Estimation of the biomechanical mammographic deformation of the breast using machine learning models.

BACKGROUND: A typical problem in the registration of MRI and X-ray mammography is the nonlinear deformation applied to the breast during mammography. We have developed a method for virtual deformation of the breast using a biomechanical model automatically constructed from MRI. The virtual deformation is applied in two steps: unloaded state estimation and compression simulation. The finite element method is used to solve the deformation process. However, the extensive computational cost prevents its usage in clinical routine. METHODS: We propose three machine learning models to overcome this problem: an extremely randomized tree (first model), extreme gradient boosting (second model), and deep learning-based bidirectional long short-term memory with an attention layer (third model) to predict the deformation of a biomechanical model. We evaluated our methods with 516 breasts with realistic compression ratios up to 76%. FINDINGS: We first applied one-fold validation, in which the second and third models performed better than the first model. We then applied ten-fold validation. For the unloaded state estimation, the median RMSE for the second and third models is 0.8 mm and 1.2 mm, respectively. For the compression, the median RMSE is 3.4 mm for both models. We evaluated correlations between model accuracy and characteristics of the clinical datasets such as compression ratio, breast volume, and tissue types. INTERPRETATION: Using the proposed models, we achieved accurate results comparable to the finite element model, with a speedup of factor 240 using the extreme gradient boosting model. These proposed models can replace the finite element model simulation, enabling clinically relevant real-time application.

Purification to homogeneity of B cell stimulating factor. A molecule that stimulates proliferation of multiple lymphokine-dependent cell lines.

Murine B cell stimulating factor 1 (BSF-1) was purified to homogeneity from supernatants of a stimulated thymoma cell line. A protein of 18.4 kD with a unique N-terminal amino acid sequence was identified. BSF-1 had a sp act of at least 3.28 X 10(8) U/mg. In addition to its B cell-stimulatory activity, BSF-1 also stimulated the proliferation of several IL-2- and IL-3-dependent cell lines. We conclude that BSF-1 is both a growth factor and a differentiation factor. Finally, these results also suggest additional biologic properties of BSF-1 on lineages besides B lymphocytes.

Detection and characterization of high affinity plasma membrane receptors for human interleukin 1.

Interleukin 1 (IL-1) is a polypeptide hormone that acts as a central mediator of inflammation. Since IL-1 action is presumably mediated by specific cell surface receptor(s), we have characterized the binding of this hormone to cells. Purified human IL-1 was labeled to high specific activity with 125I, using Bolton-Hunter reagent. The labeled protein binds specifically to LBRM-33-1A5 (a murine T lymphoma line previously shown to produce IL-2 in response to phytohemagglutinin and IL-1) with an affinity of approximately 0.2-2 X 10(10)/M and, at saturation, to approximately 500 receptors per cell, on intact cells at 8 degrees C in the presence of sodium azide. The affinity of unmodified IL-1 for the murine plasma membrane receptor is 0.9-2 X 10(10)/M, as measured by the inhibition of 125I-IL-1 binding. The murine receptor specificity has been confirmed by demonstrating that, among a series of 12 polypeptide hormones, only IL-1 inhibits 125I-IL-1 binding to LBRM-33-1A5 cells. Treatment of surface-bound 125I-IL-1 with bivalent water-soluble crosslinkers identified a membrane polypeptide of Mr 79,500 to which IL-1 is crosslinked. A variety of cell types have been surveyed for the capacity to bind 125I-IL-1 specifically. The presence of specific binding correlates with the capacity of the cells tested to respond to IL-1. Our results indicate that the biological effects of the polypeptide hormone IL-1 are mediated by high affinity plasma membrane receptors. The identification of these receptors should provide valuable insight into the apparently diverse biological activities of IL-1.

Human interleukin 1. Purification to homogeneity.

We have purified human interleukin 1 (IL-1) to homogeneity by a simplified procedure that results in excellent yields of pure material that retains a high level of biological activity. IL-1, secreted by human peripheral blood macrophages that have been stimulated with Staphylococcus aureus, was purified by ion exchange chromatography and affinity chromatography on Procion Red agarose. The pure protein has a specific activity of 3.2 X 10(8) U/mg in the thymocyte mitogenesis assay, and is pyrogenic. No molecular weight heterogeneity was observed, in contrast to findings for mouse IL-1 and earlier reports of human IL-1. Purified IL-1, as analyzed by two-dimensional electrophoresis/electrofocusing gels, exhibited a series of charged species with isoelectric points ranging from 6.0 to 4.9, all with a molecular weight of approximately 17,500. Amino acid analysis indicated an abundance of acidic residues, in agreement with the low isoelectric points. There is little or no cysteine in the molecule. No evidence was found for the presence of carbohydrate moieties. The overall yield for this procedure was approximately 31% of the activity contained in the initial culture supernatant.

A hypersensitive estrogen receptor-alpha mutation in premalignant breast lesions.

The best current model of breast cancer evolution suggests that most cancers arise from certain premalignant lesions. We have identified a common (34%) somatic mutation in the estrogen receptor (ER)-alpha gene in a series of 59 typical hyperplasias, a type of early premalignant breast lesion. The mutation, which affects the border of the hinge and hormone binding domains of ER-alpha, showed increased sensitivity to estrogen as compared with wild-type ER-alpha in stably transfected breast cancer cells, including markedly increased proliferation at subphysiological levels of estrogen. The mutated ER-alpha exhibits enhanced binding to the TIF-2 coactivator at low levels of hormone, which may partially explain its increased estrogen responsiveness. These data suggest that this mutation may promote or accelerate the development of cancer from premalignant breast lesions.

Tamoxifen-bound estrogen receptor (ER) strongly interacts with the nuclear matrix protein HET/SAF-B, a novel inhibitor of ER-mediated transactivation.

The estrogen receptor (ER) is a ligand-dependent transcription factor that acts in a cell- and promoter-specific manner. Evidence suggests that the activity of the ER can be regulated by a number of other stimuli (e.g. growth factors) and that the effects of the ER are modulated by nuclear factors termed coregulators. While the interplay among these factors may in part explain the pleiotropic effects elicited by the ER, there are several other less well described mechanisms of control, such as interactions with the nuclear matrix. Here we report that the nuclear matrix protein/scaffold attachment factor HET/SAF-B is an ER-interacting protein. ER and HET/SAF-B interact in in vitro binding assays, with HET binding to both the ER DNA-binding domain and the hinge region. Coimmunoprecipitation experiments reveal that HET/SAF-B and ER associate in cell lines in the presence or absence of estradiol, but binding is increased by the antiestrogen tamoxifen. HET/SAF-B enhances tamoxifen antagonism of estrogen-induced ER-mediated transactivation, but at high concentrations can inhibit both estrogen and tamoxifen-induced ER activity. HET/SAF-B-mediated repression of ER activity is dependent upon interaction with the ER-DBD. While the existence of high-affinity binding sites for the ER in the nuclear matrix has been known for some time, we now provide evidence of a specific nuclear matrix protein binding to the ER. Furthermore, our data showing that HET/SAF-B binds to ER particularly strongly in the presence of tamoxifen suggests that it may be important for the antagonist effect of tamoxifen.

Immunogenicity of a synthetic HBsAg peptide: enhancement by conjugation to a fatty acid carrier.

Effective immunization with short polypeptide antigens has typically only been possible when the peptide is conjugated to a large carrier substance, usually a protein. Such immunizations suffer from difficulties in producing conjugates of reliable composition, and from unwanted anti-carrier immune responses. When a chemically synthesized peptide, bearing hepatitis B virus a-determinant specificity, was conjugated to a dipalmityl-lysine moiety, a significant improvement in anti-hepatitis B surface antigen response was obtained, in comparison to the corresponding peptide-keyhole limpet hemocyanin conjugate. Dipalmityl lysyl peptide conjugates are readily made by standard Merrifield synthesis procedures, and are relatively free of byproducts that might cause unwanted immune responses. Gel filtration experiments suggest that the conjugates form large aggregates, possibly micelles, which may play a significant role in the enhancement of the anti-peptide response. These properties suggest that fatty acid conjugation may be a useful procedure for producing chemically synthesized peptide vaccines.

A computer program for predicting protein antigenic determinants.

A computerized method for predicting the locations of protein antigenic determinants is presented, which requires only the amino acid sequence of a protein, and no other information. This procedure has been used to predict the major antigenic determinant of the hepatitis B surface antigen, as well as antigenic sites on a series of test proteins of known antigenic structure [Hopp & Woods (1981) Proc. natn. Acad. Sci. U.S.A. 78, 3824-3828.] The method is suitable for use in smaller personal computers, and is written in the BASIC language, in order to make it available to investigators with limited computer experience and/or resources. A means of locating multiple antigenic sites on a homologous series of proteins is demonstrated using the influenza hemagglutinin as an example.

Immunochemical studies on alpha-lactalbumin.

The antigenic structural features of alpha-lactalbumin have been investigated using a radioimmunoassay, peptide inhibition of the quantitative precipitin reaction, and by immunodiffusion analysis after chemical modification of the molecule. Antigenic activity (in rabbits) was localized to several peptic fragments and the single arginine residue of bovine alpha-lactalbumin. Antigenic activity was also found to be associated with the single methionine residue. A peptic fragment containing a disulfide loop was found to possess antigenic activity in both bovine and goat alpha-lactalbumin. Radioimmunoassay cross-reactivity between the alpha-lactalbumins is correlated with amino acid sequence similarities; bovine alpha-lactalbumin antiserum cross-reacts with goat alpha-lactalbumin more extensively than with human alpha-lactalbumin, while the more distantly homologous protein, chicken lysozyme, does not cross-react at all. Nevertheless our data indicate that the alpha-lactalbumins and lysozyme share a similar distribution of antigenic determinants on their surfaces.

Metal-binding properties of a calcium-dependent monoclonal antibody.

The calcium-dependent mAb, M1 (also called anti-Flag or 4E11) was studied using a newly developed metal-sensitive enzyme-linked immunosorbent assay (ELISA). This antibody, specific for a calcium complex of the peptide antigen, Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys, has found widespread use as a mild purification reagent for Flag-epitope tagged recombinant proteins. Although M1 affinity columns release monovalent Flagged proteins in the absence of calcium, the antibody retains substantial affinity for the Flag sequence even in metal-free conditions, so that it has been impossible to use it to develop a metal-sensitive ELISA assay. This is due to the ability of the antibody to remain bound to polyvalent surface-coated antigen, for instance, when Flagged proteins are bound to ELISA plates or blotting filters. The resultant antigen polyvalence raises the avidity of the Flag antibody to a point where the reaction is essentially calcium-independent. However, when the antibody itself was made monovalent, by proteolytic cleavage to the Fab, this situation was reversed and the ELISA reaction became calcium-dependent. This new metal-dependent ELISA assay was used to explore the metal requirements of the antibody in detail. Among divalent metals, binding tapered off with increasing radius above that of calcium, or with decreasing radius below that of calcium. Several smaller metals, such as nickel, acted as inhibitors of the binding reaction. Substantial binding was demonstrated for heavy metals such as cadmium, lanthanum and samarium. Because it is of interest to use this antibody for the co-crystallization of recombinant Flag-fusion proteins, the ability to bind heavy metals was a significant finding.

Image fusion of Ultrasound Computer Tomography volumes with X-ray mammograms using a biomechanical model based 2D/3D registration.

Ultrasound Computer Tomography (USCT) is a promising breast imaging modality under development. Comparison to a standard method like mammography is essential for further development. Due to significant differences in image dimensionality and compression state of the breast, correlating USCT images and X-ray mammograms is challenging. In this paper we present a 2D/3D registration method to improve the spatial correspondence and allow direct comparison of the images. It is based on biomechanical modeling of the breast and simulation of the mammographic compression. We investigate the effect of including patient-specific material parameters estimated automatically from USCT images. The method was systematically evaluated using numerical phantoms and in-vivo data. The average registration accuracy using the automated registration was 11.9mm. Based on the registered images a method for analysis of the diagnostic value of the USCT images was developed and initially applied to analyze sound speed and attenuation images based on X-ray mammograms as ground truth. Combining sound speed and attenuation allows differentiating lesions from surrounding tissue. Overlaying this information on mammograms, combines quantitative and morphological information for multimodal diagnosis.

Evidence from sequence information that the interleukin-1 receptor is a transmembrane GTPase.

Evidence is presented that the cytoplasmic domain of the type I interleukin-1 receptor (IL-1R) may be a GTPase. This domain conserves segments of hydrophobic amino acids that suggest a structural relatedness to the ras protooncogene protein and other members of the GTPase superfamily, despite a lack of significant detectable sequence homology. When the hydrophobic segments of the IL-1R were aligned with similar segments of the GTPases, it became apparent that the IL-1Rs possess a number of conserved amino acids that represent plausible functional residues for base-specific binding of GTP, magnesium chelation, and phosphate ester hydrolysis. Furthermore, a segment of five contiguous residues were found that is identical between ras and the IL-1R, and which is positioned to form part of the guanine base binding pocket. If this model is correct, then the IL-1Rs possess a highly conserved effector protein binding region, but one that is entirely unrelated to the effector regions of other superfamily members. Therefore, if the IL-1R is indeed a GTPase, then its activation function may be directed to as-yet unrecognized effector target proteins, as part of a unique cellular signal transduction pathway.

Protein surface analysis. Methods for identifying antigenic determinants and other interaction sites.

A variety of methods are currently employed in attempts to identify antigenic determinants and other features of proteins. Most of these involve calculations based on scales of values for the 20 amino acids that reflect their likelihood of occurrence at the surface of proteins or as part of secondary structures such as helices or beta-bends. The most successful of these procedures all use scales related to the water solubility of the individual amino acids. In particular, the highest success rates are obtained using hydrophilicity scales that emphasize the charged and polar amino acids, but are not overly selective for either positive or negative charges. Such a method can correctly pinpoint major antigenic sites on the proteins of most well characterized infectious organisms. The hydrophilicity profiles also contain information concerning other types of protein interaction sites and membrane spanning segments.

Use of hydrophilicity plotting procedures to identify protein antigenic segments and other interaction sites.

Hydrophilicity analysis of the surface properties of proteins continues to be an important means for understanding the interactions that occur between proteins and other macromolecules. We have shown that the procedure of Hopp and Woods is useful in developing synthetic peptide immunogens and for understanding the relationship of protein sequence and folding to the interactions between macromolecules. Using a standardized procedure and the optimized hydrophilicity scale of amino acid values, it is possible to display the surface-exposed and buried portions of a polypeptide chain, as well as such features as membrane-spanning segments. Finally, an example was provided to show that hydrophilicity analysis has a place in protein engineering, allowing the creation of new surface segments with predictable properties.

A calcium-dependent antibody for identification and purification of recombinant proteins.

We report a straightforward methodology for purification of recombinant proteins by incorporating a short hydrophilic peptide marker segment at their N-termini. A calcium-dependent antibody that reacts primarily with the first three amino acids of this peptide segment was used to affinity purify the fusion proteins in a single chromatographic step. The marker peptide could subsequently be removed by proteolysis with the enzyme enterokinase.

Automatic multimodal 2D/3D breast image registration using biomechanical FEM models and intensity-based optimization.

Due to their different physical origin, X-ray mammography and Magnetic Resonance Imaging (MRI) provide complementary diagnostic information. However, the correlation of their images is challenging due to differences in dimensionality, patient positioning and compression state of the breast. Our automated registration takes over part of the correlation task. The registration method is based on a biomechanical finite element model, which is used to simulate mammographic compression. The deformed MRI volume can be compared directly with the corresponding mammogram. The registration accuracy is determined by a number of patient-specific parameters. We optimize these parameters--e.g. breast rotation--using image similarity measures. The method was evaluated on 79 datasets from clinical routine. The mean target registration error was 13.2mm in a fully automated setting. On basis of our results, we conclude that a completely automated registration of volume images with 2D mammograms is feasible. The registration accuracy is within the clinically relevant range and thus beneficial for multimodal diagnosis.