RETRACTED: The Fas/Fas Ligand Pathway and Bcl-2 Regulate T Cell Responses to Model Self and Foreign Antigens
Authors: D A Peterson
A K Abbas
L Van Parijs
Journal: Immunity (1998)
Discipline: IMMUNOLOGY
Keywords: Fas; Bcl-2; T cell survival; antigen; in vivo
Affiliations: Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.

Abstract:  We have examined the role of Fas and Bcl-2 in T cell survival and responses to antigen in vivo using T cells that express a transgenic antigen receptor specific for hen egg lysozyme (HEL) and that either lack functional Fas or Fas ligand (FasL) or overexpress Bcl-2 as a transgene. HEL-specific, Bcl-2-transgenic T cells showed prolonged responses to immunization with cognate peptide but were eliminated rapidly when exposed to HEL expressed systemically as a self antigen. In contrast, Fas- and FasL-defective T cells did not display exaggerated responses to immunization with HEL peptide, but did show increased expansion and survival in response to systemic self antigen and were able to activate anti-HEL (self) antibody-forming cells. Thus, Bcl-2 and Fas play different roles in the regulation of T cell responses to antigen in vivo and in self tolerance. 

Retracted: Yes

PubPeer comments:
 This a gorgeously written paper, but unfortunately there are many defects in the mathematics. Having spent much too much time myself on the earlier works of the same author, I will just point out here that the computer code reproduced in Section IV is actually not an implementation of the mathematics in the paper nor in the earlier publications (and attempts at publication) of the author. The code-line if(lambda==1) {q=A B;} else {q=B A;} shuffles the alternative orientations of S3 is an ad hoc fix discovered one of the author s computing aides, Albert Jan Wonnink, in an attempt four years ago to convert mathematical formulas into computer code. I copy-pasted the published code into GAViewer, after changing the number of trials N from 50000 to 1. Nothing happened. But then I typed in  test() to run the batch program which the code has defined. This resulted in the following output: test() neg_adotb = -0.087949 eta_ab = 275.045624 correlation = -0.087949 mean = -0.087949 + -0.549194*e2^e3 + -0.177510*e3^e1 + -0.811875*e1^e2 aveA = -0.666721 + -0.691323*e2^e3 + 0.018680*e3^e1 + -0.277863*e1^e2 aveB = 0.660582 + 0.240868*e2^e3 + -0.288674*e3^e1 + 0.649832*e1^e2 ans = 0 How a correlation can come out when only one trial has been performed is, or course, a mystery! Anyway, it is now easy to do more experiments. The computer code is just a very round-about way to compute a negative cosine by numerical simulation, and merely takes account of the well known and GA trivial fact a.b = (ab + ba) 2 I will find out how to set the random seed so as to make this experiment reproducible. Small numbers N (5 or 10 say) generate a manageable amount of printed output. And one can easily add lines to print out more intermediate results. , 
 I have put a minor modification of the GAViewer code from this paper on my home-page at https: www.math.leidenuniv.nl ~gill test.g It s a plain text file. In the code I made the sample size N equal to 4, added a  set random seed line, added lines to the code which print the seed and the sample size and the value of n from 1 to N as each  trial is performed. Instructions: Download GAViewer from http: www.geometricalgebra.net gaviewer_download.html Save  test.g in a folder called, for instance,  Test . Fire up GAViewer It has a  File menu with a menu item  load .g directory . Use this menu item to load the director  Test . This compiles all the GAViewer code in every .g file in the directory. The one I have given you includes a line batch test() . When you actually type  test() in console window (the one with a prompt ) the whole code in that file will be run. You should, altogether, get *exactly* the following output. Please let me know if you don t! Maybe some things work a tiny bit differently on different platforms (though they shouldn t). But anyway, if you repeat all this a number of times, you should every time get exactly the same output. (I do). Reading all .g files in Users richard Desktop GAViewer Test Parsing Users richard Desktop GAViewer Test test.g test() seed = 0.123400 N = 4.000000 n = 1.000000 neg_adotb = -0.613934 eta_ab = 307.874481 correlation = -0.613934 n = 2.000000 neg_adotb = -0.126766 eta_ab = 82.717224 correlation = -0.126766 n = 3.000000 neg_adotb = -0.593831 eta_ab = 306.429321 correlation = -0.593831 n = 4.000000 neg_adotb = 0.975552 eta_ab = 167.304520 correlation = 0.975552 N = 4.000000 mean = -0.089745 + 0.178404*e2^e3 + -0.294515*e3^e1 + 0.070495*e1^e2 aveA = 0.174688 + 0.136034*e2^e3 + 0.565717*e3^e1 + -0.450829*e1^e2 aveB = -0.043899 + 0.001339*e2^e3 + -0.240015*e3^e1 + -0.001439*e1^e2 ans = 0 The bottom line  ans = 0 is there because the very last command which was executed had no output of its own. So its output is called  ans and was given the value 0. The original authors draw their nice plot of the negative cosine by copy-pasting their output into Excel, binning the data for which the difference between the two directions of polarization lies in some small intervals, averaging *not* what they call the  correlation got from each trial, but something else called q, which actually has a purely imaginary quaternionic part, which tends to cancel out by the law of large numbers when N is large. That is what they call  mean (but then, per angle difference bin). This really is all fake. The  computer simulation is not complete without the post-processing, which draws the nice graph at the end. The authors should add a proper description of how they process the GAViewer output to draw their pretty negative cosine curve. Just saying  with an Excell spreadsheet is not exactly what is understood by  reproducible research . , 
 Sorry for the typesetting of computer output in the last comment. By the time the posting had passed moderation, I was not allowed to edit it any more. Hopefully this looks better: Reading all .g files in Users richard Desktop GAViewer Test Parsing Users richard Desktop GAViewer Test test.g test() seed = 0.123400 N = 4.000000 n = 1.000000 neg_adotb = -0.613934 eta_ab = 307.874481 correlation = -0.613934 n = 2.000000 neg_adotb = -0.126766 eta_ab = 82.717224 correlation = -0.126766 n = 3.000000 neg_adotb = -0.593831 eta_ab = 306.429321 correlation = -0.593831 n = 4.000000 neg_adotb = 0.975552 eta_ab = 167.304520 correlation = 0.975552 N = 4.000000 mean = -0.089745 + 0.178404e2^e3 + -0.294515e3^e1 + 0.070495e1^e2 aveA = 0.174688 + 0.136034e2^e3 + 0.565717e3^e1 + -0.450829e1^e2 aveB = -0.043899 + 0.001339e2^e3 + -0.240015e3^e1 + -0.001439*e1^e2 ans = 0 , 
 Further details can be found here: https: www.mdpi.com 1099-4300 22 1 61 , 
 I have written a brief analysis of the main mathematical error in this paper. It can be found at https: www.math.leidenuniv.nl ~gill socks.pdf Christian introduces a  handedness lambda = + - 1. Of course, it is possible to use different coordinate systems at the same time, and in particular to have both a left-handed and a right-handed coordinate system for the same vector space. It is then important to have a good notation which always makes clear which coordinate system is in force in a given mathematical expression (or given part of a mathematical expression). He is however not consistent, because he also uses the ordinary cross-product  x of real 3D vectors **a** and **b**. He should have introduced a right-handed and a left-handed cross-product, writing them, for instance, as **a** x(+) **b** and **a** x(u2013) **b** Then he could have set up his definitions and his model in a self-consistent way, though unfortunately, his main result would then no longer have been correct. , 
 #5 My paper is  Dr. Bertlmannu2019s left- and right-handed socks arXiv:2001.11338 [physics.gen-ph] https: arxiv.org abs 2001.11338 , 
 My arXiv paper that has been the subject of this thread is now published in *IEEE Access*: *IEEE Access*, vol. 8, pp 191028 - 191048, 16 October 2020, DOI: 10.1109 ACCESS.2020.3031734 It can be downloaded freely: https: ieeexplore.ieee.org stamp stamp.jsp?tp= arnumber=9226414 ... ,