Changes in interface pressures and shear stresses over time on trans-tibial amputee subjects ambulating with prosthetic limbs: comparison of diurnal and six-month differences

For trans-tibial amputees maintenance over time of a quality fit of the prosthesis to the residual limb is an important clinical challenge. The purpose of this research was to compare diurnal and long-term (5 weeks to 6 months) interface stress changes as well as variance in the change in cross-sectional area down the length of the residual limb. If long-term changes were simply accentuated diurnal fluctuations then this result would suggest similar treatment methods should be used for both conditions. Interface pressures and shear stresses at 13 sites and residual limb shape were measured on eight trans-tibial amputee subjects using patellar-tendon-bearing prostheses. Data were collected at diurnal intervals (within the same day at least 5 h apart) as well as at long-term intervals (5, 10, 15, 20, and 25 weeks apart). Absolute diurnal interface stress changes were not significantly different from those at 5-weeks intervals but were significantly smaller than those at 15, 20, and 25-weeks intervals. Mean interface stress changes increased significantly (p<0.05) for increased session-to-session intervals. Variance of the change in cross-sectional area down the length of the residual limb was significantly smaller for diurnal intervals than for 6-months intervals, indicating that long-term changes were more localized than diurnal changes. These results indicate that long-term changes are not simply accentuated diurnal fluctuations, suggesting that different treatment methods should be used to treat each condition.     

Visualize: a free and open source multifunction tool for proteomics data analysis

A major challenge in the field of high-throughput proteomics is the conversion of the large volume of experimental data that is generated into biological knowledge. Typically, proteomics experiments involve the combination and comparison of multiple data sets and the analysis and annotation of these combined results. Although there are some commercial applications that provide some of these functions, there is a need for a free, open source, multifunction tool for advanced proteomics data analysis. We have developed the Visualize program that provides users with the abilities to visualize, analyze, and annotate proteomics data; combine data from multiple runs, and quantitate differences between individual runs and combined data sets. Visualize is licensed under GNU GPL and can be downloaded from http://proteomics.mcw.edu/visualize. It is available as compiled client-based executable files for both Windows and Mac OS X platforms as well as PERL source code.     

A physiological basis for control of a prosthetic hand

Recent surveys from upper limb amputees indicate the sentiment that prosthetic hands do not function in a life-like manner and are not intuitively controlled. Thus, two methods of control for a prosthetic hand are presented. A proportional derivative (PD) force controller is compared to a novel biomimetic application of sliding mode control. The biomimetic sliding mode (BSM) controller was designed to map human muscle signals into prosthesis motor command signals in a physiologically expected manner.The BSM and PD controllers were evaluated analytically and subjectively by one amputee and nine nonamputee test subjects. The posture of the hands of the nonamputee test subjects were measured with a CyberGlove and used to determine if the position of the prosthesis (when driven by both controllers) was highly correlated to the posture of the human hands. Force tracking experiments were also performed by all test subjects with both controllers to evaluate the ability to control the applied force. Finally, a dual object lifting task was performed by all test subjects to determine if the mapping of electromyogram (EMG) signals with the BSM controller resulted in physiologically expected motions. A nonparametric Mann–Whitney U-test was performed on the subjective evaluations to determine the statistical significance of the evaluations.The BSM controller was shown to replicate the posture of the human hand much more accurately than the PD force controller. The BSM controller also enabled better average force tracking results and higher success rates with the dual object lifting experiment while the same task was nearly impossible to perform with the PD controller. Finally, the BSM controller was subjectively rated to be more similar to control in comparison to the human hand with respect to position and force.     

Modeling and optimal control of an energy-storing prosthetic knee

Advanced prosthetic knees for transfemoral amputees are currently based on controlled damper mechanisms. Such devices require little energy to operate, but can only produce negative or zero joint power, while normal knee joint function requires alternative phases of positive and negative work. The inability to generate positive work may limit the user's functional capabilities, may cause undesirable adaptive behavior, and may contribute to excessive metabolic energy cost for locomotion. In order to overcome these problems, we present a novel concept for an energy-storing prosthetic knee, consisting of a rotary hydraulic actuator, two valves, and a spring-loaded hydraulic accumulator. In this paper, performance of the proposed device will be assessed by computational modeling and by simulation of functional activities. A computational model of the hydraulic system was developed, with methods to obtain optimal valve control patterns for any given activity. The objective function for optimal control was based on tracking of joint angles, tracking of joint moments, and the energy cost of operating the valves. Optimal control solutions were obtained, based on data collected from three subjects during walking, running, and a sit-stand-sit cycle. Optimal control simulations showed that the proposed device allows near-normal knee function during all three activities, provided that the accumulator stiffness was tuned to each activity. When the energy storage mechanism was turned off in the simulations, the system functioned as a controlled damper device and optimal control results were similar to literature data on human performance with such devices. When the accumulator stiffness was tuned to walking, simulated performance for the other activities was sub-optimal but still better than with a controlled damper. We conclude that the energy-storing knee concept is valid for the three activities studied, that modeling and optimal control can assist the design process, and that further studies using human subjects are justified.     

High affinity beta-2-adrenergic receptors in mononuclear leucocytes: similar density in young and old normal subjects

In normal subjects beta-adrenergic responsiveness in the cardiovascular system has been shown to be impaired with increasing age. In order to correlate reduced hormonal responsiveness to an age-related defect at the receptor level, high affinity beta-adrenergic receptors in homogenates of human mononuclear leucocytes have been studied with a (?)-³H-dihydroalprenolol (³H-DHA) binding assay. The binding sites have been characterized by rapid kinetics, saturability, structural and sterospecificity. Binding equilibrium was obtained within 16 minutes at 37° and was reversed by 50% within 10.6 minutes. In 22 healthy subjects a binding capacity of 60 ± 8 fmol/mg protein and an equilibrium dissociation constant (K_D) of 0.6 ± 0.05 nM was found. Beta-adrenergic agonists displaced ³H-DHA binding with a potency order of isoproterenol > adrenaline > noradrenaline. The (?) isomers of beta-adrenergic agonists and antagonists were one to two orders of magnitude more potent as inhibitors of ³H-DHA binding than their corresponding (+) isomers. The binding capacity and affinity of the beta-adrenergic receptors did not differ in old, as compared to young normal subjects. Leucocytes from 14 individuals 18–40 years old had an average density of 53 ± 4 fmol/mg protein, while the average density in leucocytes from 8 individuals aged 53–65 years was 67 ± 8 fmol/mg protein. The K_D was 0.6 ± 0.05 nM in both groups. In conclusion, an age-related decrease of beta-adrenergic receptor-mediated cardiovascular functions does not seem to be reflected in the properties of beta-adrenergic receptors of mononuclear leucocytes.     

Time-dependent power spectral density estimation of surface electromyography during isometric muscle contraction: Methods and comparisons

This paper studies the time-dependent power spectral density (PSD) estimation of nonstationary surface electromyography (SEMG) signals and its application to fatigue analysis during isometric muscle contraction. The conventional time-dependent PSD estimation methods exhibit large variabilities in estimating the instantaneous SEMG parameters so that they often fail to identify the changing patterns of short-period SEMG signals and gauge the extent of fatigue in specific muscle groups. To address this problem, a time-varying autoregressive (TVAR) model is proposed in this paper to describe the SEMG signal, and then the recursive least-squares (RLS) and basis function expansion (BFE) methods are used to estimate the model coefficients and the time-dependent PSD. The instantaneous parameters extracted from the PSD estimation are evaluated and compared in terms of reliability, accuracy, and complexity. Experimental results on synthesized and real SEMG data show that the proposed TVAR-model-based PSD estimators can achieve more stable and precise instantaneous parameter estimation than conventional methods.     

Design and evaluation of control strategies for high cell density fermentations

A methodology for the design and evalution of bioprocess control strategies is presented. The strategies manage nutrient supply with demand and vary with the metabolic condition and phase of fermentation operation. Six carbon source addition strategies are based on different combinations of available measurements; they are described and evaluated under different operating conditions for yeast cultivation. It is concluded that a single control strategy is not the most appropriate under all possible operating conditions. An oxygen uptake rate-based control strategy performs better with a mean respiratory quotient (RQ) value less than 1.1 during an oxygen limitation than an ethanol control strategy which had a mean RQ of 14. The designed strategies and an approach of applying the strategy that best matches fermentation conditions consistently enables achievement of high cell densities 78.7 g DCW/L and yields 0.50 g DCW/g glucose as the mean values for three fermentations.     

High cell density and high monoclonal antibody production through medium design and rational control in a bioreactor

A simple feeding strategy was developed and successfully employed for nutritional control in a 2-L fed-batch culture of hybridoma cells. A previously developed stoichiometric model for animal cell growth was used to design a supplemental medium for feeding. Undialyzed fetal bovine serum and trace metals (Fe(2+), SeO(3) (2-), Li(+), Zn(2+), and Cu(2+)) were fed to the cells periodically in addition to the automatic feeding of other nutrients in the supplemental medium. In this study, the maximum viable cell density was increased from 6.3 x 10(6) to 1.7 x 10(7) cells/mL, and the culture span was extended from 340 to 550 hours. The final monoclonal antibody titer achieved was 2400 mg/L. The specific production rates for ammonia and lactate were further reduced from 0.0045 and 0.0048 in our previous fed-batch experiments to 0.0028 and 0.0036 mmol/10(9) cell h, respectively. Only 3.4% of the total glucose consumption was converted into lactate, compared to 67% in a conventional batch culture.     

Probability density functions useful for parametrization of heterogeneity in growth and allometry data

This paper addresses the problem of modelling heterogeneous individual characteristics in a population. A flexible unified approach for stochastic parametrization dynamics of the distribution in population data is proposed. To approximate data with multiple observations per individual, models based on Markov processes are constructed. The method can be applied to scalar or multivariate characteristics, and its application to growth and allometry data is considered. Different stochastic versions of known growth and allometry functions are developed, which enable wide applicability. Simple informative growth indices are calculated as the moments of distribution. The three-parameter Gompertz growth model for size-at-age data was reparametrized to a size-increment data model with two parameters. An erratum to this article is available at .     

Performance assessment of kernel density clustering for gene expression profile data

Kernel density smoothing techniques have been used in classification or supervised learning of gene expression profile (GEP) data, but their applications to clustering or unsupervised learning of those data have not been explored and assessed. Here we report a kernel density clustering method for analysing GEP data and compare its performance with the three most widely-used clustering methods: hierarchical clustering, K-means clustering, and multivariate mixture model-based clustering. Using several methods to measure agreement, between-cluster isolation, and withincluster coherence, such as the Adjusted Rand Index, the Pseudo F test, the r(2) test, and the profile plot, we have assessed the effectiveness of kernel density clustering for recovering clusters, and its robustness against noise on clustering both simulated and real GEP data. Our results show that the kernel density clustering method has excellent performance in recovering clusters from simulated data and in grouping large real expression profile data sets into compact and well-isolated clusters, and that it is the most robust clustering method for analysing noisy expression profile data compared to the other three methods assessed.     

Likelihood-based association analysis for nuclear families and unrelated subjects with missing genotype data

Missing data occur in genetic association studies for several reasons including missing family members and uncertain haplotype phase. Maximum likelihood is a commonly used approach to accommodate missing data, but it can be difficult to apply to family-based association studies, because of possible loss of robustness to confounding by population stratification. Here a novel likelihood for nuclear families is proposed, in which distinct sets of association parameters are used to model the parental genotypes and the offspring genotypes. This approach is robust to population structure when the data are complete, and has only minor loss of robustness when there are missing data. It also allows a novel conditioning step that gives valid analysis for multiple offspring in the presence of linkage. Unrelated subjects are included by regarding them as the children of two missing parents. Simulations and theory indicate similar operating characteristics to TRANSMIT, but with no bias with missing data in the presence of linkage. In comparison with FBAT and PCPH, the proposed model is slightly less robust to population structure but has greater power to detect strong effects. In comparison to APL and MITDT, the model is more robust to stratification and can accommodate sibships of any size. The methods are implemented for binary and continuous traits in software, UNPHASED, available from the author.     

Chronobiological aspects of TSH secretion in control subjects and in subjects with primary hypothyroidism

The circadian rhythm in plasma TSH concentration was demonstrated in euthyroid subjects and in treated hypothyroid patients. Our results suggest that two hypothalamic areas, involved in TRH secretion, are responsables in basal as well impulsive pituitary TSH dismission.     

Planning of distributed data production for High Energy and Nuclear Physics

Modern experiments in High Energy and Nuclear Physics heavily rely on distributed computations using multiple computational facilities across the world. One of the essential types of the computations is a distributed data production where petabytes of raw files from a single source has to be processed once (per production campaign) using thousands of CPUs at distant locations and the output has to be transferred back to that source. The data distribution over a large system does not necessary match the distribution of storage, network and CPU capacity. Therefore, bottlenecks may appear and lead to increased latency and degraded performance. In this paper we propose a new scheduling approach for distributed data production which is based on the network flow maximization model. In our approach a central planner defines how much input and output data should be transferred over each network link in order to maximize the computational throughput. Such plans are created periodically for a fixed planning time interval using up-to-date information on network, storage and CPU resources. The centrally created plans are executed in a distributed manner by dedicated services running at participating sites. Our simulations based on the log records from the data production framework of the experiment STAR (Solenoid Tracker at RHIC) have shown that the proposed model systematically provides a better performance compared to the simulated traditional techniques.     

Biomarkers of oxidative stress in schizophrenic and control subjects

Increasing evidence indicates that oxidative injury exists in schizophrenia. Although it may not be the main cause, oxidative damage has been suggested to contribute to the pathophysiology and may account for deteriorating course and poor outcome in schizophrenia. A human study was undertaken, therefore, to investigate possible differences in biomarkers of DNA, lipid and protein oxidation in schizophrenic (n=16) and control subjects (n=17). Plasma vitamin C levels were also compared in both groups. Cellular DNA damage and plasma protein carbonyl levels were increased in the schizophrenic group compared to control subjects but not significantly. However, DNA damage in lymphocytes from the male schizophrenic group was significantly higher than the female group. Biomarkers of lipid peroxidation and plasma vitamin C levels also revealed no significant difference between the two groups under investigation, although a significant elevation in plasma vitamin C was observed in the female control group when compared to the male groups.     

Human movement data for malaria control and elimination strategic planning

ABSTRACT: Recent increases in funding for malaria control have led to the reduction in transmission in many malaria endemic countries, prompting the national control programmes of 36 malaria endemic countries to set elimination targets. Accounting for human population movement (HPM) in planning for control, elimination and post-elimination surveillance is important, as evidenced by previous elimination attempts that were undermined by the reintroduction of malaria through HPM. Strategic control and elimination planning, therefore, requires quantitative information on HPM patterns and the translation of these into parasite dispersion. HPM patterns and the risk of malaria vary substantially across spatial and temporal scales, demographic and socioeconomic sub-groups, and motivation for travel, so multiple data sets are likely required for quantification of movement. While existing studies based on mobile phone call record data combined with malaria transmission maps have begun to address within-country HPM patterns, other aspects remain poorly quantified despite their importance in accurately gauging malaria movement patterns and building control and detection strategies, such as cross-border HPM, demographic and socioeconomic stratification of HPM patterns, forms of transport, personal malaria protection and other factors that modify malaria risk. A wealth of data exist to aid filling these gaps, which, when combined with spatial data on transport infrastructure, traffic and malaria transmission, can answer relevant questions to guide strategic planning. This review aims to (i) discuss relevant types of HPM across spatial and temporal scales, (ii) document where datasets exist to quantify HPM, (iii) highlight where data gaps remain and (iv) briefly put forward methods for integrating these datasets in a Geographic Information System (GIS) framework for analysing and modelling human population and Plasmodium falciparum malaria infection movements.     

Evidence for natural horizontal transfer of tetQ between bacteria that normally colonize humans and bacteria that normally colonize livestock.

Though numerous studies have shown that gene transfer occurs between distantly related bacterial genera under laboratory conditions, the frequency and breadth of horizontal transfer events in nature remain unknown. Previous evidence for natural intergeneric transfers came from studies of genes in human pathogens, bacteria that colonize the same host. We present evidence that natural transfer of a tetracycline resistance gene, tetQ, has occurred between bacterial genera that normally colonize different hosts. A DNA sequence comparative approach was taken to examine the extent of horizontal tetQ dissemination between species of Bacteroides, the predominant genus of the human colonic microflora, and between species of Bacteroides and of the distantly related genus Prevotella, a predominant genus of the microflora of the rumens and intestinal tracts of farm animals. Virtually identical tetQ sequences were found in a number of isolate pairs differing in taxonomy and geographic origin, indicating that extensive natural gene transmission has occurred. Among the exchange events indicated by the evidence was the very recent transfer of an allele of tetQ usually found in Prevotella spp. to a Bacteroides fragilis strain.