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1. Diploid-dominant life cycles characterize the early evolution of Fungi

Author

Amses, Kevin R, Simmons, D Rabern, Longcore, Joyce E, Mondo, Stephen J, Seto, Kensuke, Jerônimo, Gustavo H, Bonds, Anne E, Quandt, C Alisha, Davis, William J, Chang, Ying, Federici, Brian A, Kuo, Alan, LaButti, Kurt, Pangilinan, Jasmyn, Andreopoulos, William, Tritt, Andrew, Riley, Robert, Hundley, Hope, Johnson, Jenifer, Lipzen, Anna, Barry, Kerrie, Lang, B Franz, Cuomo, Christina A, Buchler, Nicolas E, Grigoriev, Igor V, Spatafora, Joseph W, Stajich, Jason E, and James, Timothy Y

Subjects
Microbiology, Biological Sciences, Evolutionary Biology, Genetics, Diploidy, Fungi, Genome, Fungal, Life Cycle Stages, Phylogeny, life cycle evolution, phylogenomics, aquatic fungi, plesiomorphy
Abstract

Most of the described species in kingdom Fungi are contained in two phyla, the Ascomycota and the Basidiomycota (subkingdom Dikarya). As a result, our understanding of the biology of the kingdom is heavily influenced by traits observed in Dikarya, such as aerial spore dispersal and life cycles dominated by mitosis of haploid nuclei. We now appreciate that Fungi comprises numerous phylum-level lineages in addition to those of Dikarya, but the phylogeny and genetic characteristics of most of these lineages are poorly understood due to limited genome sampling. Here, we addressed major evolutionary trends in the non-Dikarya fungi by phylogenomic analysis of 69 newly generated draft genome sequences of the zoosporic (flagellated) lineages of true fungi. Our phylogeny indicated five lineages of zoosporic fungi and placed Blastocladiomycota, which has an alternation of haploid and diploid generations, as branching closer to the Dikarya than to the Chytridiomyceta. Our estimates of heterozygosity based on genome sequence data indicate that the zoosporic lineages plus the Zoopagomycota are frequently characterized by diploid-dominant life cycles. We mapped additional traits, such as ancestral cell-cycle regulators, cell-membrane- and cell-wall-associated genes, and the use of the amino acid selenocysteine on the phylogeny and found that these ancestral traits that are shared with Metazoa have been subject to extensive parallel loss across zoosporic lineages. Together, our results indicate a gradual transition in the genetics and cell biology of fungi from their ancestor and caution against assuming that traits measured in Dikarya are typical of other fungal lineages.

Published
2022

2. Interleukin (IL)-1/IL-6-Inhibitor–Associated Drug Reaction With Eosinophilia and Systemic Symptoms (DReSS) in Systemic Inflammatory Illnesses

Author

Aamir, R., Abulaban, K., Adams, A., Lapsia, C. Aguiar, Akinsete, A., Akoghlanian, S., Al Manaa, M., AlBijadi, A., Allenspach, E., Almutairi, A., Alperin, R., Amarilyo, G., Ambler, W., Amoruso, M., Angeles-Han, S., Ardoin, S., Armendariz, S., Asfaw, L., Aviran Dagan, N., Bacha, C., Balboni, I., Balevic, S., Ballinger, S., Baluta, S., Barillas-Arias, L., Basiaga, M., Baszis, K., Baxter, S., Becker, M., Begezda, A., Behrens, E., Beil, E., Benseler, S., Bermudez-Santiago, L., Bernal, W., Bigley, T., Bingham, C., Binstadt, B., Black, C., Blackmon, B., Blakley, M., Bohnsack, J., Boneparth, A., Bradfield, H., Bridges, J., Brooks, E., Brothers, M., Brunner, H., Buckley, L., Buckley, M., Bukulmez, H., Bullock, D., Canna, S., Cannon, L., Canny, S., Cartwright, V., Cassidy, E., Castro, D., Chalom, E., Chang, J., Chang, M., Chang-Hoftman, A., Chen, A., Chiraseveenuprapund, P., Ciaglia, K., Co, D., Cohen, E., Collinge, J., Conlon, H., Connor, R., Cook, K., Cooper, A., Cooper, J., Corbin, K., Correll, C., Cron, R., Curry, M., Dalrymple, A., Datyner, E., Davis, T., De Ranieri, D., Dean, J., DeCoste, C., Dedeoglu, F., DeGuzman, M., Delnay, N., DeSantis, E., Devine, R., Dhalla, M., Dhanrajani, A., Dissanayake, D., Dizon, B., Drapeau, N., Drew, J., Driest, K., Du, Q., Duncan, E., Dunnock, K., Durkee, D., Dvergsten, J., Eberhard, A., Ede, K., Edelheit, B., Edens, C., El Tal, T., Elder, M., Elzaki, Y., Fadrhonc, S., Failing, C., Fair, D., Favier, L., Feldman, B., Fennell, J., Ferguson, P., Ferguson, I., Figueroa, C., Flanagan, E., Fogel, L., Fox, E., Fox, M., Franklin, L., Fuhlbrigge, R., Fuller, J., Furey, M., Futch-West, T., Gagne, S., Gennaro, V., Gerstbacher, D., Gilbert, M., Gironella, A., Glaser, D., Goh, I., Goldsmith, D., Gorry, S., Goswami, N., Gottlieb, B., Graham, T., Grevich, S., Griffin, T., Grim, A., Grom, A., Guevara, M., Hahn, T., Halyabar, O., Hamda Natur, M., Hammelev, E., Hammond, T., Harel, L., Harris, J., Harry, O., Hausmann, J., Hay, A., Hays, K., Hayward, K., Henderson, L., Henrickson, M., Hersh, A., Hickey, K., Hiraki, L., Hiskey, M., Hobday, P., Hoffart, C., Holland, M., Hollander, M., Hong, S., Horton, D., Horwitz, M., Hsu, J., Huber, A., Huberts, A., Huggins, J., Huie, L., Hui-Yuen, J., Ibarra, M., Imlay, A., Imundo, L., Inman, C., Jackson, A., James, K., Janow, G., Jared, S., Jiang, Y., Johnson, L., Johnson, N., Jones, J., Kafisheh, D., Kahn, P., Kaidar, K., Kasinathan, S., Kaur, R., Kessler, E., Kienzle, B., Kim, S., Kimura, Y., Kingsbury, D., Kitcharoensakkul, M., Klausmeier, T., Klein, K., Klein-Gitelman, M., Knight, A., Kovalick, L., Kramer, S., Kremer, C., Kudas, O., LaFlam, T., Lang, B., Lapidus, S., Lapin, B., Lasky, A., Lawler, C., Lawson, E., Laxer, R., Lee, P., Lee, T., Lee, A., Leisinger, E., Lentini, L., Lerman, M., Levinsky, Y., Levy, D., Li, S., Lieberman, S., Lim, L., Limenis, E., Lin, C., Ling, N., Lionetti, G., Livny, R., Lloyd, M., Lo, M., Long, A., Lopez-Peña, M., Lovell, D., Luca, N., Lvovich, S., Lytch, A., Ma, M., Machado, A., MacMahon, J., Madison, J., Mannion, M., Manos, C., Mansfield, L., Marston, B., Mason, T., Matchett, D., McAllister, L., McBrearty, K., McColl, J., McCurdy, D., McDaniels, K., McDonald, J., Meidan, E., Mellins, E., Mian, Z., Miettunen, P., Miller, M., Milojevic, D., Mitacek, R., Modica, R., Mohan, S., Moore, T., Moore, K., Moorthy, L., Moreno, J., Morgan, E., Moyer, A., Murante, B., Murphy, A., Muscal, E., Mwizerwa, O., Najafi, A., Nanda, K., Nasah, N., Nassi, L., Nativ, S., Natter, M., Nearanz, K., Neely, J., Newhall, L., Nguyen, A., Nigrovic, P., Nocton, J., Nolan, B., Nowicki, K., Oakes, R., Oberle, E., Ogbonnaya-Whittesley, S., Ogbu, E., Oliver, M., Olveda, R., Onel, K., Orandi, A., Padam, J., Paller, A., Pan, N., Pandya, J., Panupattanapong, S., Toledano, A. Pappo, Parsons, A., Patel, J., Patel, P., Patrick, A., Patrizi, S., Paul, S., Perfetto, J., Perron, M., Peskin, M., Ponder, L., Pooni, R., Prahalad, S., Puplava, B., Quinlan-Waters, M., Rabinovich, C., Rafko, J., Rahimi, H., Rampone, K., Ramsey, S., Randell, R., Ray, L., Reed, A., Reid, H., Reiff, D., Richins, S., Riebschleger, M., Rife, E., Riordan, M., Riskalla, M., Robinson, A., Robinson, L., Rodgers, L., Rodriquez, M., Rogers, D., Ronis, T., Rosado, A., Rosenkranz, M., Rosenwasser, N., Rothermel, H., Rothman, D., Rothschild, E., Roth-Wojcicki, E., Rouster-Stevens, K., Rubinstein, T., Rupp, J., Ruth, N., Sabbagh, S., Sadun, R., Santiago, L., Saper, V., Sarkissian, A., Scalzi, L., Schahn, J., Schikler, K., Schlefman, A., Schmeling, H., Schmitt, E., Schneider, R., Schulert, G., Schultz, K., Schutt, C., Seper, C., Sheets, R., Shehab, A., Shenoi, S., Sherman, M., Shirley, J., Shishov, M., Siegel, D., Singer, N., Sivaraman, V., Sloan, E., Smith, C., Smith, J., Smitherman, E., Soep, J., Son, Mary B., Sosna, D., Spencer, C., Spiegel, L., Spitznagle, J., Srinivasalu, H., Stapp, H., Steigerwald, K., Stephens, A., Sterba Rakovchik, Y., Stern, S., Stevens, B., Stevenson, R., Stewart, K., Stewart, W., Stingl, C., Stoll, M., Stringer, E., Sule, S., Sullivan, J., Sundel, R., Sutter, M., Swaffar, C., Swayne, N., Syed, R., Symington, T., Syverson, G., Szymanski, A., Taber, S., Tal, R., Tambralli, A., Taneja, A., Tanner, T., Tarvin, S., Tate, L., Taxter, A., Taylor, J., Tesher, M., Thakurdeen, T., Theisen, A., Thomas, B., Thomas, L., Thomas, N., Ting, T., Todd, C., Toib, D., Torok, K., Tory, H., Toth, M., Tse, S., Tsin, C., Twachtman-Bassett, J., Twilt, M., Valcarcel, T., Valdovinos, R., Vallee, A., Van Mater, H., Vandenbergen, S., Vannoy, L., Varghese, C., Vasquez, N., Vega-Fernandez, P., Velez, J., Verbsky, J., Verstegen, R., von Scheven, E., Vora, S., Wagner-Weiner, L., Wahezi, D., Waite, H., Walker, B., Walters, H., Waterfield, M., Waters, A., Weiser, P., Weiss, P., Weiss, J., Wershba, E., Westheuser, V., White, A., Widrick, K., Williams, C., Wong, S., Woolnough, L., Wright, T., Wu, E., Yalcindag, A., Yasin, S., Yeung, R., Yomogida, K., Zeft, A., Zhang, Y., Zhao, Y., Zhu, A., Saper, Vivian E., Tian, Lu, Verstegen, Ruud H.J., Conrad, Carol K., Cidon, Michal, Hopper, Rachel K., Kuo, Christin S., Osoegawa, Kazutoyo, Baszis, Kevin, Bingham, Catherine A., Ferguson, Ian, Hahn, Timothy, Horne, Annacarin, Isupova, Eugenia A., Jones, Jordan T., Kasapcopur, Özgür, Klein-Gitelman, Marisa S., Kostik, Mikhail M., Ozen, Seza, Phadke, Omkar, Prahalad, Sampath, Randell, Rachel L., Sener, Seher, Stingl, Cory, Abdul-Aziz, Rabheh, Akoghlanian, Shoghik, Al Julandani, Dalila, Alvarez, Marcela B., Bader-Meunier, Brigitte, Balay-Dustrude, Erin E., Balboni, Imelda, Baxter, Sarah K., Berard, Roberta A., Bhattad, Sagar, Bolaria, Roxana, Boneparth, Alexis, Cassidy, Elaine A., Co, Dominic O., Collins, Kathleen P., Dancey, Paul, Dickinson, Aileen M., Edelheit, Barbara S., Espada, Graciela, Flanagan, Elaine R., Imundo, Lisa F., Jindal, Ankur K., Kim, Hyoun-Ah, Klaus, Günter, Lake, Carol, Lapin, W. Blaine, Lawson, Erica F., Marmor, Itay, Mombourquette, Joy, Ogunjimi, Benson, Olveda, Rebecca, Ombrello, Michael J., Onel, Karen, Poholek, Catherine, Ramanan, Athimalaipet V., Ravelli, Angelo, Reinhardt, Adam, Robinson, Amanda D., Rouster-Stevens, Kelly, Saad, Nadine, Schneider, Rayfel, Selmanovic, Velma, Sefic Pasic, Irmina, Shenoi, Susan, Shilo, Natalie R., Soep, Jennifer B., Sura, Angeli, Taber, Sarah F., Tesher, Melissa, Tibaldi, Jessica, Torok, Kathryn S., Tsin, Cathy Mei, Vasquez-Canizares, Natalia, Villacis Nunez, Diana S., Way, Emily E., Whitehead, Benjamin, Zemel, Lawrence S., Sharma, Surbhi, Fernández-Viña, Marcelo A., and Mellins, Elizabeth D.

Published
2024
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3. Evolution of zygomycete secretomes and the origins of terrestrial fungal ecologies

Author

Chang, Ying, Wang, Yan, Mondo, Stephen, Ahrendt, Steven, Andreopoulos, William, Barry, Kerrie, Beard, Jeff, Benny, Gerald L, Blankenship, Sabrina, Bonito, Gregory, Cuomo, Christina, Desiro, Alessandro, Gervers, Kyle A, Hundley, Hope, Kuo, Alan, LaButti, Kurt, Lang, B Franz, Lipzen, Anna, O'Donnell, Kerry, Pangilinan, Jasmyn, Reynolds, Nicole, Sandor, Laura, Smith, Matthew E, Tsang, Adrian, Grigoriev, Igor V, Stajich, Jason E, and Spatafora, Joseph W

Subjects
Microbiology, Biological Sciences, Evolutionary Biology, 2.2 Factors relating to the physical environment, Biological sciences, microbial genomics, microbial metabolism, microbiology, omics
Abstract

Fungi survive in diverse ecological niches by secreting proteins and other molecules into the environment to acquire food and interact with various biotic and abiotic stressors. Fungal secretome content is, therefore, believed to be tightly linked to fungal ecologies. We sampled 132 genomes from the early-diverging terrestrial fungal lineage zygomycetes (Mucoromycota and Zoopagomycota) and characterized their secretome composition. Our analyses revealed that phylogeny played an important role in shaping the secretome composition of zygomycete fungi with trophic mode contributing a smaller amount. Reconstruction of the evolution of secreted digestive enzymes revealed lineage-specific expansions, indicating that Mucoromycota and Zoopagomycota followed different trajectories early in their evolutionary history. We identified the presence of multiple pathogenicity-related proteins in the lineages known as saprotrophs, suggesting that either the ecologies of these fungi are incompletely known, and/or that these pathogenicity-related proteins have important functions associated with saprotrophic ecologies, both of which invite further investigation.

Published
2022

4. Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes

Author

Valach, Matus, Moreira, Sandrine, Petitjean, Celine, Benz, Corinna, Butenko, Anzhelika, Flegontova, Olga, Nenarokova, Anna, Prokopchuk, Galina, Batstone, Tom, Lapébie, Pascal, Lemogo, Lionnel, Sarrasin, Matt, Stretenowich, Paul, Tripathi, Pragya, Yazaki, Euki, Nara, Takeshi, Henrissat, Bernard, Lang, B. Franz, Gray, Michael W., Williams, Tom A., Lukeš, Julius, and Burger, Gertraud

Published
2023
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5. Mitochondrial genomes of the human pathogens Coccidioides immitis and Coccidioides posadasii

Author

de Melo Teixeira, Marcus, Lang, B Franz, Matute, Daniel R, Stajich, Jason E, and Barker, Bridget M

Subjects
Biological Sciences, Genetics, Infectious Diseases, Rare Diseases, Valley Fever, Humans, Coccidioides, Phylogeny, Genome, Mitochondrial, Coccidioidomycosis, Valley fever, Onygenales, coccidioidomycosis, mitochondrial genomes, phylogenetics, fungal pathogen, group I and II introns, Biochemistry and cell biology, Statistics
Abstract

Fungal mitochondrial genomes encode genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and the molecule has been used as a molecular marker for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, approximately 150 Coccidioides isolates have been sequenced to infer patterns of variation in nuclear genomes. However, less attention has been given to the mitochondrial genomes of Coccidioides. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains of C. posadasii and C. immitis, as well as assess population variation among 77 selected genomes. The sizes of the circular-mapping molecules are 68.2 Kb in C. immitis and 75.1 Kb in C. posadasii. We identify 14 mitochondrial protein-coding genes common to most fungal mitochondria, which are largely syntenic across different populations and species of Coccidioides. Both Coccidioides species are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparisons of mitochondrial and nuclear genomes show extensive phylogenetic discordance suggesting that the evolution of the two types of genetic material is not identical. This work represents the first assessment of mitochondrial genomes among isolates of both species of Coccidioides, and provides a foundation for future functional work.

Published
2021

6. The mitochondrial genomes of the human pathogens Coccidioides immitis and C. posadasii.

Author

de Melo Teixeira, Marcus, Lang, B, Matute, Daniel, Barker, Bridget, and Stajich, Jason

Subjects
Coccidioides, Onygenales, Valley fever, coccidioidomycosis, fungal pathogen, group I and II introns, mitochondrial genomes, phylogenetics
Abstract

Fungal mitochondrial genomes encode genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and the molecule has been used as a molecular marker for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, approximately 150 Coccidioides isolates have been sequenced to infer patterns of variation of nuclear genomes. However, less attention has been given to the mitochondrial genomes of Coccidioides. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains of C. posadasii and C. immitis, as well as assess population variation among 77 selected genomes. The sizes of the circular-mapping molecules are 68.2 Kb in C. immitis and 75.1 Kb in C. posadasii. We identify fourteen mitochondrial protein-coding genes common to most fungal mitochondria, which are largely syntenic across different populations and species of Coccidioides. Both Coccidioides species are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparisons of mitochondrial and nuclear genomes show extensive phylogenetic discordance suggesting that the evolution of the two types of genetic material is not identical. This work represents the first assessment of mitochondrial genomes among isolates of both species of Coccidioides, and provides a foundation for future functional work.

Published
2021

8. 99% beta factor and directional coupling of quantum dots to fast light in photonic crystal waveguides determined by hyperspectral imaging

Author

Scarpelli, L., Lang, B., Masia, F., Beggs, D. M., Muljarov, E. A., Young, A. B., Oulton, R., Kamp, M., Höfling, S., Schneider, C., and Langbein, W.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Physics - Optics, Quantum Physics
Abstract

Spontaneous emission from excitonic transitions in InAs/GaAs quantum dots embedded in photonic crystal waveguides at 5K into non-guided and guided modes is determined by direct hyperspectral imaging. This enables measurement of the absolute coupling efficiency into the guided modes, the beta-factor, directly, without assumptions on decay rates used previously. Notably, we found beta-factors above 90% over a wide spectral range of 40meV in the fast light regime, reaching a maximum of (99 $\pm$ 1)%. We measure the directional emission of the circularly polarized transitions in a magnetic field into counter-propagating guided modes, to deduce the mode circularity at the quantum dot sites. We find that points of high directionality, up to 97%, correlate with a reduced beta-factor, consistent with their positions away from the mode field antinode. By comparison with calibrated finite-difference time-domain simulations, we use the emission energy, mode circularity and beta-factor to estimate the quantum dot position inside the photonic crystal waveguide unit cell.

Published
2019
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10. Structural characterization and evolutionary analyses of the Coccidioides immitis and Coccidioides posadasii mitochondrial genomes

Author

de Melo Teixeira, Marcus, Lang, B Franz, Matute, Daniel R, Stajich, Jason E, and Barker, Bridget

Subjects
Biological Sciences, Genetics, Emerging Infectious Diseases, Infectious Diseases, Rare Diseases, Valley Fever
Abstract

Fungal mitochondrial genomes encode for genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and these genes have been used as molecular markers for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, almost one hundred Coccidioides strains have been sequenced. The focus of these studies has been exclusively to infer patterns of variation of nuclear genomes (nucDNA). However, their mitochondrial genomes (mtDNA) have not been studied. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains of C. posadasii and C. immitis , as well as assess population variation among 77 published genomes. The circular-mapping mtDNA molecules are 68.2 Kb in C. immitis and 75.1 Kb in C. posadasii . We identified the fourteen mitochondrial protein-coding genes common to most fungal mitochondria, including genes encoding the small and large ribosomal RNAs ( rns and rnl ), the RNA subunit of RNAse P ( rnp B), and 26 tRNAs organized in polycistronic transcription units, which are mostly syntenic across different populations and species of Coccidioides . Both Coccidioides species are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparison of the mtDNA and nucDNA genomes shows discordance, possibly due to differences in patterns of inheritance. In summary, this work represents the first complete assessment of mitochondrial genomes among several isolates of both species of Coccidioides , and provides a foundation for future functional work.

Published
2020

11. Health Equity Implications of Missing Data Among Youths With Childhood‐Onset Systemic Lupus Erythematosus: A Proof‐of‐Concept Study in the Childhood Arthritis and Rheumatology Research Alliance Registry

Author

Woo, Jennifer M. P., Simmonds, Faith, Dennos, Anne, Son, Mary Beth F., Lewandowski, Laura B., Rubinstein, Tamar B., Abel, N., Abulaban, K., Adams, A., Adams, M., Agbayani, R., Aiello, J., Akoghlanian, S., Alejandro, C., Allenspach, E., Alperin, R., Alpizar, M., Amarilyo, G., Ambler, W., Anderson, E., Ardoin, S., Armendariz, S., Baker, E., Balboni, I., Balevic, S., Ballenger, L., Ballinger, S., Balmuri, N., Barbar‐Smiley, F., Barillas‐Arias, L., Basiaga, M., Baszis, K., Becker, M., Bell‐Brunson, H., Beltz, E., Benham, H., Benseler, S., Bernal, W., Beukelman, T., Bigley, T., Binstadt, B., Black, C., Blakley, M., Bohnsack, J., Boland, J., Boneparth, A., Bowman, S., Bracaglia, C., Brooks, E., Brothers, M., Brown, A., Brunner, H., Buckley, M., Buckley, M., Bukulmez, H., Bullock, D., Cameron, B., Canna, S., Cannon, L., Carper, P., Cartwright, V., Cassidy, E., Cerracchio, L., Chalom, E., Chang, J., Chang‐Hoftman, A., Chauhan, V., Chira, P., Chinn, T., Chundru, K., Clairman, H., Co, D., Confair, A., Conlon, H., Connor, R., Cooper, A., Cooper, J., Cooper, S., Correll, C., Corvalan, R., Costanzo, D., Cron, R., Curiel‐Duran, L., Curington, T., Curry, M., Dalrymple, A., Davis, A., Davis, C., Davis, C., Davis, T., De Benedetti, F., De Ranieri, D., Dean, J., Dedeoglu, F., DeGuzman, M., Delnay, N., Dempsey, V., DeSantis, E., Dickson, T., Dingle, J., Donaldson, B., Dorsey, E., Dover, S., Dowling, J., Drew, J., Driest, K., Du, Q., Duarte, K., Durkee, D., Duverger, E., Dvergsten, J., Eberhard, A., Eckert, M., Ede, K., Edelheit, B., Edens, C., Edens, C., Edgerly, Y., Elder, M., Ervin, B., Fadrhonc, S., Failing, C., Fair, D., Falcon, M., Favier, L., Federici, S., Feldman, B., Fennell, J., Ferguson, I., Ferguson, P., Ferreira, B., Ferrucho, R., Fields, K., Finkel, T., Fitzgerald, M., Fleming, C., Flynn, O., Fogel, L., Fox, E., Fox, M., Franco, L., Freeman, M., Fritz, K., Froese, S., Fuhlbrigge, R., Fuller, J., George, N., Gerhold, K., Gerstbacher, D., Gilbert, M., Gillispie‐Taylor, M., Giverc, E., Godiwala, C., Goh, I., Goheer, H., Goldsmith, D., Gotschlich, E., Gotte, A., Gottlieb, B., Gracia, C., Graham, T., Grevich, S., Griffin, T., Griswold, J., Grom, A., Guevara, M., Guittar, P., Guzman, M., Hager, M., Hahn, T., Halyabar, O., Hammelev, E., Hance, M., Hanson, A., Harel, L., Haro, S., Harris, J., Harry, O., Hartigan, E., Hausmann, J., Hay, A., Hayward, K., Heiart, J., Hekl, K., Henderson, L., Henrickson, M., Hersh, A., Hickey, K., Hill, P., Hillyer, S., Hiraki, L., Hiskey, M., Hobday, P., Hoffart, C., Holland, M., Hollander, M., Hong, S., Horwitz, M., Hsu, J., Huber, A., Huggins, J., Hui‐Yuen, J., Hung, C., Huntington, J., Huttenlocher, A., Ibarra, M., Imundo, L., Inman, C., Insalaco, A., Jackson, A., Jackson, S., James, K., Janow, G., Jaquith, J., Jared, S., Johnson, N., Jones, J., Jones, J., Jones, J., Jones, K., Jones, S., Joshi, S., Jung, L., Justice, C., Justiniano, A., Karan, N., Kaufman, K., Kemp, A., Kessler, E., Khalsa, U., Kienzle, B., Kim, S., Kimura, Y., Kingsbury, D., Kitcharoensakkul, M., Klausmeier, T., Klein, K., Klein‐Gitelman, M., Kompelien, B., Kosikowski, A., Kovalick, L., Kracker, J., Kramer, S., Kremer, C., Lai, J., Lam, J., Lang, B., Lapidus, S., Lapin, B., Lasky, A., Latham, D., Lawson, E., Laxer, R., Lee, P., Lee, P., Lee, T., Lentini, L., Lerman, M., Levy, D., Li, S., Lieberman, S., Lim, L., Lin, C., Ling, N., Lingis, M., Lo, M., Lovell, D., Lowman, D., Luca, N., Lvovich, S., Madison, C., Madison, J., Manzoni, S. Magni, Malla, B., Maller, J., Malloy, M., Mannion, M., Manos, C., Marques, L., Martyniuk, A., Mason, T., Mathus, S., McAllister, L., McCarthy, K., McConnell, K., McCormick, E., McCurdy, D., Stokes, P. McCurdy, McGuire, S., McHale, I., McMonagle, A., McMullen‐Jackson, C., Meidan, E., Mellins, E., Mendoza, E., Mercado, R., Merritt, A., Michalowski, L., Miettunen, P., Miller, M., Milojevic, D., Mirizio, E., Misajon, E., Mitchell, M., Modica, R., Mohan, S., Moore, K., Moorthy, L., Morgan, S., Dewitt, E. Morgan, Moss, C., Moussa, T., Mruk, V., Murphy, A., Muscal, E., Nadler, R., Nahal, B., Nanda, K., Nasah, N., Nassi, L., Nativ, S., Natter, M., Neely, J., Nelson, B., Newhall, L., Ng, L., Nicholas, J., Nicolai, R., Nigrovic, P., Nocton, J., Nolan, B., Oberle, E., Obispo, B., OʼBrien, B., OʼBrien, T., Okeke, O., Oliver, M., Olson, J., OʼNeil, K., Onel, K., Orandi, A., Orlando, M., Osei‐Onomah, S., Oz, R., Pagano, E., Paller, A., Pan, N., Panupattanapong, S., Pardeo, M., Paredes, J., Parsons, A., Patel, J., Pentakota, K., Pepmueller, P., Pfeiffer, T., Phillippi, K., Phillippi, K., Marafon, D. Pires, Ponder, L., Pooni, R., Prahalad, S., Pratt, S., Protopapas, S., Puplava, B., Quach, J., Quinlan‐Waters, M., Rabinovich, C., Radhakrishna, S., Rafko, J., Raisian, J., Rakestraw, A., Ramirez, C., Ramsay, E., Ramsey, S., Randell, R., Reed, A., Reed, A., Reed, A., Reid, H., Remmel, K., Repp, A., Reyes, A., Richmond, A., Riebschleger, M., Ringold, S., Riordan, M., Riskalla, M., Ritter, M., Rivas‐Chacon, R., Robinson, A., Rodela, E., Rodriquez, M., Rojas, K., Ronis, T., Rosenkranz, M., Rosolowski, B., Rothermel, H., Rothman, D., Roth‐Wojcicki, E., Rouster‐Stevens, K., Rubinstein, T., Ruth, N., Saad, N., Sabbagh, S., Sacco, E., Sadun, R., Sandborg, C., Sanni, A., Santiago, L., Sarkissian, A., Savani, S., Scalzi, L., Schanberg, L., Scharnhorst, S., Schikler, K., Schlefman, A., Schmeling, H., Schmidt, K., Schmitt, E., Schneider, R., Schollaert‐Fitch, K., Schulert, G., Seay, T., Seper, C., Shalen, J., Sheets, R., Shelly, A., Shenoi, S., Shergill, K., Shirley, J., Shishov, M., Shivers, C., Silverman, E., Singer, N., Sivaraman, V., Sletten, J., Smith, A., Smith, C., Smith, J., Smith, J., Smitherman, E., Soep, J., Son, M., Spence, S., Spiegel, L., Spitznagle, J., Sran, R., Srinivasalu, H., Stapp, H., Steigerwald, K., Rakovchik, Y. Sterba, Stern, S., Stevens, A., Stevens, B., Stevenson, R., Stewart, K., Stingl, C., Stokes, J., Stoll, M., Stringer, E., Sule, S., Sumner, J., Sundel, R., Sutter, M., Syed, R., Syverson, G., Szymanski, A., Taber, S., Tal, R., Tambralli, A., Taneja, A., Tanner, T., Tapani, S., Tarshish, G., Tarvin, S., Tate, L., Taxter, A., Taylor, J., Terry, M., Tesher, M., Thatayatikom, A., Thomas, B., Tiffany, K., Ting, T., Tipp, A., Toib, D., Torok, K., Toruner, C., Tory, H., Toth, M., Tse, S., Tubwell, V., Twilt, M., Uriguen, S., Valcarcel, T., Van Mater, H., Vannoy, L., Varghese, C., Vasquez, N., Vazzana, K., Vehe, R., Veiga, K., Velez, J., Verbsky, J., Vilar, G., Volpe, N., von Scheven, E., Vora, S., Wagner, J., Wagner‐Weiner, L., Wahezi, D., Waite, H., Walker, J., Walters, H., Muskardin, T. Wampler, Waqar, L., Waterfield, M., Watson, M., Watts, A., Weiser, P., Weiss, J., Weiss, P., Wershba, E., White, A., Williams, C., Wise, A., Woo, J., Woolnough, L., Wright, T., Wu, E., Yalcindag, A., Yee, M., Yen, E., Yeung, R., Yomogida, K., Yu, Q., Zapata, R., Zartoshti, A., Zeft, A., Zeft, R., Zhang, Y., Zhao, Y., Zhu, A., and Zic, C.

Published
2023
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12. Childhood‐Onset Lupus Nephritis in the Childhood Arthritis and Rheumatology Research Alliance Registry: Short‐Term Kidney Status and Variation in Care

Author

Smitherman, Emily A., Chahine, Rouba A., Beukelman, Timothy, Lewandowski, Laura B., Rahman, A. K. M. Fazlur, Wenderfer, Scott E., Curtis, Jeffrey R., Hersh, Aimee O., Abel, N., Abulaban, K., Adams, A., Adams, M., Agbayani, R., Aiello, J., Akoghlanian, S., Alejandro, C., Allenspach, E., Alperin, R., Alpizar, M., Amarilyo, G., Ambler, W., Anderson, E., Ardoin, S., Armendariz, S., Baker, E., Balboni, I., Balevic, S., Ballenger, L., Ballinger, S., Balmuri, N., Barbar‐Smiley, F., Barillas‐Arias, L., Basiaga, M., Baszis, K., Becker, M., Bell‐Brunson, H., Beltz, E., Benham, H., Benseler, S., Bernal, W., Beukelman, T., Bigley, T., Binstadt, B., Black, C., Blakley, M., Bohnsack, J., Boland, J., Boneparth, A., Bowman, S., Bracaglia, C., Brooks, E., Brothers, M., Brown, A., Brunner, H., Buckley, M., Buckley, M., Bukulmez, H., Bullock, D., Cameron, B., Canna, S., Cannon, L., Carper, P., Cartwright, V., Cassidy, E., Cerracchio, L., Chalom, E., Chang, J., Chang‐Hoftman, A., Chauhan, V., Chira, P., Chinn, T., Chundru, K., Clairman, H., Co, D., Confair, A., Conlon, H., Connor, R., Cooper, A., Cooper, J., Cooper, S., Correll, C., Corvalan, R., Costanzo, D., Cron, R., Curiel‐Duran, L., Curington, T., Curry, M., Dalrymple, A., Davis, A., Davis, C., Davis, C., Davis, T., De Benedetti, F., De Ranieri, D., Dean, J., Dedeoglu, F., DeGuzman, M., Delnay, N., Dempsey, V., DeSantis, E., Dickson, T., Dingle, J., Donaldson, B., Dorsey, E., Dover, S., Dowling, J., Drew, J., Driest, K., Du, Q., Duarte, K., Durkee, D., Duverger, E., Dvergsten, J., Eberhard, A., Eckert, M., Ede, K., Edelheit, B., Edens, C., Edens, C., Edgerly, Y., Elder, M., Ervin, B., Fadrhonc, S., Failing, C., Fair, D., Falcon, M., Favier, L., Federici, S., Feldman, B., Fennell, J., Ferguson, I., Ferguson, P., Ferreira, B., Ferrucho, R., Fields, K., Finkel, T., Fitzgerald, M., Fleming, C., Flynn, O., Fogel, L., Fox, E., Fox, M., Franco, L., Freeman, M., Fritz, K., Froese, S., Fuhlbrigge, R., Fuller, J., George, N., Gerhold, K., Gerstbacher, D., Gilbert, M., Gillispie‐Taylor, M., Giverc, E., Godiwala, C., Goh, I., Goheer, H., Goldsmith, D., Gotschlich, E., Gotte, A., Gottlieb, B., Gracia, C., Graham, T., Grevich, S., Griffin, T., Griswold, J., Grom, A., Guevara, M., Guittar, P., Guzman, M., Hager, M., Hahn, T., Halyabar, O., Hammelev, E., Hance, M., Hanson, A., Harel, L., Haro, S., Harris, J., Harry, O., Hartigan, E., Hausmann, J., Hay, A., Hayward, K., Heiart, J., Hekl, K., Henderson, L., Henrickson, M., Hersh, A., Hickey, K., Hill, P., Hillyer, S., Hiraki, L., Hiskey, M., Hobday, P., Hoffart, C., Holland, M., Hollander, M., Hong, S., Horwitz, M., Hsu, J., Huber, A., Huggins, J., Hui‐Yuen, J., Hung, C., Huntington, J., Huttenlocher, A., Ibarra, M., Imundo, L., Inman, C., Insalaco, A., Jackson, A., Jackson, S., James, K., Janow, G., Jaquith, J., Jared, S., Johnson, N., Jones, J., Jones, J., Jones, J., Jones, K., Jones, S., Joshi, S., Jung, L., Justice, C., Justiniano, A., Karan, N., Kaufman, K., Kemp, A., Kessler, E., Khalsa, U., Kienzle, B., Kim, S., Kimura, Y., Kingsbury, D., Kitcharoensakkul, M., Klausmeier, T., Klein, K., Klein‐Gitelman, M., Kompelien, B., Kosikowski, A., Kovalick, L., Kracker, J., Kramer, S., Kremer, C., Lai, J., Lam, J., Lang, B., Lapidus, S., Lapin, B., Lasky, A., Latham, D., Lawson, E., Laxer, R., Lee, P., Lee, P., Lee, T., Lentini, L., Lerman, M., Levy, D., Li, S., Lieberman, S., Lim, L., Lin, C., Ling, N., Lingis, M., Lo, M., Lovell, D., Lowman, D., Luca, N., Lvovich, S., Madison, C., Madison, J., Manzoni, S. Magni, Malla, B., Maller, J., Malloy, M., Mannion, M., Manos, C., Marques, L., Martyniuk, A., Mason, T., Mathus, S., McAllister, L., McCarthy, K., McConnell, K., McCormick, E., McCurdy, D., Stokes, P. McCurdy, McGuire, S., McHale, I., McMonagle, A., McMullen‐Jackson, C., Meidan, E., Mellins, E., Mendoza, E., Mercado, R., Merritt, A., Michalowski, L., Miettunen, P., Miller, M., Milojevic, D., Mirizio, E., Misajon, E., Mitchell, M., Modica, R., Mohan, S., Moore, K., Moorthy, L., Morgan, S., Dewitt, E. Morgan, Moss, C., Moussa, T., Mruk, V., Murphy, A., Muscal, E., Nadler, R., Nahal, B., Nanda, K., Nasah, N., Nassi, L., Nativ, S., Natter, M., Neely, J., Nelson, B., Newhall, L., Ng, L., Nicholas, J., Nicolai, R., Nigrovic, P., Nocton, J., Nolan, B., Oberle, E., Obispo, B., OʼBrien, B., OʼBrien, T., Okeke, O., Oliver, M., Olson, J., OʼNeil, K., Onel, K., Orandi, A., Orlando, M., Osei‐Onomah, S., Oz, R., Pagano, E., Paller, A., Pan, N., Panupattanapong, S., Pardeo, M., Paredes, J., Parsons, A., Patel, J., Pentakota, K., Pepmueller, P., Pfeiffer, T., Phillippi, K., Marafon, D. Pires, Phillippi, K., Ponder, L., Pooni, R., Prahalad, S., Pratt, S., Protopapas, S., Puplava, B., Quach, J., Quinlan‐Waters, M., Rabinovich, C., Radhakrishna, S., Rafko, J., Raisian, J., Rakestraw, A., Ramirez, C., Ramsay, E., Ramsey, S., Randell, R., Reed, A., Reed, A., Reed, A., Reid, H., Remmel, K., Repp, A., Reyes, A., Richmond, A., Riebschleger, M., Ringold, S., Riordan, M., Riskalla, M., Ritter, M., Rivas‐Chacon, R., Robinson, A., Rodela, E., Rodriquez, M., Rojas, K., Ronis, T., Rosenkranz, M., Rosolowski, B., Rothermel, H., Rothman, D., Roth‐Wojcicki, E., Rouster – Stevens, K., Rubinstein, T., Ruth, N., Saad, N., Sabbagh, S., Sacco, E., Sadun, R., Sandborg, C., Sanni, A., Santiago, L., Sarkissian, A., Savani, S., Scalzi, L., Schanberg, L., Scharnhorst, S., Schikler, K., Schlefman, A., Schmeling, H., Schmidt, K., Schmitt, E., Schneider, R., Schollaert‐Fitch, K., Schulert, G., Seay, T., Seper, C., Shalen, J., Sheets, R., Shelly, A., Shenoi, S., Shergill, K., Shirley, J., Shishov, M., Shivers, C., Silverman, E., Singer, N., Sivaraman, V., Sletten, J., Smith, A., Smith, C., Smith, J., Smith, J., Smitherman, E., Soep, J., Son, M., Spence, S., Spiegel, L., Spitznagle, J., Sran, R., Srinivasalu, H., Stapp, H., Steigerwald, K., Rakovchik, Y. Sterba, Stern, S., Stevens, A., Stevens, B., Stevenson, R., Stewart, K., Stingl, C., Stokes, J., Stoll, M., Stringer, E., Sule, S., Sumner, J., Sundel, R., Sutter, M., Syed, R., Syverson, G., Szymanski, A., Taber, S., Tal, R., Tambralli, A., Taneja, A., Tanner, T., Tapani, S., Tarshish, G., Tarvin, S., Tate, L., Taxter, A., Taylor, J., Terry, M., Tesher, M., Thatayatikom, A., Thomas, B., Tiffany, K., Ting, T., Tipp, A., Toib, D., Torok, K., Toruner, C., Tory, H., Toth, M., Tse, S., Tubwell, V., Twilt, M., Uriguen, S., Valcarcel, T., Van Mater, H., Vannoy, L., Varghese, C., Vasquez, N., Vazzana, K., Vehe, R., Veiga, K., Velez, J., Verbsky, J., Vilar, G., Volpe, N., von Scheven, E., Vora, S., Wagner, J., Wagner‐Weiner, L., Wahezi, D., Waite, H., Walker, J., Walters, H., Muskardin, T. Wampler, Waqar, L., Waterfield, M., Watson, M., Watts, A., Weiser, P., Weiss, J., Weiss, P., Wershba, E., White, A., Williams, C., Wise, A., Woo, J., Woolnough, L., Wright, T., Wu, E., Yalcindag, A., Yee, M., Yen, E., Yeung, R., Yomogida, K., Yu, Q., Zapata, R., Zartoshti, A., Zeft, A., Zeft, R., Zhang, Y., Zhao, Y., Zhu, A., and Zic, C.

Published
2023
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14. Second moment of the pion distribution amplitude with the momentum smearing technique

Author

RQCD Collaboration, Bali, G. S., Braun, V. M., Göckeler, M., Gruber, M., Hutzler, F., Korcyl, P., Lang, B., and Schäfer, A.

Subjects
High Energy Physics - Lattice, High Energy Physics - Phenomenology
Abstract

Using the second moment of the pion distribution amplitude as an example, we investigate whether lattice calculations of matrix elements of local operators involving covariant derivatives may benefit from the recently proposed momentum smearing technique for hadronic interpolators. Comparing the momentum smearing technique to the traditional Wuppertal smearing we find - at equal computational cost - a considerable reduction of the statistical errors. The present investigation was carried out using $N_f=2+1$ dynamical non-perturbatively order $a$ improved Wilson fermions on lattices of different volumes and pion masses down to 220 MeV.

Published
2017
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15. A biofertilizing fungal endophyte of cranberry plants suppresses the plant pathogen Diaporthe

Author

Thimmappa, Bhagya C., Salhi, Lila Naouelle, Forget, Lise, Sarrasin, Matt, Bustamante Villalobos, Peniel, Henrissat, Bernard, Lang, B. Franz, Burger, Gertraud, Thimmappa, Bhagya C., Salhi, Lila Naouelle, Forget, Lise, Sarrasin, Matt, Bustamante Villalobos, Peniel, Henrissat, Bernard, Lang, B. Franz, and Burger, Gertraud

Abstract

Fungi colonizing plants are gaining attention because of their ability to promote plant growth and suppress pathogens. While most studies focus on endosymbionts from grasses and legumes, the large and diverse group of ericaceous plants has been much neglected. We recently described one of the very few fungal endophytes promoting the growth of the Ericaceae Vaccinium macrocarpon (American cranberry), notably the Codinaeella isolate EC4. Here, we show that EC4 also suppresses fungal pathogens, which makes it a promising endophyte for sustainable cranberry cultivation. By dual-culture assays on agar plates, we tested the potential growth suppression (or biocontrol) of EC4 on other microbes, notably 12 pathogenic fungi and one oomycete reported to infect not only cranberry but also blueberry, strawberry, tomato plants, rose bushes and olive trees. Under greenhouse conditions, EC4 protects cranberry plantlets infected with one of the most notorious cranberry-plant pathogens, Diaporthe vaccinii, known to cause upright dieback and berry rot. The nuclear genome sequence of EC4 revealed a large arsenal of genes potentially involved in biocontrol. About ∼60 distinct clusters of genes are homologs of secondary metabolite gene clusters, some of which were shown in other fungi to synthesize nonribosomal peptides and polyketides, but in most cases, the exact compounds these clusters may produce are unknown. The EC4 genome also encodes numerous homologs of hydrolytic enzymes known to degrade fungal cell walls. About half of the nearly 250 distinct glucanases and chitinases are likely involved in biocontrol because they are predicted to be secreted outside the cell. Transcriptome analysis shows that the expression of about a quarter of the predicted secondary-metabolite gene clusters and glucan and chitin-degrading genes of EC4 is stimulated when it is co-cultured with D. vaccinii. Some of the differentially expressed EC4 genes are alternatively spliced

Published
2024

18. Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

Author

Corrochano, Luis M, Kuo, Alan, Marcet-Houben, Marina, Polaino, Silvia, Salamov, Asaf, Villalobos-Escobedo, José M, Grimwood, Jane, Álvarez, M Isabel, Avalos, Javier, Bauer, Diane, Benito, Ernesto P, Benoit, Isabelle, Burger, Gertraud, Camino, Lola P, Cánovas, David, Cerdá-Olmedo, Enrique, Cheng, Jan-Fang, Domínguez, Angel, Eliáš, Marek, Eslava, Arturo P, Glaser, Fabian, Gutiérrez, Gabriel, Heitman, Joseph, Henrissat, Bernard, Iturriaga, Enrique A, Lang, B Franz, Lavín, José L, Lee, Soo Chan, Li, Wenjun, Lindquist, Erika, López-García, Sergio, Luque, Eva M, Marcos, Ana T, Martin, Joel, McCluskey, Kevin, Medina, Humberto R, Miralles-Durán, Alejandro, Miyazaki, Atsushi, Muñoz-Torres, Elisa, Oguiza, José A, Ohm, Robin A, Olmedo, María, Orejas, Margarita, Ortiz-Castellanos, Lucila, Pisabarro, Antonio G, Rodríguez-Romero, Julio, Ruiz-Herrera, José, Ruiz-Vázquez, Rosa, Sanz, Catalina, Schackwitz, Wendy, Shahriari, Mahdi, Shelest, Ekaterina, Silva-Franco, Fátima, Soanes, Darren, Syed, Khajamohiddin, Tagua, Víctor G, Talbot, Nicholas J, Thon, Michael R, Tice, Hope, de Vries, Ronald P, Wiebenga, Ad, Yadav, Jagjit S, Braun, Edward L, Baker, Scott E, Garre, Victoriano, Schmutz, Jeremy, Horwitz, Benjamin A, Torres-Martínez, Santiago, Idnurm, Alexander, Herrera-Estrella, Alfredo, Gabaldón, Toni, and Grigoriev, Igor V

Subjects
Microbiology, Biochemistry and Cell Biology, Biological Sciences, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Evolution, Molecular, Gene Duplication, Genome, Fungal, Light, Mucor, Multigene Family, Perception, Phycomyces, Signal Transduction, Transcription, Genetic, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Psychology
Abstract

Plants and fungi use light and other signals to regulate development, growth, and metabolism. The fruiting bodies of the fungus Phycomyces blakesleeanus are single cells that react to environmental cues, including light, but the mechanisms are largely unknown [1]. The related fungus Mucor circinelloides is an opportunistic human pathogen that changes its mode of growth upon receipt of signals from the environment to facilitate pathogenesis [2]. Understanding how these organisms respond to environmental cues should provide insights into the mechanisms of sensory perception and signal transduction by a single eukaryotic cell, and their role in pathogenesis. We sequenced the genomes of P. blakesleeanus and M. circinelloides and show that they have been shaped by an extensive genome duplication or, most likely, a whole-genome duplication (WGD), which is rarely observed in fungi [3-6]. We show that the genome duplication has expanded gene families, including those involved in signal transduction, and that duplicated genes have specialized, as evidenced by differences in their regulation by light. The transcriptional response to light varies with the developmental stage and is still observed in a photoreceptor mutant of P. blakesleeanus. A phototropic mutant of P. blakesleeanus with a heterozygous mutation in the photoreceptor gene madA demonstrates that photosensor dosage is important for the magnitude of signal transduction. We conclude that the genome duplication provided the means to improve signal transduction for enhanced perception of environmental signals. Our results will help to understand the role of genome dynamics in the evolution of sensory perception in eukaryotes.

Published
2016

19. Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system

Author

Horváthová, Lenka, Žárský, Vojtěch, Pánek, Tomáš, Derelle, Romain, Pyrih, Jan, Motyčková, Alžběta, Klápšťová, Veronika, Vinopalová, Martina, Marková, Lenka, Voleman, Luboš, Klimeš, Vladimír, Petrů, Markéta, Vaitová, Zuzana, Čepička, Ivan, Hryzáková, Klára, Harant, Karel, Gray, Michael W., Chami, Mohamed, Guilvout, Ingrid, Francetic, Olivera, Franz Lang, B., Vlček, Čestmír, Tsaousis, Anastasios D., Eliáš, Marek, and Doležal, Pavel

Published
2021
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22. Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte?

Author

Ševčíková, Tereza, Horák, Aleš, Klimeš, Vladimír, Zbránková, Veronika, Demir-Hilton, Elif, Sudek, Sebastian, Jenkins, Jerry, Schmutz, Jeremy, Přibyl, Pavel, Fousek, Jan, Vlček, Čestmír, Lang, B Franz, Oborník, Miroslav, Worden, Alexandra Z, and Eliáš, Marek

Subjects
Plastids, DNA, Sequence Analysis, DNA, Evolution, Molecular, Phylogeny, Symbiosis, Genome, Plastid, Rhodophyta, Stramenopiles, Evolution, Molecular, Genome, Plastid, Sequence Analysis
Abstract

Algae with secondary plastids of a red algal origin, such as ochrophytes (photosynthetic stramenopiles), are diverse and ecologically important, yet their evolutionary history remains controversial. We sequenced plastid genomes of two ochrophytes, Ochromonas sp. CCMP1393 (Chrysophyceae) and Trachydiscus minutus (Eustigmatophyceae). A shared split of the clpC gene as well as phylogenomic analyses of concatenated protein sequences demonstrated that chrysophytes and eustigmatophytes form a clade, the Limnista, exhibiting an unexpectedly elevated rate of plastid gene evolution. Our analyses also indicate that the root of the ochrophyte phylogeny falls between the recently redefined Khakista and Phaeista assemblages. Taking advantage of the expanded sampling of plastid genome sequences, we revisited the phylogenetic position of the plastid of Vitrella brassicaformis, a member of Alveolata with the least derived plastid genome known for the whole group. The results varied depending on the dataset and phylogenetic method employed, but suggested that the Vitrella plastids emerged from a deep ochrophyte lineage rather than being derived vertically from a hypothetical plastid-bearing common ancestor of alveolates and stramenopiles. Thus, we hypothesize that the plastid in Vitrella, and potentially in other alveolates, may have been acquired by an endosymbiosis of an early ochrophyte.

Published
2015

23. Mitochondrial Genomes in Fungi

Author

Lang, B. Franz, Wells, Robert D., editor, Bond, Judith S., editor, Klinman, Judith, editor, Masters, Bettie Sue Siler, editor, Bell, Ellis, Managing Editor, and Kaguni, Laurie S., Book Editor

Published
2018
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25. Comparative Effectiveness of a Second Tumor Necrosis Factor Inhibitor Versus a Non–Tumor Necrosis Factor Biologic in the Treatment of Patients With Polyarticular‐Course Juvenile Idiopathic Arthritis

Author

Mannion, Melissa L., Amin, Shahla, Balevic, Stephen, Chang, Min‐Lee, Correll, Colleen K., Kearsley‐Fleet, Lianne, Hyrich, Kimme L., Beukelman, Timothy, Aamir, R., Abulaban, K., Adams, A., Aguiar Lapsia, C., Akinsete, A., Akoghlanian, S., Al Manaa, M., AlBijadi, A., Allenspach, E., Almutairi, A., Alperin, R., Amarilyo, G., Ambler, W., Amoruso, M., Angeles‐Han, S., Ardoin, S., Armendariz, S., Asfaw, L., Aviran Dagan, N., Bacha, C., Balboni, I., Balevic, S., Ballinger, S., Baluta, S., Barillas‐Arias, L., Basiaga, M., Baszis, K., Baxter, S., Becker, M., Begezda, A., Behrens, E., Beil, E., Benseler, S., Bermudez‐Santiago, L., Bernal, W., Bigley, T., Bingham, C., Binstadt, B., Black, C., Blackmon, B., Blakley, M., Bohnsack, J., Boneparth, A., Bradfield, H., Bridges, J., Brooks, E., Brothers, M., Brunner, H., Buckley, L., Buckley, M., Buckley, M., Bukulmez, H., Bullock, D., Canna, S., Cannon, L., Canny, S., Cartwright, V., Cassidy, E., Castro, D., Chalom, E., Chang, J., Chang, M., Chang, J., Chang‐Hoftman, A., Chen, A., Chiraseveenuprapund, P., Ciaglia, K., Co, D., Cohen, E., Collinge, J., Conlon, H., Connor, R., Cook, K., Cooper, A., Cooper, J., Corbin, K., Correll, C., Cron, R., Curry, M., Dalrymple, A., Datyner, E., Davis, T., De Ranieri, D., Dean, J., DeCoste, C., Dedeoglu, F., DeGuzman, M., Delnay, N., DeSantis, E., Devine, R., Dhalla, M., Dhanrajani, A., Dissanayake, D., Dizon, B., Drapeau, N., Drew, J., Driest, K., Du, Q., Duncan, E., Dunnock, K., Durkee, D., Dvergsten, J., Eberhard, A., Ede, K., Edelheit, B., Edens, C., El Tal, T., Elder, M., Elzaki, Y., Fadrhonc, S., Failing, C., Fair, D., Favier, L., Feldman, B., Fennell, J., Ferguson, P., Ferguson, I., Figueroa, C., Flanagan, E., Fogel, L., Fox, E., Fox, M., Franklin, L., Fuhlbrigge, R., Fuller, J., Furey, M., Futch‐West, T., Gagne, S., Gennaro, V., Gerstbacher, D., Gilbert, M., Gironella, A., Glaser, D., Goh, I., Goldsmith, D., Gorry, S., Goswami, N., Gottlieb, B., Graham, T., Grevich, S., Griffin, T., Grim, A., Grom, A., Guevara, M., Hahn, T., Halyabar, O., Hamda Natur, M., Hammelev, E., Hammond, T., Harel, L., Harris, J., Harry, O., Hausmann, J., Hay, A., Hays, K., Hayward, K., Henderson, L., Henrickson, M., Hersh, A., Hickey, K., Hiraki, L., Hiskey, M., Hobday, P., Hoffart, C., Holland, M., Hollander, M., Hong, S., Horton, D., Horwitz, M., Hsu, J., Huber, A., Huberts, A., Huggins, J., Huie, L., Hui‐Yuen, J., Ibarra, M., Imlay, A., Imundo, L., Inman, C., Jackson, A., James, K., Janow, G., Jared, S., Jiang, Y., Johnson, L., Johnson, N., Jones, J., Kafisheh, D., Kahn, P., Kaidar, K., Kasinathan, S., Kaur, R., Kessler, E., Kienzle, B., Kim, S., Kimura, Y., Kingsbury, D., Kitcharoensakkul, M., Klausmeier, T., Klein, K., Klein‐Gitelman, M., Knight, A., Kovalick, L., Kramer, S., Kremer, C., Kudas, O., LaFlam, T., Lang, B., Lapidus, S., Lapin, B., Lasky, A., Lawler, C., Lawson, E., Laxer, R., Lee, P., Lee, P., Lee, T., Lee, A., Leisinger, E., Lentini, L., Lerman, M., Levinsky, Y., Levy, D., Li, S., Lieberman, S., Lim, L., Limenis, E., Lin, C., Ling, N., Lionetti, G., Livny, R., Lloyd, M., Lo, M., Long, A., Lopez‐Peña, M., Lovell, D., Luca, N., Lvovich, S., Lytch, A., Ma, M., Machado, A., MacMahon, J., Madison, J., Mannion, M., Manos, C., Mansfield, L., Marston, B., Mason, T., Matchett, D., McAllister, L., McBrearty, K., McColl, J., McCurdy, D., McDaniels, K., McDonald, J., Meidan, E., Mellins, E., Mian, Z., Miettunen, P., Miller, M., Milojevic, D., Mitacek, R., Modica, R., Mohan, S., Moore, T., Moore, K., Moorthy, L., Moreno, J., Morgan, E., Moyer, A., Murante, B., Murphy, A., Muscal, E., Mwizerwa, O., Najafi, A., Nanda, K., Nasah, N., Nassi, L., Nativ, S., Natter, M., Nearanz, K., Neely, J., Newhall, L., Nguyen, A., Nigrovic, P., Nocton, J., Nolan, B., Nowicki, K., Oakes, R., Oberle, E., Ogbonnaya‐Whittesley, S., Ogbu, E., Oliver, M., Olveda, R., Onel, K., Orandi, A., Padam, J., Paller, A., Pan, N., Pandya, J., Panupattanapong, S., Toledano, A. Pappo, Parsons, A., Patel, J., Patel, P., Patrick, A., Patrizi, S., Paul, S., Perfetto, J., Perron, M., Peskin, M., Ponder, L., Pooni, R., Prahalad, S., Puplava, B., Quinlan‐Waters, M., Rabinovich, C., Rafko, J., Rahimi, H., Rampone, K., Ramsey, S., Randell, R., Ray, L., Reed, A., Reed, A., Reid, H., Reiff, D., Richins, S., Riebschleger, M., Rife, E., Riordan, M., Riskalla, M., Robinson, A., Robinson, L., Rodgers, L., Rodriquez, M., Rogers, D., Ronis, T., Rosado, A., Rosenkranz, M., Rosenwasser, N., Rothermel, H., Rothman, D., Rothschild, E., Roth‐Wojcicki, E., Rouster‐Stevens, K., Rubinstein, T., Rupp, J., Ruth, N., Sabbagh, S., Sadun, R., Santiago, L., Saper, V., Sarkissian, A., Scalzi, L., Schahn, J., Schikler, K., Schlefman, A., Schmeling, H., Schmitt, E., Schneider, R., Schulert, G., Schultz, K., Schutt, C., Seper, C., Sheets, R., Shehab, A., Shenoi, S., Sherman, M., Shirley, J., Shishov, M., Siegel, D., Singer, N., Sivaraman, V., Sloan, E., Smith, C., Smith, J., Smitherman, E., Soep, J., Son, Mary B., Sosna, D., Spencer, C., Spiegel, L., Spitznagle, J., Srinivasalu, H., Stapp, H., Steigerwald, K., Stephens, A., Sterba Rakovchik, Y., Stern, S., Stevens, B., Stevenson, R., Stewart, K., Stewart, W., Stingl, C., Stoll, M., Stringer, E., Sule, S., Sullivan, J., Sundel, R., Sutter, M., Swaffar, C., Swayne, N., Syed, R., Symington, T., Syverson, G., Szymanski, A., Taber, S., Tal, R., Tambralli, A., Taneja, A., Tanner, T., Tarvin, S., Tate, L., Taxter, A., Taylor, J., Tesher, M., Thakurdeen, T., Theisen, A., Thomas, B., Thomas, L., Thomas, N., Ting, T., Todd, C., Toib, D., Toib, D., Torok, K., Tory, H., Toth, M., Tse, S., Tsin, C., Twachtman‐Bassett, J., Twilt, M., Valcarcel, T., Valdovinos, R., Vallee, A., Van Mater, H., Vandenbergen, S., Vannoy, L., Varghese, C., Vasquez, N., Vega‐Fernandez, P., Velez, J., Verbsky, J., Verstegen, R., Scheven, E., Vora, S., Wagner‐Weiner, L., Wahezi, D., Waite, H., Walker, B., Walters, H., Waterfield, M., Waters, A., Weiser, P., Weiss, P., Weiss, J., Wershba, E., Westheuser, V., White, A., Widrick, K., Williams, C., Wong, S., Woolnough, L., Wright, T., Wu, E., Yalcindag, A., Yasin, S., Yeung, R., Yomogida, K., Zeft, A., Zhang, Y., Zhao, Y., and Zhu, A.

Abstract

The objective of this study was to compare the effectiveness of a second tumor necrosis factor inhibitor (TNFi) versus a non‐TNFi biologic following discontinuation of a TNFi for patients with polyarticular‐course juvenile idiopathic arthritis (pJIA). Using the Childhood Arthritis and Rheumatology Research Alliance Registry, patients with pJIA who started receiving a second biologic following a first TNFi were identified. Patients were required to have no active uveitis on the index date and a visit six months after the index date. Outcome measures included Clinical Juvenile Arthritis Disease Activity Score with a maximum of 10 active joints (cJADAS10), cJADAS10 inactive disease (ID; ≤2.5) and cJADAS10 minimal disease activity (MiDA; ≤5). Multiple imputation was used to account for missing data. Adjusted odds ratios (aORs) were calculated using propensity score quintiles to compare outcomes at six months following second biologic initiation. There were 216 patients included, 84% initially received etanercept, and most patients stopped receiving it because of its ineffectiveness (74%). A total of 183 (85%) started receiving a second TNFi, and 33 (15%) started receiving a non‐TNFi. Adalimumab was the most common second biologic received (71% overall, 84% of second TNFi), and tocilizumab was the most common non‐TNFi second biologic received (9% overall, 58% of non‐TNFi). There was no difference between receiving TNFi versus non‐TNFi in cJADAS10 ID (29% vs 25%; aOR 1.23, 95% confidence interval [CI] 0.47–3.20) or at least MiDA (43% vs 39%; aOR 1.11, 95% CI 0.47–2.62) at six months. Most patients with pJIA started receiving TNFi rather than non‐TNFi as their second biologic, and there were no differences in disease activity at six months.

Published
2024
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26. Down Syndrome–Associated Arthritis Cohort in the New Childhood Arthritis and Rheumatology Research Alliance Registry: Clinical Characteristics, Treatment, and Outcomes

Author

Jones, Jordan T., Smith, Chelsey, Becker, Mara L., Lovell, Daniel, Abel, N., Abulaban, K., Adams, A., Adams, M., Agbayani, R., Akoghlanian, S., Al Ahmed, O., Allenspach, E., Alperin, R., Alpizar, M., Amarilyo, G., Anastasopoulos, D., Anderson, E., Andrew, M., Ardalan, K., Ardoin, S., Baker, E., Balboni, I., Balevic, S., Ballenger, L., Ballinger, S., Balmuri, N., Barbar‐Smiley, F., Barillas‐Arias, L., Basiaga, M., Baszis, K., Bell‐Brunson, H., Beltz, E., Benham, H., Benseler, S., Bernal, W., Beukelman, T., Bigley, T., Binstadt, B., Birmingham, J., Black, C., Blakley, M., Bohnsack, J., Boland, J., Boneparth, A., Bowman, S., Brooks, E., Brown, A., Brunner, H., Buckley, M., Buckley, M., Bukulmez, H., Bullington, A., Bullock, D., Cameron, B., Canna, S., Cannon, L., Carpenter, S., Carper, P., Cartwright, V., Cassidy, E., Cerracchio, L., Chalom, E., Chang, J., Chang‐Hoftman, A., Chauhan, V., Chira, P., Chiu, Y., Chundru, K., Clairman, H., Co, D., Collins, K., Confair, A., Conlon, H., Connor, R., Cooper, A., Cooper, J., Cooper, S., Correll, C., Corvalan, R., Cospito, T., Costanzo, D., Cron, R., Curry, M., Dalrymple, A., Davis, A., Davis, C., Davis, C., Davis, T., De Ranieri, D., Dean, J., Dedeoglu, F., DeGuzman, M., Delnay, N., Dempsey, V., DeSantis, E., Dickson, T., Dingle, J., Dionizovik‐Dimanovski, M., Donaldson, B., Dorsey, E., Dover, S., Dowling, J., Drew, J., Driest, K., Drummond, K., Du, Q., Duarte, K., Durkee, D., Duverger, E., Dvergsten, J., Eberhard, A., Eckert, M., Ede, K., Edens, C., Edens, C., Edgerly, Y., Elder, M., Fadrhonc, S., Failing, C., Fair, D., Falcon, M., Favier, L., Feldman, B., Ferguson, I., Ferguson, P., Ferreira, B., Ferrucho, R., Fields, K., Finkel, T., Fitzgerald, M., Fleck, D., Fleming, C., Flynn, O., Fogel, L., Fox, E., Fox, M., Franco, L., Freeman, M., Froese, S., Fuhlbrigge, R., Fuller, J., George, N., Gergely, T., Gerhold, K., Gerstbacher, D., Gilbert, M., Gillispie‐Taylor, M., Giverc, E., Goh, I., Goldberg, T., Goldsmith, D., Gotschlich, E., Gotte, A., Gottlieb, B., Gracia, C., Graham, T., Grevich, S., Griffin, T., Griswold, J., Guevara, M., Guittar, P., Gurion, R., Guzman, M., Hahn, T., Halyabar, O., Hammelev, E., Hance, M., Hansman, E., Hanson, A., Harel, L., Haro, S., Harris, J., Hartigan, E., Hausmann, J., Hay, A., Hayward, K., Heiart, J., Hekl, K., Henderson, L., Henrickson, M., Hersh, A., Hickey, K., Hillyer, S., Hiraki, L., Hiskey, M., Hobday, P., Hoffart, C., Holland, M., Hollander, M., Hong, S., Horwitz, M., Hsu, J., Huber, A., Huggins, J., Hughes, R., Hui‐Yuen, J., Hung, C., Huntington, J., Huttenlocher, A., Ibarra, M., Imundo, L., Inman, C., Iqbal, S., Jackson, A., Jackson, S., James, K., Janow, G., Jaquith, J., Jared, S., Johnson, N., Jones, J., Jones, J., Jones, J., Jones, K., Jones, S., Joshi, S., Jung, L., Justice, C., Justiniano, A., Kahn, P., Karan, N., Kaufman, K., Kemp, A., Kessler, E., Khaleel, M., Khalsa, U., Kienzle, B., Kim, S., Kimura, Y., Kingsbury, D., Kitcharoensakkul, M., Klausmeier, T., Klein, K., Klein‐Gitelman, M., Kosikowski, A., Kovalick, L., Kracker, J., Kramer, S., Kremer, C., Lai, J., Lang, B., Lapidus, S., Lasky, A., Latham, D., Lawson, E., Laxer, R., Lee, P., Lee, P., Lee, T., Lentini, L., Lerman, M., Levy, D., Li, S., Lieberman, S., Lim, L., Lin, C., Ling, N., Lingis, M., Lo, M., Lovell, D., Luca, N., Lvovich, S., Ma, M., Mackey, C., Madison, C., Madison, J., Malla, B., Maller, J., Malloy, M., Mannion, M., Manos, C., Marques, L., Martyniuk, A., Mason, T., Mathus, S., McAllister, L., McCallum, B., McCarthy, K., McConnell, K., McCurdy, D., McCurdy Stokes, P., McGuire, S., McHale, I., McHugh, A., McKibben, K., McMonagle, A., McMullen‐Jackson, C., Meidan, E., Mellins, E., Mendoza, E., Mercado, R., Merritt, A., Michalowski, L., Miettunen, P., Miller, M., Mirizio, E., Misajon, E., Mitchell, M., Modica, R., Mohan, S., Moore, K., Moorthy, L., Morgan, S., Morgan Dewitt, E., Morris, S., Moss, C., Moussa, T., Mruk, V., Mulvhihill, E., Muscal, E., Nahal, B., Nanda, K., Nassi, L., Nativ, S., Natter, M., Neely, J., Nelson, B., Newhall, L., Ng, L., Nguyen, E., Nicholas, J., Nigrovic, P., Nocton, J., Oberle, E., Obispo, B., O’Brien, B., O’Brien, T., O’Connor, M., Oliver, M., Olson, J., O’Neil, K., Onel, K., Orlando, M., Oz, R., Pagano, E., Paller, A., Pan, N., Panupattanapong, S., Paredes, J., Parsons, A., Patel, J., Pentakota, K., Pepmueller, P., Pfeiffer, T., Phillippi, K., Phillippi, K., Ponder, L., Pooni, R., Prahalad, S., Pratt, S., Protopapas, S., Punaro, M., Puplava, B., Quach, J., Quinlan‐Waters, M., Quintero, A., Rabinovich, C., Radhakrishna, S., Rafko, J., Raisian, J., Rakestraw, A., Ramsay, E., Ramsey, S., Reed, A., Reed, A., Reed, A., Reid, H., Reyes, A., Richmond, A., Riebschleger, M., Ringold, S., Riordan, M., Riskalla, M., Ritter, M., Rivas‐Chacon, R., Roberson, S., Robinson, A., Rodela, E., Rodriquez, M., Rojas, K., Ronis, T., Rosenkranz, M., Rosenwasser Raines, N., Rosolowski, B., Rothermel, H., Rothman, D., Roth‐Wojcicki, E., Rouster–Stevens, K., Rubinstein, T., Ruth, N., Saad, N., Sabatino, M., Sabbagh, S., Sadun, R., Sandborg, C., Sanni, A., Sarkissian, A., Savani, S., Scalzi, L., Schanberg, L., Scharnhorst, S., Schikler, K., Schmeling, H., Schmidt, K., Schmitt, E., Schneider, R., Schollaert‐Fitch, K., Schulert, G., Seay, T., Seper, C., Shalen, J., Sheets, R., Shelly, A., Shen, B., Shenoi, S., Shergill, K., Shiff, N., Shirley, J., Shishov, M., Silverman, E., Singer, N., Sivaraman, V., Sletten, J., Smith, A., Smith, C., Smith, J., Smith, J., Smitherman, E., Snider, C., Soep, J., Son, M., Soybilgic, A., Spence, S., Spiegel, L., Spitznagle, J., Sran, R., Srinivasalu, H., Stapp, H., Stasek, J., Steigerwald, K., Sterba Rakovchik, Y., Stern, S., Stevens, A., Stevens, B., Stevenson, R., Stewart, K., Stingl, C., Stokes, J., Stoll, M., Stoops, S., Strelow, J., Stringer, E., Sule, S., Sumner, J., Sundel, R., Sura, A., Sutter, M., Syed, R., Taber, S., Tal, R., Tambralli, A., Taneja, A., Tanner, T., Tapani, S., Tarshish, G., Tarvin, S., Tate, L., Taxter, A., Taylor, J., Terry, M., Tesher, M., Thatayatikom, A., Thomas, B., Ting, T., Tipp, A., Toib, D., Torok, K., Toruner, C., Tory, H., Toth, M., Treemarcki, E., Tse, S., Tubwell, V., Twilt, M., Uriguen, S., Valcarcel, T., Van Mater, H., Vannoy, L., Varghese, C., Vasquez, N., Vazzana, K., Vega‐Fernandes, P., Vehe, R., Veiga, K., Velez, J., Verbsky, J., Volpe, N., von Scheven, E., Vora, S., Wagner, J., Wagner‐Weiner, L., Wahezi, D., Waite, H., Walker, J., Walters, H., Wampler Muskardin, T., Wang, C., Waqar, L., Waterfield, M., Watson, M., Watts, A., Waugaman, B., Weiser, P., Weiss, J., Weiss, P., Wershba, E., White, A., Williams, C., Wise, A., Woo, J., Woolnough, L., Wright, T., Wu, E., Yalcindag, A., Yee, M., Yen, E., Yeung, R., Yomogida, K., Yu, Q., Zapata, R., Zartoshti, A., Zeft, A., Zeft, R., Zemel, L., Zhang, Y., Zhao, Y., Zhu, A., and Zic, C.

Published
2021
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28. Comparison of the efficacy and safety of remifentanil versus different pharmacological approaches on prevention of etomidate-induced myoclonus: a meta-analysis of randomized controlled trials

Author

Lang B, Zhang L, Li F, Lin Y, Zhang W, and Yang C

Subjects
remifentanil, etomidate, myoclonus, meta-analysis, fentanyl, midazolam, Therapeutics. Pharmacology, RM1-950
Abstract

Bingchen Lang,1 Lingli Zhang,1–3 Fengshan Li,1 Yunzhu Lin,1 Wensheng Zhang,4 Chunsong Yang11Department of Pharmacy, West China Second University Hospital, Sichuan University, Chengdu, People’s Republic of China; 2Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu, People’s Republic of China; 3Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, People’s Republic of China; 4Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, People’s Republic of ChinaObjective: Myoclonus was considered as one conundrum in etomidate induction, which led to multiple risks during clinical anesthesia. The present study was conducted to compare the efficacy of pretreatment with remifentanil to different pharmacological approaches on reducing etomidate-induced myoclonus.Methods: We searched PubMed, Embase, Cochrane Library, and China National Knowledge Infrastructure from the inception to October 2018. Randomized controlled trials comparing remifentanil versus other pharmacological approaches in reducing etomidate-induced myoclonus were eligible to be analyzed.Results: Overall, 13 trials with 1,392 patients met with the inclusion criteria. 1) Pretreatment with remifentanil could reduce the incidence of etomidate-induced myoclonus compared to placebo and fentanyl; few differences were found between the use of remifentanil and the use of midazolam: (incidence of myoclonus: 5.56% with remifentanil vs 71.65% with saline, RR=0.08, with 95% CI [0.05, 0.12], P

Published
2019

29. Charm-Production in e^+e^- Annihilation Around 4 GeV

Author

Lang, B. W.

Subjects
High Energy Physics - Experiment
Abstract

Using the CLEO-c detector at the Cornell Electron Storage Ring, we have measured inclusive and exclusive cross sections for the production of $D^+$, $D^0$ and $D_s^+$ mesons in $e^{+}e^{-}$ annihilations at thirteen center-of-mass energies between 3.97 and 4.26 GeV. Exclusive cross sections are presented for final states consisting of two charmed mesons ($D\bar{D}$, $D^{*}\bar{D}$, $D^{*}\bar{D}^{*}$, $D_s^+ D_s^-$, $D_s^{*+} D_s^-$, and $D_s^{*+} D_s^{*-}$) and for processes in which the charmed meson pair is accompanied by a pion., Comment: 8 pages, 8 figures, to be published in the proceedings of CHARM07, Ithaca, NY, August 2007, eConf C070805

Published
2007

30. Signatures of Random Matrix Theory in the Discrete Energy Spectra of Subnanosize Metallic Clusters

Author

Adams, L. L. A., Lang, B. W., Chen, Yu, and Goldman, A. M.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Lead clusters deposited on Si(111) substrates have been studied at low temperatures using scanning tunneling microscopy and spectroscopy. The current-voltage characteristics exhibit current peaks that are irregularly spaced and varied in height. The statistics of the distribution of peak heights and spacings are in agreement with random matrix theory for several clusters. The distributions have also been studied as a function of cluster shape., Comment: 10 pages, 9 figures, to appear in Phys. Rev. B

Published
2007
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31. An iterative method to compute the sign function of a non-Hermitian matrix and its application to the overlap Dirac operator at nonzero chemical potential

Author

Bloch, J., Frommer, A., Lang, B., and Wettig, T.

Subjects
High Energy Physics - Lattice
Abstract

The overlap Dirac operator in lattice QCD requires the computation of the sign function of a matrix. While this matrix is usually Hermitian, it becomes non-Hermitian in the presence of a quark chemical potential. We show how the action of the sign function of a non-Hermitian matrix on an arbitrary vector can be computed efficiently on large lattices by an iterative method. A Krylov subspace approximation based on the Arnoldi algorithm is described for the evaluation of a generic matrix function. The efficiency of the method is spoiled when the matrix has eigenvalues close to a function discontinuity. This is cured by adding a small number of critical eigenvectors to the Krylov subspace, for which we propose two different deflation schemes. The ensuing modified Arnoldi method is then applied to the sign function, which has a discontinuity along the imaginary axis. The numerical results clearly show the improved efficiency of the method. Our modification is particularly effective when the action of the sign function of the same matrix has to be computed many times on different vectors, e.g., if the overlap Dirac operator is inverted using an iterative method., Comment: 11 pages, 4 figures; minor changes, as published in Comput. Phys. Commun.

Published
2007

32. Pinning frequencies of the collective modes in $\alpha$-uranium

Author

Mihaila, B., Opeil, C. P., Drymiotis, F. R., Smith, J. L., Cooley, J. C., Manley, M. E., Migliori, A., Mielke, C., Lookman, T., Saxena, A., Bishop, A. R., Blagoev, K. B., Thoma, D. J., Lang, B. E., Boerio-Goates, J., Woodfield, B. F., Schmiedeshoff, G. M., and Lashley, J. C.

Subjects
Condensed Matter - Other Condensed Matter
Abstract

Uranium is the only known element that features a charge-density wave (CDW) and superconductivity. We report a comparison of the specific heat of single-crystal and polycrystalline $\alpha$-uranium. \red{Away from the the phase transition the specific heat of the polycrystal is larger than that of the single crystal, and the aim of this paper is to explain this difference.} In the single crystal we find excess contributions to the heat capacity at 41 K, 38 K, and 23 K, with a Debye temperature, $\Theta_D$ = 256 K. In the polycrystalline sample the heat capacity curve is thermally broadened ($\Theta_D$ = 184 K), but no excess heat capacity was observed. The excess heat capacity, $C_\phi$ (taken as the difference between the single crystal and polycrystal heat capacities) is well described in terms of collective-mode excitations above their respective pinning frequencies. This attribution is represented by a modified Debye spectrum with two cutoff frequencies, a pinning frequency, $\nu_o$, for the pinned CDW (due to grain boundaries in the polycrystal), and a normal Debye acoustic frequency occurring in the single crystal. We explain the 50-year-old difference in Debye temperatures between heat capacity and ultrasonic measurements.

Published
2006
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33. Observation of discrete energy levels in a quantum confined system

Author

Adams, L. L. A., Lang, B. W., and Goldman, A. M.

Subjects
Condensed Matter - Other Condensed Matter, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Low temperature scanning tunneling microscope images and spectroscopic data have been obtained on subnanometer size Pb clusters fabricated using the technique of buffer layer assisted growth. Discrete energy levels were resolved in current-voltage characteristics as current peaks rather than current steps. Distributions of peak voltage spacings and peak current heights were consistent with Wigner-Dyson and Porter-Thomas distributions respectively, suggesting the relevance of random matrix theory to the description of the electronic eigenstates of the clusters. The observation of peaks rather than steps in the current-voltage characteristics is attributed to a resonant tunneling process involving the discrete energy levels of the cluster, the tip, and the states at the interface between the cluster and the substrate surface., Comment: 4 pages, 4 figures

Published
2005
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34. Juvenile Spondyloarthritis in the Childhood Arthritis and Rheumatology Research Alliance Registry: High Biologic Use, Low Prevalence of HLA–B27, and Equal Sex Representation in Sacroiliitis

Author

Rumsey, Dax G., Lougee, Aimee, Matsouaka, Roland, Collier, David H., Schanberg, Laura E., Schenfeld, Jennifer, Shiff, Natalie J., Stoll, Matthew L., Stryker, Scott, Weiss, Pamela F., Beukelman, Timothy, Abel, N., Abulaban, K., Adams, A., Adams, M., Agbayani, R., Aiello, J., Akoghlanian, S., Alejandro, C., Allenspach, E., Alperin, R., Alpizar, M., Amarilyo, G., Ambler, W., Anderson, E., Ardoin, S., Armendariz, S., Baker, E., Balboni, I., Balevic, S., Ballenger, L., Ballinger, S., Balmuri, N., Barbar‐Smiley, F., Barillas‐Arias, L., Basiaga, M., Baszis, K., Becker, M., Bell‐Brunson, H., Beltz, E., Benham, H., Benseler, S., Bernal, W., Bigley, T., Binstadt, B., Black, C., Blakley, M., Bohnsack, J., Boland, J., Boneparth, A., Bowman, S., Bracaglia, C., Brooks, E., Brothers, M., Brown, A., Brunner, H., Buckley, M., Buckley, M., Bukulmez, H., Bullock, D., Cameron, B., Canna, S., Cannon, L., Carper, P., Cartwright, V., Cassidy, E., Cerracchio, L., Chalom, E., Chang, J., Chang‐Hoftman, A., Chauhan, V., Chira, P., Chinn, T., Chundru, K., Clairman, H., Co, D., Confair, A., Conlon, H., Connor, R., Cooper, A., Cooper, J., Cooper, S., Correll, C., Corvalan, R., Costanzo, D., Cron, R., Curiel‐Duran, L., Curington, T., Curry, M., Dalrymple, A., Davis, A., Davis, C., Davis, C., Davis, T., De Benedetti, F., De Ranieri, D., Dean, J., Dedeoglu, F., DeGuzman, M., Delnay, N., Dempsey, V., DeSantis, E., Dickson, T., Dingle, J., Donaldson, B., Dorsey, E., Dover, S., Dowling, J., Drew, J., Driest, K., Du, Q., Duarte, K., Durkee, D., Duverger, E., Dvergsten, J., Eberhard, A., Eckert, M., Ede, K., Edelheit, B., Edens, C., Edens, C., Edgerly, Y., Elder, M., Ervin, B., Fadrhonc, S., Failing, C., Fair, D., Falcon, M., Favier, L., Federici, S., Feldman, B., Fennell, J., Ferguson, I., Ferguson, P., Ferreira, B., Ferrucho, R., Fields, K., Finkel, T., Fitzgerald, M., Fleming, C., Flynn, O., Fogel, L., Fox, E., Fox, M., Franco, L., Freeman, M., Fritz, K., Froese, S., Fuhlbrigge, R., Fuller, J., George, N., Gerhold, K., Gerstbacher, D., Gilbert, M., Gillispie‐Taylor, M., Giverc, E., Godiwala, C., Goh, I., Goheer, H., Goldsmith, D., Gotschlich, E., Gotte, A., Gottlieb, B., Gracia, C., Graham, T., Grevich, S., Griffin, T., Griswold, J., Grom, A., Guevara, M., Guittar, P., Guzman, M., Hager, M., Hahn, T., Halyabar, O., Hammelev, E., Hance, M., Hanson, A., Harel, L., Haro, S., Harris, J., Harry, O., Hartigan, E., Hausmann, J., Hay, A., Hayward, K., Heiart, J., Hekl, K., Henderson, L., Henrickson, M., Hersh, A., Hickey, K., Hill, P., Hillyer, S., Hiraki, L., Hiskey, M., Hobday, P., Hoffart, C., Holland, M., Hollander, M., Hong, S., Horwitz, M., Hsu, J., Huber, A., Huggins, J., Hui‐Yuen, J., Hung, C., Huntington, J., Huttenlocher, A., Ibarra, M., Imundo, L., Inman, C., Insalaco, A., Jackson, A., Jackson, S., James, K., Janow, G., Jaquith, J., Jared, S., Johnson, N., Jones, J., Jones, J., Jones, J., Jones, K., Jones, S., Joshi, S., Jung, L., Justice, C., Justiniano, A., Karan, N., Kaufman, K., Kemp, A., Kessler, E., Khalsa, U., Kienzle, B., Kim, S., Kimura, Y., Kingsbury, D., Kitcharoensakkul, M., Klausmeier, T., Klein, K., Klein‐Gitelman, M., Kompelien, B., Kosikowski, A., Kovalick, L., Kracker, J., Kramer, S., Kremer, C., Lai, J., Lam, J., Lang, B., Lapidus, S., Lapin, B., Lasky, A., Latham, D., Lawson, E., Laxer, R., Lee, P., Lee, P., Lee, T., Lentini, L., Lerman, M., Levy, D., Li, S., Lieberman, S., Lim, L., Lin, C., Ling, N., Lingis, M., Lo, M., Lovell, D., Lowman, D., Luca, N., Lvovich, S., Madison, C., Madison, J., Magni Manzoni, S., Malla, B., Maller, J., Malloy, M., Mannion, M., Manos, C., Marques, L., Martyniuk, A., Mason, T., Mathus, S., McAllister, L., McCarthy, K., McConnell, K., McCormick, E., McCurdy, D., McCurdy Stokes, P., McGuire, S., McHale, I., McMonagle, A., McMullen‐Jackson, C., Meidan, E., Mellins, E., Mendoza, E., Mercado, R., Merritt, A., Michalowski, L., Miettunen, P., Miller, M., Milojevic, D., Mirizio, E., Misajon, E., Mitchell, M., Modica, R., Mohan, S., Moore, K., Moorthy, L., Morgan, S., Morgan Dewitt, E., Moss, C., Moussa, T., Mruk, V., Murphy, A., Muscal, E., Nadler, R., Nahal, B., Nanda, K., Nasah, N., Nassi, L., Nativ, S., Natter, M., Neely, J., Nelson, B., Newhall, L., Ng, L., Nicholas, J., Nicolai, R., Nigrovic, P., Nocton, J., Nolan, B., Oberle, E., Obispo, B., O’Brien, B., O’Brien, T., Okeke, O., Oliver, M., Olson, J., O’Neil, K., Onel, K., Orandi, A., Orlando, M., Osei‐Onomah, S., Oz, R., Pagano, E., Paller, A., Pan, N., Panupattanapong, S., Pardeo, M., Paredes, J., Parsons, A., Patel, J., Pentakota, K., Pepmueller, P., Pfeiffer, T., Phillippi, K., Pires Marafon, D., Phillippi, K., Ponder, L., Pooni, R., Prahalad, S., Pratt, S., Protopapas, S., Puplava, B., Quach, J., Quinlan‐Waters, M., Rabinovich, C., Radhakrishna, S., Rafko, J., Raisian, J., Rakestraw, A., Ramirez, C., Ramsay, E., Ramsey, S., Randell, R., Reed, A., Reed, A., Reed, A., Reid, H., Remmel, K., Repp, A., Reyes, A., Richmond, A., Riebschleger, M., Ringold, S., Riordan, M., Riskalla, M., Ritter, M., Rivas‐Chacon, R., Robinson, A., Rodela, E., Rodriquez, M., Rojas, K., Ronis, T., Rosenkranz, M., Rosolowski, B., Rothermel, H., Rothman, D., Roth‐Wojcicki, E., Rouster – Stevens, K., Rubinstein, T., Ruth, N., Saad, N., Sabbagh, S., Sacco, E., Sadun, R., Sandborg, C., Sanni, A., Santiago, L., Sarkissian, A., Savani, S., Scalzi, L., Scharnhorst, S., Schikler, K., Schlefman, A., Schmeling, H., Schmidt, K., Schmitt, E., Schneider, R., Schollaert‐Fitch, K., Schulert, G., Seay, T., Seper, C., Shalen, J., Sheets, R., Shelly, A., Shenoi, S., Shergill, K., Shirley, J., Shishov, M., Shivers, C., Silverman, E., Singer, N., Sivaraman, V., Sletten, J., Smith, A., Smith, C., Smith, J., Smith, J., Smitherman, E., Soep, J., Son, M., Spence, S., Spiegel, L., Spitznagle, J., Sran, R., Srinivasalu, H., Stapp, H., Steigerwald, K., Sterba Rakovchik, Y., Stern, S., Stevens, A., Stevens, B., Stevenson, R., Stewart, K., Stingl, C., Stokes, J., Stringer, E., Sule, S., Sumner, J., Sundel, R., Sutter, M., Syed, R., Syverson, G., Szymanski, A., Taber, S., Tal, R., Tambralli, A., Taneja, A., Tanner, T., Tapani, S., Tarshish, G., Tarvin, S., Tate, L., Taxter, A., Taylor, J., Terry, M., Tesher, M., Thatayatikom, A., Thomas, B., Tiffany, K., Ting, T., Tipp, A., Toib, D., Torok, K., Toruner, C., Tory, H., Toth, M., Tse, S., Tubwell, V., Twilt, M., Uriguen, S., Valcarcel, T., Van Mater, H., Vannoy, L., Varghese, C., Vasquez, N., Vazzana, K., Vehe, R., Veiga, K., Velez, J., Verbsky, J., Vilar, G., Volpe, N., von Scheven, E., Vora, S., Wagner, J., Wagner‐Weiner, L., Wahezi, D., Waite, H., Walker, J., Walters, H., Wampler Muskardin, T., Waqar, L., Waterfield, M., Watson, M., Watts, A., Weiser, P., Weiss, J., Wershba, E., White, A., Williams, C., Wise, A., Woo, J., Woolnough, L., Wright, T., Wu, E., Yalcindag, A., Yee, M., Yen, E., Yeung, R., Yomogida, K., Yu, Q., Zapata, R., Zartoshti, A., Zeft, A., Zeft, R., Zhang, Y., Zhao, Y., Zhu, A., and Zic, C.

Published
2021
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35. Three-dimensional Continuum Radiative Transfer Images of a Molecular Cloud Core Evolution

Author

Steinacker, J., Lang, B., Burkert, A., Bacmann, A., and Henning, Th.

Subjects
Astrophysics
Abstract

We analyze a three-dimensional smoothed particle hydrodynamics simulation of an evolving and later collapsing pre-stellar core. Using a three-dimensional continuum radiative transfer program, we generate images at 7 micron, 15 micron, 175 micron, and 1.3 mm for different evolutionary times and viewing angles. We discuss the observability of the properties of pre-stellar cores for the different wavelengths. For examples of non-symmetric fragments, it is shown that, misleadingly, the density profiles derived from a one-dimensional analysis of the corresponding images are consistent with one-dimensional core evolution models. We conclude that one-dimensional modeling based on column density interpretation of images does not produce reliable structural information and that multidimensional modeling is required., Comment: accepted by ApJL, 4 pages, 4 figures

Published
2004
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36. Insights into the Origin of Metazoan Filopodia and Microvilli

Author

Sebé-Pedrós, Arnau, Burkhardt, Pawel, Sánchez-Pons, Núria, Fairclough, Stephen R, Lang, B Franz, King, Nicole, and Ruiz-Trillo, Iñaki

Subjects
1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Actins, Animals, Biological Evolution, Carrier Proteins, Cell Movement, Choanoflagellata, Gelsolin, Humans, Mesomycetozoea, Microfilament Proteins, Microvilli, Myosins, Phylogeny, Pseudopodia, cdc42 GTP-Binding Protein, fascin, choanoflagellate, Capsaspora, Cdc42, formin evolution, gelsolin evolution, filopodia, pseudopodia, Biochemistry and Cell Biology, Evolutionary Biology, Genetics
Abstract

Filopodia are fine actin-based cellular projections used for both environmental sensing and cell motility, and they are essential organelles for metazoan cells. In this study, we reconstruct the origin of metazoan filopodia and microvilli. We first report on the evolutionary assembly of the filopodial molecular toolkit and show that homologs of many metazoan filopodial components, including fascin and myosin X, were already present in the unicellular or colonial progenitors of metazoans. Furthermore, we find that the actin crosslinking protein fascin localizes to filopodia-like structures and microvilli in the choanoflagellate Salpingoeca rosetta. In addition, homologs of filopodial genes in the holozoan Capsaspora owczarzaki are upregulated in filopodia-bearing cells relative to those that lack them. Therefore, our findings suggest that proteins essential for metazoan filopodia and microvilli are functionally conserved in unicellular and colonial holozoans and that the last common ancestor of metazoans bore a complex and specific filopodial machinery.

Published
2013

37. Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta

Author

Fairclough, Stephen R, Chen, Zehua, Kramer, Eric, Zeng, Qiandong, Young, Sarah, Robertson, Hugh M, Begovic, Emina, Richter, Daniel J, Russ, Carsten, Westbrook, M Jody, Manning, Gerard, Lang, B Franz, Haas, Brian, Nusbaum, Chad, and King, Nicole

Abstract

Abstract Background Metazoan multicellularity is rooted in mechanisms of cell adhesion, signaling, and differentiation that first evolved in the progenitors of metazoans. To reconstruct the genome composition of metazoan ancestors, we sequenced the genome and transcriptome of the choanoflagellate Salpingoeca rosetta, a close relative of metazoans that forms rosette-shaped colonies of cells. Results A comparison of the 55 Mb S. rosetta genome with genomes from diverse opisthokonts suggests that the origin of metazoans was preceded by a period of dynamic gene gain and loss. The S. rosetta genome encodes homologs of cell adhesion, neuropeptide, and glycosphingolipid metabolism genes previously found only in metazoans and expands the repertoire of genes inferred to have been present in the progenitors of metazoans and choanoflagellates. Transcriptome analysis revealed that all four S. rosetta septins are upregulated in colonies relative to single cells, suggesting that these conserved cytokinesis proteins may regulate incomplete cytokinesis during colony development. Furthermore, genes shared exclusively by metazoans and choanoflagellates were disproportionately upregulated in colonies and the single cells from which they develop. Conclusions The S. rosetta genome sequence refines the catalog of metazoan-specific genes while also extending the evolutionary history of certain gene families that are central to metazoan biology. Transcriptome data suggest that conserved cytokinesis genes, including septins, may contribute to S. rosetta colony formation and indicate that the initiation of colony development may preferentially draw upon genes shared with metazoans, while later stages of colony maturation are likely regulated by genes unique to S. rosetta.

Published
2013

38. Genome sequence of the opportunistic human pathogen Magnusiomyces capitatus

Author

Brejová, Bronislava, Lichancová, Hana, Brázdovič, Filip, Hegedűsová, Eva, Forgáčová Jakúbková, Michaela, Hodorová, Viktória, Džugasová, Vladimíra, Baláž, Andrej, Zeiselová, Lucia, Cillingová, Andrea, Neboháčová, Martina, Raclavský, Vladislav, Tomáška, Ľubomír, Lang, B. Franz, Vinař, Tomáš, and Nosek, Jozef

Published
2019
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39. Elastic and thermodynamic properties of the shape-memory alloy AuZn

Author

Darling, T. W., Chu, F., Migliori, A., thoma, D. J., Lashley, J. C., Lang, B. E., Boerio-Goates, J., and Woodfield, B. F.

Subjects
Condensed Matter - Materials Science
Abstract

The current work reports on the elastic shear moduli, internal friction, and the specific heat of the B2 cubic ordered alloy AuZn as a function of temperature. Measurements were made on single-crystal and polycrystalline samples using Resonant Ultrasound Spectroscopy (RUS), semi-adiabatic calorimetry and stress-strain measurements. Our results confirm that this alloy exhibits the shape-memory effect and a phase transition at 64.75 K that appears to be continuous (second-order) from the specific heat data. It is argued that the combination of equiatomic composition and a low transformation temperature constrain the chemical potential and its derivatives to exhibit behavior that lies at the borderline between that of a first-order (discontinuous) and a continuous phase transition. The acoustic dissipation does not peak at the transtion temperature as expected, but shows a maximum well into the low-temperature phase. The Debye temeprature value of 219 K, obtained from the low-temperature specific heat data is in favorable agreement with that determined from the acoustic data (207 K) above the transition., Comment: 25 pages, 6 figures, submitted to Phys. Rev. B

Published
2001
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40. Pretreatment with lidocaine reduces both incidence and severity of etomidate-induced myoclonus: a meta-analysis of randomized controlled trials

Author

Lang B, Zhang L, Yang C, Lin Y, Zhang W, and Li F

Subjects
lidocaine, etomidate, myoclonus, meta-analysis, Therapeutics. Pharmacology, RM1-950
Abstract

Bingchen Lang,1 Lingli Zhang,1–3 Chunsong Yang,1 Yunzhu Lin,1 Wensheng Zhang,4 Fengshan Li1 1Department of Pharmacy, West China Second University Hospital, Sichuan University, Chengdu, People’s Republic of China; 2Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, People’s Republic of China; 3Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu, People’s Republic of China; 4Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, People’s Republic of China Objective: One conundrum that frequently occurs during clinical anesthesia is etomidate-induced myoclonus, which results in multiple risks. The aim of the study was to evaluate systematically the effect of pretreatment with lidocaine on preventing etomidate-induced myoclonus. Materials and methods: The literature search was performed from the inception to April 2018 in PubMed, Embase, Cochrane Library, and China National Knowledge Infrastructure. All randomized controlled trials that used lidocaine to prevent etomidate-induced myoclonus were enrolled. The primary outcome included the incidence and severity of etomidate-induced myoclonus. The data were combined to calculate the risk ratio and relevant 95% CI. A meta-analysis was performed following the guidelines of the Cochrane Reviewer’s Handbook and the Preferred Reporting Items for Systematic Reviews and Meta Analyses statement. Results: A total of eight studies were enrolled, and the existing evidence indicated that 1) pretreatment with lidocaine can reduce the incidence of etomidate-induced myoclonus (the incidence of myoclonus: 37.6% in lidocaine vs 73.6% in saline, risk ratio =0.46, with 95% CI [0.34, 0.63], P

Published
2018

41. Surgical significance and efficacy of epidermal growth factor receptor tyrosine kinase inhibitors in patients with primary lung adenosquamous carcinoma

Author

Zhang C, Yang H, Lang B, Yu X, Xiao P, Zhang D, Fan L, and Zhang X

Subjects
Lung adenosquamous carcinoma, EGFR, surgery, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Chao Zhang,1,* Haitang Yang,2–4,* Baoping Lang,1 Xiangdong Yu,1 Peng Xiao,1 Dian Zhang,1 Liwen Fan,5 Xiao Zhang1 1Department of Thoracic Surgery, The Affiliated Luoyang Central Hospital of Zhengzhou University, Luoyang, China; 2Division of General Thoracic Surgery, Inselspital, Bern University Hospital, Bern, Switzerland; 3Department for BioMedical Research, University of Bern, Bern, Switzerland; 4Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland; 5Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China *These authors contributed equally to this work Background: Primary adenosquamous carcinoma (ASC) of the lung is a rare and aggressive disease. The accurate diagnosis of ASC based on small biopsies is challenging because of the mixed components within the tumor, and this may lead to suboptimal treatment. Furthermore, information about the efficacy of epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) in lung ASC is limited. Patients and methods: Data on a cohort of patients with lung ASC who underwent surgery between October 2008 and December 2016 at a single institution were retrospectively reviewed. Results: This study analyzed 148 patients. Differences between the pre- and post-resection diagnosis were observed. Based on the results of preoperative biopsy, patients were diagnosed as having squamous cell carcinoma (n=26), adenocarcinoma (n=20), poorly differentiated carcinoma (n=20), and large cell carcinoma (n=1), and finally diagnosed as having ASC based on histopathological examination of the surgical specimens. Thirty patients (20.3%) with EGFR-sensitizing mutations (TKI group) were treated with EGFR-TKIs after surgery, whereas the remaining patients (79.7%) with unknown EGFR-mutation status received chemotherapy or chemoradiotherapy alone (non-TKI group). TKI treatment was associated with better median overall survival (OS) (HR=0.619; p=0.034). Multivariate analysis identified the presence of EGFR-TKI treatment as an independent prognostic factor for OS (HR=0.471; p=0.003). Conclusion: Discrepancies between the pre- and post-operative diagnosis reflect the inadequacy of non-resection approaches to the diagnosis of ASC. ASC patients harboring EGFR-sensitizing mutations who were treated with EGFR-TKIs showed a significantly better prognosis than those receiving chemotherapy or chemoradiotherapy alone. Keywords: adenosquamous carcinoma, lung, EGFR, surgery, recurrence

Published
2018

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