Cell modeling with reusable agent-based formalisms

Biologists are building increasingly complex models and simulations of cells and other biological entities, and are looking at alternatives to traditional representations. Making use of the object-oriented (OO) paradigm, the Unified Modeling Language (UML) and Real-time Object-Oriented Modeling (ROOM) visual formalisms, and the Rational Rose RealTime (RRT) visual modeling tool, we summarize a previously-described multi-step process for constructing top-down models of cells. We first construct a simple model of a cell using an architecture in which all objects are containers, agents, or passive objects. We then reuse these architectural principles and components to extend our simple cell model into a more complex cell, the goal being to demonstrate that encapsulation familiar to artificial intelligence researchers can be employed by systems biologists in their models. A red blood cell is embedded in a straight-forward manner within a larger system, which is in turn iteratively embedded within still larger systems, including a blood vessel, a circulatory system, a human being, and a simple ecology. Each complexity increment reuses the same architectural principles, including the use of agents, each of which continuously either moves passive small molecules between containers, or transforms these passive objects from one type into another. We show how it is possible to start with a direct diagrammatic representation of a biological structure such as a cell, using terminology familiar to biologists, and by following a process of gradually adding more and more detail, arrive at a system with structure and behavior of arbitrary complexity that can run and be observed on a computer.     

Hydrogen-assisted cracking studies of 4340 steel by using the optical method of caustics

The optical method of caustics is used to measure the effect of hydrogen on the localized deformation within the fracture process zone (PZ). In particular, the role of the PZ in hydrogen-assisted cracking (HAC) of 4340 steel in hydrogen gas at 1 atm is examined. No change in the caustic diameter was detected prior to crack initiation but an “anomalous” enlargement of the caustic diameter as a function of crack growth was observed as a result of crack tunneling. The “center” of the caustic follows the position of the internal crack front, thus providing a simple means to monitor the growth of internal cracks. It is demonstrated that the technique provides a sensitive means for detecting HAC initiation (the smallest crack depth change detected is 35 μm) and insight into the three-dimensional character of the PZ.     

Reconceptualizing classroom-based research in computers and composition

In this article, Webb maps out three dominant forms of research that have been undertaken in the field of computers and composition—theoretical, case studies, and limited quantitative. She then identifies a fourth mode that has begun to appear—a multimodal approach. Arguing for ways in which this method could help us answer research questions that have been previously unanswerable by other research methods, she calls for the field to reconsider incorporating this multimodal approach more within our research studies.     

Peer interaction and learning with computers in small groups

While anecdotal reports of computer use in classrooms suggest that students often work together, few studies have focused on the interaction between students or on its consequences for achievement. This paper reviews the research on peer interaction with computers to determine its effects on learning. The purposes of this review are to determine (a) the advantages or disadvantages of group work for learning, (b) the kinds of verbal interaction that occur when students work together at the computer, and (c) the kinds of interaction that are beneficial or detrimental for learning. This paper considers the possible cognitive and socioemotional processes that mediate the effects of peer interaction on learning, and discusses the implications of the research findings for the design of computer software.     

An investigation into the occurrence of sewage fungus in rivers containing papermill effluents—IV. Growth in experimental channels dosed with effluents and pure compounds

Wastewaters from the manufacture of pulp and paper have given rise to problems of excessive microbial growth in rivers over a number of years. This paper is the first in a series of four articles describing research undertaken by PIRA at four U.K. paper/board mills (one integrated with pulp production) over the period 1978–1980. This first paper briefly reviews the published literature on sewage fungus growth from pulp and paper mill discharges up to 1978, but mainly describes previously unpublished work undertaken by PIRA over the period 1965–1975. This introductory paper thus provides a state-of-the-art review of methods to control sewage fungus growth from pulp and paper mill effluents prior to commencement of the research described in the following three articles.     

Effectiveness of automatic sprinkler systems in exhibition halls

In cooperation with Mayor Daley's Committee to investigate the McCormick Place Fire, Underwriters' Laboratories tested the effectiveness of automatic sprinkler systems in a simulated exhibition hall having ceiling heights of 30 ft and 50 ft. The results may prove surprising to some who doubt the value of sprinklers in high-ceilinged structures, such as McCormick Place. Fire Protection Department Underwriters' Laboratories, Inc.     

Insulin-like growth factor-I-mediated neurite outgrowth in vitro requires mitogen-activated protein kinase activation

Insulin-like growth factor-I (IGF-I) induces neuronal differentiation in vitro. In the present study, we examined the signaling pathway underlying IGF-I-mediated neurite outgrowth. In SH-SY5Y human neuroblastoma cells, treatment with IGF-I induced concentration- and time-dependent tyrosine phosphorylation of the type I IGF receptor (IGF-IR) and extracellular signal-regulated protein kinases (ERK) 1 and 2. These effects of IGF-I were blocked by a neutralizing antibody against IGF-IR. Whereas IGF-IR phosphorylation was observed within 1 min, maximal phosphorylation of ERKs was not reached for 30 min. Both IGF-IR and ERK phosphorylation were maintained for at least 24 h. Also, the concentration dependence of IGF-I-stimulated IGF-IR and ERK tyrosine phosphorylation paralleled that of IGF-I-mediated neurite outgrowth. We further examined the role of mitogen-activated protein kinase activation in IGF-I-stimulated neuronal differentiation using the mitogen-activated protein kinase/ERK kinase inhibitor PD98059. Whereas PD98059 had no effect on IGF-IR phosphorylation, PD98059 reduced IGF-I-mediated ERK tyrosine phosphorylation and ERK phosphorylation of the substrate Elk-1. PD98059 also produced a parallel reduction of IGF-I-stimulated neurite outgrowth. Finally, consistent with its ability to block neuronal differentiation, PD98059 inhibited IGF-I-dependent changes of GAP-43 and c-myc gene expression. Together these results suggest that activation of ERKs is essential for IGF-I-stimulated neuronal differentiation.     

The value of immediate cytologic evaluation for needle aspiration lung biopsy

RATIONALE AND OBJECTIVES: The authors evaluate the role of immediate cytologic evaluation (ICE) with fine-needle aspiration biopsy (FNAB) for lung lesions at highest risk for pneumothorax. METHODS: A prospective randomized study was conducted of 80 patients with lung lesions surrounded by aerated parenchyma undergoing FNAB with and without ICE (47 and 33 patients, respectively). An analysis of needle passes, procedure time, complications, specimen adequacy, diagnostic yield, and accuracy of procedure was made. RESULTS: There was an increased number of needle passes with ICE (> or = three passes: 23% [11 biopsies] versus 3% [1 biopsy]; P = 0.01). Fluoroscopic procedures took longer with ICE (median time: 15 versus 9 minutes; P = 0.002) with no difference in complication rates. Specimen adequacy was similar (74% and 64%) and the procedure was diagnostic in 79% (37 biopsies) with ICE and in 70% (33 biopsies) without ICE. There were no significant differences in the sensitivity, specificity, or accuracy of the biopsy. CONCLUSIONS: Immediate cytologic evaluation improved results marginally with increased procedure time and needle passes. Immediate cytologic evaluation may be most useful for lesions at lowest risk of complications to assure that a second procedure is not required.     

Dioctyl sodium sulphosuccinate increases net ultrafiltration in peritoneal dialysis

BACKGROUND: The surface-active substance dioctyl sodium sulphosuccinate (DSS) has been reported to increase the peritoneal clearances of urea and creatinine. This study investigated the effects of DSS on the fluid and solute transport characteristics of the peritoneum. DESIGN: A 4-h single-dwell experiment session of peritoneal dialysis using 25 ml of 3.86% glucose dialysis solution with an intraperitoneal volume maker was performed in 16 male Sprague-Dawley rats. In eight rats, 0.005% (50 p.p.m.) DSS was added to the dialysis fluid. No DSS was given to the other eight rats (control group). The transport of fluid, glucose, potassium, sodium, urea, phosphate and urate were analysed. RESULTS: There was a significant increase in the intraperitoneal volume in the DSS group. At 240 min, the drain volume in DSS group (33.0 +/- 2.9 ml) was significantly higher compared to the control group (28.8 +/- 2.1 ml, P < 0.01). This increase in the drain volume was mainly due to a decrease in peritoneal fluid absorption rate in the DSS group (0.040 +/- 0.013 ml/min) as compared to the control group (0.054 +/- 0.010 ml/min, P < 0.05). There was no significant difference in the diffusive permeability and sieving coefficient for the small solutes between these two groups. However, the clearances for urea and sodium were higher in the DSS group, mainly due to the increase in the dialysate volume. CONCLUSION: Our results suggest that DSS significantly increases the net ultrafiltration of peritoneal dialysis. This effect, which was mainly due to a decrease in the fluid absorption rate, contributed to the increased clearances for urea and sodium. DSS did not alter the diffusive permeability and sieving coefficient for the small solutes.