Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing.

Cardiac experimental electrophysiology is in need of a well-defined Minimum Information Standard for recording, annotating, and reporting experimental data. As a step towards establishing this, we present a draft standard, called Minimum Information about a Cardiac Electrophysiology Experiment (MICEE). The ultimate goal is to develop a useful tool for cardiac electrophysiologists which facilitates and improves dissemination of the minimum information necessary for reproduction of cardiac electrophysiology research, allowing for easier comparison and utilisation of findings by others. It is hoped that this will enhance the integration of individual results into experimental, computational, and conceptual models. In its present form, this draft is intended for assessment and development by the research community. We invite the reader to join this effort, and, if deemed productive, implement the Minimum Information about a Cardiac Electrophysiology Experiment standard in their own work.

Systems biology: an approach.

In just over a decade, Systems Biology has moved from being an idea, or rather a disparate set of ideas, to a mainstream feature of research and funding priorities. Institutes, departments, and centers of various flavors of Systems Biology have sprung up all over the world. An Internet search now produces more than 2 million hits. Of the 2,800 entries in PubMed with "Systems Biology" in either the title or the abstract, only two papers were published before 2000, and >90% were published in the past five years. In this article, we interpret Systems Biology as an approach rather than as a field or a destination of research. We illustrate that this approach is productive for the exploration of systems behavior, or "phenotypes," at all levels of structural and functional complexity, explicitly including the supracellular domain, and suggest how this may be related conceptually to genomes and biochemical networks. We discuss the role of models in Systems Biology and conclude with a consideration of their utility in biomedical research and development.

Dynamics of neutrophil aggregation in couette flow revealed by videomicroscopy: effect of shear rate on two-body collision efficiency and doublet lifetime.

During inflammation, neutrophil capture by vascular endothelial cells is dependent on L-selectin and beta(2)-integrin adhesion receptors. One of us (S.I.S.) previously demonstrated that homotypic neutrophil aggregation is analogous to this process in that it is also mediated by these receptors, thus providing a model for studying the dynamics of neutrophil adhesion. In the present work, we set out to confirm the hypothesis that cell-cell adhesion via selectins serves to increase the lifetimes of neutrophil doublets formed through shear-induced two-body collisions. In turn, this would facilitate the engagement of more stable beta(2)-integrin bonds and thus increase the two-body collision efficiency (fraction of collisions resulting in the formation of nonseparating doublets). To this end, suspensions of unstimulated neutrophils were subjected to a uniform shear field in a transparent counter-rotating cone and plate rheoscope, and the formation of doublets and growth of aggregates recorded using high-speed videomicroscopy. The dependence of neutrophil doublet lifetime and two-body collision-capture efficiency on shear rate, G, from 14 to 220 s(-1) was investigated. Bond formation during a two-body collision was indicated by doublets rotating well past the orientation predicted for break-up of doublets of inert spheres. A striking dependence of doublet lifetime on shear rate was observed. At low shear (G = 14 s(-1)), no collision capture occurred, and doublet lifetimes were no different from those of neutrophils pretreated with a blocking antibody to L-selectin, or in Ca(++)-depleted EDTA buffers. At G > or = 66 s(-1), doublet lifetimes increased, with increasing G reaching values twice those for the L-selectin-blocked controls. This correlated with capture efficiencies in excess of 20%, and, at G > or = 110 s(-1), led to the rapid formation of large aggregates, and this in the absence of exogenous chemotactic stimuli. Moreover, the aggregates almost completely broke up when the shear rate was reduced below 66 s(-1). Partial inhibition of aggregate formation was achieved by blocking beta(2)-integrin receptors with antibody. By direct observation of the shear-induced interactions between neutrophils, these data reveal that steady application of a threshold level of shear rate is sufficient to support homotypic neutrophil aggregation.

Neutralase reverses the anti-coagulant but not the anti-thrombotic activity of heparin in a rabbit model of venous thrombosis.

Neutralase (heparinase I; E.C. 4.2.2.7) is a heparin-degrading enzyme undergoing clinical evaluation as an alternative to protamine for reversing the anticoagulant effects of heparin in coronary bypass surgery. The objective of this study was to assess the relative effects of Neutralase and protamine on reversal of heparin-dependent elevations in coagulation parameters and inhibition of clot formation in a rabbit vena caval stasis model. Rabbits were treated with saline or heparin (300 U/kg) for 10 minutes, followed by saline, protamine (2.6 mg/kg), or Neutralase (10 or 30 microg/kg, representing 1.23 IU/kg and 3.69 IU/kg, respectively). Twenty minutes later, venous stasis was induced, and vena caval clots were excised, weighed, and characterized. Coagulation parameters [activated partial thromboplastin time (aPTT) and thrombin clotting time (TCT)] and antiFactor IIa and Xa levels were measured throughout the protocol. Both protamine and Neutralase reversed heparin-mediated increases in aPTT (>300 seconds to 26-35 seconds) and TCT (>300 seconds to 29-56 seconds) to values that were not different from saline-treated, nonheparinized animals. Thrombus weight in the nonheparinized saline group was 62+/-7 mg; heparin-treated animals had no detectable clots. Protamine reversal of heparin was associated with clot formation (89+/-20 mg) while Neutralase reversal was not (no clots). Heparin-induced increases in antiFactor IIa activity were reversed similarly by protamine and Neutralase (from 4.3-8.8 U/ml to 0.2-0.3 U/ml) while antiFactor Xa activity was differentially reversed (from 3.9-5.9 U/ml to 0.7-1.3 U/ml Neutralase; 5.5 U/ml to 0.02 U/ml protamine). These results are consistent with a hypothesis that Neutralase cleaves heparin into fragments, which are devoid of antiFactor IIa activity that retain modest antiFactor Xa activity, resulting in reversal of anticoagulant, but not antithrombotic, heparin activity. This property of Neutralase may be beneficial in reducing post-surgical thrombotic events after reversal of heparin.

Matrix metalloproteinases and metalloproteinase inhibitors in human interphotoreceptor matrix and vitreous.

PURPOSE: We wished to establish which matrix metalloproteinases (MMPs) and metalloproteinase inhibitors (TIMPs) were present in human interphotoreceptor matrix (IPM) and vitreous. METHODS: IPM and vitreous were obtained from postmortem human eyebank eyes. Western immunoblots were probed with antibodies against human MMPs and TIMPs. Assays specific for elastase activity were also performed. RESULTS: Immunoblot analysis indicated the presence of MMP-1 (interstitial collagenase), MMP-2 and MMP-9 (gelatinases A and B), MMP-3 (stromelysin-1) and TIMP-1, -2 and -3 in both IPM and vitreous. MMP-7 (matrilysin) and MMP-12 (metalloelastase) were not found in either IPM or vitreous. CONCLUSIONS: This is the first demonstration of the MMPs and TIMPs in human IPM and of the TIMPs in human vitreous. While these enzymes are most likely involved in normal turnover within the extracellular matrices that surround the neural retina, they may also play a role in a number of retinal diseases, particularly proliferative diabetic retinopathy and age-related macular degeneration.

Association of matrix metalloproteinases with interphotoreceptor retinoid binding protein.

PURPOSE: Interphotoreceptor retinoid binding protein (IRBP) is one of the major components of the interphotoreceptor matrix (IPM) where it may function in retinoid transport between the photoreceptor cells and the retinal pigment epithelium. In the course of studies of the metalloproteinases (MPs) of the IPM, we found that some MPs remain associated with IRBP through the standard purification scheme. We wished to report this finding as a caution to those working with IRBP prepared from fresh tissue. METHODS: IRBP was prepared from bovine IPM by procedures commonly used for its purification, including ion exchange, concanavalin A affinity and gel filtration chromatographies. The MPs were detected by zymography, both gelatin and casein, run with and without preactivation. RESULTS: Through each step of the purification both gelatinase and, especially, caseinase (stromelysin) activities were associated with IRBP. Inclusion of gelatin affinity chromatography did not totally remove the gelatinases. Much of this activity was latent and was only revealed following fractionation or by preactivation before zymography. Whether the fractionation steps remove an inhibitor or simply provide conditions appropriate for the activation of the latent zymogen forms is not known. CONCLUSIONS: The close association of the MPs and IRBP may suggest a functional role for this complex. As a practical consideration, it is likely that many preparations of IRBP may be contaminated with one or more MPs. We found no evidence for any other class of proteinase. Caution should thus be exercised in using an IRBP preparation purified from fresh tissue. It should be monitored for proteinase activity by zymography and/or prepared or stored in the presence of EDTA or dithiothreitol as much as possible.

The effect of the referring dialysis center on renal transplant results.

Between 1/1/76 and 12/31/86, 448 patients underwent transplantation (360 first transplants). Of these, 286 (230 first) were referred by 5 dialysis centers, each referring more than 40 recipients. The remainder were referred by a large number of centers. Using our 5 largest referral centers, we studied the effect of dialysis center on graft and patient survival. There was no difference between dialysis centers in patient survival. Actuarial graft survival differed significantly for all cadaver transplants and for first cadaver transplants (P less than 105). Significant differences persisted when groups were subdivided by type of immunosuppression (azathioprine vs cyclosporine). Demographic (age, race, cause of renal disease) and immunologic (transfusions, PRA, matching) differences between groups did not explain the difference in graft survival. We conclude that referring dialysis center is a previously unrecognized factor affecting transplant outcome. Further studies with larger numbers will be required to determine the underlying reasons for ths phenomenon.

Individualization of immediate posttransplant immunosuppression. The value of antilymphocyte globulin in patients with delayed graft function.

In patients with delayed graft function (DGF), the use of cyclosporine (CsA) has been reported to prolong DGF, increase the number of required dialyses, increase the duration of hospitalization, and be associated with decreased graft survival. Routine postoperative antilymphocyte globulin (ALG) use has been advocated, but ALG is associated with increased viral infection. We studied outcome of individualization of immunosuppression. Between 11/84 and 8/86, first-cadaver transplant recipients whose serum creatinine (Cr) fell greater than or equal to 30% in the first 24 hr (immediate function) were started on CsA and prednisone (P) (group 1, n = 26). The remainder were randomized to P and azathioprine (group 2, n = 32) or P and ALG (group 3, n = 26), and switched to CsA when serum Cr fell greater than 30% (minimum 5 days ALG for the ALG group). P taper was the same in all groups. Patients with DGF (groups 2 and 3) had longer preservation time and higher peak PRA (P less than .05) than group 1. Groups were otherwise equivalent. One and 2-year patient survival was 96% (3 cardiovascular deaths; all with functioning grafts). One-year graft survival was 87% for group 1, 87% for group 2, and 82% for group 3(NS). In patients requiring dialysis, mean day off dialysis was 12 +/- 3 in both groups 2 and 3. Mean hospital stay was 12.5 +/- 1.3 days for group 1, 21.6 +/- 2.1 days for group 2 (P less than .05 vs. 1 & 3), and 14.5 +/- 1.2 days for group 3 (NS vs. 1). The increased hospital stay for group 2 patients was mainly due to increased in-hospital rejections: 75% for group 2, (P less than .05 vs. group 1 [35%], and group 3 [11.5%]). In addition, more group 2 in-hospital 1st rejections were steroid resistant as compared to group 1; 46% group 1 patients have remained rejection free as compared to 0% group 2 (P less than .05 vs. 1 and 3) and 35% of group 3 (P less than .05 vs. 1 and 2). Mean serum creatinine at 6-12 months remained higher in patients with DGF (group 1 P less than .05 vs. 2 and 3). Rejection was the major cause of graft loss in all groups.(ABSTRACT TRUNCATED AT 400 WORDS)

Timing of cyclosporine administration in patients with delayed graft function.

Cyclosporine in renal transplant recipients with delayed graft function (DGF) has been reported to decrease graft survival and prolong both DGF and hospitalization. In some centers, antilymphocyte globulin (ALG) has been used perioperatively to obviate these problems, but ALG is associated with increased viral infections. In this study, first cadaver transplant recipients with a fall in serum creatinine level of greater than or equal to 30% in the first 24 hr were started on prednisone (P) and cyclosporine (Group 1, n = 18). Those whose creatinine level did not fall were started on P and azathioprine (Group 2, n = 23) and switched to P and cyclosporine when serum creatinine fell 30%. One-year patient survival was 98%. One-year graft survival was 83% for both Groups 1 and 2 (NS). Results were compared to historical controls with DGF who received P and cyclosporine (Group 3, n = 19). Patients with DGF and requiring dialysis had fewer dialyses (P less than 0.05) and a shorter hospital stay (P less than 0.05) if started on azathioprine, as compared to those started on cyclosporine. Patients with DGF had a higher serum creatinine at 12 months than those with immediate function (P less than 0.05). We conclude that withholding cyclosporine until DGF is resolving decreases the duration of dialysis, decreases hospital stay, and without the use of prophylactic ALG, is associated with graft survival equivalent to that in patients with immediate function.