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Biomedical subjects

Richard J Morris

Publications and source records attributed to Richard J Morris.

At least 19 recordsLinked to original sources
PubMed2006

Voice onset time for female trained and untrained singers during speech and singing.

UNLABELLED: The purpose of this study was to examine the voice onset times of female trained and untrained singers during spoken and sung tasks. Thirty females were digitally recorded speaking and singing short phrases containing the English stop consonants /p/ and /b/ in the word-initial position. Voice onset time was measured for each phoneme and statistically analyzed. Mixed-ANOVAs revealed significantly longer voice onset time durations during speech for /p/ as compared to sung productions. No significant differences between the trained singers and untrained singers were observed. In addition, no task differences occurred for the /b/ productions. The results indicated that the type of phonatory task influences VOT for voiceless stops in females. LEARNING OUTCOMES: As a result of this activity, the reader will be able to (1) understand articulatory and phonatory differences between spoken and sung productions; (2) understand the articulatory and phonatory timing differences between trained singers and untrained singers during spoken and sung productions.

Adult↗
PubMed2006

Assessing fears and related anxieties in children and adolescents with learning disabilities or mild mental retardation.

The purpose of the present study was to examine self-reported fears and related anxieties in children and adolescents (7-18 years of age) having learning disabilities (LD) or mild mental retardation (MIMR), and whether these fears and related anxieties differ based on gender and age. Students responded to two well validated instruments, The Fear Survey Schedule for Children-Revised and Revised Children's Manifest Anxiety Scale. The results revealed age, gender, and disability interaction effects. Adolescent boys having mild mental retardation reported highest levels of fear related to failure and criticism, a finding that was different from those reported in previous studies. In addition, girls reported higher levels than boys of total fear, fears related to minor injury and small animals, and worry/oversensitivity. Age main effects were also observed where younger students from both the LD and the MIMR groups reported higher levels of non-specific general anxiety. Implications and directions for future research were presented.

Adolescent↗
PubMed2006

Acoustic analysis of the interaction of choral arrangements, musical selection, and microphone location.

Acoustic differences were evaluated among three choral arrangements and two choral textures recorded at three microphone locations. A choir was recorded when singing two musical selections of different choral texture, one homophonic and one polyphonic. Both musical selections were sung in three choral arrangements: block sectional, sectional-in-columns, and mixed. Microphones were placed at the level of the choristers, the conductor, and the audience. The recordings at each location were analyzed using long-term average spectrum (LTAS). The LTAS from the mixed arrangement exhibited more signal amplitude than the other arrangements in the range of 1000-3500Hz. When considering the musical selections, the chorus produced more signal amplitude in the region of 1800-2200Hz for the homophonic selection. In addition, the LTAS produced by the choir for the homophonic selection varied across the microphone locations. As for the microphone location, the LTAS of the signal detected directly in front of the chorus had a greater slope than the other two locations. Thus, the acoustic signal near the choristers differed from the signals near the conductor and in the audience. Conductors may be using acoustic information from the region of the second and third formants when they decide how to arrange a choir for a particular musical selection.

Acoustic Stimulation↗
PubMed2006

A method for localizing ligand binding pockets in protein structures.

The accurate identification of ligand binding sites in protein structures can be valuable in determining protein function. Once the binding site is known, it becomes easier to perform in silico and experimental procedures that may allow the ligand type and the protein function to be determined. For example, binding pocket shape analysis relies heavily on the correct localization of the ligand binding site. We have developed SURFNET-ConSurf, a modular, two-stage method for identifying the location and shape of potential ligand binding pockets in protein structures. In the first stage, the SURFNET program identifies clefts in the protein surface that are potential binding sites. In the second stage, these clefts are trimmed in size by cutting away regions distant from highly conserved residues, as defined by the ConSurf-HSSP database. The largest clefts that remain tend to be those where ligands bind. To test the approach, we analyzed a nonredundant set of 244 protein structures from the PDB and found that SURFNET-ConSurf identifies a ligand binding pocket in 75% of them. The trimming procedure reduces the original cleft volumes by 30% on average, while still encompassing an average 87% of the ligand volume. From the analysis of the results we conclude that for those cases in which the ligands are found in large, highly conserved clefts, the combined SURFNET-ConSurf method gives pockets that are a better match to the ligand shape and location. We also show that this approach works better for enzymes than for nonenzyme proteins.

Algorithms↗
PubMed2006

Effects of vocal training and phonatory task on voice onset time.

OBJECTIVES/HYPOTHESIS: The purpose of this study was to examine the temporal-acoustic differences between trained singers and nonsingers during speech and singing tasks. METHODS: Thirty male participants were separated into two groups of 15 according to level of vocal training (ie, trained or untrained). The participants spoke and sang carrier phrases containing English voiced and voiceless bilabial stops, and voice onset time (VOT) was measured for the stop consonant productions. RESULTS: Mixed analyses of variance revealed a significant main effect between speech and singing for /p/ and /b/, with VOT durations longer during speech than singing for /p/, and the opposite true for /b/. Furthermore, a significant phonatory task by vocal training interaction was observed for /p/ productions. CONCLUSIONS: The results indicated that the type of phonatory task influences VOT and that these influences are most obvious in trained singers secondary to the articulatory and phonatory adjustments learned during vocal training.

Adult↗
PubMed2005

An evaluation of spherical designs for molecular-like surfaces.

The use of spherical harmonics in the molecular sciences is widespread. They have been employed with success in, for instance, the crystallographic fast rotation function, small-angle scattering particle reconstruction, molecular surface visualisation, protein-protein docking, active site analysis and protein function prediction. The calculation of spherical harmonic expansion coefficients requires integration over the full sphere and can be a computationally cumbersome and also numerically sensitive (with respect to the integration weights) procedure. It is shown here how the use of spherical t-designs and pre-computed near-equal weight integration layouts can significantly reduce the computational effort in the determination of spherical harmonic expansion coefficients for molecular surfaces, thus giving rise to a robust and highly efficient algorithm for the construction of molecular-like objects.

Cellulase↗
PubMed2005

Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.

MOTIVATION: An increasing number of protein structures are being determined for which no biochemical characterization is available. The analysis of protein structure and function assignment is becoming an unexpected challenge and a major bottleneck towards the goal of well-annotated genomes. As shape plays a crucial role in biomolecular recognition and function, the examination and development of shape description and comparison techniques is likely to be of prime importance for understanding protein structure-function relationships. RESULTS: A novel technique is presented for the comparison of protein binding pockets. The method uses the coefficients of a real spherical harmonics expansion to describe the shape of a protein's binding pocket. Shape similarity is computed as the L2 distance in coefficient space. Such comparisons in several thousands per second can be carried out on a standard linux PC. Other properties such as the electrostatic potential fit seamlessly into the same framework. The method can also be used directly for describing the shape of proteins and other molecules. AVAILABILITY: A limited version of the software for the real spherical harmonics expansion of a set of points in PDB format is freely available upon request from the authors. Binding pocket comparisons and ligand prediction will be made available through the protein structure annotation pipeline Profunc (written by Roman Laskowski) which will be accessible from the EBI website shortly.

Algorithms↗
PubMed2005

Comparisons of voice onset time for trained male singers and male nonsingers during speaking and singing.

This study was designed to examine the temporal acoustic differences between male trained singers and nonsingers during speaking and singing across voiced and voiceless English stop consonants. Recordings were made of 5 trained singers and 5 nonsingers, and acoustically analyzed for voice onset time (VOT). A mixed analysis of variance showed that the male trained singers had significantly longer mean VOT than did the nonsingers during voiceless stop production. Sung productions of voiceless stops had significantly longer mean VOTs than did the spoken productions. No significant differences were observed for the voiced stops, nor were any interactions observed. These results indicated that vocal training and phonatory task have a significant influence on VOT.

Analysis of Variance↗
PubMed2005

The effects of fundamental frequency level on voice onset time in normal adult male speakers.

The purpose of this study was to examine the effect of fundamental frequency (F(0)) on stop consonant voice onset time (VOT). VOT was measured from the recordings of 56 young men reading phrases containing all 6 English voiced and voiceless stops in word-initial position across high-, medium-, and low-F(0) levels. Separate analyses of variance for the voiced and voiceless stops revealed no significant main effect for F(0) for the voiced stops but a significant F(0) effect for the voiceless stops. Across the voiceless stops, productions at high F(0)s displayed significantly shorter VOTs than productions at low or mid F(0)s. The findings indicated that researchers must take into account the F(0) level at which voiceless stop VOT is measured.

Adult↗
PubMed2004

Statistical pattern recognition for macromolecular crystallographers.

A selection of pattern-recognition techniques is presented with a special focus on those methods that may be of interest to macromolecular crystallographers not indifferent to automated protein model building. An overview of the most common pattern-recognition approaches is given and some popular model-building packages are briefly reviewed within this context.

Algorithms↗
PubMed2004

Towards complete validated models in the next generation of ARP/wARP.

The design of a new versatile control system that will underlie future releases of the automated model-building package ARP/wARP is presented. A sophisticated expert system is under development that will transform ARP/wARP from a very useful model-building aid to a truly automated package capable of delivering complete, well refined and validated models comparable in quality to the result of intensive manual checking, rebuilding, hypothesis testing, refinement and validation cycles of an experienced crystallographer. In addition to the presentation of this control system, recent advances, ideas and future plans for improving the current model-building algorithms, especially for completing partially built models, are presented. Furthermore, a concept for integrating validation routines into the iterative model-building process is also presented.

Algorithms↗
PubMed2004

On the interpretation and use of <|E|2>(d*) profiles.

Profiles of squared normalized structure factors, <|E|(2)>(d*), have been computed for a large number of proteins and nucleic acids. These are interpreted in terms of their underlying structural features. It is also shown that the 'solvent dip' at around 6.3 A resolution is to a large extent a protein secondary-structure effect that is enhanced by the water structure. A hierarchical classification of protein structures based on their <|E|(2)>(d*) profiles is briefly outlined, together with the use of <|E|(2)>(d*) profiles as an improvement over Wilson absolute scale estimation and as a novel solvent-modelling method.

Cluster Analysis↗
PubMed2003

Breaking good resolutions with ARP/wARP.

New procedures are outlined that enable ARP/wARP to automatically build protein models with diffraction data extending to about 2.5 A. An overview of ongoing research is given and possible future advances are discussed.

Algorithms↗
PubMed2003

Sheldrick's 1.2 A rule and beyond.

An average profile of squared normalized structure factors as a function of resolution, /E/2>(d*), calculated from a large ensemble of high-resolution protein models, is presented. An interpretation is given that provides a structural explanation for Sheldrick's 1.2 A rule for the applicability of direct methods. The implications for the potential effectiveness of extended direct methods, incorporating stereochemical knowledge, are discussed.

Algorithms↗
PubMed2002

Advantages of high-resolution phasing: MAD to atomic resolution.

The structure of the endoglucanase A from Clostridium thermocellum CelA was re-solved by three-wavelength MAD. Experimental phases were obtained in the resolution range 25-1.0 A. Various structure-solution approaches were tested in order to quantify the contribution of each wavelength. Two-wavelength MAD phasing was sufficient to obtain excellent experimental phases. SAD at the remote wavelength also resulted in interpretable maps. The three-wavelength MAD electron-density map was of excellent quality: for parts of the structure, atom types and bond types could be easily assigned. Double bonds in peptide links and side chains could be located owing to their increased electron density indicating their pi character. Comparison with a previously determined structure of CelA at 1.65 A showed that, apart from a few additional multiple conformers and differently oriented side chains, major differences occur at the protein-solvent interface. A complete additional solvent shell could be observed and the inner shells have been completed. The high accuracy of the structure allowed unambiguous assignment of the protonation state for the active-site catalytic carboxylates.

Cellulase↗
PubMed2002

ARP/wARP's model-building algorithms. I. The main chain.

Algorithms underlying the automatic model-building functionality of the ARP/wARP software suite are presented. Finding the most likely set of Calpha atoms from a given set of atoms is formulated as a constrained integer programming problem. The objective function is a density-weighted score for the match between observed and expected chain conformation. Graph-search algorithms are presented that find solutions to this problem in an efficient manner.

Algorithms↗