20,069 results on '"Schmutz"'
Search Results
2. The Impacts of Climate Change on Coastal Georgia Heritage Tourism Sites
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Corkran, Reilly T., Potter, Amy E., and Schmutz, Phillip P.
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- 2023
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3. Non-exchangeable networks of integrate-and-fire neurons: spatially-extended mean-field limit of the empirical measure
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Jabin, Pierre-Emmanuel, Schmutz, Valentin, and Zhou, Datong
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Mathematics - Probability ,Mathematics - Analysis of PDEs ,Quantitative Biology - Neurons and Cognition - Abstract
The dynamics of exchangeable or spatially-structured networks of $N$ interacting stochastic neurons can be described by deterministic population equations in the mean-field limit $N\to\infty$, when synaptic weights scale as $O(1/N)$. This asymptotic behavior has been proven in several works but a general question has remained unanswered: does the $O(1/N)$ scaling of synaptic weights, by itself, suffice to guarantee the convergence of network dynamics to a deterministic population equation, even when networks are not assumed to be exchangeable or spatially structured? In this work, we consider networks of stochastic integrate-and-fire neurons with arbitrary synaptic weights satisfying only a $O(1/N)$ scaling condition. Borrowing results from the theory of dense graph limits (graphons), we prove that, as $N\to\infty$, and up to the extraction of a subsequence, the empirical measure of the neurons' membrane potentials converges to the solution of a spatially-extended mean-field partial differential equation (PDE). Our proof requires analytical techniques that go beyond standard propagation of chaos methods. In particular, we introduce a weak metric that depends on the dense graph limit kernel and we show how the weak convergence of the initial data can be obtained by propagating the regularity of the limit kernel along the dual-backward equation associated with the spatially-extended mean-field PDE. Overall, this result invites us to re-interpret spatially-extended population equations as universal mean-field limits of networks of neurons with $O(1/N)$ synaptic weight scaling., Comment: 49 pages
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- 2024
4. Local electrochemical characterization of active Mg-Fe materials: from pure Mg to Mg50-Fe composites
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Ott, Noémie, Fillon, Aurélien Tournier, Renk, Oliver, Kremmer, Thomas, Pogatscher, Stefan, Suter, Thomas, and Schmutz, Patrik
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Condensed Matter - Materials Science ,Physics - Instrumentation and Detectors - Abstract
This study demonstrates the applicability of the scanning electrochemical nanocapillary (SEN) technique to characterize the local surface reactivity of active systems, such as Mg-based materials. Owing to its confined electrolyte configuration, one undeniable strength of the method is to provide with unprecedented resolution direct visualization and assessment of the presence, distribution and nobility of different phases. High lateral resolution open-circuit potential (OCP) scans on single Fe-rich particles in Mg confirms that these particles serve as local cathodes while evidencing enhanced surface activation at the interfacial area between the particle and the Mg matrix. Valuable insights about nanoscale galvanic coupling within an intermetallic particle can therefore be retrieved, which are otherwise not accessible. On more complex systems, such as Mg50-Fe composites, the SEN technique allows individual assessment of the reactivity of the different microscale phases. By combining OCP scans and local potentiodynamic polarization measurements, we reveal that changes in surface reactivity and stability of Mg-rich phases in these composites are directly correlated to their different microstructure, i.e. phase spacing and composition, which are intrinsically linked to their processing parameters. The SEN technique is therefore an excellent tool to help us refine our mechanistic understanding of initial stages of corrosion in heterogeneous materials.
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- 2024
5. Beach User Perception of the Economic and Ecological Services of Sand Dunes at Pensacola Beach, Florida
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Harris, Emily, Schmutz, Phillip P., Jackson, Chloe A., Anaya, Miranda, Johnson, Martha, and Chapman, Guy
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- 2020
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6. Scleral Fixation of a Toric Lens to Treat Corneal Astigmatism in Eyes without Capsular Support
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Ward MS, Hou AC, Murphy DA, Schmutz MA, and Riaz KM
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aphakia ,toric ,suture fixation ,secondary lens ,astigmatism ,Ophthalmology ,RE1-994 - Abstract
Matthew S Ward,1 Andrew C Hou,2 David A Murphy,2 Mason A Schmutz,3 Kamran M Riaz2 1Riverwoods Eye Center, Provo, UT, USA; 2Dean McGee Eye Institute, University of Oklahoma, Oklahoma City, OK, USA; 3Excel Eye Center, Saratoga Springs, UT, USACorrespondence: Kamran M RiazDean McGee Eye Institute, University of Oklahoma, 608 Stanton L Young Blvd, Suite 313, Oklahoma City, OK, 73104, USATel +1 405-271-1095Fax +1 405-271-3680Email Kamran-Riaz@dmei.orgPurpose: To describe surgical technique and report short-term visual outcomes after suture-fixation of a single-piece eyelet-toric (SET) intraocular lens (IOL) for treatment of concurrent aphakia and astigmatism.Design: Retrospective, noncomparative, and non-consecutive case series.Methods: This was a case series of eleven eyes who underwent successful SET. Eligible eyes had loss of capsular support or aphakia with a minimum of symmetric corneal astigmatism 1.75 diopters (D). Outcome measures included uncorrected distance visual acuity (UDVA), corrected distance visual acuity (CDVA), magnitude of residual refractive cylinder, and complications resulting from the SET procedure.Results: Preoperative UDVA and CDVA in logMAR scale were 1.46 and 0.45, respectively. Mean preoperative keratometric and refractive cylinder were 3.67 D and 2.52D, respectively. Postoperative UDVA and CDVA were 0.51 and 0.27, respectively, three months after surgery (POM3). Residual refractive cylinder at POM3 was 0.93 D.Conclusion: SET technique reduced refractive cylinder and improved UDVA and CDVA. SET may be adapted by surgeons using a readily available IOL and familiar scleral-fixation maneuvers.Keywords: aphakia, toric, suture fixation, secondary lens, astigmatism
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- 2021
7. Unlocking saponin biosynthesis in soapwort
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Jo, Seohyun, El-Demerdash, Amr, Owen, Charlotte, Srivastava, Vikas, Wu, Dewei, Kikuchi, Shingo, Reed, James, Hodgson, Hannah, Harkess, Alex, Shu, Shengqiang, Plott, Chris, Jenkins, Jerry, Williams, Melissa, Boston, Lori-Beth, Lacchini, Elia, Qu, Tongtong, Goossens, Alain, Grimwood, Jane, Schmutz, Jeremy, Leebens-Mack, Jim, and Osbourn, Anne
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Biological Sciences ,Industrial Biotechnology ,Biotechnology ,Complementary and Integrative Health ,Medicinal and Biomolecular Chemistry ,Biochemistry and Cell Biology ,Biochemistry & Molecular Biology ,Biochemistry and cell biology ,Medicinal and biomolecular chemistry - Abstract
Soapwort (Saponaria officinalis) is a flowering plant from the Caryophyllaceae family with a long history of human use as a traditional source of soap. Its detergent properties are because of the production of polar compounds (saponins), of which the oleanane-based triterpenoid saponins, saponariosides A and B, are the major components. Soapwort saponins have anticancer properties and are also of interest as endosomal escape enhancers for targeted tumor therapies. Intriguingly, these saponins share common structural features with the vaccine adjuvant QS-21 and, thus, represent a potential alternative supply of saponin adjuvant precursors. Here, we sequence the S. officinalis genome and, through genome mining and combinatorial expression, identify 14 enzymes that complete the biosynthetic pathway to saponarioside B. These enzymes include a noncanonical cytosolic GH1 (glycoside hydrolase family 1) transglycosidase required for the addition of D-quinovose. Our results open avenues for accessing and engineering natural and new-to-nature pharmaceuticals, drug delivery agents and potential immunostimulants.
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- 2024
8. Tuning the water intrinsic permeability of PEGDA hydrogel membranes by adding free PEG chains of varying molar masses
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Eddine, Malak Alaa, Carvalho, Alain, Schmutz, M., Salez, Thomas, de Chateauneuf-Randon, Sixtine, Bresson, Bruno, Pantoustier, Nadège, Monteux, C., and Belbekhouche, S.
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Condensed Matter - Soft Condensed Matter ,Physics - Chemical Physics - Abstract
We explore the effect of poly (ethylene glycol) (PEG) molar mass on the intrinsic permeability and structural characteristics of poly (ethylene glycol) diacrylate PEGDA/PEG composite hydrogel membranes. We observe that by varying the PEG content and molar mass, we can finely adjust the water intrinsic permeability over several orders of magnitude. Notably, we show the existence of a maximum water intrinsic permeability, already identified in a previous study to be located at the critical overlap concentration C^* of PEG chains, for the highest PEG molar mass studied. Furthermore, we note that the maximum intrinsic permeability follows a non-monotonic evolution with respect to the PEG molar mass and reaches its peak at 35 000 g.mol-1. Besides our results show that a significant fraction of PEG chains is irreversibly trapped within the PEGDA matrix even for the shortest molar masses down to 600 g.mol-1. This observation suggests the possibility of covalent grafting of PEG chains to the PEGDA matrix. CryoSEM and AFM measurements demonstrate the presence of large micron-sized cavities separated by PEGDA-rich walls whose nanometric structure strongly depends on the PEG content. By combining our permeability and structural measurements, we suggest that the PEG chains trapped inside the PEGDA rich walls induce nanoscale defects in the cross linking density, resulting in an increased permeability below C^*. Conversely, above C^*, we speculate that partially-trapped PEG chains may form a brush-like arrangement on the surface of the PEGDA-rich walls, leading to a reduction in permeability. These two opposing effects are anticipated to exhibit molar-mass-dependent trends, contributing to the non-monotonic variation of the maximum intrinsic permeability at C^*. Overall, our results demonstrate the potential to fine-tune the properties of hydrogel membranes, offering new opportunities in separation applications.
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- 2024
9. Improving population estimates of threatened spectacled eiders: correcting aerial counts for visibility bias
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Lewis, TL, Swaim, MA, Schmutz, JA, and Fischer, JB
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Zoology ,QL1-991 ,Botany ,QK1-989 - Abstract
Listed as ‘threatened’ under the US Endangered Species Act in 1993, the spectacled eider Somateria fischeri population in western Alaska, USA, has since rebounded, prompting an assessment of their suitability for delisting. This assessment, however, is limited by aerial-based population estimates that are incompletely corrected for unobserved eiders. Notably, aerial counts of eiders are corrected with a visibility correction factor (VCF), calculated as the ratio of ground-based nest counts to aerial pair counts, which disregards spatial variation in eider density. Accordingly, we (1) stratified our study area into zones of low, medium, and high eider density, (2) developed density-adjusted VCFs for each stratum, (3) evaluated the influence of several ecological factors on VCFs, and (4) estimated eider population size using our density-adjusted VCFs. For the low-density stratum, we estimated a VCF (± SE) of 1.35 ± 0.15, indicating that aerial counts of eider pairs closely matched ground counts of nests. In medium and high-density strata, VCFs increased to 2.46 ± 0.17 and 3.09 ± 0.19, respectively, suggesting that aerial detection decreased as eider densities increased. VCFs also increased for surveys that occurred late relative to nest initiation. Population estimates produced with our density-adjusted VCFs were 42% (5580 eiders) lower, on average, than those produced with the traditional VCF, which is currently used. Such large differences underscore the importance of accounting for density when correcting counts for incomplete detection, and, for threatened species such as spectacled eiders, may determine whether populations retain protected status.
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- 2019
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10. Comprehensive evaluation of Manikin-based airway training with second generation supraglottic airway devices
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Schmutz A, Bohn E, Spaeth J, and Heinrich S
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Emergency airway management ,Supraglottic airway device ,SAD ,Airway training manikin ,Failed intubation: treatment ,LMA: intubation guide ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Axel Schmutz, Erich Bohn, Johannes Spaeth, Sebastian Heinrich Department of Anesthesiology and Critical Care, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany Background: Supraglottic airway devices (SADs) are an essential second line tool during difficult airway management after failed tracheal intubation. Particularly for such challenging situations the handling of an SAD requires sufficient training. We hypothesized that the feasibility of manikin-based airway management with second generation SADs depends on the type of manikin.Methods: Two airway manikins (TruCorp AirSim® and Laerdal Resusci Anne® Airway Trainer™) were evaluated by 80 experienced anesthesia providers using 5 different second generation SADs (LMA® Supreme™ [LMA], Ambu® AuraGain™, i-gel®, KOO™-SGA and LTS-D™). The primary outcome of the study was feasibility of ventilation measured by assessment of the manikins’ lung distention. As secondary outcome measures, oropharyngeal leakage pressure (OLP), ease of gastric tube insertion the insertion time, position and subjective assessments were evaluated.Results: Ventilation was feasible with all combinations of SAD and manikin. By contrast, an OLP exceeding 10 cm H2O could be reached with most of the SADs in the TruCorp but with the LTS-D only in the Laerdal manikin. Gastric tube insertion was successful in above 90% in the Laerdal vs 87% in the TruCorp manikin (P
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- 2019
11. Genome resources for three modern cotton lines guide future breeding efforts.
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Sreedasyam, Avinash, Lovell, John, Mamidi, Sujan, Khanal, Sameer, Jenkins, Jerry, Plott, Christopher, Bryan, Kempton, Li, Zhigang, Shu, Shengqiang, Carlson, Joseph, Goodstein, David, De Santiago, Luis, Kirkbride, Ryan, Calleja, Sebastian, Campbell, Todd, Koebernick, Jenny, Dever, Jane, Scheffler, Jodi, Pauli, Duke, Jenkins, Johnie, McCarty, Jack, Williams, Melissa, Boston, LoriBeth, Webber, Jenell, Udall, Joshua, Chen, Z, Bourland, Fred, Stiller, Warwick, Saski, Christopher, Grimwood, Jane, Chee, Peng, Jones, Don, and Schmutz, Jeremy
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Gossypium ,Genome ,Plant ,Plant Breeding ,Cotton Fiber ,Genetic Variation ,Phenotype - Abstract
Cotton (Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars (UGA230, UA48 and CSX8308) and updating the TM-1 cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from Pima cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.
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- 2024
12. The complex polyploid genome architecture of sugarcane
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Healey, AL, Garsmeur, O, Lovell, JT, Shengquiang, S, Sreedasyam, A, Jenkins, J, Plott, CB, Piperidis, N, Pompidor, N, Llaca, V, Metcalfe, CJ, Doležel, J, Cápal, P, Carlson, JW, Hoarau, JY, Hervouet, C, Zini, C, Dievart, A, Lipzen, A, Williams, M, Boston, LB, Webber, J, Keymanesh, K, Tejomurthula, S, Rajasekar, S, Suchecki, R, Furtado, A, May, G, Parakkal, P, Simmons, BA, Barry, K, Henry, RJ, Grimwood, J, Aitken, KS, Schmutz, J, and D’Hont, A
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Agricultural ,Veterinary and Food Sciences ,Biological Sciences ,Genetics ,Agricultural Biotechnology ,Crop and Pasture Production ,Horticultural Production ,Human Genome ,Biotechnology ,Zero Hunger ,Chromosomes ,Plant ,Genome ,Plant ,Haplotypes ,Hybridization ,Genetic ,Plant Breeding ,Polyploidy ,Saccharum ,Reference Standards ,DNA ,Plant ,General Science & Technology - Abstract
Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.
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- 2024
13. Neue Wege in der interdisziplinären Fließgewässerforschung – Vorstellung des FWF-Doktoratsprogramms „Industrialisierte Flusslandschaften“ im Rahmen der Doktoratsschule HR21 an der BOKU Wien
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Hein, T., Bondar-Kunze, E., Ertl, T., Graf, W., Habersack, H., Haidvogl, G., Hauer, C., Hood-Nowotny, R., Laaha, G., Mehdi-Schulz, B., Mitter, H., Schinegger, R., Schmid, E., Schmid, M., Schmutz, S., Seher, W., Stockinger, M., Stöglehner, G., Stumpp, C., Weigelhofer, G., and Langergraber, G.
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- 2024
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14. Curbing the major and growing threats from invasive alien species is urgent and achievable
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Roy, Helen E., Pauchard, Aníbal, Stoett, Peter J., Renard Truong, Tanara, Meyerson, Laura A., Bacher, Sven, Galil, Bella S., Hulme, Philip E., Ikeda, Tohru, Kavileveettil, Sankaran, McGeoch, Melodie A., Nuñez, Martin A., Ordonez, Alejandro, Rahlao, Sebataolo J., Schwindt, Evangelina, Seebens, Hanno, Sheppard, Andy W., Vandvik, Vigdis, Aleksanyan, Alla, Ansong, Michael, August, Tom, Blanchard, Ryan, Brugnoli, Ernesto, Bukombe, John K., Bwalya, Bridget, Byun, Chaeho, Camacho-Cervantes, Morelia, Cassey, Phillip, Castillo, María L., Courchamp, Franck, Dehnen-Schmutz, Katharina, Zenni, Rafael Dudeque, Egawa, Chika, Essl, Franz, Fayvush, Georgi, Fernandez, Romina D., Fernandez, Miguel, Foxcroft, Llewellyn C., Genovesi, Piero, Groom, Quentin J., González, Ana Isabel, Helm, Aveliina, Herrera, Ileana, Hiremath, Ankila J., Howard, Patricia L., Hui, Cang, Ikegami, Makihiko, Keskin, Emre, Koyama, Asuka, Ksenofontov, Stanislav, Lenzner, Bernd, Lipinskaya, Tatsiana, Lockwood, Julie L., Mangwa, Dongang C., Martinou, Angeliki F., McDermott, Shana M., Morales, Carolina L., Müllerová, Jana, Mungi, Ninad Avinash, Munishi, Linus K., Ojaveer, Henn, Pagad, Shyama N., Pallewatta, Nirmalie P. K. T. S., Peacock, Lora R., Per, Esra, Pergl, Jan, Preda, Cristina, Pyšek, Petr, Rai, Rajesh K., Ricciardi, Anthony, Richardson, David M., Riley, Sophie, Rono, Betty J., Ryan-Colton, Ellen, Saeedi, Hanieh, Shrestha, Bharat B., Simberloff, Daniel, Tawake, Alifereti, Tricarico, Elena, Vanderhoeven, Sonia, Vicente, Joana, Vilà, Montserrat, Wanzala, Wycliffe, Werenkraut, Victoria, Weyl, Olaf L. F., Wilson, John R. U., Xavier, Rafael O., and Ziller, Sílvia R.
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- 2024
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15. Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment.
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Ma, Xiao, Vanneste, Steffen, Chang, Jiyang, Ambrosino, Luca, Barry, Kerrie, Bayer, Till, Bobrov, Alexander, Boston, LoriBeth, Campbell, Justin, Chen, Hengchi, Chiusano, Maria, Dattolo, Emanuela, Grimwood, Jane, He, Guifen, Jenkins, Jerry, Khachaturyan, Marina, Marín-Guirao, Lázaro, Mesterházy, Attila, Muhd, Danish-Daniel, Pazzaglia, Jessica, Plott, Chris, Rajasekar, Shanmugam, Rombauts, Stephane, Ruocco, Miriam, Scott, Alison, Tan, Min, Van de Velde, Jozefien, Vanholme, Bartel, Webber, Jenell, Wong, Li, Yan, Mi, Sung, Yeong, Novikova, Polina, Schmutz, Jeremy, Reusch, Thorsten, Procaccini, Gabriele, Olsen, Jeanine, and Van de Peer, Yves
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Alismatales ,Zosteraceae ,Ecosystem - Abstract
We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the savannahs of the sea are of major concern in times of climate change and loss of biodiversity.
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- 2024
16. Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs
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Bredeson, Jessen V, Mudd, Austin B, Medina-Ruiz, Sofia, Mitros, Therese, Smith, Owen Kabnick, Miller, Kelly E, Lyons, Jessica B, Batra, Sanjit S, Park, Joseph, Berkoff, Kodiak C, Plott, Christopher, Grimwood, Jane, Schmutz, Jeremy, Aguirre-Figueroa, Guadalupe, Khokha, Mustafa K, Lane, Maura, Philipp, Isabelle, Laslo, Mara, Hanken, James, Kerdivel, Gwenneg, Buisine, Nicolas, Sachs, Laurent M, Buchholz, Daniel R, Kwon, Taejoon, Smith-Parker, Heidi, Gridi-Papp, Marcos, Ryan, Michael J, Denton, Robert D, Malone, John H, Wallingford, John B, Straight, Aaron F, Heald, Rebecca, Hockemeyer, Dirk, Harland, Richard M, and Rokhsar, Daniel S
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Ecological Applications ,Bioinformatics and Computational Biology ,Biological Sciences ,Genetics ,Environmental Sciences ,Human Genome ,Generic health relevance ,Animals ,Chromatin ,Evolution ,Molecular ,Genome ,Anura ,Xenopus ,Centromere - Abstract
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
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- 2024
17. X-ray Observations of the Enigmatic Wolf-Rayet System Theta Mus: Two's Company But Three's a Crowd
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Skinner, Stephen L., Zhekov, Svetozar A., Guedel, Manuel, and Schmutz, Werner
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
Theta Mus is a remarkable spectroscopic binary (SB) consisting of a carbon-type Wolf-Rayet star and OV companion (WC6+O6-7V) in a 19-day orbit. In addition an O-supergiant is visually detected at a small offset of 46 mas and if gravitationally bound to the SB system would have an orbital period of many decades. Theta Mus is X-ray bright and a nonthermal radio source as commonly observed in massive colliding wind (CW) binaries. We present new Chandra X-ray observations of Theta Mus which complement previous XMM-Newton observations. The X-ray emission consists of a cool nearly steady weakly-absorbed plasma component with broad redshifted emission lines located in an extended region far from the SB system. Hotter plasma is also present traced by Fe XXV emission. The observed flux in the 2-5 keV range dropped significantly on a timescale of less than 5 years. The flux decrease can be attributed to an increase in absorption toward the hotter plasma which is likely located in the confined wind interaction region of the short-period SB system. The X-ray emission of Theta Mus is remarkably similar to the WC+O binary gamma^2 Vel including carbon recombination spectral lines but both systems show unusual line centroid properties that challenge CW models., Comment: 22 pages, 4 figures, 3 tables
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- 2023
18. In Search of Meaning and Relevance: Applying Participant-Centered Learning at Holocaust Sites
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Wolfgang Schmutz, Yariv Lapid, and Paul Salmons
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Educational visits to historical sites related to the Holocaust face significant constraints: Groups have limited time to see the site; guides are meeting students for the first time; they do not know them or what preparation (if any) students have had. Teachers and students expect guides to share their expertise, show them the most important parts of the site, and relate the historical narrative. Guides, similarly, often feel a tremendous responsibility to share their knowledge and impart meaning, perhaps even more so in the case of the Holocaust. All of these factors can lead to highly guide-centered tours and very passive participants. We, the authors, argue that this approach disempowers the learner and may miss opportunities for deeper engagement. Therefore, we propose a more participant-centered approach based on social constructivist pedagogy that encourages deep conversations about ethical issues and in which students are more actively involved in their own meaning-making.
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- 2024
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19. Changes in the Total Solar Irradiance and climatic effects
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Schmutz Werner K.
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total solar irradiance ,tsi ,observations ,radiometry ,space mission ,maunder minimum ,terrestrial climate ,climate variations ,Meteorology. Climatology ,QC851-999 - Abstract
The correlation between the averaged reconstructed March temperature record for Kyoto, Japan, and the reconstructed Total Solar Irradiance (TSI) over 660 years from 1230 to 1890 gives evidence with 98% probability that the Little Ice Age with four cold periods is forced by variations of TSI. If the correlation is restricted to the period 1650–1890, with two cold periods in the 17th and 19th century and for which two independent reconstructed March temperature records are available, the probability of solar forcing increases to 99.99%. As solar irradiance variations have a global effect there has to be a global climatic solar forcing impact. However, by how much global temperature were lower during these minima and with what amplitude TSI was varying is not accurately known. The two quantities, global temperature and TSI, are linked by the energy equilibrium equation for the Earth system. The derivation of this equation with respect to a variation of the solar irradiance has two terms: A direct forcing term, which can be derived analytically and quantified accurately from the Stefan-Boltzmann law, and a second term, describing indirect influences on the surface temperature. If a small TSI variation should force a large temperature variation, then it has to be the second indirect term that strongly amplifies the effect of the direct forcing. The current knowledge is summarized by three statements:During the minima periods in the 13th, 15/16th, 17th, and 19th centuries the terrestrial climate was colder by 0.5–1.5 °C;Indirect Top-down and Bottom-up mechanisms do not amplify direct forcing by a large amount, i.e. indirect solar forcing is of the same magnitude (or smaller) as direct solar forcing;The radiative output of the Sun cannot be lower by more than 2 Wm−2 below the measured present-day TSI value during solar cycle minimum.These three statements contradict each other and it is concluded that at least one is not correct. Which one is a wrong statement is presently not known conclusively. It is argued that it is the third statement and it is speculated that over centennial time scales the Sun might vary its radiance significantly more than observed so far during the last 40 years of space TSI measurements. To produce Maunder minimum type cold climate excursions, a TSI decrease of the order of 10 Wm−2 is advocated.
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- 2021
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20. A remarkable change in inhibition potency and selectivity of isofagomine by simple N-modification
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Culum, André, Prasch, Herwig, Dorn, Tobias, Fischer, Roland, Gardić, Ema, Schmutz, Franziska, Steinbrugger, Magdalena, Stütz, Arnold E., Weber, Patrick, Wrodnigg, Tanja M., and Thonhofer, Martin
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- 2024
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21. Metrology of Rydberg states of the hydrogen atom
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Scheidegger, Simon, Agner, Josef A., Schmutz, Hansjürg, and Merkt, Frédéric
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Physics - Atomic Physics - Abstract
We present a method to precisly measure the frequencies of transitions to high-$n$ Rydberg states of the hydrogen atom which are not subject to uncontrolled systematic shifts caused by stray electric fields. The method consists in recording Stark spectra of the field-insensitive $k=0$ Stark states and the field-sensitive $k=\pm2$ Stark states, which are used to calibrate the electric field strength. We illustrate this method with measurements of transitions from the $2\,\text{s}(f=0\text{ and } 1)$ hyperfine levels in the presence of intentionally applied electric fields with strengths in the range between $0.4$ and $1.6\,$Vcm$^{-1}$. The slightly field-dependent $k=0$ level energies are corrected with a precisely calculated shift to obtain the corresponding Bohr energies $\left(-cR_{\mathrm{H}}/n^2\right)$. The energy difference between $n=20$ and $n=24$ obtained with our method agrees with Bohr's formula within the $10\,$kHz experimental uncertainty. We also determined the hyperfine splitting of the $2\,\text{s}$ state by taking the difference between transition frequencies from the $2\,\text{s}(f=0 \text{ and }1)$ levels to the $n=20,k=0$ Stark states. Our results demonstrate the possibility of carrying out precision measurements in high-$n$ hydrogenic quantum states.
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- 2023
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22. Sieving and clogging in PEG-PEGDA hydrogel membranes
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Eddine, Malak Alaa, Carvalho, Alain, Schmutz, M., Salez, Thomas, de Chateauneuf-Randon, Sixtine, Bresson, Bruno, Belbekhouche, S., and Monteux, C.
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Condensed Matter - Soft Condensed Matter - Abstract
Hydrogels are promising systems for separation applications due to their structural characteristics (i.e. hydrophilicity and porosity). In our study, we investigate the permeation of suspensions of rigid latex particles of different sizes through free-standing hydrogel membranes prepared by photopolymerization of a mixture of poly (ethylene glycol) diacrylate (PEGDA) and large poly (ethylene glycol) (PEG) chains of 300 000 g.mol-1 in the presence of a photoinitiator. Atomic force microscopy (AFM) and cryoscanning electron microscopy (cryoSEM) were employed to characterize the structure of the hydrogel membranes. We find that the 20 nm particle permeation depends on both the PEGDA/PEG composition and the pressure applied during filtration. In contrast, we do not measure a significant permeation of the 100 nm and 1 $\mu$m particles, despite the presence of large cavities of 1 $\mu$m evidenced by cryoSEM images. We suggest that the PEG chains induce local nanoscale defects in the cross-linking of PEGDA-rich walls separating the micron size cavities, that control the permeation of particles and water. Moreover, we discuss the decline of the permeation flux observed in the presence of latex particles, compared to that of pure water. We suggest that a thin layer of particles forms on the surface of the hydrogels.
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- 2023
23. In situ monitoring of block copolymer self-assembly through controlled dialysis with light and neutron scattering detection
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Fauquignon, Martin, Porcar, Lionel, Brûlet, Annie, Meins, Jean-François Le, Sandre, Olivier, Chapel, Jean-Paul, Schmutz, Marc, and Schatz, Christophe
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Condensed Matter - Soft Condensed Matter - Abstract
Solution self-assembly of amphiphilic block copolymers (BCs) is typically performed by a solvent-to-water exchange. However, BC assemblies are often trapped in metastable states depending on the mixing conditions such as the magnitude and rate of water addition. BC self-assembly can be performed under near thermodynamic control by dialysis, which accounts for a slow and gradual water addition. In this Letter we report the use of a specifically designed dialysis cell to continuously monitor by dynamic light scattering and small-angle neutron scattering the morphological changes of PDMS-b-PEG BCs self-assemblies during THF-to-water exchange. The complete phase diagrams of near-equilibrium structures can then be established. Spherical micelles first form before evolving to rod-like micelles and vesicles, decreasing the total developed interfacial area of self-assembled structures in response to increasing interfacial energy as the water content increases. The dialysis kinetics can be tailored to the time scale of BC self-assembly by modifying the membrane pore size, which is of interest to study the interplay between thermodynamics and kinetics in self-assembly pathways.
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- 2023
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24. Imaging-assisted single-photon Doppler-free laser spectroscopy and the ionization energy of metastable triplet helium
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Clausen, Gloria, Scheidegger, Simon, Agner, Josef A., Schmutz, Hansjürg, and Merkt, Frédéric
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Physics - Atomic Physics - Abstract
Skimmed supersonic beams provide intense, cold, collision-free samples of atoms and molecules are one of the most widely used tools in atomic and molecular laser spectroscopy. High-resolution optical spectra are typically recorded in a perpendicular arrangement of laser and supersonic beams to minimize Doppler broadening. Typical Doppler widths are nevertheless limited to tens of MHz by the residual transverse-velocity distribution in the gas-expansion cones. We present an imaging method to overcome this limitation which exploits the correlation between the positions of the atoms and molecules in the supersonic expansion and their transverse velocities - and thus their Doppler shifts. With the example of spectra of $(1\mathrm{s})(n\mathrm{p})\,^3\mathrm{P}_{0-2}\leftarrow (1\mathrm{s})(2\mathrm{s})\,^3\mathrm{S}_1$ transitions to high Rydberg states of metastable triplet He, we demonstrate the suppression of the residual Doppler broadening and a reduction of the full linewidths at half maximum to only about 1 MHz in the UV. Using a retro-reflection arrangement for the laser beam and a cross-correlation method, we determine Doppler-free spectra without any signal loss from the selection, by imaging, of atoms within ultranarrow transverse-velocity classes. As an illustration, we determine the ionization energy of triplet metastable He and confirm the significant discrepancy between recent experimental (Clausen et al., Phys. Rev. Lett. 127 093001 (2021)) and high-level theoretical (Patk\'os et al., Phys. Rev. A 103 042809 (2021)) values of this quantity.
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- 2023
25. SPICE Connection Mosaics to link the Sun's surface and the heliosphere
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Varesano, T., Hassler, D. M., Prado, N. Zambrana, Plowman, J., Del Zanna, G., Parenti, S., Mason, H. E., Giunta, A., Auchere, F., Carlsson, M., Fludra, A., Peter, H., Muller, D., Williams, D., Cuadrado, R. Aznar, Barczynski, K., Buchlin, E., Caldwell, M., Fredvik, T., Grundy, T., Guest, S., Harra, L., Janvier, M., Kucera, T., Leeks, S., Schmutz, W., Schuehle, U., Sidher, S., Teriaca, L., Thompson, W., and Yardley, S. L.
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Astrophysics - Solar and Stellar Astrophysics - Abstract
We present an analysis of the first connection mosaic made by the SPICE instrument on board of the ESA / NASA Solar Orbiter mission on March 2nd, 2022. The data will be used to map coronal composition that will be compared with in-situ measurements taken by SWA/HIS to establish the coronal origin of the solar wind plasma observed at Solar Orbiter. The SPICE spectral lines were chosen to have varying sensitivity to the First Ionization Potential (FIP) effect, and therefore the radiances of the spectral lines will vary significantly depending on whether the elemental composition is coronal or photospheric. We investigate the link between the behavior of sulfur with the hypothesis that Alfv\'en waves drive FIP fractionation above the chromosphere. We perform temperature diagnostics using line ratios and Emission Measure (EM) loci, and compute relative FIP biases using three different approaches (two line ratio (2LR), ratios of linear combinations of spectral lines (LCR), and differential emission measure (DEM) inversion) to perform composition diagnostics in the corona. We then compare the SPICE composition analysis and EUI data of the potential solar wind source regions to the SWA / HIS data products. Radiance maps are extracted from SPICE spectral data cubes, with values matching previous observations. We find isothermal plasma of around LogT = 5.8 for the active region loops targeted, and that higher FIP-bias values are present at the footpoints of the coronal loops associated with two active regions. Comparing the results with the SWA/HIS data products encourages us to think that Solar Orbiter was connected to a source of slow solar wind during this observation campaign. We demonstrate FIP fractionation in observations of the upper chromosphere and transition region, emphasized by the behavior of the intermediate-FIP element sulfur., Comment: 20 pages, 19 figures, submitted to A&A on August 3rd, accepted on February 12th, 2024
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- 2023
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26. A multiple spacecraft detection of the 2 April 2022 M-class flare and filament eruption during the first close Solar Orbiter perihelion
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Janvier, M., Mzerguat, S., Young, P. R., Buchlin, É., Manou, A., Pelouze, G., Long, D. M., Green, L., Warmuth, A., Schuller, F., Démoulin, P., Calchetti, D., Kahil, F., Rubio, L. Bellot, Parenti, S., Baccar, S., Barczynski, K., Harra, L. K., Hayes, L. A., Thompson, W. T., Müller, D., Baker, D., Yardley, S., Berghmans, D., Verbeeck, C., Smith, P. J., Peter, H., Cuadrado, R. Aznar, Musset, S., Brooks, D. H., Rodriguez, L., Auchère, F., Carlsson, M., Fludra, A., Hassler, D., Williams, D., Caldwell, M., Fredvik, T., Giunta, A., Grundy, T., Guest, S., Kraaikamp, E., Leeks, S., Plowman, J., Schmutz, W., Schühle, U., Sidher, S. D., Teriaca, L., Solanki, S. K., Iniesta, J. C. del Toro, Woch, J., Gandorfer, A., Hirzberger, J., Suarez, D. Orozco, Appourchaux, T., Valori, G., Sinjan, J., Albert, K., and Volkmer, R.
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Astrophysics - Solar and Stellar Astrophysics - Abstract
The Solar Orbiter mission completed its first remote-sensing observation windows in the spring of 2022. On 2/4/2022, an M-class flare followed by a filament eruption was seen both by the instruments on board the mission and from several observatories in Earth's orbit. The complexity of the observed features is compared with the predictions given by the standard flare model in 3D. We use the observations from a multi-view dataset, which includes EUV imaging to spectroscopy and magnetic field measurements. These data come from IRIS, SDO, Hinode, as well as several instruments on Solar Orbiter. Information given by SDO/HMI and Solar Orbiter PHI/HRT shows that a parasitic polarity emerging underneath the filament is responsible for bringing the flux rope to an unstable state. As the flux rope erupts, Hinode/EIS captures blue-shifted emission in the transition region and coronal lines in the northern leg of the flux rope prior to the flare peak. Solar Orbiter SPICE captures the whole region, complementing the Doppler diagnostics of the filament eruption. Analyses of the formation and evolution of a complex set of flare ribbons and loops show that the parasitic emerging bipole plays an important role in the evolution of the flaring region. While the analysed data are overall consistent with the standard flare model, the present particular magnetic configuration shows that surrounding magnetic activity such as nearby emergence needs to be taken into account to fully understand the processes at work. This filament eruption is the first to be covered from different angles by spectroscopic instruments, and provides an unprecedented diagnostic of the multi-thermal structures present before and during the flare. This dataset of an eruptive event showcases the capabilities of coordinated observations with the Solar Orbiter mission., Comment: Accepted for publication in the Astronomy & Astrophysics special edition "Solar Orbiter First Results (Nominal Mission Phase)" (23/05/2023)
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- 2023
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27. The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum
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Lei, Li, Gordon, Sean P, Liu, Lifeng, Sade, Nir, Lovell, John T, Del Mar Rubio Wilhelmi, Maria, Singan, Vasanth, Sreedasyam, Avinash, Hestrin, Rachel, Phillips, Jeremy, Hernandez, Bryan T, Barry, Kerrie, Shu, Shengqiang, Jenkins, Jerry, Schmutz, Jeremy, Goodstein, David M, Thilmony, Roger, Blumwald, Eduardo, and Vogel, John P
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Biochemistry and Cell Biology ,Biological Sciences ,Genetics ,Mathematical Sciences ,Statistics ,Humans ,Brachypodium ,Genome ,Plant ,Biomass ,Transcriptome ,Stress ,Physiological ,genome ,perennial grass ,transcriptome ,abiotic stress ,transposable element ,Plant Genetics and Genomics ,Biochemistry and cell biology - Abstract
Perennial grasses are important forage crops and emerging biomass crops and have the potential to be more sustainable grain crops. However, most perennial grass crops are difficult experimental subjects due to their large size, difficult genetics, and/or their recalcitrance to transformation. Thus, a tractable model perennial grass could be used to rapidly make discoveries that can be translated to perennial grass crops. Brachypodium sylvaticum has the potential to serve as such a model because of its small size, rapid generation time, simple genetics, and transformability. Here, we provide a high-quality genome assembly and annotation for B. sylvaticum, an essential resource for a modern model system. In addition, we conducted transcriptomic studies under 4 abiotic stresses (water, heat, salt, and freezing). Our results indicate that crowns are more responsive to freezing than leaves which may help them overwinter. We observed extensive transcriptional responses with varying temporal dynamics to all abiotic stresses, including classic heat-responsive genes. These results can be used to form testable hypotheses about how perennial grasses respond to these stresses. Taken together, these results will allow B. sylvaticum to serve as a truly tractable perennial model system.
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- 2023
28. Secreted Effector Proteins of Poplar Leaf Spot and Stem Canker Pathogen Sphaerulina musiva Manipulate Plant Immunity and Contribute to Virulence in Diverse Ways.
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Zhao, Yao, Zheng, Xinyue, Tabima, Javier F, Zhu, Sheng, Søndreli, Kelsey L, Hundley, Hope, Bauer, Diane, Barry, Kerrie, Zhang, Yaxin, Schmutz, Jeremy, Wang, Yuanchao, LeBoldus, Jared M, and Xiong, Qin
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Plant Biology ,Biological Sciences ,Infectious Diseases ,Populus ,Virulence ,Ascomycota ,Plant Immunity ,Plant Diseases ,Sphaerulina musiva ,candidate secreted effector proteins ,plant immunity ,poplar ,prediction ,subcellular localization ,virulence ,Genetics ,Microbiology ,Plant Biology & Botany ,Plant biology - Abstract
Fungal effectors play critical roles in manipulating plant immune responses and promoting colonization. Sphaerulina musiva is a heterothallic ascomycete fungus that causes Septoria leaf spot and stem canker disease in poplar (Populus spp.) plantations. This disease can result in premature defoliation, branch and stem breakage, increased mortality, and plantation failure. However, little is known about the interaction between S. musiva and poplar. Previous work predicted 142 candidate secreted effector proteins in S. musiva (SmCSEPs), 19 of which were selected for further functional characterization in this study. SmCSEP3 induced plant cell death in Nicotiana benthamiana, while 8 out of 19 tested SmCSEPs suppressed cell death. The signal peptides of these eight SmCSEPs exhibited secretory activity in a yeast signal sequence trap assay. Confocal microscopy revealed that four of these eight SmCSEPs target both the cytoplasm and the nucleus, whereas four predominantly localize to discrete punctate structures. Pathogen challenge assays in N. benthamiana demonstrated that the transient expression of six SmCSEPs promoted Fusarium proliferatum infection. The expression of these six SmCSEP genes were induced during infection. SmCSEP2, SmCSEP13, and SmCSEP25 suppressed chitin-triggered reactive oxygen species burst and callose deposition in N. benthamiana. The candidate secreted effector proteins of S. musiva target multiple compartments in the plant cell and modulate different pattern-triggered immunity pathways. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2023.
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- 2023
29. Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses
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Andrei S. Steindorff, Maria Victoria Aguilar-Pontes, Aaron J. Robinson, Bill Andreopoulos, Kurt LaButti, Alan Kuo, Stephen Mondo, Robert Riley, Robert Otillar, Sajeet Haridas, Anna Lipzen, Jane Grimwood, Jeremy Schmutz, Alicia Clum, Ian D. Reid, Marie-Claude Moisan, Gregory Butler, Thi Truc Minh Nguyen, Ken Dewar, Gavin Conant, Elodie Drula, Bernard Henrissat, Colleen Hansel, Steven Singer, Miriam I. Hutchinson, Ronald P. de Vries, Donald O. Natvig, Amy J. Powell, Adrian Tsang, and Igor V. Grigoriev
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Biology (General) ,QH301-705.5 - Abstract
Abstract Thermophily is a trait scattered across the fungal tree of life, with its highest prevalence within three fungal families (Chaetomiaceae, Thermoascaceae, and Trichocomaceae), as well as some members of the phylum Mucoromycota. We examined 37 thermophilic and thermotolerant species and 42 mesophilic species for this study and identified thermophily as the ancestral state of all three prominent families of thermophilic fungi. Thermophilic fungal genomes were found to encode various thermostable enzymes, including carbohydrate-active enzymes such as endoxylanases, which are useful for many industrial applications. At the same time, the overall gene counts, especially in gene families responsible for microbial defense such as secondary metabolism, are reduced in thermophiles compared to mesophiles. We also found a reduction in the core genome size of thermophiles in both the Chaetomiaceae family and the Eurotiomycetes class. The Gene Ontology terms lost in thermophilic fungi include primary metabolism, transporters, UV response, and O-methyltransferases. Comparative genomics analysis also revealed higher GC content in the third base of codons (GC3) and a lower effective number of codons in fungal thermophiles than in both thermotolerant and mesophilic fungi. Furthermore, using the Support Vector Machine classifier, we identified several Pfam domains capable of discriminating between genomes of thermophiles and mesophiles with 94% accuracy. Using AlphaFold2 to predict protein structures of endoxylanases (GH10), we built a similarity network based on the structures. We found that the number of disulfide bonds appears important for protein structure, and the network clusters based on protein structures correlate with the optimal activity temperature. Thus, comparative genomics offers new insights into the biology, adaptation, and evolutionary history of thermophilic fungi while providing a parts list for bioengineering applications.
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- 2024
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30. Stakeholders' views on the global guidelines for the sustainable use of non‐native trees
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Ana Novoa, Giovanni Vimercati, Giuseppe Brundu, David M. Richardson, Urs Schaffner, Antonio Brunori, Thomas Campagnaro, Susan Canavan, Laura Celesti‐Grapow, Michele Dechoum, Katharina Dehnen‐Schmutz, Jean‐Marc Dufour‐Dror, Franz Essl, S. Luke Flory, Heinke Jäger, Jasmin Joshi, Marion Karmann, Barbara Langdon, Katharina Lapin, Johannes Le Roux, Vanessa Lozano, Mauro Masiero, Laura A. Meyerson, Martin A. Nuñez, Aníbal Pauchard, Jan Pergl, Annabel J. Porté, Petr Pyšek, Jana Pyšková, Jonatan Rodriguez, Ross T. Shackleton, Joaquim S. Silva, Tommaso Sitzia, Laura Verbrugge, Michaela Vítková, Yitbarek Tibebe Weldesemaet, Marjana Westergren, and John R. U. Wilson
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agroforestry ,alien species ,forestry ,invasion risk ,online survey ,ornamental trees ,Human ecology. Anthropogeography ,GF1-900 ,Ecology ,QH540-549.5 - Abstract
Abstract A large number of non‐native trees (NNTs) have been introduced globally and widely planted, contributing significantly to the world's economy. Although some of these species present a limited risk of spreading beyond their planting sites, a growing number of NNTs are spreading and becoming invasive leading to diverse negative impacts on biodiversity, ecosystem functions and human well‐being. To help minimize the negative impacts and maximize the economic benefits of NNTs, Brundu et al. developed eight guidelines for the sustainable use of NNTs globally—the Global Guidelines for the Use of NNTs (GG‐NNTs). Here, we used an online survey to assess perceptions of key stakeholders towards NNTs, and explore their knowledge of and compliance with the GG‐NNTs. Our results show that stakeholders are generally aware that NNTs can provide benefits and cause negative impacts, often simultaneously and they consider that their organization complies with existing regulations and voluntary agreements concerning NNTs. However, they are not aware of or do not apply most of the eight recommendations included in the GG‐NNTs. We conclude that effectively managing invasions linked to NNTs requires both more communication efforts using an array of channels for improving stakeholder awareness and implementation of simple measures to reduce NNT impacts (e.g. via GG‐NNTs), and a deeper understanding of the barriers and reluctance of stakeholders to manage NNT invasions. Read the free Plain Language Summary for this article on the Journal blog.
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- 2024
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31. Beyond the disk: EUV coronagraphic observations of the Extreme Ultraviolet Imager on board Solar Orbiter
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Auchère, Berghmans, Dumesnil, Halain, -P., J., Mercier, Rochus, Delmotte, François, Hermans, Hervier, Kraaikamp, Meltchakov, Morinaud, Philippon, Smith, J., P., Stegen, Verbeeck, Zhang, Y., X., Andretta, Abbo, Buchlin, Frassati, Gissot, Gyo, Harra, Jerse, Landini, Mierla, Nicula, Parenti, Renotte, Romoli, Russano, Sasso, Schühle, Schmutz, Soubrié, Susino, Teriaca, West, Zhukov, and N, A.
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Astrophysics - Solar and Stellar Astrophysics - Abstract
Most observations of the solar corona beyond 2 Rs consist of broadband visible light imagery from coronagraphs. The associated diagnostics mainly consist of kinematics and derivations of the electron number density. While the measurement of the properties of emission lines can provide crucial additional diagnostics of the coronal plasma (temperatures, velocities, abundances, etc.), these observations are comparatively rare. In visible wavelengths, observations at these heights are limited to total eclipses. In the VUV range, very few additional observations have been achieved since the pioneering results of UVCS. One of the objectives of the Full Sun Imager (FSI) channel of the EUI telescope on board the Solar Orbiter mission has been to provide very wide field-of-view EUV diagnostics of the morphology and dynamics of the solar atmosphere in temperature regimes that are typical of the lower transition region and of the corona. FSI carries out observations in two narrowbands of the EUV spectrum centered on 17.4 nm and 30.4 nm that are dominated, respectively, by lines of Fe IX/X (formed in the corona around 1 MK) and by the resonance line of He II (formed around 80 kK in the lower transition region). Unlike previous EUV imagers, FSI includes a moveable occulting disk that can be inserted in the optical path to reduce the amount of instrumental stray light to a minimum. FSI detects signals at 17.4 nm up to the edge of its FOV (7~Rs), which is about twice further than was previously possible. Comparisons with observations by the LASCO and Metis coronagraphs confirm the presence of morphological similarities and differences between the broadband visible light and EUV emissions, as documented on the basis of prior eclipse and space-based observations. The very-wide-field observations of FSI are paving the way for future dedicated instruments.
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- 2023
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32. Slow Solar Wind Connection Science during Solar Orbiter's First Close Perihelion Passage
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Yardley, Stephanie L., Owen, Christopher J., Long, David M., Baker, Deborah, Brooks, David H., Polito, Vanessa, Green, Lucie M., Matthews, Sarah, Owens, Mathew, Lockwood, Mike, Stansby, David, James, Alexander W., Valori, Gherado, Giunta, Alessandra, Janvier, Miho, Ngampoopun, Nawin, Mihailescu, Teodora, To, Andy S. H., van Driel-Gesztelyi, Lidia, Demoulin, Pascal, D'Amicis, Raffaella, French, Ryan J., Suen, Gabriel H. H., Roulliard, Alexis P., Pinto, Rui F., Reville, Victor, Watson, Christopher J., Walsh, Andrew P., De Groof, Anik, Williams, David R., Zouganelis, Ioannis, Muller, Daniel, Berghmans, David, Auchere, Frederic, Harra, Louise, Scheuhle, Udo, Barczynski, Krysztof, Buchlin, Eric, Cuadrado, Regina Aznar, Kraaikamp, Emil, Mandal, Sudip, Parenti, Susanna, Peter, Hardi, Rodriguez, Luciano, Schwanitz, Conrad, Smith, Phil, Teriaca, Luca, Verbeeck, Cis, Zhukov, Andrei N., De Pontieu, Bart, Horbury, Tim, Solanki, Sami K., Iniesta, Jose Carlos del Toro, Woch, Joachim, Gandorfer, Achim, Hirzberger, Johann, Suarez, David Orozco, Appourchaux, Thierry, Calchetti, Daniele, Sinjan, Jonas, Kahil, Fatima, Albert, Kinga, Volkmer, Reiner, Carlsson, Mats, Fludra, Andrzej, Hassler, Don, Caldwell, Martin, Fredvik, Terje, Grundy, Tim, Guest, Steve, Haberreiter, Margit, Leeks, Sarah, Pelouze, Gabriel, Plowman, Joseph, Schmutz, Werner, Sidher, Sunil, Thompson, William T., Louarn, Philippe, and Federov, Andrei
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Astrophysics - Solar and Stellar Astrophysics ,Physics - Space Physics - Abstract
The Slow Solar Wind Connection Solar Orbiter Observing Plan (Slow Wind SOOP) was developed to utilise the extensive suite of remote sensing and in situ instruments on board the ESA/NASA Solar Orbiter mission to answer significant outstanding questions regarding the origin and formation of the slow solar wind. The Slow Wind SOOP was designed to link remote sensing and in situ measurements of slow wind originating at open-closed field boundaries. The SOOP ran just prior to Solar Orbiter's first close perihelion passage during two remote sensing windows (RSW1 and RSW2) between 2022 March 3-6 and 2022 March 17-22, while Solar Orbiter was at a heliocentric distance of 0.55-0.51 and 0.38-0.34 au from the Sun, respectively. Coordinated observation campaigns were also conducted by Hinode and IRIS. The magnetic connectivity tool was used, along with low latency in situ data, and full-disk remote sensing observations, to guide the target pointing of Solar Orbiter. Solar Orbiter targeted an active region complex during RSW1, the boundary of a coronal hole, and the periphery of a decayed active region during RSW2. Post-observation analysis using the magnetic connectivity tool along with in situ measurements from MAG and SWA/PAS, show that slow solar wind, with velocities between 210 and 600 km/s, arrived at the spacecraft originating from two out of the three of the target regions. The Slow Wind SOOP, despite presenting many challenges, was very successful, providing a blueprint for planning future observation campaigns that rely on the magnetic connectivity of Solar Orbiter., Comment: 24 pages, 10 figures
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- 2023
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33. Interview – Que pouvons-nous attendre de l’application de la notion de Trame verte et bleue dans les territoires ?
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SCHMUTZ, Thomas
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TRAME VERTE ET BLEUE ,AMENAGEMENT ,TERRITOIRES ,PAYSAGES ,Environmental technology. Sanitary engineering ,TD1-1066 ,Environmental sciences ,GE1-350 - Abstract
L’élaboration progressive de la Trame verte et bleue a d'ores et déjà commencé à modifier les méthodes des équipes techniques – concepteurs, gestionnaires de sites – et les paysages qu'ils façonnent. L’entretien avec Thomas Schmutz, ingénieur conseil impliqué sur la prise en compte de la TVB, apporte des premiers retours d'expérience.
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- 2014
34. Focus – « Grenelliser » nos aménagements : quelques retours d’expérience sur ce qui a changé
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SCHMUTZ, Thomas
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TRAME VERTE ET BLEUE ,AMENAGEMENT ,TERRITOIRES ,PAYSAGES ,Environmental technology. Sanitary engineering ,TD1-1066 ,Environmental sciences ,GE1-350 - Abstract
Les quelques exemples présentés ici illustrent les nouveaux défis que les équipes techniques commencent à relever, depuis la conception jusqu’à la valorisation auprès des usagers.
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- 2014
35. Stationäre Versorgung von Menschen mit psychogenen nichtepileptischen Anfällen in Epilepsiezentren? Eine kritische Stellungnahme
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Krämer, Günter and Schmutz, Matthias
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- 2024
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36. Transformation of learning and teaching in rehabilitation sciences
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Visser, Monique, Oosthuizen, Helena, Louw, Alwyn J.N., Unger, Marianne, Keiller, Lianne, Inglis-Jassiem, Gakeemah, Hanekom, Susan D., de Beer, Alida, Gaskin, Ashley, Bardien, Faeza, Manas, Lorisha, Coetzee, Marisa, de Wit, Monique, Nizeyimana, Eugene, Dawood, Gouwa, Plastow, Nicola, Joseph, Conran, Louw, Quinette, Kloppers, Maatje, Bester, Juanita, Baxter, Anja, Denton, ELLA PRU, Koegelenberg, Ané, Burchell, Helena J., Simpson, Tayla-leigh, van Wyk, Marnie, Ernstzen, Dawn Verna, Schmutz, Anna M. S., Meyer, Ilse S., Filies, Gerard, Müller, Jana, Gerber, Berna, Berner, Karina, Pefile, Ntsikelelo, Charumbira, Maria Yvonne, Ernstzen, Dawn Verna, Jacobs-Nzuzi Khuabi, Lee-Ann, and Bardien, Faeza
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Curriculum reform ,transformative learning ,leadership ,interprofessional education ,clinical competence ,peer teaching and learning ,learning technologies ,thema EDItEUR::M Medicine and Nursing::MQ Nursing and ancillary services::MQS Physiotherapy - Abstract
This is the second book in the 'Health, Functioning and Technology' series. The focus of this book is on teaching, learning and assessment in rehabilitation education within the African context. The primary contributors to the book are authors from occupational therapy, physiotherapy and speech-language therapy in South Africa. The authors discuss local contextual drivers for renewing rehabilitation professions curricula that support graduates in becoming competent, socially accountable, and dynamic. The foundational element of the chapters in the book is the African context and evidence-informed educational practice. We include the impact of the COVID-19 pandemic on teaching, learning, student support and the integration of technology to assist in achieving the goals of the curricula. Through the different themes of transformative learning, curriculum renewal, technology for learning and clinical training key topics are covered on responsive curricula, leadership, interprofessional education, clinical competence, critical consciousness, peer teaching and learning, learning technologies, student support and emergency remote teaching and learning.
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- 2022
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37. JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom
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Sreedasyam, Avinash, Plott, Christopher, Hossain, Shakhawat, Lovell, John T, Grimwood, Jane, Jenkins, Jerry W, Daum, Christopher, Barry, Kerrie, Carlson, Joseph, Shu, Shengqiang, Phillips, Jeremy, Amirebrahimi, Mojgan, Zane, Matthew, Wang, Mei, Goodstein, David, Haas, Fabian B, Hiss, Manuel, Perroud, Pierre-François, Jawdy, Sara S, Yang, Yongil, Hu, Rongbin, Johnson, Jenifer, Kropat, Janette, Gallaher, Sean D, Lipzen, Anna, Shakirov, Eugene V, Weng, Xiaoyu, Torres-Jerez, Ivone, Weers, Brock, Conde, Daniel, Pappas, Marilia R, Liu, Lifeng, Muchlinski, Andrew, Jiang, Hui, Shyu, Christine, Huang, Pu, Sebastian, Jose, Laiben, Carol, Medlin, Alyssa, Carey, Sankalpi, Carrell, Alyssa A, Chen, Jin-Gui, Perales, Mariano, Swaminathan, Kankshita, Allona, Isabel, Grattapaglia, Dario, Cooper, Elizabeth A, Tholl, Dorothea, Vogel, John P, Weston, David J, Yang, Xiaohan, Brutnell, Thomas P, Kellogg, Elizabeth A, Baxter, Ivan, Udvardi, Michael, Tang, Yuhong, Mockler, Todd C, Juenger, Thomas E, Mullet, John, Rensing, Stefan A, Tuskan, Gerald A, Merchant, Sabeeha S, Stacey, Gary, and Schmutz, Jeremy
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Human Genome ,Generic health relevance ,Gene Expression Regulation ,Plant ,Genes ,Plant ,Genome ,Plant ,Phylogeny ,Software ,Transcriptome ,Atlases as Topic ,Environmental Sciences ,Information and Computing Sciences ,Developmental Biology ,Biological sciences ,Chemical sciences ,Environmental sciences - Abstract
Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.
- Published
- 2023
38. Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina).
- Author
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Van de Peer, Yves, Olsen, Jeanine, Reusch, Thorsten, Cusson, Mathieu, Emmett Duffy, J, Joel Fodrie, F, Gill, Diana, Grimwood, Jane, Hori, Masakazu, Hovel, Kevin, Hughes, A, Jahnke, Marlene, Jenkins, Jerry, Keymanesh, Keykhosrow, Kruschel, Claudia, Mamidi, Sujan, Menning, Damian, Moksnes, Per-Olav, Nakaoka, Masahiro, Pennacchio, Christa, Reiss, Katrin, Rossi, Francesca, Ruesink, Jennifer, Schultz, Stewart, Talbot, Sandra, Unsworth, Richard, Ward, David, Dagan, Tal, Schmutz, Jeremy, Yu, Lei, Khachaturyan, Marina, Matschiner, Michael, Healey, Adam, Bauer, Diane, Stachowicz, John, Eisen, Jonathan, and Cameron, Brenda
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Ecosystem ,Zosteraceae ,Canada ,Phylogeography ,Oceans and Seas - Abstract
Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.
- Published
- 2023
39. Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii
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Weng, Xiaoyu, Song, Haili, Sreedasyam, Avinash, Haque, Taslima, Zhang, Li, Chen, Cindy, Yoshinaga, Yuko, Williams, Melissa, O’Malley, Ronan C, Grimwood, Jane, Schmutz, Jeremy, and Juenger, Thomas E
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Ecotype ,Panicum ,Transcriptome ,Inflorescence ,Epigenome ,Gene Expression Regulation ,Plant ,DNA Methylation ,Agricultural and Veterinary Sciences ,Plant Biology & Botany ,Plant biology - Abstract
The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the 2 major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and Ka/Ks ratio results characterized the evolutionary features of DMR-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology.
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- 2023
40. Toward High Efficiency Water Processed Organic Photovoltaics: Controlling the Nanoparticle Morphology with Surface Energies
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Laval, Hugo, Holmes, Alexandre, Marcus, Matthew A, Watts, Benjamin, Bonfante, Gwenaël, Schmutz, Marc, Deniau, Elise, Szymanski, Robin, Lartigau‐Dagron, Christine, Xu, Xiaoxue, Cairney, Julie M, Hirakawa, Kazuhiko, Awai, Fumiyasu, Kubo, Takaya, Wantz, Guillaume, Bousquet, Antoine, Holmes, Natalie P, and Chambon, Sylvain
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Engineering ,Macromolecular and Materials Chemistry ,Materials Engineering ,Chemical Sciences ,Nanotechnology ,Bioengineering ,Affordable and Clean Energy ,Interdisciplinary Engineering ,Macromolecular and materials chemistry ,Materials engineering - Abstract
Here efficient organic photovoltaic devices fabricated from water-based colloidal dispersions with donor:acceptor composite nanoparticles achieving up to 9.98% power conversion efficiency (PCE) are reported. This high efficiency for water processed organic solar cells is attributed to morphology control by surface energy matching between the donor and the acceptor materials. Indeed, due to a low interfacial energy between donor and the acceptor, no large phase separation occurs during the nanoparticle formation process as well as upon thermal annealing. Indeed, synchrotron-based scanning transmission X-ray microscopy reveals that the internal morphology of composite nanoparticles is intermixed as well as the active layer morphology after thermal treatment. The PCE of this system reaches 85% that of devices prepared from chlorinated solvent. The gap between water-based inks and organic solvent-based inks gets narrower, which is promising for the development of eco-friendly processing and fabrication of organic photovoltaics.
- Published
- 2023
41. Flow dynamics
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Schmutz, Thomas, Le Terrier, Christophe, and Ribordy, Vincent
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- 2024
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- View/download PDF
42. Correction: The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes
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Masonbrink, Rick, Maier, Tom R., Muppirala, Usha, Seetharam, Arun S., Lord, Etienne, Juvale, Parijat S., Schmutz, Jeremy, Johnson, Nathan T., Korkin, Dmitry, Mitchum, Melissa G., Mimee, Benjamin, den Akker, Sebastian Eves-van, Hudson, Matthew, Severin, Andrew J., and Baum, Thomas J.
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- 2024
- Full Text
- View/download PDF
43. How the mapping of threshold concepts across a master’s programme in health professions education could support the development of mastersness
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Archer, E., Schmutz, A. M. S., Volschenk, M., and Jacobs, C.
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- 2024
- Full Text
- View/download PDF
44. Developing a capacity-building intervention for healthcare workers to improve communication skills and awareness of hard of hearing and D/deaf patients: results from a participatory action research study
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Grazioli, Véronique S., Graells, Madison, Schmutz, Elodie, Cantero, Odile, Sebaï, Tanya, Favre, Vanessa, Richème-Roos, Jessica, Morisod, Kevin, Jeanneret, Michel, Singy, Pascal, and Bodenmann, Patrick
- Published
- 2024
- Full Text
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45. Gender and Cultural Consecration in Popular Music
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Schmutz, Vaughn and Faupel, Alison
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- 2011
- Full Text
- View/download PDF
46. Emergent rate-based dynamics in duplicate-free populations of spiking neurons
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Schmutz, Valentin, Brea, Johanni, and Gerstner, Wulfram
- Subjects
Quantitative Biology - Neurons and Cognition - Abstract
Can Spiking Neural Networks (SNNs) approximate the dynamics of Recurrent Neural Networks (RNNs)? Arguments in classical mean-field theory based on laws of large numbers provide a positive answer when each neuron in the network has many "duplicates", i.e. other neurons with almost perfectly correlated inputs. Using a disordered network model that guarantees the absence of duplicates, we show that duplicate-free SNNs can converge to RNNs, thanks to the concentration of measure phenomenon. This result reveals a general mechanism underlying the emergence of rate-based dynamics in large SNNs., Comment: 41 pages, 4 figures
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- 2023
47. Are labels informative in semi-supervised learning? -- Estimating and leveraging the missing-data mechanism
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Sportisse, Aude, Schmutz, Hugo, Humbert, Olivier, Bouveyron, Charles, and Mattei, Pierre-Alexandre
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Statistics - Machine Learning - Abstract
Semi-supervised learning is a powerful technique for leveraging unlabeled data to improve machine learning models, but it can be affected by the presence of ``informative'' labels, which occur when some classes are more likely to be labeled than others. In the missing data literature, such labels are called missing not at random. In this paper, we propose a novel approach to address this issue by estimating the missing-data mechanism and using inverse propensity weighting to debias any SSL algorithm, including those using data augmentation. We also propose a likelihood ratio test to assess whether or not labels are indeed informative. Finally, we demonstrate the performance of the proposed methods on different datasets, in particular on two medical datasets for which we design pseudo-realistic missing data scenarios.
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- 2023
48. Evaluating Utah's Rural Online Initiative: Empowering Organizational Leaders through Remote Work
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Hill, Paul A., Ali, Amanda D., Narine, Lendel K., Schmutz, Andrea T., Riskas, Tyson M., and Spielmaker, Debra M.
- Abstract
Compared to urban counties, Utah's rural counties experienced high levels of unemployment. Informed by a statewide needs assessment, Utah State University Extension developed a remote work leadership course to equip business leaders with knowledge and skills to create remote jobs as a solution to rural unemployment. This descriptive evaluation study collected data from course participants (N = 62). Findings showed short-term outcomes were achieved; participants experienced increases in knowledge and skills and had more positive intentions toward creating remote jobs and hiring employees from rural counties. Extension professionals can design and evaluate their programs using the framework in this study.
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- 2022
49. Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet
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Devos, Katrien M, Qi, Peng, Bahri, Bochra A, Gimode, Davis M, Jenike, Katharine, Manthi, Samuel J, Lule, Dagnachew, Lux, Thomas, Martinez-Bello, Liliam, Pendergast, Thomas H, Plott, Chris, Saha, Dipnarayan, Sidhu, Gurjot S, Sreedasyam, Avinash, Wang, Xuewen, Wang, Hao, Wright, Hallie, Zhao, Jianxin, Deshpande, Santosh, de Villiers, Santie, Dida, Mathews M, Grimwood, Jane, Jenkins, Jerry, Lovell, John, Mayer, Klaus FX, Mneney, Emmarold E, Ojulong, Henry F, Schatz, Michael C, Schmutz, Jeremy, Song, Bo, Tesfaye, Kassahun, and Odeny, Damaris A
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Agricultural ,Veterinary and Food Sciences ,Biological Sciences ,Genetics ,Humans ,Infant ,Eleusine ,Plant Breeding ,Genome ,Plant ,Phenotype ,Africa ,Eastern - Abstract
Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a 'poor man's crop', finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.
- Published
- 2023
50. The diatom Fragilariopsis cylindrus: A model alga to understand cold‐adapted life
- Author
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Otte, Antonia, Winder, Johanna C, Deng, Longji, Schmutz, Jeremy, Jenkins, Jerry, Grigoriev, Igor V, Hopes, Amanda, and Mock, Thomas
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Microbiology ,Biological Sciences ,Ecology ,Life Below Water ,Diatoms ,Cold Temperature ,Temperature ,Oceans and Seas ,Fragilariopsis ,cold adaptation ,diatom ,evolution ,genome ,phytoplankton ,Plant Biology ,Fisheries Sciences ,Marine Biology & Hydrobiology ,Fisheries sciences ,Plant biology - Abstract
Diatoms are significant primary producers especially in cold, turbulent, and nutrient-rich surface oceans. Hence, they are abundant in polar oceans, but also underpin most of the polar food webs and related biogeochemical cycles. The cold-adapted pennate diatom Fragilariopsis cylindrus is considered a keystone species in polar oceans and sea ice because it can thrive under different environmental conditions if temperatures are low. In this perspective paper, we provide insights into the latest molecular work that has been done on F. cylindrus and discuss its role as a model alga to understand cold-adapted life.
- Published
- 2023
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