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At least 1,081 records · Page 60Linked to original sources
PubMed2006

Analysis of EMG patterns of control subjects and subjects with ACL deficiency during an unanticipated walking cut task.

PURPOSE: The purpose of this study was to describe the muscle activation patterns of the vastus lateralis (VL), medial hamstrings (MH) and lateral hamstrings (LH) associated with subjects that were anterior cruciate ligament (ACL) deficient and controls. METHODS: A total of 54 subjects participated in this study including 25 ACL deficient subjects subdivided into copers (n=9) and non-copers (n=16) using clinical criteria. Muscle activation patterns were recorded at 1000 Hz during an unanticipated side step cut task. The root mean square processed data (time constant 11 ms) were ensemble averaged from 20% of stance before heel strike to toe off. Using the first five harmonics of the Fourier Coefficients as features, muscle activation patterns were divided using a cluster analysis algorithm. RESULTS: A majority (76-93%) of control subjects used three muscle activation patterns for each muscle. The coper group preferentially used a particular VL and MH activation pattern >2 times more frequently than controls. The non-coper group also preferentially used a MH activation pattern >2 times more frequently than controls and utilized a unique MH and LH activation pattern, distinct from the copers and controls. CONCLUSIONS: Specific muscle activation patterns distinguish subsets of subjects that are healthy and injured, suggesting possible patterns of muscle activation that contribute to coping status.

Adaptation, Physiological↗
PubMed2004

Modeling of growing networks with directional attachment and communities.

In this paper, we propose a new network growth model and its learning algorithm to more precisely model such a real-world growing network as the Web. Unlike the conventional models, we have incorporated directional attachment and community structure for this purpose. We show that the proposed model exhibits a degree distribution with a power-law tail, which is an important characteristic of many large-scale real-world networks including the Web. Using real Web data, we experimentally show that predictive ability can be improved by incorporating directional attachment and community structure. Also, using synthetic data, we experimentally show that predictive ability can definitely be improved by incorporating community structure.

Algorithms↗
PubMedDate not supplied

New hybrid count- and geometry-based method for quantification of left ventricular volumes and ejection fraction from ECG-gated SPECT: methodology and validation.

BACKGROUND: We have previously developed a new method for quantitative assessment of left ventricular (LV) volumes and ejection fraction (EF) from electrocardiography-gated single photon emission computed tomography (SPECT). The aims of this study were to present the methodology, to validate the gated SPECT cardiac quantification (GSCQ) method in phantoms and patients, and to determine normal values of LVEF. METHODS AND RESULTS: A simple thresholding technique was used to generate binary images from nongated SPECT images. The K-means cluster classification algorithm was used to separate the LV region from non-LV regions on the binary images. A count- and geometry-based algorithm was applied to define endocardial and epicardial boundaries for calculation of LV volumes and LVEF. Overall correlation between GSCQ-quantified volumes and actual phantom volumes was good ( r = 0.97 and standard error of estimation (SEE) = 9.99 mL for normal phantoms, r = 0.99 and SEE = 6.97 mL for phantoms with defects). In patient studies, LVEF derived by GSCQ from SPECT and from equilibrium radionuclide angiography also showed good correlation ( r = 0.90 and SEE = 6.2%). The lower limit of normal LVEF from 8-frame gated SPECT by use of GSCQ was 45%. Quantification of LVEF by the GSCQ method was highly producible and was not significantly affected by the presence of myocardial perfusion defects or intense gastrointestinal activity. CONCLUSIONS: The GSCQ method provides reliable and consistent assessments of LV volumes and EF. This methodology is less affected by intense gastrointestinal activity than other methods.

Adult↗
PubMed2003

Cloning, molecular characterization, and expression analysis of Copine 8.

Copines are ubiquitously expressed, phospholipid-binding proteins that have been conserved through evolution. In this paper, we report the cloning and molecular characterization of a new member of the Copine family, Copine 8. This gene has been isolated and characterized using a combination of bioinformatic and experimental approaches. Using an algorithm to cluster ESTs (expressed sequence tags) that are available through the public "GoldenPath" database, Copine 8 was initially identified as a gene predominantly expressed in prostate and testis. Cloning and molecular analysis revealed that this gene is expressed in low-levels in most tissues examined. Two different isoforms of this gene have been isolated. Strongest expression of Copine 8 mRNA is seen in the prostate, heart, and brain. Taken together, this data suggest that Copine 8 may have an important role to play in prostate regulation and development.

Alternative Splicing↗
PubMed2000

Pattern classification by a neurofuzzy network: application to vibration monitoring.

An innovative neurofuzzy network is proposed herein for pattern classification applications, specifically for vibration monitoring. A fuzzy set interpretation is incorporated into the network design to handle imprecise information. A neural network architecture is used to automatically deduce fuzzy if-then rules based on a hybrid supervised learning scheme. The neurofuzzy classifier proposed is equipped with a one-pass, on-line, and incremental learning algorithm. This network can be considered a self-organized classifier with the ability to adaptively learn new information without forgetting old knowledge. The classification performance of the proposed neurofuzzy network is validated on the Fisher's Iris data, which is a well-known benchmark data set. For the generalization capability, the neurofuzzy network can achieve 97.33% correct classification. In addition, to demonstrate the efficiency and effectiveness of the proposed neurofuzzy paradigm, numerical simulations have been performed using the Westland data set. The Westland data set consists of vibration data collected from a US Navy CH-46E helicopter test stand. Using a simple fast Fourier transform technique for feature extraction, the proposed neurofuzzy network has shown promising results. Using various torque levels for training and testing, the network achieved 100% correct classification.

Algorithms↗
PubMed2001

Basic microarray analysis: grouping and feature reduction.

DNA microarray technologies are useful for addressing a broad range of biological problems - including the measurement of mRNA expression levels in target cells. These studies typically produce large data sets that contain measurements on thousands of genes under hundreds of conditions. There is a critical need to summarize this data and to pick out the important details. The most common activities, therefore, are to group together microarray data and to reduce the number of features. Both of these activities can be done using only the raw microarray data (unsupervised methods) or using external information that provides labels for the microarray data (supervised methods). We briefly review supervised and unsupervised methods for grouping and reducing data in the context of a publicly available suite of tools called CLEAVER, and illustrate their application on a representative data set collected to study lymphoma.

Algorithms↗
PubMed2001

Hypothalamic pituitary gonadal axis dysregulation in depressed women.

In order to examine HPG axis regulation in women with major depression, luteinizing hormone (LH) pulsativity was studied in 26 depressed and 24 normal women. Blood was sampled every 10 min for an 8-h period during the first week of their menstrual cycle. LH pulsatile release was analyzed using the computerized cluster analysis algorithm of Veldhuis and Johnson and spectral analysis. Compared to control women, depressed women had slower frequency dysrhythmic LH pulsatility. These results are consistent with a previously published pilot study which reported results of the first 23 subjects [Am. J. Psychiat. 154 (1997) 1454].

Adolescent↗
PubMed2002

Identification of individual walking patterns using time discrete and time continuous data sets.

Scientific studies typically treat data by studying effects of groups. Clinical therapy typically treats patients on a subject specific basis. Consequently, scientific and clinical attempts to help patients are often not coordinated. The purposes of this study were (a) to identify subject and group specific locomotion characteristics quantitatively, using time discrete and time continuous data and (b) to assess the advantages and disadvantages of the two approaches. Kinematic and kinetic gait pattern of 13 female subjects walking in dress shoes with different heel heights (14, 37, 54 and 85 mm) were analysed. The results of this study showed that subject specific gait characteristics could be better identified with the time continuous than with the time discrete approach. Thus, the time continuous approach using artificial networks is an effective tool for identifying subject and group specific locomotion characteristics.

Adult↗
PubMed2003

Continuous, intermitted and sporadic motor unit activity in the trapezius muscle during prolonged computer work.

The Cinderella hypothesis postulates the continuous activity of specific motor units (MUs) during low-level muscle contraction. The MUs may become metabolically overloaded, with the subject developing muscle pain and strain. The hypothesis requires MUs that are active for a time long enough to actually damage muscle fibers. The aim of this study was to determine if there are continuously active MUs in the right trapezius muscle during normal computer work using a computer mouse. Fourteen healthy subjects executed an interactive computer-learning program (ErgoLight) for 30 min. Six-channel intramuscular EMG and two-channel surface EMG signals were recorded from two positions of the trapezius muscle. Decomposition was achieved with automated, multi-channel, long-term decomposition software (EMG-LODEC). In two out of the 14 subjects, three MUs were continuously active throughout the 30 min. Although the majority of the MUs were active during only part of the experimental session, an ordered on-off behavior (e.g. substitution) pattern was not observed. As long-lasting activity was verified in some subjects, the results support the Cinderella hypothesis. However, it cannot be concluded here how long the MUs could stay active. If continuous activity overloads low threshold MUs, the potential exists for selective fibre injuries in low threshold MUs of the trapezius muscle in subjects exposed to long-term computer work.

Adult↗
PubMed2003

Characterization of sexual dimorphism in the human corpus callosum.

Despite decades of research, there is still no agreement over the presence of gender-based morphologic differences in the human corpus callosum. We approached the problem using a highly precise computational technique for shape comparison. Starting with a prospectively acquired sample of cranial MRIs of healthy volunteers (age ranges 18-84), the variations of individual callosa are quantified with respect to a reference callosum shape in the form of Jacobian determinant maps derived from the geometric transformations that map the reference callosum into anatomic alignment with the subject callosa. Voxelwise t tests performed over the determinant values demonstrated that females had a larger splenium than males (P < 0.001 uncorrected for multiple comparisons) while males possessed a larger genu (P < 0.001). In addition, pointwise Pearson plots using age as a correlate showed a different pattern of age-related changes in male and female callosa, with female splenia tending to expand more with age, while the male genu tended to contract. Our results demonstrate significant morphologic differences in the corpus callosum between genders and a possible sex difference in the neuro-developmental cycle.

Adolescent↗
PubMedDate not supplied

Automated recognition of spontaneous versus voluntary cough.

Cough or cough epochs may be an important and persistent symptom in many respiratory diseases requiring both a continuous and objective observation. The research presented in this paper is aimed at assessing a blind data-based classification between 'spontaneous' and 'voluntary' human cough on individual sound samples. Cough sounds were registered in the free acoustic field on 3 pathological and 9 healthy non-smoking subjects, all aged between 20 and 30. Each sound is represented by the normalized power spectral density (PSD). Different transformations of the cough PSD-vector are chosen as input features to the classification algorithm. An experimental error rate comparison between different neural and fuzzy classification networks is performed. All evaluated algorithms used the Euclidean metric. This resulted in a correct class-discrimination between 'spontaneous' and 'voluntary' cough for 96% of the cough database.

Acoustics↗
PubMedDate not supplied

Symplectic molecular dynamics simulations on specially designed parallel computers.

We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables the use of longer simulation time steps. The low-frequency motion is treated numerically on specially designed parallel computers, which decreases the computational time of each simulation time step. The combination of these approaches means that less time is required and fewer steps are needed and so enables fast MD simulations. We study the computational performance of MD simulation of molecular systems on specialized computers and provide a comparison to standard personal computers. The combination of the SISM with two specialized parallel computers is an effective way to increase the speed of MD simulations up to 16-fold over a single PC processor.

Algorithms↗
PubMedDate not supplied

Novel statistical approach for primary high-throughput screening hit selection.

The standard activity threshold-based method (the "top X" approach), currently widely used in the high-throughput screening (HTS) data analysis, is ineffective at identifying good-quality hits. We have proposed a novel knowledge-based statistical approach, driven by the hidden structure-activity relationship (SAR) within a screening library, for primary hit selection. Application to an in-house ultrahigh-throughput screening (uHTS) campaign has demonstrated it can directly identify active scaffolds containing valuable SAR information with a greatly improved confirmation rate compared to the standard "top X" method (from 55% to 85%). This approach may help produce high-quality leads and expedite the hit-to-lead process in drug discovery.

Algorithms↗
PubMedDate not supplied

GLARE: a new approach for filtering large reagent lists in combinatorial library design using product properties.

We present a novel computer algorithm, called GLARE (Global Library Assessment of REagents), that addresses the issue of optimal reagent selection in combinatorial library design. This program reduces or eliminates the time a medicinal chemist spends examining reagents which a priori cannot be part of a "good" library. Our approach takes the large reagent sets returned by standard chemical database queries and produces often considerably reduced reagent sets that are well-behaved with respect to a specific template. The pruning enforces "goodness" constraints such as the Lipinski rule of five on the product properties such that any reagent selection from the resulting sets produces only "good" products. The algorithm we implemented has three important features: (i) As opposed to genetic algorithms or other stochastic algorithms, GLARE uses a deterministic greedy procedure that smoothly filters out nonviable reagents. (ii) The pruning method can be biased to produce reagent sets with a balanced size, conserving proportionally more reagents in smaller sets. (iii) For very large combinatorial libraries, a partitioning scheme allows libraries as large as 10(12) to be evaluated in 0.25 s on an IBM AMD Opteron processor. This algorithm is validated on a diverse set of 12 libraries. The results that we obtained show an excellent compliance to the product property requirements and very fast timings.

Algorithms↗
PubMed2004

Mechanisms for gas adsorption and desorption in silica aerogels: the effect of temperature.

We present a theoretical study of the adsorption and desorption mechanisms of fluids in silica aerogels, focusing on the effect of temperature. We adopt a coarse-grained lattice description in which the gel structure is generated by a diffusion-limited cluster-cluster aggregation algorithm and the fluid configurations are computed using local mean-field (i.e., density functional) theory. Our calculations reproduce qualitatively the changes in the shape of the hysteresis loops observed with (4)He in gels of varying porosity. We study in detail the morphology of the condensation and evaporation events that correspond to the irreversible processes (avalanches) which are at the origin of the hysteresis. Depending on porosity and temperature, these avalanches may be localized, involve regions that extend beyond the gel correlation length, or even span the entire sample. This makes difficult the characterization of aerogels based on analyzing sorption isotherms.

Adsorption↗
PubMed1997

Dependence estimation for marginal models of multivariate survival data.

We have previously (Segal and Neuhaus, 1993) devised methods for obtaining marginal regression coefficients and associated variance estimates for multivariate survival data, using a synthesis of the Poisson regression formulation for univariate censored survival analysis and generalized estimating equations (GEE's). The method is parametric in that a baseline survival distribution is specified. Analogous semiparametric models, with unspecified baseline survival, have also been developed (Wei, Lin and Weissfeld, 1989; Lin, 1994). Common to both these approaches is the provision of robust variances for the regression parameters. However, none of this work has addressed the more difficult area of dependence estimation. While GEE approaches ostensibly provide such estimates, we show that there are problems adopting these with multivariate survival data. Further, we demonstrate that these problems can affect estimation of the regression coefficients themselves. An alternate, ad hoc approach to dependence estimation, based on design effects, is proposed and evaluated via simulation and illustrative examples.

Algorithms↗
PubMed2004

Genomic portraits of the nervous system in health and disease.

As the human genome project moves toward its goal of sequencing the entire human genome, gene expression profiling by DNA microarray technology is being employed to rapidly screen genes for biological information. In this review, we will introduce DNA microarray technology, outline the basic experimental paradigms and data analysis methods, and then show with some examples how gene expression profiling can be applied to the study of the central nervous system in health and disease.

Algorithms↗