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2. Considerations and consequences of allowing DNA sequence data as types of fungal taxa

Author

Zamora, Juan Carlos, Svensson, Måns, Kirschner, Roland, Olariaga, Ibai, Ryman, Svengunnar, Parra, Luis Alberto, Geml, József, Rosling, Anna, Adamčík, Slavomír, Ahti, Teuvo, Aime, M. Catherine, Ainsworth, A. Martyn, Albert, László, Albertó, Edgardo, García, Alberto Altés, Ageev, Dmitry, Agerer, Reinhard, Aguirre-Hudson, Begoña, Ammirati, Joe, Andersson, Harry, Angelini, Claudio, Antonín, Vladimír, Aoki, Takayuki, Aptroot, André, Argaud, Didier, Sosa, Blanca Imelda Arguello, Aronsen, Arne, Arup, Ulf, Asgari, Bita, Assyov, Boris, Atienza, Violeta, Bandini, Ditte, Baptista-Ferreira, João Luís, Baral, Hans-Otto, Baroni, Tim, Barreto, Robert Weingart, Beker, Henry, Bell, Ann, Bellanger, Jean-Michel, Bellù, Francesco, Bemmann, Martin, Bendiksby, Mika, Bendiksen, Egil, Bendiksen, Katriina, Benedek, Lajos, Bérešová-Guttová, Anna, Berger, Franz, Berndt, Reinhard, Bernicchia, Annarosa, Biketova, Alona Yu., Bizio, Enrico, Bjork, Curtis, Boekhout, Teun, Boertmann, David, Böhning, Tanja, Boittin, Florent, Boluda, Carlos G., Boomsluiter, Menno W., Borovička, Jan, Brandrud, Tor Erik, Braun, Uwe, Brodo, Irwin, Bulyonkova, Tatiana, Burdsall, Jr., Harold H., Buyck, Bart, Burgaz, Ana Rosa, Calatayud, Vicent, Callac, Philippe, Campo, Emanuele, Candusso, Massimo, Capoen, Brigitte, Carbó, Joaquim, Carbone, Matteo, Castañeda-Ruiz, Rafael F., Castellano, Michael A., Chen, Jie, Clerc, Philippe, Consiglio, Giovanni, Corriol, Gilles, Courtecuisse, Régis, Crespo, Ana, Cripps, Cathy, Crous, Pedro W., da Silva, Gladstone Alves, da Silva, Meiriele, Dam, Marjo, Dam, Nico, Dämmrich, Frank, Das, Kanad, Davies, Linda, De Crop, Eske, De Kesel, Andre, De Lange, Ruben, De Madrignac Bonzi, Bárbara, dela Cruz, Thomas Edison E., Delgat, Lynn, Demoulin, Vincent, Desjardin, Dennis E., Diederich, Paul, Dima, Bálint, Dios, Maria Martha, Divakar, Pradeep Kumar, Douanla-Meli, Clovis, Douglas, Brian, Drechsler-Santos, Elisandro Ricardo, Dyer, Paul S., Eberhardt, Ursula, Ertz, Damien, Esteve-Raventós, Fernando, Salazar, Javier Angel Etayo, Evenson, Vera, Eyssartier, Guillaume, Farkas, Edit, Favre, Alain, Fedosova, Anna G., Filippa, Mario, Finy, Péter, Flakus, Adam, Fos, Simón, Fournier, Jacques, Fraiture, André, Franchi, Paolo, Molano, Ana Esperanza Franco, Friebes, Gernot, Frisch, Andreas, Fryday, Alan, Furci, Giuliana, Márquez, Ricardo Galán, Garbelotto, Matteo, García-Martín, Joaquina María, Otálora, Mónica A. García, Sánchez, Dania García, Gardiennet, Alain, Garnica, Sigisfredo, Benavent, Isaac Garrido, Gates, Genevieve, da Gerlach, Alice Cruz Lima, Ghobad-Nejhad, Masoomeh, Gibertoni, Tatiana B., Grebenc, Tine, Greilhuber, Irmgard, Grishkan, Bella, Groenewald, Johannes Z., Grube, Martin, Gruhn, Gérald, Gueidan, Cécile, Gulden, Gro, Gusmão, Luis F. P., Hafellner, Josef, Hairaud, Michel, Halama, Marek, Hallenberg, Nils, Halling, Roy E., Hansen, Karen, Harder, Christoffer Bugge, Heilmann-Clausen, Jacob, Helleman, Stip, Henriot, Alain, Hernandez-Restrepo, Margarita, Herve, Raphaël, Hobart, Caroline, Hoffmeister, Mascha, Høiland, Klaus, Holec, Jan, Holien, Håkon, Hughes, Karen, Hubka, Vit, Huhtinen, Seppo, Ivančević, Boris, Jagers, Marian, Jaklitsch, Walter, Jansen, AnnaElise, Jayawardena, Ruvishika S., Jeppesen, Thomas Stjernegaard, Jeppson, Mikael, Johnston, Peter, Jørgensen, Per Magnus, Kärnefelt, Ingvar, Kalinina, Liudmila B., Kantvilas, Gintaras, Karadelev, Mitko, Kasuya, Taiga, Kautmanová, Ivona, Kerrigan, Richard W., Kirchmair, Martin, Kiyashko, Anna, Knapp, Dániel G., Knudsen, Henning, Knudsen, Kerry, Knutsson, Tommy, Kolařík, Miroslav, Kõljalg, Urmas, Košuthová, Alica, Koszka, Attila, Kotiranta, Heikki, Kotkova, Vera, Koukol, Ondřej, Kout, Jiří, Kovács, Gábor M., Kříž, Martin, Kruys, Åsa, Kučera, Viktor, Kudzma, Linas, Kuhar, Francisco, Kukwa, Martin, Kumar, T. K. Arun, Kunca, Vladimír, Kušan, Ivana, Kuyper, Thomas W., Lado, Carlos, Læssøe, Thomas, Lainé, Patrice, Langer, Ewald, Larsson, Ellen, Larsson, Karl-Henrik, Laursen, Gary, Lechat, Christian, Lee, Serena, Lendemer, James C., Levin, Laura, Lindemann, Uwe, Lindström, Håkan, Liu, Xingzhong, Hernandez, Regulo Carlos Llarena, Llop, Esteve, Locsmándi, Csaba, Lodge, Deborah Jean, Loizides, Michael, Lőkös, László, Luangsa-ard, Jennifer, Lüderitz, Matthias, Lumbsch, Thorsten, Lutz, Matthias, Mahoney, Dan, Malysheva, Ekaterina, Malysheva, Vera, Manimohan, Patinjareveettil, Marin-Felix, Yasmina, Marques, Guilhermina, Martínez-Gil, Rubén, Marson, Guy, Mata, Gerardo, Matheny, P. Brandon, Mathiassen, Geir Harald, Matočec, Neven, Mayrhofer, Helmut, Mehrabi, Mehdi, Melo, Ireneia, Mešić, Armin, Methven, Andrew S., Miettinen, Otto, Romero, Ana M. Millanes, Miller, Andrew N., Mitchell, James K., Moberg, Roland, Moreau, Pierre-Arthur, Moreno, Gabriel, Morozova, Olga, Morte, Asunción, Muggia, Lucia, González, Guillermo Muñoz, Myllys, Leena, Nagy, István, Nagy, László G., Neves, Maria Alice, Niemelä, Tuomo, Nimis, Pier Luigi, Niveiro, Nicolas, Noordeloos, Machiel E., Nordin, Anders, Noumeur, Sara Raouia, Novozhilov, Yuri, Nuytinck, Jorinde, Ohenoja, Esteri, Fiuza, Patricia Oliveira, Orange, Alan, Ordynets, Alexander, Ortiz-Santana, Beatriz, Pacheco, Leticia, Pál-Fám, Ferenc, Palacio, Melissa, Palice, Zdeněk, Papp, Viktor, Pärtel, Kadri, Pawlowska, Julia, Paz, Aurelia, Peintner, Ursula, Pennycook, Shaun, Pereira, Olinto Liparini, Daniëls, Pablo Pérez, Capella, Miquel À. Pérez-De-Gregorio, del Amo, Carlos Manuel Pérez, Gorjón, Sergio Pérez, Pérez-Ortega, Sergio, Pérez-Vargas, Israel, Perry, Brian A., Petersen, Jens H., Petersen, Ronald H., Pfister, Donald H., Phukhamsakda, Chayanard, Piątek, Marcin, Piepenbring, Meike, Pino-Bodas, Raquel, Esquivel, Juan Pablo Pinzón, Pirot, Paul, Popov, Eugene S., Popoff, Orlando, Álvaro, María Prieto, Printzen, Christian, Psurtseva, Nadezhda, Purahong, Witoon, Quijada, Luis, Rambold, Gerhard, Ramírez, Natalia A., Raja, Huzefa, Raspé, Olivier, Raymundo, Tania, Réblová, Martina, Rebriev, Yury A., García, Juan de Dios Reyes, Ripoll, Miguel Ángel Ribes, Richard, Franck, Richardson, Mike J., Rico, Víctor J., Robledo, Gerardo Lucio, Barbosa, Flavia Rodrigues, Rodriguez-Caycedo, Cristina, Rodriguez-Flakus, Pamela, Ronikier, Anna, Casas, Luis Rubio, Rusevska, Katerina, Saar, Günter, Saar, Irja, Salcedo, Isabel, Martínez, Sergio M. Salcedo, Montoya, Carlos A. Salvador, Sánchez-Ramírez, Santiago, Sandoval-Sierra, J. Vladimir, Santamaria, Sergi, Monteiro, Josiane Santana, Schroers, Hans Josef, Schulz, Barbara, Schmidt-Stohn, Geert, Schumacher, Trond, Senn-Irlet, Beatrice, Ševčíková, Hana, Shchepin, Oleg, Shirouzu, Takashi, Shiryaev, Anton, Siepe, Klaus, Sir, Esteban B., Sohrabi, Mohammad, Soop, Karl, Spirin, Viacheslav, Spribille, Toby, Stadler, Marc, Stalpers, Joost, Stenroos, Soili, Suija, Ave, Sunhede, Stellan, Svantesson, Sten, Svensson, Sigvard, Svetasheva, Tatyana Yu., Świerkosz, Krzysztof, Tamm, Heidi, Taskin, Hatira, Taudière, Adrien, Tedebrand, Jan-Olof, Lahoz, Raúl Tena, Temina, Marina, Thell, Arne, Thines, Marco, Thor, Göran, Thüs, Holger, Tibell, Leif, Tibell, Sanja, Timdal, Einar, Tkalčec, Zdenko, Tønsberg, Tor, Trichies, Gérard, Triebel, Dagmar, Tsurykau, Andrei, Tulloss, Rodham E., Tuovinen, Veera, Sosa, Miguel Ulloa, Urcelay, Carlos, Valade, François, Garza, Ricardo Valenzuela, van den Boom, Pieter, Van Vooren, Nicolas, Vasco-Palacios, Aida M., Vauras, Jukka, Santos, Juan Manuel Velasco, Vellinga, Else, Verbeken, Annemieke, Vetlesen, Per, Vizzini, Alfredo, Voglmayr, Hermann, Volobuev, Sergey, von Brackel, Wolfgang, Voronina, Elena, Walther, Grit, Watling, Roy, Weber, Evi, Wedin, Mats, Weholt, Øyvind, Westberg, Martin, Yurchenko, Eugene, Zehnálek, Petr, Zhang, Huang, Zhurbenko, Mikhail P., and Ekman, Stefan

Published
2018
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3. Which is the best postoperative chemotherapy regimen in patients with rectal cancer after neoadjuvant therapy?

Author

Peng Gao, Yong-xi Song, Jing-xu Sun, Xiao-wan Chen, Ying-ying Xu, Jun-hua Zhao, Xuan-zhang Huang, Hui-mian Xu, and Zhen-ning Wang

Subjects
POSTOPERATIVE care, CANCER chemotherapy, RECTAL cancer patients, RECTAL cancer treatment, OXALIPLATIN, FLUOROURACIL, THERAPEUTICS
Abstract

Background There is no general agreement about whether patients who have already received neoadjuvant chemoradiotherapy need further postoperative chemotherapy based on 5-fluorouracil(5-FU) or 5-FU plus oxaliplatin. Methods Medicare beneficiaries from 1992 to 2008 with Union for International Cancer Control ypStages I to III primary carcinoma of the rectum who underwent 5-FU-based neoadjuvant chemoradiotherapy and surgery for curative intent were identified through the Surveillance, Epidemiology, and End Results (SEER)-Medicare-linked database. A Cox proportional hazards model and propensity score-matched techniques were used to evaluate the effect of treatment on survival. Results For patients with resected rectal cancer who have already received 5-FU-based neoadjuvant chemoradiotherapy, postoperative 5-FU-based chemotherapy did not prolong cancer-specific survival (CSS) in ypStage I (P = 0.960) and ypStage II (P = 0.134); however, it significantly improved the CSS in ypStage III (hazard ratio = 1.547, 95% CI = 1.101-2.173, P = 0.012). No significant differences in survival between the 5-FU group and oxaliplatin group were observed. Conclusions For patients with resected rectal cancer who have already received 5-FU-based neoadjuvant chemoradiotherapy, postoperative 5-FU-based chemotherapy prolongs the CSS of groups in ypStage III. Adding oxaliplatin to fluoropyrimidines in the postoperative chemotherapy did not improve the CSS for patients who received neoadjuvant chemoradiotherapy. [ABSTRACT FROM AUTHOR]

Published
2014
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4. Fast-track surgery versus traditional perioperative care in laparoscopic colorectal cancer surgery: a meta-analysis.

Author

Jun-hua Zhao, Jing-xu Sun, Peng Gao, Xiao-wan Chen, Yong-xi Song, Xuan-zhang Huang, Hui-mian Xu, and Zhen-ning Wang

Subjects
COLON cancer treatment, PROCTOLOGY, LAPAROSCOPY, META-analysis, RANDOMIZED controlled trials
Abstract

Background: Both laparoscopic and fast-track surgery (FTS) have shown some advantages in colorectal surgery. However, the effectiveness of using both methods together is unclear. We performed this meta-analysis to compare the effects of FTS with those of traditional perioperative care in laparoscopic colorectal cancer surgery. Methods: We searched the PubMed, EMBASE, Cochrane Library, and Ovid databases for eligible studies until April 2014. The main end points were the duration of the postoperative hospital stay, time to first flatus after surgery, time of first bowel movement, total postoperative complication rate, readmission rate, and mortality. Results: Five randomized controlled trials and 5 clinical controlled trials with 1,317 patients were eligible for analysis. The duration of the postoperative hospital stay (weighted mean difference [WMD], -1.64 days; 95% confidence interval [CI], -2.25 to -1.03; p < 0.001), time to first flatus (WMD, -0.40 day; 95% CI, -0.77 to -0.04; p = 0.03), time of first bowel movement (WMD, -0.98 day; 95% CI, -1.45 to -0.52; p < 0.001), and total postoperative complication rate (risk ratio [RR], 0.67; 95% CI, 0.56-0.80; p < 0.001) were significantly reduced in the FTS group. No significant differences were noted in the readmission rate (RR, 0.64; 95% CI, 0.41-1.01; p = 0.06) or mortality (RR, 1.55; 95% CI, 0.42-5.71; p = 0.51). Conclusion: Among patients undergoing laparoscopic colorectal cancer surgery, FTS is associated with a significantly shorter postoperative hospital stay, more rapid postoperative recovery, and, notably, greater safety than is expected from traditional care. [ABSTRACT FROM AUTHOR]

Published
2014
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5. Microbiota-activated CD103 + DCs stemming from microbiota adaptation specifically drive γδT17 proliferation and activation.

Author

Fleming C, Cai Y, Sun X, Jala VR, Xue F, Morrissey S, Wei YL, Chien YH, Zhang HG, Haribabu B, Huang J, and Yan J

Subjects
Animals, Antigens, CD metabolism, Bacteria classification, Bacteria genetics, Bacteria isolation & purification, DNA, Bacterial genetics, DNA, Ribosomal genetics, Gastrointestinal Microbiome, Integrin alpha Chains metabolism, Mice, Mice, Knockout, Microbiota, Phylogeny, RNA, Ribosomal, 16S genetics, Receptors, Interleukin-17 genetics, Sequence Analysis, DNA methods, Bacteria growth & development, Dendritic Cells immunology, Mouth microbiology, Th17 Cells immunology
Abstract

Background: IL-17-producing γδT cells (γδT17) promote autoinflammatory diseases and cancers. Yet, γδT17 peripheral regulation has not been thoroughly explored especially in the context of microbiota-host interaction. The potent antigen-presenting CD103 + dendritic cell (DC) is a key immune player in close contact with both γδT17 cells and microbiota. This study presents a novel cellular network among microbiota, CD103 + DCs, and γδT17 cells., Methods: Immunophenotyping of IL-17r -/- mice and IL-17r -/- IRF8 -/- mice were performed by ex vivo immunostaining and flow cytometric analysis. We observed striking microbiome differences in the oral cavity and gut of IL-17r -/- mice by sequencing 16S rRNA gene (v1-v3 region) and analyzed using QIIME 1.9.0 software platform. Principal coordinate analysis of unweighted UniFrac distance matrix showed differential clustering for WT and IL-17r -/- mice., Results: We found drastic homeostatic expansion of γδT17 in all major tissues, most prominently in cervical lymph nodes (cLNs) with monoclonal expansion of Vγ6 γδT17 in IL-17r -/- mice. Ki-67 staining and in vitro CFSE assays showed cellular proliferation due to cell-to-cell contact stimulation with microbiota-activated CD103 + DCs. A newly developed double knockout mice model for IL-17r and CD103 + DCs (IL-17r -/- IRF8 -/- ) showed a specific reduction in Vγ6 γδT17. Vγ6 γδT17 expansion is inhibited in germ-free mice and antibiotic-treated specific pathogen-free (SPF) mice. Microbiota transfer using cohousing of IL-17r -/- mice with wildtype mice induces γδT17 expansion in the wildtype mice with increased activated CD103 + DCs in cLNs. However, microbiota transfer using fecal transplant through oral gavage to bypass the oral cavity showed no difference in colon or systemic γδT17 expansion., Conclusions: These findings reveal for the first time that γδT17 cells are regulated by microbiota dysbiosis through cell-to-cell contact with activated CD103 + DCs leading to drastic systemic, monoclonal expansion. Microbiota dysbiosis, as indicated by drastic bacterial population changes at the phylum and genus levels especially in the oral cavity, was discovered in mice lacking IL-17r. This network could be very important in regulating both microbiota and immune players. This critical regulatory pathway for γδT17 could play a major role in IL-17-driven inflammatory diseases and needs further investigation to determine specific targets for future therapeutic intervention.

Published
2017
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