Biomedical subjects

Stephen B Johnson

Publications and source records attributed to Stephen B Johnson.

At least 19 recordsLinked to original sources

PubMed2006

Bridging the gap between biological and clinical informatics in a graduate training program.

Several training programs in biomedical informatics in the United States are attempting to integrate biological and clinical informatics. However, significant differences in the cultures underlying these two disciplines pose barriers to a uniform educational solution. This paper recounts the experience at Columbia University in adapting a graduate program with an initial focus on clinical informatics to train bioinformaticians. The analysis begins by considering the development of the medical and biological informatics cultures over a 17-year period. Then we review how two separate curricula evolved to serve the needs of each group. Interviews with bioinformatics students and faculty indicated some dissatisfaction with the curriculum that developed within clinical informatics. Their comments are considered in the light of an analysis of the relationship between the application domains of biomedical informatics as a discipline. In response, a new curriculum was developed in which bioinformatics and clinical informatics are regarded as subdivisions of the same subject. A key feature of this curriculum is a new course, Theory and Methods in Biomedical Informatics, which presents informatics principles in their general form, and illustrates their application with examples drawn from across the biomedical spectrum. The paper concludes with suggestions for integrating informatics training programs at other institutions.

Computational Biology↗

PubMed2006

Reengineering clinical research with informatics.

The future success of the translational research spectrum depends on the clinical research enterprise's ability to break through the barriers that constrain its productivity. As more basic science discoveries emerge, our ability to effectively translate this knowledge into improved patient care rests squarely on the manner in which we answer clinical questions. Informatics--the science of effective information use--is poised to help advance the conduct of science. However, incorporating informatics into the enterprise comes with its own set of challenges. To harness the benefits of improved information use, it is important to first establish how information flows within research. A thoughtful implementation of informatics--one that factors in social and organizational nuances--will undoubtedly lead to a more efficient and effective clinical research enterprise.

Biomedical Research↗

PubMed2006

Is the Health Level 7/LOINC document ontology adequate for representing nursing documents?

The use of nursing documents from different electronic health record (EHR) systems is challenging due to inconsistency in document naming across systems and institutions. Mapping each local document name to standard document ontology may enable health care professionals to navigate and retrieve documents efficiently for multiple purposes such as quality assurance, outcomes research or public health reporting. The purpose of this study was to evaluate the sufficiency of the Health Level 7 (HL7)/Logical Observation Identifiers, Names, and Codes (LOINC) document ontology for representing nursing document names. We collected 94 nursing document types from the Eclipsys Clinical Information System (CIS) and the Columbia Medical Entities Dictionary (MED) and mapped them to the components of the HL7/LOINC document ontology. Seventy-five (79.8%) nursing document names were completely represented and 19 (20.2%) document names were partially represented. In order for the HL7/LOINC document ontology to be of more use in implementing EHRs that support nursing documentation, Subject Matter Domain and Type of Service axes require extension and clarification.

Humans↗

PubMed2006

Markup of temporal information in electronic health records.

Temporal information plays a critical role in the understanding of clinical narrative (i.e., free text). We developed a representation for marking up temporal information in a narrative, consisting of five elements: 1) reference point, 2) direction, 3) number, 4) time unit, and 5) pattern. We identified 254 temporal expressions from 50 discharge summaries and represented them using our scheme. The overall inter-rater reliability among raters applying the representation model was 75 percent agreement. The model can contribute to temporal reasoning in computer systems for decision support, data mining, and process and outcomes analyses by providing structured temporal information.

Hospitals, Religious↗

PubMed2005

Graph theoretic modeling of large-scale semantic networks.

During the past several years, social network analysis methods have been used to model many complex real-world phenomena, including social networks, transportation networks, and the Internet. Graph theoretic methods, based on an elegant representation of entities and relationships, have been used in computational biology to study biological networks; however they have not yet been adopted widely by the greater informatics community. The graphs produced are generally large, sparse, and complex, and share common global topological properties. In this review of research (1998-2005) on large-scale semantic networks, we used a tailored search strategy to identify articles involving both a graph theoretic perspective and semantic information. Thirty-one relevant articles were retrieved. The majority (28, 90.3%) involved an investigation of a real-world network. These included corpora, thesauri, dictionaries, large computer programs, biological neuronal networks, word association networks, and files on the Internet. Twenty-two of the 28 (78.6%) involved a graph comprised of words or phrases. Fifteen of the 28 (53.6%) mentioned evidence of small-world characteristics in the network investigated. Eleven (39.3%) reported a scale-free topology, which tends to have a similar appearance when examined at varying scales. The results of this review indicate that networks generated from natural language have topological properties common to other natural phenomena. It has not yet been determined whether artificial human-curated terminology systems in biomedicine share these properties. Large network analysis methods have potential application in a variety of areas of informatics, such as in development of controlled vocabularies and for characterizing a given domain.

Algorithms↗

PubMed2005

Role of organic acids in promoting colloidal transport of mercury from mine tailings.

A number of factors affect the transport of dissolved and particulate mercury (Hg) from inoperative Hg mines, including the presence of organic acids in the rooting zone of vegetated mine waste. We examined the role of the two most common organic acids in soils (oxalic and citric acid) on Hg transport from such waste by pumping a mixed organic acid solution (pH 5.7) at 1 mL/min through Hg mine tailings columns. For the two total organic acid concentrations investigated (20 microM and 1 mM), particle-associated Hg was mobilized, with the onset of particulate Hg transport occurring later for the lower organic acid concentration. Chemical analyses of column effluent indicate that 98 wt % of Hg mobilized from the column was particulate. Hg speciation was determined using extended X-ray absorption fine structure spectroscopy and transmission electron microscopy, showing that HgS minerals are dominant in the mobilized particles. Hg adsorbed to colloids is another likely mode of transport due to the abundance of Fe-(oxyhydr)oxides, Fe-sulfides, alunite, and jarosite in the tailings to which Hg(II) adsorbs. Organic acids produced by plants are likely to enhance the transport of colloid-associated Hg from vegetated Hg mine tailings by dissolving cements to enable colloid release.

Chemical Fractionation↗

PubMed2005

Adsorption of organic matter at mineral/water interfaces. 6. Effect of inner-sphere versus outer-sphere adsorption on colloidal stability.

The effects of the adsorption modes of several low molecular weight (LMW) organic anions (maleate, oxalate, and citrate) on the colloidal stability of corundum-water suspensions have been examined using electrokinetic and shear yield stress (tau(y)) measurements over a broad range of pH conditions and LMW organic anion concentrations. Consistent with previous studies, increasing concentrations of maleate, oxalate, and citrate progressively shift the electrokinetic isoelectric point and pH of the maximum shear yield stress (tau(y,max)) to more acidic conditions. Due to its predominant electrostatic driving force for adsorption, outer-spherically adsorbed maleate possesses a very limited ability to charge reverse the corundum-water interface or bind to the negatively charged corundum surface. By contrast, inner-spherically adsorbed oxalate and citrate can significantly charge reverse the corundum-water interface, with the extent of charge reversal being related to the relative binding strengths of the oxalate and citrate anions. Adsorbed maleate, oxalate, and citrate generate steric barriers to interparticle approach, leading to substantial reductions in the magnitude of tau(y,max) at low to intermediate concentrations of those LMW anions. At the highest anion concentrations investigated, however, increases in tau(y,max) are observed, and can be attributed to the formation of bridging Al(III)-organic surface precipitates, as suggested by in situ attenuated total reflectance Fourier transform infrared spectroscopic measurements of corundum-oxalate suspensions at high oxalate concentrations. The extent of precipitate formation is greatest for the corundum-oxalate system due to the strong dissolution-enhancing properties of the inner-spherically adsorbed oxalate anion (i.e., its ability to generate enhanced concentrations of dissolved Al(III) which can then participate in precipitate formation). The effects of the LMW organic anion adsorption modes on both the forms of the measured tau(y) versus pH data, and the ability to quantitatively compare tau(y) and zeta potential data measured at different corundum concentrations, are also discussed.

Journal Article↗

PubMed2005

Adsorption of organic matter at mineral/water interfaces. IV. Adsorption of humic substances at boehmite/water interfaces and impact on boehmite dissolution.

The adsorption of Suwannee River fulvic acid (SRFA) and Pahokee peat humic acid (PPHA) at the boehmite (gamma-AlOOH)/water interface and the impact of SRFA on boehmite dissolution have been examined over a wide range of solution pH conditions (pH 2-12), SRFA surface coverages (Gamma(SRFA), total SRFA binding site concentration normalized by the boehmite surface area) of 0.0-5.33 micromol m(-2), and PPHA surface coverages (Gamma(PPHA), PPHA binding site concentration normalized by boehmite surface area) of 0.0-4.0 micromol m(-2), using macroscopic adsorption and in situ attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. At relatively high SRFA surface coverages (Gamma(SRFA) = 5.33 micromol m(-2)), in situ ATR-FTIR spectral features of adsorbed SRFA are very similar to those measured for SRFA in solution at approximately 1-3 pH units higher. At sub-monolayer surface coverages (Gamma(SRFA) = 1.20 and 2.20 micromol m(-2)), several new peaks and enhancements of the intensities of a number of existing peaks are observed. The latter spectral changes arise from several nonorganic extrinsic species (i.e., adsorbed carbonate and water, for alkaline solution conditions), partially protonated SRFA carboxyl functional groups (near-neutral pH conditions), and small quantities of inner-spherically adsorbed SRFA carboxyl groups and/or Al(III)-SRFA complexes (for acidic conditions). The spectra of PPHA adsorbed at boehmite/water interfaces also showed changes generally consistent with our observations for SRFA sorbed on boehmite. These observations confirm that SRFA and PPHA are predominantly adsorbed at the boehmite/water interface in an outer-sphere fashion, with minor inner-sphere adsorption complexes being formed only under quite acidic conditions. They also suggest that the positively charged boehmite/water interface stabilizes SRFA and PPHA carboxyl functional groups against protonation at lower pH. Measurements of the concentration of dissolved Al(III) ions in the absence and presence of SRFA showed that the boehmite dissolution process is clearly inhibited by the adsorption of SRFA, which is consistent with previous observations that outer-spherically adsorbed organic anions inhibit Al-(oxyhydr)oxide dissolution.

Journal Article↗

PubMed2005

ISO reference terminology models for nursing: applicability for natural language processing of nursing narratives.

Natural language processing (NLP) systems have demonstrated utility in parsing narrative texts for purposes such as surveillance and decision support. However, there has been little work related to NLP of nursing narratives. The purpose of this study was to compare the semantic categories of a NLP system (Medical Language Extraction and Encoding [MedLEE] system) with the semantic domains, categories, and attributes of the International Standards Organization (ISO) reference terminology models for nursing diagnoses and nursing actions. All but two MedLEE diagnosis and procedure-related semantic categories mapped to ISO models. In some instances, we found exact correspondence between the semantic structures of MedLEE and the ISO models. In other situations (e.g. aspects of Site or Location), the ISO model was not as granular as MedLEE. For clinical procedure and non-invasive examination, two ISO nursing action model components (Action and Target) mapped to a single MedLEE semantic category. The ISO models are applicable to NLP of nursing narratives. However, the ISO models require additional specification of selected semantic categories for the abstract semantic domains in order to achieve the objective of using NLP to parse and encode data from nursing narratives. Our analysis also suggests areas for extension of MedLEE particularly in regard to represent nursing actions.

Diagnosis, Computer-Assisted↗

PubMed2005

Adsorption of organic matter at mineral/water interfaces: 5. Effects of adsorbed natural organic matter analogues on mineral dissolution.

The effects of the adsorption of pyromellitate, an analogue for natural organic matter, on the dissolution behavior of corundum (alpha-Al2O3) have been examined over a wide range of pyromellitate concentrations (0-2.5 mM) and pH conditions (2-10). The adsorption modes of pyromellitate on corundum have first been examined using in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy and are shown to be dominated by a fully deprotonated, outer-sphere pyromellitate species ([triple bond]AlOH2+. . .Pyr4-) at pH >/= 5.0. At lower pH conditions, however, an additional protonated outer-sphere species ([triple bond]AlOH2+. . .H2Pyr2-) and an inner-sphere species are also evident. In accordance with the ATR-FTIR findings, modeling of macroscopic pyromellitate adsorption data using an extended constant capacitance treatment was possible using two outer-sphere ([triple bond]AlOH2+. . .Pyr4- and [triple bond]AlOH2+. . .H2Pyr2-) and one inner-sphere ([triple bond]AlPyr3-) adsorbed pyromellitate species. The presence of adsorbed pyromellitate strongly inhibited the dissolution of corundum under acidic (pH < 5) conditions, consistent with a mechanism previously proposed by Johnson et al. whereby outer-spherically adsorbed Pyr4- species sterically protect dissolution-active surface sites from attack by dissolution-promoting species such as protons. A reduction in the protolytic dissolution rate of corundum results. A reference Suwannee River fulvic acid, which also adsorbs to aluminum (oxyhydr)oxide surfaces in a predominantly outer-sphere manner, was similarly shown to strongly inhibit the dissolution of corundum at pH = 3.

Journal Article↗

PubMed2005

Breaking the translational barriers: the value of integrating biomedical informatics and translational research.

The conduct of translational health research has become a vital national enterprise. However, multiple barriers prevent the effective translation of basic science discoveries into clinical and community practice. New information technology (IT) applications could help address these barriers. Unfortunately, owing to a combination of organizational, technical, and social factors, neither physician-investigators and research staff nor their clinical and community counterparts have harnessed such applications. Recently, at the request of the Institute of Medicine's Clinical Research Roundtable, a qualitative study of these factors was conducted at several leading academic medical centers. We explore the current status of IT in the translational research domain, describe the qualitative results, and conclude with a proposed set of initiatives to further increase the integration of IT into translational research.

Biomedical Research↗

PubMed2005

Analyzing the structure and content of public health messages.

BACKGROUND: Health messages are crucial to the field of public health in effecting behavior change, but little research is available to assist writers in composing the overall structure of a message. In order to develop software to assist non-expert message writers in constructing effective messages, the structure of existing health messages must be understood, and an appropriate method for analyzing health message structure developed. METHODS: 72 messages from expert sources were used for development of the method, which was then tested for reproducibility using ten randomly selected health messages. Four raters analyzed the messages and inter-coder agreement was calculated. RESULTS: A method for analyzing the structure of the messages was developed using sublanguage analysis and discourse analysis. Overall kappa between four coders was 0.69, demonstrating "substantial agreement." CONCLUSION: A novel framework for characterizing health message structure and a method for analyzing messages appears to be reproducible.

Communication↗

PubMed2005

Document ontology: supporting narrative documents in electronic health records.

Electronic health records (EHRs) are beginning to manage an increasing volume of narrative data, such as clinical notes pertaining to admission, patient progress, shift change, follow-up, consultation, procedures, etc. These documents fall into a wide variety of classes, based on who is writing them, for what purpose, and in which location, suggesting the need for a document ontology (DO) to model our knowledge of health care documents and their properties. This paper focuses on one aspect of the Health Level 7 (HL7)/ Logical Observation Identifiers, Names, and Codes (LOINC) DO, the Subject Matter Domain (SMD). We created a new polyhierarchical structure for the SMD that combines the current value lists from the LOINC database with another value list from the American Board of Medical Specialties (ABMS). We refined and evaluated the new structure through expert review of the ontology, a survey of medical specialty boards, and specification of SMDs for a corpus of clinical notes.

Attitude of Health Personnel↗

PubMed2005

Clinicians' perceptions of usability of eNote.

The purpose of this evaluation was to assess perceptions of usability of a new semi-structured electronic clinical note. Two focus groups were held, one with attending physicians and one with residents. Physicians described their experiences with eNote and their perceptions about the system. Transcripts of the focus groups underwent content analysis, and four major themes emerged. These were "time", "hardware-system issues", "eNote application issues", and "patients' perceptions."

Attitude of Health Personnel↗

PubMed2004

Adsorption of organic matter at mineral/water interfaces: 3. Implications of surface dissolution for adsorption of oxalate.

The adsorption of oxalate on a model aluminum oxide, corundum (alpha-Al2O3), has been examined over a broad range of oxalate concentrations (0.125-25.0 mM) and pH conditions (2-10). In situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) measurements indicate that at low to intermediate concentrations ([oxalate] < or = 2.50 mM), oxalate adsorbs to corundum predominantly as a bidentate, mononuclear, inner-sphere complex involving both carboxyl groups. Significant contributions from outer-spherically bound oxalate and aqueous Ox(2-) are additionally observed at higher oxalate concentrations. Consistent with the ATR-FTIR findings, macroscopic adsorption data measured for oxalate concentrations of 0.125-2.50 mM can be generally well modeled with a single bidentate, inner-sphere oxalate complex using the charge distribution multisite complexation (CD-MUSIC) model. However, at intermediate oxalate concentrations (0.50 and 1.25 mM) and pH <5, the extent of oxalate adsorption measured experimentally is found to fall significantly below that predicted by CD-MUSIC simulations. The latter finding is interpreted in terms of competition for oxalate from dissolved Al(III), the formation of which is promoted by the dissolution-enhancing properties of the adsorbed oxalate anion. In accordance with this expectation, increasing concentrations of dissolved Al(III) in solution are found to significantly decrease the extent of oxalate adsorption on corundum under acidic pH conditions, presumably through promoting the formation of Al(III)-oxalate complexes with reduced affinities for the corundum surface compared with the uncomplexed oxalate anion.

Journal Article↗

PubMed2004

In situ characterization of aluminum-containing mineral-microorganism aqueous suspensions using scanning transmission X-ray microscopy.

In situ characterization of colloidal particles under hydrous conditions is one of the key requirements for understanding their state of aggregation and impact on the transport of pollutants in aqueous environments. Scanning transmission X-ray microscopy (STXM) is one of the few techniques that can satisfy this need by providing element- and chemical-state-specific 2-D maps at a spatial resolution better than 50 nm using soft X-rays from synchrotron radiation wiggler or undulator sources tuned to the absorption edges of different elements. X-ray absorption near-edge structure (XANES) spectra can also be collected simultaneously at a similar spatial resolution and can provide phase identification in many cases. In this study, we report STXM images and XANES spectroscopy measurements at or above the Al K-edge (E = 1559.6 eV) of various Al-containing minerals and synthetic oxides [alpha-Al2O3 (corundum), gamma-Al2O3, gamma-AlOOH (boehmite), alpha-Al(OH)3 (bayerite), KAl2(AlSi3O10)(OH)2 (muscovite), (Al,Mg)8(Si4O10)4(OH)8.nH2O (montmorillonite), and Mg6Al2(OH)16CO3.4H2O (hydrotalcite)] and demonstrate the capability of this spectromicroscopic tool to identify different Al-containing mineral colloids in multiphase mixtures in aqueous solution. We also demonstrate that STXM imaging at or above the C K-edge (E = 284.2 eV) and Al K-edge can provide unique information on the interactions between bacteria and Al-containing nanoparticles in aqueous suspensions. STXM images of a mixture of Caulobacter crescentus and montmorillonite and corundum particles just above the C and Al K-edges show that the mineral particles and bacteria are closely associated in aggregates, which is likely due to the binding of bacteria to clay and corundum particles by extracellular polysaccharides.

Aluminum↗

PubMed2004

Modeling electronic discharge summaries as a simple temporal constraint satisfaction problem.

OBJECTIVE: To model the temporal information contained in medical narrative reports as a simple temporal constraint satisfaction problem. DESIGN: A constraint satisfaction problem is defined by time points and constraints (inequalities between points). A time interval comprises a pair of points and a constraint. Five complete electronic discharge summaries and paragraphs from 226 other discharge summaries were studied. Medical events were represented as intervals, and assertions about events were represented as constraints. Through a consensus process, a set of encoding procedures and a list of issues related to encoding were generated. MEASUREMENTS: Instances of temporal disjunction and contradiction and distribution of temporal constraints were used. RESULTS: An average of 95 medical events (range, 46-151) and 234 temporal assertions (range, 118-388) were identified per complete discharge summary. Nondefinitional assertions were explicit (36%) or implicit (64%) and absolute (17%), qualitative (72%), or metric (11%). Implicit assertions were based on domain knowledge and assumptions, e.g., the section of the report determined the ordering of events. Issues included linking events, intermittence, periodicity, granularity, vagueness, ambiguity, uncertainty, and plans. ions such as intermittence were not represented explicitly. The temporal network was sparse: Only 0.80% (range, 0.42%-1.38%) of possible constraints were instantiated. No instances of discontinuous temporal disjunction were found in the complete summaries or the 226 paragraphs. One instance of temporal contradiction was found (intrareport rate of 0.2 with a 95% confidence interval of 0.005-1.114). CONCLUSION: A simple temporal constraint satisfaction problem appears sufficient to represent most temporal assertions in discharge summaries and may be useful for encoding electronic medical records.

Algorithms↗

PubMed2004

Adsorption of Suwannee River fulvic acid on aluminum oxyhydroxide surfaces: an in situ ATR-FTIR study.

The adsorption of Suwannee River fulvic acid (SRFA) on boehmite, gamma-AlO(OH), has been examined by both macroscopic adsorption and in situ ATR-FTIR spectroscopic techniques. At a SRFA concentration approaching surface saturation (F = 5.3 micromol m(-2)), adsorption is at a maximum at low pH and decreases as pH is increased. The ATR-FTIR spectral features of adsorbed SRFA are very similar to those measured approximately 1-2 pH units higher in solution, indicating that (i) the SRFA appears to be predominantly adsorbed at the boehmite/water interface in an outer-sphere complexation mode and (ii) the positively charged boehmite/water interface stabilizes SRFA molecules against protonation at low pH.

Adsorption↗