An application of principal component analysis for lower body kinematics between loaded and unloaded walking

Load carriage is a very common daily activity at home and in the workplace. Generally, the load is in the form of an external load carried by an individual, it could also be the excessive body mass carried by an overweight individual. To quantify the effects of carrying extra weight, whether in the form of an external load or excess body mass, motion capture data were generated for a diverse subject set. This consisted of twenty-three subjects generating one hundred fifteen trials for each loading condition. This study applied principal component analysis (PCA) to motion capture data in order to analyze the lower body gait patterns for four loading conditions: normal weight unloaded, normal weight loaded, overweight unloaded and overweight loaded.PCA has been shown to be a powerful tool for analyzing complex gait data. In this analysis, it is shown that in order to quantify the effects of external loads and/or for both normal weight and overweight subjects, the first principal component (PC1) is needed. For the work in this paper, PCs were generated from lower body joint angle data. The PC1 of the hip angle and PC1 of the ankle angle are shown to be an indicator of external load and BMI effects on temporal gait data.     

Application of principal component analysis in clinical gait research: Identification of systematic differences between healthy and medial knee-osteoarthritic gait

For a successful completion of a movement task the motor control system has to observe a multitude of internal constraints that govern the coordination of its segments. The purpose of this study was to apply principal component (PC) analysis to detect differences in the segmental coordination between healthy subjects and patients with medial knee osteoarthritis (OA). It was hypothesized that (1) systematic differences in patterns of whole body movement would be identifiable with this method even in small sample sized groups and that (2) these differences will include compensatory movements in the OA patients in both the lower and upper body segments. Marker positions and ground reaction forces of three gait trials of 5 healthy and 5 OA participants with full body marker sets were analyzed using a principal component analysis. Group differences in the PC-scores were determined for the first 10 PC-vectors and a linear combination of those PC-vectors where differences were found defined a discriminant vector. Projecting the original trials onto this discriminant vector yielded significant group differences (t(d=8)=3.011; p=0.017) with greater upper body movement in patients with knee OA that was correlated with the medial–lateral ground reaction force. These results help to characterize the adaptation of whole-body gait patterns to knee OA in a relatively small population and may provide an improved basis for the development of interventions to modify knee load. The PC-based motion analysis offered a highly sensitive approach to identify characteristic whole body patterns of movement associated with pathological gait.     

基于空间ICA和时间相关方法的人脑视觉皮层V5区的功能连通性研究

利用功能磁共振成像技术,将空间ICA和时间相关方法相结合来研究不同活动状态下人脑视觉皮层V5区的功能连通性。首先利用空间ICA处理组块视觉运动刺激的数据,定位V5区;然后分别计算静息和连续视觉运动刺激两种稳态下V5区与其它脑区低频振荡的时间相关,检测出该区的功能连通网络。实验结果表明,静息时V5区的功能连通网络更广泛,且与已知的解剖连通一致;当被试接受连续视觉运动刺激时,与V5区连通的脑区网络局限在视觉皮层,此时的网络特定于处理视觉运动这一任务。     

Evaluating the link between photosynthetic capacity and leaf vascular organization with principal component analysis

Photosynthetica - Significant linear relationships between photosynthetic capacity and principal components loaded by phloem cell numbers and tracheary elements per minor vein as well as the latter...     

Correlation between qualitatively distributed predicting variables and chemical terms in acridine derivatives using principal component analysis

When biological variables are not continuously distributed, the multiple and multivariate regression analysis cannot be used to correlate these variables against chemical regressors. As the employment of discriminant analysis requires the homogeneity of dispersion matrices and, that n_hp where n_h= degree of freedom of hypothesis, p =number of chemical terms, the reliability and validity of this method is highly questionable here. An alternative method is based on the principal component analysis where multicategory variables of drug responses can be classified into measures of inactive, slightly active, sufficiently active, and highly active drugs, for instance. The rules for classification are based on biological sources that can be expressed by chemical terms, too. An example adapted from antitumor action of acridine derivatives shows the working technique.     

Using principal component analysis to find correlations between loop-related and thermodynamic variables for G-quadruplex-forming sequences

The application of Principal Component Analysis (PCA) is proposed here as a simple means of revealing correlations between thermodynamic variables corresponding to folding equilibria of intramolecular G-quadruplexes and Watson–Crick duplexes, and the length of loops in the corresponding guanine-rich DNA sequences. To this end, two previously studied data sets were analyzed (Arora and Maiti, J. Phys. Chem. B. 2009 and Kumar and Maiti, Nucleic Acids. Res. 2008). All of the sequences considered shared the common structure 5’- GGG - loop1 - GGG - loop2 - GGG - loop3 - GGG -3’. PCA of these data sets supported a series of correlations between the variables studied. First, the association of loop length with thermodynamic stability and quadruplex structure was corroborated. Secondly, it is proposed that the addition of ethylene glycol produces a stronger stabilization on those sequences showing long loop1 and/or loop3. Thirdly, it is proposed that a low content of adenine in loop1 and/or loop3 will produce an increase in the stability of G-quadruplex and its related Watson–Crick duplex.     

A study of pattern and process in coastal vegetation using principal components analysis

A study is made of the dune system at Tentsmuir Point National Nature Reserve, Scotland, using transects crossing the vegetation zonation. Principal Components Analysis and tabular ordination are used to analyse the data, and an attempt is made to relate the results obtained to the dynamics of the system. The effects of different management regimes are considered, and it is concluded that the establishment of pine on the area has the largest effect on the development of the vegetation. Reduction in grazing pressure by rabbits is found to increase species diversity slightly, but has no major influence as yet on vegetation development. While some information on the dynamics of the vegetation can be inferred, the problems involved in this are considered to be large, and the study raises a number of questions to be studied in greater detail. It is concluded that permanent plots would be the most effective method to employ.Nomenclature follows Clapham, Tutin & Warburg (1962) for vascular plants, Watson (1968) for bryophytes, and Duncan (1970) for lichens.We should like to thank Dr. R. A. H. Smith of the Nature Conservancy Council for her assistance and permission to work on Tentsmuir Point N. N. R., and Mr. J. G. Young, then warden at Tentsmuir for his help at the start of the project. We are grateful to Dr. R. Meutzelfeldt for computational advice. In addition, one of us (R.J.H.) would like to thank Dr. E. van der Maarel and Dr. R. S. Clymo for their tuition during the Nordic Council for Ecology course Numerical Methods in Vegetation Analysis' in Lund, September, 1979.     

Relationships between induction of anesthesia and mitotic spindle disturbances studied by means of principal component analysis

A dataset comprising the activity of 30 compounds in 4 biological tests--anesthesia of tadpoles, anesthesia of frog heart, abnormal growth and spindle disturbances in Allium root tips--was re-evaluated by means of principal component analysis. A two-component model is required to explain the variation in biological activity of the compounds. It is found that abnormal growth is different from the other biological responses. When this test is excluded, as much as 90% of the variation is explained by a one-component model, the determining factor most probably being the lipophilic character of the compounds. Mammalian mitotic cells respond in a similar way to mitotic cells of Allium root tips. It is suggested that possible regularities in the dose-response relationships for anesthesia, teratogenic effects and generation of abnormal chromosome numbers require further exploration.     

Relationships between soil bulk electrical conductivity and the principal component analysis of topography and soil fertility values

Measures of soil electrical conductivity (EC) and elevation are relatively inexpensive to collect and result in dense data sets which allow for mapping with limited interpolation. Conversely, soil fertility information is expensive to collect so that relatively few samples are taken and mapping requires extensive interpolation with large estimation errors, resulting in limited usefulness for site-specific applications in precision agriculture. Principal component (PC) analysis and cokriging can be applied to create meaningful field scale summaries of groups of attributes and to decrease the estimation error of maps of the summarized attributes. Deep (0–90 cm) and shallow (0–30 cm) EC, elevation, and soil fertility attributes were measured in fields under corn (Zea mays L.) and soybean (Glycine max L.) rotations, at two sites in Illinois (IL) and two sites in Missouri (MO). Soil fertility and topography attributes were summarized by PC analysis. The first topography PC (TopoPC1) contrasted flow accumulation against elevation and curvature, to describe the main topographic pattern of the fields. The first soil fertility PC (SoilPC1) consistently grouped together cation exchange capacity (CEC), Ca, Mg, and organic matter (OM). SoilPC1 was well correlated to soil EC for all sites and cokriging with EC had higher r ² in the crossvariogram models compared to ordinary kriging. The second and third soil fertility PCs (SoilPC2 and SoilPC3) were concerned with soil pH and P, and reflected historic land use patterns. Maps of SoilPC2 and SoilPC3 had little relationship to soil EC or topography and so could not be improved by cokriging.     

香菇数量性状的相关性分析和主成分分析

对110个香菇杂交菌株16个数量性状进行表型、遗传和环境相关性分析及主成分分析。由分析结果可知,单菇鲜重与有关单菇的其他5个性状在表型、遗传和环境等3个方面都存在极显著的正相关,与菇数存在3种极显著的负相关,与CMC酶活性、木聚糖酶活性分别呈显著和极显著遗传负相关。鲜菇总重与出菇期和原基期呈极显著的表型和遗传负相关,与菇数、两种菌丝生长速度及菌盖厚度呈极显著的遗传正相关。结果表明,在香菇育种工作中,菌丝生长速度和酶活性,可以作为对单菇性状和鲜菇总重进行选择的间接指标之一。主成分分析结果表明,16个性状可以缩减为6个主成分,按方差贡献率大小分别命名为单菇、发育、产量、酶活、原基和转色因子,6个主成分的方差累积贡献率为80.75%。在香菇育种中,可以按照育种目标对上述主成分因子或其分量进行单独选择。     

Examination through a principal component analysis of the phosphorus exchanges between sediments and water in trophically different reservoirs

Phosphorus exchange at the sediment-water interface coupled with several parameters were assessed in several reservoirs with geologically different catchment basins and different trophic status in Morocco and France.The results showed that these exchanges were regulated by a combination of factors: physical chemical variability of the environment, the geological composition of catchment basins and the trophic status of the lake.In the hypereutrophic Villerest, iron-bound phosphorus is the major form of phosphorus trapped by the sediment whereas, in Moroccan reservoirs, calcium-bound phosphorus prevailed.We suggest that a drastic control of phosphorus inputs into the waters must be done through a large program of dephosphatization of tributaries to avoid Microcystis aeruginosa bloom formation in Villerest (Aleya et al., 1993) and calcium-bound phosphorus dissociation in Moroccan reservoirs with upward release of bioavailable phosphorus.

---

Résumé Les échanges de phosphore au niveau de l'interface eau-sédiment couplés á la distribution temporelle de divers éléments chimiques et biologiques ont été étudiés dans divers réservoirs de niveaux trophiques différents, au Maroc et en France.Nos résultats mettent clairement en évidence une influence directe de l'environnement physico-chimique, de la nature géologique des bassins versants et de l'état trophique du lac sur la dynamique du phosphore au sein de cette interface.De plus, il apparait que dans le lac hypereutrophe de Villerest (Roanne, France), le phosphore est majoritairement complexé au fer alors que dans les retenues marocaines, ce sont les complexes phosphore-calcium qui prédominent.Nous préconisons un contrôle drastique des apports en phosphore á travers l'installation et la multiplication d'unités de déphosphatation afin d'éviter d'une part, la prolifération massive de la Cyanobactérie Microcystis aeruginosa á Villetest (Aleya et al., 1994) et d'autre part la dissociation des complexes phhosphore-calcium au sein des retenues marocaines avec libération de phosphore biodisponible.

     

Harmonicity and anharmonicity in protein dynamics: A normal mode analysis and principal component analysis

A comparison of a normal mode analysis and principal component analysis of a 200-ps molecular dynamics trajectory of bovine pancreatic trypsin inhibitor in vacuum has been made in order to further elucidate the harmonic and anharmonic aspects in the dynamics of proteins. An anharmonicity factor is defined which measures the degree of anharmonicity in the modes, be they principal modes or normal modes, and it is shown that the principal mode system naturally divides into anharmonic modes with peak frequencies below 80 cm^?1, and harmonic modes with frequencies above this value. In general the larger the mean-square fluctuation of a principal mode, the greater the degree of anharmonicity in its motion. The anharmonic modes represent only 12% of the total number of variables, but account for 98% of the total mean-square fluctuation. The transitional nature of the anharmonic motion is demonstrated. The results strongly suggest that in a large subspace, the free energy surface, as probed by the simulation, is approximated by a multi-dimensional parabola which is just a resealed version of the parabola corresponding to the harmonic approximation to the conformational energy surface at a single minimum. After 200 ps, the resealing factor, termed the “normal mode resealing factor,” has apparently converged to a value whereby the mean-square fluctuation within the subspace is about twice that predicted by the normal mode analysis. © 1995 Wiley-Liss, Inc.     

Predicting timing of foot strike during running,independent of striking technique,using principal component analysis of joint angles

As 3-dimensional (3D) motion-capture for clinical gait analysis continues to evolve, new methods must be developed to improve the detection of gait cycle events based on kinematic data. Recently, the application of principal component analysis (PCA) to gait data has shown promise in detecting important biomechanical features. Therefore, the purpose of this study was to define a new foot strike detection method for a continuum of striking techniques, by applying PCA to joint angle waveforms. In accordance with Newtonian mechanics, it was hypothesized that transient features in the sagittal-plane accelerations of the lower extremity would be linked with the impulsive application of force to the foot at foot strike. Kinematic and kinetic data from treadmill running were selected for 154 subjects, from a database of gait biomechanics. Ankle, knee and hip sagittal plane angular acceleration kinematic curves were chained together to form a row input to a PCA matrix. A linear polynomial was calculated based on PCA scores, and a 10-fold cross-validation was performed to evaluate prediction accuracy against gold-standard foot strike as determined by a 10 N rise in the vertical ground reaction force. Results show 89–94% of all predicted foot strikes were within 4 frames (20 ms) of the gold standard with the largest error being 28 ms. It is concluded that this new foot strike detection is an improvement on existing methods and can be applied regardless of whether the runner exhibits a rearfoot, midfoot, or forefoot strike pattern.     

Multiple-breed genomic evaluation by principal component analysis in small size populations

In this study, the effects of breed composition and predictor dimensionality on the accuracy of direct genomic values (DGV) in a multiple breed (MB) cattle population were investigated. A total of 3559 bulls of three breeds were genotyped at 54 001 single nucleotide polymorphisms: 2093 Holstein (H), 749 Brown Swiss (B) and 717 Simmental (S). DGV were calculated using a principal component (PC) approach for either single (SB) or MB scenarios. Moreover, DGV were computed using all SNP genotypes simultaneously with SNPBLUP model as comparison. A total of seven data sets were used: three with a SB each, three with different pairs of breeds (HB, HS and BS), and one with all the three breeds together (HBS), respectively. Editing was performed separately for each scenario. Reference populations differed in breed composition, whereas the validation bulls were the same for all scenarios. The number of SNPs retained after data editing ranged from 36 521 to 41 360. PCs were extracted from actual genotypes. The total number of retained PCs ranged from 4029 to 7284 in Brown Swiss and HBS respectively, reducing the number of predictors by about 85% (from 82% to 89%). In all, three traits were considered: milk, fat and protein yield. Correlations between deregressed proofs and DGV were used to assess prediction accuracy in validation animals. In the SB scenarios, average DGV accuracy did not substantially change when either SNPBLUP or PC were used. Improvement of DGV accuracy were observed for some traits in Brown Swiss, only when MB reference populations and PC approach were used instead of SB-SNPBLUP (+10% HBS, +16%HB for milk yield and +3% HBS and +7% HB for protein yield, respectively). With the exclusion of the abovementioned cases, similar accuracies were observed using MB reference population, under the PC or SNPBLUP models. Random variation owing to sampling effect or size and composition of the reference population may explain the difficulty in finding a defined pattern in the results.     

基于主成分分析的广西省干旱时空格局

广西省地处喀斯特地貌区,土壤保水效率低,且年降水时空分布不均,研究干旱时空分布尤为重要。基于广西省1981—2010年20个气象站实测和2011—2100年HadGEM2-ES模型模拟数据,利用标准化降水指数(SPI, Standardized Precipitation Index)和标准化降水蒸散指数(SPEI,Standardized Precipitation Evapotranspiration Index),分析广西省干旱的时空变化。对不同时间尺度的SPI和SPEI应用主成分分析(PCA,Principal Component Analysis)确定干旱的空间模式,结果揭示了3个空间分布明确的区域:桂东北地区(PC1),桂西北地区(PC2)和桂南地区(PC3)。各区域干旱的时空变化和频率分布差异显著。PC1和PC3的SPEI-12呈负增长趋势,PC2的SPEI-12呈正增长趋势,且PC1、PC2和PC3的SPI-12均大于SPEI-12。年尺度(SPEI-12)上PC1和PC3的干旱频率大于PC2,其干旱频率分别为34.24%和35.83%。SPI和SPEI在空间和时间尺度...     

A combined FT-IR microscopy and principal component analysis on softwood cell walls

A combined FT-IR microscopy and principle component analysis was used to investigate chemical variations between softwood species as well as types of wood cell walls; latewood tracheids, earlywood tracheids and earlywood ray parenchyma cells. The method allowed us to detect small spectral differences between cell types rather than species and to predict characteristic chemical components of each cell type. The method enabled information to be obtained which allowed a evaluation of the polysaccharide composition even in lignified woody plant cell walls.     

On the resolving power of principal component analysis in plant community ordination

Summary A comparison between centered and non-centered principal component analysis is made on the basis of the resolving power of the methods. The results indicate the appropriateness of using a centered PCA when the aim is an ordination of plant communities, and the noncentered PCA when the aim is to elicit the taxonomic structure of a collection.Contribution from the Working Group for Data-Processing in Phytosociology, International Society for Vegetation Science.This work was supported by the Italian C.N.R. and the Centro di Calcolo dell'Università di Trieste within the framework of a broader project entitled I metodi statistici e le loro applicazioni mediante l'uso dell'elaboratore.