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Wang S, Wu W, Cai A, Xu Y, Vardhanabhuti V, Liu F, Yu H. Image-spectral decomposition extended-learning assisted by sparsity for multi-energy computed tomography reconstruction. Quant Imaging Med Surg 2023; 13:610-630. [PMID: 36819292 PMCID: PMC9929415 DOI: 10.21037/qims-22-235] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022]
Abstract
Background Multi-energy computed tomography (CT) provides multiple channel-wise reconstructed images, and they can be used for material identification and k-edge imaging. Nonetheless, the projection datasets are frequently corrupted by various noises (e.g., electronic, Poisson) in the acquisition process, resulting in lower signal-noise-ratio (SNR) measurements. Multi-energy CT images have local sparsity, nonlocal self-similarity in spatial dimension, and correlation in spectral dimension. Methods In this paper, we propose an image-spectral decomposition extended-learning assisted by sparsity (IDEAS) method to fully exploit these intrinsic priors for multi-energy CT image reconstruction. Particularly, a nonlocal low-rank Tucker decomposition (TD) is employed to utilize the correlation and nonlocal self-similarity priors. Moreover, considering the advantages of multi-task tensor dictionary learning (TDL) in sparse representation, an adaptive spatial dictionary and an adaptive spectral dictionary are trained during the iterative reconstruction process. Furthermore, a weighted total variation (TV) regularization term is employed to encourage local sparsity. Results Numerical simulation, physical phantom, and preclinical mouse experiments are performed to validate the proposed IDEAS algorithm. Specifically, in the simulation experiments, the proposed IDEAS reconstructed high-quality images that are very close to the references. For example, the root mean square error (RMSE) of IDEAS image in energy bin 1 is as low as 0.0672, while the RMSE of other methods are higher than 0.0843. Besides, the structural similarity (SSIM) of IDEAS reconstructed image in energy bin 1 is greater than 0.98. For material decomposition, the RMSE of IDEAS bone component is as low as 0.0152, and other methods are higher than 0.0199. In addition, the computational cost of IDEAS is as low as 98.8 s for one iteration, and the competing tensor decomposition method is higher than 327 s. Conclusions To further improve the quality of the reconstructed multi-energy CT images, multiple prior regularizations are introduced to the multi-energy CT reconstructed model, leading to an IDEAS method. Both qualitative and quantitative evaluation of our results confirm the outstanding performance of the proposed algorithm compared to the state-of-the-arts.
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Yang Y, Chen H, Ji M, Wu J, Chen X, Liu F, Rao S. A new radiomics approach combining the tumor and peri-tumor regions to predict lymph node metastasis and prognosis in gastric cancer. Gastroenterol Rep (Oxf) 2023; 7:goac080. [PMID: 36627981 PMCID: PMC9825201 DOI: 10.1093/gastro/goac080] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 01/09/2023] Open
Abstract
Objective The development of non-invasive methods for evaluating lymph node metastasis (LNM) preoperatively in gastric cancer (GC) is necessary. In this study, we developed a new radiomics model combining features from the tumor and peri-tumor regions for predicting LNM and prognoses. Methods This was a retrospective observational study. In this study, two cohorts of patients with GC treated in Zhongshan Hospital Fudan University (Shanghai, China) were included. In total, 193 patients were assigned to the internal training/validation cohort; another 98 patients were assigned to the independent testing cohort. The radiomics features were extracted from venous phase computerized tomography (CT) images. The radiomics model was constructed and the output was defined as the radiomics score (RS). The performance of the RS and CT-defined N status (ctN) for predicting LNM was compared using the area under the curve (AUC). The 5-year overall survival and progression-free survival were compared between different subgroups using Kaplan-Meier curves. Results In both cohorts, the RS was significantly higher in the LNM-positive group than that in the LNM-negative group (all P < 0.001). The radiomics model combining features from the tumor and peri-tumor regions achieved the highest AUC in predicting LNM (AUC, 0.779 and 0.724, respectively), which performed better than the radiomics model based only on the tumor region and ctN (AUC, 0.717, 0.622 and 0.710, 0.603, respectively). The differences in 5-year overall survival and progression-free survival between high-risk and low-risk groups were significant (both P < 0.001). Conclusions The radiomics model combining features from the tumor and peri-tumor regions could effectively predict the LNM in GC. Risk stratification based on the RS was capable of distinguishing patients with poor prognoses.
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YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV. Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Wang S, Cai A, Wu W, Zhang T, Liu F, Yu H. IMD-MTFC: Image-domain Material Decomposition via Material-image Tensor Factorization and Clustering for Spectral CT. IEEE TRANSACTIONS ON RADIATION AND PLASMA MEDICAL SCIENCES 2023. [DOI: 10.1109/trpms.2023.3234613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu 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KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Wu Z, Yan S, Liu Z, Jing C, Liu F, Yu J, Li Z, Zhang J, Zang L, Hao H, Zheng C, Li Y, Fan L, Huang H, Liang P, Wu B, Zhu J, Niu Z, Zhu L, Song W, You J, Wang Q, Li Z, Ji J. Postoperative abdominal complications of gastric and colorectal cancer surgeries in China: a multicentered prospective registry-based cohort study. Sci Bull (Beijing) 2022; 67:2517-2521. [PMID: 36604028 DOI: 10.1016/j.scib.2022.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/15/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
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Liu F, Wu X, You C, Ge S, Zou Y, Sun X. Aligning Source Visual and Target Language Domains for Unpaired Video Captioning. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2022; 44:9255-9268. [PMID: 34855588 DOI: 10.1109/tpami.2021.3132229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Training supervised video captioning model requires coupled video-caption pairs. However, for many targeted languages, sufficient paired data are not available. To this end, we introduce the unpaired video captioning task aiming to train models without coupled video-caption pairs in target language. To solve the task, a natural choice is to employ a two-step pipeline system: first utilizing video-to-pivot captioning model to generate captions in pivot language and then utilizing pivot-to-target translation model to translate the pivot captions to the target language. However, in such a pipeline system, 1) visual information cannot reach the translation model, generating visual irrelevant target captions; 2) the errors in the generated pivot captions will be propagated to the translation model, resulting in disfluent target captions. To address these problems, we propose the Unpaired Video Captioning with Visual Injection system (UVC-VI). UVC-VI first introduces the Visual Injection Module (VIM), which aligns source visual and target language domains to inject the source visual information into the target language domain. Meanwhile, VIM directly connects the encoder of the video-to-pivot model and the decoder of the pivot-to-target model, allowing end-to-end inference by completely skipping the generation of pivot captions. To enhance the cross-modality injection of the VIM, UVC-VI further introduces a pluggable video encoder, i.e., Multimodal Collaborative Encoder (MCE). The experiments show that UVC-VI outperforms pipeline systems and exceeds several supervised systems. Furthermore, equipping existing supervised systems with our MCE can achieve 4% and 7% relative margins on the CIDEr scores to current state-of-the-art models on the benchmark MSVD and MSR-VTT datasets, respectively.
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You C, Zhao R, Liu F, Dong S, Chinchali S, Topcu U, Staib L, Duncan JS. Class-Aware Adversarial Transformers for Medical Image Segmentation. ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 2022; 35:29582-29596. [PMID: 37533756 PMCID: PMC10395073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Transformers have made remarkable progress towards modeling long-range dependencies within the medical image analysis domain. However, current transformer-based models suffer from several disadvantages: (1) existing methods fail to capture the important features of the images due to the naive tokenization scheme; (2) the models suffer from information loss because they only consider single-scale feature representations; and (3) the segmentation label maps generated by the models are not accurate enough without considering rich semantic contexts and anatomical textures. In this work, we present CASTformer, a novel type of adversarial transformers, for 2D medical image segmentation. First, we take advantage of the pyramid structure to construct multi-scale representations and handle multi-scale variations. We then design a novel class-aware transformer module to better learn the discriminative regions of objects with semantic structures. Lastly, we utilize an adversarial training strategy that boosts segmentation accuracy and correspondingly allows a transformer-based discriminator to capture high-level semantically correlated contents and low-level anatomical features. Our experiments demonstrate that CASTformer dramatically outperforms previous state-of-the-art transformer-based approaches on three benchmarks, obtaining 2.54%-5.88% absolute improvements in Dice over previous models. Further qualitative experiments provide a more detailed picture of the model's inner workings, shed light on the challenges in improved transparency, and demonstrate that transfer learning can greatly improve performance and reduce the size of medical image datasets in training, making CASTformer a strong starting point for downstream medical image analysis tasks.
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Wu W, Yu H, Liu F, Zhang J, Vardhanabhuti V, Chen J. Spectral CT reconstruction via Spectral-Image Tensor and Bidirectional Image-gradient minimization. Comput Biol Med 2022; 151:106080. [PMID: 36327881 DOI: 10.1016/j.compbiomed.2022.106080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/19/2022] [Accepted: 09/03/2022] [Indexed: 12/27/2022]
Abstract
It is challenging to obtain good image quality in spectral computed tomography (CT) as the photon-number for the photon-counting detectors is limited for each narrow energy bin. This results in a lower signal to noise ratio (SNR) for the projections. To handle this issue, we first formulate the weight bidirectional image gradient with L0-norm constraint of spectral CT image. Then, as a new regularizer, bidirectional image gradient with L0-norm constraint is introduced into the tensor decomposition model, generating the Spectral-Image Tensor and Bidirectional Image-gradient Minimization (SITBIM) algorithm. Finally, the split-Bregman method is employed to optimize the proposed SITBIM mathematical model. The experiments on the numerical mouse phantom and real mouse experiments are designed to validate and evaluate the SITBIM method. The results demonstrate that the SITBIM can outperform other state-of-the-art methods (including TVM, TV + LR, SSCMF and NLCTF). INDEX TERMS: -spectral CT, image reconstruction, tensor decomposition, unidirectional image gradient, image similarity.
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Lin L, Wang AP, Dou JT, Chen Y, Liu FL, Ma H, Zheng LG, Dong SY, Wang YM, Mu Y. [Predictive value of hemoglobin glycation index for chronic kidney disease]. ZHONGHUA NEI KE ZA ZHI 2022; 61:1310-1317. [PMID: 36456510 DOI: 10.3760/cma.j.cn112138-20220508-00347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Objective: To investigate the influence of hemoglobin glycation index (HGI) on the risk of incident chronic kidney disease (CDK) among nondiabetic patients. Methods: Prospective cohort study. At baseline, a total of 7 407 nondiabetic patients without a history of CKD from Pingguoyuan Community of the Shijingshan District in Beijing were included from December 2011 to August 2012, who were then divided into three groups according to the tertiles of their baseline HGI levels. The CKD incidence rate was compared among the different HGI groups at last follow-up. Cox multivariable regression was applied to evaluate whether HGI measures predicted CKD risk. Test for trend across tertiles were examined using ordinal values in separate models. Results: The mean age of the subjects was (56.4±7.5) years, and 4 933 (66.6%) were female. At mean follow-up of 3.23 years, 107 (1.4%) individuals developed CKD. The incidence of CKD was gradually increasing from the low to high HGI groups [1.1% (28/2 473) vs. 1.2% (31/2 564) vs. 2.0% (48/2 370), P=0.016]. In the multivariate Cox regression analysis, after adjustment for potential confounders, the high HGI group had a 68.5% increased risk of CKD compared with the low HGI group (HR=1.685, 95%CI 1.023 to 2.774). CKD risk increased with increasing HGI tertiles (P for trend=0.028). Conclusion: High HGI is associated with an increased risk for CKD in the nondiabetic population, indicating that HGI may help identify individuals at high risk for CKD.
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Li Y, Liu FL, Yuan J, Li ZW, Liu NX, Guan N. [Meta-analysis of the interventional effects of music therapy on pain and anxiety of burn patients in wound dressing change]. ZHONGHUA SHAO SHANG YU CHUANG MIAN XIU FU ZA ZHI 2022; 38:1079-1084. [PMID: 36418266 DOI: 10.3760/cma.j.cn501120-20210716-00252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Objective: To evaluate the interventional effects of music therapy on pain and anxiety of burn patients in wound dressing change. Methods: The meta-analysis method was adopted. Databases including China National Knowledge Internet, Wanfang Database, and VIP database were retrieved with the search terms in Chinese version of ", , /, /", and PubMed, Embase, and Cochrane Library were retrieved with the search terms in English version of "music, burn, dressing change/wound dressing, pain/ache/sore" to obtain the publicly published randomized controlled trials on the application of music therapy for wound dressing change in burn patients from the establishment of each database to May 2021. The outcome indexes included pain score/percentage and anxiety score after dressing change. Rev Man 5.4 and Stata 14.0 statistical software were used to conduct a meta-analysis of eligible studies. Results: A total of 520 burn patients from 7 studies were included, including 260 patients in music therapy group who received music therapy and 260 patients in routine dressing change group who received routine dressing change. The bias risk of all the 7 included studies was uncertain. Compared with those in routine dressing change group, the pain percentages (relative risk=0.06, 95% confidence interval=0.01-0.41, P<0.01) and pain scores after dressing change (standardized mean difference (SMD)=-0.91, 95% confidence interval=-1.61--0.22, P<0.05) of patients in music therapy group were significantly lower. Subgroup analysis showed that music type and timing of intervention might be the source of heterogeneity in pain scores after dressing change. The anxiety scores of patients in music therapy group were significantly lower than those in routine dressing change group (SMD=-0.64, 95% confidence interval=-1.09--0.19, P<0.01). There was no publication bias in pain or anxiety scores after dressing change. Conclusions: Music therapy can relieve the pain and anxiety of burn patients during dressing change.
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Ramonfaur DR, Buckley LB, Arthur VA, Claggett BC, Ndumele CN, Walker KAW, Kitzman DK, Konety SK, Schrack JS, Liu FL, Windham BGW, Palta PP, Coresh JC, Yu BY, Shah AMS. Proteomic biomarkers associated with incident heart failure and frailty in late life. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Heart failure (HF) and frailty are highly prevalent in late life and commonly co-exist, but the mechanisms underlying their bi-directional relationship are incompletely understood. This study aimed to identify shared molecular pathways associated with incident HF and frailty in late life.
Methods
Among participants in the Atherosclerosis Risk in Communities (ARIC) study, a communit-based cohort study in the United States, 4,877 plasma proteins were measured using an aptamer-affinity assay (Somascan v4) at study Visit 3 (V3; 1993–1994; n=10,368, age 60±6 years; 822 incident HF events) and at study Visit 5 (V5; 2011–2013; n=3,908, age 75±5 years; 336 incident HF events). Frailty was assessed at V5 using Fried criteria, which incorporates gait speed, grip strength, low energy expenditure, weight loss, and exhaustion. We examined the association of proteins at V3 with incident HF after V3 with Bonferroni corrected P<0.05 using multivariable Cox proportional hazard regression models. For HF-associated proteins at V3, we assessed the association of V5 protein levels with incident HF after V5. For the resulting HF-associated proteins, multivariable logistic regression was used to assess associations of V5 protein values with prevalent frailty at V5 (n=223 cases) and with incident frailty by study Visit 6 (2016–2018; n=152 incident cases). All models adjusted for age, sex, race, hypertension, diabetes, cardiovascular disease, BMI, atrial fibrillation, and stroke. The set of HF-related proteins that associated with incident frailty at FDR <0.05 using Benjamini-Hochberg correction was tested for pathway enrichment using the Reactome database.
Results
Of 289 proteins associated with incident HF post-V3 at p<1.0x10–5 (0.05/4,877), 84 were significantly associated with incident HF post-V5 at p<1.7x10–4 (0.05/289). Among 4,131 HF-free participants at V5, 48 of these 84 HF-associated proteins associated with prevalent frailty at p<5.9x10–4 (0.05/84). Among Visit 5 participants who completed a frailty assessment and were free of both prevalent HF and frailty (n=3,908), 31of 48 candidate proteins were also significantly associated with incident frailty at FDR 0.05, 18 of which were significantly associated with incident frailty at p<1.0x10–3 (0.05/48; Figure 1). The 31 proteins associated with incident frailty at FDR 0.05 enriched for collagen biosynthesis, formation, and trimerization (COL28A1, COL6A3, EFEMP1), and cytokine immune pathways and TNF receptor binding (TNFRSF1A and B, VEGFA, B2M, and HAVCR2) in pathway enrichment analysis.
Conclusions
Collagen metabolism and immune pathways may be shared biologic pathways between HF and frailty in late-life.
Funding Acknowledgement
Type of funding sources: Public Institution(s). Main funding source(s): The Atherosclerosis Risk in Communities study has been funded in whole or in part with Federal funds from the National Heart, Lung, and Blood Institute, National Institutes of Health, Department of Health and Human Services.
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Liu Y, Yue W, Yu S, Zhou T, Zhang Y, Zhu R, Song B, Guo T, Liu F, Huang Y, Wu T, Wang H. A physical perspective to understand myelin II: The physical origin of myelin development. Front Neurosci 2022; 16:951998. [PMID: 36263368 PMCID: PMC9574017 DOI: 10.3389/fnins.2022.951998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
The physical principle of myelin development is obtained from our previous study by explaining Peter’s quadrant mystery: an externally applied negative and positive E-field can promote and inhibit the growth of the inner tongue of the myelin sheath, respectively. In this study, this principle is considered as a fundamental hypothesis, named Hypothesis-E, to explain more phenomena about myelin development systematically. Specifically, the g-ratio and the fate of the Schwann cell’s differentiation are explained in terms of the E-field. Moreover, an experiment is proposed to validate this theory.
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Liu Y, Yue W, Yu S, Zhou T, Zhang Y, Zhu R, Song B, Guo T, Liu F, Huang Y, Wu T, Wang H. A physical perspective to understand myelin. I. A physical answer to Peter’s quadrant mystery. Front Neurosci 2022; 16:951942. [PMID: 36225732 PMCID: PMC9548592 DOI: 10.3389/fnins.2022.951942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/05/2022] [Indexed: 11/28/2022] Open
Abstract
In the development of oligodendrocytes in the central nervous systems, the inner and outer tongue of the myelin sheath tend to be located within the same quadrant, which was named as Peters quadrant mystery. In this study, we conduct in silico investigations to explore the possible mechanisms underlying the Peters quadrant mystery. A biophysically detailed model of oligodendrocytes was used to simulate the effect of the actional potential-induced electric field across the myelin sheath. Our simulation suggests that the paranodal channel connecting the inner and outer tongue forms a low impedance route, inducing two high-current zones at the area around the inner and outer tongue. When the inner tongue and outer tongue are located within the same quadrant, the interaction of these two high-current-zones will induce a maximum amplitude and a polarity reverse of the voltage upon the inner tongue, resulting in the same quadrant phenomenon. This model indicates that the growth of myelin follows a simple principle: an external negative or positive E-field can promote or inhibit the growth of the inner tongue, respectively.
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Chen L, Liu FL. [Dilemmas in definition and classification of adenocarcinoma of esophagogastric junction: from history to current status]. ZHONGHUA WAI KE ZA ZHI [CHINESE JOURNAL OF SURGERY] 2022; 60:813-818. [PMID: 36058706 DOI: 10.3760/cma.j.cn112139-20220424-00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In recent years, adenocarcinoma of esophagogastric junction (AEG) has received increased attention from the academic community. However, the esophagogastric junction (EGJ) straddles two anatomical regions: the thoracic cavity and the abdominal cavity. The histological features of the EGJ are different from those of the esophagus and stomach. There are general disagreements among the related disciplines regarding the definition and classification of AEG. By summarizing the views of different disciplines, including endoscopy, radiography, and pathology, a more comprehensive definition of the EGJ was formulated in the Japanese Classification of Gastric Carcinoma (the 15th edition), and the principle of endoscopic diagnostic priority was established. In recent years, with the development of physiological and anatomical studies, the EGJ has gradually expanded conceptually into a complex functional anatomical region covering the distal esophagus to the proximal stomach. The venous and lymphatic vessels in the EGJ are characterized by bidirectional flow, which is an important anatomical basis for the invasion and metastasis patterns of tumors in this region. The clinical practice of EGJ cancer has been promoted by the creation of Nishi and Siewert classification systems. With the support of a series of clinical studies for its scientificity and effectiveness, the Siewert classification is widely accepted by the international community, and successively introduced into major international practice guidelines. In general, the staging and management of Siewert Ⅰ and Ⅱ AEG are recommended as esophageal cancer, while Siewert Ⅲ AEG is recommended for gastric cancer. However, in the Japanese guidelines for the treatment of esophageal and gastric cancers, the Nishi classification is still used to define and classify EGJ cancer. Recent year, a Chinese consensus on the surgical treatment of AEG was formulated by multidisciplinary experts. The main controversies were summarized in the consensus, and proposals that incorporate the domestic situation were also presented. At present, only by returning to the basic anatomical and physiological perspectives, strengthening multidisciplinary communication and cooperation, and with the help of emerging bioinformatics, digital, and material technology, can it be possible to get out of the dilemma faced by traditional AEG classification and staging system.
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Yang L, Wu JZ, You J, Fan L, Jing CQ, Wang Q, Yan S, Yu J, Zang L, Xing JD, Hu WQ, Liu F. [A multicenter retrospective study on the efficacy of different anti-reflux reconstruction methods after proximal gastrectomy for gastric cancer]. ZHONGHUA WAI KE ZA ZHI [CHINESE JOURNAL OF SURGERY] 2022; 60:838-845. [PMID: 36058710 DOI: 10.3760/cma.j.cn112139-20220418-00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Objective: To examine the clinical efficacy of 3 anti-reflux methods of digestive tract reconstruction after proximal gastrectomy for gastric cancer. Methods: The clinical data and follow-up data of gastric cancer patients who underwent anti-reflux reconstruction after proximal gastrectomy in 11 medical centers of China from September 2016 to August 2021 were retrospectively collected, including 273 males and 65 females, aging of (63±10) years (range: 28 to 91 years). Among them, 159 cases were performed with gastric tube anastomosis (GTA), 107 cases with double tract reconstruction (DTR), and 72 cases with double-flap technique (DFT), respectively. The duration of operation, length of postoperative hospital stay and early postoperative complications (referring to Clavien-Dindo classification) of different anti-reflux reconstruction methods were assessed. Body mass index, hemoglobin and albumin were used to reflect postoperative nutritional status. Reflux esophagitis was graded according to Los Angeles criteria based on the routinely gastroscopy within 12 months after surgery. The postoperative quality of life (QoL) was evaluated by Visick score system. The ANOVA analysis, Kruskal-Wallis rank sum test, χ2 test and Fisher's exact test were used for comparison between multiple groups, and further comparison among groups were performed with LSD, Tamhane's test or Bonferroni corrected χ2 test. The mixed effect model was used to compare the trends of Body mass index, hemoglobin and albumin over time among different groups. Results: The operation time of DFT was significantly longer than that of GTA and DTR ((352±63) minutes vs. (221±66) minutes, (352±63) minutes vs. (234±61) minutes, both P<0.01). The incidence of early complications with Clavien-Dindo grade Ⅱ to Ⅴ in GTA, DFT and DTR groups was 17.0% (27/159), 9.7% (7/72) and 10.3% (11/107), respectively, without significant difference among these three groups (χ2=3.51, P=0.173). Body mass index decreased more significantly in GTA than DFT group at 6 and 12 months after surgery (mean difference=1.721 kg/m2, P<0.01; mean difference=2.429 kg/m2, P<0.01). body mass index decreased significantly in DTR compared with DFT at 12 months after surgery (mean difference=1.319 kg/m2, P=0.027). There was no significant difference in hemoglobin or albumin fluctuation between different reconstruction methods perioperative. The incidence of reflux esophagitis one year after surgery in DTR group was 12.9% (4/31), which was lower than that in DFT (45.9% (17/37), χ2=8.63, P=0.003). Follow-up of postoperative quality of life showed the incidence of Visick grade 2 to 4 in DFT group was lower than that in GTA group (10.4% (7/67) vs. 34.6% (27/78), χ2=11.70, P=0.018), while there was no significant difference between DFT and DTR group (10.4% (7/67) vs. 22.2% (8/36, P>0.05). Conclusions: Compared with GTA and DTR, DFT is more time-consuming, but there is no significant difference in early complications among three methods. DFT reconstruction is more conducive to maintain postoperative nutritional status and improve QoL, especially compared with GTA. The risk of reflux esophagitis after DTR reconstruction is lower than that of DFT.
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Jiang Q, Tian C, Wu H, Min L, Chen H, Chen L, Liu F, Sun Y. Tertiary lymphoid structure patterns predicted anti-PD1 therapeutic responses in gastric cancer. Chin J Cancer Res 2022; 34:365-382. [PMID: 36199531 PMCID: PMC9468020 DOI: 10.21147/j.issn.1000-9604.2022.04.05] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/04/2022] [Indexed: 10/24/2023] Open
Abstract
OBJECTIVE Recent studies have highlighted the distinct value of tertiary lymphoid structure (TLS) for immunotherapeutic response prediction. However, it remains unclear whether TLS could play such roles in gastric cancer (GC). METHODS In this study, tumor tissue slices from 292 GC patients from Zhongshan Hospital were firstly reviewed to explore the correlation between TLS and clinical characteristics. Subsequently, we curated 38 reported genes that may function as triggers of TLS and performed consensus molecular subtyping in public RNA-seq datasets to determine TLS patterns in GC. Based on the differentially expressed genes acquired from two TLS patterns, we quantified TLS-related genes on the principal component analysis (PCA) algorithm to develop TLS score. A Zhongshan immunotherapy cohort including 13 patients who received programmed cell death 1 (PD1) blockade therapy was established to conduct RNA sequencing analysis and multiplex immunohistochemistry (mIHC) tests using formalin-fixed and paraffin-embedded (FFPE) tissues. The corresponding TLS score and immune cell counts were further compared based on therapeutic response variations. RESULTS Mature TLS was revealed as an independent prognostic factor in 292 GC patients. Patients with higher TLS score was characterized by prolonged survival time and superior response to immunotherapy. TLS score was correlated with immunotherapy-related characters, such as microsatellite instability (MSI) and tumor mutation burden (TMB). In addition, RNA-seq data analysis in the Zhongshan immunotherapy cohort indicated that a higher TLS score was correlated with a superior response to PD1 blockade therapy. mIHC tests also revealed that PD1+CD8+ T cell counts were significantly increased in the high-TLS score group. CONCLUSIONS This study highlighted that TLS was significantly associated with immune landscape diversity and complexity. Quantitatively evaluating TLS patterns of individual tumor will strengthen our understanding of TME characteristics and promote more effective immunotherapy strategies.
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Xu L, Xiang P, Zhang B, Yang K, Liu F, Wang Z, Jin Y, Deng L, Gan W, Song Z. Host Species Influence the Gut Microbiota of Endemic Cold-Water Fish in Upper Yangtze River. Front Microbiol 2022; 13:906299. [PMID: 35923412 PMCID: PMC9339683 DOI: 10.3389/fmicb.2022.906299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
The fish gut microbiome plays an important role in nutrition absorption and energy metabolism. Studying the gut microbes of cold-water fish is important to understand the dietary adaptation strategies in extreme environments. In this study, the gut samples of Schizothorax wangchiachii (SW, herbivorous), Schizothorax kozlovi (SK, omnivorous), and Percocypris pingi (PP, carnivorous) in the upper Yangtze River were collected, and we sequenced 16S rRNA amplicon to study the potential relationship between gut microbes and host species. The results showed that gut microbial composition and diversity were significantly different between the three cold-water fishes. These fishes had different key taxa in their gut microbes, including bacteria involved in the breakdown of food (e.g., Cetobacterium, Aeromonas, and Clostridium sensu stricto 10). The highest alpha diversity indices (e.g., Chao 1 index) were identified in the herbivore (SW), followed by the carnivore (PP), and the lowest in the omnivore (SK). Non-metric multidimensional scaling (NMDS) results revealed that the gut microbial community of these species was different between host species. The neutral community model (NCM) showed that the microbial community structure of SW was shaped by stochastic processes, and the highest species dispersal was found in SW, followed by PP, and the lowest in SK. The results of niche breadth agreed with these findings. Our results demonstrated that host species influenced the gut microbiome composition, diversity, and microbial community assembly processes of the three cold-water fishes. These findings implied that the variation of gut microbiome composition and function plays a key role in digesting and absorbing nutrients from different foods in cold-water fish.
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He D, Chen M, Chang L, Gu J, Liu F, Gao X, Ruan Y. De novo pyrimidine synthesis fuels glycolysis and confers chemoresistance in gastric cancer. Cancer Lett 2022; 549:215837. [DOI: 10.1016/j.canlet.2022.215837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/16/2022] [Accepted: 07/21/2022] [Indexed: 11/27/2022]
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Chen L, Sun J, Chen H, Liu F. Perioperative Safety Evaluation of Gastrointestinal Surgery in Patients With Prosthetic Valves. Heart Surg Forum 2022; 25:E305-E313. [DOI: 10.1532/hsf.4533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/07/2022] [Indexed: 11/20/2022]
Abstract
Background: In patients with prosthetic valves, the perioperative outcomes, as well as the risk factors, following gastrointestinal surgery remain to be defined.
Methods: From January 2010 to March 2018, the clinical data of 69 cases with prosthetic valves after gastrointestinal surgery retrospectively were collected. Univariate and multivariate analysis were applied to identify the risk factors associated with significant bleeding events and non-hemorrhagic complications.
Results: Among 69 cases, 9 patients (13.0%) presented major bleeding events, and 21 patients (30.4%) presented non-hemorrhagic complications. Major bleeding events were significantly higher in patients with simple aortic valve replacement (AVR) than in other types of prosthetic valves (27.6% vs. 2.5%, P = 0.003), and there was no significant difference in the incidence of non-hemorrhagic complications. Simple AVR was the significant risk factor for major bleeding events (P = 0.043). Significant risk factors for non-hemorrhagic complications were operative duration ≥ 160 minutes (P = 0.021), duration from heart valve replacement to gastrointestinal surgery ≥ 84 months (P = 0.039), and simple AVR (P = 0.047).
Conclusion: The patients with simple AVR had a much higher bleeding risk following gastrointestinal surgery.
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Cai TY, Liu FL. [Application value and difficulty analysis of fluorescence laparoscopy in lymphadenectomy of gastric cancer]. ZHONGHUA WEI CHANG WAI KE ZA ZHI = CHINESE JOURNAL OF GASTROINTESTINAL SURGERY 2022; 25:295-299. [PMID: 35461195 DOI: 10.3760/cma.j.cn441530-20220111-00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gastric cancer is one of the most common gastrointestinal malignancies, and the incidence and mortality of gastric cancer remain high in China. In recent years, with the rapid popularization of laparoscopic technology, fluorescent laparoscopic technology is increasingly getting mature, providing a new method for accurate clinical tracing of lymph nodes and prediction of tumor metastasis lymph nodes. A large number of scientific research experiments and clinical trials have shown that, laparoscopic lymph node diagnosis technology based on the fluorescent indocyanine green (ICG) can significantly improve the efficiency of lymphadenectomy and prediction accuracy of lymph node metastasis, and can reveal a more accurate scope of lymphadenectomy in gastric cancer for surgeons, so as to avoid excessive adenectomy as well as iatrogenic injuries on patients. Although the status of the technology in gastric cancer surgery mentioned above continues improving, the overall operation process details of ICG fluorescence imaging, standardized fluorescence detecting equipment, and postoperative pathological examination process still need to be further optimized.
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Zhao JJ, Liu FL. [Laparoscopic proximal gastrectomy and lymph node resection in adenocarcinoma of the esophagogastric junction]. ZHONGHUA WEI CHANG WAI KE ZA ZHI = CHINESE JOURNAL OF GASTROINTESTINAL SURGERY 2022; 25:114-119. [PMID: 35176821 DOI: 10.3760/cma.j.cn441530-20211103-00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The proportion of adenocarcinoma of the esophagogastric junction (AEG) in gastric cancer is gradually increasing. Due to the unique anatomical structure and biological characteristics of the tumor at this site, AEG has a certain degree of complexity in many aspects of diagnosis and treatment, which brings difficulties to the operation method, the selection of the resection range, the lymph node dissection and the treatment decision-making. Therefore, AEG has always been the focus of academic debate. With the development of minimally invasive surgery in recent years, laparoscopic technology has been increasingly mature and widely used in the treatment of gastrointestinal tumors. Compared with distal gastric cancer, the minimally invasive treatment of AEG is in a lagging state, and there are also a series of problems that have not yet reached a consensus. This article reviews and summarizes the recent research progress in two aspects: proximal gastrectomy for AEG and lymph node dissection. Laparoscopic-assisted proximal gastrectomy is safe for early proximal gastric cancer and has a long-term survival outcome not inferior to total gastrectomy, but the surgical indications must be strictly selected. Abdominal lymph node metastasis of AEG is mainly in group 1, 2, 3, and 7, and mediastinal lymph node metastasis is closely related to the length of the infiltrated esophagus. The abdominal transhiatal (TH) approach can obtain a sufficient number of harvested lymph node, and has good safety and efficacy, which is the first-choice of surgical approach for early AEG. The results of the CLASS-10 clinical trial can provide a higher level of evidence for laparoscopic mediastinal lymph node dissection. Laparoscopic surgery for AEG should be carried out in experienced medical center based on clinical research.
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Hong X, Liu F. Editorial: Molecular Biomarkers for Gastric Cancer. Front Oncol 2022; 12:850373. [PMID: 35186772 PMCID: PMC8850303 DOI: 10.3389/fonc.2022.850373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/17/2022] [Indexed: 01/04/2023] Open
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Wu J, Tang Z, Zhao G, Zang L, Li Z, Zang W, Li Z, Qu J, Yan S, Zheng C, Ji G, Zhu L, Zhao Y, Zhang J, Huang H, Hao Y, Fan L, Xu H, Li Y, Yang L, Song W, Zhu J, Zhang W, Li M, Qin X, Liu F. Incidence and risk factors for postoperative pancreatic fistula in 2089 patients treated by radical gastrectomy: A prospective multicenter cohort study in China. Int J Surg 2022; 98:106219. [PMID: 34990829 DOI: 10.1016/j.ijsu.2021.106219] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To determine the incidence of clinically relevant postoperative pancreatic fistula (CR-POPF) following radical gastrectomy and to identify independent risk factors of CR-POPF. BACKGROUND CR-POPF and its sequelae are potential complications following radical gastrectomy. The reported incidence of CR-POPF was quite different across various regions, and no consensus was reached. METHODS Between December 2017 to November 2018, patients who underwent radical gastrectomy from 22 centers across 13 regions in China were prospectively recruited. The primary endpoint was the occurrence of CR-POPF, defined by the International Study Group of Pancreatic Fistula (ISGPF) in 2016. Clinically relevant change and short-term outcomes were recorded to diagnose and grade the POPF. Multivariate regression analyses were performed to identify independent risk factors of clinically relevant postoperative pancreatic fistula (CR-POPF). RESULTS A total of 2089 cases were analyzed. The incidence of biochemical leakage (BL) and CR-POPF were 19.6% and 1.1% respectively. All CR-POPF patients recovered well after appropriate treatment and no Grade C POPF were recorded. Logistic regression analysis showed pTNM III (OR, 2.940; 95% CI 1.180-7.325; P = 0.021) and LigaSure usage (OR, 6.618; 95% CI 1.847-23.707; P = 0.004) were independent risk factors of CR-POPF. LigaSure usage (OR, 4.817; 95% CI 1.184-19.598; P = 0.028), the drain amylase content (D-AMY) on postoperative day 3 (POD3) ≥5 times the upper limit of normal amylase (OR, 3.476; 95% CI 1.240-9.744; P = 0.018) and open surgery (OR, 2.463; 95% CI 1.003-6.050; P = 0.049) were independent predictors for identifying CR-POPF from BL. CONCLUSION In rich-experienced gastric cancer centers, there is high prevalence of BL secondary to radical gastrectomy without clinical impact. Fewer patients suffered Grade B POPF, and Grade C POPF was less common. The patients with pTNM III or LigaSure usage were prone to suffer CR-POPF. Surgery procedure, LigaSure usage combined with D-AMY measurement on POD3 are promising for early identification of CR-POPF.
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Tan C, Yu H, Xi Y, Li L, Liao M, Liu F, Duan L. Multi source translation based projection completion for interior region of interest tomography with CBCT. OPTICS EXPRESS 2022; 30:2963-2980. [PMID: 35209426 DOI: 10.1364/oe.442287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Interior tomography by rotary computed tomography (RCT) is an effective method to improve the detection efficiency and achieve high-resolution imaging for the region of interest (ROI) within a large-scale object. However, because only the X-rays through the ROI can be received by detector, the projection data is inevitably truncated, resulting in truncation artifacts in the reconstructed image. When the ROI is totally within the object, the solution of the problem is not unique, which is named interior problem. Fortunately, projection completion (PC) is an effective technique to solve the interior problem. In this study, we proposed a multi source translation CT based PC method (mSTCT-PC) to cope with the interior problem. Firstly, mSTCT-PC employs multi-source translation to sparsely obtain the global projection which covered the whole object. Secondly, the sparse global projection is utilized to fill up the truncated projection of ROI. The global projection and truncated projection are obtained under the same geometric parameters. Therefore, it omits the registration of projection. To verify the feasibility of this method, simulation and practical experiments were implemented. Compared with the results of ROI reconstructed by filtered back-projection (FBP), simultaneous iterative reconstruction technique-total variation (SIRT-TV) and the multi-resolution based method (mR-PC), the proposed mSTCT-PC is good at mitigating truncation artifacts, preserving details and improving the accuracy of ROI images.
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