Abstract：
:The immune system is characterized by high combinatorial complexity that necessitates the use of specialized computational tools for analysis of immunological data. Machine learning (ML) algorithms are used in combination with classical experimentation for the selection of vaccine targets and in computational simulations that reduce the number of necessary experiments. The development of ML algorithms requires standardized data sets, consistent measurement methods, and uniform scales. To bridge the gap between the immunology community and the ML community, we designed a repository for machine learning in immunology named Dana-Farber Repository for Machine Learning in Immunology (DFRMLI). This repository provides standardized data sets of HLA-binding peptides with all binding affinities mapped onto a common scale. It also provides a list of experimentally validated naturally processed T cell epitopes derived from tumor or virus antigens. The DFRMLI data were preprocessed and ensure consistency, comparability, detailed descriptions, and statistically meaningful sample sizes for peptides that bind to various HLA molecules. The repository is accessible at http://bio.dfci.harvard.edu/DFRMLI/.
journal_name
J Immunol Methodsjournal_title
Journal of immunological methodsauthors
Zhang GL,Lin HH,Keskin DB,Reinherz EL,Brusic Vdoi
10.1016/j.jim.2011.07.007subject
Has Abstractpub_date
2011-11-30 00:00:00pages
18-25issue
1-2eissn
0022-1759issn
1872-7905pii
S0022-1759(11)00177-3journal_volume
374pub_type
杂志文章abstract：:An antibody binding-inhibition test is described, which allows the detection of P. falciparum in red blood cells (RBC) infected in vitro, using a crossreacting, monoclonal anti-P. berghei antibody and P. berghei coated microtiter plates. Experiments carried out to determine the coating efficiency of various P. berghei...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/0022-1759(85)90231-5
更新日期：1985-09-03 00:00:00
abstract：:The neutrophilic granulocyte is the most numerous leukocyte in peripheral blood. The development from a multipotent progenitor cell to a mature neutrophil takes place in the bone marrow over a period of 10-14 days. In order to understand the cellular mechanisms behind this process, it is necessary to investigate cells...
journal_title：Journal of immunological methods
pub_type： 杂志文章,评审
doi：10.1016/s0022-1759(99)00176-3
更新日期：1999-12-17 00:00:00
abstract：:A panel of 18 monoclonal antibodies was raised to the human calcitonin gene related peptide (CGRP). Of these mabs, seven were specific for alpha CGRP and five for beta CGRP, while the remainder reacted with both alpha and beta CGRP. Nine different epitopes on CGRP were defined with these mabs. In addition, the mabs we...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/0022-1759(90)90115-c
更新日期：1990-11-06 00:00:00
abstract：:Flow cytometry has been utilized to evaluate the stability of antibody production by unstable subclones of a human x human x mouse heterohybridoma. Heterogeneity of cell-associated immunoglobulin heavy chain expression was demonstrated in different subclones and an increased frequency of cells containing low levels of...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/0022-1759(94)90247-x
更新日期：1994-03-29 00:00:00
abstract：:Antibody molecules bind to antigen with six complementary determining region (CDR) loops, three of which are located on each variable heavy (V(H)) and light (V(L)) chains. Discovery and optimization of antibodies that bind antigen using in vitro techniques require diversification of one or more of these CDRs. Since an...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/j.jim.2006.09.006
更新日期：2006-12-20 00:00:00
abstract：:The early successes of highly active anti-retroviral therapies (HAART) for the treatment of HIV-1-infection and AIDS have raised the question as to whether there is a legitimate role for gene therapy in the treatment of this chronic infectious disease. However, in many patients the profound suppression of viral replic...
journal_title：Journal of immunological methods
pub_type： 杂志文章,评审
doi：10.1016/s0022-1759(99)00159-3
更新日期：1999-12-10 00:00:00
abstract：:Fungi represent emerging infectious threats to human populations worldwide. Mice and other laboratory animals have proved invaluable in modeling clinical syndromes associated with superficial and life-threatening invasive mycoses. This review outlines salient features of common vertebrate animal model systems to study...
journal_title：Journal of immunological methods
pub_type： 杂志文章,评审
doi：10.1016/j.jim.2014.03.022
更新日期：2014-08-01 00:00:00
abstract：:An enzyme-linked immunosorbent assay was developed for quantitation of complement C3b receptors (C3bR) on human erythrocytes fixed in monolayer to microtiter plates. The disadvantages of macro test tube systems (large consumption of sample material and reagents, tedious washing procedures, cell loss and hemolysis) wer...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/0022-1759(85)90211-x
更新日期：1985-08-02 00:00:00
abstract：:A dot-ELISA technique for the detection of G. lamblia specific antigen in stool eluates of clinical cases of giardiasis was developed and evaluated employing monospecific antibodies to a G. lamblia specific coproantigen with a molecular mass of 66 kDa. The assay detected 22 (91.7%) of the 24 microscopically confirmed ...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/0022-1759(91)90030-j
更新日期：1991-03-21 00:00:00
abstract：:The identification of T cell epitopes that elicit a weak T cell response is technically challenging due to the relatively low resolution of many available screening assays. Peptide immunization can confirm the immunogenicity of a given peptide, however, this also often induces a low frequency response in lymphoid orga...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/s0022-1759(02)00106-0
更新日期：2002-08-01 00:00:00
abstract：:We describe techniques to detect nuclear transcription factors in thymocyte subsets using flow cytometry. We have adapted a method that minimizes autofluorescence of fixed cells, thereby allowing the detection of proteins expressed at low levels. An accompanying method in which the cytoplasm is removed from stained ce...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/s0022-1759(03)00184-4
更新日期：2003-08-01 00:00:00
abstract：:The aim of the study was to develop a novel system permitting automated analysis of multicolor immunofluorescence-staining of cells in solid tissues which would be comparable to the analytical capacity of flow cytometry. In the user friendly automated data acquisition and image processing system which was established,...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/s0022-1759(99)00240-9
更新日期：2000-04-03 00:00:00
abstract：:We describe a rapid in vitro assay for the evaluation of in vivo properties of conjugate vaccines. Using human and murine monoclonal antibodies (mAb) specific for lipopolysaccharides (LPS), isolated from Pseudomonas aeruginosa, we determined in a competitive binding assay the amount of LPS or conjugate vaccine which w...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/0022-1759(90)90367-5
更新日期：1990-10-19 00:00:00
abstract：:We report the development of an expression system for the production of soluble, calmodulin (CaM)-tagged proteins in Drosophila Schneider S2 cells and the subsequent use of these proteins for the selection of phage displayed antibodies. The CaM-tag permitted the purification of recombinant protein to >90% purity in a ...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/j.jim.2006.08.003
更新日期：2006-10-20 00:00:00
abstract：:We describe here the use of a new agarose for isoelectric focusing of body fluids and tissue proteins. Macromolecular proteins even when significantly greater in size than 1 X 10(6) mol.wt. were easily and rapidly focused. ...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/0022-1759(79)90130-3
更新日期：1979-01-01 00:00:00
abstract：:Household contacts of tuberculosis patients are at high risk of infection and development of active disease. In this study we evaluated the cytokine production and mRNA expression of IFN-γ, TNF-α, IL-10&IL-6 stimulated with r32kDa M. bovis BCGAg in active pulmonary tuberculosis patients (APTB), household contacts (HHC...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/j.jim.2016.02.012
更新日期：2016-05-01 00:00:00
abstract：:Somatic cell hybridization between the YACUT T cell lymphoma cell line with normal lymphocytes activated in secondary mixed lymphocyte cultures (MLCs) consistently yielded IL-2-dependent CD4- CD8 alpha+ beta- Fc gamma RIII+ hybrids with cytotoxic function. The hybrids expressed T cell receptors other than that of YACU...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/0022-1759(96)00030-0
更新日期：1996-06-10 00:00:00
abstract：:Pathologic rheumatoid factor (RF) levels are hallmarks of several human diseases. Production of monoclonal RF in vitro is essential for studies of the antigenic specificities of RF, as well as for a dissection of the mechanisms of aberrant RF+ B cell activation. We have expanded upon previous methods to develop a flow...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/j.jim.2010.09.022
更新日期：2011-01-05 00:00:00
abstract：:The periodate oxidation and chromium chloride coupling methods were compared for their ability to sensitize indicator erythrocytes with staphylococcal lipoteichoic acid (LTA) for the detection of specific antibody. Erythrocytes, sensitized with periodiate-activated lipoteichoic acid, were found to be superior for use ...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/0022-1759(80)90070-8
更新日期：1980-01-01 00:00:00
abstract：:Conditions were optimized for measuring the activity of myeloperoxidase (MPO) and the eosinophil peroxidase (EPO) with tetramethylbenzidine (TMB) as the substrate. Detergents caused a small increase in the measured activity of the purified enzymes and were required when isolated neutrophils or eosinophils were assayed...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/0022-1759(90)90020-v
更新日期：1990-01-24 00:00:00
abstract：:A simple technique for raising specific antiserum to the native molecule of Epstein-Barr virus (EBV)-encoded nuclear antigen-2 (EBNA-2) from Raji cells is described. The procedure involves the use of immunoblotting to identify the EBNA-2 polypeptide followed by subsequent excision from an SDS-gel and immunization of e...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/0022-1759(86)90543-0
更新日期：1986-03-13 00:00:00
abstract：:Cell-based assays to monitor antigen-specific T-cell responses are characterized by their high complexity and should be conducted under controlled conditions to lower multiple possible sources of assay variation. However, the lack of standard reagents makes it difficult to directly compare results generated in one lab...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/j.jim.2018.04.007
更新日期：2018-07-01 00:00:00
abstract：:Bromodeoxyuridine (BrdU) is used to label synthesizing DNA and to chase label-retaining cell (LRC). As stem cells divide slowly in adult tissues, they can be visualized as LRCs. In order to identify LRCs in hard tissue, we examined optimal conditions of fixation, demineralization, and DNA denaturation/antigen retrieva...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/j.jim.2008.07.013
更新日期：2008-11-30 00:00:00
abstract：:Near-infrared Raman spectroscopy may provide a highly sensitive, noninvasive means to identify activation status of leukocytes. The purpose of the current study was to establish Raman spectroscopic characteristics of T cell activation. Activation of the RsL.11 T cell clone in vitro with Con A resulted in specific decr...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/j.jim.2004.11.020
更新日期：2005-02-01 00:00:00
abstract：:Respiratory enteric orphan virus (reovirus) has been used to study many aspects of the biology and genetics of viruses, viral infection, pathogenesis, and the immune response to virus infection. This report describes the functional activity of virus labeled with Alexa Fluor 488, a stable fluorescent dye. Matrix assist...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/j.jim.2006.05.008
更新日期：2006-07-31 00:00:00
abstract：:Autoimmune (Hashimoto's) thyroiditis is a chronic inflammatory disease which affects >3% of the population and shows an increasing prevalence with increasing age. Anti-thyroid autoantibodies, particularly against thyroperoxidase (also known as thyroid peroxidase or TPO), occur commonly in humans with autoimmune thyroi...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/j.jim.2007.04.002
更新日期：2007-06-30 00:00:00
abstract：:We developed a dual wavelength spectrophotometric assay that permitted beta-lactamase and beta-galactosidase activities to be measured concurrently in a single sample. We also constructed a target cell, E. coli ML-35p, that was substantially cryptic for its periplasmic beta-lactamase and cytoplasmic beta-galactosidase...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/0022-1759(88)90414-0
更新日期：1988-04-06 00:00:00
abstract：:The reverse haemolytic plaque assay has been adapted to detect and measure the release of such cytokines as interleukin-1, -2 and -6, GM colony-stimulating factor or interferon-gamma by individual human cells derived from either peripheral blood or enzymatically dispersed breast carcinomas. Since each of these peptide...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/0022-1759(90)90340-2
更新日期：1990-02-20 00:00:00
abstract：:An improved microassay for quantitation of murine macrophage-mediated antibody-dependent cellular cytotoxicity (ADCC) has been developed. The method is based on the turbidimetric measurement of sheep erythrocyte or nucleated (L1210) target cell suspensions at 630 nm with an automatic microtiter plate densitometer. The...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/0022-1759(86)90262-0
更新日期：1986-01-22 00:00:00
abstract：:We have used a conceptually novel way to construct antibody mimics based on the binding of a noncatalytic enzyme to its substrate. Bacteriophage-derived endosialidase cleaves polysialic acid (polySia), an important oncofetal and bacterial antigen, which is poorly immunogenic. We fused to green fluorescent protein (GFP...
journal_title：Journal of immunological methods
pub_type： 杂志文章
doi：10.1016/j.jim.2004.10.006
更新日期：2004-12-01 00:00:00
