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Effect of registration on cyclical kinematic data.

ABSTRACT: Given growing interest in functional data analysis (FDA) as a useful method for analyzing human movement data, it is critical to understand the effects of standard FDA procedures, including registration, on biomechanical analyses. Registration is used to reduce phase variability between curves while preserving the individual curve's shape and amplitude. The application of three methods available to assess registration could benefit those in the biomechanics community using FDA techniques: comparison of mean curves, comparison of average RMS values, and assessment of time-warping functions. Therefore, the present study has two purposes. First, the necessity of registration applied to cyclical data after time normalization is assessed. Second, we illustrate the three methods for evaluating registration effects. Masticatory jaw movements of 22 healthy adults (2 males, 21 females) were tracked while subjects chewed a gum-based pellet for 20s. Motion data were captured at 60 Hz with two gen-locked video cameras. Individual chewing cycles were time normalized and then transformed into functional observations. Registration did not affect mean curves and warping functions were linear. Although registration decreased the RMS, indicating a decrease in inter-subject variability, the difference was not statistically significant. Together these results indicate that registration may not always be necessary for cyclical chewing data. An important contribution of this paper is the illustration of three methods for evaluating registration that are easy to apply and useful for judging whether the extra data manipulation is necessary.

SUBMITTER: Crane EA

PROVIDER: S-EPMC2931315 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature

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Effect of registration on cyclical kinematic data.

Crane Elizabeth A EA Cassidy Ruth B RB Rothman Edward D ED Gerstner Geoffrey E GE

Journal of biomechanics 20100801 12

Given growing interest in functional data analysis (FDA) as a useful method for analyzing human movement data, it is critical to understand the effects of standard FDA procedures, including registration, on biomechanical analyses. Registration is used to reduce phase variability between curves while preserving the individual curve's shape and amplitude. The application of three methods available to assess registration could benefit those in the biomechanics community using FDA techniques: compar ...[more]

PMID: 20537335

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Project description:BackgroundEconomically developed countries have recruited large numbers of overseas health workers to fill domestic shortages. Recognition of the negative impact this can have on health care in developing countries led the United Kingdom Department of Health to issue a Code of Practice for National Health Service (NHS) employers in 1999 providing ethical guidance on international recruitment. Case reports suggest this guidance had limited influence in the context of other NHS policy priorities.MethodsThe temporal association between trends in new professional registrations from doctors qualifying overseas and relevant United Kingdom government policy is reported. Government policy documents were identified by a literature review; further information was obtained, when appropriate, through requests made under the Freedom of Information Act. Data on new professional registration of doctors were obtained from the General Medical Council (GMC).ResultsNew United Kingdom professional registrations by doctors trained in Africa and south Asia more than doubled from 3105 in 2001 to 7343 in 2003, as NHS Trusts sought to achieve recruitment targets specified in the 2000 NHS Plan; this occurred despite ethical guidance to avoid active recruitment of doctors from resource-poor countries. Registration of such doctors declined subsequently, but in response to other government policy initiatives. A fall in registration of South African-trained doctors from 3206 in 2003 to 4 in 2004 followed a Memorandum of Understanding with South Africa signed in 2003. Registrations from India and Pakistan fell from a peak of 4626 in 2004 to 1169 in 2007 following changes in United Kingdom immigration law in 2005 and 2006. Since 2007, registration of new doctors trained outside the European Economic Area has remained relatively stable, but in 2010 the United Kingdom still registered 722 new doctors trained in Africa and 1207 trained in India and Pakistan.ConclusionsEthical guidance was ineffective in preventing mass registration by doctors trained in resource-poor countries between 2001 and 2004 because of competing NHS policy priorities. Changes in United Kingdom immigration laws and bilateral agreements have subsequently reduced new registrations, but about 4000 new doctors a year continue to register who trained in Africa, Asia and less economically developed European countries.

Project description:BackgroundThe cyclical nature of gene expression in the intraerythrocytic development cycle (IDC) of the malaria parasite, Plasmodium falciparum, confounds the accurate detection of specific transcriptional differences, e.g. as provoked by the development of drug resistance. In lab-based studies, P. falciparum cultures are synchronized to remove this confounding factor, but the rapid detection of emerging resistance to artemisinin therapies requires rapid analysis of transcriptomes extracted directly from clinical samples. Here we propose the use of cyclical regression covariates (CRC) to eliminate the major confounding effect of developmentally driven transcriptional changes in clinical samples. We show that elimination of this confounding factor reduces both Type I and Type II errors and demonstrate the effectiveness of this approach using a published dataset of 1043 transcriptomes extracted directly from patient blood samples with different patient clearance times after treatment with artemisinin.ResultsWe apply this method to two publicly available datasets and demonstrate its ability to reduce the confounding of differences in transcript levels due to misaligned intraerythrocytic development time. Adjusting the clinical 1043 transcriptomes dataset with CRC results in detection of fewer functional categories than previously reported from the same data set adjusted using other methods. We also detect mostly the same functional categories, but observe fewer genes within these categories. Finally, the CRC method identifies genes in a functional category that was absent from the results when the dataset was adjusted using other methods. Analysis of differential gene expression in the clinical data samples that vary broadly for developmental stage resulted in the detection of far fewer transcripts in fewer functional categories while, at the same time, identifying genes in two functional categories not present in the unadjusted data analysis. These differences are consistent with the expectation that CRC reduces both false positives and false negatives with the largest effect on datasets from samples with greater variance in developmental stage.ConclusionsCyclical regression covariates have immediate application to parasite transcriptome sequencing directly from clinical blood samples and to cost-constrained in vitro experiments.

Project description:We present an algorithm, QBKR (Quaternary Backbone Kinematic Reconstruction), a fast analytical method for an all-atom backbone reconstruction of proteins and linear or cyclic peptide chains from Cα coordinate traces. Unlike previous analytical methods for deriving all-atom representations from coarse-grained models that rely on canonical geometry with planar peptides in the trans conformation, our de novo kinematic model incorporates noncanonical, cis-trans, geometry naturally. Perturbations to this geometry can be effected with ease in our formulation, for example, to account for a continuous change from cis to trans geometry. A simple optimization of a spring-based objective function is employed for Cα-Cα distance variations that extend beyond the cis-trans limit. The kinematic construction produces a linked chain of peptide units, Cα-C-N-Cα, hinged at the Cα atoms spanning all possible planar and nonplanar peptide conformations. We have combined our method with a ring closure algorithm for the case of ring peptides and missing loops in a protein structure. Here, the reconstruction proceeding from both the N and C termini of the protein backbone (or in both directions from a starting position for rings) requires freedom in the position of one Cα atom (a capstone) to achieve a successful loop or ring closure. A salient feature of our reconstruction method is the ability to enrich conformational ensembles to produce alternative feasible conformations in which H-bond forming C-O or N-H pairs in the backbone can reverse orientations, thus addressing a well-known shortcoming in Cα-based RMSD structure comparison, wherein very close structures may lead to significantly different overall H-bond behavior. We apply the fixed Cα-based design to the reverse reconstruction from noisy Cryo-EM data, a posteriori to the optimization. Our method can be applied to speed up the process of an all-atom description from voluminous experimental data or subpar electron density maps.

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Effect of registration on cyclical kinematic data.

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Effect of registration on cyclical kinematic data.

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