Relational Capacity: Broadening the Notion of Decision-Making Capacity in Paediatric Healthcare

Problems arise when applying the current procedural conceptualization of decision-making capacity to paediatric healthcare: Its emphasis on content-neutrality and rational cognition as well as its implicit assumption that capacity is an ability that resides within a person jeopardizes children’s position in decision-making. The purpose of the paper is to challenge this dominant account of capacity and provide an alternative for how capacity should be understood in paediatric care. First, the influence of developmental psychologist Jean Piaget upon the notion of capacity is discussed, followed by an examination of Vygostky’s contextualist view on children’s development, which emphasizes social interactions and learning for decision-making capacity. In drawing parallels between autonomy and capacity, substantive approaches to relational autonomy are presented that underline the importance of the content of a decision. The authors then provide a relational reconceptualization of capacity that leads the focus away from the individual to include important social others such as parents and physicians. Within this new approach, the outcome of adults’ decision-making processes is accepted as a guiding factor for a good decision for the child. If the child makes a choice that is not approved by adults, the new conceptualization emphasizes mutual exchange and engagement by both parties.     

Implementation and application of a versatile clustering tool for tandem mass spectrometry data

High-throughput proteomics experiments typically generate large amounts of peptide fragmentation mass spectra during a single experiment. There is often a substantial amount of redundant fragmentation of the same precursors among these spectra, which is usually considered a nuisance. We here discuss the potential of clustering and merging redundant spectra to turn this redundancy into a useful property of the dataset. To this end, we have created the first general-purpose, freely available open-source software application for clustering and merging MS/MS spectra. The application also introduces a novel approach to calculating the similarity of fragmentation mass spectra that takes into account the increased precision of modern mass spectrometers, and we suggest a simple but effective improvement to single-linkage clustering. The application and the novel algorithms are applied to several real-life proteomic datasets and the results are discussed. An analysis of the influence of the different algorithms available and their parameters is given, as well as a number of important applications of the overall approach.     

Medical plan-analysis by computer

The traditional approach to computer-assisted medical decision-making involves designing a computer system which simulates a physician's decision-making process. This paper describes a different approach: Medical Plan-Analysis (MPA). Instead of trying to tell a physician how best to manage a patient, an MPA system critiques a physician's management plan. It is anticipated that this approach may have a number of potential social, medical, and medicolegal advantages. The MPA approach has been implemented in ATTENDING, a system designed using Artificial Intelligence techniques to critique a physician's plan for anesthetic management.     

Carrying capacity of wetlands for massive migratory waterfowl

Although it has been documented that waterfowl can cause water quality problems when their populations are large relative to the size or volume of the water body, the question as to how many waterbirds a wetland or a lake can support remains unanswered. A method to quantify the carrying capacity of a water body with regard to massive waterfowl was developed through the study of five wetlands that are used as the wintering ground by a large number of waterfowl in Japan. It takes into consideration water depth, retention time, and in-lake phosphorus concentration. For one of the sites, Sakata Lagoon, which is a registered Ramsar wetland in Japan, the assessment of its carrying capacity suggests that the number of waterfowl should be reduced by half to sustain the water quality of this wetland. Based on the comparison among the five wetlands, a simple indicator was proposed for quick diagnosis. Moreover, a general plot of permissible loading of phosphorus (kg/ha/year) by waterfowl was presented. Besides, this study shed some new light on potential toxicity and accumulation of waterfowl feces at lakebed. Finally, a proposal to increase the carrying capacity of Sakata Lagoon is discussed.     

Dynamic domain threading

A modeling method is described that avoids the need to consider the domain structure of the template used for modeling, and automatically extracts compact fragments of structure that would be of a suitable size to build the model. This aids automation as the size or nature of the template structure can be ignored and does not have to be broken into domain (or multi-domain) units beforehand. The approach leads to the generation of a large number of models each based on slightly differing domain definitions and this variation was further increased by considering alternative secondary structure predictions. Each model, of which there may be thousands, takes the form of a complete alpha-carbon trace and some methods (including residue burial) were investigated for their power to discriminate good models from bad models using decoys. The method is also compared to an earlier retroviral capsid modeling problem for which the X-ray structure is now known. Some potential extensions of the approach to more distant modeling problems are discussed.     

Patterns of parasitism by insect parasitoids in patchy environments

Abstract. 1. This paper shows how the different spatial patterns of per cent parasitism in patches of different host density can be explained within a single model framework that takes into account the parasitoid's aggregative response, and the factors limiting the degree of host exploitation within patches.
2. Two contrasting laboratory examples are presented in which the distribution of searching parasitoids and the resulting levels of parasitism in different patches are both known for a range of parasitoid densities.
3. A model is described predicting the number of hosts parasitized per patch, in which the number of parasitoids searching is determined from a simple expression allowing different degrees of aggregation.
4. The model generates patterns of parasitism encompassing the two laboratory examples and a wide range of examples from the field.
5. The importance of density dependent spatial distributions of parasitism to population stability is briefly discussed.     

A STATISTICAL ANALYSIS OF DIFFERENCE TESTS WITH REPLICATIONS

This paper proposes a statistical method for difference tests with repetitions. Classical methods for difference tests are based upon the binomial distribution, and are not concerned with the number of repetitions per judge. But when more than one replication of a difference test is required, judgements from different judges are more independent than replicates from the same judge; these two cannot be combined in the classical methods. In this paper, we propose another approach that takes into account two points: the number of repetitions per judge, and the differences within subjects. Two examples are presented to illustrate this approach.     

The reduction of formaldehyde by bacterial cells

Formaldehyde is reduced to methyl alcohol by living cells of a creatinine-decomposing strain of Pseudomonas aeruginosa. The amount of HCHO taken up in 30 minutes by 3 x 10(10) cells of this organism is termed its reducing capacity. It was found to be 400 to 480 microg. The reaction takes place over wide pH and temperature ranges, is independent of the concentration of formaldehyde as long as the latter is not high enough to exert a toxic effect on the cell, but depends on the number of bacteria present. In cultures, 3 to 7 days old, there is a decline in reducing capacity without a proportionate decrease in the number of viable cells. On the other hand in cultures, 2 to 4 weeks old, the number of viable cells determines the amount of HCHO taken up. N/100 NaOH depresses the reducing capacity of the organism without affecting bacterial viability. Exposure of bacterial suspensions to temperatures of 46-52 degrees C. for 10 minutes causes a far more rapid decrease in the number of viable cells than in reducing capacity. Incubation of cellular suspensions with nutrient substances, which are able to support adequately the growth of the organism, for 30 minutes prior to the addition of HCHO, induces increases in reducing capacity. The uptake of HCHO by different microorganisms seems to be related to their gaseous and nutritional requirements. Strains of P. aeruginosa and P. fluorescens are predominantly aerobic, least fastidious in their nutritional requirements, most active against HCHO, and least susceptible to the action of aureomycin and chloromycetin. The potential significance of cellular reducing capacity is discussed.     

An ecological approach to restructuring school biology

As a follow-up to the human-centred and cybernetic structuring principles described by Kattman and Schaefer in J. Biol. Educ. 10 (3), an ecological structuring principle is discussed. This principle takes the dynamic and reciprocal relationships between man and his environment as the basis of his existence. The reciprocal relationships are characterized as the biological capacity for self-preservation, reproduction, and adaptation. Several examples from a teaching syllabus are given to illustrate this approach.     

A line-balancing strategy for designing flexible assembly systems

We present a rough-cut analysis tool that quickly determines a few potential cost-effective designs at the initial design stage of flexible assembly systems (FASs) prior to a detailed analysis such as simulation. It uses quantitative methods for selecting and configuring the components of an FAS suitable for medium to high volumes of several similar products. The system is organized as a series of assembly stations linked with an automated material-handling system moving parts in a unidirectional flow. Each station consists of a single machine or of identical parallel machines. The methods exploit the ability of flexible hardware to switch almost instantaneously from product to product. Our approach is particularly suitable where the product mix is expected to be stable, since we combine the hardware-configuration phase with the task-allocation phase. For the required volume of products, we use integer programming to select the number of stations and the number of machines at each station and to allocate tasks to stations. We use queueing network analysis, which takes into account the mean and variance of processing times among different products to determine the necessary capacity of the material-handling system. We iterate between the two analyses to find the combined solution with the lowest costs. Work-in-process costs are also included in the analysis. Computational results are presented.     

An evolutionary model for maximum likelihood alignment of DNA sequences

Summary Most algorithms for the alignment of biological sequences are not derived from an evolutionary model. Consequently, these alignment algorithms lack a strong statistical basis. A maximum likelihood method for the alignment of two DNA sequences is presented. This method is based upon a statistical model of DNA sequence evolution for which we have obtained explicit transition probabilities. The evolutionary model can also be used as the basis of procedures that estimate the evolutionary parameters relevant to a pair of unaligned DNA sequences. A parameter-estimation approach which takes into account all possible alignments between two sequences is introduced; the danger of estimating evolutionary parameters from a single alignment is discussed.     

Invertebrate Strategies in Comparative Learning Studies

Despite the overwhelming variety and abundance of invertebratespecies the contribution of invertebrate studies to our understandingof the behavioral and physiological bases of learning has beenminimal. Although anthropocentric biases may be responsiblefor the inordinate number of studies performed with the usuallaboratory animals, clearly a vigorous extension of the comparativeapproach in the behavioral sciences is demanded. Several featuresof the comparative approach are outlined and suggestions aremade which minimize any of its inherent difficulties. A multi-leveland polythetic approach is proposed which considers multiplecharacteristics supplemented by evidence obtained at other levelsto establish a meaningful behavioral taxonomy. Controlled systematicvariation may be used to analyze the functional relations ofthe performance of different species on the same behavioraltask. Another strategy compares simplified and complex versionsof the same system in order to assess the quantitative and qualitativerelationships between complexity and capacity. The structureof many invertebrate species renders them ideally suited tosuch analysis. Data on habituation obtained in Limulus polyphemusemploying such a paradigm is discussed. The relationships betweenelectrophysiological habituation and levels of neural complexityare clearly demonstrated. Future contributions from this preparationas well as from other invertebrate species are also discussed.     

Animal exchange ratios: an alternative point of view

An alternative interpretation is provided of the concepts of carrying capacity and exchange ratios, particularly suitable for game animal species, based on management models for a given area of rangeland or pasture. It involves modelling animal population dynamics as discrete‐time logistic equations. Carrying capacity is then generated endogenously using rainfall as a proxy. The model interaction parameters, also generated endogenously, represent the animal exchange ratios. Because these two parameters are generated endogenously, this approach takes into account all the animals' habitat requirements (food, cover, water and space) simultaneously, unlike other approaches that tend to consider food requirements only. This makes the approach amenable to multi‐species situations. It also captures the ecological definition of population growth models where the realized rather than the theoretical carrying capacity is determined endogenously.     

Migration,a complex phenomenon

Migration is a complex phenomenon, the dynamics of which demand a systems analysis which goes beyond demographic, economic and spatial considerations to include the facts of individual behaviour and factors in decision-making, and at the same time takes into account how these change with time and affect each other. The first part of this article puts forward asystemic view of the migratory process in the general sense according to the mechanisms and dynamic behavior that generate it. The second part describes an application of this approach: systems analysis thus results in the development not only of an analytical model but also a management model. The material for this part concerns inter-regional migratory movement in Senegal over the period 1960–1980.     

Methods for Quick Consensus Estimation

A method that allows estimating consensus trees without exhaustive searches is described. The method consists of comparing the results of different independent superficial searches. The results of the searches are then summarized through a majority rule, consensed with the strict consensus tree of the best trees found overall. This assumes that to the extent that a group is recovered by most searches, it is more likely to be actually supported by the data. The effect of different parameters on the accuracy and reliability of the results is discussed. Increasing the cutoff frequency decreases the number of spurious groups, although it also decreases the number of correct nodes recovered. Collapsing trees during swapping reduces the number of spurious groups without significantly decreasing the number of correct nodes recovered. A way to collapse branches considering suboptimal trees is described, which can be extended as a measure of relative support for groups; the relative support is based on the Bremer support, but takes into account relative amounts of favorable and contradictory evidence. More exhaustive searches increase the number of correct nodes recovered, but leave unaffected (or increase) the number of spurious groups. Within some limits, the number of replications does not strongly affect the accuracy of the results, so that using relatively small numbers of replications normally suffices to produce a reliable estimation.     

What behaviour in economic games tells us about the evolution of non-human species' economic decision-making behaviour

In the past decade, there has been a surge of interest in using games derived from experimental economics to test decision-making behaviour across species. In most cases, researchers are using the games as a tool, for instance, to understand what factors influence decision-making, how decision-making differs across species or contexts, or to ask broader questions about species’ propensities to cooperate or compete. These games have been quite successful in this regard. To what degree, however, do these games tap into species'' economic decision-making? For the purpose of understanding the evolution of economic systems in humans, this is the key question. To study this, we can break economic decision-making down into smaller components, each of which is a potential step in the evolution of human economic behaviour. We can then use data from economic games, which are simplified, highly structured models of decision-making and therefore ideal for the comparative approach, to directly compare these components across species and contexts, as well as in relation to more naturalistic behaviours, to better understand the evolution of economic behaviour and the social and ecological contexts that influenced it. The comparative approach has successfully informed us about the evolution of other complex traits, such as language and morality, and should help us more deeply understand why and how human economic systems evolved.This article is part of the theme issue ‘Existence and prevalence of economic behaviours among non-human primates’.     

An examination of on-line machine learning approaches for pseudo-random generated data

A pseudo-random generator is an algorithm to generate a sequence of objects determined by a truly random seed which is not truly random. It has been widely used in many applications, such as cryptography and simulations. In this article, we examine current popular machine learning algorithms with various on-line algorithms for pseudo-random generated data in order to find out which machine learning approach is more suitable for this kind of data for prediction based on on-line algorithms. To further improve the prediction performance, we propose a novel sample weighted algorithm that takes generalization errors in each iteration into account. We perform intensive evaluation on real Baccarat data generated by Casino machines and random number generated by a popular Java program, which are two typical examples of pseudo-random generated data. The experimental results show that support vector machine and k-nearest neighbors have better performance than others with and without sample weighted algorithm in the evaluation data set.     

Kinetic study of the pathway of melanizationn between l-dopa and dopachrome

The first part of the melanization pathway from l-dopa to dopachrome has been studied as a system of various chemical reactions coupled by an enzymatic reaction. A theoretical and experimental kinetic approach is proposed for such a system. Rate constants for the implicated chemical steps at different pH and temperature values can be evaluated from measurement of the lag period arising from the accumulation of dopachrome that takes place when l-Dopa was oxidized at acid pH. The thermodynamic parameters of the chemical steps, the deprotonation of dopaquinone-H⁺ into dopaquinone and the internal cyclization of dopaquinone into leukodopachrome, have been obtained. From the results presented, an alternative series of chemical reactions to the Raper-Mason scheme are proposed and discussed.     

Information pyramids for informed biodiversity conservation

We discuss a paradigm for informed ecosystem management that provides a quantitative and rigorous foundation for informing conservation decisions and sustainable ecosystem management. Information pyramids incorporate conceptual and technological advances in ecosystem depiction and provide a framework for the integration and generalization of raw data into forms that are spatially extensive and at the appropriate level of generalization for a particular use. The basic tenets of the pyramid are: (1) Higher levels of the pyramid are entirely derived from a foundation of underlying data. (2) The process of generalization and integration upward should be objective and explicit. (3) Pyramids for different purposes often overlap, with common data and common methods for integration. (4) All levels of the pyramid should be developed together, including base data, methods and kinds of integration, and algorithms for using the information for planning and decision-making. Information pyramids are a powerful approach to organizing research science, and provide a mechanism by which research, data collection, storage and generalization can be focused on conservation outcomes. Common data and methods lead to increased efficiency, while also allowing for separate disciplines and programs. A case study of an integrated pyramid from New Zealand is discussed, which illustrates the characteristics of information pyramids. Components of this pyramid are discussed that provide examples of integration and generalization at various levels of the pyramid, from base data, to derived data, to spatial predictions and classifications, to a method of integrating this information into conservation decisions.     

The ethical acceptability of animal experiments: a proposal for a system to support decision-making

We describe a system to support decision-making on the ethical acceptability of animal experiments for scientific researchers and others responsible for ethical decision-making in animal experiments. The system consists of eight steps. Each step contains a number of substantive questions or a computational rule, leading to a well-articulated moral judgment on specific animal experiments. The system comprises a number of moral assumptions and pre-emptive norms, but leaves enough room for moral discretion and personal responsibility. The general ethical ideas behind the moral choices and assumptions are sketched and potential objections to the overall approach are discussed.