John Dowling - Academia.edu (original) (raw)
Papers by John Dowling
Introduction: Emergency department (ED) records and over-the-counter (OTC) sales data are two of ... more Introduction: Emergency department (ED) records and over-the-counter (OTC) sales data are two of the most commonly used sources of data for syndromic surveillance. The majority of detection algorithms monitor these data sources separately and either do not combine them or combine them in an ad hoc fashion. This report outlines a new causal model that combines the two data sources
Archives of Dermatology, 2003
Amia Annual Symposium Proceedings, 2005
Encoder is a Windows-based program that assists researchers and their staff in coding free text c... more Encoder is a Windows-based program that assists researchers and their staff in coding free text clinical reports into structured databases that are ready for analysis. This software represents approximately 5000 person-hours of programmer time. Researchers at the ...
Journal of Clinical Pathology, 1983
The exanthem of epidemic polyarthritis, a disease caused by Ross River (RR) virus, was examined t... more The exanthem of epidemic polyarthritis, a disease caused by Ross River (RR) virus, was examined three days after onset of the common erythematous and the rare purpuric forms of the eruption. The dermis showed a light perivascular infiltrate of mononuclear cells in both, with extravasation of erythrocytes in the latter. No immunoglobulins (IgM, IgG, IgA) or complement components (Clq, C3)
Cancer Research, 1987
A monoclonal antibody, Leo Mel 3, raised against a melanoma cell line (LiBr), binds to a carbohyd... more A monoclonal antibody, Leo Mel 3, raised against a melanoma cell line (LiBr), binds to a carbohydrate determinant of cell surface gangliosides, the simplest of which is (>,»-This monoclonal antibody was screened for by its capacity to block the recognition and lysis of the melanoma cells by cytotoxic T-lymphocytes with anomalous killer cell function, illustrating a novel approach for identifying monoclonal antibody to biologically relevant tumor-associated antigens. Leo Mel 3 reacted selectively with melanoma cells by indirect immunofluorescent and inimunoperoxidase staining; it reacted with tissue from all primary and metastatic melanomas tested, and it bound to cells from all but one of six cultured melanoma cell lines. Leo Mel 3 did not react with a variety of carcinomas, lymphomas, leukemias, and other neuroectodermal tumors, nor with adult or fetal tissues, except fetal liver. Very weak staining of cutaneous basal melanocytes was noted in a minority of skin sections, and 50 to 80% of melanocytes in four of seven benign nevi showed weak to moderate reactivity. The antibody was relatively specific for human adherent melanoma cells, since it did not bind to the adherent murine B16 melanoma line nor to a nonadherent human melanoma cell line . Expression of the Leo Mel 3-defined antigen was unrelated to changes in cell cycle. When cells from an adherent melanoma cell line were detached and maintained briefly in suspension culture, the cells became markedly less reactive with Leo Mel 3 and, after readherence to plastic, they rapidly reexpressed higher levels of the ganglioside antigen; since Leo Mel 3 prevented attachment and growth of melanoma cells in vitro, a functional role for the ganglioside is suggested in cell adhesion and metastasis. Differentiation of melanoma cells with dimethyl sulfoxide, retinole acid, and theophylline resulted in a marked and selective increase in the amount of Leo Mel 3-defined antigen, together with an increase in the target cell binding ability of these cells, assessed by cold target competition assays using anomalous killer cells.
Amia Annual Symposium Proceedings Amia Symposium Amia Symposium, Feb 1, 2006
Objective Determine how four contextual features (Validity, Certainty, Directionality, and Tempor... more Objective Determine how four contextual features (Validity, Certainty, Directionality, and Temporality) contribute to classification of respiratory syndrome-related clinical conditions as acute, chronic, or absent from manual annotations in Emergency Department Reports. Based on the results, we will direct our research towards automatic identification of the contextual features found to be discriminating.Methods A physician annotated all instances of 56 clinical conditions in 120 ED reports and encoded four contextual features for every annotation. We classified clinical conditions using the contextual features and measured agreement to reference standard classifications made by the physician using a weighted kappa (Κw).Results Κw was 0.518 when not using any of the features and 0.953 when using all of the features.Conclusion Validity, Directionality, and Temporality all improved accuracy. Negation (Directionality) was the most important feature for improving accuracy. Using Certainty made the classification worse.
Working Papers, Nov 1, 2005
Forecasting the future of the CARs, particularly a decade ahead, is a daunting task in view of un... more Forecasting the future of the CARs, particularly a decade ahead, is a daunting task in view of uncertainties in the world economy and the region as well as questions about the reliability of national statistics. Not surprisingly, there have been few previous attempts to do so. Fortunately, future studies and scenario planning is an expanding international field. The world's leading multinational corporations and economies undertake such exercises on a regular basis as an input into business planning and long-term policy development.
... lack of revenue, weak domestic investment and failure to attract foreign directinvestment (FD... more ... lack of revenue, weak domestic investment and failure to attract foreign directinvestment (FDI). ... attracting FDI into the oil and gas sector. ... While the oil exporting countries of Kazakhstan, Azerbaijan and Turkmenistan are showing ...
This paper presents a coherent and systematic analysis of the collapse and subsequent revival of ... more This paper presents a coherent and systematic analysis of the collapse and subsequent revival of the Central Asian Republics (CARs) since 1990. The focus is on the pattern of growth and structural change during the cycle of decline and subsequent revival in the CARs which have been inadequately analyzed in the literature on transition. The paper relates economic performance to initial conditions, country characteristics and policies. Within this framework, it proposes a simple typology of policies (including a new Type III set of policies on regional cooperation and industrial competitiveness) and relates them to the cycle of decline and revival in the CARs. It goes on to examine medium-term prospects and policy needs for the CARs.
Journal American Water Works Association, 1998
Hospital-acquired Legionnaires' disease, associated with contaminated hot water plumbing syst... more Hospital-acquired Legionnaires' disease, associated with contaminated hot water plumbing systems, is a well-documented problem in hospitals and may also be a problem in nursing homes. In this study, four nursing homes were surveyed to determine the extent to which potable hot water systems were colonized by Legionetta pneumophila and to measure microbial and chemical factors related to legionellae contamination. The
Studies in health technology and informatics
Clinical conditions described in patients' dictated reports are necessary for automated detec... more Clinical conditions described in patients' dictated reports are necessary for automated detection of patients with respiratory illnesses such as inhalational anthrax and pneumonia. We applied MetaMap to emergency department reports to extract a set of 71 clinical conditions relevant to detection of a lower respiratory outbreak. We indexed UMLS terms in emergency department reports with MetaMap, filtered the indexed output with a specialized lexicon of UMLS terms for the domain, and mapped the clinical conditions of interest to concepts in the lexicon. We compared MetaMap's ability to accurately identify the conditions against a physician's manual annotations and evaluated incorrectly indexed features to determine what additional processing is necessary. MetaMap identified the clinical conditions with a recall of 0.72 and a precision of 0.56. Necessary processing beyond MetaMap's indexing includes finding validation, temporal discrimination, anatomic location discrimi...
This paper presents a coherent and systematic analysis of the collapse and subsequent revival of ... more This paper presents a coherent and systematic analysis of the collapse and subsequent revival of the Central Asian Republics (CARs) since 1990. The focus is on the pattern of growth and structural change during the cycle of decline and subsequent revival in the CARs which have been inadequately analyzed in the literature on transition. The paper relates economic performance to
Studies in health technology and informatics
The purpose of this study was to determine whether the level of influenza in a population correla... more The purpose of this study was to determine whether the level of influenza in a population correlates with the number of times that internet users access information about influenza on health-related Web sites. We obtained Web access logs from the Healthlink Web site. Web access logs contain information about the user and the information the user accessed, and are maintained electronically by most Web sites, including Healthlink. We developed weekly counts of the number of accesses of selected influenza-related articles on the Healthlink Web site and measured their correlation with traditional influenza surveillance data from the Centers for Disease Control and Prevention (CDC) using the cross-correlation function (CCF). We defined timeliness as the time lag at which the correlation was a maximum. There was a moderately strong correlation between the frequency of influenza-related article accesses and the CDC's traditional surveillance data, but the results on timeliness were inc...
0.9606 (0.9551-0.9649) 0.9815 (0.978-0.9856) Syndrome 2 - Gastrointestinal 0.9823 (0.9797-0.9851)... more 0.9606 (0.9551-0.9649) 0.9815 (0.978-0.9856) Syndrome 2 - Gastrointestinal 0.9823 (0.9797-0.9851) 0.9885 (0.9858-0.9919) Syndrome 3 - Constitutional 0.9293 (0.9207-0.9383) 0.9555 (0.9493-0.9619)
Cancer research, 1987
A monoclonal antibody, Leo Mel 3, raised against a melanoma cell line (LiBr), binds to a carbohyd... more A monoclonal antibody, Leo Mel 3, raised against a melanoma cell line (LiBr), binds to a carbohydrate determinant of cell surface gangliosides, the simplest of which is GD3. This monoclonal antibody was screened for by its capacity to block the recognition and lysis of the melanoma cells by cytotoxic T-lymphocytes with anomalous killer cell function, illustrating a novel approach for identifying monoclonal antibody to biologically relevant tumor-associated antigens. Leo Mel 3 reacted selectively with melanoma cells by indirect immunofluorescent and immunoperoxidase staining; it reacted with tissue from all primary and metastatic melanoma tested, and it bound to cells from all but one of six cultured melanoma cell lines. Leo Mel 3 did not react with a variety of carcinomas, lymphomas, leukemias, and other neuroectodermal tumors, nor with adult or fetal tissues, except fetal liver. Very weak staining of cutaneous basal melanocytes was noted in a minority of skin sections, and 50 to 80...
Applied and environmental microbiology, 1995
We evaluated the use of peptone-yeast extract (PY) medium, different strains of Hartmannella verm... more We evaluated the use of peptone-yeast extract (PY) medium, different strains of Hartmannella vermiformis, and gentamicin in a coculture system to improve the discrimination of virulent and avirulent strains of Legionella pneumophila. H. vermiformis ATCC 50256 was unique among four strains of H. vermiformis, in that it multiplied equally well in Medium 1034 and PY medium (Medium 1034 without fetal calf serum, folic acid, hemin, and yeast nucleic acid and with a 50% reduction of peptone). However, both a virulent strain of L. pneumophila and its avirulent derivative strain multiplied in cocultures when PY medium was used. The multiplication of this avirulent strain was greatly reduced by incorporating gentamicin (1 (mu)g/ml) into the cocultivation system. Five virulent-avirulent sets of L. pneumophila strains were then tested for multiplication in cocultures with H. vermiformis ATCC 50256 and the gentamicin-containing PY medium. Only the virulent strains multiplied. The modified cocul...
MMWR. Morbidity and mortality weekly report, Jan 26, 2005
Emergency department (ED) records and over-the-counter (OTC) sales data are two of the most commo... more Emergency department (ED) records and over-the-counter (OTC) sales data are two of the most commonly used sources of data for syndromic surveillance. The majority of detection algorithms monitor these data sources separately and either do not combine them or combine them in an ad hoc fashion. This report outlines a new causal model that combines the two data sources coherently to perform outbreak detection. This report describes the extension of the Population-wide Anomaly Detection and Assessment (PANDA) Bayesian biologic surveillance algorithm to combine information from multiple data streams. It also outlines the assumptions and techniques used to make this approach scalable for real-time surveillance of a large population. A causal Bayesian network model used previously was extended to incorporate evidence from daily OTC sales data. At the level of individual persons, the actions that result in the purchase of OTC products and in admission to an ED were modeled. Preliminary resu...
Australian and New Zealand journal of medicine, 1994
The American journal of pathology, 1980
The fine structure of "Pittsburgh Pneumonia Agent" (PPA) was studied in infected human ... more The fine structure of "Pittsburgh Pneumonia Agent" (PPA) was studied in infected human lung, guinea pig omentum, yolk sac membrane, Vero cell culture, and after cultivation of the organism on buffered charcoal yeast extract agar. The organism is a prokaryotic cell with the general features of a gram-negative bacillus. PPA is ultrastructurally distinctive because of an unusually thick, electron-dense band present within the periplasmic space adjacent to the outer membrane of the cell wall. This band, presumably a mucopeptide (peptidoglycan) layer, was seen in about 95% of organisms in human lung but less frequently under certain conditions of laboratory infection or cultivation. Future studies are required to determine whether this ultrastructural dimorphism of PPA is related to variation in other properties of this bacterium, eg, gram-variability, acid-fastness, colony morphology, and virulence.
Introduction: Emergency department (ED) records and over-the-counter (OTC) sales data are two of ... more Introduction: Emergency department (ED) records and over-the-counter (OTC) sales data are two of the most commonly used sources of data for syndromic surveillance. The majority of detection algorithms monitor these data sources separately and either do not combine them or combine them in an ad hoc fashion. This report outlines a new causal model that combines the two data sources
Archives of Dermatology, 2003
Amia Annual Symposium Proceedings, 2005
Encoder is a Windows-based program that assists researchers and their staff in coding free text c... more Encoder is a Windows-based program that assists researchers and their staff in coding free text clinical reports into structured databases that are ready for analysis. This software represents approximately 5000 person-hours of programmer time. Researchers at the ...
Journal of Clinical Pathology, 1983
The exanthem of epidemic polyarthritis, a disease caused by Ross River (RR) virus, was examined t... more The exanthem of epidemic polyarthritis, a disease caused by Ross River (RR) virus, was examined three days after onset of the common erythematous and the rare purpuric forms of the eruption. The dermis showed a light perivascular infiltrate of mononuclear cells in both, with extravasation of erythrocytes in the latter. No immunoglobulins (IgM, IgG, IgA) or complement components (Clq, C3)
Cancer Research, 1987
A monoclonal antibody, Leo Mel 3, raised against a melanoma cell line (LiBr), binds to a carbohyd... more A monoclonal antibody, Leo Mel 3, raised against a melanoma cell line (LiBr), binds to a carbohydrate determinant of cell surface gangliosides, the simplest of which is (>,»-This monoclonal antibody was screened for by its capacity to block the recognition and lysis of the melanoma cells by cytotoxic T-lymphocytes with anomalous killer cell function, illustrating a novel approach for identifying monoclonal antibody to biologically relevant tumor-associated antigens. Leo Mel 3 reacted selectively with melanoma cells by indirect immunofluorescent and inimunoperoxidase staining; it reacted with tissue from all primary and metastatic melanomas tested, and it bound to cells from all but one of six cultured melanoma cell lines. Leo Mel 3 did not react with a variety of carcinomas, lymphomas, leukemias, and other neuroectodermal tumors, nor with adult or fetal tissues, except fetal liver. Very weak staining of cutaneous basal melanocytes was noted in a minority of skin sections, and 50 to 80% of melanocytes in four of seven benign nevi showed weak to moderate reactivity. The antibody was relatively specific for human adherent melanoma cells, since it did not bind to the adherent murine B16 melanoma line nor to a nonadherent human melanoma cell line . Expression of the Leo Mel 3-defined antigen was unrelated to changes in cell cycle. When cells from an adherent melanoma cell line were detached and maintained briefly in suspension culture, the cells became markedly less reactive with Leo Mel 3 and, after readherence to plastic, they rapidly reexpressed higher levels of the ganglioside antigen; since Leo Mel 3 prevented attachment and growth of melanoma cells in vitro, a functional role for the ganglioside is suggested in cell adhesion and metastasis. Differentiation of melanoma cells with dimethyl sulfoxide, retinole acid, and theophylline resulted in a marked and selective increase in the amount of Leo Mel 3-defined antigen, together with an increase in the target cell binding ability of these cells, assessed by cold target competition assays using anomalous killer cells.
Amia Annual Symposium Proceedings Amia Symposium Amia Symposium, Feb 1, 2006
Objective Determine how four contextual features (Validity, Certainty, Directionality, and Tempor... more Objective Determine how four contextual features (Validity, Certainty, Directionality, and Temporality) contribute to classification of respiratory syndrome-related clinical conditions as acute, chronic, or absent from manual annotations in Emergency Department Reports. Based on the results, we will direct our research towards automatic identification of the contextual features found to be discriminating.Methods A physician annotated all instances of 56 clinical conditions in 120 ED reports and encoded four contextual features for every annotation. We classified clinical conditions using the contextual features and measured agreement to reference standard classifications made by the physician using a weighted kappa (Κw).Results Κw was 0.518 when not using any of the features and 0.953 when using all of the features.Conclusion Validity, Directionality, and Temporality all improved accuracy. Negation (Directionality) was the most important feature for improving accuracy. Using Certainty made the classification worse.
Working Papers, Nov 1, 2005
Forecasting the future of the CARs, particularly a decade ahead, is a daunting task in view of un... more Forecasting the future of the CARs, particularly a decade ahead, is a daunting task in view of uncertainties in the world economy and the region as well as questions about the reliability of national statistics. Not surprisingly, there have been few previous attempts to do so. Fortunately, future studies and scenario planning is an expanding international field. The world's leading multinational corporations and economies undertake such exercises on a regular basis as an input into business planning and long-term policy development.
... lack of revenue, weak domestic investment and failure to attract foreign directinvestment (FD... more ... lack of revenue, weak domestic investment and failure to attract foreign directinvestment (FDI). ... attracting FDI into the oil and gas sector. ... While the oil exporting countries of Kazakhstan, Azerbaijan and Turkmenistan are showing ...
This paper presents a coherent and systematic analysis of the collapse and subsequent revival of ... more This paper presents a coherent and systematic analysis of the collapse and subsequent revival of the Central Asian Republics (CARs) since 1990. The focus is on the pattern of growth and structural change during the cycle of decline and subsequent revival in the CARs which have been inadequately analyzed in the literature on transition. The paper relates economic performance to initial conditions, country characteristics and policies. Within this framework, it proposes a simple typology of policies (including a new Type III set of policies on regional cooperation and industrial competitiveness) and relates them to the cycle of decline and revival in the CARs. It goes on to examine medium-term prospects and policy needs for the CARs.
Journal American Water Works Association, 1998
Hospital-acquired Legionnaires' disease, associated with contaminated hot water plumbing syst... more Hospital-acquired Legionnaires' disease, associated with contaminated hot water plumbing systems, is a well-documented problem in hospitals and may also be a problem in nursing homes. In this study, four nursing homes were surveyed to determine the extent to which potable hot water systems were colonized by Legionetta pneumophila and to measure microbial and chemical factors related to legionellae contamination. The
Studies in health technology and informatics
Clinical conditions described in patients' dictated reports are necessary for automated detec... more Clinical conditions described in patients' dictated reports are necessary for automated detection of patients with respiratory illnesses such as inhalational anthrax and pneumonia. We applied MetaMap to emergency department reports to extract a set of 71 clinical conditions relevant to detection of a lower respiratory outbreak. We indexed UMLS terms in emergency department reports with MetaMap, filtered the indexed output with a specialized lexicon of UMLS terms for the domain, and mapped the clinical conditions of interest to concepts in the lexicon. We compared MetaMap's ability to accurately identify the conditions against a physician's manual annotations and evaluated incorrectly indexed features to determine what additional processing is necessary. MetaMap identified the clinical conditions with a recall of 0.72 and a precision of 0.56. Necessary processing beyond MetaMap's indexing includes finding validation, temporal discrimination, anatomic location discrimi...
This paper presents a coherent and systematic analysis of the collapse and subsequent revival of ... more This paper presents a coherent and systematic analysis of the collapse and subsequent revival of the Central Asian Republics (CARs) since 1990. The focus is on the pattern of growth and structural change during the cycle of decline and subsequent revival in the CARs which have been inadequately analyzed in the literature on transition. The paper relates economic performance to
Studies in health technology and informatics
The purpose of this study was to determine whether the level of influenza in a population correla... more The purpose of this study was to determine whether the level of influenza in a population correlates with the number of times that internet users access information about influenza on health-related Web sites. We obtained Web access logs from the Healthlink Web site. Web access logs contain information about the user and the information the user accessed, and are maintained electronically by most Web sites, including Healthlink. We developed weekly counts of the number of accesses of selected influenza-related articles on the Healthlink Web site and measured their correlation with traditional influenza surveillance data from the Centers for Disease Control and Prevention (CDC) using the cross-correlation function (CCF). We defined timeliness as the time lag at which the correlation was a maximum. There was a moderately strong correlation between the frequency of influenza-related article accesses and the CDC's traditional surveillance data, but the results on timeliness were inc...
0.9606 (0.9551-0.9649) 0.9815 (0.978-0.9856) Syndrome 2 - Gastrointestinal 0.9823 (0.9797-0.9851)... more 0.9606 (0.9551-0.9649) 0.9815 (0.978-0.9856) Syndrome 2 - Gastrointestinal 0.9823 (0.9797-0.9851) 0.9885 (0.9858-0.9919) Syndrome 3 - Constitutional 0.9293 (0.9207-0.9383) 0.9555 (0.9493-0.9619)
Cancer research, 1987
A monoclonal antibody, Leo Mel 3, raised against a melanoma cell line (LiBr), binds to a carbohyd... more A monoclonal antibody, Leo Mel 3, raised against a melanoma cell line (LiBr), binds to a carbohydrate determinant of cell surface gangliosides, the simplest of which is GD3. This monoclonal antibody was screened for by its capacity to block the recognition and lysis of the melanoma cells by cytotoxic T-lymphocytes with anomalous killer cell function, illustrating a novel approach for identifying monoclonal antibody to biologically relevant tumor-associated antigens. Leo Mel 3 reacted selectively with melanoma cells by indirect immunofluorescent and immunoperoxidase staining; it reacted with tissue from all primary and metastatic melanoma tested, and it bound to cells from all but one of six cultured melanoma cell lines. Leo Mel 3 did not react with a variety of carcinomas, lymphomas, leukemias, and other neuroectodermal tumors, nor with adult or fetal tissues, except fetal liver. Very weak staining of cutaneous basal melanocytes was noted in a minority of skin sections, and 50 to 80...
Applied and environmental microbiology, 1995
We evaluated the use of peptone-yeast extract (PY) medium, different strains of Hartmannella verm... more We evaluated the use of peptone-yeast extract (PY) medium, different strains of Hartmannella vermiformis, and gentamicin in a coculture system to improve the discrimination of virulent and avirulent strains of Legionella pneumophila. H. vermiformis ATCC 50256 was unique among four strains of H. vermiformis, in that it multiplied equally well in Medium 1034 and PY medium (Medium 1034 without fetal calf serum, folic acid, hemin, and yeast nucleic acid and with a 50% reduction of peptone). However, both a virulent strain of L. pneumophila and its avirulent derivative strain multiplied in cocultures when PY medium was used. The multiplication of this avirulent strain was greatly reduced by incorporating gentamicin (1 (mu)g/ml) into the cocultivation system. Five virulent-avirulent sets of L. pneumophila strains were then tested for multiplication in cocultures with H. vermiformis ATCC 50256 and the gentamicin-containing PY medium. Only the virulent strains multiplied. The modified cocul...
MMWR. Morbidity and mortality weekly report, Jan 26, 2005
Emergency department (ED) records and over-the-counter (OTC) sales data are two of the most commo... more Emergency department (ED) records and over-the-counter (OTC) sales data are two of the most commonly used sources of data for syndromic surveillance. The majority of detection algorithms monitor these data sources separately and either do not combine them or combine them in an ad hoc fashion. This report outlines a new causal model that combines the two data sources coherently to perform outbreak detection. This report describes the extension of the Population-wide Anomaly Detection and Assessment (PANDA) Bayesian biologic surveillance algorithm to combine information from multiple data streams. It also outlines the assumptions and techniques used to make this approach scalable for real-time surveillance of a large population. A causal Bayesian network model used previously was extended to incorporate evidence from daily OTC sales data. At the level of individual persons, the actions that result in the purchase of OTC products and in admission to an ED were modeled. Preliminary resu...
Australian and New Zealand journal of medicine, 1994
The American journal of pathology, 1980
The fine structure of "Pittsburgh Pneumonia Agent" (PPA) was studied in infected human ... more The fine structure of "Pittsburgh Pneumonia Agent" (PPA) was studied in infected human lung, guinea pig omentum, yolk sac membrane, Vero cell culture, and after cultivation of the organism on buffered charcoal yeast extract agar. The organism is a prokaryotic cell with the general features of a gram-negative bacillus. PPA is ultrastructurally distinctive because of an unusually thick, electron-dense band present within the periplasmic space adjacent to the outer membrane of the cell wall. This band, presumably a mucopeptide (peptidoglycan) layer, was seen in about 95% of organisms in human lung but less frequently under certain conditions of laboratory infection or cultivation. Future studies are required to determine whether this ultrastructural dimorphism of PPA is related to variation in other properties of this bacterium, eg, gram-variability, acid-fastness, colony morphology, and virulence.