814 results on '"Goff, A."'
Search Results
2. Anticipating in vitro gametogenesis: Hopes and concerns for IVG among diverse stakeholders
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Le Goff, Anne, Hein, Robbin Jeffries, Hart, Ariel N, Roberson, Isaias, and Landecker, Hannah L
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Biochemistry and Cell Biology ,Biological Sciences ,Contraception/Reproduction ,Infertility ,Reproductive health and childbirth ,Humans ,Gametogenesis ,Female ,Male ,Adult ,Stakeholder Participation ,Reproductive Techniques ,Assisted ,Germ Cells ,LGBTQ+ ,assisted reproduction ,focus groups ,gametes ,in vitro gametogenesis ,infertility ,qualitative research ,regenerative medicine ,reproductive justice ,stem cells ,Clinical Sciences ,Biochemistry and cell biology - Abstract
In vitro gametogenesis (IVG), the reconstitution of germ cell development in vitro, is an emerging stem cell-based technology with profound implications for reproductive science. Despite researchers' long-term goals for future clinical applications, little is currently known about the views of IVG held by the stakeholders potentially most affected by its introduction in humans. We conducted focus groups and interviews with 80 individuals with lived experience of infertility and/or LGBTQ+ family formation in the US, two intersecting groups of potential IVG users. Respondents expressed hope that IVG would lead to higher reproductive success than current assisted reproductive technology (ART), alleviate suffering associated with ART use, and promote greater social inclusion, while expressing concerns predominantly framed in terms of equity and safety. These findings underscore the importance of sustained engagement with stakeholders with relevant experience to anticipate the implications of IVG for research and clinical translation.
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- 2024
3. Clinical validation of C12FDG as a marker associated with senescence and osteoarthritic phenotypes
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Hambright, William S, Duke, Victoria R, Goff, Adam D, Goff, Alex W, Minas, Lucas T, Kloser, Heidi, Gao, Xueqin, Huard, Charles, Guo, Ping, Lu, Aiping, Mitchell, John, Mullen, Michael, Su, Charles, Tchkonia, Tamara, Netto, Jair M Espindola, Robbins, Paul D, Niedernhofer, Laura J, Kirkland, James L, Bahney, Chelsea S, Philippon, Marc, and Huard, Johnny
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Biomedical and Clinical Sciences ,Clinical Sciences ,Arthritis ,Clinical Research ,Aging ,Prevention ,Detection ,screening and diagnosis ,4.1 Discovery and preclinical testing of markers and technologies ,Inflammatory and immune system ,Musculoskeletal ,Good Health and Well Being ,aging ,cell senescence ,osteoarthritis ,senolytics ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences - Abstract
Chronic conditions associated with aging have proven difficult to prevent or treat. Senescence is a cell fate defined by loss of proliferative capacity and the development of a pro-inflammatory senescence-associated secretory phenotype comprised of cytokines/chemokines, proteases, and other factors that promotes age-related diseases. Specifically, an increase in senescent peripheral blood mononuclear cells (PBMCs), including T cells, is associated with conditions like frailty, rheumatoid arthritis, and bone loss. However, it is unknown if the percentage of senescent PBMCs associated with age-associated orthopedic decline could be used for potential diagnostic or prognostic use in orthopedics. Here, we report senescent cell detection using the fluorescent compound C12FDG to quantify PBMCs senescence across a large cohort of healthy and osteoarthritic patients. There is an increase in the percent of circulating C12FDG+ PBMCs that is commensurate with increases in age and senescence-related serum biomarkers. Interestingly, C12FDG+ PBMCs and T cells also were found to be elevated in patients with mild to moderate osteoarthritis, a progressive joint disease that is strongly associated with inflammation. The percent of C12FDG+ PBMCs and age-related serum biomarkers were decreased in a small subgroup of study participants taking the senolytic drug fisetin. These results demonstrate quantifiable measurements in a large group of participants that could create a composite score of healthy aging sensitive enough to detect changes following senolytic therapy and may predict age-related orthopedic decline. Detection of peripheral senescence in PBMCs and subsets using C12FDG may be clinically useful for quantifying cellular senescence and determining how and if it plays a pathological role in osteoarthritic progression.
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- 2024
4. Using graph neural networks to reconstruct charged pion showers in the CMS High Granularity Calorimeter
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Aamir, M., Acar, B., Adamov, G., Adams, T., Adloff, C., Afanasiev, S., Agrawal, C., Ahmad, A., Ahmed, H. A., Akbar, S., Akchurin, N., Akgul, B., Akgun, B., Akpinar, R. O., Aktas, E., AlKadhim, A., Alexakhin, V., Alimena, J., Alison, J., Alpana, A., Alshehri, W., Dominguez, P. Alvarez, Alyari, M., Amendola, C., Amir, R. B., Andersen, S. B., Andreev, Y., Antoszczuk, P. D., Aras, U., Ardila, L., Aspell, P., Avila, M., Awad, I., Aydilek, O., Azimi, Z., Pretel, A. Aznar, Bach, O. A., Bainbridge, R., Bakshi, A., Bam, B., Banerjee, S., Barney, D., Bayraktar, O., Beaudette, F., Beaujean, F., Becheva, E., Behera, P. K., Belloni, A., Bergauer, T., Besancon, M., Bylund, O. Bessidskaia, Bhatt, L., Bhowmil, D., Blekman, F., Blinov, P., Bloch, P., Bodek, A., Boger, a., Bonnemaison, A., Bouyjou, F., Brennan, L., Brondolin, E., Brusamolino, A., Bubanja, I., Perraguin, A. Buchot, Bunin, P., Misura, A. Burazin, Butler-nalin, A., Cakir, A., Callier, S., Campbell, S., Canderan, K., Cankocak, K., Cappati, A., Caregari, S., Carron, S., Carty, C., Cauchois, A., Ceard, L., Cerci, S., Chang, P. J., Chatterjee, R. M., Chatterjee, S., Chattopadhyay, P., Chatzistavrou, T., Chaudhary, M. S., Chauhan, A., Chen, J. A., Chen, J., Chen, Y., Cheng, K., Cheung, H., Chhikara, J., Chiron, A., Chiusi, M., Chokheli, D., Chudasama, R., Clement, E., Mendez, S. Coco, Coko, D., Coskun, K., Couderc, F., Crossman, B., Cui, Z., Cuisset, T., Cummings, G., Curtis, E. M., D'Alfonso, M., D-hler-ball, J., Dadazhanova, O., Damgov, J., Das, I., DasGupta, S., Dauncey, P., Mendes, A. David Tinoco, Davies, G., Davignon, O., DeLa, P. deBarbaroC., DeSilva, M., DeWit, A., Debbins, P., Defranchis, M. M., Delagnes, E., Devouge, P., Dewangan, C., DiGuglielmo, G., Diehl, L., Dilsiz, K., Dincer, G. G., Dittmann, J., Dragicevic, M., Du, D., Dubinchik, B., Dugad, S., Dulucq, F., Dumanoglu, I., Duran, B., Dutta, S., Dutta, V., Dychkant, A., Dünser, M., Edberg, T., Ehle, I. T., Berni, A. El, Elias, F., Eno, S. C., Erdogan, E. N., Erkmen, B., Ershov, Y., Ertorer, E. Y., Extier, S., Eychenne, L., Fedar, Y. E., Fedi, G., De Almeida, J. P. Figueiredo De De Sá Sousa, Alves, B. A. Fontana Santos Santos, Frahm, E., Francis, K., Freeman, J., French, T., Gaede, F., Gandhi, P. K., Ganjour, S., Garcia-Bellido, A., Gastaldi, F., Gazi, L., Gecse, Z., Gerwig, H., Gevin, O., Ghosh, S., Gill, K., Gleyzer, S., Godinovic, N., Goek, M., Goettlicher, P., Goff, R., Golunov, A., Gonultas, B., Martínez, J. D. González, Gorbounov, N., Gouskos, L., Gray, A., Gray, L., Grieco, C., Groenroos, S., Groner, D., Gruber, A., Grummer, A., Grönroos, S., Guilloux, F., Guler, Y., Gungordu, A. D., Guo, J., Guo, K., Guler, E. Gurpinar, Gutti, H. K., Guvenli, A. A., Gülmez, E., Hacisahinoglu, B., Halkin, Y., Machado, G. Hamilton Ilha, Hare, H. S., Hatakeyama, K., Heering, A. H., Hegde, V., Heintz, U., Hinton, N., Hinzmann, A., Hirschauer, J., Hitlin, D., Hos, İ., Hou, B., Hou, X., Howard, A., Howe, C., Hsieh, H., Hsu, T., Hua, H., Hummer, F., Imran, M., Incandela, J., Iren, E., Isildak, B., Jackson, P. S., Jackson, W. J., Jain, S., Jana, P., Jaroslavceva, J., Jena, S., Jige, A., Jordano, P. P., Joshi, U., Kaadze, K., Kafizov, A., Kalipoliti, L., Tharayil, A. Kallil, Kaluzinska, O., Kamble, S., Kaminskiy, A., Kanemura, M., Kanso, H., Kao, Y., Kapic, A., Kapsiak, C., Karjavine, V., Karmakar, S., Karneyeu, A., Kaya, M., Topaksu, A. Kayis, Kaynak, B., Kazhykarim, Y., Khan, F. A., Khudiakov, A., Kieseler, J., Kim, R. S., Klijnsma, T., Kloiber, E. G., Klute, M., Kocak, Z., Kodali, K. R., Koetz, K., Kolberg, T., Kolcu, O. B., Komaragiri, J. R., Komm, M., Kopsalis, I., Krause, H. A., Krawczyk, M. A., Vinayakam, T. R. Krishnaswamy, Kristiansen, K., Kristic, A., Krohn, M., Kronheim, B., Krüger, K., Kudtarkar, C., Kulis, S., Kumar, M., Kumar, N., Kumar, S., Verma, R. Kumar, Kunori, S., Kunts, A., Kuo, C., Kurenkov, A., Kuryatkov, V., Kyre, S., Ladenson, J., Lamichhane, K., Landsberg, G., Langford, J., Laudrain, A., Laughlin, R., Lawhorn, J., Dortz, O. Le, Lee, S. W., Lektauers, A., Lelas, D., Leon, M., Levchuk, L., Li, A. J., Li, J., Li, Y., Liang, Z., Liao, H., Lin, K., Lin, W., Lin, Z., Lincoln, D., Linssen, L., Litomin, A., Liu, G., Liu, Y., Lobanov, A., Lohezic, V., Loiseau, T., Lu, C., Lu, R., Lu, S. Y., Lukens, P., Mackenzie, M., Magnan, A., Magniette, F., Mahjoub, A., Mahon, D., Majumder, G., Makarenko, V., Malakhov, A., Malgeri, L., Mallios, S., Mandloi, C., Mankel, A., Mannelli, M., Mans, J., Mantilla, C., Martinez, G., Massa, C., Masterson, P., Matthewman, M., Matveev, V., Mayekar, S., Mazlov, I., Mehta, A., Mestvirishvili, A., Miao, Y., Milella, G., Mirza, I. R., Mitra, P., Moccia, S., Mohanty, G. B., Monti, F., Moortgat, F., Murthy, S., Music, J., Musienko, Y., Nabili, S., Nayak, S., Nelson, J. W., Nema, A., Neutelings, I., Niedziela, J., Nikitenko, A., Noonan, D., Noy, M., Nurdan, K., Obraztsov, S., Ochando, C., Ogul, H., Olsson, J., Onel, Y., Ozkorucuklu, S., Paganis, E., Palit, P., Pan, R., Pandey, S., Pantaleo, F., Papageorgakis, C., Paramesvaran, S., Paranjpe, M. M., Parolia, S., Parsons, A. G., Parygin, P., Paulini, M., Paus, C., Peñaló, K., Pedro, K., Pekic, V., Peltola, T., Peng, B., Perego, A., Perini, D., Petrilli, A., Pham, H., Pierre-Emile, T., Podem, S. K., Popov, V., Portales, L., Potok, O., Pradeep, P. B., Pramanik, R., Prosper, H., Prvan, M., Qasim, S. R., Qu, H., Quast, T., Trivino, A. Quiroga, Rabour, L., Raicevic, N., Rajpoot, H., Rao, M. A., Rapacz, K., Redjeb, W., Reinecke, M., Revering, M., Roberts, A., Rohlf, J., Rosado, P., Rose, A., Rothman, S., Rout, P. K., Rovere, M., Rumerio, P., Rusack, R., Rygaard, L., Ryjov, V., Sadivnycha, S., Sahin, M. Ö., Sakarya, U., Salerno, R., Saradhy, R., Saraf, M., Sarbandi, K., Sarkisla, M. A., Satyshev, I., Saud, N., Sauvan, J., Schindler, G., Schmidt, A., Schmidt, I., Schmitt, M. H., Sculac, A., Sculac, T., Sedelnikov, A., Seez, C., Sefkow, F., Selivanova, D., Selvaggi, M., Sergeychik, V., Sert, H., Shahid, M., Sharma, P., Sharma, R., Sharma, S., Shelake, M., Shenai, A., Shih, C. W., Shinde, R., Shmygol, D., Shukla, R., Sicking, E., Silva, P., Simsek, C., Simsek, E., Sirasva, B. K., Sirois, Y., Song, S., Song, Y., Soudais, G., Sriram, S., StJacques, R. R., StahlLeiton, A. G., Steen, A., Stein, J., Strait, J., Strobbe, N., Su, X., Sukhov, E., Suleiman, A., Cerci, D. Sunar, Suryadevara, P., Swain, K., Syal, C., Tali, B., Tanay, K., Tang, W., Tanvir, A., Tao, J., Tarabini, A., Tatli, T., Taylor, R., Taysi, Z. C., Teafoe, G., Tee, C. Z., Terrill, W., Thienpont, D., Thomas, R., Titov, M., Todd, C., Todd, E., Toms, M., Tosun, A., Troska, J., Tsai, L., Tsamalaidze, Z., Tsionou, D., Tsipolitis, G., Tsirigoti, M., Tu, R., Polat, S. N. Tural, Undleeb, S., Usai, E., Uslan, E., Ustinov, V., Vernazza, E., Viahin, O., Viazlo, O., Vichoudis, P., Vijay, A., Virdee, T., Voirin, E., Vojinovic, M., Voytishin, N., Vámi, T. Á., Wade, A., Walter, D., Wang, C., Wang, F., Wang, J., Wang, K., Wang, X., Wang, Y., Wang, Z., Wanlin, E., Wayne, M., Wetzel, J., Whitbeck, A., Wickwire, R., Wilmot, D., Wilson, J., Wu, H., Xiao, M., Yang, J., Yazici, B., Ye, Y., Yetkin, T., Yi, R., Yohay, R., Yu, T., Yuan, C., Yuan, X., Yuksel, O., YushmanoV, I., Yusuff, I., Zabi, A., Zareckis, D., Zarubin, A., Zehetner, P., Zghiche, A., Zhang, C., Zhang, D., Zhang, H., Zhang, J., Zhang, Z., Zhao, X., Zhong, J., Zhou, Y., and Zorbilmez, Ç.
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Physics - Instrumentation and Detectors ,High Energy Physics - Experiment ,Physics - Data Analysis, Statistics and Probability - Abstract
A novel method to reconstruct the energy of hadronic showers in the CMS High Granularity Calorimeter (HGCAL) is presented. The HGCAL is a sampling calorimeter with very fine transverse and longitudinal granularity. The active media are silicon sensors and scintillator tiles readout by SiPMs and the absorbers are a combination of lead and Cu/CuW in the electromagnetic section, and steel in the hadronic section. The shower reconstruction method is based on graph neural networks and it makes use of a dynamic reduction network architecture. It is shown that the algorithm is able to capture and mitigate the main effects that normally hinder the reconstruction of hadronic showers using classical reconstruction methods, by compensating for fluctuations in the multiplicity, energy, and spatial distributions of the shower's constituents. The performance of the algorithm is evaluated using test beam data collected in 2018 prototype of the CMS HGCAL accompanied by a section of the CALICE AHCAL prototype. The capability of the method to mitigate the impact of energy leakage from the calorimeter is also demonstrated., Comment: Prepared for submission to JINST
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- 2024
5. When is IV identification agnostic about outcomes?
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Goff, Leonard
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Economics - Econometrics - Abstract
Many identification results in instrumental variables (IV) models have the property that identification holds with no restrictions on the joint distribution of potential outcomes or how these outcomes are correlated with selection behavior. This enables many IV models to allow for arbitrary heterogeneity in treatment effects and the possibility of selection on gains in the outcome variable. I call this type of identification result "outcome-agnostic", and provide a necessary and sufficient condition for counterfactual means or treatment effects to be identified in an outcome-agnostic manner, when the instruments and treatments have finite support. In addition to unifying many existing IV identification results, this characterization suggests a brute-force approach to revealing all restrictions on selection behavior that yield identification of treatment effect parameters. While computationally intensive, the approach uncovers even in simple settings new selection models that afford identification of interpretable causal parameters.
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- 2024
6. The $e$-positivity of the chromatic symmetric function for twinned paths and cycles
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Banaian, Esther, Celano, Kyle, Chang-Lee, Megan, Colmenarejo, Laura, Goff, Owen, Kimble, Jamie, Kimpel, Lauren, Lentfer, John, Liang, Jinting, and Sundaram, Sheila
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Mathematics - Combinatorics ,05E05, 05C15 - Abstract
The operation of twinning a graph at a vertex was introduced by Foley, Ho\`ang, and Merkel (2019), who conjectured that twinning preserves $e$-positivity of the chromatic symmetric function. A counterexample to this conjecture was given by Li, Li, Wang, and Yang (2021). In this paper, we prove that $e$-positivity is preserved by the twinning operation on cycles, by giving an $e$-positive generating function for the chromatic symmetric function, as well as an $e$-positive recurrence. We derive similar $e$-positive generating functions and recurrences for twins of paths. Our methods make use of the important triple deletion formulas of Orellana and Scott (2014), as well as new symmetric function identities., Comment: 35 pages, 2 tables, 9 figures
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- 2024
7. MacroQueue: Automating Measurements in High-Dimensional Parameter Spaces
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Goff, Brad M. and Gupta, Jay A.
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Physics - Instrumentation and Detectors ,Condensed Matter - Materials Science - Abstract
Laboratory measurements often use several instruments to fully explore the relevant parameter space; such as, an external lock-in amplifier, an electromagnet, an RF generator, etc.. Ordinarily, these instruments have to be individually controlled and their parameters have to be manually recorded. MacroQueue enables effortless measurements throughout these high-dimensional parameter space systems. MacroQueue is a modular software designed for controlling and automating various laboratory equipment in sync without requiring coding ability. Currently, it includes functions to control the 3 major commercial scanning tunneling microscopes, CreaTec, RHK, and Scienta Omicron in combination with any other instruments that are a part of the systems. It can be extended to control any instrument that can be controlled via Python., Comment: 4 pages; 3 figures
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- 2024
8. DESI 2024 VI: Cosmological Constraints from the Measurements of Baryon Acoustic Oscillations
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DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Alexander, D. M., Alvarez, M., Alves, O., Anand, A., Andrade, U., Armengaud, E., Avila, S., Aviles, A., Awan, H., Bahr-Kalus, B., Bailey, S., Baltay, C., Bault, A., Behera, J., BenZvi, S., Bera, A., Beutler, F., Bianchi, D., Blake, C., Blum, R., Brieden, S., Brodzeller, A., Brooks, D., Buckley-Geer, E., Burtin, E., Calderon, R., Canning, R., Rosell, A. Carnero, Cereskaite, R., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chen, X., Claybaugh, T., Cole, S., Cuceu, A., Davis, T. M., Dawson, K., de la Macorra, A., de Mattia, A., Deiosso, N., Dey, A., Dey, B., Ding, Z., Doel, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Fagrelius, P., Fanning, K., Ferraro, S., Ereza, J., Findlay, N., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Frenk, C. S., Garcia-Quintero, C., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Green, D., Gruen, D., Gsponer, R., Gutierrez, G., Guy, J., Hadzhiyska, B., Hahn, C., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Juneau, S., Karaçaylı, N. G., Kehoe, R., Kent, S., Kirkby, D., Kremin, A., Krolewski, A., Lai, Y., Lan, T. -W., Landriau, M., Lang, D., Lasker, J., Goff, J. M. Le, Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Linder, E., Lodha, K., Magneville, C., Manera, M., Margala, D., Martini, P., Maus, M., McDonald, P., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Miquel, R., Moon, J., Moore, S., Moustakas, J., Mudur, N., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nguyen, N. M., Nie, J., Niz, G., Noriega, H. E., Padmanabhan, N., Paillas, E., Palanque-Delabrouille, N., Pan, J., Penmetsa, S., Percival, W. J., Pieri, M. M., Pinon, M., Poppett, C., Porredon, A., Prada, F., Pérez-Fernández, A., Pérez-Ràfols, I., Rabinowitz, D., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Ravoux, C., Rashkovetskyi, M., Rezaie, M., Rich, J., Rocher, A., Rockosi, C., Roe, N. A., Rosado-Marin, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Samushia, L., Sanchez, E., Saulder, C., Schlafly, E. F., Schlegel, D., Schubnell, M., Seo, H., Shafieloo, A., Sharples, R., Silber, J., Slosar, A., Smith, A., Sprayberry, D., Tan, T., Tarlé, G., Taylor, P., Trusov, S., Ureña-López, L. A., Vaisakh, R., Valcin, D., Valdes, F., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., Weinberg, D. H., White, M., Yu, J., Yu, Y., Yuan, S., Yèche, C., Zaborowski, E. A., Zarrouk, P., Zhang, H., Zhao, C., Zhao, R., Zhou, R., Zhuang, T., and Zou, H.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
We present cosmological results from the measurement of baryon acoustic oscillations (BAO) in galaxy, quasar and Lyman-$\alpha$ forest tracers from the first year of observations from the Dark Energy Spectroscopic Instrument (DESI), to be released in the DESI Data Release 1. DESI BAO provide robust measurements of the transverse comoving distance and Hubble rate, or their combination, relative to the sound horizon, in seven redshift bins from over 6 million extragalactic objects in the redshift range $0.1
-1$ and $w_a<0$. This preference is 2.6$\sigma$ for the DESI+CMB combination, and persists or grows when SN~Ia are added in, giving results discrepant with the $\Lambda$CDM model at the $2.5\sigma$, $3.5\sigma$ or $3.9\sigma$ levels for the addition of Pantheon+, Union3, or DES-SN5YR datasets respectively. For the flat $\Lambda$CDM model with the sum of neutrino mass $\sum m_\nu$ free, combining the DESI and CMB data yields an upper limit $\sum m_\nu < 0.072$ $(0.113)$ eV at 95% confidence for a $\sum m_\nu>0$ $(\sum m_\nu>0.059)$ eV prior. These neutrino-mass constraints are substantially relaxed in models beyond $\Lambda$CDM. [Abridged.], Comment: This DESI Collaboration Key Publication is part of the 2024 publication series using the first year of observations (see https://data.desi.lbl.gov/doc/papers). Typos corrected and a new figure and discussion added to Appendix A - Published
- 2024
9. DESI 2024 IV: Baryon Acoustic Oscillations from the Lyman Alpha Forest
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DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Alexander, D. M., Alvarez, M., Alves, O., Anand, A., Andrade, U., Armengaud, E., Avila, S., Aviles, A., Awan, H., Bailey, S., Baltay, C., Bault, A., Bautista, J., Behera, J., BenZvi, S., Beutler, F., Bianchi, D., Blake, C., Blum, R., Brieden, S., Brodzeller, A., Brooks, D., Buckley-Geer, E., Burtin, E., Calderon, R., Canning, R., Rosell, A. Carnero, Cereskaite, R., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chen, X., Claybaugh, T., Cole, S., Cuceu, A., Davis, T. M., Dawson, K., de la Cruz, R., de la Macorra, A., de Mattia, A., Deiosso, N., Dey, A., Dey, B., Ding, J., Ding, Z., Doel, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Fagrelius, P., Fanning, K., Ferraro, S., Ereza, J., Findlay, N., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Garcia-Quintero, C., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Green, D., Gruen, D., Gsponer, R., Gutierrez, G., Guy, J., Hadzhiyska, B., Hahn, C., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Juneau, S., Karaçayli, N. G., Kehoe, R., Kent, S., Kirkby, D., Kremin, A., Krolewski, A., Lai, Y., Lan, T. -W., Landriau, M., Lang, D., Lasker, J., Goff, J. M. Le, Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Linder, E., Lodha, K., Magneville, C., Manera, M., Margala, D., Martini, P., Maus, M., McDonald, P., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Miquel, R., Moon, J., Moore, S., Moustakas, J., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nguyen, N. M., Nie, J., Niz, G., Noriega, H. E., Padmanabhan, N., Paillas, E., Palanque-Delabrouille, N., Pan, J., Penmetsa, S., Percival, W. J., Pieri, M. M., Pinon, M., Poppett, C., Porredon, A., Prada, F., Pérez-Fernández, A., Pérez-Ràfols, I., Rabinowitz, D., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Ravoux, C., Rezaie, M., Rich, J., Rocher, A., Rockosi, C., Roe, N. A., Rosado-Marin, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Samushia, L., Sanchez, E., Saulder, C., Schlafly, E. F., Schlegel, D., Schubnell, M., Seo, H., Sharples, R., Silber, J., Sinigaglia, F., Slosar, A., Smith, A., Sprayberry, D., Tan, T., Tarlé, G., Trusov, S., Vaisakh, R., Valcin, D., Valdes, F., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., Weinberg, D. H., White, M., Yu, J., Yu, Y., Yuan, S., Yèche, C., Zaborowski, E. A., Zarrouk, P., Zhang, H., Zhao, C., Zhao, R., Zhou, R., and Zou, H.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
We present the measurement of Baryon Acoustic Oscillations (BAO) from the Lyman-$\alpha$ (Ly$\alpha$) forest of high-redshift quasars with the first-year dataset of the Dark Energy Spectroscopic Instrument (DESI). Our analysis uses over $420\,000$ Ly$\alpha$ forest spectra and their correlation with the spatial distribution of more than $700\,000$ quasars. An essential facet of this work is the development of a new analysis methodology on a blinded dataset. We conducted rigorous tests using synthetic data to ensure the reliability of our methodology and findings before unblinding. Additionally, we conducted multiple data splits to assess the consistency of the results and scrutinized various analysis approaches to confirm their robustness. For a given value of the sound horizon ($r_d$), we measure the expansion at $z_{\rm eff}=2.33$ with 2\% precision, $H(z_{\rm eff}) = (239.2 \pm 4.8) (147.09~{\rm Mpc} /r_d)$ km/s/Mpc. Similarly, we present a 2.4\% measurement of the transverse comoving distance to the same redshift, $D_M(z_{\rm eff}) = (5.84 \pm 0.14) (r_d/147.09~{\rm Mpc})$ Gpc. Together with other DESI BAO measurements at lower redshifts, these results are used in a companion paper to constrain cosmological parameters., Comment: This DESI Collaboration Key Publication is part of the 2024 publication series using the first year of observations (see https://data.desi.lbl.gov/doc/papers)
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- 2024
10. Validation of the DESI 2024 Ly$\alpha$ forest BAO analysis using synthetic datasets
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Cuceu, Andrei, Herrera-Alcantar, Hiram K., Gordon, Calum, Martini, Paul, Guy, Julien, Font-Ribera, Andreu, Gonzalez-Morales, Alma X., Karim, M. Abdul, Aguilar, J., Ahlen, S., Armengaud, E., Bault, A., Brooks, D., Claybaugh, T., de la Macorra, A., Doel, P., Fanning, K., Ferraro, S., Forero-Romero, J. E., Gaztañaga, E., Gontcho, S. Gontcho A, Gutierrez, G., Honscheid, K., Howlett, C., Karaçaylı, N. G., Kirkby, D., Kremin, A., Landriau, M., Goff, J. M. Le, Guillou, L. Le, Levi, M. E., Manera, M., Meisner, A., Miquel, R., Moustakas, J., Muñoz-Gutiérrez, A., Myers, A. D., Niz, G., Palanque-Delabrouille, N., Percival, W. J., Poppett, C., Prada, F., Pérez-Ràfols, I., Ramírez-Pérez, C., Ravoux, C., Rezaie, M., Rossi, G., Sanchez, E., Schlegel, D., Schubnell, M., Seo, H., Sprayberry, D., Tan, T., Tarlé, G., Vargas-Magaña, M., Walther, M., Weaver, B. A., Zhou, R., and Zou, H.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
The first year of data from the Dark Energy Spectroscopic Instrument (DESI) contains the largest set of Lyman-$\alpha$ (Ly$\alpha$) forest spectra ever observed. This data, collected in the DESI Data Release 1 (DR1) sample, has been used to measure the Baryon Acoustic Oscillation (BAO) feature at redshift $z=2.33$. In this work, we use a set of 150 synthetic realizations of DESI DR1 to validate the DESI 2024 Ly$\alpha$ forest BAO measurement. The synthetic data sets are based on Gaussian random fields using the log-normal approximation. We produce realistic synthetic DESI spectra that include all major contaminants affecting the Ly$\alpha$ forest. The synthetic data sets span a redshift range $1.8
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- 2024
11. DESI 2024 III: Baryon Acoustic Oscillations from Galaxies and Quasars
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DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Alexander, D. M., Alvarez, M., Alves, O., Anand, A., Andrade, U., Armengaud, E., Avila, S., Aviles, A., Awan, H., Bailey, S., Baltay, C., Bault, A., Behera, J., BenZvi, S., Beutler, F., Bianchi, D., Blake, C., Blum, R., Brieden, S., Brodzeller, A., Brooks, D., Buckley-Geer, E., Burtin, E., Calderon, R., Canning, R., Rosell, A. Carnero, Cereskaite, R., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chen, X., Claybaugh, T., Cole, S., Cuceu, A., Davis, T. M., Dawson, K., de la Macorra, A., de Mattia, A., Deiosso, N., Dey, A., Dey, B., Ding, Z., Doel, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Fagrelius, P., Fanning, K., Ferraro, S., Ereza, J., Findlay, N., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Garcia-Quintero, C., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Green, D., Gruen, D., Gsponer, R., Gutierrez, G., Guy, J., Hadzhiyska, B., Hahn, C., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Juneau, S., Karaçaylı, N. G., Kehoe, R., Kent, S., Kirkby, D., Kremin, A., Krolewski, A., Lai, Y., Lan, T. -W., Landriau, M., Lang, D., Lasker, J., Goff, J. M. Le, Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Linder, E., Lodha, K., Magneville, C., Manera, M., Margala, D., Martini, P., Maus, M., McDonald, P., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Miquel, R., Moon, J., Moore, S., Moustakas, J., Mudur, N., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nguyen, N. M., Nie, J., Niz, G., Noriega, H. E., Padmanabhan, N., Paillas, E., Palanque-Delabrouille, N., Pan, J., Penmetsa, S., Percival, W. J., Pieri, M., Pinon, M., Poppett, C., Porredon, A., Prada, F., Pérez-Fernández, A., Pérez-Ràfols, I., Rabinowitz, D., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Rezaie, M., Rich, J., Rocher, A., Rockosi, C., Roe, N. A., Rosado-Marin, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Samushia, L., Sanchez, E., Saulder, C., Schlafly, E. F., Schlegel, D., Schubnell, M., Seo, H., Sharples, R., Silber, J., Slosar, A., Smith, A., Sprayberry, D., Swanson, J., Tan, T., Tarlé, G., Trusov, S., Vaisakh, R., Valcin, D., Valdes, F., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., Weinberg, D. H., White, M., Yu, J., Yu, Y., Yuan, S., Yèche, C., Zaborowski, E. A., Zarrouk, P., Zhang, H., Zhao, C., Zhao, R., Zhou, R., and Zou, H.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
We present the DESI 2024 galaxy and quasar baryon acoustic oscillations (BAO) measurements using over 5.7 million unique galaxy and quasar redshifts in the range 0.1
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- 2024
12. Current Postlaunch Implementation of State Mandates of Newborn Screening for Critical Congenital Heart Disease by Pulse Oximetry in U.S. States and Hospitals
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Sakai-Bizmark, Rie, Chang, Ruey-Kang R, Martin, Gerard R, Hom, Lisa A, Marr, Emily H, Ko, Jamie, Goff, Donna A, Mena, Laurie A, von Kohler, Connie, Bedel, Lauren EM, Murillo, Mary, Estevez, Dennys, and Hays, Ron D
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Health Services and Systems ,Biomedical and Clinical Sciences ,Health Sciences ,Congenital Structural Anomalies ,Clinical Research ,Rare Diseases ,Pediatric ,Health Services ,Cardiovascular ,Heart Disease ,Humans ,Oximetry ,Heart Defects ,Congenital ,Neonatal Screening ,Infant ,Newborn ,United States ,Guideline Adherence ,Surveys and Questionnaires ,Hospitals ,Mandatory Programs ,RUSP ,pulse oximetry screening ,CFIR ,implementation ,newborn screening ,CCHD ,congenital heart disease ,nurses ,Clinical Sciences ,Paediatrics and Reproductive Medicine ,Obstetrics & Reproductive Medicine ,Paediatrics ,Reproductive medicine ,Midwifery - Abstract
ObjectiveOur objective was to gauge adherence to nationally endorsed protocols in implementation of pulse oximetry (POx) screening for critical congenital heart disease (CCHD) in infants after mandate by all states and to assess associated characteristics.Study designBetween March and October 2019, an online questionnaire was administered to nurse supervisors who oversee personnel conducting POx screening. The questionnaire used eight questions regarding performance and interpretation of screening protocols to measure policy consistency, which is adherence to nationally endorsed protocols for POx screening developed by professional medical societies. Multilevel linear regression models evaluated associations between policy consistency and characteristics of hospitals and individuals, state of hospital location, early versus late mandate adopters, and state reporting requirements.ResultsResponses from 189 nurse supervisors spanning 38 states were analyzed. Only 17% received maximum points indicating full policy consistency, and 24% selected all four options for potential hypoxia that require a repeat screen. Notably, 33% did not recognize ≤90% SpO2 as an immediate failed screen and 31% responded that an infant with SpO2 of 89% in one extremity will be rescreened by nurses in an hour rather than receiving an immediate physician referral. Lower policy consistency was associated with lack of state reporting mandates (beta = -1.23 p = 0.01) and early adoption by states (beta = -1.01, p
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- 2024
13. Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface.
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Nielsen, Torben, Kuehl, Jennifer, Hunt, Kristopher, Chandonia, John-Marc, Huang, Jiawen, Thorgersen, Michael, Poole, Farris, Stahl, David, Deutschbauer, Adam, Arkin, Adam, Adams, Michael, Goff, Jennifer, Szink, Elizabeth, Durrence, Konnor, Chakraborty, Romy, and Lui, Lauren
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Acid tolerance ,Contamination ,Heavy metals ,Mobile genetic elements ,Nitrate ,Pangenome - Abstract
Castellaniella species have been isolated from a variety of mixed-waste environments including the nitrate and multiple metal-contaminated subsurface at the Oak Ridge Reservation (ORR). Previous studies examining microbial community composition and nitrate removal at ORR during biostimulation efforts reported increased abundances of members of the Castellaniella genus concurrent with increased denitrification rates. Thus, we asked how genomic and abiotic factors control the Castellaniella biogeography at the site to understand how these factors may influence nitrate transformation in an anthropogenically impacted setting. We report the isolation and characterization of several Castellaniella strains from the ORR subsurface. Five of these isolates match at 100% identity (at the 16S rRNA gene V4 region) to two Castellaniella amplicon sequence variants (ASVs), ASV1 and ASV2, that have persisted in the ORR subsurface for at least 2 decades. However, ASV2 has consistently higher relative abundance in samples taken from the site and was also the dominant blooming denitrifier population during a prior biostimulation effort. We found that the ASV2 representative strain has greater resistance to mixed metal stress than the ASV1 representative strains. We attribute this resistance, in part, to the large number of unique heavy metal resistance genes identified on a genomic island in the ASV2 representative genome. Additionally, we suggest that the relatively lower fitness of ASV1 may be connected to the loss of the nitrous oxide reductase (nos) operon (and associated nitrous oxide reductase activity) due to the insertion at this genomic locus of a mobile genetic element carrying copper resistance genes. This study demonstrates the value of integrating genomic, environmental, and phenotypic data to characterize the biogeography of key microorganisms in contaminated sites.
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- 2024
14. An Investigation of the Factors Influencing Evolutionary Dynamics in the Joint Evolution of Robot Body and Control
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Goff, Léni K. Le, Buchanan, Edgar, and Hart, Emma
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Computer Science - Robotics - Abstract
In evolutionary robotics, jointly optimising the design and the controller of robots is a challenging task due to the huge complexity of the solution space formed by the possible combinations of body and controller. We focus on the evolution of robots that can be physically created rather than just simulated, in a rich morphological space that includes a voxel-based chassis, wheels, legs and sensors. On the one hand, this space offers a high degree of liberty in the range of robots that can be produced, while on the other hand introduces a complexity rarely dealt with in previous works relating to matching controllers to designs and in evolving closed-loop control. This is usually addressed by augmenting evolution with a learning algorithm to refine controllers. Although several frameworks exist, few have studied the role of the \textit{evolutionary dynamics} of the intertwined `evolution+learning' processes in realising high-performing robots. We conduct an in-depth study of the factors that influence these dynamics, specifically: synchronous vs asynchronous evolution; the mechanism for replacing parents with offspring, and rewarding goal-based fitness vs novelty via selection. Results show that asynchronicity combined with goal-based selection and a `replace worst' strategy results in the highest performance., Comment: 9 pages, 8 figures
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- 2024
15. Understanding fitness landscapes in morpho-evolution via local optima networks
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Thomson, Sarah L., Goff, Léni K. Le, Hart, Emma, and Buchanan, Edgar
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Computer Science - Artificial Intelligence - Abstract
Morpho-evolution (ME) refers to the simultaneous optimisation of a robot's design and controller to maximise performance given a task and environment. Many genetic encodings have been proposed which are capable of representing design and control. Previous research has provided empirical comparisons between encodings in terms of their performance with respect to an objective function and the diversity of designs that are evaluated, however there has been no attempt to explain the observed findings. We address this by applying Local Optima Network (LON) analysis to investigate the structure of the fitness landscapes induced by three different encodings when evolving a robot for a locomotion task, shedding new light on the ease by which different fitness landscapes can be traversed by a search process. This is the first time LON analysis has been applied in the field of ME despite its popularity in combinatorial optimisation domains; the findings will facilitate design of new algorithms or operators that are customised to ME landscapes in the future., Comment: Submitted to GECCO-2024
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- 2024
16. Recommendations for public action towards sustainable generative AI systems
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Goff, Thomas Le
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Computer Science - Computers and Society - Abstract
Growing awareness of the environmental impact of digital technologies has led to several isolated initiatives to promote sustainable practices. However, despite these efforts, the environmental footprint of generative AI, particularly in terms of greenhouse gas emissions and water consumption, remains considerable. This contribution first presents the components of this environmental footprint, highlighting the massive CO2 emissions and water consumption associated with training large language models, thus underlining the need to rethink learning and inference methods. The paper also explores the factors and characteristics of models that have an influence on their environmental footprint and demonstrates the existence of solutions to reduce it, such as using more efficient processors or optimising the energy performance of data centres. The potentially harmful effects of AI on the planet and its ecosystem have made environmental protection one of the founding principles of AI ethics at international and European levels. However, this recognition has not yet translated into concrete measures to address it.To address this issue, our contribution puts forward twelve pragmatic recommendations for public action to promote sustainable generative AI, in particular by building a long-term strategy to achieve carbon neutrality for AI models, encouraging international cooperation to set common standards, supporting scientific research and developing appropriate legal and regulatory frameworks.This paper seeks to inform the members of the Interministerial Committee on Generative AI about the environmental challenges of this technology by providing a brief review of the scientific literature on the subject and proposing concrete recommendations of public policy actions to reconcile technological innovation with the need to protect our environment., Comment: in French language
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- 2024
17. Adoptive transfer of personalized neoantigen-reactive TCR-transduced T cells in metastatic colorectal cancer: phase 2 trial interim results
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Parkhurst, Maria, Goff, Stephanie L., Lowery, Frank J., Beyer, Rachel K., Halas, Hyunmi, Robbins, Paul F., Prickett, Todd D., Gartner, Jared J., Sindiri, Sivasish, Krishna, Sri, Zacharakis, Nikolaos, Ngo, Lien, Ray, Satyajit, Bera, Alakesh, Shepherd, Ryan, Levin, Noam, Kim, Sanghyun P., Copeland, Amy, Nah, Shirley, Levi, Shoshana, Parikh, Neilesh, Kwong, Mei Li M., Klemen, Nicholas D., Yang, James C., and Rosenberg, Steven A.
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- 2024
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18. When National Origins Equal Socio-economic Background: The Effect of the Ethno-class Parental Background on the Education of Children Coming of Age in Switzerland
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Guichard, Eduardo, Chimienti, Milena, Bolzman, Claudio, and Le Goff, Jean-Marie
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- 2024
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19. Physiological regulation of neuronal Wnt activity is essential for TDP-43 localization and function
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Zhang, Nan, Westerhaus, Anna, Wilson, Macey, Wang, Ethan, Goff, Loyal, and Sockanathan, Shanthini
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- 2024
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20. Clinical outcomes of subtalar arthroereisis for the treatment of stage 1 flexible progressive collapsing foot deformity
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Lewis, Thomas L., Goff, Thomas A. J., Ray, Robbie, Dhaliwal, Jagwinder, Carmody, David, and Wines, Andrew P.
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- 2024
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21. The God behind the Marble: The Fate of Art in the German Aesthetic State
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Goff, Alice, author and Goff, Alice
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- 2024
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22. NCI10066: a Phase 1/2 study of olaparib in combination with ramucirumab in previously treated metastatic gastric and gastroesophageal junction adenocarcinoma
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Cecchini, Michael, Cleary, James M, Shyr, Yu, Chao, Joseph, Uboha, Nataliya, Cho, May, Shields, Anthony, Pant, Shubham, Goff, Laura, Spencer, Kristen, Kim, Edward, Stein, Stacey, Kortmansky, Jeremy S, Canosa, Sandra, Sklar, Jeffrey, Swisher, Elizabeth M, Radke, Marc, Ivy, Percy, Boerner, Scott, Durecki, Diane E, Hsu, Chih-Yuan, LoRusso, Patricia, and Lacy, Jill
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Biomedical and Clinical Sciences ,Clinical Sciences ,Oncology and Carcinogenesis ,Clinical Trials and Supportive Activities ,Cancer ,Clinical Research ,Evaluation of treatments and therapeutic interventions ,6.2 Cellular and gene therapies ,6.1 Pharmaceuticals ,Humans ,Ramucirumab ,Stomach Neoplasms ,Phthalazines ,Adenocarcinoma ,Esophagogastric Junction ,Antineoplastic Combined Chemotherapy Protocols ,Esophageal Neoplasms ,Piperazines ,Public Health and Health Services ,Oncology & Carcinogenesis ,Oncology and carcinogenesis - Abstract
BackgroundOur preclinical work revealed tumour hypoxia induces homologous recombination deficiency (HRD), increasing sensitivity to Poly (ADP-ribose) polymerase inhibitors. We aimed to induce tumour hypoxia with ramucirumab thereby sensitising tumours to olaparib.Patients and methodsThis multi-institution single-arm Phase 1/2 trial enrolled patients with metastatic gastroesophageal adenocarcinoma refractory to ≥1 systemic treatment. In dose escalation, olaparib was evaluated at escalating dose levels with ramucirumab 8 mg/kg day 1 in 14-day cycles. The primary endpoint of Phase 1 was the recommended Phase 2 dose (RP2D), and in Phase 2 the primary endpoint was the overall response rate (ORR).ResultsFifty-one patients received ramucirumab and olaparib. The RP2D was olaparib 300 mg twice daily with ramucirumab 8 mg/kg. In evaluable patients at the RP2D the ORR was 6/43 (14%) (95% CI 4.7-25.6). The median progression-free survival (PFS) was 2.8 months (95% CI 2.3-4.2) and median overall survival (OS) was 7.3 months (95% CI 5.7-13.0). Non-statistically significant improvements in PFS and OS were observed for patients with tumours with mutations in HRD genes.ConclusionsOlaparib and ramucirumab is well-tolerated with efficacy that exceeds historical controls with ramucirumab single agent for gastric cancer in a heavily pre-treated patient population.
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- 2024
23. Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes
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Goff, Jennifer L, Lui, Lauren M, Nielsen, Torben N, Poole, Farris L, Smith, Heidi J, Walker, Kathleen F, Hazen, Terry C, Fields, Matthew W, Arkin, Adam P, and Adams, Michael WW
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Microbiology ,Biological Sciences ,Ecology ,Genetics ,mobilome ,plasmids ,phages ,evolution ,metagenome - Abstract
Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.
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- 2024
24. The Science of Precision Prevention: Research Opportunities and Clinical Applications to Reduce Cardiovascular Health Disparities.
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Pearson, Thomas, Vitalis, Debbie, Pratt, Charlotte, Campo, Rebecca, Armoundas, Antonis, Au, David, Beech, Bettina, Brazhnik, Olga, Chute, Christopher, Davidson, Karina, Diez-Roux, Ana, Fine, Lawrence, Gabriel, Davera, Groenveld, Peter, Hall, Jaclyn, Hamilton, Alison, Hu, Hui, Ji, Heng, Kind, Amy, Kraus, William, Krumholz, Harlan, Mensah, George, Merchant, Raina, Mozaffarian, Dariush, Murray, David, Neumark-Sztainer, Dianne, Goff, David, and Petersen, Maya
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data science ,health equity ,health promotion ,implementation science ,personalized medicine ,precision analytics - Abstract
Precision prevention embraces personalized prevention but includes broader factors such as social determinants of health to improve cardiovascular health. The quality, quantity, precision, and diversity of data relatable to individuals and communities continue to expand. New analytical methods can be applied to these data to create tools to attribute risk, which may allow a better understanding of cardiovascular health disparities. Interventions using these analytic tools should be evaluated to establish feasibility and efficacy for addressing cardiovascular disease disparities in diverse individuals and communities. Training in these approaches is important to create the next generation of scientists and practitioners in precision prevention. This state-of-the-art review is based on a workshop convened to identify current gaps in knowledge and methods used in precision prevention intervention research, discuss opportunities to expand trials of implementation science to close the health equity gaps, and expand the education and training of a diverse precision prevention workforce.
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- 2024
25. Takanga 'Enau Fohe: A Scoping Review of the Educational Successes and Challenges of Pacific Learners in Australia 2010-2021
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Maryanne Pale, Lyn Kee, Bin Wu, and Wendy Goff
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International literature has recognised the importance of education research with Pacific learners. In an Australian context, the early years learning framework for Australia and the Australian curriculum emphasise that education sectors should work towards cultivating respect for cultural diversity and to develop intercultural understanding and intercultural capabilities. As such, the call to better understand the cultural complexities that underpins Pacific learners and their interactions with educational processes remains pertinent. This scoping review offers an important synthesis of empirical research on the educational successes and challenges of Pacific learners in Australian educational settings from 2010 to 2021. While this study offers critical insights for teacher education and research, the findings also revealed paucities in education research with Pacific learners. Thereby, propositions for future and ongoing education research with Pacific learners in Australia are offered in this article.
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- 2024
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26. Autologous stem cell boost improves persistent immune effector cell associated hematotoxicity following BCMA directed chimeric antigen receptor T (CAR T) cell therapy in multiple myeloma
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Mohan, Meera, Szabo, Aniko, Patwari, Anannya, Esselmann, Jean, Patel, Tanvi, Bachu, Ramya, Rein, Lisa E., Janardan, Abhishek, Bhatlapenumarthi, Vineel, Annyapu, Evanka, Skoog, Catherine, Goff, Areyl, Hadidi, Samer Al, Radhakrishnan, Sabarinath Venniyil, Thanendrarajan, Sharmilan, Zangari, Maurizio, Shah, Nirav, van Rhee, Frits, Dhakal, Binod, Hamadani, Mehdi, D’Souza, Anita, and Schinke, Carolina
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- 2024
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27. Unmasking Bartonella henselae infection in the shadows of long COVID thanks to clinical metagenomics
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Aubry, Aurélien, Corvilain, Emilie, Ghelfenstein-Ferreira, Théo, Camelena, François, Meignin, Véronique, Berçot, Béatrice, Le Goff, Jérôme, and Salmona, Maud
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- 2024
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28. Coffee trees intercropped with common beans: An opportunity to regulate the aphid Toxoptera aurantii (Boyer de Fonscolombe) (Hemiptera: Aphididae) in coffee agroecosystems
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Harelimana, Anastase, Le Goff, Guillaume, Rukazambuga, Daniel, and Hance, Thierry
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- 2024
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29. Takanga ‘enau fohe: a scoping review of the educational successes and challenges of Pacific learners in Australia 2010–2021
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Pale, Maryanne, Kee, Lyn, Wu, Bin, and Goff, Wendy
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- 2024
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30. Is the fine-tuning evidence for a multiverse?
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Goff, Philip
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- 2024
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31. Breaking bad news: an active learning method for medical students
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Laura Polivka, C. Delcour, H. Dufresne, S. Bartoli, P. Bataille, L. Bekel, J. Bonigen, E. Deladrière, S. Dimarcq, A. Felix, C. Havas, H. Le Goff, M. Levy, E. Riback, A. Welfringer-Morin, V. Houdouin, S. Hadj-Rabia, C. Bodemer, A. Faye, and I. Melki
- Subjects
Breaking bad news ,Objective structured clinical examination (OSCE) ,Announcement ,Discussion group ,S-P-w-ICE-S protocol ,Special aspects of education ,LC8-6691 ,Medicine - Abstract
Abstract Background Breaking bad news is one of the most difficult aspects of communication in medicine. The objective of this study was to assess the relevance of a novel active learning course on breaking bad news for fifth-year students. Methods Students were divided into two groups: Group 1, the intervention group, participated in a multidisciplinary formative discussion workshop on breaking bad news with videos, discussions with a pluri-professional team, and concluding with the development of a guide on good practice in breaking bad news through collective intelligence; Group 2, the control group, received no additional training besides conventional university course. The relevance of discussion-group-based active training was assessed in a summative objective structured clinical examination (OSCE) station particularly through the students’ communication skills. Results Thirty-one students were included: 17 in Group 1 and 14 in Group 2. The mean (range) score in the OSCE was significantly higher in Group 1 than in Group 2 (10.49 out of 15 (7; 13) vs. 7.80 (4.75; 12.5), respectively; p = 0.0007). The proportion of students assessed by the evaluator to have received additional training in breaking bad news was 88.2% (15 of the 17) in Group 1 and 21.4% (3 of the 14) in Group 2 (p = 0.001). The intergroup differences in the Rosenberg Self-Esteem Scale and Jefferson Scale of Empathy scores were not significant, and both scores were not correlated with the students’ self-assessed score for success in the OSCE. Conclusion Compared to the conventional course, this new active learning method for breaking bad news was associated with a significantly higher score in a summative OSCE. A longer-term validation study is needed to confirm these exploratory data.
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- 2024
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32. Real-world multidisciplinary outcomes of onasemnogene abeparvovec monotherapy in patients with spinal muscular atrophy type 1: experience of the French cohort in the first three years of treatment
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Isabelle Desguerre, Rémi Barrois, Frédérique Audic, Christine Barnerias, Brigitte Chabrol, Jean Baptiste Davion, Julien Durigneux, Caroline Espil-Taris, Marta Gomez-Garcia de la Banda, Marine Guichard, Arnaud Isapof, Marie Christine Nougues, Vincent Laugel, Laure Le Goff, Sandra Mercier, Anne Pervillé, Christian Richelme, Marie Thibaud, Catherine Sarret, Cyril Schweitzer, Hervé Testard, Valérie Trommsdorff, Catherine Vanhulle, Ulrike Walther-Louvier, Cécilia Altuzarra, Mondher Chouchane, Juliette Ropars, Susana Quijano-Roy, and Claude Cances
- Subjects
Spinal muscular atrophy ,Gene transfer therapy ,Real-world outcome ,Medicine - Abstract
Abstract Background Spinal muscular atrophy type 1 (SMA1) is the most severe and early form of SMA, a genetic disease with motor neuron degeneration. Onasemnogene abeparvovec gene transfer therapy (GT) has changed the natural history of SMA1, but real-world data are scarce. Methods A French national expert committee identified 95 newly diagnosed treatment-naive SMA1 patients between June 2019 and June 2022. We prospectively report on children treated with GT as the first and only therapy who had more than one-year of follow-up. Results Forty-six SMA1 patients received GT. Twelve patients received other treatments. Patients with respiratory insufficiency were oriented toward palliative care after discussion with families. Twenty-nine of the treated patients with more than 12 months of follow-up were included in the follow-up analysis. Among them, 17 had 24 months of follow-up. The mean age at treatment was 7.5 (2.1–12.5) months. Twenty-two patients had two SMN2 copies, and seven had three copies. One infant died in the month following GT due to severe thrombotic microangiopathy, and another died due to respiratory distress. Among the 17 patients with 24 months of follow-up, 90% required spinal bracing (15/17), three patients required nocturnal noninvasive ventilation, and two needed gastrostomy. Concerning motor milestones at the 24-month follow-up, all patients held their head, 15/17 sat for 30 s unassisted, and 12/17 stood with aid. Motor scores (CHOPINTEND and HINE-2) and thoracic circumference significantly improved in all patients. Conclusions Our study shows favorable motor outcomes and preserved respiratory and feeding functions in treatment-naive SMA1 infants treated by GT as the first and only therapy before respiratory and bulbar dysfunctions occurred. Nevertheless, almost all patients developed spinal deformities.
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- 2024
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33. Conserved transcriptional regulation by BRN1 and BRN2 in neocortical progenitors drives mammalian neural specification and neocortical expansion
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Soraia Barão, Yijun Xu, José P. Llongueras, Rachel Vistein, Loyal Goff, Kristina J. Nielsen, Byoung-Il Bae, Richard S. Smith, Christopher A. Walsh, Genevieve Stein-O’Brien, and Ulrich Müller
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Science - Abstract
Abstract The neocortex varies in size and complexity among mammals due to the tremendous variability in the number and diversity of neuronal subtypes across species. The increased cellular diversity is paralleled by the expansion of the pool of neocortical progenitors and the emergence of indirect neurogenesis during brain evolution. The molecular pathways that control these biological processes and are disrupted in neurological disorders remain largely unknown. Here we show that the transcription factors BRN1 and BRN2 have an evolutionary conserved function in neocortical progenitors to control their proliferative capacity and the switch from direct to indirect neurogenesis. Functional studies in mice and ferrets show that BRN1/2 act in concert with NOTCH and primary microcephaly genes to regulate progenitor behavior. Analysis of transcriptomics data from genetically modified macaques provides evidence that these molecular pathways are conserved in non-human primates. Our findings thus demonstrate that BRN1/2 are central regulators of gene expression programs in neocortical progenitors critical to determine brain size during evolution.
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- 2024
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34. Assessment of multi-professional primary healthcare center quality by patients with multimorbidity
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Antoine Dany, Paul Aujoulat, Floriane Colin, Jean-Yves Le Reste, and Delphine Le Goff
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Multimorbidity ,Primary health care ,Quality of health care ,Patient satisfaction ,Face validity ,Public aspects of medicine ,RA1-1270 - Abstract
Abstract Background The main aim of this study was to build an item bank for assessing the care quality of multi-professional healthcare centers (MPHCC) from the perspective of patients with multimorbidity. This study was part of the QUALSOPRIM (QUALité des SOins PRIMaires; primary healthcare quality) research project to create a psychometrically robust self-administered questionnaire to assess healthcare quality. Methods First, twelve experts built an item bank using data from a previous qualitative work and a systematic literature review. Second, the validity of each item was assessed in a sample of patients. Adult patients with multimorbidity were recruited from six French MPHCC. Items were assessed based on ceiling effects, the level of missing or neutral responses and patient feedback. Patient feedback was recorded after the item bank completion. Based on results, items were validated, improved, or removed during expert meetings. In case of disagreement the Delphi method was used to reach consensus. Results The study sample included 209 outpatients. The most frequent medical conditions were cardiovascular risk factors, cardiovascular diseases and rheumatological conditions. In total, a bank of 109 items classified in nine domains was built. The validity assessment led to the removal of 34 items. Retained items explored a variety of topics related to care quality: availability, accessibility, premises’ layout and building, technical care, expertise, organization, relationships with caregivers and communication, involvement and personal relationships. Conclusions This study allowed cross-validation of a bank of 75 items, leading to a complete picture of the patient perception of care quality items. Overall, patients were generally satisfied with their care at the MPHCC. Nonetheless, there were still numerous items on subjects for which patients’ satisfaction could be improved.
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- 2024
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35. Unravelling large-scale patterns and drivers of biodiversity in dry rivers
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Arnaud Foulquier, Thibault Datry, Roland Corti, Daniel von Schiller, Klement Tockner, Rachel Stubbington, Mark O. Gessner, Frédéric Boyer, Marc Ohlmann, Wilfried Thuiller, Delphine Rioux, Christian Miquel, Ricardo Albariño, Daniel C. Allen, Florian Altermatt, Maria Isabel Arce, Shai Arnon, Damien Banas, Andy Banegas-Medina, Erin Beller, Melanie L. Blanchette, Joanna Blessing, Iola Gonçalves Boëchat, Kate Boersma, Michael Bogan, Núria Bonada, Nick Bond, Katherine Brintrup, Andreas Bruder, Ryan Burrows, Tommaso Cancellario, Cristina Canhoto, Stephanie Carlson, Núria Cid, Julien Cornut, Michael Danger, Bianca de Freitas Terra, Anna Maria De Girolamo, Rubén del Campo, Verónica Díaz Villanueva, Fiona Dyer, Arturo Elosegi, Catherine Febria, Ricardo Figueroa Jara, Brian Four, Sarig Gafny, Rosa Gómez, Lluís Gómez-Gener, Simone Guareschi, Björn Gücker, Jason Hwan, J. Iwan Jones, Patrick S. Kubheka, Alex Laini, Simone Daniela Langhans, Bertrand Launay, Guillaume Le Goff, Catherine Leigh, Chelsea Little, Stefan Lorenz, Jonathan Marshall, Eduardo J. Martin Sanz, Angus McIntosh, Clara Mendoza-Lera, Elisabeth I. Meyer, Marko Miliša, Musa C. Mlambo, Manuela Morais, Nabor Moya, Peter Negus, Dev Niyogi, Iluminada Pagán, Athina Papatheodoulou, Giuseppe Pappagallo, Isabel Pardo, Petr Pařil, Steffen U. Pauls, Marek Polášek, Pablo Rodríguez-Lozano, Robert J. Rolls, Maria Mar Sánchez-Montoya, Ana Savić, Oleksandra Shumilova, Kandikere R. Sridhar, Alisha Steward, Amina Taleb, Avi Uzan, Yefrin Valladares, Ross Vander Vorste, Nathan J. Waltham, Dominik H. Zak, and Annamaria Zoppini
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Science - Abstract
Abstract More than half of the world’s rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries on four continents. Both direct factors, such as nutrient and carbon availability, and indirect factors such as climate influence the local biodiversity of most taxa. Limited resource availability and prolonged dry phases favor oligotrophic microbial taxa. Co-variation among taxa, particularly Bacteria, Fungi, Algae and Protozoa, explain more spatial variation in community composition than dispersal or environmental gradients. This finding suggests that biotic interactions or unmeasured ecological and evolutionary factors may strongly influence communities during dry phases, altering biodiversity responses to global changes.
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- 2024
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36. Economic analysis of digital motor rehabilitation technologies: a systematic review
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Koffi Adzinyo Agbemanyole, Kokouvi Geovani Agbohessou, Christelle Pons, Philippe Lenca, Olivier Rémy-Néris, and Myriam Le Goff-Pronost
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Cost-effectiveness analysis ,Disability ,Rehabilitation technologies ,QALY ,Systematic review ,Medicine (General) ,R5-920 - Abstract
Abstract Rehabilitation technologies offer promising opportunities for interventions for patients with motor disabilities. However, their use in routine care remains limited due to their high cost and persistent doubts about their cost-effectiveness. Providing solid evidence of the economic efficiency of rehabilitation technologies would help dispel these doubts in order to better take advantage of these technologies. In this context, this systematic review aimed to examine the cost-effectiveness of rehabilitation interventions based on the use of digital technologies. In total, 660 articles published between 2011 and 2021 were identified, of which eleven studies met all the inclusion criteria. Of these eleven studies, seven proved to be cost-effective, while four were not. Four studies used cost-utility analyses (CUAs) and seven used cost-minimization analyses (CMAs). The majority (ten studies) focused on the rehabilitation of the upper and/or lower limbs after a stroke, while only one study examined the rehabilitation of the lower limbs after knee arthroplasty. Regarding the evaluated devices, seven studies analyzed the cost-effectiveness of robotic rehabilitation and four analyzed rehabilitation with virtual reality.The assessment of the quality of the included studies using the CHEERS (Consolidated Health Economic Evaluation Reporting Standards) suggested that the quality was related to the economic analysis method: all studies that adopted a cost-utility analysis obtained a high quality score (above 80%), while the quality scores of the cost-minimization analyses were average, with the highest score obtained by a CMA being 72%. The average quality score of all the articles was 75%, ranging between 52 and 100. Of the four studies with a considering score, two concluded that there was equivalence between the intervention and conventional care in terms of cost-effectiveness, one concluded that the intervention dominated, while the last one concluded that usual care dominated. This suggests that even considering the quality of the included studies, rehabilitation interventions based on digital technologies remain cost-effective, they improved health outcomes and quality of life for patients with motor disorders while also allowing cost savings.
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- 2024
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37. Helicobacter pylori associated primary cutaneous nodular amyloidosis improvement through debulking and cauterization
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Victoria Garfinkel, BSA and Heather Woodworth Goff, MD, MPH
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Helicobacter pylori ,Helicobacter pylori with cutaneous involvement ,primary cutaneous amyloidosis ,primary cutaneous nodular amyloidosis ,primary cutaneous nodular amyloidosis and infection ,primary cutaneous nodular amyloidosis and treatment ,Dermatology ,RL1-803 - Published
- 2024
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38. Co-producing age-friendly community interventions
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Goff, Mhorag, primary and Doran, Patty, additional
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- 2024
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39. Sartre and Honneth on conflict and recognition
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Le Goff, Alice, primary
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- 2024
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40. Deepening critical theory
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Bankovsky, Miriam, primary and Le Goff, Alice, additional
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- 2024
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41. Language Matters
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Knutson, Douglas, primary, Goldbach, Chloe, additional, Kler, Satveer, additional, Rodríguez-Ordóñez, Itxaso, additional, McDurmon, Parker, additional, and Goff, Benton, additional
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- 2024
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42. Get creative: Bird photography doesn't have to follow a documentary approach, says Martin Goff, so get creative with your shots
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Goff, Martin
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Photography - Abstract
Bird photography is often seen as a more representational genre rather than an interpretive one, so experimentation with different styles tends to be less common. Unlike many other genres of [...]
- Published
- 2024
43. Computation Efficient Structure-Aware PSI from Incremental Function Secret Sharing.
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Gayathri Garimella, Benjamin Goff, and Peihan Miao 0001
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- 2024
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44. Improving Efficiency of Evolving Robot Designs via Self-Adaptive Learning Cycles and an Asynchronous Architecture.
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Leni K. Le Goff and Emma Hart
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- 2024
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45. Control Allocation for Optimal and Resilient Operation of the MMC.
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Grégoire Le Goff, Marc Bodson, and Maurice Fadel
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- 2024
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46. A Stochastic Expectation Maximization Algorithm for the Estimation of Wastewater Treatment Plant Ammonium Concentration.
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Victor Bertret, Roman Le Goff Latimier, and Valérie Monbet
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- 2024
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47. Computation Efficient Structure-Aware PSI from Incremental Function Secret Sharing
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Garimella, Gayathri, Goff, Benjamin, Miao, Peihan, Goos, Gerhard, Series Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Reyzin, Leonid, editor, and Stebila, Douglas, editor
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- 2024
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48. Formal Definition of Hexahedral Blocking operations Using n-G-Maps
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Postat, Valentin, Goff, Nicolas Le, Calderan, Simon, Ledoux, Franck, Hutzler, Guillaume, Barth, Timothy J., Series Editor, Griebel, Michael, Series Editor, Keyes, David E., Series Editor, Nieminen, Risto M., Series Editor, Roose, Dirk, Series Editor, Schlick, Tamar, Series Editor, Ruiz-Gironés, Eloi, editor, Sevilla, Rubén, editor, and Moxey, David, editor
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- 2024
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49. The Case for Panpsychism
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Goff, Philip, Walach, Harald, Series Editor, Schmidt, Stefan, Series Editor, Schooler, Jonathan, Editorial Board Member, Beauregard, Mario, Editorial Board Member, Forman, Robert, Editorial Board Member, Wallace, B. Alan, Editorial Board Member, Satsangi, Prem Saran, editor, Horatschek, Anna Margaretha, editor, and Srivastav, Anand, editor
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- 2024
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50. Reactivation of Epstein–Barr virus among intensive care patients: a prospective observational study
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Guiouillier, François, Derely, Jean, Salvadori, Alexandre, Pochard, Jonas, Le Goff, Jérôme, Martinez, Thibault, Raffin, Florent, Laitselart, Philippe, Beaucreux, Charlotte, Priou, Sonia, Conan, Pierre-Louis, Foissaud, Vincent, Servonnet, Aurélie, Vest, Philippe, Boutonnet, Mathieu, de Rudnicki, Stéphane, Bigaillon, Christine, and Libert, Nicolas
- Published
- 2024
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