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PubMed2002

Diversity-stability relationships in community ecology: re-examination of the portfolio effect.

In plant communities, the portfolio effect, also called "statistical averaging effect", expresses the fact that stability in aggregate community properties such as biomass productivity generally rises with species diversity, simply because of the statistical averaging of the fluctuations in species' properties. This paper essentially upgrades the previous formulations of the portfolio effect, first developed by Doak and collaborators and then by Tilman. It uses a theoretical approach based on simple statistical relationships and some simplifying assumptions proposed by these authors. The new formulation presented extends and improves the previous relationships in the sense that it takes into account simultaneously a varying scaling power of the variance, the interaction effect between species, the heterogeneity in species productivity and interspecies correlated responses to the environment. It appears that the simple statistical averaging, as inferred from this formulation, does not necessarily lead to a positive correlation between species diversity and community stability.

Ecosystem↗
PubMed1975

Correlation analysis of units recorded in the cat dorsal lateral geniculate nucleus.

Spike activity was simultaneously recorded from pairs of units consisting of both optic tract fibers and relay cells in the cat dLGN. The unit pairs were classified with regard to the types of receptive fields involved, the relative location of receptive fields, and their occular drive. Statistical dependencies between the discharge patterns of the simultaneously observed units were assessed by computing their auto- and crosscorrelogram during a period of maintained discharge. Two distinctly different types of statistical dependence were observed. Unit pairs having like and overlapping receptive field centers exhibited statistical dependencies manifested in their crosscorrelograms by a peak near the origin. Conversely, unit pairs having opposite and overlapping receptive field centers were characterized by a prominent valley in their crosscorrelograms near the origin. These statistical dependencies are inferred to represent functional interaction most probably occurring in the retina and characterized by a common element exerting an influence on both units.

Action Potentials↗
PubMedDate not supplied

Selective ordering of preoperative investigations by anesthesiologists reduces the number and cost of tests.

PURPOSE: Preoperative investigations are frequently ordered according to care maps or protocols. We hypothesized that selective ordering of investigations by anesthesiology staff would reduce the number and cost of testing. METHODS: Prospective descriptive double cohort study carried out over 17 weeks in a tertiary care preadmission clinic. In Group 1, testing followed usual practice (based on standing preoperative orders) while in Group 2 testing was initiated only on the order of an attending anesthesiologist or anesthesiology resident. Postoperative complications were categorized and confirmed by an internist blinded to group assignment. Fisher's exact test, Chi-square and Student's t test were used to compare the groups as appropriate. Statistical significance was inferred at P < 0.05. RESULTS: Data were obtained from 507 patients in Group 1 and 431 patients in Group 2. Demographics and ASA risk score were similar in both groups. The mean number of tests ordered did not differ between groups. The mean cost of investigations was reduced from 124 dollars in Group 1 to 95 dollars in Group 2 (P < 0.05). If data for patients assessed by staff anesthesiologists only were considered, the mean cost of testing was reduced to 73 dollars. The number and cost of tests ordered by anesthesia residents were similar to that in Group 1. More complications were noted in Group 2, but these did not appear to be related to the altered test ordering practice. CONCLUSION: Selective test ordering by staff anesthesiologists reduces the number and cost of preoperative investigations. Educational efforts should be directed towards improving resident and staff preoperative test ordering practices.

Aged↗
PubMed2006

BIOREL: the benchmark resource to estimate the relevance of the gene networks.

The progress of high-throughput methodologies in functional genomics has lead to the development of statistical procedures to infer gene networks from various types of high-throughput data. However, due to the lack of common standards, the biological significance of the results of the different studies is hard to compare. To overcome this problem we propose a benchmark procedure and have developed a web resource (BIOREL), which is useful for estimating the biological relevance of any genetic network by integrating different sources of biological information. The associations of each gene from the network are classified as biologically relevant or not. The proportion of genes in the network classified as "relevant" is used as the overall network relevance score. Employing synthetic data we demonstrated that such a score ranks the networks fairly in respect to the relevance level. Using BIOREL as the benchmark resource we compared the quality of experimental and theoretically predicted protein interaction data.

Computational Biology↗
PubMed2005

Conjunction revisited.

The aim of this note is to revisit the analysis of conjunctions in imaging data. We review some conceptual issues that have emerged from recent discussion (Nichols, T., Brett, M., Andersson, J., Wager, T., Poline, J.-B., 2004. Valid Conjunction Inference with the Minimum Statistic.) and reformulate the conjunction of null hypotheses as a conjunction of k or more effects. Analyses based on minimum statistics have typically used the null hypothesis that k = 0. This enables inferences about one or more effects (k > 0). However, this does not provide control over false-positive rates (FPR) for inferences about a conjunction of k = n effects, over n tests. This is the key point made by Nichols et al., who suggest a procedure based on supremum P values that provides an upper bound on FPR for k = n. Although valid, this is a very conservative procedure, particularly in the context of multiple comparisons. We suggest that an inference on a conjunction of k = n effects is generally unnecessary and distinguish between congruent contrasts that test for the same treatment and incongruent contrasts of the sort used in cognitive conjunctions. For congruent contrasts, the usual inference, k > 0, is sufficient. With incongruent contrasts it is sufficient to infer a conjunction of k >u effects, where u is the number of contrasts that share some uninteresting effect. The issues highlighted by Nichols et al., have important implications for the design and analysis of cognitive conjunction studies and have motivated a change to the SPM software, that affords a test for the more general hypothesis k >u. This more general conjunction test is described.

Arousal↗
PubMed2005

Uncertainty, neuromodulation, and attention.

Uncertainty in various forms plagues our interactions with the environment. In a Bayesian statistical framework, optimal inference and prediction, based on unreliable observations in changing contexts, require the representation and manipulation of different forms of uncertainty. We propose that the neuromodulators acetylcholine and norepinephrine play a major role in the brain's implementation of these uncertainty computations. Acetylcholine signals expected uncertainty, coming from known unreliability of predictive cues within a context. Norepinephrine signals unexpected uncertainty, as when unsignaled context switches produce strongly unexpected observations. These uncertainty signals interact to enable optimal inference and learning in noisy and changeable environments. This formulation is consistent with a wealth of physiological, pharmacological, and behavioral data implicating acetylcholine and norepinephrine in specific aspects of a range of cognitive processes. Moreover, the model suggests a class of attentional cueing tasks that involve both neuromodulators and shows how their interactions may be part-antagonistic, part-synergistic.

Acetylcholine↗
PubMed1996

Full reconstruction of Markov models on evolutionary trees: identifiability and consistency.

A Markov model of evolution of characters on a phylogenetic tree consists of a tree topology together with a specification of probability transition matrices on the edges of the tree. Previous work has shown that, under mild conditions, the tree topology may be reconstructed, in the sense that the topology is identifiable from knowledge of the joint distribution of character states at pairs of terminal nodes of the tree. Also, the method of maximum likelihood is statistically consistent for inferring the tree topology. In this article we answer the analogous questions for reconstructing the full model, including the edge transition matrices. Under mild conditions, such full reconstruction is achievable, not by using pairs of terminal nodes, but rather by using triples of terminal nodes. The identifiability result generalizes previous results that were restricted either to characters having two states or to transition matrices having special structure. The proof develops matrix relationships that may be exploited to identify the model. We also use the identifiability result to prove that the method of maximum likelihood is consistent for reconstructing the full model.

Animals↗
PubMed1992

An evaluation of pre-registration midwifery education in England. Research design: a case study approach.

In this paper some aspects of research design are described and discussed. A national study to evaluate pre-registration midwifery education in England is currently in progress. As part of that study six case study sites have been selected. How those sites were selected and the theory and method of the case study approach are discussed in this paper. The value of the case study approach is discussed as are methodological issues of the case study method. What is a case? Are case studies representative? How can you generalise from case studies? What is theoretical sampling? What is the difference between statistical and logical inference? These are some of the questions raised and examined. It is suggested that an understanding of these theoretical issues and the research process is important to understand the research findings. By making the research design explicit and describing the research process the study also adopts a reflexive approach.

Education, Nursing↗
PubMedDate not supplied

Public perceptions of a rural emergency medical services system.

INTRODUCTION: To determine the awareness of citizens and physicians concerning the capabilities of a rural emergency medical services (EMS) system. HYPOTHESIS: Citizens and physicians are unaware of the capabilities of the EMS system. METHODS: Residents were selected randomly from the local telephone directory and asked a series of structured questions about their EMS agency. A written survey was distributed to area physicians. Chi-square analysis was used to compare the proportion of respondents who knew the available interventions in their community with the proportion of those who did not. Statistical significance was inferred at p < 0.01. RESULTS: A total of 49% of the citizens were able to identify available skills, and 41.4% of the physicians were able to identify available skills. Physicians were less likely than were the citizens to be able to identify the skills performed by each provider (p < 0.001). CONCLUSION: This study indicates that both physicians and the lay public have little understanding of the capabilities of their EMS system.

Attitude of Health Personnel↗
PubMed2003

Real-time observation of surface reactivity and mobility with scanning tunneling microscopy.

Scanning tunneling microscopy allows the direct observation of reactions on surfaces on the atomic scale that otherwise must be inferred from the statistical behavior of hundred of trillions of molecules or atoms. Since the study of the details of reactions on this length scale began, our conception of surface reactivity has changed profoundly. In this Account we focus attention on our real-time observations of reactions for a number of systems, including the island growth of surface oxide on Cu(110), the anisotropic and site-specific reactivity of this oxide with carbon monoxide and ammonia, the collective motion of laterally interacting O(a) and SO(3)(a), and the incorporation of metal atoms into the structures of molecular intermediates formed in the reaction of ammonia with O(a) on Ag(110). These nanoscale, time-resolved movies capture the events as they occur, providing a dynamic picture of the distribution of reactants and products on the surface, thus providing a better understanding of the roles of reactant distribution and site specificity in surface reactivity.

Journal Article↗
PubMed1983

[Significance of vascular changes in the colposcopic diagnosis of precancerous and early stages of cervical cancer].

Blood vessels are visible in an average of 80% of patients on whom colposcopy is performed. This percentage share increases if there are pathological changes. The following vascular types occur as characteristic criteria in cervical intraepithelial neoplasia (CIN) and in carcinoma, their classification being based on structural properties such as calibre, long and intercapillary spaces, shape and arrangement of the vessels, as well as their functional state: Abnormal vessels; pathological vessels of the 1st and 2nd degree; uncharacteristic vessels (also known as "troubled vessels"). The author discusses the architecture, adaptive vasodilation and formation of new vessels in connection with morphological changes in the epithelium. Their occurrence is evaluated statistically, and an inference is drawn from these studies on the efficiency of vascular diagnosis. The following conclusions are arrived at on the basis of the examined material: The abnormal vessel result from a proliferation of the abnormal or dysplastic epithelium. The pathological vessels of the 1st degree occur as maximum type of adaptive vascular change resulting in the course of carcinomatous proliferation. The pathological changes of the 2nd degree, on the other hand, become visible as new formations in invasively growing carcinomas only. There is a connection between the presence of pathological types of vessels and the carcinomatous degeneration of the epithelium and the invasive growth. Assessment of the vessels must be performed parallel to the assessment of the epithelium via acetic acid or lactic acid test. This facilitates colposcopic diagnosis of precarcinomic and early stages of cervical carcinoma and enables conclusions to be drawn on an invasive growth of the carcinoma.

Blood Vessels↗
PubMed2000

Factors predicting prolonged length of stay after carotid endarterectomy.

BACKGROUND: Over the last several years, implementation of critical pathways in patients undergoing carotid endarterectomy has decreased postoperative length of stay significantly. Discharge the day after surgery has become commonplace in many centers, including our own. Unfortunately, managed care may interpret this refinement as a standard of care and limit reimbursement or even disallow admissions extending beyond 1 day. We therefore examined our carotid registry to identify risk factors associated with postoperative length of stay exceeding 1 day. METHODS: We retrospectively reviewed all patients undergoing carotid endarterectomy at our academic center from May 1996 through April 1999. Combined procedures and patients undergoing subsequent noncarotid-related procedures on those admissions were excluded. The charts were inspected for atherosclerosis risk factors, including sex and age, specific attending surgeon, side of the surgery, use of intravenous vasoactive drugs, actual preoperative blood pressure, and presence of neurologic symptoms or postoperative complications. Multiple regression analysis was performed on all collected variables. Statistical significance was inferred for P less than.05. RESULTS: A total of 188 patients met the study criteria and had complete, retrievable medical records. A mean postoperative length of stay of 1.65 +/- 0.08 days and a mean total length of stay of 2.17 +/- 0.14 days were observed. Fifty-seven percent of patients went home the day after surgery. There was a 1.6% stroke-mortality rate. Significant predictors of a prolonged stay, listed in order of decreasing importance on the basis of their calculated contribution to prolonging the postoperative length of stay, are as follows (P value; beta coefficient): postoperative complications (<.0001; 1.03), age > 79 years (.008; 0.547), diabetes mellitus (.011; 0.407), female sex (.007; 0.398), and intravenous vasodilator requirement (. 035; 0.382). Other atherosclerosis risk factors, prior neurologic symptoms, the postoperative use of vasopressors, and reoperative surgery did not contribute to extended length of stay. CONCLUSIONS: Discharge on the first postoperative day is feasible in many, but not all, patients undergoing carotid endarterectomy. Our data help define subsets of patients at risk for prolonged postoperative stay. Targeting these subsets for preoperative medical and social interventions may allow safe early discharge more frequently.

Aged↗
PubMed2002

Waiting time information services: what are the implications of waiting list behaviour for their design?

In some countries, patients requiring elective surgery can access comparative waiting time information for various surgical units. What someone can deduce from this information will depend upon how the statistics are derived, and how waiting lists behave. However, empirical analyses of waiting list behaviour are scarce. This study analysed three years of waiting list data collected at one hospital in Sydney, Australia. The results highlight various issues that raise questions about using particular waiting time statistics to make inferences about patient waiting times. In particular, the results highlight the considerable variation in behaviour that can exist between surgeons in the same specialty, and that can occur over time.

Censuses↗
PubMed2005

Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups.

We explored the epidemic history of HIV-1 subtype B in the United Kingdom by using statistical methods that infer the population history of pathogens from sampled gene sequence data. Phylogenetic analysis of HIV-1 pol gene sequences from Britain showed at least six large transmission chains, indicating a genetically variable, but epidemiologically homogeneous, epidemic among men having sex with men. Through coalescent-based analysis, we showed that these chains arose through separate introductions of subtype B strains into the United Kingdom in the early to mid-1980s. After an initial period of exponential growth, the rate of spread generally slowed in the early 1990s, which is more likely to correlate with behavior change than with reduced infectiousness resulting from highly active antiretroviral therapy. Our results provide insights into the complexity of HIV-1 epidemics that must be considered when developing HIV monitoring and prevention initiatives.

Disease Outbreaks↗
PubMed2000

Field investigation comparing diffusion badge and charcoal tube monitoring for styrene.

A short investigation was completed to compare organic vapor monitor and charcoal tube results for airborne styrene in three fiberglass boat manufacturing plants. Time-weighted average results were compared for 15 paired samples (12 breathing zone/3 area). Linear regression analysis showed a strong predictive relationship and an R2 value of 0.96. The organic vapor monitors had 31 percent higher results than the charcoal tubes across the range of concentrations 5.6 ppm to 150 ppm. Paired t-test validated this inference by demonstrating statistically significant differences between the means.

Air Pollutants, Occupational↗
PubMed2004

Incorporating genotyping uncertainty in haplotype inference for single-nucleotide polymorphisms.

The accuracy of the vast amount of genotypic information generated by high-throughput genotyping technologies is crucial in haplotype analyses and linkage-disequilibrium mapping for complex diseases. To date, most automated programs lack quality measures for the allele calls; therefore, human interventions, which are both labor intensive and error prone, have to be performed. Here, we propose a novel genotype clustering algorithm, GeneScore, based on a bivariate t-mixture model, which assigns a set of probabilities for each data point belonging to the candidate genotype clusters. Furthermore, we describe an expectation-maximization (EM) algorithm for haplotype phasing, GenoSpectrum (GS)-EM, which can use probabilistic multilocus genotype matrices (called "GenoSpectrum") as inputs. Combining these two model-based algorithms, we can perform haplotype inference directly on raw readouts from a genotyping machine, such as the TaqMan assay. By using both simulated and real data sets, we demonstrate the advantages of our probabilistic approach over the current genotype scoring methods, in terms of both the accuracy of haplotype inference and the statistical power of haplotype-based association analyses.

Algorithms↗
PubMed2006

Evolutionary simulations to detect functional lineage-specific genes.

MOTIVATION: Supporting the functionality of recent duplicate gene copies is usually difficult, owing to high sequence similarity between duplicate counterparts and shallow phylogenies, which hamper both the statistical and experimental inference. RESULTS: We developed an integrated evolutionary approach to identify functional duplicate gene copies and other lineage-specific genes. By repeatedly simulating neutral evolution, our method estimates the probability that an ORF was selectively conserved and is therefore likely to represent a bona fide coding region. In parallel, our method tests whether the accumulation of non-synonymous substitutions reveals signatures of selective constraint. We show that our approach has high power to identify functional lineage-specific genes using simulated and real data. For example, a coding region of average length (approximately 1400 bp), restricted to hominoids, can be predicted to be functional in approximately 94-100% of cases. Notably, the method may support functionality for instances where classical selection tests based on the ratio of non-synonymous to synonymous substitutions fail to reveal signatures of selection. Our method is available as an automated tool, ReEVOLVER, which will also be useful to systematically detect functional lineage-specific genes of closely related species on a large scale. AVAILABILITY: ReEVOLVER is available at http://www.unil.ch/cig/page7858.html.

Animals↗
PubMed1989

Molecular phylogeny of the kingdoms Animalia, Plantae, and Fungi.

The branching order of the kingdoms Animalia, Plantae, and Fungi has been a controversial issue. Using the transformed distance method and the maximum parsimony method, we investigated this problem by comparing the sequences of several kinds of macromolecules in organisms spanning all three kingdoms. The analysis was based on the large-subunit and small-subunit ribosomal RNAs, 10 isoacceptor transfer RNA families, and six highly conserved proteins. All three sets of sequences support the same phylogenetic tree: plants and animals are sibling kingdoms that have diverged more recently than the fungi. The ribosomal RNA and protein data sets are large enough so that in both cases the inferred phylogeny is statistically significant. The present report appears to be the first to provide statistically conclusive molecular evidence for the phylogeny of the three kingdoms. The determination of this phylogeny will help us to understand the evolution of various molecular, cellular, and developmental characters shared by any two of the three kingdoms. Noting that the large-subunit rRNA sequences have evolved at similar rates in the three kingdoms, we estimated the ratio of the time since the animal-plant split to the time since the fungal divergence to be 0.90.

Animal Population Groups↗