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PubMed1975

Calculation of predictive odds for possible carriers of heamophilia.

Betting odds for possible carriers of haemophilia have been calculated using data derived from normal and known carrier populations. For each possible carrier the concentration of factor VIII-related antigen and factor VIII biological activity was measured and used to determine the probability of the individual being a carrier. The calculations indicated that, of the 32 possible carriers, 11 were likely to be normal (odds of more than 5:1) while 11 were likely to be haemophilia carriers (again odds of more than 5:1).

Antigens↗
PubMed2001

Towards an inclusive philosophy for phylogenetic inference.

We defend and expand on our earlier proposal for an inclusive philosophical framework for phylogenetics, based on an interpretation of Popperian corroboration that is decoupled from the popular falsificationist interpretation of Popperian philosophy. Any phylogenetic inference method can provide Popperian "evidence" or "test statements" based on the method's goodness-of-fit values for different tree hypotheses. Corroboration, or the severity of that test, requires that the evidence is improbable without the hypothesis, given only background knowledge that includes elements of chance. This framework contrasts with attempted Popperian justifications for cladistic parsimony--in which evidence is the data, background knowledge is restricted to descent with modification, and "corroboration," as a by-product of nonfalsification, is to be measured by cladistic parsimony. Recognition that cladistic "corroboration" reflects only goodness-of-fit, not corroboration/severity, makes it clear that standard cladistic prohibitions, such as restrictions on the evolutionary models to be included in "background knowledge," have no philosophical status. The capacity to assess Popperian corroboration neither justifies nor excludes any phylogenetic method, but it does provide a framework in phylogenetics for learning from errors--cases where apparent good evidence is probable even without the hypothesis. We explore these issues in the context of corroboration assessments applied to likelihood methods and to a new form of parsimony. These different forms of evidence and corroboration assessment point also to a new way to combine evidence--not at the level of overall fit, but at the level of overall corroboration/severity. We conclude that progress in an inclusive phylogenetics will be well served by the rejection of cladistic philosophy.

Likelihood Functions↗
PubMed2002

[Increase in surgical safety].

The authors discuss the problem of operation period safety. It is postulated that the patients' safety depends on the members of operative team. To analyze this aspect the method of theory of probabilities was used. The significant dependence of complication probability on the duration of operation period and associated factor of tiredness of surgical staff is shown in the article. The way of forming the operative team taking into account the psychophysical qualities of its members is proposed.

Humans↗
PubMed2003

Failed refutations: further comments on parsimony and likelihood methods and their relationship to Popper's degree of corroboration.

Kluge's (2001, Syst. Biol. 50:322-330) continued arguments that phylogenetic methods based on the statistical principle of likelihood are incompatible with the philosophy of science described by Karl Popper are based on false premises related to Kluge's misrepresentations of Popper's philosophy. Contrary to Kluge's conjectures, likelihood methods are not inherently verificationist; they do not treat every instance of a hypothesis as confirmation of that hypothesis. The historical nature of phylogeny does not preclude phylogenetic hypotheses from being evaluated using the probability of evidence. The low absolute probabilities of hypotheses are irrelevant to the correct interpretation of Popper's concept termed degree of corroboration, which is defined entirely in terms of relative probabilities. Popper did not advocate minimizing background knowledge; in any case, the background knowledge of both parsimony and likelihood methods consists of the general assumption of descent with modification and additional assumptions that are deterministic, concerning which tree is considered most highly corroborated. Although parsimony methods do not assume (in the sense of entailing) that homoplasy is rare, they do assume (in the sense of requiring to obtain a correct phylogenetic inference) certain things about patterns of homoplasy. Both parsimony and likelihood methods assume (in the sense of implying by the manner in which they operate) various things about evolutionary processes, although violation of those assumptions does not always cause the methods to yield incorrect phylogenetic inferences. Test severity is increased by sampling additional relevant characters rather than by character reanalysis, although either interpretation is compatible with the use of phylogenetic likelihood methods. Neither parsimony nor likelihood methods assess test severity (critical evidence) when used to identify a most highly corroborated tree(s) based on a single method or model and a single body of data; however, both classes of methods can be used to perform severe tests. The assumption of descent with modification is insufficient background knowledge to justify cladistic parsimony as a method for assessing degree of corroboration. Invoking equivalency between parsimony methods and likelihood models that assume no common mechanism emphasizes the necessity of additional assumptions, at least some of which are probabilistic in nature. Incongruent characters do not qualify as falsifiers of phylogenetic hypotheses except under extremely unrealistic evolutionary models; therefore, justifications of parsimony methods as falsificationist based on the idea that they minimize the ad hoc dismissal of falsifiers are questionable. Probabilistic concepts such as degree of corroboration and likelihood provide a more appropriate framework for understanding how phylogenetics conforms with Popper's philosophy of science. Likelihood ratio tests do not assume what is at issue but instead are methods for testing hypotheses according to an accepted standard of statistical significance and for incorporating considerations about test severity. These tests are fundamentally similar to Popper's degree of corroboration in being based on the relationship between the probability of the evidence e in the presence versus absence of the hypothesis h, i.e., between p(e|hb) and p(e|b), where b is the background knowledge. Both parsimony and likelihood methods are inductive in that their inferences (particular trees) contain more information than (and therefore do not follow necessarily from) the observations upon which they are based; however, both are deductive in that their conclusions (tree lengths and likelihoods) follow necessarily from their premises (particular trees, observed character state distributions, and evolutionary models). For these and other reasons, phylogenetic likelihood methods are highly compatible with Karl Popper's philosophy of science and offer several advantages over parsimony methods in this context.

Knowledge↗
PubMed2002

[Theoretic medicine in Egypt].

Egyptian medical writings - especially those surviving on papyri - provide a rich material for historical research. They did not only serve the memory of old healing methods and practices, but that of contemporary medical theories and views as well. On the one hand, Egyptians knew illnesses caused by factors physicians could easily identify by mere empirism, or by their anatomical or physiological knowledge. (Their main physiological theory was probably based on the idea of specific materials circulating through a system of canals (mtw) in the body. It produced illness, either by the system being blocked, or by its original materials changed into the pathogenic material (wxdw). On the other hand however, they supposed the existence of illnesses, caused by the activity of supernatural forces or demons. The two different but parallel etiologies demanded different therapies. Consequently, besides physical also magical therapies were used, and in the healing process the healer him/herself played a double role. Egyptian thinking regarded both ways of healing - the physical and the magical - as equally useful and rational. This richly documented article gives an overview of the Egyptian medical heritage, as illustrated by the original texts and objects.

Egypt, Ancient↗
PubMed2003

[A novel approach for peptide identification by tandem mass spectrometry].

High throughput scoring algorithms that are used to find the match of a tandem mass spectrum to a predicted mass spectrum of a peptide within a database have been applied in shotgun proteomics. However, these algorithms could produce a significant number of incorrect peptide identifications. Here a novel approach was developed to scoring tandem mass spectra against a peptide database, in which fragment ion probabilities, number of enzymatic termini of candidate peptides, matching quality and match pattern between experimental and theoretical spectrum were considered. Benchmarking the novel scorer on a large set of experimental MS/MS spectra, it is demonstrated that PepSearch performs significantly better than the widely used software SEQUEST. The PepSearch software is available at http://compbio.sibsnet.org/projects/pepsearch.

Databases, Protein↗
PubMedDate not supplied

[Design and analysis of a study on reliability and validity of diagnostic tests in urological clinical research].

Diagnosis is a process characterized by uncertainty, which the researcher can approach through knowledge based on the theory of probability, and, as such, it is part of the general decision-making process. To use a test is a process that helps to confirm or refuse the initial probability of the patient to be sick. In this article, we analyze the essential characteristics of diagnostic tests and the principles of effective evaluation of the studies about these tests. We explain in detail what reliability of an instrument is, the types of reliability that there are, and how to analyze them. So that, we introduce concepts such as Pearson's correlation coefficient, intra-class correlation coefficient, and Cohen's Kappa coefficient. Another topic described in this article is measurement of validity, defining the types of validity to be considered on an instrument. Finally, we treat the general principles that rule the design and execution of a study for the evaluation of diagnostic tests, the structure followed by these studies, and mainly the analysis, intention of which is to evaluate to what extent that diagnostic test differentiates between subjects with and without the disease studied. We explore the concepts of sensitivity, specificity, predictive values, and probability ratios, and ROC curves are explained.

Biomedical Research↗
PubMedDate not supplied

Probability.

Explore the source record for details and available documents.

Epidemiology↗
PubMed2004

A randomised controlled trial of three pragmatic approaches to initiate increased physical activity in sedentary patients with risk factors for cardiovascular disease.

BACKGROUND: Physical activity is a major modifiable risk factor for cardiovascular disease, but it is unclear what combination of feasible approaches, using existing resources in primary care, work best to initiate increased physical activity. AIM: To assess three approaches to initiate increased physical activity. DESIGN OF STUDY: Randomised controlled (2 X 2 X 2) factorial trial. SETTING: Four general practices. METHOD: One hundred and fifty-one sedentary patients with computer documented risk factors for cardiovascular disease were randomised to eight groups defined by three factors: prescription by general practitioners (GPs) for brisk exercise not requiring a leisure facility (for example, walking) 30 minutes per day, 5 days per week; counselling by practice nurses, based on psychological theory to modify intentions and perceived control of behaviour, and using behavioural implementation techniques (for example, contracting, 'rehearsal'); use of the Health Education Authority booklet 'Getting active, feeling fit'. RESULTS: Single interventions had modest effects. There was a trend from the least intensive interventions (control +/- booklet) to the more intensive interventions (prescription and counselling combined +/- booklet) for both increased physical activity and fitness (test for trend, P = 0.02 and P = 0.05, respectively). Only with the most intense intervention (prescription and counselling combined) were there significant increases in both physical activity and fitness from baseline (Godin score = 14.4, 95% confidence interval [CI] = 7.8 to 21, which was equivalent to three 15-minute sessions of brisk exercise and a 6-minute walking distance = 28.5 m, respectively, 95% CI = 11.1 to 45.8). Counselling only made a difference among those individuals with lower intention at baseline. CONCLUSION: Feasible interventions using available staff, which combine exercise prescription and counselling explicitly based on psychological theory, can probably initiate important increases in physical activity.

Analysis of Variance↗
PubMed2004

Statistical characteristics of mechanical heart valve cavitation in accelerated testing.

BACKGROUND AND AIM OF THE STUDY: Cavitation damage has been observed on mechanical heart valves (MHVs) undergoing accelerated testing. Cavitation itself can be modeled as a stochastic process, as it varies from beat to beat of the testing machine. This in-vitro study was undertaken to investigate the statistical characteristics of MHV cavitation. METHODS: A 25-mm St. Jude Medical bileaflet MHV (SJM 25) was tested in an accelerated tester at various pulse rates, ranging from 300 to 1,000 bpm, with stepwise increments of 100 bpm. A miniature pressure transducer was placed near a leaflet tip on the inflow side of the valve, to monitor regional transient pressure fluctuations at instants of valve closure. The pressure trace associated with each beat was passed through a 70 kHz high-pass digital filter to extract the high-frequency oscillation (HFO) components resulting from the collapse of cavitation bubbles. Three intensity-related measures were calculated for each HFO burst: its time span; its local root-mean-square (LRMS) value; and the area enveloped by the absolute value of the HFO pressure trace and the time axis, referred to as cavitation impulse. These were treated as stochastic processes, of which the first-order probability density functions (PDFs) were estimated for each test rate. RESULTS: Both the LRMS value and cavitation impulse were log-normal distributed, and the time span was normal distributed. These distribution laws were consistent at different test rates. CONCLUSION: The present investigation was directed at understanding MHV cavitation as a stochastic process. The results provide a basis for establishing further the statistical relationship between cavitation intensity and time-evolving cavitation damage on MHV surfaces. These data are required to assess and compare the performance of MHVs of different designs.

Acceleration↗
PubMedDate not supplied

A mathematical approach to medical diagnosis: application to congenital heart disease.1961.

An equation of conditional probability is derived to express the logical process used by a clinician in making a diagnosis based on clinical data. Solutions of this equation take the form of a differential diagnosis. The probability that each disease represents the correct diagnosis in any particular patient can be calculated. Sufficient statistical data regarding the incidence of clinical signs, symptoms, and electrocardiographic findings in patients with congenital heart disease have been assembled to allow application of this approach to differential diagnosis in this field. This approach provides a means by which electronic computing equipment can be used to advantage in clinical medicine.

Diagnosis, Computer-Assisted↗
PubMed2005

Management of the single liver nodule in a cirrhotic patient: a decision analysis model.

The widespread use of liver imaging in patients with cirrhosis results in the discovery of small (<3 cm) nodules. Although the subsequent management of these patients is variable, it is generally focused on the diagnosis and treatment of hepatocellular carcinoma (HCC). We aimed to compare the 3-year survival associated with several competing strategies used in the management of patients with compensated liver cirrhosis in whom a single small liver lesion is detected during surveillance. We constructed a decision analysis model using a decision tree and Markov model. We assumed that all patients undergo an initial "diagnostic phase" consisting of an imaging study and serum alpha-fetoprotein (AFP). Patients with a "positive initial diagnostic phase" for HCC are referred for either imaging-guided biopsy (IGB) or surgical resection or orthotopic liver transplantation (OLT) without preceding IGB. IGB, if positive for HCC, was followed by OLT, surgical resection, or local therapy. Patients with a "negative initial diagnostic phase" undergo either repeat diagnostic testing (imaging, AFP) every 4 months or are referred for either OLT, surgical resection, or IGB followed by interventions. Probability assumptions were estimated from the published literature. The outcomes compared were 3-year overall survival and recurrence-free survival. When the initial diagnostic phase is positive for HCC, OLT it is associated with the longest survival. In the sensitivity analysis, when the 3-year overall survival for patients referred to OLT is <54%, surgical resection or IGB preceding therapy become more favorable strategies. This 3-year overall survival (<54%) associated with OLT is reached after a waiting time of 4 months on the transplant list, if a 4% monthly dropout rate is assumed. When the initial diagnostic phase is negative for HCC, then performing IGB, before proceeding to therapeutic intervention, is associated with the longest 3-year overall survival. If the IGB is positive, subsequent OLT is associated with the longest survival. The higher the predictive value of the initial diagnostic phase for HCC, the more favorable is OLT (for the "positive results" arm), and follow-up testing (for the "negative results" arm). In conclusion, given a high pretest likelihood of HCC in a single liver nodule detected during surveillance in patients with cirrhosis, IGB may not be required in the presence of a positive noninvasive diagnostic testing. The long waiting time prior to OLT limits its advantage over surgical resection in the treatment of patients with early HCC.

Biopsy↗
PubMedDate not supplied

Statistical properties of the USP dissolution test with pooled samples.

The Montecarlo simulation method is used to study the statistical properties of the USP pooled dissolution test. In this paper, the statistical behavior of the dissolution test for pooled samples is studied, including: a) the operating characteristic curve showing the probability of passing the test versus the mean amount dissolved, b) the influence of measurement uncertainty on the result of the test, c) an analysis of the dependence of the statistical behavior on the underlying distribution of the individual amounts dissolved, d) a comparison of the statistical behavior of the unit dissolution test versus the pooled dissolution test, e) the average number of stages needed to reach a decision presented as a function of parameters of the lot, f) the relative influence of the three stages of the test on the probability of acceptance.

Algorithms↗