2,068 results on '"A. Sonnenschein"'
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2. European genetic resources conservation in a rapidly changing world: three existential challenges for the crop, forest and animal domains in the 21st century
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European Commission, Bojkovski, Danijela [0009-0001-9491-0181], Kharrat, Magda Bou Dagher [0000-0001-7969-1673], Bozzano, Michele [0000-0003-1577-6509], Hiemstra, S. J. [0000-0002-8634-3658], Kraigher, Hojka [0000-0001-5696-2178], Laloë, Denis [0000-0001-8359-0760], Restoux, Gwendal [0000-0001-7771-9476], Sharrock, Suzanne [0000-0001-5212-2956], Sturaro, Enrico [0000-0001-9508-5622], van Hintum, Theo [0000-0003-4953-4700], Westergren, Marjana [0000-0002-4204-0161], Maxted, Nigel [0000-0002-2112-0947], Alía Miranda, Ricardo [0000-0002-9426-0967], Bytyqi, Hysen [0000-0001-7352-695X], Castellanos Moncho, Montserrat [0009-0008-3845-6173], Dorđević-Milošević, Suzana [0000-0003-2401-8742], Esposito, Edoardo [0000-0003-2414-6488], Farsakoglou, Anna Maria [0000-0002-1906-2813], Gandini, G. [0000-0003-1049-967X], Hermanowicz, Ewa [0000-0002-8941-7114], Honkatukia, Mervi [0000-0003-4839-2931], Kreft, Ivan [0000-0003-3339-8476], Lovrić, Nataša [0000-0002-5107-9260], Magos Brehm, Joana [0000-0002-6444-6488], Martín-Collado, Daniel [0000-0002-2087-961X], Niggli, Claudio [0000-0002-4164-9194], Notivol, Eduardo [0000-0003-4272-4536], Raggi, Lorenzo [0000-0003-0484-8669], Rusanen, Mari [0000-0002-2207-6984], Sonnenschein, Katja K. [0000-0001-6248-9559], Tixier-Boichard, M. [0000-0001-5944-7884], Trudic, Branislav [0000-0003-0385-547X], Ureña, Luis Pablo [0000-0001-8861-1452], Sustar Vozlic, Jelka [0000-0003-0998-9890], Wolter, Frank [0000-0002-4470-606X], Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72], Lefèvre, François, Bojkovski, Danijela, Kharrat, Magda Bou Dagher, Bozzano, Michele, Charvolin-Lemaire, Eléonore, Hiemstra, S. J., Kraigher, Hojka, Laloë, Denis, Restoux, Gwendal, Sharrock, Suzanne, Sturaro, Enrico, van Hintum, Theo, Westergren, Marjana, Maxted, Nigel, Alía Miranda, Ricardo, Bytyqi, Hysen, Castellanos Moncho, Montserrat, Cvelbar, Joži J., Dorđević-Milošević, Suzana, Esposito, Edoardo, Farsakoglou, Anna Maria, Fernández Martín, Jesús, Gandini, G., Hermanowicz, Ewa, Honkatukia, Mervi, Kreft, Ivan, Lovrić, Nataša, Magos Brehm, Joana, Martín-Collado, Daniel, Niggli, Claudio, Notivol, Eduardo, Raggi, Lorenzo, Rusanen, Mari, Schröder, Stefan, Smith, Paul P., Sonnenschein, Katja K., Tixier-Boichard, M., Trudic, Branislav, Ureña, Luis Pablo, Sustar Vozlic, Jelka, Walshe, Sharon, Woelders, Henri, Wolter, Frank, European Commission, Bojkovski, Danijela [0009-0001-9491-0181], Kharrat, Magda Bou Dagher [0000-0001-7969-1673], Bozzano, Michele [0000-0003-1577-6509], Hiemstra, S. J. [0000-0002-8634-3658], Kraigher, Hojka [0000-0001-5696-2178], Laloë, Denis [0000-0001-8359-0760], Restoux, Gwendal [0000-0001-7771-9476], Sharrock, Suzanne [0000-0001-5212-2956], Sturaro, Enrico [0000-0001-9508-5622], van Hintum, Theo [0000-0003-4953-4700], Westergren, Marjana [0000-0002-4204-0161], Maxted, Nigel [0000-0002-2112-0947], Alía Miranda, Ricardo [0000-0002-9426-0967], Bytyqi, Hysen [0000-0001-7352-695X], Castellanos Moncho, Montserrat [0009-0008-3845-6173], Dorđević-Milošević, Suzana [0000-0003-2401-8742], Esposito, Edoardo [0000-0003-2414-6488], Farsakoglou, Anna Maria [0000-0002-1906-2813], Gandini, G. [0000-0003-1049-967X], Hermanowicz, Ewa [0000-0002-8941-7114], Honkatukia, Mervi [0000-0003-4839-2931], Kreft, Ivan [0000-0003-3339-8476], Lovrić, Nataša [0000-0002-5107-9260], Magos Brehm, Joana [0000-0002-6444-6488], Martín-Collado, Daniel [0000-0002-2087-961X], Niggli, Claudio [0000-0002-4164-9194], Notivol, Eduardo [0000-0003-4272-4536], Raggi, Lorenzo [0000-0003-0484-8669], Rusanen, Mari [0000-0002-2207-6984], Sonnenschein, Katja K. [0000-0001-6248-9559], Tixier-Boichard, M. [0000-0001-5944-7884], Trudic, Branislav [0000-0003-0385-547X], Ureña, Luis Pablo [0000-0001-8861-1452], Sustar Vozlic, Jelka [0000-0003-0998-9890], Wolter, Frank [0000-0002-4470-606X], Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72], Lefèvre, François, Bojkovski, Danijela, Kharrat, Magda Bou Dagher, Bozzano, Michele, Charvolin-Lemaire, Eléonore, Hiemstra, S. J., Kraigher, Hojka, Laloë, Denis, Restoux, Gwendal, Sharrock, Suzanne, Sturaro, Enrico, van Hintum, Theo, Westergren, Marjana, Maxted, Nigel, Alía Miranda, Ricardo, Bytyqi, Hysen, Castellanos Moncho, Montserrat, Cvelbar, Joži J., Dorđević-Milošević, Suzana, Esposito, Edoardo, Farsakoglou, Anna Maria, Fernández Martín, Jesús, Gandini, G., Hermanowicz, Ewa, Honkatukia, Mervi, Kreft, Ivan, Lovrić, Nataša, Magos Brehm, Joana, Martín-Collado, Daniel, Niggli, Claudio, Notivol, Eduardo, Raggi, Lorenzo, Rusanen, Mari, Schröder, Stefan, Smith, Paul P., Sonnenschein, Katja K., Tixier-Boichard, M., Trudic, Branislav, Ureña, Luis Pablo, Sustar Vozlic, Jelka, Walshe, Sharon, Woelders, Henri, and Wolter, Frank
- Abstract
Even though genetic resources represent a fundamental reservoir of options to achieve sustainable development goals in a changing world, they are overlooked in the policy agenda and severely threatened. The conservation of genetic resources relies on complementary in situ and ex situ approaches appropriately designed for each type of organism. Environmental and socioeconomic changes raise new challenges and opportunities for sustainable use and conservation of genetic resources. Aiming at a more integrated and adaptive approach, European scientists and genetic resources managers with long experience in the agricultural crop, animal and forestry domains joined their expertise to address three critical challenges: (1) how to adapt genetic resources conservation strategies to climate change, (2) how to promote in situ conservation strategies and (3) how can genetic resources conservation contribute to and benefit from agroecological systems. We present here 31 evidence-based statements and 88 key recommendations elaborated around these questions for policymakers, conservation actors and the scientific community. We anticipate that stakeholders in other genetic resources domains and biodiversity conservation actors across the globe will have interest in these crosscutting and multi-actor recommendations, which support several biodiversity conservation policies and practices.
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- 2024
3. From spectral to scattering form factor
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Bianchi, Massimo, Firrotta, Maurizio, Sonnenschein, Jacob, Weissman, Dorin, Bianchi, Massimo, Firrotta, Maurizio, Sonnenschein, Jacob, and Weissman, Dorin
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We propose a novel indicator for chaotic quantum scattering processes, the scattering form factor (ScFF). It is based on mapping the locations of peaks in the scattering amplitude to random matrix eigenvalues, and computing the analog of the spectral form factor (SFF). We compute the spectral and scattering form factors of several non-chaotic systems. We determine the ScFF associated with the phase shifts of the leaky torus, closely related to the distribution of the zeros of Riemann zeta function. We compute the ScFF for the decay amplitude of a highly excited string states into two tachyons. We show that it displays the universal features expected from random matrix theory - a decline, a ramp and a plateau - and is in general agreement with the Gaussian unitary ensemble. It also shows some new features, owning to the special structure of the string amplitude, including a "bump" before the ramp associated with gaps in the average eigenvalue density. The "bump" is removed for highly excited string states with an appropriate state dependent unfolding. We also discuss the SFF for the Gaussian $\beta$- ensemble, writing an interpolation between the known results of the Gaussian orthogonal, unitary, and symplectic ensembles., Comment: 47 pages, 17 figures
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- 2024
4. Novel knotted non-abelian gauge fields
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Nastase, Horatiu, Sonnenschein, Jacob, Nastase, Horatiu, and Sonnenschein, Jacob
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In analogy to null electromagnetic fields we define null YM fields. We show that the null non-abelian $SU(N)$ gauge fields admit a set of $2 N^2$ conserved "helicities". We derive null YM solutions that carry finite helicities by uplifting the abelian Hopfion solution and their generalizations. Another method that we implement is to deform YM solutions which do not carry helicities into ones that have nontrivial helicities. A nontrivial non-Abelian solution with helicities is found as a wave of infinite energy. We also discuss non-abelian generalizations of the Bateman parameterization for null abelian gauge fields., Comment: 33 pages, 1 figure; references added; summary of main points added in Introduction
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- 2024
5. Taming the Zoo of Tetraquarks and Pentaquarks using the HISH Model
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Sonnenschein, Jacob, Green, Michal Michael, Sonnenschein, Jacob, and Green, Michal Michael
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In this paper we scan over all possible charmed tetraquarks and pentaquarks. Using the holography inspired stringy hadron (HISH) model we determine the trajectories associated with each of the exotic hadron candidates. The trajectories include further exotic states with higher angular momentum or higher stringy excited states. A trajectory is a property of a genuine exotic hadron and can be used to distinguish between the latter and a molecule. We examine 71 tetraquarks and 210 pentaquarks. Few of these states have already been found but most of the predicted zoo have yet not been discovered. We analyze the strong decay processes of these exotic hadrons and compute the corresponding decay widths of part of them.
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- 2024
6. Validating and constructing behavioral models for simulation and projection using automated knowledge extraction
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Sonnenschein, Tabea, de Wit, G Ardine, den Braver, Nicole R, Vermeulen, Roel, Scheider, Simon, Sonnenschein, Tabea, de Wit, G Ardine, den Braver, Nicole R, Vermeulen, Roel, and Scheider, Simon
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Human behavior may be one of the most challenging phenomena to model and validate. This paper proposes a method for automatically extracting and compiling evidence on human behavior determinants into a knowledge graph. The method (1) extracts associations of behavior determinants and choice options in relation to study groups and moderators from published studies using Natural Language Processing and Deep Learning, (2) synthesizes the extracted evidence into a knowledge graph, and (3) sub-selects the model components and relationships that are relevant and robust. The method can be used to either (4a) construct a structurally valid simulation model before proceeding with calibration or (4b) to validate the structure of existing simulation models. To demonstrate the feasibility of the method, we discuss an example implementation with mode of transport as behavior choice. We find that including non-frequently studied significant behavior determinants drastically improves the model's explanatory power in comparison to only including frequently studied variables. The paper serves as a proof-of-concept which can be reused, extended or adapted for various purposes.
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- 2024
7. The Conflict between Regulatory Agencies over the 20,000-Fold Lowering of the Tolerable Daily Intake (TDI) for Bisphenol A (BPA) by the European Food Safety Authority (EFSA)
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vom Saal, Frederick S., Antoniou, Michael, Belcher, Scott M., Bergman, Åke, Bhandari, Ramji K., Birnbaum, Linda S., Cohen, Aly, Collins, Terrence J., Demeneix, Barbara, Fine, Anne Marie, Flaws, Jodi A., Gayrard, Veronique, Goodson III, William H., Gore, Andrea C., Heindel, Jerrold J., Hunt, Patricia A., Iguchi, Taisen, Kassotis, Christopher D., Kortenkamp, Andreas, Mesnage, Robin, Muncke, Jane, Myers, John Peterson, Nadal, Angel, Newbold, Retha R., Padmanabhan, Vasantha, Palanza, Paola, Palma, Zandra, Parmigiani, Stefano, Patrick, Lyn, Prins, Gail S., Rosenfeld, Cheryl S., Skakkebaek, Niels E., Sonnenschein, Carlos, Soto, Ana M., Swan, Shanna H., Taylor, Julia A., Toutain, Pierre-Louis, von Hippel, Frank A., Welshons, Wade V., Zalko, Daniel, Zoeller, R. Thomas, vom Saal, Frederick S., Antoniou, Michael, Belcher, Scott M., Bergman, Åke, Bhandari, Ramji K., Birnbaum, Linda S., Cohen, Aly, Collins, Terrence J., Demeneix, Barbara, Fine, Anne Marie, Flaws, Jodi A., Gayrard, Veronique, Goodson III, William H., Gore, Andrea C., Heindel, Jerrold J., Hunt, Patricia A., Iguchi, Taisen, Kassotis, Christopher D., Kortenkamp, Andreas, Mesnage, Robin, Muncke, Jane, Myers, John Peterson, Nadal, Angel, Newbold, Retha R., Padmanabhan, Vasantha, Palanza, Paola, Palma, Zandra, Parmigiani, Stefano, Patrick, Lyn, Prins, Gail S., Rosenfeld, Cheryl S., Skakkebaek, Niels E., Sonnenschein, Carlos, Soto, Ana M., Swan, Shanna H., Taylor, Julia A., Toutain, Pierre-Louis, von Hippel, Frank A., Welshons, Wade V., Zalko, Daniel, and Zoeller, R. Thomas
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Background: The European Food Safety Authority (EFSA) recommended lowering their estimated tolerable daily intake (TDI) for bisphenol A (BPA) 20,000-fold to 0.2 ng/kg body weight (BW)/day. BPA is an extensively studied high production volume endocrine disrupting chemical (EDC) associated with a vast array of diseases. Prior risk assessments of BPA by EFSA as well as the US Food and Drug Administration (FDA) have relied on industry-funded studies conducted under good laboratory practice protocols (GLP) requiring guideline end points and detailed record keeping, while also claiming to examine (but rejecting) thousands of published findings by academic scientists. Guideline protocols initially formalized in the mid-twentieth century are still used by many regulatory agencies. EFSA used a 21st century approach in its reassessment of BPA and conducted a transparent, but time-limited, systematic review that included both guideline and academic research. The German Federal Institute for Risk Assessment (BfR) opposed EFSA’s revision of the TDI for BPA. Objectives: We identify the flaws in the assumptions that the German BfR, as well as the FDA, have used to justify maintaining the TDI for BPA at levels above what a vast amount of academic research shows to cause harm. We argue that regulatory agencies need to incorporate 21st century science into chemical hazard identifications using the CLARITY-BPA (Consortium Linking Academic and Regulatory Insights on BPA Toxicity) nonguideline academic studies in a collaborative government–academic program model. Discussion: We strongly endorse EFSA’s revised TDI for BPA and support the European Commission’s (EC) apparent acceptance of this updated BPA risk assessment. We discuss challenges to current chemical risk assessment assumptions about EDCs that need to be addressed by regulatory agencies to, in our opinion, become truly protective of public health. Addressing these challenges will hopefully result in BPA, and eventually other s
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- 2024
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8. Monitoring of species' genetic diversity in Europe varies greatly and overlooks potential climate change impacts
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Pearman, Peter B., Broennimann, Olivier, Aavik, Tsipe, Albayrak, Tamer, Alves, Paulo C., Aravanopoulos, F. A., Bertola, Laura D., Biedrzycka, Aleksandra, Buzan, Elena, Cubric-Curik, Vlatka, Djan, Mihajla, Fedorca, Ancuta, Fuentes Pardo, Angela P., Fussi, Barbara, Godoy, Jose A., Gugerli, Felix, Hoban, Sean, Holderegger, Rolf, Hvilsom, Christina, Iacolina, Laura, Kalamujic Stroil, Belma, Klinga, Peter, Konopinski, Maciej K., Kopatz, Alexander, Laikre, Linda, Lopes-Fernandes, Margarida, Mcmahon, Barry John, Mergeay, Joachim, Neophytou, Charalambos, Pálsson, Snæbjoern, Paz-Vinas, Ivan, Posledovich, Diana, Primmer, Craig R., Raeymaekers, Joost A. M., Rinkevich, Baruch, Rolecková, Barbora, Runis, Dainis, Schuerz, Laura, Segelbacher, Gernot, Kavcic Sonnenschein, Katja, Stefanovic, Milomir, Thurfjell, Henrik, Träger, Sabrina, Tsvetkov, Ivaylo N., Velickovic, Nevena, Vergeer, Philippine, Vernesi, Cristiano, Vilà, Carles, Westergren, Marjana, Zachos, Frank E., Guisan, Antoine, Bruford, Michael, Pearman, Peter B., Broennimann, Olivier, Aavik, Tsipe, Albayrak, Tamer, Alves, Paulo C., Aravanopoulos, F. A., Bertola, Laura D., Biedrzycka, Aleksandra, Buzan, Elena, Cubric-Curik, Vlatka, Djan, Mihajla, Fedorca, Ancuta, Fuentes Pardo, Angela P., Fussi, Barbara, Godoy, Jose A., Gugerli, Felix, Hoban, Sean, Holderegger, Rolf, Hvilsom, Christina, Iacolina, Laura, Kalamujic Stroil, Belma, Klinga, Peter, Konopinski, Maciej K., Kopatz, Alexander, Laikre, Linda, Lopes-Fernandes, Margarida, Mcmahon, Barry John, Mergeay, Joachim, Neophytou, Charalambos, Pálsson, Snæbjoern, Paz-Vinas, Ivan, Posledovich, Diana, Primmer, Craig R., Raeymaekers, Joost A. M., Rinkevich, Baruch, Rolecková, Barbora, Runis, Dainis, Schuerz, Laura, Segelbacher, Gernot, Kavcic Sonnenschein, Katja, Stefanovic, Milomir, Thurfjell, Henrik, Träger, Sabrina, Tsvetkov, Ivaylo N., Velickovic, Nevena, Vergeer, Philippine, Vernesi, Cristiano, Vilà, Carles, Westergren, Marjana, Zachos, Frank E., Guisan, Antoine, and Bruford, Michael
- Abstract
Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring. Overlaying GME with areas where the ranges of selected species of conservation interest approach current and future climate niche limits helps identify whether GME coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area, financial resources and conservation policy influence GME, high values of which only partially match species' joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Our results illuminate the need in Europe for expanded investment in genetic monitoring across climate gradients occupied by focal species, a need arguably greatest in southeastern European countries. This need could be met in part by expanding the European Union's Birds and Habitats Directives to fully address the conservation and monitoring of genetic diversity. Comparing data on genetic monitoring efforts across Europe with the distributions of areas at species' climatic niche margins, the authors show that monitoring efforts should be expanded to populations at trailing niche margins to include genetic variation that may prove important for adaptation to ongoing climate warming.
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- 2024
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9. Beperkte herinneringen, rekbare getuigenissen. De culturele herinnering aan de deportatie van het Apeldoornsche Bosch en het perspectief van de patiënten
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Koning, Pepijn de, Sonnenschein, Johan (Thesis Advisor), Koning, Pepijn de, and Sonnenschein, Johan (Thesis Advisor)
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Het Apeldoornsche Bosch was een Joodse psychiatrische instelling die van 1909 tot 1943 in Apeldoorn gevestigd was. De nazi-ontruiming in de nacht van 21 op 22 januari 1943 leidde tot de deportatie van bijna 1200 patiënten en een deel van het personeel naar het vernietigingskamp Auschwitz, waar alle patiënten werden vermoord. De naoorlogse culturele herinnering aan het Apeldoornsche Bosch wordt gekenmerkt door een gebrek aan (geschreven) getuigenissen van de patiëntenslachtoffers. De centrale vraag in dit onderzoek is daarom hoe deze gewelddadige, massale tragedie kan worden herinnerd vanuit het perspectief van de patiënten, een slachtoffergroep die vooral bestaat uit mensen met een disability. In dit onderzoek wordt een alternatief herinneringsmodel geïntroduceerd dat rekening houdt met het perspectief van de patiënten, om zo een inclusievere herinnering aan het Apeldoornsche Bosch mogelijk te maken. Dit onderzoek maakt gebruik van een narratieve methode om de naoorlogse culturele herinnering aan de deportatie van het Apeldoornsche Bosch te analyseren, zoals die wordt verbeeld in literaire werken, tv-films, toneelstukken en tentoonstellingen. Geconcludeerd werd dat de narratieven die voor 2000 zijn gepubliceerd zich voornamelijk richten op het verplegend personeel. Een terugkerende trope in deze verhalen is het morele dilemma waar het verplegend personeel mee te maken kreeg aan de vooravond van de evacuatie: vluchten en onderduiken of bij de zorgafhankelijke patiënten blijven en mee op transport gaan. De patiënten staan in deze narratieven in dienst van de karaktersering van de centrale, niet-disabled personages en fungeren daarmee als disabled enablers (Knittel, Historical 75). Vanaf de jaren 2000 wordt deze asymmetrie in perspectieven langzaamaan opgemerkt en een punt van kritische reflectie vanuit disabled perspectief. Enkele werken koppelen dan de geschiedenis van het Apeldoornsche Bosch aan de eugenetische ideologieën van de Duitse nazibezetters en de geschiede
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- 2024
10. (On)duidelijk, (niet)mensgericht en (on)conventioneel: de (on)mogelijkheden voor de activismeroman
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Duistermaat, Charlotte, Sonnenschein, Johan (Thesis Advisor), Duistermaat, Charlotte, and Sonnenschein, Johan (Thesis Advisor)
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Het huwelijk tussen de literaire roman en activisme is niet geheel voor de hand liggend. Het schrijven van een roman duurt lang, terwijl bij activisme vaak haast is geboden. En terwijl romans in de kritische receptie gewaardeerd worden om hun nuance en ambiguïteit, vereist een activistisch standpunt juist helderheid. Toch is de combinatie activisme en romans niet onmogelijk, blijkt onder andere uit de verschillende pogingen tot het schrijven van activistische literatuur sinds de negentiende eeuw. In deze scriptie staan die pogingen centraal, met name de hedendaagse pogingen, in een tijd waarin protest en demonstraties steeds meer deel uitmaken van de dagelijkse orde. Ik analyseer hedendaagse, Nederlandstalige romans over activisme, ook wel activismeromans genoemd, waarbij mijn doel is om de hedendaagse activismeroman en de kritische receptie daarvan in kaart te brengen. Daarnaast wil ik de activismeroman op de kaart zetten, door te laten zien dat activisme wel degelijk weerklank vindt in de hedendaagse Nederlandse romans en dat dit daarnaast al een rijke geschiedenis kent. De onderzoeksvraag van deze scriptie luidt: Hoe krijgt activisme vorm in de Nederlandstalige literaire cultuur? Om die vraag te beantwoorden voer ik een tweeledige analyse uit, die bestaat uit enerzijds een analyse van de kritische receptie van activismeromans en anderzijds een close reading van de romans zelf. Het vertrekpunt van beide analyses wordt gevormd door begrippenparen die ik vanuit de theorie abstraheer en die een belangrijke rol spelen in de kritische receptie en conceptie van de activismeroman. De romans die centraal staan in de analyse behandelen uiteenlopende activistische thema’s en zijn Zee Nu (2022) van Eva Meijer, En toen ging hij (2023) van Jannah Loontjens en De schoft (2023) van Marente de Moor. In het besluit confronteer ik de resultaten van beide analyses met elkaar, om zo aan te wijzen waar de zere plekken voor de activismeroman zitten. Hierbij laat ik zien dat de besproke
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- 2024
11. Validating and constructing behavioral models for simulation and projection using automated knowledge extraction
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Urban Accessibility and Social Inclusion, IRAS OH Epidemiology Chemical Agents, IRAS – One Health Chemical, Sonnenschein, Tabea, de Wit, G Ardine, den Braver, Nicole R, Vermeulen, Roel, Scheider, Simon, Urban Accessibility and Social Inclusion, IRAS OH Epidemiology Chemical Agents, IRAS – One Health Chemical, Sonnenschein, Tabea, de Wit, G Ardine, den Braver, Nicole R, Vermeulen, Roel, and Scheider, Simon
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- 2024
12. Probing efficient microbial CO2 utilisation through metabolic and process modelling
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Gorter de Vries, Philip J., Mol, Viviënne, Sonnenschein, Nikolaus, Jensen, Torbjørn Ølshøj, Nielsen, Alex Toftgaard, Gorter de Vries, Philip J., Mol, Viviënne, Sonnenschein, Nikolaus, Jensen, Torbjørn Ølshøj, and Nielsen, Alex Toftgaard
- Abstract
Acetogenic gas fermentation is increasingly studied as a promising technology to upcycle carbon-rich waste gasses. Currently the product range is limited, and production yields, rates and titres for a number of interesting products do not allow for economically viable processes. By pairing process modelling and host-agnostic metabolic modelling, we compare fermentation conditions and various products to optimise the processes. The models were then used in a simulation of an industrial-scale bubble column reactor. We find that increased temperatures favour gas transfer rates, particularly for the valuable and limiting H2, while furthermore predicting an optimal feed composition of 9:1 mol H2 to mol CO2. Metabolically, the increased non-growth associated maintenance requirements of thermophiles favours the formation of catabolic products. To assess the expansion of the product portfolio beyond acetate, both a product volatility analysis and a metabolic pathway model were implemented. In-situ recovery of volatile products is shown to be within range for acetone but challenging due to the extensive evaporation of water, while the direct production of more valuable compounds by acetogens is metabolically unfavourable compared to acetate and ethanol. We discuss alternative approaches to overcome these challenges to utilise acetogenic CO2 fixation to produce a wider range of carbon negative chemicals.
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- 2024
13. Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum
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Jian, Jianbo, Wu, Zhangyan, Silva-Núñez, Arisbe, Liu, Yun, Li, Xiaohui, Zheng, Xiaomin, Luo, Bei, Fang, Xiaodong, Workman, Christopher T., Larsen, Thomas Ostenfeld, Hansen, Per Juel, Sonnenschein, Eva C., Jian, Jianbo, Wu, Zhangyan, Silva-Núñez, Arisbe, Liu, Yun, Li, Xiaohui, Zheng, Xiaomin, Luo, Bei, Fang, Xiaodong, Workman, Christopher T., Larsen, Thomas Ostenfeld, Hansen, Per Juel, and Sonnenschein, Eva C.
- Abstract
Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms worldwide, which are often associated with massive fish-kills and subsequent economic losses. In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P. parvum strains UTEX 2797 and CCMP 3037, representing producers of type A prymnesins. Our results show that the P. parvum strains have a moderate haptophyte genome size of 97.56 and 107.32 Mb. The genome assemblies present one of highest contiguous assembled contig sequences to date consisting of 463 and 362 contigs with a contig N50 of 596.99 kb and 968.39 kb for strain UTEX 2797 and CCMP 3037, respectively. The assembled contigs of UTEX 2797 and CCMP 3037 were anchored to 34 scaffolds, with a scaffold N50 of 5.35 Mb and 3.61 Mb, respectively, accounting for 93.2 % and 97.9 % of the total length. Each plastid genome comprises a circular contig. A total of 20,578 and 19,426 protein-coding genes were annotated for UTEX 2797 and CCMP 3037. The expanded gene family analysis showed that starch and sucrose metabolism, sulfur metabolism, energy metabolism and ABC transporters are involved in the evolution of P. parvum. Polyketide synthase (PKSs) genes responsible for the production of secondary metabolites such as prymnesins displayed different expression patterns under nutrient limitation. Repeat expanded and horizontal gene transfer may be two contributing factors to the high number of PKS genes found in this species. The two high quality P. parvum genomes will serve as valuable resources for ecological, genetic, and toxicological studies of haptophytes that can be used to monitor and potentially manage harmful blooms of ichthyotoxic P. parvum in the future.
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- 2024
14. Monitoring of species’ genetic diversity in Europe varies greatly and overlooks potential climate change impacts
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Pearman, Peter, Broennimann, Olivier, Aavik, Tsipe, Albayrak, Tamer, Alves, Paulo, Aravanopoulos, F.A., Bertola, Laura, Biedrzycka, Aleksandra, Buzan, Elena, Cubric-Curik, Vlatka, Djan, Mihajla, Fedorca, Ancuta, Fuentes-Pardo, Angela, Fussi, Barbara, Godoy, José, Gugerli, Felix, Hoban, Sean, Holderegger, Rolf, Hvilsom, Christina, Iacolina, Laura, Kalamujic Stroil, Belma, Klinga, Peter, Konopiński, Maciej K., Kopatz, Alexander, Laikre, Linda, Lopes-Fernandes, Margarida, McMahon, Barry John, Mergeay, Joachim, Neophytou, Charalambos, Pálsson, Snæbjörn, Paz-Vinas, Ivan, Posledovich, Diana, Primmer, Craig, Raeymaekers, Joost, Rinkevich, Baruch, Rolečková, Barbora, Ruņģis, Dainis, Schuerz, Laura, Segelbacher, Gernot, Kavčič Sonnenschein, Katja, Stefanovic, Milomir, Thurfjell, Henrik, Träger, Sabrina, Tsvetkov, Ivaylo, Velickovic, Nevena, Vergeer, Philippine, Vernesi, Cristiano, Vilà, Carles, Westergren, Marjana, Zachos, Frank, Pearman, Peter, Broennimann, Olivier, Aavik, Tsipe, Albayrak, Tamer, Alves, Paulo, Aravanopoulos, F.A., Bertola, Laura, Biedrzycka, Aleksandra, Buzan, Elena, Cubric-Curik, Vlatka, Djan, Mihajla, Fedorca, Ancuta, Fuentes-Pardo, Angela, Fussi, Barbara, Godoy, José, Gugerli, Felix, Hoban, Sean, Holderegger, Rolf, Hvilsom, Christina, Iacolina, Laura, Kalamujic Stroil, Belma, Klinga, Peter, Konopiński, Maciej K., Kopatz, Alexander, Laikre, Linda, Lopes-Fernandes, Margarida, McMahon, Barry John, Mergeay, Joachim, Neophytou, Charalambos, Pálsson, Snæbjörn, Paz-Vinas, Ivan, Posledovich, Diana, Primmer, Craig, Raeymaekers, Joost, Rinkevich, Baruch, Rolečková, Barbora, Ruņģis, Dainis, Schuerz, Laura, Segelbacher, Gernot, Kavčič Sonnenschein, Katja, Stefanovic, Milomir, Thurfjell, Henrik, Träger, Sabrina, Tsvetkov, Ivaylo, Velickovic, Nevena, Vergeer, Philippine, Vernesi, Cristiano, Vilà, Carles, Westergren, Marjana, and Zachos, Frank
- Abstract
Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring. Overlaying GME with areas where the ranges of selected species of conservation interest approach current and future climate niche limits helps identify whether GME coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area, financial resources and conservation policy influence GME, high values of which only partially match species’ joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Our results illuminate the need in Europe for expanded investment in genetic monitoring across climate gradients occupied by focal species, a need arguably greatest in southeastern European countries. This need could be met in part by expanding the European Union’s Birds and Habitats Directives to fully address the conservation and monitoring of genetic diversity.
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- 2024
15. Submitted candidate projects for validation as population genetic diversity monitoring.
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Pearman, Peter, Broennimann, Olivier, Aavik, Tsipe, Albayrak, Tamer, Alves, Paulo, Aravanopoulos, F.A., Bertola, Laura, Biedrzycka, Aleksandra, Buzan, Elena, Cubric-Curik, Vlatka, Djan, Mihajla, Fedorca, Ancuta, Fuentes-Pardo, Angela, Fussi, Barbara, Godoy, José, Gugerli, Felix, Hoban, Sean, Holderegger, Rolf, Hvilsom, Christina, Iacolina, Laura, Kalamujic Stroil, Belma, Klinga, Peter, Konopiński, Maciej K., Kopatz, Alexander, Laikre, Linda, Lopes-Fernandes, Margarida, McMahon, Barry John, Mergeay, Joachim, Neophytou, Charalambos, Pálsson, Snæbjörn, Paz-Vinas, Ivan, Posledovich, Diana, Primmer, Craig, Raeymaekers, Joost, Rinkevich, Baruch, Rolečková, Barbora, Ruņģis, Dainis, Schuerz, Laura, Segelbacher, Gernot, Kavčič Sonnenschein, Katja, Stefanovic, Milomir, Thurfjell, Henrik, Träger, Sabrina, Tsvetkov, Ivaylo, Velickovic, Nevena, Vergeer, Philippine, Vernesi, Cristiano, Vilà, Carles, Westergren, Marjana, Zachos, Frank, Pearman, Peter, Broennimann, Olivier, Aavik, Tsipe, Albayrak, Tamer, Alves, Paulo, Aravanopoulos, F.A., Bertola, Laura, Biedrzycka, Aleksandra, Buzan, Elena, Cubric-Curik, Vlatka, Djan, Mihajla, Fedorca, Ancuta, Fuentes-Pardo, Angela, Fussi, Barbara, Godoy, José, Gugerli, Felix, Hoban, Sean, Holderegger, Rolf, Hvilsom, Christina, Iacolina, Laura, Kalamujic Stroil, Belma, Klinga, Peter, Konopiński, Maciej K., Kopatz, Alexander, Laikre, Linda, Lopes-Fernandes, Margarida, McMahon, Barry John, Mergeay, Joachim, Neophytou, Charalambos, Pálsson, Snæbjörn, Paz-Vinas, Ivan, Posledovich, Diana, Primmer, Craig, Raeymaekers, Joost, Rinkevich, Baruch, Rolečková, Barbora, Ruņģis, Dainis, Schuerz, Laura, Segelbacher, Gernot, Kavčič Sonnenschein, Katja, Stefanovic, Milomir, Thurfjell, Henrik, Träger, Sabrina, Tsvetkov, Ivaylo, Velickovic, Nevena, Vergeer, Philippine, Vernesi, Cristiano, Vilà, Carles, Westergren, Marjana, and Zachos, Frank
- Abstract
A data set of submitted candidate projects for evaluation of validity as Category II population genetic monitoring, with repeated sampling over time and at least one indicator of population genetic diversity., A data set of submitted candidate projects for evaluation of validity as Category II population genetic monitoring, with repeated sampling over time and at least one indicator of population genetic diversity.
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- 2024
16. Long-Term Follow-Up of High-Risk Breast Lesions at Vacuum-Assisted Biopsy without Subsequent Surgical Resection
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Elfgen, Constanze; https://orcid.org/0000-0001-6092-6612, Varga, Zsuzsanna; https://orcid.org/0000-0002-2855-983X, Breitling, Katrin, Pauli, Eliane, Schwegler-Guggemos, Daniela, Kampmann, Gert, Kubik-Huch, Rahel A; https://orcid.org/0000-0002-3636-8697, Leo, Cornelia; https://orcid.org/0000-0003-1601-0281, Lepori, Domenico, Sonnenschein, Martin, Tausch, Christoph, Schrading, Simone, Elfgen, Constanze; https://orcid.org/0000-0001-6092-6612, Varga, Zsuzsanna; https://orcid.org/0000-0002-2855-983X, Breitling, Katrin, Pauli, Eliane, Schwegler-Guggemos, Daniela, Kampmann, Gert, Kubik-Huch, Rahel A; https://orcid.org/0000-0002-3636-8697, Leo, Cornelia; https://orcid.org/0000-0003-1601-0281, Lepori, Domenico, Sonnenschein, Martin, Tausch, Christoph, and Schrading, Simone
- Abstract
INTRODUCTION B3-lesions of the breast are a heterogeneous group of neoplasms, associated with a higher risk of breast cancer. Recent studies show a low upgrade rate into malignancy after subsequent open surgical excision (OE) of most B3-lesions when proven by vacuum-assisted biopsy (VAB). However, there is a lack of long-term follow-up data after VAB of high-risk lesions. The primary aim of this study was to demonstrate whether follow-up of B3 lesions is a beneficial and reliable alternative to OE in terms of long-term outcome. The secondary aim was to identify patient and lesion characteristics of B3 lesions for which OE is still necessary. METHODS This retrospective multicenter study was conducted at 8 Swiss breast centers between 2010 and 2019. A total of 278 women (mean age: 53.5 ± 10.7 years) with 286 B3-lesions who had observation only and who had at least 24 months of follow-up were included. Any event during follow-up (ductal carcinoma in situ [DCIS], invasive cancer, new B3-lesion) was systematically recorded. Data from women who had an event during follow-up were compared with those who did not. The results for the different B3 lesions were analyzed using the t test and Fisher's exact test. A p value of <0.05 was considered statistically significant. RESULTS The median follow-up interval was 59 months (range: 24-143 months) with 52% (148/286) having a follow-up of more than 5 years. During follow-up, in 42 women, 44 suspicious lesions occurred, with 36.4% (16/44) being invasive cancer and 6.8% (3/44) being DCIS. Thus, 6.6% (19/286) of all women developed malignancy during follow-up after a median follow-up interval of 6.5 years (range: 31-119 months). The initial histology of the B3 lesion influenced the subsequent occurrence of a malignant lesion during follow-up (p < 0.038). The highest malignancy-developing rate was observed in atypical ductal hyperplasia (ADH) (24%, 19/79), while all other B3-lesions had malignant findings ipsi- and contralateral betwe
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- 2024
17. Literaire pornografie, vrijheid en objectificatie: Objectivering van het meisje in Mieke Maaike’s obscene jeugd, Eros en de eenzame man en Menuet
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Hooijdonk, Mina van, Sonnenschein, Johan (Thesis Advisor), Hooijdonk, Mina van, and Sonnenschein, Johan (Thesis Advisor)
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In deze scriptie onderzoek ik op welke manier de feministische objectificatietheorie inzicht geeft in de representatie van het meisje in drie werken van de Vlaamse schrijver Louis Paul Boon, te weten Mieke Maaike’s obscene jeugd (1972), Eros en de eenzame man (1980) en Menuet (1955). Om ten behoeve van de uiteindelijke analyse een werkdefinitie te vormen van objectificatie, wordt gebruik gemaakt van de objectificatietheorie van Martha Nussbaum. Volgens deze theorie is objectificeren het behandelen of bezien van een persoon als een object voor eigen (seksueel) belang waardoor zijn of haar menselijkheid verloren gaat. Door bovendien in te gaan op pornografie als literair genre in het sociale klimaat van de jaren zestig wordt aangetoond dat de verbeelde vrijheid binnen dit genre naar voren komt als hypermannelijk: zo ook in de publicaties van Boon. Deze andere, meer feministische lezing van zijn werken toont aan dat het meisje in deze publicaties op verschillende manieren veelvuldig wordt geobjectificeerd waarbij er sprake is van ongelijke genderrollen.
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- 2024
18. Antagonistic activity of Phaeobacter piscinae against the emerging fish pathogen Vibrio crassostreae in aquaculture feed algae
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Roager, Line, Athena-Vasileiadi, Despoina, Gram, Lone, Sonnenschein, Eva C., Roager, Line, Athena-Vasileiadi, Despoina, Gram, Lone, and Sonnenschein, Eva C.
- Abstract
Aquaculture provides a rich resource of high-quality protein; however, the production is challenged by emerging pathogens such as Vibrio crassostreae. While probiotic bacteria have been proposed as a sustainable solution to reduce pathogen load in aquaculture, their application requires a comprehensive assessment across the aquaculture food chain. The purpose of this study was to determine the antagonistic effect of the potential probiotic bacterium Phaeobacter piscinae against the emerging fish pathogen V. crassostreae in aquaculture feed algae that can be an entry point for pathogens in fish and shellfish aquaculture. P. piscinae strain S26 produces the antibacterial compound tropodithietic acid (TDA). In a plate-based assay, P. piscinae S26 was equally to more effective than the well-studied Phaeobacter inhibens DSM17395 in its inhibition of the fish pathogens Vibrio anguillarum 90-11-286 and V. crassostreae DMC-1. When co-cultured with the microalgae Tetraselmis suecica and Isochrysis galbana, P. piscinae S26 reduced the maximum cell density of V. crassostreae DMC-1 by 2 log and 3-4 log fold, respectively. A TDA-deficient mutant of P. piscinae S26 inhibited V. crassostreae DMC-1 to a lesser extent than the wild type, suggesting that the antagonistic effect involves TDA and other factors. TDA is the prime antagonistic agent of the inhibition of V. anguillarum 90-11-286. Comparative genomics of V. anguillarum 90-11-286 and V. crassostreae DMC-1 revealed that V. crassostreae DMC-1 carries a greater arsenal of antibiotic resistance genes potentially contributing to the reduced effect of TDA. In conclusion, P. piscinae S26 is a promising new candidate for inhibition of emerging pathogens such as V. crassostreae DMC-1 in algal feed systems and could contribute to a more sustainable aquaculture industry. IMPORTANCE The globally importan
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- 2024
19. Documenting the Child's Everyday Home Experiences: The Ecological Inventory as a Resource for Teachers. Instructional Resource No. 11.
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National Reading Research Center, Athens, GA., National Reading Research Center, College Park, MD., and Sonnenschein, Susan
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This paper describes the Ecological Inventory, a technique developed to document the range and frequency of literacy-related activities available in pre-kindergartners' everyday lives. This technique can be used by teachers to broaden understanding of their students' home-based experiences. Results from the Ecological Inventory can be used as a basis for improved understanding between teachers and parents, for developing classroom educational plans, and for identifying the socialization agents in children's lives. Contains 25 references. Appendixes present guidelines for telling parents about the diaries, guidelines for diary keeping, and the Ecological Inventory. (Author/RS)
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- 1995
20. Measuring chaos in string scattering processes
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Bianchi, Massimo, Firrotta, Maurizio, Sonnenschein, Jacob, Weissman, Dorin, Bianchi, Massimo, Firrotta, Maurizio, Sonnenschein, Jacob, and Weissman, Dorin
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We analyze the amplitudes of one highly excited string (HES) state with two or three tachyons in open bosonic string theory. We argue that these processes are chaotic by showing that the spacing ratios of successive peaks in the angular dependence of the amplitudes are distributed as predicted by the $\beta$-ensemble of random matrix theory (RMT). We show how the continuous parameter $\beta$ depends on the level and helicity of the scattered HES state. We derive the scattering amplitude of an HES and three tachyons and show that it takes the form of the Veneziano amplitude times a dressing factor, and that the dressing is chaotic as a function of the scattering angle, in the sense that its spacing ratios match with RMT predictions.
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- 2023
21. Euler fluid in 2+1 dimensions as a gauge theory, and an action for the Euler fluid in any dimension
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Nastase, Horatiu, Sonnenschein, Jacob, Nastase, Horatiu, and Sonnenschein, Jacob
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In this paper we parallel the construction of Tong of a gauge theory for shallow water, by writing a gauge theory for the Euler fluid in 2+1 dimensions. We then extend it to an Euler fluid coupled to electromagnetic background. We argue that the gauge theory formulation provides a topological argument for the quantization of 2+1 dimensional Euler Hopfion solution. In the process, we find a (non-gauge) action for the Euler fluid that can be extended to any dimension, including the physical 3+1 dimensions. We discuss several aspects of the ABC flow., Comment: 20 pages, no figures; reference added, connection to previous Euler fluid action explained; references added
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- 2023
22. Assoziation von OxLDL-Antikörpern bei primärem Sjögren-Syndrom und atherosklerotischen Veränderungen der A. carotis
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Zehrfeld, N, Abelmann, M, Benz, S, Armbruster, FP, Beider, S, Dopfer-Jablonka, A, Witte, T, Seeliger, T, Skripuletz, T, Derda, AA, Sonnenschein, K, Ernst, D, Zehrfeld, N, Abelmann, M, Benz, S, Armbruster, FP, Beider, S, Dopfer-Jablonka, A, Witte, T, Seeliger, T, Skripuletz, T, Derda, AA, Sonnenschein, K, and Ernst, D
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- 2023
23. Die Organbeteiligung bei primärem Sjögren-Syndrom ist mit atherosklerotischer Plaquebildung & erhöhter Intima-Media Dicke der A.carotis assoziiert
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Zehrfeld, N, Benz, S, Beider, S, Dopfer-Jablonka, A, Emelie, K, Witte, T, Skripuletz, T, Seeliger, T, Derda, AA, Sonnenschein, K, Ernst, D, Zehrfeld, N, Benz, S, Beider, S, Dopfer-Jablonka, A, Emelie, K, Witte, T, Skripuletz, T, Seeliger, T, Derda, AA, Sonnenschein, K, and Ernst, D
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- 2023
24. The COVID-19 pandemic: changes in parent–child activities at home from spring 2020 to spring 2021 from a cross-cultural viewp
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Meoded Karabanov, Galia, Aram, Dorit, López Escribano, María Del Carmen, Shtereva, Katerina, Asaf, Merav, Ziv, Margalit, Stites, Michele, Sonnenschein, Susan, Meoded Karabanov, Galia, Aram, Dorit, López Escribano, María Del Carmen, Shtereva, Katerina, Asaf, Merav, Ziv, Margalit, Stites, Michele, and Sonnenschein, Susan
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The study was conducted in accordance with the Declaration of Helsinki, and approved by the Institutional Review Board (or Ethics Committee) of Tel Aviv University (protocol code 0001208-1 March 2020 and 0001208-2 April 2021). Referencias bibliográficas: • Bornstein M.H. Introduction: The SARS-CoV-2 pandemic—Issues for families, parents and children Psychological Insights for Understanding COVID-19 and Families, Parents, and Children Bornstein M.H. Routledge Oxfordshire, UK 2021 1 68 • Prime H. Wade M. Browne D.T. Risk and resilience in family well-being during the COVID-19 pandemic Am. Psychol. 2020 75 631 643 10.1037/amp0000660 • Brown S.M. Doom J.R. Lechuga-Peña S. Watamura S.E. Koppels T. Stress and parenting during the global COVID-19 pandemic Child Abus. Negl. 2020 110 104699 10.1016/j.chiabu.2020.104699 • Deoni S.C. Beauchemin J. Volpe A. D’Sa V. the RESONANCE Consortium Impact of the COVID-19 pandemic on early childhood cognitive development: Initial findings in a longitudinal observational study of child health MedRxiv 2021 10.1101/2021.08.10.21261846 • Harkness S. Super C.M. Culture and parenting Handbook of Parenting Bornstein M.H. Lawrence Erlbaum Associates Mahwah, NJ, USA 2002 Volume 2 253 280 • Super C.M. Harkness S. The developmental niche: A conceptualization at the interface of child and culture Int. J. Behav. Dev. 1986 9 545 569 10.1177/016502548600900409 • Harkness S. Super C.M. Moscardino U. Rha J. Blom M. Huitrón B. Johnston C. Sutherland M.A. Hyun O.K. Axia G. et al. Cultural models and developmental agendas: Implications for arousal and self-regulation in early infancy J. Dev. • Keeter S. McGeeney K. Coverage Error in Internet Survey Pew Research Centre Washington, DC, USA 2015 Available online: https://www.pewresearch.org/methods/2015/09/22/coverage-error-in-internet-surveys (accessed on 1 July 2023) • Kogan V. Lavertu S. The COVID-19 Pandemic and Student Achievement on Ohio’s Third-Grade English Language Arts Assessment Ohio State Universit, This study explored young children’s (2–8 years old) daily activities during the first lockdown with the outbreak of the COVID-19 pandemic (spring/2020, T1) and a year later (spring/2021, T2) from a cross-cultural perspective. It describes parent–child literacy and digital activities in Bulgaria, Israel, and Spain. Participating parents (747 in T1 and 432 in T2) answered online questionnaires about the frequency of parent–child literacy activities (alphabetic, book reading, and play) and digital activities (joint activities, selecting content, scaffolding) and the child’s screen time. The findings indicated moderate parent–child literacy and digital activities during the time points. A series of ANCOVAs revealed differences between time periods and cultures beyond the demographic measures (child’s age, parent’s education and age, and family size). During the first lockdown, parent–child joint digital activities and the child’s screen time were higher than a year later. A year later, parents were more involved in book reading, literacy play activities, and scaffolding their children’s use of digital devices. Interactions between the period and culture showed that Bulgarian and Spanish parents were more involved in their children’s literacy and digital activities than Israeli parents. Spanish children had more independent screen time than Bulgarian and Israeli children. Associations between literacy and digital activities implied a consistent parenting style across the activities., Depto. de Investigación y Psicología en Educación, Fac. de Educación, TRUE, pub
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- 2023
25. Search for a Dark-Matter-Induced Cosmic Axion Background with ADMX
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Nitta, T, Nitta, T, Braine, T, Du, N, Guzzetti, M, Hanretty, C, Leum, G, Rosenberg, LJ, Rybka, G, Sinnis, J, Clarke, John, Siddiqi, I, Awida, MH, Chou, AS, Hollister, M, Knirck, S, Sonnenschein, A, Wester, W, Gleason, JR, Hipp, AT, Sikivie, P, Sullivan, NS, Tanner, DB, Khatiwada, R, Carosi, G, Robertson, N, Duffy, LD, Boutan, C, Lentz, E, Oblath, NS, Taubman, MS, Yang, J, Daw, EJ, Perry, MG, Bartram, C, Buckley, JH, Gaikwad, C, Hoffman, J, Murch, KW, Goryachev, M, Hartman, E, McAllister, BT, Quiskamp, A, Thomson, C, Tobar, ME, Dror, JA, Murayama, H, Rodd, NL, Nitta, T, Nitta, T, Braine, T, Du, N, Guzzetti, M, Hanretty, C, Leum, G, Rosenberg, LJ, Rybka, G, Sinnis, J, Clarke, John, Siddiqi, I, Awida, MH, Chou, AS, Hollister, M, Knirck, S, Sonnenschein, A, Wester, W, Gleason, JR, Hipp, AT, Sikivie, P, Sullivan, NS, Tanner, DB, Khatiwada, R, Carosi, G, Robertson, N, Duffy, LD, Boutan, C, Lentz, E, Oblath, NS, Taubman, MS, Yang, J, Daw, EJ, Perry, MG, Bartram, C, Buckley, JH, Gaikwad, C, Hoffman, J, Murch, KW, Goryachev, M, Hartman, E, McAllister, BT, Quiskamp, A, Thomson, C, Tobar, ME, Dror, JA, Murayama, H, and Rodd, NL
- Abstract
We report the first result of a direct search for a cosmic axion background (CaB)-a relativistic background of axions that is not dark matter-performed with the axion haloscope, the Axion Dark Matter eXperiment (ADMX). Conventional haloscope analyses search for a signal with a narrow bandwidth, as predicted for dark matter, whereas the CaB will be broad. We introduce a novel analysis strategy, which searches for a CaB induced daily modulation in the power measured by the haloscope. Using this, we repurpose data collected to search for dark matter to set a limit on the axion photon coupling of a CaB originating from dark matter cascade decay via a mediator in the 800-995 MHz frequency range. We find that the present sensitivity is limited by fluctuations in the cavity readout as the instrument scans across dark matter masses. Nevertheless, we suggest that these challenges can be surmounted using superconducting qubits as single photon counters, and allow ADMX to operate as a telescope searching for axions emerging from the decay of dark matter. The daily modulation analysis technique we introduce can be deployed for various broadband rf signals, such as other forms of a CaB or even high-frequency gravitational waves.
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- 2023
26. GenSynthPop: Generating a Spatially Explicit Synthetic Population of Agents and Households from Aggregated Data
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Pellegrino, M., de Mooij, J., Sonnenschein, T., Dastani, M., Ettema, D., Logan, B., Verstegen, J.A., Pellegrino, M., de Mooij, J., Sonnenschein, T., Dastani, M., Ettema, D., Logan, B., and Verstegen, J.A.
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Synthetic populations are microscopic representations of actual citizens living in a specific area. They play an increasingly important role in studying and modeling citizens and are often used to build agent-based social simulations.Traditional approaches for synthesizing populations use a detailed sample of the population (which may not be available) or combine data into a single joint distribution, and draw agents or households from these. In this paper, we propose a sample-free approach where synthetic individuals and households directly represent the estimated joint distribution to which attributes are iteratively added, conditioned on previous attributes such that the relative frequencies within each joint group of attributes are maintained.
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- 2023
27. Low Frequency (100-600 MHz) Searches with Axion Cavity Haloscopes
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Chakrabarty, S., Gleason, J. R., Han, Y., Hipp, A. T., Solano, M., Sikivie, P., Sullivan, N. S., Tanner, D. B., Goryachev, M., Hartman, E., McAllister, B. T., Quiskamp, A., Thomson, C., Tobar, M. E., Awida, M. H., Chou, A. S., Hollister, M., Knirck, S., Sonnenschein, A., Wester, W., Braine, T., Guzzetti, M., Hanretty, C., Leum, G., Rosenberg, L. J, Rybka, G., Sinnis, J., Clarke, John, Siddiqi, I., Khatiwada, R., Carosi, G., Du, N., Robertson, N., Duffy, L. D., Boutan, C., Oblath, N. S., Taubman, M. S., Yang, J., Lentz, E., Daw, E. J., Perry, M. G., Bartram, C., Buckley, J. H., Gaikwad, C., Hoffman, J., Murch, K. W., Nitta, T., Chakrabarty, S., Gleason, J. R., Han, Y., Hipp, A. T., Solano, M., Sikivie, P., Sullivan, N. S., Tanner, D. B., Goryachev, M., Hartman, E., McAllister, B. T., Quiskamp, A., Thomson, C., Tobar, M. E., Awida, M. H., Chou, A. S., Hollister, M., Knirck, S., Sonnenschein, A., Wester, W., Braine, T., Guzzetti, M., Hanretty, C., Leum, G., Rosenberg, L. J, Rybka, G., Sinnis, J., Clarke, John, Siddiqi, I., Khatiwada, R., Carosi, G., Du, N., Robertson, N., Duffy, L. D., Boutan, C., Oblath, N. S., Taubman, M. S., Yang, J., Lentz, E., Daw, E. J., Perry, M. G., Bartram, C., Buckley, J. H., Gaikwad, C., Hoffman, J., Murch, K. W., and Nitta, T.
- Abstract
We investigate reentrant and dielectric loaded cavities for the purpose of extending the range of axion cavity haloscopes to lower masses, below the range where the Axion Dark Matter eXperiment (ADMX) has already searched. Reentrant and dielectric loaded cavities were simulated numerically to calculate and optimize their form factors and quality factors. A prototype reentrant cavity was built and its measured properties were compared with the simulations. We estimate the sensitivity of axion dark matter searches using reentrant and dielectric loaded cavities inserted in the existing ADMX magnet at the University of Washington and a large magnet being installed at Fermilab., Comment: 33 pages, 24 figures
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- 2023
28. Chemotaxis increases metabolic exchanges between marine picophytoplankton and heterotrophic bacteria
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Raina, J-B, Giardina, M, Brumley, DRR, Clode, PLL, Pernice, M, Guagliardo, P, Bougoure, J, Mendis, H, Smriga, S, Sonnenschein, ECC, Ullrich, MSS, Stocker, R, Seymour, JRR, Raina, J-B, Giardina, M, Brumley, DRR, Clode, PLL, Pernice, M, Guagliardo, P, Bougoure, J, Mendis, H, Smriga, S, Sonnenschein, ECC, Ullrich, MSS, Stocker, R, and Seymour, JRR
- Abstract
Behaviours such as chemotaxis can facilitate metabolic exchanges between phytoplankton and heterotrophic bacteria, which ultimately regulate oceanic productivity and biogeochemistry. However, numerically dominant picophytoplankton have been considered too small to be detected by chemotactic bacteria, implying that cell-cell interactions might not be possible between some of the most abundant organisms in the ocean. Here we examined how bacterial behaviour influences metabolic exchanges at the single-cell level between the ubiquitous picophytoplankton Synechococcus and the heterotrophic bacterium Marinobacter adhaerens, using bacterial mutants deficient in motility and chemotaxis. Stable-isotope tracking revealed that chemotaxis increased nitrogen and carbon uptake of both partners by up to 4.4-fold. A mathematical model following thousands of cells confirmed that short periods of exposure to small but nutrient-rich microenvironments surrounding Synechococcus cells provide a considerable competitive advantage to chemotactic bacteria. These findings reveal that transient interactions mediated by chemotaxis can underpin metabolic relationships among the ocean's most abundant microorganisms.
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- 2023
29. Search for inelastic dark matter-nucleus scattering with the PICO-60 CF$_{3}$I and C$_{3}$F$_{8}$ bubble chambers
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Adams, E., Ali, B., Arnquist, I. J., Baxter, D., Behnke, E., Bressler, M., Broerman, B., Chen, C. J., Clark, K., Collar, J. I., Cooper, P. S., Cripe, C., Crisler, M., Dahl, C. E., Das, M., Fallows, S., Farine, J., Filgas, R., Viltres, A. García, Giroux, G., Harris, O., Hillier, T., Hoppe, E. W., Jackson, C. M., Jin, M., Krauss, C. B., Kumar, V., Laurin, M., Lawson, I., Leblanc, A., Leng, H., Levine, I., Licciardi, C., Lippincott, W. H., Mitra, P., Monette, V., Moore, C., Neilson, R., Noble, A. J., Nozard, H., Pal, S., Piro, M. -C., Plante, A., Priya, S., Rethmeier, C., Robinson, A. E., Savoie, J., Sonnenschein, A., Starinski, N., Štekl, I., Tiwari, D., Vázquez-Jáuregui, E., Wichoski, U., Zacek, V., Zhang, J., Adams, E., Ali, B., Arnquist, I. J., Baxter, D., Behnke, E., Bressler, M., Broerman, B., Chen, C. J., Clark, K., Collar, J. I., Cooper, P. S., Cripe, C., Crisler, M., Dahl, C. E., Das, M., Fallows, S., Farine, J., Filgas, R., Viltres, A. García, Giroux, G., Harris, O., Hillier, T., Hoppe, E. W., Jackson, C. M., Jin, M., Krauss, C. B., Kumar, V., Laurin, M., Lawson, I., Leblanc, A., Leng, H., Levine, I., Licciardi, C., Lippincott, W. H., Mitra, P., Monette, V., Moore, C., Neilson, R., Noble, A. J., Nozard, H., Pal, S., Piro, M. -C., Plante, A., Priya, S., Rethmeier, C., Robinson, A. E., Savoie, J., Sonnenschein, A., Starinski, N., Štekl, I., Tiwari, D., Vázquez-Jáuregui, E., Wichoski, U., Zacek, V., and Zhang, J.
- Abstract
PICO bubble chambers have exceptional sensitivity to inelastic dark matter-nucleus interactions due to a combination of their extended nuclear recoil energy detection window from a few keV to $O$(100 keV) or more and the use of iodine as a heavy target. Inelastic dark matter-nucleus scattering is interesting for studying the properties of dark matter, where many theoretical scenarios have been developed. This study reports the results of a search for dark matter inelastic scattering with the PICO-60 bubble chambers. The analysis reported here comprises physics runs from PICO-60 bubble chambers using CF$_{3}$I and C$_{3}$F$_{8}$. The CF$_{3}$I run consisted of 36.8 kg of CF$_{3}$I reaching an exposure of 3415 kg-day operating at thermodynamic thresholds between 7 and 20 keV. The C$_{3}$F$_{8}$ runs consisted of 52 kg of C$_{3}$F$_{8}$ reaching exposures of 1404 kg-day and 1167 kg-day running at thermodynamic thresholds of 2.45 keV and 3.29 keV, respectively. The analysis disfavors various scenarios, in a wide region of parameter space, that provide a feasible explanation of the signal observed by DAMA, assuming an inelastic interaction, considering that the PICO CF$_{3}$I bubble chamber used iodine as the target material., Comment: 7 pages, 3 figures
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- 2023
30. Third International Consensus Conference on lesions of uncertain malignant potential in the breast (B3 lesions).
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Elfgen, C., Leo, C., Kubik-Huch, R.A., Muenst, S., Schmidt, N., Quinn, C., McNally, S., Diest, P.J. van, Mann, R.M., Bago-Horvath, Z., Bernathova, M., Regitnig, P., Fuchsjäger, M., Schwegler-Guggemos, D., Maranta, M., Zehbe, S., Tausch, C., Güth, U., Fallenberg, E.M., Schrading, S., Kothari, A., Sonnenschein, M., Kampmann, G., Kulka, J., Tille, J.C., Körner, M., Decker, T., Lax, S.F., Daniaux, M., Bjelic-Radisic, V., Kacerovsky-Strobl, S., Condorelli, R., Gnant, M., Varga, Z., Elfgen, C., Leo, C., Kubik-Huch, R.A., Muenst, S., Schmidt, N., Quinn, C., McNally, S., Diest, P.J. van, Mann, R.M., Bago-Horvath, Z., Bernathova, M., Regitnig, P., Fuchsjäger, M., Schwegler-Guggemos, D., Maranta, M., Zehbe, S., Tausch, C., Güth, U., Fallenberg, E.M., Schrading, S., Kothari, A., Sonnenschein, M., Kampmann, G., Kulka, J., Tille, J.C., Körner, M., Decker, T., Lax, S.F., Daniaux, M., Bjelic-Radisic, V., Kacerovsky-Strobl, S., Condorelli, R., Gnant, M., and Varga, Z.
- Abstract
01 juli 2023, Contains fulltext : 294873.pdf (Publisher’s version ) (Open Access), The heterogeneous group of B3 lesions in the breast harbors lesions with different malignant potential and progression risk. As several studies about B3 lesions have been published since the last Consensus in 2018, the 3rd International Consensus Conference discussed the six most relevant B3 lesions (atypical ductal hyperplasia (ADH), flat epithelial atypia (FEA), classical lobular neoplasia (LN), radial scar (RS), papillary lesions (PL) without atypia, and phyllodes tumors (PT)) and made recommendations for diagnostic and therapeutic approaches. Following a presentation of current data of each B3 lesion, the international and interdisciplinary panel of 33 specialists and key opinion leaders voted on the recommendations for further management after core-needle biopsy (CNB) and vacuum-assisted biopsy (VAB). In case of B3 lesion diagnosis on CNB, OE was recommended in ADH and PT, whereas in the other B3 lesions, vacuum-assisted excision was considered an equivalent alternative to OE. In ADH, most panelists (76%) recommended an open excision (OE) after diagnosis on VAB, whereas observation after a complete VAB-removal on imaging was accepted by 34%. In LN, the majority of the panel (90%) preferred observation following complete VAB-removal. Results were similar in RS (82%), PL (100%), and FEA (100%). In benign PT, a slim majority (55%) also recommended an observation after a complete VAB-removal. VAB with subsequent active surveillance can replace an open surgical intervention for most B3 lesions (RS, FEA, PL, PT, and LN). Compared to previous recommendations, there is an increasing trend to a de-escalating strategy in classical LN. Due to the higher risk of upgrade into malignancy, OE remains the preferred approach after the diagnosis of ADH.
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- 2023
31. Simultaneous application of enzyme and thermodynamic constraints to metabolic models using an updated Python implementation of GECKO
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Carrasco Muriel, Jorge, Long, Christopher, Sonnenschein, Nikolaus, Carrasco Muriel, Jorge, Long, Christopher, and Sonnenschein, Nikolaus
- Abstract
Genome-scale metabolic (GEM) models are knowledge bases of the reactions and metabolites of a particular organism. These GEM models allow for the simulation of the metabolism, for example, calculating growth and production yields-based on the stoichiometry, reaction directionality, and uptake rates of the metabolic network. Over the years, several extensions have been added to take into account other actors in metabolism, going beyond pure stoichiometry. One such extension is enzyme-constrained models, which enable the integration of proteomics data into GEM models containing the necessary kcat values for their enzymes. Given its relatively recent formulation, there are still challenges in standardization and data reconciliation between the model and the experimental measurements. In this work, we present geckopy 3.0 (genome-scale model with enzyme constraints, using Kinetics and Omics in Python), an actualization from scratch of the previous Python implementation of the same name. This update tackles the aforementioned challenges, to reach maturity in enzyme-constrained modeling. With the new geckopy, proteins are typed in the Systems Biology Markup Language (SBML) document, taking advantage of the SBML Groups extension, in compliance with community standards. In addition, a suite of relaxation algorithms-in the form of linear and mixed-integer linear programming problems-has been added to facilitate the reconciliation of raw proteomics data with the metabolic model. Several functionalities to integrate experimental data were implemented, including an interface layer with pytfa for the usage of thermodynamics and metabolomics constraints. Finally, the relaxation algorithms were benchmarked against public proteomics data sets in Escherichia coli for different conditions, revealing targets for improving the enzyme-constrained model and/or the proteomics pipeline. IMPORTANCE The metabolism of biologica
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- 2023
32. CRI-SPA: a high-throughput method for systematic genetic editing of yeast libraries
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Cachera, Paul, Olsson, Helén, Coumou, Hilde, Jensen, Mads L, Sánchez, Benjamín J., Strucko, Tomas, van den Broek, Marcel, Daran, Jean-Marc, Jensen, Michael K., Sonnenschein, Nikolaus, Lisby, Michael, Mortensen, Uffe H., Cachera, Paul, Olsson, Helén, Coumou, Hilde, Jensen, Mads L, Sánchez, Benjamín J., Strucko, Tomas, van den Broek, Marcel, Daran, Jean-Marc, Jensen, Michael K., Sonnenschein, Nikolaus, Lisby, Michael, and Mortensen, Uffe H.
- Abstract
Biological functions are orchestrated by intricate networks of interacting genetic elements. Predicting the interaction landscape remains a challenge for systems biology and new research tools allowing simple and rapid mapping of sequence to function are desirable. Here, we describe CRI-SPA, a method allowing the transfer of chromosomal genetic features from a CRI-SPA Donor strain to arrayed strains in large libraries of Saccharomyces cerevisiae. CRI-SPA is based on mating, CRISPR-Cas9-induced gene conversion, and Selective Ploidy Ablation. CRI-SPA can be massively parallelized with automation and can be executed within a week. We demonstrate the power of CRI-SPA by transferring four genes that enable betaxanthin production into each strain of the yeast knockout collection (≈4800 strains). Using this setup, we show that CRI-SPA is highly efficient and reproducible, and even allows marker-free transfer of genetic features. Moreover, we validate a set of CRI-SPA hits by showing that their phenotypes correlate strongly with the phenotypes of the corresponding mutant strains recreated by reverse genetic engineering. Hence, our results provide a genome-wide overview of the genetic requirements for betaxanthin production. We envision that the simplicity, speed, and reliability offered by CRI-SPA will make it a versatile tool to forward systems-level understanding of biological processes.
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- 2023
33. First Results from a Broadband Search for Dark Photon Dark Matter in the $44$ to $52\,\mu$eV range with a coaxial dish antenna
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Knirck, Stefan, Hoshino, Gabe, Awida, Mohamed H., Cancelo, Gustavo I., Di Federico, Martin, Knepper, Benjamin, Lapuente, Alex, Littmann, Mira, Miller, David W., Mitchell, Donald V., Rodriguez, Derrick, Ruschman, Mark K., Sawtell, Matthew A., Stefanazzi, Leandro, Sonnenschein, Andrew, Teafoe, Gary W., Bowring, Daniel, Carosi, G., Chou, Aaron, Chang, Clarence L., Dona, Kristin, Khatiwada, Rakshya, Kurinsky, Noah A., Liu, Jesse, Pena, Cristián, Salemi, Chiara P., Wang, Christina W., Yu, Jialin, Knirck, Stefan, Hoshino, Gabe, Awida, Mohamed H., Cancelo, Gustavo I., Di Federico, Martin, Knepper, Benjamin, Lapuente, Alex, Littmann, Mira, Miller, David W., Mitchell, Donald V., Rodriguez, Derrick, Ruschman, Mark K., Sawtell, Matthew A., Stefanazzi, Leandro, Sonnenschein, Andrew, Teafoe, Gary W., Bowring, Daniel, Carosi, G., Chou, Aaron, Chang, Clarence L., Dona, Kristin, Khatiwada, Rakshya, Kurinsky, Noah A., Liu, Jesse, Pena, Cristián, Salemi, Chiara P., Wang, Christina W., and Yu, Jialin
- Abstract
We present first results from a dark photon dark matter search in the mass range from 44 to 52 $\mu{\rm eV}$ ($10.7 - 12.5\,{\rm GHz}$) using a room-temperature dish antenna setup called GigaBREAD. Dark photon dark matter converts to ordinary photons on a cylindrical metallic emission surface with area $0.5\,{\rm m}^2$ and is focused by a novel parabolic reflector onto a horn antenna. Signals are read out with a low-noise receiver system. A first data taking run with 24 days of data does not show evidence for dark photon dark matter in this mass range, excluding dark photon - photon mixing parameters $\chi \gtrsim 10^{-12}$ in this range at 90% confidence level. This surpasses existing constraints by about two orders of magnitude and is the most stringent bound on dark photons in this range below 49 $\mu$eV., Comment: 6 pages, 4 figures, matches published version
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- 2023
- Full Text
- View/download PDF
34. Axion Dark Matter eXperiment: Run 1A Analysis Details
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Boutan, C., LaRoque, B. H., Lentz, E., Oblath, N. S., Taubman, M. S., Tedeschi, J., Yang, J., Jones, A. M., Braine, T., Crisosto, N., Rosenberg, L. J, Rybka, G., Will, D., Zhang, D., Kimes, S., Ottens, R., Bartram, C., Bowring, D., Cervantes, R., Chou, A. S., Knirck, S., Mitchell, D. V., Sonnenschein, A., Wester, W., Khatiwada, R., Carosi, G., Du, N., Durham, S., O'Kelley, S. R., Woollett, N., Duffy, L. D., Bradley, R., Clarke, J., Siddiqi, I., Agrawal, A., Dixit, A. V., Gleason, J. R., Hipp, A. T., Jois, S., Sikivie, P., Sullivan, N. S., Tanner, D. B., Buckley, J. H., Gaikwad, C., Henriksen, E. A., Hoffman, J., Murch, K. W., Harrington, P. M., Daw, E. J., Perry, M. G., Hilton, G. C., Boutan, C., LaRoque, B. H., Lentz, E., Oblath, N. S., Taubman, M. S., Tedeschi, J., Yang, J., Jones, A. M., Braine, T., Crisosto, N., Rosenberg, L. J, Rybka, G., Will, D., Zhang, D., Kimes, S., Ottens, R., Bartram, C., Bowring, D., Cervantes, R., Chou, A. S., Knirck, S., Mitchell, D. V., Sonnenschein, A., Wester, W., Khatiwada, R., Carosi, G., Du, N., Durham, S., O'Kelley, S. R., Woollett, N., Duffy, L. D., Bradley, R., Clarke, J., Siddiqi, I., Agrawal, A., Dixit, A. V., Gleason, J. R., Hipp, A. T., Jois, S., Sikivie, P., Sullivan, N. S., Tanner, D. B., Buckley, J. H., Gaikwad, C., Henriksen, E. A., Hoffman, J., Murch, K. W., Harrington, P. M., Daw, E. J., Perry, M. G., and Hilton, G. C.
- Abstract
The ADMX collaboration gathered data for its Run 1A axion dark matter search from January to June 2017, scanning with an axion haloscope over the frequency range 645-680 MHz (2.66-2.81 ueV in axion mass) at DFSZ sensitivity. The resulting axion search found no axion-like signals comprising all the dark matter in the form of a virialized galactic halo over the entire frequency range, implying lower bound exclusion limits at or below DFSZ coupling at the 90% confidence level. This paper presents expanded details of the axion search analysis of Run 1A, including review of relevant experimental systems, data-taking operations, preparation and interpretation of raw data, axion search methodology, candidate handling, and final axion limits., Comment: 27 pages, 19 figures, accepted for publication in PRD
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- 2023
35. CRI-SPA: a high-throughput method for systematic genetic editing of yeast libraries
- Author
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Cachera, Paul (author), Olsson, Helén (author), Coumou, Hilde (author), Jensen, Mads L. (author), Sánchez, Benjamín J. (author), Strucko, Tomas (author), van den Broek, M.A. (author), Daran, J.G. (author), Jensen, Michael K. (author), Sonnenschein, Nikolaus (author), Lisby, Michael (author), Mortensen, Uffe H. (author), Cachera, Paul (author), Olsson, Helén (author), Coumou, Hilde (author), Jensen, Mads L. (author), Sánchez, Benjamín J. (author), Strucko, Tomas (author), van den Broek, M.A. (author), Daran, J.G. (author), Jensen, Michael K. (author), Sonnenschein, Nikolaus (author), Lisby, Michael (author), and Mortensen, Uffe H. (author)
- Abstract
Biological functions are orchestrated by intricate networks of interacting genetic elements. Predicting the interaction landscape remains a challenge for systems biology and new research tools allowing simple and rapid mapping of sequence to function are desirable. Here, we describe CRI-SPA, a method allowing the transfer of chromosomal genetic features from a CRI-SPA Donor strain to arrayed strains in large libraries of Saccharomyces cerevisiae. CRI-SPA is based on mating, CRISPR-Cas9-induced gene conversion, and Selective Ploidy Ablation. CRI-SPA can be massively parallelized with automation and can be executed within a week. We demonstrate the power of CRI-SPA by transferring four genes that enable betaxanthin production into each strain of the yeast knockout collection (≈4800 strains). Using this setup, we show that CRI-SPA is highly efficient and reproducible, and even allows marker-free transfer of genetic features. Moreover, we validate a set of CRI-SPA hits by showing that their phenotypes correlate strongly with the phenotypes of the corresponding mutant strains recreated by reverse genetic engineering. Hence, our results provide a genome-wide overview of the genetic requirements for betaxanthin production. We envision that the simplicity, speed, and reliability offered by CRI-SPA will make it a versatile tool to forward systems-level understanding of biological processes., BT/Industriele Microbiologie
- Published
- 2023
- Full Text
- View/download PDF
36. European Medicines Agency Conflicts With the European Food Safety Authority (EFSA) on Bisphenol A Regulation
- Author
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Zoeller, R. Thomas, Birnbaum, Linda S., Collins, Terrence J., Heindel, Jerrold, Hunt, Patricia A., Iguchi, Taisen, Kortenkamp, Andreas, Myers, John Peterson, Vom Saal, Frederick S., Sonnenschein, Carlos, Soto, Ana M., Zoeller, R. Thomas, Birnbaum, Linda S., Collins, Terrence J., Heindel, Jerrold, Hunt, Patricia A., Iguchi, Taisen, Kortenkamp, Andreas, Myers, John Peterson, Vom Saal, Frederick S., Sonnenschein, Carlos, and Soto, Ana M.
- Abstract
The European Food Safety Authority (EFSA) has revised their estimate of the toxicity of bisphenol A (BPA) and, as a result, have recommended reducing the tolerable daily intake (TDI) by 20 000-fold. This would essentially ban the use of BPA in food packaging such as can liners, plastic food containers, and in consumer products. To come to this conclusion, EFSA used a systematic approach according to a pre-established protocol and included all guideline and nonguideline studies in their analysis. They found that Th-17 immune cells increased with very low exposure to BPA and used this endpoint to revise the TDI to be human health protective. A number of regulatory agencies including the European Medicines Agency (EMA) have written formal disagreements with several elements of EFSA's proposal. The European Commission will now decide whether to accept EFSA's recommendation over the objections of EMA. If the Commission accepts EFSA's recommendation, it will be a landmark action using knowledge acquired through independent scientific studies focused on biomarkers of chronic disease to protect human health. The goal of this Perspective is to clearly articulate the monumental nature of this debate and decision and to explain what is at stake. Our perspective is that the weight of evidence clearly supports EFSA's proposal to reduce the TDI by 20 000-fold.
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- 2023
- Full Text
- View/download PDF
37. CRI-SPA:a high-throughput method for systematic genetic editing of yeast libraries
- Author
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Cachera, Paul, Olsson, Helén, Coumou, Hilde, Jensen, Mads L, Sánchez, Benjamín j, Strucko, Tomas, Van den broek, Marcel, Daran, Jean-marc, Jensen, Michael k, Sonnenschein, Nikolaus, Lisby, Michael, Mortensen, Uffe h, Cachera, Paul, Olsson, Helén, Coumou, Hilde, Jensen, Mads L, Sánchez, Benjamín j, Strucko, Tomas, Van den broek, Marcel, Daran, Jean-marc, Jensen, Michael k, Sonnenschein, Nikolaus, Lisby, Michael, and Mortensen, Uffe h
- Abstract
Biological functions are orchestrated by intricate networks of interacting genetic elements. Predicting the interaction landscape remains a challenge for systems biology and new research tools allowing simple and rapid mapping of sequence to function are desirable. Here, we describe CRI-SPA, a method allowing the transfer of chromosomal genetic features from a CRI-SPA Donor strain to arrayed strains in large libraries of Saccharomyces cerevisiae. CRI-SPA is based on mating, CRISPR-Cas9-induced gene conversion, and Selective Ploidy Ablation. CRI-SPA can be massively parallelized with automation and can be executed within a week. We demonstrate the power of CRI-SPA by transferring four genes that enable betaxanthin production into each strain of the yeast knockout collection (≈4800 strains). Using this setup, we show that CRI-SPA is highly efficient and reproducible, and even allows marker-free transfer of genetic features. Moreover, we validate a set of CRI-SPA hits by showing that their phenotypes correlate strongly with the phenotypes of the corresponding mutant strains recreated by reverse genetic engineering. Hence, our results provide a genome-wide overview of the genetic requirements for betaxanthin production. We envision that the simplicity, speed, and reliability offered by CRI-SPA will make it a versatile tool to forward systems-level understanding of biological processes., Biological functions are orchestrated by intricate networks of interacting genetic elements. Predicting the interaction landscape remains a challenge for systems biology and new research tools allowing simple and rapid mapping of sequence to function are desirable. Here, we describe CRI-SPA, a method allowing the transfer of chromosomal genetic features from a CRI-SPA Donor strain to arrayed strains in large libraries of Saccharomyces cerevisiae. CRI-SPA is based on mating, CRISPR-Cas9-induced gene conversion, and Selective Ploidy Ablation. CRI-SPA can be massively parallelized with automation and can be executed within a week. We demonstrate the power of CRI-SPA by transferring four genes that enable betaxanthin production into each strain of the yeast knockout collection (≈4800 strains). Using this setup, we show that CRI-SPA is highly efficient and reproducible, and even allows marker-free transfer of genetic features. Moreover, we validate a set of CRI-SPA hits by showing that their phenotypes correlate strongly with the phenotypes of the corresponding mutant strains recreated by reverse genetic engineering. Hence, our results provide a genome-wide overview of the genetic requirements for betaxanthin production. We envision that the simplicity, speed, and reliability offered by CRI-SPA will make it a versatile tool to forward systems-level understanding of biological processes.
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- 2023
38. Inklusive Medienbildung in beruflichen (Bildungs-)Kontexten: Konzeptionelle Ansätze und Perspektiven für ihre Weiterentwicklung
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Sonnenschein, Nele and Sonnenschein, Nele
- Abstract
Im Diskurs um Inklusive Medienbildung stellen Überlegungen mit Bezug auf berufliche (Bildungs-)Kontexte weitgehend eine Leerstelle dar, obgleich dieses Handlungsfeld angesichts der fortlaufenden Digitalisierung der Arbeitswelt für eine Auseinandersetzung mit Fragen an der Schnittstelle von Inklusion, Teilhabe, digitalen Medien und Medienbildung hochgradig relevant erscheint. So gilt es beispielsweise, Möglichkeiten für die berufliche Teilhabe von Menschen mit Behinderungen unter den spezifischen Bedingungen digital geprägter Arbeitsprozesse und -aufgaben näher zu betrachten. Lediglich aus einigen innovativen Forschungs- und Entwicklungsprojekten, die sich vorwiegend praxisorientiert mit Möglichkeiten zur Förderung beruflicher Inklusion durch digitale Medien auseinandergesetzt haben, liegen erste konzeptionelle Ansätze vor. Diese werden im Beitrag anhand ausgewählter Beispiele aufgearbeitet und aus der Perspektive der Inklusiven Medienbildung diskutiert. Die vorliegenden Ansätze lassen sich mit Blick auf die adressierten Zielgruppen, fachlichen Kontexte sowie die Konzepte zum inklusiven Medieneinsatz insgesamt als sehr spezifisch beschreiben und bedürfen einer theoretischen und konzeptionellen Weiterentwicklung. Als gewinnbringende Perspektive für die Umsetzung einer Inklusiven Medienbildung in beruflichen (Bildungs-)Kontexten stellt sich in diesem Zusammenhang ein pädagogisch begleiteter Einsatz digitaler Medien heraus, der auf Unterstützung im Arbeitsprozess, im beruflichen Wissens- und Kompetenzerwerb wie auch auf Persönlichkeitsbildung abzielt., In the discourse on inclusive media education, considerations related to vocational (educational) contexts are largely a research gap, although this field seems highly relevant for addressing questions at the intersection of inclusion, participation, digital media and media education in the view of the continuous digitalization of the working world. For example, it is necessary to take a closer look at possibilities for the professional participation of people with disabilities under the specific conditions of digitally shaped work processes and tasks. Only a few innovative research and development projects, which have primarily dealt with practice-oriented possibilities for promoting professional inclusion by using digital media, have produced initial conceptual approaches. These are reviewed in this article by using selected examples and discussed from the perspective of inclusive media education. Overall, the existing approaches can be described as very specific with regard to the addressed target groups, professional contexts as well as the concepts for inclusive media use and require further theoretical development. A profitable perspective for the implementation of inclusive media education in vocational (educational) contexts seems to be a pedagogically supported use of digital media, which focuses on support in the working process, the acquisition of professional knowledge and skills as well as on personal development.
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- 2023
39. Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition
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Roager, Line, Sonnenschein, Eva C., Gram, Lone, Roager, Line, Sonnenschein, Eva C., and Gram, Lone
- Abstract
Microalgae are very important as primary producers in the ocean, but also as forthcoming sustainable producers of biotechnologically interesting compounds. Accordingly, the bacterial microbiomes associated with microalgae are attracting increasing attention due to their effects on the growth and health of microalgae. The bacterial communities associated with microalgae are vital for the growth and health of the host, and engineering algal microbiomes can enhance the fitness of the algae. Characterization of these microbiomes mostly relies on sequencing of DNA, which can be extracted with an array of protocols that potentially impact DNA quantity and quality and thus potentially affect subsequent analyses of microbiome composition. Here, we extracted DNA from Isochrysis galbana, Tetraselmis suecica, and Conticribra weissflogii microbiomes using four different protocols. DNA yield and quality was greatly impacted by the choice of extraction protocol, whereas microbiome composition determined by 16S rRNA gene amplicon sequencing was only impacted to a minor degree, with microalgal host species being the main determinant of microbiome composition. The I. galbana microbiome was dominated by the genus Alteromonas, whereas the microbiome associated with T. suecica was dominated by Marinobacteraceae and Rhodobacteraceae family members. While these two families were also prevalent in the microbiome associated with C. weissflogii, Flavobacteriaceae and Cryomorphaceae were also highly dominant. Phenol-chloroform extraction resulted in higher DNA quality and quantity compared to commercial kits; however, because they have other advantages such as high throughput and low toxicity, commercial kits can be employed to great benefit for the characterization of microalgal microbiomes. IMPORTANCE Microalgae are very important as primary producers in the ocean, but also as forthcoming sustainable producers of biotechnologically
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- 2023
40. Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals
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Lennen, Rebecca M., Lim, Hyun Gyu, Jensen, Kristian, Mohammed, Elsayed T., Phaneuf, Patrick V., Noh, Myung Hyun, Malla, Sailesh, Börner, Rosa A., Chekina, Ksenia, Özdemir, Emre, Bonde, Ida, Koza, Anna, Maury, Jérôme, Pedersen, Lasse E., Schöning, Lars Y., Sonnenschein, Nikolaus, Palsson, Bernhard O., Nielsen, Alex T., Sommer, Morten O.A., Herrgård, Markus J., Feist, Adam M., Lennen, Rebecca M., Lim, Hyun Gyu, Jensen, Kristian, Mohammed, Elsayed T., Phaneuf, Patrick V., Noh, Myung Hyun, Malla, Sailesh, Börner, Rosa A., Chekina, Ksenia, Özdemir, Emre, Bonde, Ida, Koza, Anna, Maury, Jérôme, Pedersen, Lasse E., Schöning, Lars Y., Sonnenschein, Nikolaus, Palsson, Bernhard O., Nielsen, Alex T., Sommer, Morten O.A., Herrgård, Markus J., and Feist, Adam M.
- Abstract
Although strain tolerance to high product concentrations is a barrier to the economically viable biomanufacturing of industrial chemicals, chemical tolerance mechanisms are often unknown. To reveal tolerance mechanisms, an automated platform was utilized to evolve Escherichia coli to grow optimally in the presence of 11 industrial chemicals (1,2-propanediol, 2,3-butanediol, glutarate, adipate, putrescine, hexamethylenediamine, butanol, isobutyrate, coumarate, octanoate, hexanoate), reaching tolerance at concentrations 60%–400% higher than initial toxic levels. Sequencing genomes of 223 isolates from 89 populations, reverse engineering, and cross-compound tolerance profiling were employed to uncover tolerance mechanisms. We show that: 1) cells are tolerized via frequent mutation of membrane transporters or cell wall-associated proteins (e.g., ProV, KgtP, SapB, NagA, NagC, MreB), transcription and translation machineries (e.g., RpoA, RpoB, RpoC, RpsA, RpsG, NusA, Rho), stress signaling proteins (e.g., RelA, SspA, SpoT, YobF), and for certain chemicals, regulators and enzymes in metabolism (e.g., MetJ, NadR, GudD, PurT); 2) osmotic stress plays a significant role in tolerance when chemical concentrations exceed a general threshold and mutated genes frequently overlap with those enabling chemical tolerance in membrane transporters and cell wall-associated proteins; 3) tolerization to a specific chemical generally improves tolerance to structurally similar compounds whereas a tradeoff can occur on dissimilar chemicals, and 4) using pre-tolerized starting isolates can hugely enhance the subsequent production of chemicals when a production pathway is inserted in many, but not all, evolved tolerized host strains, underpinning the need for evolving multiple parallel populations. Taken as a whole, this study provides a comprehensive genotype-phenotype map based on identified mutations and growth phenotypes for 223 chemical tolerant isolates.
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- 2023
41. Search for a dark-matter induced Cosmic Axion Background with ADMX
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ADMX Collaboration, Nitta, T., Braine, T., Du, N., Guzzetti, M., Hanretty, C., Leum, G., Rosenberg, L. J, Rybka, G., Sinnis, J., Clarke, John, Siddiqi, I., Awida, M. H., Chou, A. S., Hollister, M., Knirck, S., Sonnenschein, A., Wester, W., Gleason, J. R., Hipp, A. T., Sikivie, P., Sullivan, N. S., Tanner, D. B., Khatiwada, R., Carosi, G., Robertson, N., Duffy, L. D., Boutan, C., Lentz, E., Oblath, N. S., Taubman, M. S., Yang, J., Daw, E. J., Perry, M. G., Bartram, C., Buckley, J. H., Gaikwad, C., Hoffman, J., Murch, K. W., Goryachev, M., Hartman, E., McAllister, B. T., Quiskamp, A., Thomson, C., Tobar, M. E., Dror, J. A., Murayama, H., Rodd, N. L., ADMX Collaboration, Nitta, T., Braine, T., Du, N., Guzzetti, M., Hanretty, C., Leum, G., Rosenberg, L. J, Rybka, G., Sinnis, J., Clarke, John, Siddiqi, I., Awida, M. H., Chou, A. S., Hollister, M., Knirck, S., Sonnenschein, A., Wester, W., Gleason, J. R., Hipp, A. T., Sikivie, P., Sullivan, N. S., Tanner, D. B., Khatiwada, R., Carosi, G., Robertson, N., Duffy, L. D., Boutan, C., Lentz, E., Oblath, N. S., Taubman, M. S., Yang, J., Daw, E. J., Perry, M. G., Bartram, C., Buckley, J. H., Gaikwad, C., Hoffman, J., Murch, K. W., Goryachev, M., Hartman, E., McAllister, B. T., Quiskamp, A., Thomson, C., Tobar, M. E., Dror, J. A., Murayama, H., and Rodd, N. L.
- Abstract
We report the first result of a direct search for a Cosmic ${\it axion}$ Background (C$a$B) - a relativistic background of axions that is not dark matter - performed with the axion haloscope, the Axion Dark Matter eXperiment (ADMX). Conventional haloscope analyses search for a signal with a narrow bandwidth, as predicted for dark matter, whereas the C$a$B will be broad. We introduce a novel analysis strategy, which searches for a C$a$B induced daily modulation in the power measured by the haloscope. Using this, we repurpose data collected to search for dark matter to set a limit on the axion photon coupling of a C$a$B originating from dark matter cascade decay via a mediator in the 800-995 MHz frequency range. We find that the present sensitivity is limited by fluctuations in the cavity readout as the instrument scans across dark matter masses. Nevertheless, we suggest that these challenges can be surmounted using superconducting qubits as single photon counters, and allow ADMX to operate as a telescope searching for axions emerging from the decay of dark matter. The daily modulation analysis technique we introduce can be deployed for various broadband RF signals, such as other forms of a C$a$B or even high-frequency gravitational waves., Comment: 9 pages, 4 figures
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- 2023
- Full Text
- View/download PDF
42. Van arcadia tot activisme? Een ecokritische lezing van de verbeelding van plaats, identiteit en landschap in de Friestalige poëzie van Obe Postma
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Schuurmans, Rymke, Sonnenschein, Johan (Thesis Advisor), Schuurmans, Rymke, and Sonnenschein, Johan (Thesis Advisor)
- Abstract
Sinds enkele jaren spreken Friezen van ‘lânskipspine’ bij het aanzien van hun landschap dat door de intensieve veeteelt steeds meer is veranderd in een monocultuur. Het gaat niet alleen om een ecologische pijn, maar ook om een cultuurhistorische: het landschap wordt gezien als een onderdeel van de Friese identiteit. In deze scriptie wordt dit verband tussen ecologisch en cultuurhistorisch bewustzijn vanuit een ecokritisch perspectief onderzocht in de poëzie van Frieslands meest canonieke dichter: Obe Postma (1868-1963). Postma dichtte zijn hele leven over het Friese landschap en zijn poëzie beschouw ik daarom als een ‘poëzie van plaats’. Aan de hand van dit idee van plaats breng ik in deze scriptie inzichten uit de ecokritiek samen met onderzoek naar Friese cultuur. Plaatsverbondenheid werd in de vroege ecokritiek sterk gewaardeerd, omdat de lokale betrokkenheid en kennis van een plaats tot een ecologisch bewustzijn zou leiden en een verlangen om de natuurlijke omgeving te beschermen. De verbeelding van plaats gaat vaak gepaard met de pastorale, waarbij het platteland wordt voorgesteld als een ‘natuurlijk’ toevluchtsoord weg van industrialisering en verstedelijking. De pastorale speelt ook een belangrijke rol in de negentiende-eeuwse constructie van Friese cultuur als een authentieke en oeroude plattelandscultuur tegenover het verstedelijkte Holland. De verbeelding van ‘plaats’ en de ‘pastorale’ is later binnen de ecokritiek bekritiseerd omdat ze ecologisch bewustzijn en milieubewust handelen juist ook kunnen tegenwerken. Zo houden ze een statische en gesimplificeerde versie van de natuur in stand, verbloemen ze misstanden op het platteland en dragen ze bij aan nationalistische sentimenten. In de analyse onderzoek ik in hoeverre Postma’s poëzie een ecokritisch potentieel laat zien dan wel meer beantwoordt aan conservatieve uitwerkingen. Ik concludeer dat Postma’s poëzie als een vorm van protoecologische poëzie beschouwd kan worden. Postma’s poëzie verwoordt een ecoc
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- 2023
43. Third International Consensus Conference on lesions of uncertain malignant potential in the breast (B3 lesions)
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Pathologie, Cancer, Elfgen, Constanze, Leo, Cornelia, Kubik-Huch, Rahel A., Muenst, Simone, Schmidt, Noemi, Quinn, Cecily, McNally, Sorcha, van Diest, Paul J., Mann, Ritse M., Bago-Horvath, Zsuzsanna, Bernathova, Maria, Regitnig, Peter, Fuchsjäger, Michael, Schwegler-Guggemos, Daniela, Maranta, Martina, Zehbe, Sabine, Tausch, Christoph, Güth, Uwe, Fallenberg, Eva Maria, Schrading, Simone, Kothari, Ashutosh, Sonnenschein, Martin, Kampmann, Gert, Kulka, Janina, Tille, Jean Christophe, Körner, Meike, Decker, Thomas, Lax, Sigurd F., Daniaux, Martin, Bjelic-Radisic, Vesna, Kacerovsky-Strobl, Stephanie, Condorelli, Rosaria, Gnant, Michael, Varga, Zsuzsanna, Pathologie, Cancer, Elfgen, Constanze, Leo, Cornelia, Kubik-Huch, Rahel A., Muenst, Simone, Schmidt, Noemi, Quinn, Cecily, McNally, Sorcha, van Diest, Paul J., Mann, Ritse M., Bago-Horvath, Zsuzsanna, Bernathova, Maria, Regitnig, Peter, Fuchsjäger, Michael, Schwegler-Guggemos, Daniela, Maranta, Martina, Zehbe, Sabine, Tausch, Christoph, Güth, Uwe, Fallenberg, Eva Maria, Schrading, Simone, Kothari, Ashutosh, Sonnenschein, Martin, Kampmann, Gert, Kulka, Janina, Tille, Jean Christophe, Körner, Meike, Decker, Thomas, Lax, Sigurd F., Daniaux, Martin, Bjelic-Radisic, Vesna, Kacerovsky-Strobl, Stephanie, Condorelli, Rosaria, Gnant, Michael, and Varga, Zsuzsanna
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- 2023
44. Third International Consensus Conference on lesions of uncertain malignant potential in the breast (B3 lesions)
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Elfgen, Constanze; https://orcid.org/0000-0001-6092-6612, Leo, Cornelia; https://orcid.org/0000-0003-1601-0281, Kubik-Huch, Rahel A; https://orcid.org/0000-0002-3636-8697, Muenst, Simone, Schmidt, Noemi, Quinn, Cecily, McNally, Sorcha, van Diest, Paul J, Mann, Ritse M, Bago-Horvath, Zsuzsanna; https://orcid.org/0000-0002-8555-7806, Bernathova, Maria, Regitnig, Peter, Fuchsjäger, Michael, Schwegler-Guggemos, Daniela, Maranta, Martina, Zehbe, Sabine, Tausch, Christoph, Güth, Uwe; https://orcid.org/0000-0002-1849-5131, Fallenberg, Eva Maria, Schrading, Simone, Kothari, Ashutosh, Sonnenschein, Martin, Kampmann, Gert, Kulka, Janina, Tille, Jean-Christoph, Körner, Meike, Decker, Thomas, Lax, Sigurd F, Daniaux, Martin, Varga, Zsuzsanna; https://orcid.org/0000-0002-2855-983X, et al, Elfgen, Constanze; https://orcid.org/0000-0001-6092-6612, Leo, Cornelia; https://orcid.org/0000-0003-1601-0281, Kubik-Huch, Rahel A; https://orcid.org/0000-0002-3636-8697, Muenst, Simone, Schmidt, Noemi, Quinn, Cecily, McNally, Sorcha, van Diest, Paul J, Mann, Ritse M, Bago-Horvath, Zsuzsanna; https://orcid.org/0000-0002-8555-7806, Bernathova, Maria, Regitnig, Peter, Fuchsjäger, Michael, Schwegler-Guggemos, Daniela, Maranta, Martina, Zehbe, Sabine, Tausch, Christoph, Güth, Uwe; https://orcid.org/0000-0002-1849-5131, Fallenberg, Eva Maria, Schrading, Simone, Kothari, Ashutosh, Sonnenschein, Martin, Kampmann, Gert, Kulka, Janina, Tille, Jean-Christoph, Körner, Meike, Decker, Thomas, Lax, Sigurd F, Daniaux, Martin, Varga, Zsuzsanna; https://orcid.org/0000-0002-2855-983X, and et al
- Abstract
The heterogeneous group of B3 lesions in the breast harbors lesions with different malignant potential and progression risk. As several studies about B3 lesions have been published since the last Consensus in 2018, the 3rd International Consensus Conference discussed the six most relevant B3 lesions (atypical ductal hyperplasia (ADH), flat epithelial atypia (FEA), classical lobular neoplasia (LN), radial scar (RS), papillary lesions (PL) without atypia, and phyllodes tumors (PT)) and made recommendations for diagnostic and therapeutic approaches. Following a presentation of current data of each B3 lesion, the international and interdisciplinary panel of 33 specialists and key opinion leaders voted on the recommendations for further management after core-needle biopsy (CNB) and vacuum-assisted biopsy (VAB). In case of B3 lesion diagnosis on CNB, OE was recommended in ADH and PT, whereas in the other B3 lesions, vacuum-assisted excision was considered an equivalent alternative to OE. In ADH, most panelists (76%) recommended an open excision (OE) after diagnosis on VAB, whereas observation after a complete VAB-removal on imaging was accepted by 34%. In LN, the majority of the panel (90%) preferred observation following complete VAB-removal. Results were similar in RS (82%), PL (100%), and FEA (100%). In benign PT, a slim majority (55%) also recommended an observation after a complete VAB-removal. VAB with subsequent active surveillance can replace an open surgical intervention for most B3 lesions (RS, FEA, PL, PT, and LN). Compared to previous recommendations, there is an increasing trend to a de-escalating strategy in classical LN. Due to the higher risk of upgrade into malignancy, OE remains the preferred approach after the diagnosis of ADH.
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- 2023
45. Non-Virialized Axion Search Sensitive to Doppler Effects in the Milky Way Halo
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Bartram, C., Braine, T., Cervantes, R., Crisosto, N., Du, N., Goodman, C., Guzzetti, M., Hanretty, C., Lee, S., Leum, G., Rosenberg, L. J., Rybka, G., Sinnis, J., Zhang, D., Awida, M. H., Bowring, D., Chou, A. S., Hollister, M., Knirck, S., Sonnenschein, A., Wester, W., Khatiwada, R., Brodsky, J., Carosi, G., Duffy, L. D., Goryachev, M., McAllister, B., Quiskamp, A., Thomson, C., Tobar, M. E., Boutan, C., Jones, M., LaRoque, B. H., Lentz, E., Man, N. E., Oblath, N. S., Taubman, M. S., Yang, J., Clarke, John, Siddiqi, I., Agrawal, A., Dixit, A. V., Gleason, J. R., Han, Y., Hipp, A. T., Jois, S., Sikivie, P., Sullivan, N. S., Tanner, D. B., Daw, E. J., Perry, M. G., Buckley, J. H., Gaikwad, C., Hoffman, J., Murch, K. W., Russell, J., Bartram, C., Braine, T., Cervantes, R., Crisosto, N., Du, N., Goodman, C., Guzzetti, M., Hanretty, C., Lee, S., Leum, G., Rosenberg, L. J., Rybka, G., Sinnis, J., Zhang, D., Awida, M. H., Bowring, D., Chou, A. S., Hollister, M., Knirck, S., Sonnenschein, A., Wester, W., Khatiwada, R., Brodsky, J., Carosi, G., Duffy, L. D., Goryachev, M., McAllister, B., Quiskamp, A., Thomson, C., Tobar, M. E., Boutan, C., Jones, M., LaRoque, B. H., Lentz, E., Man, N. E., Oblath, N. S., Taubman, M. S., Yang, J., Clarke, John, Siddiqi, I., Agrawal, A., Dixit, A. V., Gleason, J. R., Han, Y., Hipp, A. T., Jois, S., Sikivie, P., Sullivan, N. S., Tanner, D. B., Daw, E. J., Perry, M. G., Buckley, J. H., Gaikwad, C., Hoffman, J., Murch, K. W., and Russell, J.
- Abstract
The Axion Dark Matter eXperiment (ADMX) has previously excluded Dine-Fischler-Srednicki-Zhitnisky (DFSZ) axions between 680-790 MHz under the assumption that the dark matter is described by the isothermal halo model. However, the precise nature of the velocity distribution of dark matter is still unknown, and alternative models have been proposed. We report the results of a non-virialized axion search over the mass range 2.81-3.31 {\mu}eV, corresponding to the frequency range 680-800 MHz. This analysis marks the most sensitive search for non-virialized axions sensitive to Doppler effects in the Milky Way Halo to date. Accounting for frequency shifts due to the detector's motion through the Galaxy, we exclude cold flow relic axions with a velocity dispersion of order 10^-7 c with 95% confidence.
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- 2023
46. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
- Author
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Lieven, Christian [0000-0001-5377-4091], Beber, Moritz E. [0000-0003-2406-1978], Olivier, Brett G. [0000-0002-5293-5321], Ataman, Meric [0000-0002-7942-9226], Babaei, Parizad [0000-0001-9411-0427], Bartell, Jennifer A. [0000-0003-2750-9678], Blank, Lars M. [0000-0003-0961-4976], Chauhan, Siddharth [0000-0001-6674-895X], Correia, Kevin [0000-0001-7130-1765], Diener, Christian [0000-0002-7476-0868], Dräger, Andreas [0000-0002-1240-5553], Ebert, Birgitta E. [0000-0001-9425-7509], Edirisinghe, Janaka N. [0000-0003-2493-234X], Faria, José P. [0000-0001-9302-7250], Feist, Adam M. [0000-0002-8630-4800], Fengos, Georgios [0000-0001-8110-8424], Fleming, Ronan M. T. [0000-0001-5346-9812], García-Jiménez, Beatriz [0000-0002-8129-6506], Hatzimanikatis, Vassily [0000-0001-6432-4694], Van Helvoirt, Wout [0000-0002-9143-9726], Henry, Christopher S. [0000-0001-8058-9123], Hermjakob, Henning [0000-0001-8479-0262], Herrgård, Markus J. [0000-0003-2377-9929], Kaafarani, Ali [0000-0002-2805-310X], Kim, Hyun Uk [0000-0001-7224-642X], King, Zachary [0000-0003-1238-1499], Klamt, Steffen [0000-0003-2563-7561], Klipp, Edda [0000-0002-0567-7075], Koehorst, Jasper J. [0000-0001-8172-8981], König, Matthias [0000-0003-1725-179X], Lakshmanan, Meiyappan [0000-0003-2356-3458], Lee, Dong-Yup [0000-0003-0901-708X], Lee, Sang Yup [0000-0003-0599-3091], Lee, Sunjae [0000-0002-6428-5936], Lewis, Nathan E. [0000-0001-7700-3654], Liu, Filipe [0000-0001-8701-2984], Ma, Hongwu [0000-0001-5325-2314], Mahadevan, Radhakrishnan [0000-0002-1270-9063], Maia, Paulo [0000-0002-0848-8683], Mardinoglu, Adil [0000-0002-4254-6090], Medlock, Gregory L. [0000-0002-1571-0801], Monk, Jonathan M. [0000-0002-3895-8949], Nielsen, Jens [0000-0002-9955-6003], Nielsen, Lars K. [0000-0001-8191-3511], Nogales, Juan [0000-0002-4961-0833], Palsson, Bernhard Ø [0000-0003-2357-6785], Papin, Jason A. [0000-0002-2769-5805], Patil, Kiran R. [0000-0002-6166-8640], Poolman, Mark [0000-0002-3972-5418], Price, Nathan D. [0000-0002-4157-0267], Resendis-Antonio, Osbaldo [0000-0001-5220-541X], Richelle, Anne [0000-0003-1491-114X], Rocha, Isabel [0000-0001-9494-3410], Sánchez, Benjamín J. [0000-0001-6093-4110], Schaap, Peter J. [0000-0002-4346-6084], Sheriff, Rahuman S Malik [0000-0003-0705-9809], Shoaie, Saeed [0000-0001-5834-4533], Sonnenschein, Nikolaus [0000-0002-7581-4936], Teusink, Bas [0000-0003-3929-0423], Vilaça, Paulo [0000-0002-1098-5849], Vik, Jon Olav [0000-0002-7778-4515], Wodke, Judith A. H. [0009-0009-9712-060X], Xavier, Joana C. [0000-0001-9242-8968], Zakhartsev, Maksim [0000-0002-7973-9902], Zhang, Cheng [0000-0002-3721-8586], Lieven, Christian, Beber, Moritz E., Olivier, Brett G., Bergmann, Frank T., Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A., Blank, Lars M., Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E., Edirisinghe, Janaka N., Faria, José P., Feist, Adam M., Fengos, Georgios, Fleming, Ronan M. T., García-Jiménez, Beatriz, Hatzimanikatis, Vassily, Van Helvoirt, Wout, Henry, Christopher S., Hermjakob, Henning, Herrgård, Markus J., Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda, Koehorst, Jasper J., König, Matthias, Lakshmanan, Meiyappan, Lee, Dong-Yup, Lee, Sang Yup, Lee, Sunjae, Lewis, Nathan E., Liu, Filipe, Ma, Hongwu, Machado, Daniel, Mahadevan, Radhakrishnan, Maia, Paulo, Mardinoglu, Adil, Medlock, Gregory L., Monk, Jonathan M., Nielsen, Jens, Nielsen, Lars K., Nogales, Juan, Nookaew, Intawat, Palsson, Bernhard Ø, Papin, Jason A., Patil, Kiran R., Poolman, Mark, Price, Nathan D., Resendis-Antonio, Osbaldo, Richelle, Anne, Rocha, Isabel, Sánchez, Benjamín J., Schaap, Peter J., Sheriff, Rahuman S Malik, Shoaie, Saeed, Sonnenschein, Nikolaus, Teusink, Bas, Vilaça, Paulo, Vik, Jon Olav, Wodke, Judith A. H., Xavier, Joana C., Yuan, Qianqian, Zakhartsev, Maksim, Zhang, Cheng, Lieven, Christian [0000-0001-5377-4091], Beber, Moritz E. [0000-0003-2406-1978], Olivier, Brett G. [0000-0002-5293-5321], Ataman, Meric [0000-0002-7942-9226], Babaei, Parizad [0000-0001-9411-0427], Bartell, Jennifer A. [0000-0003-2750-9678], Blank, Lars M. [0000-0003-0961-4976], Chauhan, Siddharth [0000-0001-6674-895X], Correia, Kevin [0000-0001-7130-1765], Diener, Christian [0000-0002-7476-0868], Dräger, Andreas [0000-0002-1240-5553], Ebert, Birgitta E. [0000-0001-9425-7509], Edirisinghe, Janaka N. [0000-0003-2493-234X], Faria, José P. [0000-0001-9302-7250], Feist, Adam M. [0000-0002-8630-4800], Fengos, Georgios [0000-0001-8110-8424], Fleming, Ronan M. T. [0000-0001-5346-9812], García-Jiménez, Beatriz [0000-0002-8129-6506], Hatzimanikatis, Vassily [0000-0001-6432-4694], Van Helvoirt, Wout [0000-0002-9143-9726], Henry, Christopher S. [0000-0001-8058-9123], Hermjakob, Henning [0000-0001-8479-0262], Herrgård, Markus J. [0000-0003-2377-9929], Kaafarani, Ali [0000-0002-2805-310X], Kim, Hyun Uk [0000-0001-7224-642X], King, Zachary [0000-0003-1238-1499], Klamt, Steffen [0000-0003-2563-7561], Klipp, Edda [0000-0002-0567-7075], Koehorst, Jasper J. [0000-0001-8172-8981], König, Matthias [0000-0003-1725-179X], Lakshmanan, Meiyappan [0000-0003-2356-3458], Lee, Dong-Yup [0000-0003-0901-708X], Lee, Sang Yup [0000-0003-0599-3091], Lee, Sunjae [0000-0002-6428-5936], Lewis, Nathan E. [0000-0001-7700-3654], Liu, Filipe [0000-0001-8701-2984], Ma, Hongwu [0000-0001-5325-2314], Mahadevan, Radhakrishnan [0000-0002-1270-9063], Maia, Paulo [0000-0002-0848-8683], Mardinoglu, Adil [0000-0002-4254-6090], Medlock, Gregory L. [0000-0002-1571-0801], Monk, Jonathan M. [0000-0002-3895-8949], Nielsen, Jens [0000-0002-9955-6003], Nielsen, Lars K. [0000-0001-8191-3511], Nogales, Juan [0000-0002-4961-0833], Palsson, Bernhard Ø [0000-0003-2357-6785], Papin, Jason A. [0000-0002-2769-5805], Patil, Kiran R. [0000-0002-6166-8640], Poolman, Mark [0000-0002-3972-5418], Price, Nathan D. [0000-0002-4157-0267], Resendis-Antonio, Osbaldo [0000-0001-5220-541X], Richelle, Anne [0000-0003-1491-114X], Rocha, Isabel [0000-0001-9494-3410], Sánchez, Benjamín J. [0000-0001-6093-4110], Schaap, Peter J. [0000-0002-4346-6084], Sheriff, Rahuman S Malik [0000-0003-0705-9809], Shoaie, Saeed [0000-0001-5834-4533], Sonnenschein, Nikolaus [0000-0002-7581-4936], Teusink, Bas [0000-0003-3929-0423], Vilaça, Paulo [0000-0002-1098-5849], Vik, Jon Olav [0000-0002-7778-4515], Wodke, Judith A. H. [0009-0009-9712-060X], Xavier, Joana C. [0000-0001-9242-8968], Zakhartsev, Maksim [0000-0002-7973-9902], Zhang, Cheng [0000-0002-3721-8586], Lieven, Christian, Beber, Moritz E., Olivier, Brett G., Bergmann, Frank T., Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A., Blank, Lars M., Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E., Edirisinghe, Janaka N., Faria, José P., Feist, Adam M., Fengos, Georgios, Fleming, Ronan M. T., García-Jiménez, Beatriz, Hatzimanikatis, Vassily, Van Helvoirt, Wout, Henry, Christopher S., Hermjakob, Henning, Herrgård, Markus J., Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda, Koehorst, Jasper J., König, Matthias, Lakshmanan, Meiyappan, Lee, Dong-Yup, Lee, Sang Yup, Lee, Sunjae, Lewis, Nathan E., Liu, Filipe, Ma, Hongwu, Machado, Daniel, Mahadevan, Radhakrishnan, Maia, Paulo, Mardinoglu, Adil, Medlock, Gregory L., Monk, Jonathan M., Nielsen, Jens, Nielsen, Lars K., Nogales, Juan, Nookaew, Intawat, Palsson, Bernhard Ø, Papin, Jason A., Patil, Kiran R., Poolman, Mark, Price, Nathan D., Resendis-Antonio, Osbaldo, Richelle, Anne, Rocha, Isabel, Sánchez, Benjamín J., Schaap, Peter J., Sheriff, Rahuman S Malik, Shoaie, Saeed, Sonnenschein, Nikolaus, Teusink, Bas, Vilaça, Paulo, Vik, Jon Olav, Wodke, Judith A. H., Xavier, Joana C., Yuan, Qianqian, Zakhartsev, Maksim, and Zhang, Cheng
- Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper. MEMOTE for standardized genome-scale metabolic model testing (http://hdl.handle.net/10261/230245) Nature Biotechnology, Volume 38, Issue 3, Pages 272 - 276, 1 March 2020
- Published
- 2020
47. A Note on Shape Invariant Potentials for Discretized Hamiltonians
- Author
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Sonnenschein, Jonas, Tsulaia, Mirian, Sonnenschein, Jonas, and Tsulaia, Mirian
- Abstract
Using the method of the "exact discretization" of the Schr\"odinger equation, we propose a particular discretized version of the N=2 Supersymmetric Quantum Mechanics. After defining the corresponding shape invariance condition, we show that the energy spectra and wavefunctions for discretized Quantum Mechanical systems can be found using the technique of N=2 Supersymmetric Quantum Mechanics exactly the same way as it is done for their continuous counterparts. As a demonstration of the present method, we find the energy spectrum for a discretized Coulomb potential and its ground state wave function., Comment: 10 pages, LaTeX, References added
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- 2022
- Full Text
- View/download PDF
48. Agent-based Modeling of Urban Exposome Interventions: Prospects, Model Architectures and Methodological Challenges
- Author
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Sonnenschein, Tabea, Scheider, Simon, de Wit, G Ardine, Tonne, Cathryn, Vermeulen, Roel, Sonnenschein, Tabea, Scheider, Simon, de Wit, G Ardine, Tonne, Cathryn, and Vermeulen, Roel
- Abstract
With ever more people living in cities worldwide, it becomes increasingly important to understand and improve the impact of the urban habitat on livability, health behaviors and health outcomes. However, implementing interventions that tackle the exposome in complex urban systems can be costly and have long-term, sometimes unforeseen, impacts. Hence, it is crucial to assess the health impact, cost-effectiveness, and social distributional impacts of possible urban exposome interventions before implementing them. Spatial agent-based modeling can capture complex behavior-environment interactions, exposure dynamics, and social outcomes in a spatial context. This paper discusses model architectures and methodological challenges for successfully modeling urban exposome interventions using spatial agent-based modeling. We review the potential and limitations of the method; model components required to capture active and passive exposure and intervention effects; human-environment interactions and their integration into the macro-level health impact assessment and social costs benefit analysis; strategies for model calibration. Major challenges for a successful application of agent-based modeling to urban exposome intervention assessment are (1) the design of realistic behavioral models that can capture different types of exposure and that respond to urban interventions, (2) the mismatch between the possible granularity of exposure estimates and the evidence for corresponding exposure-response functions, (3) the scalability issues that emerge when aiming to estimate long-term effects such as health and social impacts based on high-resolution models of human-environment interactions, (4) as well as the data- and computational complexity of calibrating the resulting agent-based model. Although challenges exist, strategies are proposed to improve the implementation of ABM in exposome research.
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- 2022
49. Environmental risk factors of type 2 diabetes-an exposome approach
- Author
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Beulens, Joline W J, Pinho, Maria G M, Abreu, Taymara C, den Braver, Nicole R, Lam, Thao M, Huss, Anke, Vlaanderen, Jelle, Sonnenschein, Tabea, Siddiqui, Noreen Z, Yuan, Zhendong, Kerckhoffs, Jules, Zhernakova, Alexandra, Brandao Gois, Milla F, Vermeulen, Roel C H, Beulens, Joline W J, Pinho, Maria G M, Abreu, Taymara C, den Braver, Nicole R, Lam, Thao M, Huss, Anke, Vlaanderen, Jelle, Sonnenschein, Tabea, Siddiqui, Noreen Z, Yuan, Zhendong, Kerckhoffs, Jules, Zhernakova, Alexandra, Brandao Gois, Milla F, and Vermeulen, Roel C H
- Abstract
Type 2 diabetes is one of the major chronic diseases accounting for a substantial proportion of disease burden in Western countries. The majority of the burden of type 2 diabetes is attributed to environmental risks and modifiable risk factors such as lifestyle. The environment we live in, and changes to it, can thus contribute substantially to the prevention of type 2 diabetes at a population level. The ‘exposome’ represents the (measurable) totality of environmental, i.e. nongenetic, drivers of health and disease. The external exposome comprises aspects of the built environment, the social environment, the physico-chemical environment and the lifestyle/food environment. The internal exposome comprises measurements at the epigenetic, transcript, proteome, microbiome or metabolome level to study either the exposures directly, the imprints these exposures leave in the biological system, the potential of the body to combat environmental insults and/or the biology itself. In this review, we describe the evidence for environmental risk factors of type 2 diabetes, focusing on both the general external exposome and imprints of this on the internal exposome. Studies provided established associations of air pollution, residential noise and area-level socioeconomic deprivation with an increased risk of type 2 diabetes, while neighbourhood walkability and green space are consistently associated with a reduced risk of type 2 diabetes. There is little or inconsistent evidence on the contribution of the food environment, other aspects of the social environment and outdoor temperature. These environmental factors are thought to affect type 2 diabetes risk mainly through mechanisms incorporating lifestyle factors such as physical activity or diet, the microbiome, inflammation or chronic stress. To further assess causality of these associations, future studies should focus on investigating the longitudinal effects of our environment (and changes to it) in relation to type 2 diab
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- 2022
50. The Rebirth of Urban Subcenters: How Subway Expansion Impacts the Spatial Structure and Mix of Amenities in European Cities
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Sonnenschein, Tabea, Scheider, Simon, Zheng, Siqi, Sonnenschein, Tabea, Scheider, Simon, and Zheng, Siqi
- Abstract
Why do some neighborhoods thrive, and others do not? While the importance of the local amenity mix has been established as a key determinant of local livability, its link to urban transport infrastructure remains understudied, partially due to a lack of data. Using spatiotemporal social media data from Foursquare, we analyze the impact of metro stations which opened between 2014 and 2017 on the amenity mix of surrounding neighborhoods in nine European cities: Rome, Milan, Barcelona, Budapest, Warsaw, Sofia, Vienna, Helsinki, and Stuttgart. Thereby, we study three properties of the local amenity mix: its density, multifunctionality, and the heterogeneity between amenity types. For this purpose, we propose a new measurement of multifunctionality, which calculates the entropy of the locally present amenity set incorporating the degree of similarity between amenity types. For causal inference, we use Difference-in-Difference Regression based on Propensity Score Matching and Entropy Balancing. Our findings show that in most cities, subway expansion had a significant positive impact on the local amenity density and multifunctionality and that especially the social amenities—Arts & Entertainment, Restaurants and Nightlife—responded strongly. Moreover, considerable agglomeration forces seem to prevail, causing existing subcenters to benefit most from new metro stations.
- Published
- 2022
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