Equipoise, knowledge and ethics in clinical research and practice

It is widely maintained that a clinical trial is ethical only if some form of equipoise between the treatments being compared obtains. To be in equipoise between two treatments A and B is to be cognitively indifferent between the statement 'A is strictly more effective than B' and its negation. It is natural to claim that equipoise regarding A and B is necessary for randomised assignment to treatments A and B to be beneficent and non-maleficent and is sufficient for such an assignment to be fair. Cashing this out precisely is difficult, and various forms of equipoise have been discussed which consider whose equipoise is relevant to the decision. This is to make judgement of equipoise something to be managed socially, while its prima facie significance is supposedly cognitive. Recent reconstructions of equipoise-like concepts in epistemology give clues about how to understand equipoise cognitively. In this paper I examine some of this work and discuss how successful it has been. I suggest that while this work is promising, it still has far to go, and that while equipoise remains the best theory we have of the cognitive justification for clinical trials, it is nonetheless incoherent.     

Failure to Maintain Glycolysis in Anoxic Nerve Terminals

Synaptosomal glycolysis is stimulated eight- to 10-fold when the respiratory chain is inhibited by cyanide or by anoxia. However, the stimulation is transient and after 15 min declines toward the preanoxic rate. The decline is not seen when Ca2+ is absent or when the respiratory chain is inhibited by rotenone. The decline in glycolysis is reversible, is not due to substrate exhaustion, and is the cause, rather than the effect, of lowered synaptosomal ATP/ADP ratios. The failure to maintain glycolysis when the terminal oxidase of the respiratory chain is inhibited may have relevance to the sensitivity of the brain to anoxic damage.     

Site of graviperception in roots: a re-examination

Two lines of evidence have been cited to support the assertion that the root cap is the sole site of graviperception in the root. The first evidence is based on surgical removal of the cap, which abolishes the response to gravity. This is sufficient to conclude that the cap is involved in gravitropism, but not to conclude that the cap is the site of graviperception. The second is based on the results of centrifugation experiments, in which different parts of the plant are subjected to different centrifugal forces. The data from such experiments have been cited to support the conclusion that the perception of gravity is limited to the rootcap. However, these data actually support the conclusion that gravity is perceived throughout the root tip, and not only in the root cap. We believe that the data support the conclusion that the root cap is involved in root gravitropism, but that there is inadequate evidence to conclude that the cap is the sole site of graviperception.     

Analytical studies of injury criteria for the thorax

The viscous criterion is a recently developed criterion to assess injury severity of the human thorax. In the viscous criterion, the peak viscous response, which is defined as the maximum product of deformation velocity and compression of an object, is proposed as a predictor of injury risk. However, the physical meaning of the criterion is not very clear. In this paper, the mathematical properties of the viscous criterion are analyzed. A mechanical thorax model is then used to relate the criterion to the physical quantities of the model using energy concepts. It is found that the so-called peak viscous response is strongly related to the peak energy storing rate of the thorax which is not related to the viscosity of the thorax. It is also shown that the viscous response of the thorax is given by the integral of the velocity squared with respect to time. The analysis is further expanded to a more general case to result in four criteria based upon the energy concepts. A hypothesis for injury assessment is proposed by using the four criteria.     

Oxidation of glycine by Phaseolus leghaemoglobin with associated catabolic reactions at the haem.

Leghaemoglobin from the root nodules of kidney bean (Phaseolus vulgaris) reacts in alkaline glycine solutions as a glycine oxidase in a reaction that may also be regarded as a coupled oxidation. Leghaemoglobin is reduced to the ferrous form by glycinate, the oxygen complex is formed, and finally the haem is attacked to yield a green reaction product. Glycine is simultaneously oxidized to glyoxylate, and hydrogen peroxide is generated. The initial velocity of the formation of the green product is proportional to the concentrations of leghaemoglobin and glycine, and the optimum pH for the reaction is 10.2. The green product is not formed if carbon monoxide, azide of imidazole is bound to the haem, whereas oxidation of glycine to glyoxylate is not inhibited by azide and not essentially by carbon monoxide. Haem breakdown is activated by digestion of leghaemoglobin by carboxypeptidase, and partly inhibited by catalase and superoxide dismutase.     

马陆在森林生态系统物质转化中的功能研究

马陆是森林生态系统重要的分解者,在帽儿山林区,马陆摄食量随温度的升高而增加。据初步估算,马陆地对凋落物的分解量约占该地区年平均凋落物量的０．２１％。马陆对同一种、不同腐解程度的叶片摄食不同,对妆分解凋落物的摄食量大于对未分解凋落物的摄食量。在不同温度条件下,马陆的生态效率不同,其同化效率随温度升高而降低,而粪便率则随温度升高而增加。在不同林型下个体数量分布不均匀。通常、阔叶林＞针阔叶混交林＞针叶林。在土壤的垂直分布上,具有明显的表聚现象。马陆的个体数量季节变化明显,以夏末最多,冬末最少。     

Children as means and ends in large-scale medical research

This paper considers the often-expressed fear that medical research may use children merely as means, and not respect them as ends in themselves - especially insofar as they are deemed less able to consent than adults. The main focus is on large-scale genetic, socio-medical and epidemiological research. The theoretical starting point of the paper is that to be treated as an end in oneself is to be regarded as - and to act as - a participant in cooperative endeavours. This participatory status is certainly connected with individual authority to consent and dissent; and there is no doubt that consent plays an important role when adults participate in many research projects. However, insofar as consent is located within structures of human cooperation, the authority to consent is not a straightforward privilege. Rather, consent is bound up with responsibility for one's choices and commitment to shared terms of cooperation. Given this understanding, it is argued that consent should not be our principal concern when we involve children in research. This is not because of children's (possible) incompetence to consent as such, but rather because children are still learning how to respect and assess the cooperative terms involved in our institutional lives. Instead, our leading concern should be with the terms regulating their involvement in research. Given suitable safeguards, research is one way in which children may learn what it is to bear responsibilities and to act as an end in oneself - that is, to cooperate with others on reasonable terms and for worthy ends.     

Genetic Control of Phosphorus Assimilation in NEUROSPORA CRASSA: Dose-Dependent Dominance and Recessiveness in Constitutive Mutants

Mutants called nuc-1c, constitutive for alkaline phosphatase synthesis, were isolated and mapped very close to nuc-1 mutants in which this enzyme is not expressed. nuc-1 is epistatic to nuc-1c. nuc-1c acts only if it is cis to normal nuc-1 function. The preparation of partial diploids heterozygous for various nuc-1 alleles is described; nuc-1c is dominant to nuc-1+, which in turn is dominant to nuc-1. In heterocaryons with nuc-1+, nuc-1c is dominant when it is present in high proportion, but essentially recessive if it is present in low proportions. In heterocaryons with nuc-1, nuc-1c is again dominant when present in high proportions, but in low proportions it "complements" to give essentially normal repressibility. A model of regulation consistent with these findings is presented.     

The kinetics of hemolytic plaque formation. III. Inhibition of plaques by antigen.

Equations are presented which can be used to describe the inhibition of plaques by multifunctional antigen which binds γG antibody bivalently. The interaction is treated as a bimolecular reaction which is irreversible within the time of the experiment. It is shown that under these conditions the characteristics of the inhibition curve, and their relationship to kinetic and thermodynamic parameters are strongly dependent upon how antibody interacts with RBCs. When the epitope coating is dense, multivalent attachment of antibody is likely and the interaction is considered irreversible. When the epitope coating is sparse, only rapid, reversible univalent attachment is considered and local equilibrium is assumed to hold.The first case leads to an abrupt inhibition curve whose position is determined by the forward rate constant and RBC density. The second case leads to broad asymmetric curves. For this situation the relation between the extent of inhibition and the affinity of the population is generally complicated and reliable affinity information is difficult to obtain. This is contrasted to results obtained previously for unifunctional inhibitors from which reliable affinity information can, in principle, be obtained. The results emphasize the need for carefully designed experiments if affinity information is to be obtained from inhibition studies.     

The Medawar Lecture 2004 the truth about science

The attitudes of scientists towards the philosophy of science is mixed and includes considerable indifference and some hostility. This may be due in part to unrealistic expectation and to misunderstanding. Philosophy is unlikely directly to improve scientific practices, but scientists may find the attempt to explain how science works and what it achieves of considerable interest nevertheless. The present state of the philosophy of science is illustrated by recent work on the 'truth hypothesis', according to which, science is generating increasingly accurate representations of a mind-independent and largely unobservable world. According to Karl Popper, although truth is the aim of science, it is impossible to justify the truth hypothesis. According to Thomas Kuhn, the truth hypothesis is false, because scientists can only describe a world that is partially constituted by their own theories and hence not mind-independent. The failure of past scientific theories has been used to argue against the truth hypothesis; the success of the best current theories has been used to argue for it. Neither argument is sound.     

The unfolding of the P pili quaternary structure by stretching is reversible, not plastic

P pili are protein filaments expressed by uropathogenic Escherichia coli that mediate binding to glycolipids on epithelial cell surfaces, which is a prerequisite for bacterial infection. When a bacterium, attached to a cell surface, is exposed to external forces, the pili, which are composed of approximately 10(3) PapA protein subunits arranged in a helical conformation, can elongate by unfolding to a linear conformation. This property is considered important for the ability of a bacterium to withstand shear forces caused by urine flow. It has hitherto been assumed that this elongation is plastic, thus constituting a permanent conformational deformation. We demonstrate, using optical tweezers, that this is not the case; the unfolding of the helical structure to a linear conformation is fully reversible. It is surmised that this reversibility helps the bacteria regain close contact to the host cells after exposure to significant shear forces, which is believed to facilitate their colonization.     

Codon bias and gene expression.

The frequencies with which individual synonymous codons are used to code their cognate amino acids is quite variable from genome to genome and within genomes, from gene to gene. One particularly well documented codon bias is that associated with highly expressed genes in bacteria as well as in yeast; this is the so-called major codon bias. Here, it is suggested that the major codon bias is not an arrangement for regulating individual gene expression. Instead, the data suggest that this codon bias, which is correlated with a corresponding bias of tRNA abundance, is a global arrangement for optimizing the growth efficiency of cells. On the practical side, it is suggested that heterologous gene expression is not as sensitive to codon bias as previously thought, but that it is quite sensitive to other characteristics of the heterologous gene.     

Permutation tests for the correlation among genetic distances and measures of heterosis

It is often found that heterosis tends to increase with genetic distance of the parents, though the correlation is not usually very close. It is therefore important to test the null hypothesis that the correlation is zero. The present work shows that standard procedures tend to yield too liberal tests, owing to the lack of independence among genetic distances and among heterosis estimates. A valid alternative is to use a permutation test, which was first suggested by Mantel [(1967) Cancer Res 27: 209–220). This test is well-known among plant breeders and geneticists, who often use it to test the correlation among two distance matrices. Its use is not restricted to the comparison of distance matrices. This is demonstrated in the present work, using two published datasets on marker-based genetic distances of maize inbreds or populations and heterosis of their crosses. It is shown that the test is also applicable in the presence of missing data.     

Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling

A molecular dynamics study of pig heart citrate synthase is presented that aims to directly address the question of whether, for this enzyme, the ligand-induced closed domain conformation is accessible to the open unliganded enzyme. The approach utilises the technique of essential dynamics sampling, which is used in two modes. In exploring mode, the enzyme is encouraged to explore domain conformations it might not normally sample in free molecular dynamics simulation. In targeting mode, the enzyme is encouraged to adopt the domain conformation of a target structure. Using both modes extensively, it has been found that when the enzyme is prepared from a crystallographic open-domain structure and is in the unliganded state, it is unable to adopt the crystallographic closed-domain conformation of the liganded enzyme. Likewise, when the enzyme is prepared from the crystallographic closed liganded conformation with the ligands removed, it is unable to adopt the crystallographic open domain conformation. Structural investigations point to a common structural difference that is the source of this energy barrier; namely, the shift of alpha-helix 328-341 along its own axis relative to the large domain. Without this shift, the domains are unable to close or open fully. The charged substrate, oxaloacetate, binds near the base of this helix in the large domain and the interaction of Arg329 at the base of the helix with oxaloacetate is one that is consistent with the shift of this helix in going from the crystallographic open to closed structure. Therefore, the results suggest that without the substrate the enzyme remains in a partially open conformation ready to receive the substrate. In this way, the efficiency of the enzyme should be increased over one that is closed part of the time, with its binding site inaccessible to the substrate.     

Two types of hormone-responsive adenylate cyclase in the rat liver

We have demonstrated the existence of two types of hormone-responsive adenylate cyclase in the isolated perfused rat liver. One, less abundant, is linked to glycogenolysis and the other is not. Glucagon stimulates mainly the glycogenolysis-linked fraction and, to a lesser extent, the fraction which is not linked to glycogenolysis. The suppressive effect of insulin is specific for the glucagon-responsive adenylate cyclase and is inhibited by 3-isobutyl-1-methylxanthine (IBMX). However, this mechanism can explain only partly the ability of insulin to suppress glycogenolysis, and is not observed when cAMP is increased sufficiently by glucagon. Secretin-responsive adenylate cyclase is not linked to glycogenolysis and is suppressed specifically by oxymetazoline. The capacity of this suppressive effect is large and not inhibited by IBMX. These results suggest that there is a functional compartmentalization of cAMP within the hepatocyte or among hepatocytes.     

Hydrolysis of 5,10-methenyltetrahydrofolate to 5-formyltetrahydrofolate at pH 2.5 to 4.5

At pH 4.0 to 4.5, 5,10-methenyltetrahydrofolate is hydrolyzed to only 5-formyltetrahydrofolate if reducing agents are present or iron-redox cycling is suppressed. At pH 4.0, the equilibrium position for this hydrolysis is approximately equal concentrations of both folates. If no reducing agents are used or iron-redox cycling is promoted, considerable amounts of 10-formyldihydrofolate are also formed. It is likely that 10-formyldihydrofolate has been misidentified as 5,10-hydroxymethylenetetrahydrofolate, which was reported to accumulate during the hydrolysis of 5, 10-methenyltetrahydrofolate to 5-formyltetrahydrofolate [Stover, P. and Schirch, V. (1992) Biochemistry 31, 2148-2155 and 2155-2164; (1990) J. Biol. Chem. 265, 14227-14233]. Since 5, 10-hydroxymethylenetetrahydrofolate is reported to be the viable in vivo substrate for serine hydroxymethyltransferase-catalyzed formation of 5-formyltetrahydrofolate, and 5, 10-hydroxymethylenetetrahydrofolate probably does not accumulate, the above folate metabolism is now doubtful. It is hypothesized that mildly acidic subcellular organelles provide an environment for the hydrolysis of 5,10-methenyltetrahydrofolate to 5-formyltetrahydrofolate in vivo, and there is no requirement for enzyme catalysis. Finally, 10-formyltetrahydrofolate is susceptible to iron-catalyzed oxidation to 10-formyldihydrofolate at pH 4 to 4.5.     

A transient histone hyperacetylation signal marks nucleosomes for remodeling at the PHO8 promoter in vivo.

Chromatin remodeling of the yeast PHO8 promoter requires the SAGA histone acetyltransferase complex. We report here that SAGA is necessary and sufficient to establish an activator-dependent hyperacetylation peak over the PHO8 promoter that is restricted to those nucleosomes that are remodeled upon activation. This local hyperacetylated state is observed upon activation in the absence of the SWI/SNF complex when the remodeling process is frozen subsequent to activator binding. Hyperacetylation is lost, however, if remodeling is permitted to go to completion. Thus, a transient histone hyperacetylation signal is shown to be a prerequisite for, and determinant of, the domain of nucleosome remodeling in vivo.     

Aspects of the Clausius-Shannon Identity: Emphasis on the components of transitive information in linear,branched and composite physical systems

In this paper I consider how information is required to specify various systems. It is shown that the transitive information of any physical system, is distributed among three distinct components. One of these, the selective component, is required to specify the elemental parts of the system. Another, the connective component, is required to specify the macrostructure of the system; that is the way the parts are put together. And a third, the conformative component, is required to specify the intrinsic complexion or microstructure of the system. An interesting method for analyzing branched systems which takes account of connective ambiguity is described in some detail. The relationship between information and entropy, known as the Clausius-Shannon Identity, is then discussed with reference to selected thermodynamic models: and that aspect of information which is often overlooked, namely the distinction, between transitive and intransitive information is highlighted. The applications (or perhaps more correctly, the limitations of applying this treatment) to problems of biological interest are also indicated.     

Sequential allocation in clinical trials comparing two exponential survival curves.

The problem of comparing two medical treatments with respect to survival is considered. Treatment outcome is assumed to follow an exponential distribution. The ratio of expected survivals associated with the two treatments is the clinical parameter of interest. A nuisance parameter is present, but it is removed by an invariance reduction and a sequential probability ratio test is applied to the invariant likelihood ratio. A class of data-dependent treatment assignment rules is identified over which the probability of correct treatment selection at the termination of the trial is approximately constant. A cost function, the weighted sum of total patients in the trial and the number assigned to the inferior treatment is introduced, and a treatment allocation rule conjectured to minimize the expected cost is constructed. Both analytic and simulation results show that it is an improvement over rules previously proposed. The methodology contained herein can be used to construct near-optimal rules in other testing contexts.