CiteULike: Tag accuracy

Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees

Barry Hall — 2007-04-02T08:10:06-00:00

PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e51.

Metrics of phylogenetic tree reliability, such as parametric bootstrap percentages or Bayesian posterior probabilities, represent internal measures of the topological reproducibility of a phylogenetic tree, while the recently introduced aLRT (approximate likelihood ratio test) assesses the likelihood that a branch exists on a maximum-likelihood tree. Although those values are often equated with phylogenetic tree accuracy, they do not necessarily estimate how well a reconstructed phylogeny represents cladistic relationships that actually exist in nature. The authors have therefore attempted to quantify how well bootstrap percentages, posterior probabilities, and aLRT measures reflect the probability that a deduced phylogenetic clade is present in a known phylogeny. The authors simulated the evolution of bacterial genes of varying lengths under biologically realistic conditions, and reconstructed those known phylogenies using both maximum likelihood and Bayesian methods. Then, they measured how frequently clades in the reconstructed trees exhibiting particular bootstrap percentages, aLRT values, or posterior probabilities were found in the true trees. The authors have observed that none of these values correlate with the probability that a given clade is present in the known phylogeny. The major conclusion is that none of the measures provide any information about the likelihood that an individual clade actually exists. It is also found that the mean of all clade support values on a tree closely reflects the average proportion of all clades that have been assigned correctly, and is thus a good representation of the overall accuracy of a phylogenetic tree.

Accuracy of structure-based sequence alignments of automatic methods

Changhoon Kim — 2007-09-22T08:07:12-00:00

BMC Bioinformatics, Vol. 8 (20 September 2007), 355.

A taxonomy of indoor and outdoor positioning techniques for mobile location services

Vasileios Zeimpekis — 2005-06-27T18:17:07-00:00

SIGecom Exch., Vol. 3, No. 4. (2003), pp. 19-27.

How many planes are required to get an accurate and timesaving measurement of left ventricular volume and function by real-time three-dimensional echocardiography in acute myocardial infarction?

GH Yao — 2008-03-01T22:52:04-00:00

Ultrasound Med Biol, Vol. 33, No. 10. (October 2007), pp. 1572-1578.

To derive the optimal cutting planes of real-time 3-D echocardiography (RT-3DE) for measuring left ventricular volume and ejection fraction (EF) in the presence of left ventricular regional wall motion abnormalities, 14 open-chest dogs were studied with RT-3DE full volume imaging and 2-D echocardiography (2DE) after left anterior descending coronary arteries were occluded for 90 min. Left ventricular end diastolic volume (EDV), end systolic volume (ESV), stroke volume (SV) and EF were measured off-line with 2DE and RT-3DE (2-, 4- and 8-plane) methods. The autopsy EDV was estimated by the volume of saline solution injected into the excised heart and served as the reference volume (RefV) for comparison with EDV measured by 2DE and RT-3DE. Agreement analysis was performed according to the method of Bland and Altman. There were excellent correlations between 2DE, RT-3DE (2-plane) and RT-3DE (4-plane) methods on one hand, and RT-3DE (8-plane) method on the other in the measurements of EDV, ESV and SV (r = 0.84-0.99). However, 2DE and RT-3DE (2-plane) measurements significantly underestimated RT-3DE (8-plane) (p < 0.01), whereas no significant differences between RT-3DE (4-plane) and RT-3DE (8-plane) were found in terms of EDV, ESV and SV measurements. The values of EF determined by 2DE, RT-3DE (2-plane) and RT-3DE (4-plane) methods correlated highly with that by RT-3DE (8-plane) (r = 0.82-0.98) and there was no significant difference between the two measurements. EDV values determined by 2DE, RT-3DE (2-plane), RT-3DE (4-plane) and RT-3DE (8-plane) correlated highly with RefV (r = 0.84, r = 0.92, r = 0.94 and r = 0.97, respectively) and there was no significant difference between RefV and EDV by RT-3DE (4-plane) and RT-3DE (8-plane). In contrast, EDV measured by 2DE and RT-3DE (2-plane) methods underestimated RefV significantly (p < 0.01). In conclusion, RT-3DE allows reliable and reproducible measurement of left ventricular volume and EF, even in the presence of left ventricular regional wall motion abnormalities. RT-3DE (4-plane) is the method of choice for an accurate and timesaving quantification of left ventricular volume and function.

Accuracy of Radiography, Nuclear Scintigraphy, and Histopathology for Determining the Proximal Extent of Distal Radius Osteosarcoma in Dogs

Nicole Leibman — 2007-07-26T22:22:26-00:00

Veterinary Surgery, Vol. 30, No. 3. (2001), pp. 240-245.

Objective- To compare the accuracy of radiography, nuclear scintigraphy, and histopathology for determining the proximal extent of distal radius osteosarcoma in dogs. Study Design- Retrospective clinical study. Sample Population- Twenty client-owned dogs taken to Colorado State University with osteosarcoma of the distal radius. Methods- Medical records of 20 dogs with confirmed osteosarcoma that underwent a limb-salvage procedure were reviewed. Measurements were performed directly from the lateral view of each radius, from both the scintigram and the radiograph, to determine the length of the radius and the distance from the proximal extent of the tumor to the distal radiographic or scintographic extent of the radius. The ratio of distal radial involvement to total radius length was calculated. A similar ratio was also determined using the macroslide, which included the entire portion of bone that was excised during the limb-salvage procedure. All 3 methods of measurement were compared. Results- Nuclear scintigraphy significantly overestimated tumor length when compared with macroslide specimen measurements. Radiography also overestimated tumor length, but these results were not significantly different from macroslide specimen measurements. Conclusions- Both radiography and nuclear scintigraphy overestimate the extent of distal radiaus osteosarcoma in dogs when compared with histopathologic macroslides of the same lesions. Nuclear scintigraphy overestimated tumor extent to a larger degree than did radiography. Clinical Relevance- Although radiography is a more accurate method of measurement of the extent of distal radius osteosarcoma, because nuclear scintigraphy overestimates tumor length to a greater degree, scintigraphy may provide a larger margin of safety for determining the site of proximal osteotomy during a limb-salvage procedure. However, caution should be taken when utilizing scintigraphy, because this method may overestimate length of radius involved to such an extent as to cause the surgeon to believe that a patient is not a suitable limb-salvage candidate. cCopyright 2001 by The American College of Veterinary Surgeons

In vivo T2-weighted magnetic resonance imaging can accurately determine the ischemic area at risk for 2-day-old nonreperfused myocardial infarction.

GS Tilak — 2008-03-01T19:47:14-00:00

Invest Radiol, Vol. 43, No. 1. (January 2008), pp. 7-15.

OBJECTIVES: To determine whether in vivo T2-weighted cardiac magnetic resonance imaging (MRI) delineates the area at risk (AAR) in 2-day-old nonreperfused myocardial infarction (MI). AAR was defined as the size of the perfusion defect on day 0. MI and the residual ischemic viable border zone comprise the AAR. MATERIALS AND METHODS: Fourteen dogs with permanent coronary artery occlusion were imaged on day 0 and day 2. The size of the AAR as measured by first-pass magnetic resonance perfusion on day 0 was compared with retrospectively determined AAR using day 2 T2-weighted MRI. Triphenyltetrazolium chloride staining was used to measure infarct size. Microspheres were used to detect residual perfusion. RESULTS: Hyperintense zones on day 2 T2-weighted magnetic resonance images accurately depicted the AAR as measured by first-pass perfusion on day 0 (38.9 +/- 3.0 vs. 36.3% +/- 3.3% of left ventricular, P = 0.07). Good correlation (R = 0.91) and Bland-Altman agreement was observed between the AAR measurements and the corresponding T2-weighted hyperintense regions. Both measures of AAR were larger than the infarcted zone (25.6% +/- 2.5% of left ventricular area; P < 0.001). CONCLUSIONS: Hyperintense regions visualized with in vivo T2-weighted cardiac MRI allow determination of the AAR 2 days postinfarction in nonreperfused MI.

Accuracy of the withdrawal reflex for localization of the site of cervical disk herniation in dogs: 35 cases (2004-2007).

F Forterre — 2008-03-01T19:41:05-00:00

J Am Vet Med Assoc, Vol. 232, No. 4. (15 February 2008), pp. 559-563.

Objective-To evaluate the accuracy of neurologic examination versus magnetic resonance imaging (MRI) in localization of cervical disk herniation and evaluate the usefulness of withdrawal reflex testing in dogs. Design-Retrospective case series. Animals-35 client-owned dogs with a single-level cervical disk herniation as determined via MRI. Procedures-1 of 2 board-certified neurologists performed a complete neurologic examination in each dog. Clinical signs of a cervical lesion included evidence of neck pain and tetraparesis. The withdrawal reflex was used for neuroanatomic localization (C1-C5 or C6-T2). Agreement between results of neurologic and MRI examinations was determined. Results-Agreement between neurologic and MRI diagnoses was 65.8%. In 11 dogs in which the lesion was clinically localized to the C6-T2 segment on the basis of a decreased withdrawal reflex in the forelimbs, MRI revealed an isolated C1-C5 disk lesion. In 1 dog, in which the lesion was suspected to be at the C1-C5 level, MRI revealed a C6-T2 lesion. Cranial cervical lesions were significantly associated with an incorrect neurologic diagnosis regarding site of the lesion. Conclusions and Clinical Relevance-Results suggested that the withdrawal reflex in dogs with cervical disk herniation is not reliable for determining the affected site and that a decreased withdrawal reflex does not always indicate a lesion from C6 to T2.

The diagnostic accuracy of CT and MRI in the staging of pelvic lymph nodes in patients with prostate cancer: a meta-analysis

AM Hovels — 2008-02-11T10:51:40-00:00

Clinical Radiology, Vol. In Press, Corrected Proof

Aim To compare the diagnostic accuracy of computed tomography (CT) and magnetic resonance imaging (MRI) in the diagnosis of lymph node metastases in prostate cancer.Methods After a comprehensive literature search, studies were included that allowed construction of contingency tables for detection of lymph node metastases using CT or MRI. In addition, a summary receiver-operating characteristic (ROC) analysis was performed.Results A total of 24 studies were included. For CT, pooled sensitivity was 0.42 (0.26-0.56 95% CI) and pooled specificity was 0.82 (0.8-0.83 95% CI). For MRI, the pooled sensitivity was 0.39 (0.22-0.56 95% CI) and pooled specificity was 0.82 (0.79-0.83 95% CI). The differences in performance of CT and MRI were not statistically significant.Conclusion CT and MRI demonstrate an equally poor performance in the detection of lymph node metastases from prostate cancer. Reliance on either CT or MRI will misrepresent the patient's true status regarding nodal metastases, and thus misdirect the therapeutic strategies offered to the patient.

On the accuracy of MANET simulators

David Cavin — 2006-05-13T16:54:41-00:00

(2002), pp. 38-43.

Predicting Species Occurrences: Issues of Accuracy and Scale

2006-03-31T11:31:08-00:00

(31 January 2002)

Predictions about where different species are, where they are not, and how they move across a landscape or respond to human activities - if timber is harvested, for instance, or stream flow altered - are important aspects of the work of wildlife biologists, land managers, and the agencies and policymakers that govern natural resources. Despite the increased use and importance of model predictions, these predictions are seldom tested and have unknown levels of accuracy. Predicting Species Occurrences addresses those concerns, highlighting for managers and researchers the strengths and weaknesses of current approaches, as well as the magnitude of the research required to improve or test predictions of currently used models. The book is an outgrowth of an international symposium held in October 1999 that brought together scientists and researchers at the forefront of efforts to process information about species at different spatial and temporal scales. It is a comprehensive reference that offers an exhaustive treatment of the subject, with 65 chapters by leading experts from around the world that: <ul> <li>review the history of the theory and practice of modeling and present a standard terminology <li>examine temporal and spatial scales in terms of their influence on patterns and processes of species distribution <li>offer detailed discussions of state-of-the-art modeling tools and descriptions of methods for assessing model accuracy <li>discuss how to predict species presence and abundance <li>present examples of how spatially explicit data on demographics can provide important information for managers</ul> An introductory chapter by Michael A. Huston examines the ecological context in which predictions of species occurrences are made, and a concluding chapter by John A. Wiens offers an insightful review and synthesis of the topics examined along with guidance for future directions and cautions regarding misuse of models. Other contributors include Michael P. Austin, Barry R. Noon, Alan H. Fielding, Michael Goodchild, Brian A. Maurer, John T. Rotenberry, Paul Angermeier, Pierre R. Vernier, and more than a hundred others.<p>Predicting Species Occurrences offers important new information about many of the topics raised in the seminal volume Wildlife 2000 (University of Wisconsin Press, 1986) and will be the standard reference on this subject for years to come. Its state-of-the-art assessment will play a key role in guiding the continued development and application of tools for making accurate predictions and is an indispensable volume for anyone engaged in species management or conservation.

Mapping marine environments with IKONOS imagery: enhanced spatial resolution can deliver greater thematic accuracy

Peter Mumby — 2005-12-08T14:39:48-00:00

Remote Sensing of Environment, Vol. 82, No. 2-3. (October 2002), pp. 248-257.

The IKONOS 2 satellite was launched in late 1999 and carries the first commercial multispectral instrument to achieve 4 m spatial resolution. The cost and accuracy of using IKONOS imagery to map shallow-water marine environments is evaluated and compared directly to that using a suite of satellite and airborne instruments including Landsat Multispectral Scanner (MSS) and Thematic Mapper (TM), Satellite Pour l'Observation de la Terre (SPOT) High-Resolution Visible (HRV) multispectral and panchromatic, and Compact Airborne Spectrographic Imager (CASI). Evaluations were conducted in the Turks and Caicos Islands which are ideally suited to aquatic remote sensing because of the large areas of clear, shallow water containing a range of different habitats. Over 600 field sites were surveyed and used to define habitat categories, supervise image classification, and make an independent assessment of thematic map accuracy. For the high-resolution IKONOS imagery, pixel sizes were small enough to allow within-habitat textural information to be added to the classification. Making full use of this textural information in supervised classifications significantly improved (PPP2) areas. IKONOS may only be a cost-effective option if (i) independent field data are available to identify habitat patches, (ii) the area to be mapped is fairly small (2), and (iii) small-scale (<10 m) habitat dynamics are to be monitored. IKONOS data are unlikely to identify deterioration in coral reefs directly because changes in community structure cannot be resolved spectrally from the satellite.

The Shaping of Nuclear Weapon System Technology: US Fleet Ballistic Missile Guidance and Navigation: I: From Polaris to Poseidon

Donald Mackenzie — 2005-09-03T18:40:12-00:00

Social Studies of Science, Vol. 18, No. 3. (1988), pp. 419-463.

This paper (published in two Parts) presents a detailed historical case study of the evolution of the Polaris, Poseidon and Trident weapons programmes, and of the development of the guidance and navigation technologies which are essential to their role in nuclear strategies. Over the last thirty years, these technologies have changed in the direction of greatly increased missile accuracy. Simultaneously, the strategic rationale of these weapons has shifted from that of ultimate retaliatory 'counter-city' deterrent (the main perceived role of Polaris) to 'counterforce' targeting of opposing silos and command posts (a major role of Trident II). Has technological change been an independent causal factor in this sequence, bringing into being a new strategy, or is technological change the consciously intended product of political will? Part I of this paper presents the historical material as far as the production of Poseidon: Part II will complete the history, and then discuss the various analytical frameworks commonly used to explain such developments.

The Shaping of Nuclear Weapon System Technology: US Fleet Ballistic Missile Guidance and Navigation: II: 'Going for Broke' - The Path to Trident II

Donald Mackenzie — 2005-09-03T18:39:04-00:00

Social Studies of Science, Vol. 18, No. 4. (1988), pp. 581-624.

This paper (the second of two Parts) continues the historical case study of the evolution of Fleet Ballistic Missile guidance and navigation technologies by tracing the origins and development of the Trident system. This comprises a new submarine and two different missiles, Trident I (C4) and Trident II (D5), the latter of which is considered to be optimized for the destruction of 'hardened' targets such as missile silos and command posts. It thus appears to mark a significant shift from the ultimate retaliatory 'counter-city' deterrent (which was the main perceived role of Polaris). Is Trident II's technology simply the culmination of inevitable technological change, acting as an independent causal factor that itself determines strategy? Or is technological change the consciously intended product of political will? This historical case is used to discuss various analytical frameworks commonly used to explain such developments - 'Technology-out-of-Control'; 'Soft Determinism'; 'Technologists-out-of-Control'; 'Politics-in-Command'; and 'Bureaucratic Politics'. It is concluded that the material is most consistent with a 'Bureaucratic Politics' perspective, but that this unduly favours one set of 'factors' in a 'seamless web' where the 'technical' cannot readily be distinguished from the 'social'. Nevertheless, we feel it possible and useful to try to distinguish patterns in this seamless web, and close with a discussion of one such pattern - the 'black-boxing' of technical programmes.

Is feedback pedagogically correct?: Research design issues in studies of feedback on writing

Danielle Guenette — 2007-03-11T00:56:34-00:00

Journal of Second Language Writing, Vol. In Press, Corrected Proof

The debate continues between those who believe in giving corrective feedback to students to improve their written accuracy and those who do not. Indeed, the results of the many experimental studies on written corrective feedback carried out over the last 20 years have been so contradictory that second language teachers looking to support their pedagogical choice to correct, or not correct, the grammar of their students' written production are left in the midst of controversy. In this article, I examine these studies from a different perspective. Rather than interpret the conflicting results as a demonstration of the effectiveness or ineffectiveness of corrective feedback on form, I suggest that findings can be attributed to the research design and methodology, as well as to the presence of external variables that were beyond the control and vigilance of the researchers.

Influence of Heart Rate on Doppler Aortic Regurgitant Velocity Curve: Clinical Role of Heart Rate Correction of Regurgitant Pressure Half-Time.

Giovanni Gozzelino — 2008-01-22T08:34:29-00:00

Echocardiography, Vol. 16, No. 1. (January 1999), pp. 1-9.

Because it was recently suggested that pressure half-time (PHT) of aortic regurgitant velocity curve is influenced by heart rate (HR), we retrospectively analyzed 76 patients with aortic regurgitation (AR) to determine whether PHT independently correlates with HR and whether HR correction of PHT can be clinically useful. PHT correlated significantly (P < 0.001) with color Doppler relative regurgitant jet height (r = -0.62), with angiographic grading (r = -0.65), and with HR (r = -0.54); such correlations were confirmed by multivariate analysis. Tachycardia influences aortic velocity curve more than bradycardia, and this effect is more evident in patients with milder regurgitation. Two methods of HR correction of PHT were tested: relative PHT (PHT/diastolic time x 100) and corrected PHT (PHT/ radicalRR): only corrected PHT was independently related to both relative regurgitant jet height and angiographic grading (P < 0.001). HR correction of PHT by corrected PHT was of limited clinical usefulness: in fact, in the entire study population, the accuracy of the usual cutoff (< 300 msec) in detecting relevant AR was not improved by corrected PHT. However, in patients with higher HR (>/= 85 beats/min), in whom the effect of HR on aortic velocity curve appeared to be greater, corrected PHT was superior to PHT because the cutoff value of < 300 msec showed a good specificity (100%), a moderate sensitivity (66%), and a good accuracy (80%) in detecting relevant AR. Corrected PHT can be useful to confirm AR severity when a short PHT is observed in tachycardic patients.

PhyloGenie: automated phylome generation and analysis.

T Frickey — 2005-06-15T18:38:20-00:00

Nucleic Acids Res, Vol. 32, No. 17. (2004), pp. 5231-5238.

Phylogenetic reconstruction is the method of choice to determine the homologous relationships between sequences. Difficulties in producing high-quality alignments, which are the basis of good trees, and in automating the analysis of trees have unfortunately limited the use of phylogenetic reconstruction methods to individual genes or gene families. Due to the large number of sequences involved, phylogenetic analyses of proteomes preclude manual steps and therefore require a high degree of automation in sequence selection, alignment, phylogenetic inference and analysis of the resulting set of trees. We present a set of programs that automates the steps from seed sequence to phylogeny and a utility to extract all phylogenies that match specific topological constraints from a database of trees. Two example applications that show the type of questions that can be answered by phylome analysis are provided. The generation and analysis of the Thermoplasma acidophilum phylome with regard to lateral gene transfer between Thermoplasmata and Sulfolobus, showed best BLAST hits to be far less reliable indicators of lateral transfer than the corresponding protein phylogenies.The generation and analysis of the Danio rerio phylome provided more than twice as many proteins as described previously, supporting the hypothesis of an additional round of genome duplication in the actinopterygian lineage.

Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.

G Talavera — 2008-06-20T07:36:21-00:00

Systematic biology, Vol. 56, No. 4. (August 2007), pp. 564-577.

Alignment quality may have as much impact on phylogenetic reconstruction as the phylogenetic methods used. Not only the alignment algorithm, but also the method used to deal with the most problematic alignment regions, may have a critical effect on the final tree. Although some authors remove such problematic regions, either manually or using automatic methods, in order to improve phylogenetic performance, others prefer to keep such regions to avoid losing any information. Our aim in the present work was to examine whether phylogenetic reconstruction improves after alignment cleaning or not. Using simulated protein alignments with gaps, we tested the relative performance in diverse phylogenetic analyses of the whole alignments versus the alignments with problematic regions removed with our previously developed Gblocks program. We also tested the performance of more or less stringent conditions in the selection of blocks. Alignments constructed with different alignment methods (ClustalW, Mafft, and Probcons) were used to estimate phylogenetic trees by maximum likelihood, neighbor joining, and parsimony. We show that, in most alignment conditions, and for alignments that are not too short, removal of blocks leads to better trees. That is, despite losing some information, there is an increase in the actual phylogenetic signal. Overall, the best trees are obtained by maximum-likelihood reconstruction of alignments cleaned by Gblocks. In general, a relaxed selection of blocks is better for short alignment, whereas a stringent selection is more adequate for longer ones. Finally, we show that cleaned alignments produce better topologies although, paradoxically, with lower bootstrap. This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies.

Simple (Wrong) Models for Complex Trees: A Case from Retroviridae

David Posada — 2008-05-14T10:45:30-00:00

Mol Biol Evol, Vol. 18, No. 2. (1 February 2001), pp. 271-275.

Freeing phylogenies from artifacts of alignment

JL Thorne — 2008-05-14T10:35:54-00:00

Mol Biol Evol, Vol. 9, No. 6. (1 November 1992), pp. 1148-1162.

Testing for phylogenetic signal in comparative data: behavioral traits are more labile.

SP Blomberg — 2005-10-12T15:49:27-00:00

Evolution Int J Org Evolution, Vol. 57, No. 4. (April 2003), pp. 717-745.

The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal alpha = 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformations, one based on the Ornstein-Uhlenbeck (OU) model of stabilizing selection, the other based on a new model in which character evolution can accelerate or decelerate (ACDC) in rate (e.g., as may occur during or after an adaptive radiation). Maximum likelihood estimation of the OU (d) and ACDC (g) parameters can serve as tests for phylogenetic signal because an estimate of d or g near zero implies that a phylogeny with little hierarchical structure (a star) offers a good fit to the data. Transformations that improve the fit of a tree to comparative data will increase power to detect phylogenetic signal and may also be preferable for further comparative analyses, such as of correlated character evolution. Application of the methods to data from the literature revealed that, for trees with 20 or more species, 92% of traits exhibited significant phylogenetic signal (randomization test), including behavioral and ecological ones that are thought to be relatively evolutionarily malleable (e.g., highly adaptive) and/or subject to relatively strong environmental (nongenetic) effects or high levels of measurement error. Irrespective of sample size, most traits (but not body size, on average) showed less signal than expected given the topology, branch lengths, and a Brownian motion model of evolution (i.e., K was less than one), which may be attributed to adaptation and/or measurement error in the broad sense (including errors in estimates of phenotypes, branch lengths, and topology). Analysis of variance of log K for all 121 traits (from 35 trees) indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits. In addition, physiological traits (corrected for body size) showed less signal than did body size itself. For trees with 20 or more species, the estimated OU (25% of traits) and/or ACDC (40%) transformation parameter differed significantly from both zero and unity, indicating that a hierarchical tree with less (or occasionally more) structure than the original better fit the data and so could be preferred for comparative analyses.

A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in the reconstruction of phylogenetic relationships.

B Qiao — 2008-02-06T03:41:33-00:00

Infect Genet Evol, Vol. 6, No. 4. (July 2006), pp. 323-330.

Partial genome sequencing (PGS) and restriction fragment analysis (RFA) are used frequently in molecular epidemiologic investigations. The relative accuracy of PGS and RFA in phylogenetic reconstruction has not been assessed. In this study, 32 model phylogenetic trees with 16 extant lineages were generated, for which DNA sequences were simulated under varying conditions of genome length, nucleotide substitution rate, and between-site substitution rate variation. Genotyping using PGS and RFA was simulated. The effect of tree structure (stemminess, imbalance, lineage variation) on the accuracy of phylogenetic reconstruction (topological and branch length similarity) was evaluated. Overall, PGS was more accurate than RFA. The accuracy of PGS increased with increasing sequence length. The accuracy of RFA increased with the number of restriction enzymes used. In fragment size comparison, the Dice and Nei-Li algorithms differed little, with both more accurate than the Fragment Size Distribution algorithm. For RFA, higher tree stemminess and longer genome length were associated with higher topological accuracy, whereas lower tree stemminess and lower substitution rates were associated with higher branch length accuracy. For PGS, lower tree imbalance was associated with higher topological accuracy, whereas lower tree stemminess, higher substitution rate, and lower between-site substitution rate variation were associated with higher branch length accuracy. RFA had higher topological accuracy than PGS only for the shortest sequence length (200 bps) at a low substitution rate, high tree stemminess, and long genome length. PGS had equal or higher accuracy in branch length reconstruction than RFA under all conditions investigated. Thus, partial genome sequencing is recommended over restriction fragment analysis for conditions within the parameter space examined.

Bayesian coestimation of phylogeny and sequence alignment.

G Lunter — 2006-07-04T00:36:20-00:00

BMC Bioinformatics, Vol. 6 (2005)

BACKGROUND: Two central problems in computational biology are the determination of the alignment and phylogeny of a set of biological sequences. The traditional approach to this problem is to first build a multiple alignment of these sequences, followed by a phylogenetic reconstruction step based on this multiple alignment. However, alignment and phylogenetic inference are fundamentally interdependent, and ignoring this fact leads to biased and overconfident estimations. Whether the main interest be in sequence alignment or phylogeny, a major goal of computational biology is the co-estimation of both. RESULTS: We developed a fully Bayesian Markov chain Monte Carlo method for coestimating phylogeny and sequence alignment, under the Thorne-Kishino-Felsenstein model of substitution and single nucleotide insertion-deletion (indel) events. In our earlier work, we introduced a novel and efficient algorithm, termed the "indel peeling algorithm", which includes indels as phylogenetically informative evolutionary events, and resembles Felsenstein's peeling algorithm for substitutions on a phylogenetic tree. For a fixed alignment, our extension analytically integrates out both substitution and indel events within a proper statistical model, without the need for data augmentation at internal tree nodes, allowing for efficient sampling of tree topologies and edge lengths. To additionally sample multiple alignments, we here introduce an efficient partial Metropolized independence sampler for alignments, and combine these two algorithms into a fully Bayesian co-estimation procedure for the alignment and phylogeny problem. Our approach results in estimates for the posterior distribution of evolutionary rate parameters, for the maximum a-posteriori (MAP) phylogenetic tree, and for the posterior decoding alignment. Estimates for the evolutionary tree and multiple alignment are augmented with confidence estimates for each node height and alignment column. Our results indicate that the patterns in reliability broadly correspond to structural features of the proteins, and thus provides biologically meaningful information which is not existent in the usual point-estimate of the alignment. Our methods can handle input data of moderate size (10-20 protein sequences, each 100-200 bp), which we analyzed overnight on a standard 2 GHz personal computer. CONCLUSION: Joint analysis of multiple sequence alignment, evolutionary trees and additional evolutionary parameters can be now done within a single coherent statistical framework.

Informant accuracy in social network data IV: a comparison of clique-level structure in behavioral and cognitive network data

HR Bernard — 2007-09-18T13:41:34-00:00

Social Networks, Vol. 2, No. 3. (1979), pp. 191-218.

This paper examines whether clique-structure in cognitive data (i.e. recall of who one talks to) may be used as a proxy for clique-structure in behavioral data (i.e. who one actually talks to). The answer to this question is crucial to much of sociometric and social net-theoretic studies of social structure. We analysed the clique structures of the communication patterns of four naturally occurring groups of sizes 34 to 58, whose actual communications could easily be monitored, together with the groups' perceptions of their communications. The groups used were: radio hams, a college fraternity, a group of office workers, and an academic department. The analysis used clique-finding, block-modelling, and factor-analytic techniques, all employed in such a way as to maximize the accuracy of the cognitive data. After defining a way to compare clique structures between behavioral and cognitive data, we found that there was no useful relationship between the two, and furthermore there was no significant difference in performance between any of the structure-finding algorithms. We conclude that cognitive data may not be used for drawing any conclusions about behavioral social structure.

Informant accuracy in social-network data V. An experimental attempt to predict actual communication from recall data

HR Bernard — 2007-09-18T13:40:47-00:00

Social Science Research, Vol. 11, No. 1. (March 1982), pp. 30-66.

This paper seeks to discover whether the known inaccuracy of informant recall about their communication behavior can be accounted for by experimentally varying the time period over which recall takes place. The experiment took advantage of a new communications medium (computer conferencing) which enabled us to monitor automatically all the interactions involving a subset of the computer network. The experiment itself was administered entirely by the computer, which interviewed informants and recorded their responses. Variations in time period failed to account for much of the inaccuracy, which continues, as in previous experiments at an unacceptably high level. One positive finding did emerge: although the informants did not know with whom they communicated, the informants en masse seemed to know certain broad facts about the communication pattern. All other findings were negative. For example, it is impossible to predict the people an informant claimed to communicate with but did not; and it is impossible to predict who the five people are that an informant forgot to mention that she or he had communication with. Thus, despite their presumed good intentions, our findings here confirm what we have learned from six previous experiments: What people say about their communications bears no resemblance to their behavior. This suggests that other forms of data gathering, based on questions which require that informants recall their behavior, may well be suspect.

Informant Accuracy in Social Network Data II

HR Bernard — 2006-11-06T03:19:08-00:00

Human Communication Research, Vol. 4, No. 1. (1977), pp. 3-18.

This paper repeats and confirms the results of Killworth and Bernard (1976), concerning informants'ability to report their communication accurately. A variety of self-monitoring, or nearly self-monitoring, networks are used for this study. The conclusion again appears that people do not know, with any accuracy, those with whom they communicate. The expanded experimental design permits a variety of other, related questions to be answered: recall of past communication is not significantly more accurate than prediction of future communication; no one set of data is more accurate than any other; the maintenance of personal logs of communication does not improve accuracy; informants do not know if they are accurate or not; there is no reason to choose either rankings or scalings as a data instrument save for convenience. It is suggested that future research should concentrate both on improving the accuracy of data-gathering instruments and on lessening the reliance of data-processing instruments on precise data.

Informant accuracy in social network data III: A comparison of triadic structure in behavioral and cognitive data,

Peter Killworth — 2007-09-18T13:54:02-00:00

Social Networks, Vol. 2, No. 1. (1979), pp. 19-46.

This paper provides a comparison of the triadic-level structure inherent in behavioral and cognitive social network data taken on the same group, using a variety of groups whose communication could easily be monitored. It is found that many types of structure occur significantly more or less than chance in both behavioral and cognitive data, and providing that these are treated in similar ways, there is good agreement between the two structures. However, there are several ways to treat behavioral data, and these produce at least two essentially different structures. If cognitive and behavioral triads are compared, triad by triad, then there is virtually no agreement between them (even though they may both display the same structure on an overall triad census). Finally, as a demonstration of the dangers of relying solely on cognitive data, an unlikely null hypothesis is proposed. This asserts -- for demonstration purposes -- that, under many circumstances, behavioral structure never alters. Change in structure over time apparently occurs because of informant error in the reporting of the cognitive data. A pseudo-transition matrix, giving the probability that a triad is reported as one type when data are first taken, and a different type at a later date, is calculated. This compares reasonably with a genuine transition matrix evaluated for longitudinal cognitive data. It is believed that no data currently exist which can disprove this hypothesis, unlikely though it is. Much more accurate data are therefore necessary if any reliable theory of social structure is to be produced.

Completeness, conservation and error in SPH for fluids

GL Vaughan — 2007-12-09T15:07:44-00:00

International Journal for Numerical Methods in Fluids, Vol. 56, No. 1. (2008), pp. 37-62.

Smoothed particle hydrodynamics (SPH) is becoming increasingly common in the numerical simulation of complex fluid flows and an understanding of the errors is necessary. Recent advances have established techniques for ensuring completeness conditions (low-order polynomials are interpolated exactly) are enforced when estimating property gradients, but the consequences on errors have not been investigated. Here, we present an expression for the error in an SPH estimate, accounting for completeness, an expression that applies to SPH generally. We revisit the derivation of the SPH equations for fluids, paying particular attention to the conservation principles. We find that a common method for enforcing completeness violates a property required of the kernel gradients, namely that gradients with respect the two position variables be equal and opposite. In such models this means conservation principles are not enforced and we present results that show this. As an aside we show the summation interpolant for density is a solution of, and may be used in the place of, the discretized, symmetrized continuity equation. Finally, we examine two examples of discretization errors, namely numerical boundary layers and the existence of crystallized states. Copyright © 2007 John Wiley & Sons, Ltd.

Isotropic compact interpolation schemes for particle methods

Philippe Chatelain — 2008-04-22T22:22:01-00:00

Journal of Computational Physics, Vol. 227, No. 6. (1 March 2008), pp. 3244-3259.

In particle methods, an accuracy degradation can occur because of the distortion of the element positions. A solution consists in the periodic re-initialization of the particles onto regular locations, at the nodes of a lattice. This so-called redistribution works by the interpolation of particle quantities. The present work considers the design of redistribution schemes on general lattices and in particular on lattices with a higher level of symmetry than the usual cubic lattice. Such lattices allow schemes which are more compact and more isotropic. We test our schemes in the context of three-dimensional vortex methods.

An improved SPH method: Towards higher order convergence

G Oger — 2008-05-22T16:42:08-00:00

Journal of Computational Physics, Vol. 225, No. 2. (10 August 2007), pp. 1472-1492.

This paper evaluates various formulations of the SPH method for solving the Euler equations. Convergence and stability aspects are discussed and tested, taking into account subtleties induced by the presence of a free surface. The coherence between continuity and momentum equations is considered using a variational study. The use of renormalization to improve the accuracy of the simulations is investigated and discussed. A new renormalization-based formulation involving wide accuracy improvements of the scheme is introduced. The classical SPH and renormalized approaches are compared to the new method using simple test cases, thus outlining the efficiency of this new improved SPH method. Finally, the so-called "tensile instability" is shown to be prevented by this enhanced SPH method, through accuracy increases in the gradient approximations.

The accuracy of medication data in an outpatient electronic medical record

MM Wagner — 2007-12-18T18:29:02-00:00

J Am Med Inform Assoc, Vol. 3, No. 3. (1 May 1996), pp. 234-244.

The limits of localization using signal strength: a comparative study

E Elnahrawy — 2006-03-19T11:57:34-00:00

Sensor and Ad Hoc Communications and Networks, 2004. IEEE SECON 2004. 2004 First Annual IEEE Communications Society Conference on (2004), pp. 406-414.

We characterize the fundamental limits of localization using signal strength in indoor environments. Signal strength approaches are attractive because they are widely applicable to wireless sensor networks and do not require additional localization hardware. We show that although a broad spectrum of algorithms can trade accuracy for precision, none has a significant advantage in localization performance. We found that using commodity 802.11 technology over a range of algorithms, approaches and environments, one can expect a median localization error of 10 ft and 97th percentile of 30 ft. We present strong evidence that these limitations are fundamental and that they are unlikely to transcend without a fundamentally more complex environmental models or additional localization infrastructure.

On the accuracy of signal strength-based estimation techniques

AS Krishnakumar — 2006-11-02T21:16:05-00:00

INFOCOM 2005. 24th Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings IEEE, Vol. 1 (2005), pp. 642-650 vol. 1.

In this paper, we address the problem of finding the inherent uncertainty of signal strength-based location estimation techniques. We propose a mathematical model for mapping uncertainty in signal strength space to uncertainty in physical space. We then analyze this model to compute the minimum value of the uncertainty in location estimation using signal strength measurements. The results of this analysis are used to draw conclusions about the dependence of the minimum uncertainty of various factors such as the signal variance, number of APs, distance between the APs and the propagation constant. We provide an argument linking the minimum uncertainty with a lower limit on the median error in location estimation using classification techniques.

Predictability and accuracy in adaptive user interfaces

Krzysztof Gajos — 2008-06-04T19:28:05-00:00

(2008), pp. 1271-1274.

Improved Optimization for the Robust and Accurate Linear Registration and Motion Correction of Brain Images

Mark Jenkinson — 2006-10-30T06:56:47-00:00

NeuroImage, Vol. 17, No. 2. (October 2002), pp. 825-841.

Linear registration and motion correction are important components of structural and functional brain image analysis. Most modern methods optimize some intensity-based cost function to determine the best registration. To date, little attention has been focused on the optimization method itself, even though the success of most registration methods hinges on the quality of this optimization. This paper examines the optimization process in detail and demonstrates that the commonly used multiresolution local optimization methods can, and do, get trapped in local minima. To address this problem, two approaches are taken: (1) to apodize the cost function and (2) to employ a novel hybrid global-local optimization method. This new optimization method is specifically designed for registering whole brain images. It substantially reduces the likelihood of producing misregistrations due to being trapped by local minima. The increased robustness of the method, compared to other commonly used methods, is demonstrated by a consistency test. In addition, the accuracy of the registration is demonstrated by a series of experiments with motion correction. These motion correction experiments also investigate how the results are affected by different cost functions and interpolation methods.

How Is a Sensory Map Read Out? Effects of Microstimulation in Visual Area MT on Saccades and Smooth Pursuit Eye Movements

Jennifer Groh — 2007-12-12T03:37:36-00:00

J. Neurosci., Vol. 17, No. 11. (1 June 1997), pp. 4312-4330.

Cerebellar contribution to the spatial encoding of orienting gaze shifts in the head-free cat.

L Goffart — 2008-02-18T16:00:32-00:00

J Neurophysiol, Vol. 72, No. 5. (November 1994), pp. 2547-2550.

1. Cerebellar saccadic dysmetria may result from a disturbance in the processes that ensure correct execution of gaze displacement. Alternatively, an impairment in the preparatory processes that lead to the specification of the movement goal may also produce this deficit. 2. We report here on a pharmacologically induced dysmetria that suggests a cerebellar contribution to the neural processes encoding the location of the goal for orienting gaze shifts. 3. Shifts of gaze (eye-in-space) were recorded in the head-free cat after the GABA agonist muscimol was unilaterally injected into the caudal part of the fastigial nucleus. 4. Gaze saccades towards the inactivated side were hypermetric. These ipsiversive movements overshot the target by a constant error, regardless of target eccentricity and initial gaze position. 5. Gaze saccades directed away from the inactivated side undershot the target. The degree of hypometria increased when the amplitude of the required movement increased. 6. These results suggest a different contribution of the caudal fastigial nucleus to the accuracy of visually triggered gaze shifts, depending on the direction of the impending saccade. The systematic error of ipsiversive movements and the inappropriate movements evoked by presenting a target at the same physical location as gaze reveal that fastigial inactivation interfered with the processes that encode the location of a visual target.

Changes in initiation of orienting gaze shifts after muscimol inactivation of the caudal fastigial nucleus in the cat.

L Goffart — 2008-02-18T15:59:30-00:00

J Physiol, Vol. 503 ( Pt 3) (15 September 1997), pp. 657-671.

1. The production of a goal-directed saccadic gaze shift involves the specification of movement amplitude and direction, and the decision to trigger the movement. Behavioural and neurophysiological data suggest that these two functions involve separate processes which may interact. 2. The medio-posterior cerebellar areas are classically assigned a major contribution to the control of saccade metrics, and previous cerebellar lesion studies have revealed marked dysmetria of visually triggered gaze shifts. In contrast, these studies did not provide evidence for a cerebellar role in saccadic initiation. 3. In the present study, we investigated in the head-unrestrained cat the deficits in both the initiation and the metrics control of saccadic gaze shifts following pharmacological inactivation of the caudal part of the fastigial nucleus (cFN). 4. After cFN inactivation, latencies for contraversive gaze shifts increased to about 137 +/- 28% of normal, and latencies for ipsiversive gaze shifts decreased to about 84 +/- 8% of normal. Similar changes in head movement latency were observed, such that the temporal coupling between eye and head components remained largely unaffected. 5. Contraversive gaze shifts were more hypometric as their latency increased. In contrast, the degree of hypermetria in ipsiversive gaze shifts was unrelated to latency. 6. These results suggest a functional role of the medio-posterior cerebellum in gaze shift initiation and in storing information about the target location and/or the desired gaze shift amplitude.

Motion processing for saccadic eye movements in humans.

RS Gellman — 2008-02-19T09:34:09-00:00

Exp Brain Res, Vol. 84, No. 3. (1991), pp. 660-667.

1. We studied the latencies and amplitudes of saccades to moving targets in normal human subjects. Targets underwent ramp or step-ramp motions. The goal was to determine how the saccadic system uses information about target velocity. 2. For simple ramp motion saccadic latency decreased as target speed increased. A threshold distance model, which assumes that the target has to move a minimum distance before saccadic processing starts, provided a good fit to the responses of all four subjects and explains discrepancies between previously published findings. 3. A double step experiment showed that target position may have some effect on saccadic amplitude when sampled approximately 70 ms before saccade onset, but it must be sampled at least 140 ms before onset for an accurate saccade to occur. 4. Saccades to simple ramp targets approximated the target position 55 ms before saccade onset. Based on our double step results, this is more compensation than possible by a simple position estimate and implies extrapolation of target motion by the saccadic system. The lack of complete compensation may be due to an underestimate of the target speed and/or of the saccadic latency. 5. A delayed-saccade paradigm resulted in saccades with a longer, constant latency and allowed longer viewing of target motion. These saccades accounted for all but approximately 20 ms of target motion, suggesting that with more processing time of target motion a better extrapolation may be generated. 6. In a step-ramp paradigm the target stepped in one direction, then moved smoothly in the opposite direction. Saccades in this paradigm could be made in either the direction of the step or in the direction of target motion: the direction and latency were determined solely by the time at which the target crossed the fixation point. This time must be calculated from target speed and position, implying that the saccadic system must use speed information to adjust latency or to cancel unnecessary saccades.

Orienting gaze shifts during muscimol inactivation of caudal fastigial nucleus in the cat. I. Gaze dysmetria.

L Goffart — 2008-02-18T15:58:11-00:00

J Neurophysiol, Vol. 79, No. 4. (April 1998), pp. 1942-1958.

The cerebellar control of orienting behavior toward visual targets was studied in the head-unrestrained cat by analyzing the deficits of saccadic gaze shifts after unilateral injection of muscimol in the caudal part of the fastigial nucleus (cFN). Gaze shifts are rendered strongly inaccurate by muscimol cFN inactivation. The characteristics of gaze dysmetria are specific to the direction of the movement with respect to the inactivated cFN. Gaze shifts directed toward the injected side are hypermetric. Irrespective of their starting position, all these ipsiversive gaze shifts overshoot the target by a constant horizontal error (or bias) to terminate at a "shifted goal" location. In particular, when gaze is directed initially at the future target's location, a response with an amplitude corresponding to the bias moves gaze away from the actual target. Additionally, when gaze is initially in between the target and this shifted goal location, the response again is directed toward the latter. This deficit of ipsiversive gaze shifts is characterized by a consistent increase in the y intercept of the relationship between horizontal gaze amplitude and horizontal retinal error. Slight increases in the slope sometimes are observed as well. Contraversive gaze shifts are markedly hypometric and, in contrast to ipsiversive responses, they do not converge onto a shifted goal but rather underestimate target eccentricity in a proportional way. This is reflected by a decrease in the slope of the relationship between horizontal gaze amplitude and horizontal retinal error, with, for some experiments, a moderate change in the y-intercept value. The same deficits are observed in a different setup, which permits the control of initial gaze position. Correction saccades rarely are observed when visual feedback is eliminated on initiation of the primary orienting response; instead, they occur frequently when the target remains visible. Like the primary contraversive saccades, they are hypometric and the ever-decreasing series of three to five correction saccades reduces the gaze fixation error but often does not completely eliminate it. We measured the position of gaze after the final correction saccade and found that fixation of a visible target is still shifted toward the inactivated cFN by 4.9 +/- 2.4 degrees. This fixation offset is correlated to, but on average 54% smaller than, the hypermetric bias of ipsiversive responses measured in the same experiments. In conclusion, the cFN contributes to the control of saccadic shifts of the visual axis toward a visual target. The hypometria of contraversive gaze shifts suggests a cFN role in adjusting a gain in the translation of retinal signals into gaze motor commands. On the basis of the convergence of ipsiversive gaze shifts onto a shifted goal, the straightness of gaze trajectory during these responses and the production of misdirected or inappropriately initiated responses toward this shifted goal, we propose that the cFN influences the processes that specify the goal of ipsiversive gaze shifts.

Comparison of saccades perturbed by stimulation of the rostral superior colliculus, the caudal superior colliculus, and the omnipause neuron region.

NJ Gandhi — 2008-02-18T15:46:53-00:00

J Neurophysiol, Vol. 82, No. 6. (December 1999), pp. 3236-3253.

Over the past decade, considerable research efforts have been focused on the role of the rostral superior colliculus (SC) in control of saccades. The most recent theory separates the deeper intermediate layers of the SC into two functional regions: the rostral pole of these layers constitutes a fixation zone and the caudal region comprises the saccade zone. Sustained activity of fixation neurons in the fixation zone is argued to maintain fixation and help prevent saccade generation by exciting the omnipause neurons (OPNs) in the brain stem. This hypothesis is in contrast to the traditional view that the SC contains a topographic representation of the saccade motor map on which the rostral pole of the SC encodes signals for generating small saccades (<2 degrees ) instead of preventing them. There is therefore an unresolved controversy about the specific role on the most rostral region of the SC, and we reexamined its functional contribution by quantifying and comparing spatial and temporal trajectories of 30 degrees saccades perturbed by electrical stimulation of the rostral pole and more caudal regions in the SC and of the OPN region. If the rostral pole serves to preserve fixation, then saccades perturbed by stimulation should closely resemble interrupted saccades produced by stimulation of the OPN region. If it also contributes to saccade generation, then the disrupted movements would better compare with redirected saccades observed after stimulation of the caudal SC. Our experiments revealed two significant findings: 1) the locus of stimulation was the primary factor determining the perturbation effect. If the directions of the target-directed saccade and stimulation-evoked saccade were aligned and if the stimulation was delivered within approximately the rostral 2 mm (<10 degrees amplitude) of SC, the ongoing saccade stopped in midflight but then resumed after stimulation end to reach the original visually specified goal with close to normal accuracy. When stimulation was applied at more caudal sites, the ongoing saccade directly reached the target location without stopping at an intermediate position. If the directions differed considerably, both initial and resumed components were typically observed for all stimulation sites. 2) A quantitative analysis of the saccades perturbed from the fixation zone showed significant deviations from their control spatial trajectories. Thus they resembled redirected saccades induced by caudal SC stimulation and differed significantly from interrupted saccades produced by OPN stimulation. The amplitude of the initial saccade, latency of perturbation, and spatial redirection were greatest for the most caudal sites and decreased gradually for rostral sites. For stimulation sites within the rostral pole of SC, the measures formed a smooth continuation of the trends observed in the saccade zone. As these results argue for the saccade zone concept, we offer reinterpretations of the data used to support the fixation zone model. However, we also discuss scenarios that do not allow an outright rejection of the fixation zone hypothesis.

An analysis of the saccadic system by means of double step stimuli.

W Becker — 2008-02-18T15:36:34-00:00

Vision Res, Vol. 19, No. 9. (1979), pp. 967-983.

Natural and drug-induced variations of velocity and duration of human saccadic eye movements: evidence for a control of the neural pulse generator by local feedback.

R Jürgens — 2008-02-18T15:34:53-00:00

Biol Cybern, Vol. 39, No. 2. (1981), pp. 87-96.

The present report considers goal directed human saccadic eye movements. It addresses the question how a given perceived target excentricity is transformed into the innervation pattern that creates the saccade to the target. More specifically, it investigates whether this pattern is an appropriately selected preprogram or whether it is continuously controlled by a local feedback loop that compares a non-visual eye position signal to the perceived target excentricity (a visual signal would be too slow). To this end, the relation between the accuracy of saccades aimed at a given target and their velocity and duration was examined. Duration and velocity were found to vary by as much as 60% while the amplitude showed no related variation and had an almost constant accuracy of about 90%. By administrating diazepam, the variabiity of saccade duration and velocity could be further increased, but still the amplitude remained almost constant. These results favour the hypothesis that saccadic innervation is controlled by a local feedback loop.

Perturbation of combined saccade-vergence movements by microstimulation in monkey superior colliculus.

V Chaturvedi — 2008-02-20T04:28:23-00:00

J Neurophysiol, Vol. 81, No. 5. (May 1999), pp. 2279-2296.

Perturbation of combined saccade-vergence movements by microstimulation in monkey superior colliculus. This study investigated the role of the monkey superior colliculus (SC) in the control of visually (V)-guided combined saccade-vergence movements by assessing the perturbing effects of microstimulation. We elicited an electrical saccade (E) by stimulation (in 20% of trials) in the SC while the monkey was preparing a V-guided movement to a near target. The target was aligned such that E- and V-induced saccades had similar amplitudes but different directions and such that V-induced saccades had a significant vergence component (saccades to a near target). The onset of the E-stimulus was varied from immediately after V-target onset to after V-saccade onset. E-control trials, where stimulation was applied during fixation of a V-target, yielded the expected saccade but no vergence. By contrast, early perturbation trials, where the E-stimulus was applied soon after the onset of the V-target, caused an E-triggered response with a clear vergence component toward the V-target. Midflight perturbation, timed to occur just after the monkey initiated the movement toward the target, markedly curtailed the ongoing vergence component during the saccade. Examination of pooled responses from both types of perturbation trials showed weighted-averaging effects between E- and V-stimuli in both saccade and fast vergence components. Both components exhibited a progression from E- to V-dominance as the E-stimulus was delayed further. This study shows that artificial intervention in the SC, while a three-dimensional (3D) refixation is being prepared or is ongoing, can affect the timing (WHEN) and the metric specification (WHERE) of both saccades and vergence. To explain this we interpret the absence of overt vergence in the E-controls as being caused by a zero-vergence change command rather than reflecting the mere absence of a collicular vergence signal. In the perturbation trials, the E-evoked zero-vergence signal competes with the V-initiated saccade-vergence signal, thereby giving rise to a compromised 3D response. This effect would be expected if the population of movement cells at each SC site is tuned in 3D, combining the well-known topographical code for direction and amplitude with a nontopographical depth representation. On E-stimulation, the local population would yield a net saccade signal caused by the topography, but the cells coding for different depths would be excited equally, causing the vergence change to be zero.

Participation of the caudal fastigial nucleus in smooth-pursuit eye movements. I. Neuronal activity.

AF Fuchs — 2008-02-19T10:17:04-00:00

J Neurophysiol, Vol. 72, No. 6. (December 1994), pp. 2714-2728.

1. We recorded single-unit activity from neurons of an output of the cerebellum, the fastigial nucleus, in two rhesus macaques while the monkeys tracked small moving targets with their eyes. Many neurons in the caudal part of the fastigial nucleus exhibited a modulation in their discharge rates when smooth-pursuit eye movements were elicited by either sinusoidal or step-ramp motions of a small target. 2. The pursuit direction that elicited the most vigorous modulation in unit firing to sinusoidal target motion could be horizontal, vertical, or oblique. Most often, the preferred direction was in the contralateral and/or downward direction (50 of 69 neurons) or in the ipsilateral and/or upward direction (13 of 69). 3. For units whose preferred smooth-pursuit directions were either contralateral/downward or ipsilateral/upward during sinusoidal pursuit, peak firing as measured by the phase shift of periodic modulation at 0.5-0.8 Hz occurred near the time of peak velocity. The discharge of 80% of the neurons with contralateral/downward preferred directions preceded eye velocity by an average of -27 degrees; thus these neurons discharged maximally during eye acceleration. In contrast, neurons with ipsilateral/upward preferred directions lagged peak velocity by an average of +10.5 degrees and therefore discharged during eye deceleration. 4. The average eye velocity sensitivity for sinusoidal pursuit between 0.5 and 0.8 Hz was 0.83 +/- 0.57 (SD) spikes/s per degrees/s. We also tested 36 units during pursuit at a variety of frequencies in their preferred directions and found that firing rates increased monotonically with peak eye velocity. However, the firing rate saturated at velocities ranging from 20 to 60 degrees/s for different units. 5. When a monkey tracked a step-ramp target motion, three discharge patterns emerged in the 27 units tested. Just over half of the units discharged a burst of spikes that preceded (average lead of 27.4 +/- 17 ms) and lasted throughout the initial third of the eye acceleration; the burst was followed by a subsequent steady firing that continued after the eye had accelerated to its steady velocity. Fewer neurons discharged a burst that began late in the acceleration and was followed by steady firing. Occasional neurons showed only a gradual increase in firing rate during acceleration followed by a steady discharge. 6. Thirty of the 31 fastigial smooth-pursuit units tested also were modulated during sinusoidal yaw and/or pitch oscillations while the animals fixated a spot that rotated with them.(ABSTRACT TRUNCATED AT 400 WORDS)

Dissociation of eye and head components of gaze shifts by stimulation of the omnipause neuron region.

NJ Gandhi — 2008-02-18T16:30:42-00:00

J Neurophysiol, Vol. 98, No. 1. (July 2007), pp. 360-373.

Natural movements often include actions integrated across multiple effectors. Coordinated eye-head movements are driven by a command to shift the line of sight by a desired displacement vector. Yet because extraocular and neck motoneurons are separate entities, the gaze shift command must be separated into independent signals for eye and head movement control. We report that this separation occurs, at least partially, at or before the level of pontine omnipause neurons (OPNs). Stimulation of the OPNs prior to and during gaze shifts temporally decoupled the eye and head components by inhibiting gaze and eye saccades. In contrast, head movements were consistently initiated before gaze onset, and ongoing head movements continued along their trajectories, albeit with some characteristic modulations. After stimulation offset, a gaze shift composed of an eye saccade, and a reaccelerated head movement was produced to preserve gaze accuracy. We conclude that signals subject to OPN inhibition produce the eye-movement component of a coordinated eye-head gaze shift and are not the only signals involved in the generation of the head component of the gaze shift.