in ASDEX Upgrade will be described and its application for line ratio spectroscopy on helium will be demonstrated on a selected example.

Background: For biofuel production processes to be economically efficient, it is essential to maximize the production of monomeric carbohydrates from the structural carbohydrates of feedstocks. One strategy for maximizing carbohydrate production is to identify less recalcitrant feedstock cultivars by performing some type of experimental screening on a large and diverse set of candidate materials, or by identifying genetic modifications (random or directed mutations or transgenic plants) that provide decreased recalcitrance. Economic efficiency can also be increased using additional pretreatment processes such as deacetylation, which uses dilute NaOH to remove the acetyl groups of hemicellulose prior to dilute acid pretreatment. In this work, we used a laboratory-scale screening tool that mimics relevant thermochemical pretreatment conditions to compare the total sugar yield of three near-isogenic brown midrib ( bmr ) mutant lines and the wild-type (WT) sorghum cultivar. We then compared results obtained from the laboratory-scale screening pretreatment assay to a large-scale pretreatment system., Results: After pretreatment and enzymatic hydrolysis, the bmr mutants had higher total sugar yields than the WT sorghum cultivar. Increased pretreatment temperatures increased reactivity for all sorghum samples reducing the differences observed at lower reaction temperatures. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples, and reduced the differences in total sugar yields among them, but solubilized a sizable fraction of the non-structural carbohydrates. The general trends of increased total sugar yield in the bmr mutant compared to the WT seen at the laboratory scale were observed at the large-scale system. However, in the larger reactor system, the measured total sugar yields were lower and the difference in total sugar yield between the WT and bmr sorghum was larger., Conclusions: Sorghum bmr mutants, which have a reduced lignin content showed higher total sugar yields than the WT cultivar after dilute acid pretreatment and enzymatic hydrolysis. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples. However, since deacetylation also solubilizes a large fraction of the non-structural carbohydrates, the ability to derive value from these solubilized sugars will depend greatly on the proposed conversion process.

Background: In an effort to find economical, carbon-neutral transportation fuels, biomass feedstock compositional analysis methods are used to monitor, compare, and improve biofuel conversion processes. These methods are empirical, and the analytical variability seen in the feedstock compositional data propagates into variability in the conversion yields, component balances, mass balances, and ultimately the minimum ethanol selling price (MESP). We report the average composition and standard deviations of 119 individually extracted National Institute of Standards and Technology (NIST) bagasse [Reference Material (RM) 8491] run by seven analysts over 7 years. Two additional datasets, using bulk-extracted bagasse (containing 58 and 291 replicates each), were examined to separate out the effects of batch, analyst, sugar recovery standard calculation method, and extractions from the total analytical variability seen in the individually extracted dataset. We believe this is the world's largest NIST bagasse compositional analysis dataset and it provides unique insight into the long-term analytical variability. Understanding the long-term variability of the feedstock analysis will help determine the minimum difference that can be detected in yield, mass balance, and efficiency calculations., Results: The long-term data show consistent bagasse component values through time and by different analysts. This suggests that the standard compositional analysis methods were performed consistently and that the bagasse RM itself remained unchanged during this time period. The long-term variability seen here is generally higher than short-term variabilities. It is worth noting that the effect of short-term or long-term feedstock compositional variability on MESP is small, about $0.03 per gallon., Conclusions: The long-term analysis variabilities reported here are plausible minimum values for these methods, though not necessarily average or expected variabilities. We must emphasize the importance of training and good analytical procedures needed to generate this data. When combined with a robust QA/QC oversight protocol, these empirical methods can be relied upon to generate high-quality data over a long period of time.

Experiments have been performed at ASDEX Upgrade, aiming to investigate the impact of lithium in an all-metal-wall tokamak and attempting to enhance the pedestal operational space. For this purpose, a lithium pellet injector has been developed, capable of injecting pellets carrying a particle content ranging from 1.82 × 10(19) atoms (0.21 mg) to 1.64 × 10(20) atoms (1.89 mg). The maximum repetition rate is about 2 Hz. Free flight launch from the torus outboard side without a guiding tube was realized. In such a configuration, angular dispersion and speed scatter are low, and a transfer efficiency exceeding 90% was achieved in the test bed. Pellets are accelerated in a gas gun; hence special care was taken to avoid deleterious effects by the propellant gas pulse. Therefore, the main plasma gas species was applied as propellant gas, leading to speeds ranging from 420 m/s to 700 m/s. In order to minimize the residual amount of gas to be introduced into the plasma vessel, a large expansion volume equipped with a cryopump was added into the flight path. In view of the experiments, an optimal propellant gas pressure of 50 bars was chosen for operation, since at this pressure maximum efficiency and low propellant gas flux coincide. This led to pellet speeds of 585 m/s ± 32 m/s. Lithium injection has been achieved at ASDEX Upgrade, showing deep pellet penetration into the plasma, though pedestal broadening has not been observed yet.

In a wide variety of natural and laboratory magnetized plasmas, filaments appear as a result of interchange instability. These convective structures substantially enhance transport in the direction perpendicular to the magnetic field. According to filament models, their propagation may follow different regimes depending on the parallel closure of charge conservation. This is of paramount importance in magnetic fusion plasmas, as high collisionality in the scrape-off layer may trigger a regime transition leading to strongly enhanced perpendicular particle fluxes. This work reports for the first time on an experimental verification of this process, linking enhanced transport with a regime transition as predicted by models. Based on these results, a novel scaling for global perpendicular particle transport in reactor relevant tokamaks such as ASDEX-Upgrade and JET is found, leading to important implications for next generation fusion devices.

This article proposes a new method to evaluate basic characteristics of the dynamics of a coherent plasma structure (blob). With this method, one can evaluate the propagation angle of a blob in a two-dimensional plasma cross section as well as the blob velocity, size, and amplitude from one-dimensional data. The method is applied to blob measurements from the Lithium beam emission spectroscopy system in ASDEX-Upgrade. Statistical features of the observed blob velocities, angles of propagation, blob sizes, and amplitudes are discussed. The validity of the method is examined by comparing two values of the propagation angle that are evaluated in an independent manner.

The lithium beam diagnostic at ASDEX Upgrade routinely delivers electron density profiles in the plasma edge by lithium beam impact excitation spectroscopy. An accurate background subtraction requires a periodically chopped lithium beam. A new, improved chopping system was developed and installed. It involves a voltage modulation for the extractor electrode and the beam deflection plates. The modulation of the extractor electrode reduces the unused portion of lithium ions and improves the stability of the beam with respect to its position. Furthermore, the data indicate an extended emitter lifetime. The extractor chopping was also found to be insensitive to sparks. The deflection chopping experiments demonstrated beam chopping in the kilohertz range. The significantly higher modulation frequency of the deflection chopping improves background subtraction of fast transient events. It allows a more accurate density measurements in the scrape off layer during impurity injections and edge localized modes.

First experiments with nonaxisymmetric magnetic perturbations, toroidal mode number n=2, produced by newly installed in-vessel saddle coils in the ASDEX Upgrade tokamak show significant reduction of plasma energy loss and peak divertor power load associated with type-I edge localized modes (ELMs) in high-confinement mode plasmas. ELM mitigation is observed above an edge density threshold and is obtained both with magnetic perturbations that are resonant and not resonant with the edge safety factor profile. Compared with unperturbed type-I ELMy reference plasmas, plasmas with mitigated ELMs show similar confinement, similar plasma density, and lower tungsten impurity concentration.

Turbulence properties in the scrape-off layer (SOL) in the presence of ion cyclotron frequency heating (ICRH) are compared to instances where it is absent. The discharges are all in a high-confinement mode (H-mode) regime. During ICRH, the SOL plasma density increases whereas turbulence large-scale and convective structures are shown to be suppressed. The probability distribution function is thus recorded to be closer to a Gaussian, and a net decrease in the low-frequency density fluctuations is reflected in the power spectra. Consequently, the level of turbulent fluctuations decreases significantly. Turbulence suppression is also reported during edge localized modes (ELMs) where both the ELMs-induced transport and duration are strongly affected. The increase of neutrals by gas puffing did not alter this behavior. We deduce that ICRH can be used as to suppress convective transport and reduce the ELM's amplitude.

The toroidal rotation of H-mode plasmas in ASDEX Upgrade is studied in the outermost 5 cm of the confined plasma. The projection of the rotation velocity along the line of sight (approximately toroidal) is measured using charge exchange recombination spectroscopy, with a radial resolution of up to 3 mm and a temporal resolution of 1.9 ms. At about 1 cm inside the separatrix the rotation exhibits a local minimum. From there, the rotation in codirection increases towards the plasma center and towards the separatrix. The latter increase is the focus of this work. It is situated in the region of the edge transport barrier and amounts to 10-20 km/s. It is observed for D+, He2+, B5+, and C6+. The described rotation feature at the edge is not visible during an ELM crash and is probably connected to the occurrence of steep gradients in this plasma region.

Experimental x-ray spectra of the H-like 2p --> 1s (Lyman-alpha) doublet have been obtained using time-integrated high-resolution spectroscopy of a constrained-flow, laser-generated aluminum plasma. These spectra show monotonic alteration of the relative intensities of the doublet components with distance from the target surface. Excellent agreement between experiment and theory is found only if the modeling includes both ion collisional rates between the fine-structure components of the level and, more importantly, the radiative pumping of one Lyman-alpha component by the other component along the direction of the major velocity gradient (i.e., perpendicular to the direction of spectra observation). Understanding radiation transfer in plasmas with high velocity gradients is important in modeling many astrophysical objects, and this experiment acts as a benchmark for such complex calculations.

We present detailed spectroscopic analysis of the primary K-shell emission lines from a uniaxially expanding laser-produced hydrogenic and heliumlike aluminum plasma. The spectroscopic measurements are found to be consistent with time-dependent hydrodynamic properties of the plasma, measured using Thomson scattering and shadowgraphy. The K-shell population kinetics code FLY with the measured hydrodynamic parameters is used to generate spectra that are compared to the experimental spectra. Excellent agreement is found between the measured and calculated spectra for a variety of experimental target widths employed to produce plasmas with different optical depths. The peak emission from the hydrogenic Lyman series is determined to be from a temporal and spatial region where the hydrodynamic parameters are essentially constant. This allows a single steady-state solution of FLY to be used to deduce the electron temperature and density, from the measured line ratios and linewidths, for comparison with the Thomson and shadowgraphy data. These measurements are found to agree well with time-dependent calculations, and provide further validation for the FLY calculations of the ionization and excitation balance for a K-shell aluminum plasma. We also discuss the possible application of this data as a benchmark for hydrodynamic simulations and ionization/excitation balance calculations.