Identifying joint-specific gait mechanisms causing impaired gait in alkaptonuria patients.

BACKGROUND: Alkaptonuria is a rare genetic disease that leads to structural joint damage and impaired movement function. Previous research indicates that alkaptonuria affects gait, however the detailed mechanisms are unknown. RESEARCH QUESTION: What are the joint-specific gait mechanisms which contribute to impaired gait in alkaptonuria patients? METHODS: The gait of 36 alkaptonuria patients were compared to those of 21 unimpaired controls. The AKU patients were split into three age groups (young 16-29 years, n = 9, middle 30-49 years, n = 16 and old 50 + years, n = 11), and the kinematic and kinetic gait profiles were compared to speed-matched controls using a spm1d two-sample t-test. RESULTS: The young AKU group showed significant differences in the sagittal plane of the knee joint compared to speed-matched controls. The middle group showed deviations in the knee and hip joints. The old group showed significant differences in multiple joints and planes and exhibited gait mechanisms which may be compensation strategies. SIGNIFICANCE: This study is the first to identify and describe joint-specific mechanisms during gait in alkaptonuria patients. Gait deviations were evident even in young AKU patients, including a 16-year-old, much earlier than previously thought. The knee joint is an important focus of future research and potential interventions as deviations were found across all three AKU age groups.

Leaving hip rotation out of a conventional 3D gait model improves discrimination of pathological gait in cerebral palsy: A novel neural network analysis.

BACKGROUND: Complex clinical gait analysis results can be expressed as single number gait deviations by applying multivariate processing methods. The original Movement Deviation Profile (MDP) quantifies the deviation of abnormal gait using the most trusted nine dynamic joint angles of lower limbs. RESEARCH QUESTION: Which subset of joint angles maximises the ability of the MDP to separate abnormal gait from normality? What is the effect of using the best subset in a large group of patients, and in individuals? METHODS: A self-organising neural network was trained using normal gait data from 166 controls, and then the MDP of 1923 patients with cerebral palsy (3846 legs) was calculated. The same procedure was repeated with 511 combinations of the nine joint angles. The standardised distances of abnormal gait from normality were then calculated as log-transformed Z-scores to select the best combination. A mixed design ANOVA was used to assess how removing the least discriminating angle improved the separation of patients from controls. The effect of using the optimal subset of angles was also quantified for each individual leg by comparing the change in MDP to the independent FAQ levels of patients. RESULTS: Removal of hip rotation significantly (p<0.0005) increased the separation of the patient group from normality (ΔZ-score 0.24) and also at FAQ levels 7-10 (ΔZ-score 0.38, 0.27, 0.22, 0.14). The MDP of individual patients changed in a wider range of -4.65 to 1.12 Z-scores and their change matched their independent FAQ scores, with less functional patients moving further from, and more functional patients moving closer to normality. SIGNIFICANCE: In existing gait databases we recommend excluding hip rotation from data used to calculate the MDP. Alternatively, the calculation of hip rotation can be improved by post-hoc correction, but the ultimate solution is to use more accurate and reliable models of hip rotation.

Data on items of AKUSSI in Alkaptonuria collected over three years from the United Kingdom National Alkaptonuria Centre and the impact of nitisinone.

Alkaptonuria is a rare genetic disorder characterized by a high level of circulating (and urine) homogentisic acid (HGA), which contributes to ochronosis when it is deposited in connective tissue as a pigmented polymer. In an observational study carried out by National AKU Centre (NAC) in Liverpool, a total of thirty-nine AKU patients attended yearly visits in varying numbers. At each visit a mixture of clinical, joint and spinal assessments were carried out and the results calculated to yield an AKUSSI (Alkaptonuria Severity Score Index), see "Nitisinone arrests ochronosis and decreases rate of progression of Alkaptonuria: evaluation of the effect of nitisinone in the United Kingdom National Alkaptonuria Centre" (Ranganath at el., 2018). The aim of this data article is to produce visual representation of the change in the components of AKUSSI over 3 years, through radar charts. The metabolic effect of nitisinone is shown through box plots.

Nitisinone arrests ochronosis and decreases rate of progression of Alkaptonuria: Evaluation of the effect of nitisinone in the United Kingdom National Alkaptonuria Centre.

QUESTION: Does Nitisinone prevent the clinical progression of the Alkaptonuria? FINDINGS: In this observational study on 39 patients, 2 mg of daily nitisinone inhibited ochronosis and significantly slowed the progression of AKU over a three-year period. MEANING: Nitisinone is a beneficial therapy in Alkaptonuria. BACKGROUND: Nitisinone decreases homogentisic acid (HGA), but has not been shown to modify progression of Alkaptonuria (AKU). METHODS: Thirty-nine AKU patients attended the National AKU Centre (NAC) in Liverpool for assessments and treatment. Nitisinone was commenced at V1 or baseline. Thirty nine, 34 and 22 AKU patients completed 1, 2 and 3 years of monitoring respectively (V2, V3 and V4) in the VAR group. Seventeen patients also attended a pre-baseline visit (V0) in the VAR group. Within the 39 patients, a subgroup of the same ten patients attended V0, V1, V2, V3 and V4 visits constituting the SAME Group. Severity of AKU was assessed by calculation of the AKU Severity Score Index (AKUSSI) allowing comparison between the pre-nitisinone and the nitisinone treatment phases. RESULTS: The ALL (sum of clinical, joint and spine AKUSSI features) AKUSSI rate of change of scores/patient/month, in the SAME group, was significantly lower at two (0.32 ±â€¯0.19) and three (0.15 ±â€¯0.13) years post-nitisinone when compared to pre-nitisinone (0.65 ±â€¯0.15) (p < .01 for both comparisons). Similarly, the ALL AKUSSI rate of change of scores/patient/month, in the VAR group, was significantly lower at one (0.16 ±â€¯0.08) and three (0.19 ±â€¯0.06) years post-nitisinone when compared to pre-nitisinone (0.59 ±â€¯0.13) (p < .01 for both comparisons). Combined ear and ocular ochronosis rate of change of scores/patient/month was significantly lower at one, two and three year's post-nitisinone in both VAR and SAME groups compared with pre-nitisinone (p < .05). CONCLUSION: This is the first indication that a 2 mg dose of nitisinone slows down the clinical progression of AKU. Combined ocular and ear ochronosis progression was arrested by nitisinone.

Substrate and flow characteristics associated with White Sturgeon recruitment in the Columbia River Basin.

A study was conducted to identify habitat characteristics associated with age 0+ White Sturgeon (Acipenser transmontanus Richardson, 1863) recruitment in three reaches of the Columbia River Basin: Skamania reach (consistent recruitment), John Day reach (intermittent/inconsistent recruitment), and Kootenai reach (no recruitment). Our modeling approach involved numerous steps. First, we collected information about substrate, embeddedness, and hydrodynamics in each reach. Second, we developed a set of spatially explicit predictor variables. Third, we built two habitat (probability) models with Skamania reach training data where White Sturgeon recruitment was consistent. Fourth, we created spawning maps of each reach by populating the habitat models with in-reach physical metrics (substrate, embeddedness, and hydrodynamics). Fifth, we examined model accuracy by overlaying spawning locations in Skamania and Kootenai reaches with habitat predictions obtained from probability models. Sixth, we simulated how predicted habitat changed in each reach after manipulating physical conditions to more closely match Skamania reach. Model verification confirmed White Sturgeon generally spawned in locations with higher model probabilities in Skamania and Kootenai reaches, indicating the utility of extrapolating the models. Model simulations revealed significant gains in White Sturgeon habitat in all reaches when spring flow increased, gravel/cobble composition increased, or embeddedness decreased. The habitat models appear well suited to assist managers when identifying reach-specific factors limiting White Sturgeon recruitment in the Columbia River Basin or throughout its range.

A marker based kinematic method of identifying initial contact during gait suitable for use in real-time visual feedback applications.

A gait cycle is typically defined as being from heel strike or initial contact (IC) to the next ipsilateral IC using kinetic data. When these data are not available other methods of event definition are required. An algorithm based upon sagittal plane kinematics of the hip, which defines IC at contralateral peak hip extension (PHE) is presented. Kinematic and kinetic data were recorded while 10 unimpaired participants each completed a minimum of 25 overground gait cycles. The accuracy of 551 IC events was evaluated by comparing the agreement of PHE to other kinematic and kinetic algorithms. The mean temporal difference in IC between the PHE algorithm and a kinetic algorithm was +0.0006±0.008 s. The 95% Limits of Agreement was ±0.018 s. This new PHE algorithm provides simple to implement and accurate gait events for use when kinetic data are not available.

Analysis of tetraplegic reaching in their 3D workspace following posterior deltoid-triceps tendon transfer.

STUDY DESIGN: Cross-sectional study. OBJECTIVES: To quantify three-dimensional (3D) reachable workspace in different groups of tetraplegic participants and to assess their reaching performance within this workspace. SETTING: Northwest Regional Spinal Injuries Centre, UK. METHODS: The 3D reachable workspace of three groups of tetraplegics (NON-OP, operated group (OP) and tetraplegic control group (CON(Tetraplegic)) with varying levels of triceps function together with a healthy control group (CON(Healthy))) was defined by reaching to five target positions (anterior, medial, lateral, superior and inferior) located on the periphery of their workspace. Joint angles and inter-joint co-ordination were analysed after a 3D reconstruction of the thorax, humerus and forearm. The performance related variables of movement time, peak velocity, time-to-peak velocity and curvature index were also examined. RESULTS: The reachable volumes covered were consistent with the level of triceps function as CON(Healthy) covered a significantly greater volume than the tetraplegic groups and in turn the OP covered a larger workspace volume than NON-OP. The reduced workspace of tetraplegics was identified as being due to restrictions in workspace above shoulder height and across the body. Co-ordination data identified some differences in movement patterns but when reaching to targets on the workspace there were no significant differences between the OP and NON-OP groups. CONCLUSION: This study provided a detailed assessment of reachable workspace and target reaching. Tetraplegic participants found the superior and medial parts of the workspace were the most challenging directions. Standardised biomechanical analysis of tetraplegic upper-limb function is required for objective assessment.

E-MSD: an integrated data resource for bioinformatics.

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD 'atlas pages' show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples showcasing the functionality and power of these tools are available from tutorial webpages (http://www. ebi.ac.uk/msd-srv/docs/roadshow_tutorial/).

Estimation of P-values for global alignments of protein sequences.

MOTIVATION: The global alignment of protein sequence pairs is often used in the classification and analysis of full-length sequences. The calculation of a Z-score for the comparison gives a length and composition corrected measure of the similarity between the sequences. However, the Z-score alone, does not indicate the likely biological significance of the similarity. In this paper, all pairs of domains from 250 sequences belonging to different SCOP folds were aligned and Z-scores calculated. The distribution of Z-scores was fitted with a peak distribution from which the probability of obtaining a given Z-score from the global alignment of two protein sequences of unrelated fold was calculated. A similar analysis was applied to subsequence pairs found by the Smith-Waterman algorithm. These analyses allow the probability that two protein sequences share the same fold to be estimated by global sequence alignment. RESULTS: The relationship between Z-score and probability varied little over the matrix/gap penalty combinations examined. However, an average shift of +4.7 was observed for Z-scores derived from global alignment of locally-aligned subsequences compared to global alignment of the full-length sequences. This shift was shown to be the result of pre-selection by local alignment, rather than any structural similarity in the subsequences. The search ability of both methods was benchmarked against the SCOP superfamily classification and showed that global alignment Z-scores generated from the entire sequence are as effective as SSEARCH at low error rates and more effective at higher error rates. However, global alignment Z-scores generated from the best locally-aligned subsequence were significantly less effective than SSEARCH. The method of estimating statistical significance described here was shown to give similar values to SSEARCH and BLAST, providing confidence in the significance estimation. AVAILABILITY: Software to apply the statistics to global alignments is available from http://barton.ebi.ac.uk. CONTACT: geoff@ebi.ac.uk

3Dee: a database of protein structural domains.

UNLABELLED: The 3Dee database is a repository of protein structural domains. It stores alternative domain definitions for the same protein, organises domains into sequence and structural hierarchies, contains non-redundant set(s) of sequences and structures, multiple structure alignments for families of domains, and allows previous versions of the database to be regenerated. AVAILABILITY: 3Dee is accessible on the World Wide Web at the URL http://barton.ebi.ac.uk/servers/3Dee.html.

Protein structural domains: analysis of the 3Dee domains database.

The 3Dee database of domain definitions was developed as a comprehensive collection of domain definitions for all three-dimensional structures in the Protein Data Bank (PDB). The database includes definitions for complex, multiple-segment and multiple-chain domains as well as simple sequential domains, organized in a structural hierarchy. Two different snapshots of the 3Dee database were analyzed at September 1996 and November 1999. For the November 1999 release, 7,995 PDB entries contained 13,767 protein chains and gave rise to 18,896 domains. The domain sequences clustered into 1,715 domain sequence families, which were further clustered into a conservative 1,199 domain structure families (families with similar folds). The proportion of different domain structure families per domain sequence family increases from 84% for domains 1-100 residues long to 100% for domains greater than 600 residues. This is in keeping with the idea that longer chains will have more alternative folds available to them. Of the representative domains from the domain sequence families, 49% are in the range of 51-150 residues, whereas 64% of the representative chains over 200 residues have more than 1 domain. Of the representative chains, 8.5% are part of multichain domains. The largest multichain domain in the database has 14 chains and 1,400 residues, whereas the largest single-chain domain has 907 residues. The largest number of domains found in a protein is 13. The analysis shows that over the history of the PDB, new domain folds have been discovered at a slower rate than by random selection of all known folds. Between 1992 and 1997, a constant 1 in 11 new domains deposited in the PDB has shown no sequence similarity to a previously known domain sequence family, and only 1 in 15 new domain structures has had a fold that has not been seen previously. A comparison of the September 1996 release of 3Dee to the Structural Classification of Proteins (SCOP) showed that the domain definitions agreed for 80% of the representative protein chains. However, 3Dee provided explicit domain boundaries for more proteins. 3Dee is accessible on the World Wide Web at http://barton.ebi.ac.uk/servers/3Dee.html.

Application of multiple sequence alignment profiles to improve protein secondary structure prediction.

The effect of training a neural network secondary structure prediction algorithm with different types of multiple sequence alignment profiles derived from the same sequences, is shown to provide a range of accuracy from 70.5% to 76.4%. The best accuracy of 76.4% (standard deviation 8.4%), is 3.1% (Q(3)) and 4.4% (SOV2) better than the PHD algorithm run on the same set of 406 sequence non-redundant proteins that were not used to train either method. Residues predicted by the new method with a confidence value of 5 or greater, have an average Q(3) accuracy of 84%, and cover 68% of the residues. Relative solvent accessibility based on a two state model, for 25, 5, and 0% accessibility are predicted at 76.2, 79.8, and 86. 6% accuracy respectively. The source of the improvements obtained from training with different representations of the same alignment data are described in detail. The new Jnet prediction method resulting from this study is available in the Jpred secondary structure prediction server, and as a stand-alone computer program from: http://barton.ebi.ac.uk/. Proteins 2000;40:502-511.

ProtEST: protein multiple sequence alignments from expressed sequence tags.

MOTIVATION: An automatic sequence searching method (ProtEST) is described which constructs multiple protein sequence alignments from protein sequences and translated expressed sequence tags (ESTs). ProtEST is more effective than a simple TBLASTN search of the query against the EST database, as the sequences are automatically clustered, assembled, made non-redundant, checked for sequence errors, translated into protein and then aligned and displayed. RESULTS: A ProtEST search found a non-redundant, translated, error- and length-corrected EST sequence for > 58% of sequences when single sequences from 1407 Pfam-A seed alignments were used as the probe. The average family size of the resulting alignments of translated EST sequences contained > 10 sequences. In a cross-validated test of protein secondary structure prediction, alignments from the new procedure led to an improvement of 3.4% average Q3 prediction accuracy over single sequences. AVAILABILITY: The ProtEST method is available as an Internet World Wide Web service http://barton.ebi.ac.uk/servers/protest.html+ ++ The Wise2 package for protein and genomic comparisons and the ProtESTWise script can be found at http://www.sanger.ac.uk/Software/Wise2 CONTACT: geoff@ebi.ac.uk

Evaluation and improvement of multiple sequence methods for protein secondary structure prediction.

A new dataset of 396 protein domains is developed and used to evaluate the performance of the protein secondary structure prediction algorithms DSC, PHD, NNSSP, and PREDATOR. The maximum theoretical Q3 accuracy for combination of these methods is shown to be 78%. A simple consensus prediction on the 396 domains, with automatically generated multiple sequence alignments gives an average Q3 prediction accuracy of 72.9%. This is a 1% improvement over PHD, which was the best single method evaluated. Segment Overlap Accuracy (SOV) is 75.4% for the consensus method on the 396-protein set. The secondary structure definition method DSSP defines 8 states, but these are reduced by most authors to 3 for prediction. Application of the different published 8- to 3-state reduction methods shows variation of over 3% on apparent prediction accuracy. This suggests that care should be taken to compare methods by the same reduction method. Two new sequence datasets (CB513 and CB251) are derived which are suitable for cross-validation of secondary structure prediction methods without artifacts due to internal homology. A fully automatic World Wide Web service that predicts protein secondary structure by a combination of methods is available via http://barton.ebi.ac.uk/.

Deposition of macromolecular structures.

Macromolecular structures are being determined at an increasing rate, and are of interest to a wide diversity of researchers. Depositing a macromolecular structure with the Protein Data Bank makes it readily available to the community. Accuracy, consistency and machine-readability of the data are essential, as are clear indications of quality, and sufficient information to allow non-experimentalists to interpret the data. Good-quality depositions are necessary to allow this to be achieved. The PDB's AutoDep system allows deposition and some preliminary automatic checking to take place at multiple sites, prior to full processing and release of the structure by the PDB. However, depositing a structure currently requires the manual entry of a large amount of information at the time of deposition. The data-harvesting approach will allow much more information to be deposited, without placing an additional burden on the depositor. Deposition-ready files will be generated automatically during the course of a structure-determination experiment. The additional information will allow improved validation procedures to be applied to the structures, and the data to be made more useful to the wider scientific community.

Protein sequence alignment techniques.

The basic algorithms for alignment of two or more protein sequences are explained. Alternative methods for scoring substitutions and gaps (insertions and deletions) are described, as are global and local alignment methods. Multiple alignment techniques are explained, including methods for profile comparison. A summary is given of programs for the alignment and analysis of protein sequences, either from sequence alone, or from three-dimensional structure.

JPred: a consensus secondary structure prediction server.

UNLABELLED: An interactive protein secondary structure prediction Internet server is presented. The server allows a single sequence or multiple alignment to be submitted, and returns predictions from six secondary structure prediction algorithms that exploit evolutionary information from multiple sequences. A consensus prediction is also returned which improves the average Q3 accuracy of prediction by 1% to 72.9%. The server simplifies the use of current prediction algorithms and allows conservation patterns important to structure and function to be identified. AVAILABILITY: http://barton.ebi.ac.uk/servers/jpred.h tml CONTACT: geoff@ebi.ac.uk

Conservation of amino acids in multiple alignments: aspartic acid has unexpected conservation.

Analysis of the relationship between surface accessibility and amino acid conservation in multiple sequence alignments of homologous proteins confirms expected trends for hydrophobic amino acids, but reveals an unexpected difference between the conservation of Asp, Glu and Gln. Even when not in an active site, Asp is more highly conserved than Glu. There is a clear preference for conserved and buried Asp to be present in coil, but there is no tendency for Asp to conserve phi/psi in the ++ region of the Ramachandran map. Glu does not show any preference to be conserved in a particular secondary structure. Analysis of recently derived substitution matrices (e.g. BLOSUM) confirms that Glu tends to substitute more frequently with other amino acids than does Asp. Analysis of relative accessibility versus relative conservation for individual amino acid positions in alignments shows a negative correlation for all amino acid types. With the exception of Arg, Lys, Gly, Glu, Asp and Tyr, a relative conservation of > 2 suggests the amino acid will have a relative accessibility of < 50%. Observation of conserved Cys, Gly or Asp in a reliable multiple alignment suggests a position important for the structure of the protein. Furthermore, the Asp is likely to be involved in polar interactions through its side chain oxygen atoms. In contrast, Gln is the least conserved amino acid overall.