Dense Annotation of Free-Text Critical Care Discharge Summaries from an Indian Hospital and Associated Performance of a Clinical NLP Annotator.

Electronic Health Record (EHR) use in India is generally poor, and structured clinical information is mostly lacking. This work is the first attempt aimed at evaluating unstructured text mining for extracting relevant clinical information from Indian clinical records. We annotated a corpus of 250 discharge summaries from an Intensive Care Unit (ICU) in India, with markups for diseases, procedures, and lab parameters, their attributes, as well as key demographic information and administrative variables such as patient outcomes. In this process, we have constructed guidelines for an annotation scheme useful to clinicians in the Indian context. We evaluated the performance of an NLP engine, Cocoa, on a cohort of these Indian clinical records. We have produced an annotated corpus of roughly 90 thousand words, which to our knowledge is the first tagged clinical corpus from India. Cocoa was evaluated on a test corpus of 50 documents. The overlap F-scores across the major categories, namely disease/symptoms, procedures, laboratory parameters and outcomes, are 0.856, 0.834, 0.961 and 0.872 respectively. These results are competitive with results from recent shared tasks based on US records. The annotated corpus and associated results from the Cocoa engine indicate that unstructured text mining is a viable method for cohort analysis in the Indian clinical context, where structured EHR records are largely absent.

The CHEMDNER corpus of chemicals and drugs and its annotation principles.

The automatic extraction of chemical information from text requires the recognition of chemical entity mentions as one of its key steps. When developing supervised named entity recognition (NER) systems, the availability of a large, manually annotated text corpus is desirable. Furthermore, large corpora permit the robust evaluation and comparison of different approaches that detect chemicals in documents. We present the CHEMDNER corpus, a collection of 10,000 PubMed abstracts that contain a total of 84,355 chemical entity mentions labeled manually by expert chemistry literature curators, following annotation guidelines specifically defined for this task. The abstracts of the CHEMDNER corpus were selected to be representative for all major chemical disciplines. Each of the chemical entity mentions was manually labeled according to its structure-associated chemical entity mention (SACEM) class: abbreviation, family, formula, identifier, multiple, systematic and trivial. The difficulty and consistency of tagging chemicals in text was measured using an agreement study between annotators, obtaining a percentage agreement of 91. For a subset of the CHEMDNER corpus (the test set of 3,000 abstracts) we provide not only the Gold Standard manual annotations, but also mentions automatically detected by the 26 teams that participated in the BioCreative IV CHEMDNER chemical mention recognition task. In addition, we release the CHEMDNER silver standard corpus of automatically extracted mentions from 17,000 randomly selected PubMed abstracts. A version of the CHEMDNER corpus in the BioC format has been generated as well. We propose a standard for required minimum information about entity annotations for the construction of domain specific corpora on chemical and drug entities. The CHEMDNER corpus and annotation guidelines are available at: http://www.biocreative.org/resources/biocreative-iv/chemdner-corpus/.

A steady-state electrochemical model of vascular smooth muscle cells.

A model of the steady-state electrochemical response of vascular smooth muscle cells to external stimuli is presented, which accounts for K, Na, and Ca fluxes. The results of the model are broadly in accordance with experimental data 1), at various transmural pressures; 2), with channel and pump blockade; and 3), under manipulation of external ionic concentrations. The model exhibits dual stable states which sometimes coexist, and abrupt transitions between these states may account for nongraded responses in arteries as external potassium or pressure is varied. The simulations suggest that changes in the intracellular sodium concentration ([Na]i) often accompany smooth muscle responses. For example, [Na]i values vary threefold over the range of pressures from 10 to 100 mmHg.

Non-stationary fluctuation analysis of macroscopic gap junction channel records.

Non-stationary fluctuation analysis was applied to macroscopic records of junctional currents arising from homotypic Cx37 and Cx43 gap junction channels expressed in RIN cells. The data were analyzed by a modification of existing analytical methods that takes endemic uncoupling into account. The results are consistent with both channels having open probabilities ranging from 0.7 to near unity for low transjunctional voltages. The analysis also yielded estimates of single-channel conductances for the two channel types similar to those seen in single-channel recordings. The results presented here show that fluctuation analysis can be used to extract single-channel gap junctional conductances from macroscopic double whole-cell recordings. These results also constitute empirically determined estimates of the open probability that are not model-dependent.

Permeability of R6G across Cx43 hemichannels through a novel combination of patch clamp and surface enhanced Raman spectroscopy.

We have measured the permeability of rhodamine-6G across Cx43 hemichannels reconstituted on a pipette tip. Cx43 hemichannels were overexpressed in Sf9 cells, and affinity-purified. The hemichannels were reconstituted in a lipid bilayer on a pipette tip by the tip-dip method. R6G in the pipette permeated across the channels into the bath. The permeability of R6G was quantified by measuring R6G concentration in the bath after several hours by surface enhanced Raman spectroscopy (SERS) with 100 nm silver colloid particles. The ratio of the permeability of dye to salt, as extracted by this combined electrical-SERS technique, is compatible with similar ratios for other dyes across whole gap junction channels. The results for the permeability ratio were further compared to fluorescence measurements. The novel combination of patch and SERS techniques can be extended to quantifying the transport of biologically significant non-fluorescent molecules, such as cAMP and IP3, across 1 nm sized pores, such as the gap junction channel.

Cardiovascular disease in the Adventures of Sherlock Holmes.

The Adventures of Sherlock Holmes by Sir Arthur Conan Doyle contains many incidents of medical interest. While disorders of the cardiovascular system do not play an important role in these tales, there are, nevertheless, some illnesses that invite speculation. Eleven such incidents are reviewed and discussed in light of the times in which they occurred and in light of current medical knowledge.

Functional expression and biophysical properties of polymorphic variants of the human gap junction protein connexin37.

Connexin37 (Cx37) forms gap junction channels between endothelial cells, and two polymorphic Cx37 variants (Cx37-S319 and Cx37-P319) have been identified with a possible link to atherosclerosis. We studied the gap junction channel properties of these hCx37 polymorphs by expression in stably transfected communication-deficient cells (N2A and RIN). We also expressed a third, truncated variant (Cx37-fs254Delta293) and Cx37 constructs containing epitope tags added to their amino or carboxyl termini. All Cx37 constructs were produced by the transfected cells as demonstrated by RT-PCR and immunoblotting and trafficked to appositional surfaces between cells as demonstrated by immunofluorescence microscopy. Dual whole cell patch-clamping studies demonstrated that Cx37-P319, Cx37-S319, and Cx37-fs254Delta293 had large unitary conductances ( approximately 300 pS). However, addition of an amino terminal T7 tag (T7-Cx37-fs254Delta293) produced a single channel conductance of 120-145 pS with a 24-30 pS residual state. Moreover, the kinetics of the voltage-dependent decline in junctional current for T7-Cx37-fs254Delta293 were significantly slower than for the wild type, implying a destabilization of the transition state. These data suggest that the amino terminus of Cx37 plays a significant role in gating as well as conductance. The carboxyl terminal tail has lesser influence on unitary conductance and inactivation kinetics.

The influence of surface charges on the conductance of the human connexin37 gap junction channel.

The single-channel conductance of the hCx37 homotypic gap junction channel does not saturate with transjunctional voltages up to +/-75 mV, nor does it depend linearly on the intracellular electrolyte concentration. The average maximum unitary conductances measured in KCl were 175 pS (30 mM), 236 pS (55 mM), 343 pS (110 mM), and 588 pS (270 mM) in the presence of 0.1 mM MgCl(2). The unexpectedly high unitary conductance at low salt concentrations can be explained by fixed charge groups within or near the channel orifice. Fixed cytoplasmic surface charges (3.4 e) positioned adjacent (15 A) to the channel pore adequately model the data (surface charge density of 0.24 e/(nm)(2)). In other experiments, high Mg(2+) reduced the unitary conductance of hCx37 homotypic gap junction channels more than predicted by screening alone, consistent with specific effects of Mg(2+) on the channel.

A three-state model for connexin37 gating kinetics.

The gating behavior of human connexin 37 (hCx37) is unaffected by the nature of the bathing monovalent (for Na, K, Rb). It is modified by [Mg] in the millimolar range. For fitting the kinetics, we propose a simple extension to three states of the canonical 2-state model of the hemichannel. The extra closed state allows for some immobilization of a hemichannel at high transjunctional voltages. The model is reasonably efficient at fitting data at various voltage protocols. Interpreting the fits of the data at different [Mg] is consistent with a binding site for Mg.

James Bryan Herrick: a man of intellectual muscle.

James Bryan Herrick was an American physician who made several contributions to clinical medicine. Three of his most important observations are described.

Neuronal innervation, intracellular signal transduction and intercellular coupling: a model for syncytial tissue responses in the steady state.

A model tissue is proposed in which chemically responsive cells are interconnected by gap junctions and innervated by the autonomic nervous system. The model is explicitly dependent on the following physiologically relevant assumptions: (1) a fraction of the cells are directly innervated, and these cells respond to a periodic neuronal stimulus (i.e. the release of neurotransmitter) by production of an intracellular substance (i.e. second messenger molecule); (2) production of second messenger molecules modulates the amplitude of a cellular response, such as contraction or secretion; (3) intracellular formation of second messenger molecules in innervated cells is proportional to the periodicity of the neuronal stimulus, while the intracellular concentration in non-innervated cells is governed by the half-life of the second messenger molecule and the extent of cell-to-cell coupling; (4) the amplitude of the graded response of the individual cell is related to the intracellular second messenger concentration by a Michaelis-Menten function; (5) the amplitude of the graded tissue response is a function of the innervation density, the frequency of stimulation, and the extent of intercellular coupling. Thus, a stimulus-response relationship was developed, where the magnitude of the tissue response was described as a function of the total tissue stimulus. The predicted stimulus-response curve was encapsulated by two parameters: (1) the Hill-exponent, which reflects the steepness of the stimulus-response curve; and (2) the location of the stimulus-response curve, or the half-maximally effective stimulus. Both random and uniform neuronal innervation patterns were considered in model tissues with various effective dimensions. The simulations were also applied to a realistic model of vascular tissue. The shape of the stimulus-response curve is critically dependent on the geometry of innervation. For physiologically relevant (10-90% over 2-3 orders of magnitude) dose-response curves, the model yields an implicit relationship between three different dimensionless parameters. If, in a system, two of these parameters are known, the model can be used to bracket the possible range of the third parameter.

Evidence for heteromeric gap junction channels formed from rat connexin43 and human connexin37.

Homomeric gap junction channels are composed solely of one connexin type, whereas heterotypic forms contain two homomeric hemichannels but the six identical connexins of each are different from each other. A heteromeric gap junction channel is one that contains different connexins within either or both hemichannels. The existence of heteromeric forms has been suggested, and many cell types are known to coexpress connexins. To determine if coexpressed connexins would form heteromers, we cotransfected rat connexin43 (rCx43) and human connexin37 (hCx37) into a cell line normally devoid of any connexin expression and used dual whole cell patch clamp to compare the observed gap junction channel activity with that seen in cells transfected only with rCx43 or hCx37. We also cocultured cells transfected with hCx37 or rCx43, in which one population was tagged with a fluorescent marker to monitor heterotypic channel activity. The cotransfected cells possessed channel types unlike the homotypic forms of rCx43 or hCx37 or the heterotypic forms. In addition, the noninstantaneous transjunctional conductance-transjunctional voltage (Gj/Vj) relationship for cotransfected cell pairs showed a large range of variability that was unlike that of the homotypic or heterotypic form. The heterotypic cell pairs displayed asymmetric voltage dependence. The results from the heteromeric cell pairs are inconsistent with summed behavior of two independent homotypic populations or mixed populations of homotypic and heterotypic channels types. The Gj/Vj data imply that the connexin-to-connexin interactions are significantly altered in cotransfected cell pairs relative to the homotypic and heterotypic forms. Heteromeric channels are a population of channels whose characteristics could well impact differently from their homotypic counterparts with regard to multicellular coordinated responses.

Voltage sensitivity of gap junction currents in rat osteoblast-like cells.

The dependence of macroscopic gap junctional conductance (g(j)) upon transjunctional voltage (Vj) was examined in 39 paired osteoblast-like (OB) cells from primary cultures using the double whole cell patch clamp technique. OB cells were derived from calvarial explants of new-born rats. Instantaneous current-voltage (Ij-Vj) relationships of OB cell pairs (n = 6) were linear in the entire voltage range (-150 < Vj < 150 mV) examined. The steady-state Ij-Vj relationship was non-linear for V > or = +/-60 mV. The curve for the normalised steady-state junctional conductance-voltage relationship (Gss/G0-Vj) was bell-shaped, and was fitted with a two-state Boltzmann equation with a minimum conductance (Gmin) of 0.2-0.3, and a half deactivation voltage (Vo) of +/-83 mV. In two recordings unitary gap junction channel activity was observable. The linear I-V relationships revealed a single channel conductance of approximately 100 pS. Application of parathyroid hormone (10(-8) M) had no effect on the voltage dependence nor the magnitude of macroscopic currents (n = 7).

Gap junctions in excitable cells.

Gap junction channels are an integral part of the conduction or propagation of an action potential from cell to cell. Gap junctions have rather unique gating and permeability properties which permit the movement of molecules from cell to cell. These molecules may not be directly linked to action potentials but can alter nonjunctional processes within cells, which in turn can affect conduction velocity. The data described in this review reveal that, for the majority of excitable cells, there are two limiting factors, with respect to gap junctions, that affect the conduction/propagation of action potentials. These are (1) the total number of channels and (2) the selective permeability of the channels. Interestingly, voltage dependence and the time course of voltage inactivation (kinetics) are not rate limiting steps under normal physiological conditions for any of the connexins studied so far. Only specialized rectifying electrical synapses utilize strong voltage dependence and rapid kinetics to permit or deny the continued propagation of an action potential.

Human connexin 43 gap junction channel gating: evidence for mode shifts and/or heterogeneity.

The gating parameters of human connexin 43 (Cx43) gap junction channels were determined using dual whole cell patch clamp and methods designed for analysis of multichannel recordings. Under steady-state conditions, the mean open time (MOT) of Cx43 gap junction channels was computed and it ranged from 0.43 to 5.25 s. The computed mean closed times (MCT) varied from 0.21 to 1.49 s. Analysis showed that, while the MOT declined with increasing transjunctional voltage (Vj), the apparent decline in the MCT with Vj was not statistically significant. The calculated open probabilities ranged from 0.50 to 0.95. Inspection of the data showed that there was a prolonged decay in junctional current, which had a time course of 60-150 s. The analysis excluded the possibility of a homogeneous voltage inactivated/deactivated population of independent and identical Cx43 gap junction channels. The analysis provided evidence for a homogeneous population of Cx43 channels, which can mode shift under the influence of voltage. The latter case cannot be distinguished from a heterogeneous population of Cx43 channels in which one population is voltage inactivated/deactivated and another is unaffected or weakly inactivated/deactivated by voltage.

Dynamic gap junctional communication: a delimiting model for tissue responses.

Gap junctions are aqueous intercellular channels formed by a diverse class of membrane-spanning proteins, known as connexins. These aqueous pores provide partial cytoplasmic continuity between cells in most tissues, and are freely permeable to a host of physiologically relevant second messenger molecules/ionic species (e.g., Ca2+, IP3, cAMP, cGMP). Despite the fact that these second messenger molecules/ionic species have been shown to alter junctional patency, there is no clear basis for understanding how dynamic and transient changes in the intracellular concentration of second messenger molecules might modulate the extent of intercellular communication among coupled cells. Thus, we have modified the tissue monolayer model of Ramanan and Brink (1990) to account for both the up-regulatory and down-regulatory effects on junctions by second messenger molecules that diffuse through gap junctions. We have chosen the vascular wall as our morphological correlate because of its anisotropy and large investment of gap junctions. The model allows us to illustrate the putative behavior of gap junctions under a variety of physiologically relevant conditions. The modeling studies demonstrated that transient alterations in intracellular second messenger concentrations are capable of producing 50-125% changes in the number of cells recruited into a functional syncytial unit, after activation of a single cell. Moreover, the model conditions required to demonstrate such physiologically relevant changes in intercellular diffusion among coupled cells are commonly observed in intact tissues and cultured cells.