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The pointwise mutual information statistic (PMI), which measures how often two words occur together in a document corpus, is a cornerstone of recently proposed popular natural language processing algorithms such as word2vec. PMI and word2vec reveal semantic relationships between words and can be helpful in a range of applications such as document indexing, topic analysis, or document categorization. We use probability theory to demonstrate the relationship between PMI and word2vec. We use the theoretical results to demonstrate how the PMI can be modeled and estimated in a simple and straight forward manner. We further describe how one can obtain standard error estimates that account for within-patient clustering that arises from patterns of repeated words within a patient's health record due to a unique health history. We then demonstrate the usefulness of PMI on the problem of predictive identification of disease from free text notes of electronic health records. Specifically, we use our methods to distinguish those with and without type 2 diabetes mellitus in electronic health record free text data using over 400 000 clinical notes from an academic medical center.

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Based on a unifying theory presented here, it is predicted that the immune defects resulting in chronic inflammation rather than effective immune responses could be rectified by the therapeutic use of agents prepared from micro-organisms. With appropriate molecular patterns, these should be able to induce protective immunoregulatory networks or to reprogramme defective ones. In contrast to acute inflammation, chronic inflammation appears to have no beneficial role, but is a state of sustained immune reactivity in the presence or progression of a disease process. This results in an escalating cycle of tissue damage followed by unproductive tissue repair, breaks in self-tolerance, malignant transformation or deleterious changes in tissue morphology and function. Such inappropriate immune reactivity is an underlying characteristic, either in initiation or maintenance, of a diverse range of disease states including chronic infection, autoimmunity, allergy, cancer, vascular disease and metabolic alterations. Evidence is presented that the inappropriate immune reactivity is due, at least to some extent, to failures in the establishment of immunoregulatory networks as a result of hygiene-related factors. Such networks are the result of activation of antigen-presenting cells, principally dendritic cells, by molecular patterns of micro-organisms encountered sequentially during life and establishing the 'biography' of the immune system.

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The well-established model of Chagas' disease in "l" rats was used to evaluate the effects of three injections of heat-killed Gordonia bronchialis, Rhodococcus coprophilus or saline on Trypanosoma cruzi parasitaemia and acute and chronic myocarditis, sequelae of the infection. Two vaccinating injections were given prior to challenge with T. cruzi, and the third, immunotherapeutic, injection was given 7 days after challenge. Treatment with either actinomycete significantly reduced acute parasitaemia (p<0.04), modified cellular infiltration during acute myocarditis and limited chronic myocarditis (p<0.03) in comparison with the saline-treated control animals. Immunological investigations showed that both bacterial preparations achieved their results through different mechanisms. The relevance of our findings to human Chagas' disease is discussed.

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Peripheral blood mononuclear cells taken from 32 patients with Rheumatoid Arthritis (RA) receiving neither steroids nor methotrexate and 34 healthy controls were examined for lymphoproliferation in the presence of ultrasonic extracts of 14 different mycobacterial species or serotypes, of an extract of Candida albicans and of 2 mitogens. Additionally, cells were incubated for 96 hours alone, or with Mycobacterium tuberculosis (M.tb) sonicate or Concanavalin-A (Con-A), and supernatants were tested for a range of cytokines. Lymphocytes of rheumatoid patients were less reactive than controls to all the mycobacterial preparations, but no different in their responses to mitogens. Stimulation of patients' cells with M.tb sonicate induced significantly less interferon-gamma (IFN-gamma), tumour necrosis factor-alpha (TNF-alpha) and interleukin-10 (IL-10) but more transforming growth factor- beta (TGF-beta) than controls. Even stimulation with Con-A induced much less IFN-gamma in patient's cells than in those of controls. The combination of reduced responses to the mycobacterial reagents and reduced stimulation of type 1 cytokines by the sonicate of M.tb, suggests reduced responsiveness to group i, common mycobacterial antigens. Such findings need not indicate involvement of mycobacteria specifically in the disease aetiology, but provide novel information on the immunopathological abnormalities, which may explain the reported increased susceptibility to mycobacteria of RA patients.

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Two small, placebo-controlled studies of immunotherapy with heat killed Mycobacterium vaccae added to routine chemotherapy for pulmonary tuberculosis, together involving 40 HIV seronegative patients, were carried out in Argentina. The immunotherapy was associated with reduced sputum smear positivity of AFB at 1 month and a greater reduction in ESR at 2 months. In the first study radiological improvement was better (P < 0.05) among immunotherapy recipients. In the second study, weight regain and time to become apyrexial were measured and were found to be improved amongst immunotherapy recipients (P < 0.05). In the first month of treatment the levels of IgG to the 65 kDa and 70 kDa heat-shock proteins showed greater falls following immunotherapy (P < 0.05 and P < 0.001, respectively). On admission serum cytokine levels of interleukins 4 and 10 (IL-4, IL-10), interferon gamma (IFN-gamma) and tumour necrosis factor alpha (TNF-alpha) were grossly raised in comparison with a matched control group (P < 0.001). After 1 month. Levels of IL-4, IL-10 and TNF-alpha fell (P < 0.001, P < 0.01 and P < 0.01, respectively) and levels of IFN-gamma rose more (P = 0.005) in immunotherapy recipients than in those receiving chemotherapy alone. The results are in accord with a switch towards a TH1 immunological status and clinical benefit for immunotherapy recipients.

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Heparinised blood samples were obtained from 20 patients with chronic plaque psoriasis and from 13 age-matched healthy controls. After preliminary titration, mononuclear cells separated over Ficoll-Tryoson were cultured for 5 days with 10 microg ml(-1) of 15 mycobacterial preparations, or with pokeweed mitogen and concanavalin A. Stimulation indices were determined for each reagent and means were determined for patients and controls. Results for patients showed a striking reduction of responsiveness to mycobacteria, apparently due to loss of responses to group i, common mycobacterial antigens, and no differences in responses to mitogens. These observations relate psoriasis to certain other diseases, notably mycobacterial infections, rheumatoid arthritis, Chagas' disease and human immunodeficiency virus infection. The observations may be relevant to the aetiology of psoriasis, and to potential immunotherapy for the disease.

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A placebo-controlled study of immunotherapy with Mycobacterium vaccae for chronic plaque psoriasis showed improvement in the psoriasis area severity index in 19 of 21 immunotherapy recipients (P<0.005). Minor improvement, not reaching statistical significance for the group, occurred in nine of 14 placebo recipients. There were losses to follow-up and the placebo used, tetanus toxoid, was not ideal. Clinical improvement after immunotherapy persisted for 6 months and another injection of the immunotherapeutic given to a few volunteers from either group resulted in benefits lasting a year. Lymphoproliferative tests were carried out at each clinic visit, and on 50 matched controls. Starting with reduced responses to mycobacterial antigens and concanavalin A, both treatment groups showed a fall after 3 months, and diverged at 6 months with M. vaccae recipients rising to values similar to those of healthy controls, whereas placebo recipients continued to fall. Conclusions reached were that immunotherapy with M. vaccae gave long-lasting clinical benefit to most patients, with minimal side effects. This accompanied a return towards normal cellular immune responsiveness to mycobacterial antigens, which did not follow the use of the placebo.

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A total of 670 adults living or working with leprosy patients, were examined for a BCG vaccination scar, and skin-tested with four new tuberculins. Based on the results 513 were vaccinated, 65 with Bacille de Calmette et Guérin (BCG) alone, 66 with BCG plus killed Mycobacterium vaccae and 382 with killed M. vaccae alone. Skin-testing was repeated 2-3 years later on 344 subjects, when all three vaccines were found to have been highly successful in increasing responses to Tuberculin and Leprosin A (p < 0.0005) with increased immune recognition of common and species-specific antigens. Mean diameters of induration to each skin-test were greatest in recipients of BCG alone (p < 0.05), which suggests that better immuno-regulation occurs after receiving vaccines that incorporate M. vaccae. The results suggest 10(8) M. vaccae alone might prove a valuable future vaccine, which would not require selective pre-vaccination procedures.

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The immune response is impaired in the silent stage of Chagas' disease. We used quadruple skin-testing with new tuberculins in 37 adults who were symptom-free but seropositive for Trypanosoma cruzi and in 37 matched seronegative controls. Whereas 19% of controls responded to common mycobacterial antigens, none of the Chagas' seropositive group responded to them (p < 0.006), demonstrating specificity in their unresponsiveness. The enhanced tuberculin reactivity after BCG vaccination in the control group was suppressed in seropositive subjects (p < 0.002). Selective loss of response to common mycobacterial antigens may have implications for the autoimmune pathology of Chagas' disease, and for susceptibility to tuberculosis, leprosy, and HIV disease.

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Después de la administración de la inmunoterapia no deben presentarse reaciones graves y el índice bacterial debe disminuir rápidamente a cero. Las biopsias deben retornar a valores normales. La mejoría neurológica debe ser lo más completa posible. Si todo esto se puede conseguir, la lepra será una enfermedad muy distinta en el siglo XXI.

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