High density electromyography data of normally limbed and transradial amputee subjects for multifunction prosthetic control

Pattern recognition based control of powered upper limb myoelectric prostheses offers a means of extracting more information from the available muscles than conventional methods. By identifying repeatable patterns of muscle activity across multiple muscle sites rather than relying on independent EMG signals it is possible to provide more natural, reliable control of myoelectric prostheses. The purposes of this study were to (1) determine if participants can perform distinctive muscle activation patterns associated with multiple wrist and hand movements reliably and (2) to show that high density EMG can be applied individually to determine the electrode location of a clinically acceptable number of electrodes (maximally eight) to classify multiple wrist and hand movements reliably in transradial amputees. Eight normally limbed subjects (five female, three male) and four transradial amputee subjects (two traumatic and congenital) subjects participated in this study, which examined the classification accuracies of a pattern recognition control system. It was found that tasks could be classified with high accuracy (85-98%) with normally limbed subjects (10-13 tasks) and with amputees (4-6) tasks. In healthy subjects, reducing the number of electrodes to eight did not affect accuracy significantly when those electrodes were optimally placed, but did reduce accuracy significantly when those electrodes were distributed evenly. In the amputee subjects, reducing the number of electrodes up to 4 did not affect classification accuracy or the number of tasks with high accuracy, independent of whether those remaining electrodes were evenly distributed or optimally placed. The findings in healthy subjects suggest that high density EMG testing is a useful tool to identify optimal electrode sites for pattern recognition control, but its use in amputees still has to be proven. Instead of just identifying the electrode sites where EMG activity is strong, clinicians will be able to choose the electrode sites that provide the most important information for classification.     

Linking xylem diameter variations with sap flow measurements

Measurements of variation in the diameter of tree stems provide a rapid response, high resolution tool for detecting changes in water tension inside the xylem. Water movement inside the xylem is caused by changes in the water tension and theoretically, the sap flow rate should be directly proportional to the water tension gradient and, therefore, also linearly linked to the xylem diameter variations. The coefficient of proportionality describes the water conductivity and elasticity of the conducting tissue. Xylem diameter variation measurements could thus provide an alternative approach for estimating sap flow rates, but currently we lack means for calibration. On the other hand, xylem diameter variation measurements could also be used as a tool for studying xylem structure and function. If we knew both the water tension in the xylem and the sap flow rate, xylem conductivity and/or elasticity could be calculated from the slope of their relationship. In this study we measured diurnal xylem diameter variation simultaneously with sap flow rates (Granier-type thermal method) in six deciduous species (Acer rubrum L., Alnus glutinosa Miller, Betula lenta L., Fagus Sylvatica L. Quercus rubra L., and Tilia vulgaris L.) for 7–91 day periods during summers 2003, 2005 and 2006 and analyzed the relationship between these two measurements. We found that in all species xylem diameter variations and sap flow rate were linearly related in daily scale (daily average R ² = 0.61–0.87) but there was a significant variation in the daily slopes of the linear regressions. The largest variance in the slopes, however, was found between species, which is encouraging for finding a species specific calibration method for measuring sap flow rates using xylem diameter variations. At a daily timescale, xylem diameter variation and sap flow rate were related to each other via a hysteresis loop. The slopes during the morning and afternoon did not differ statistically significantly from each other, indicating no overall change in the conductivity. Because of the variance in the daily slopes, we tested three different data averaging methods to obtain calibration coefficients. The performance of the averaging methods depended on the source of variance in the data set and none of them performed best for all species. The best estimates of instantaneous sap flow rates were also given by different averaging methods than the best estimates of total daily water use. Using the linear relationship of sap flow rate and xylem diameter variations we calculated the conductance and specific conductivity of the soil–xylem–atmosphere water pathway. The conductance were of the order of magnitude 10⁻⁵ kg s⁻¹ MPa⁻¹ for all species, which compares well with measured water fluxes from broadleaved forests. Interestingly, because of the large sap wood area the conductance of Betula was approximately 10 times larger than in other species.     

Applications of species accumulation curves in large-scale biological data analysis

The species accumulation curve, or collector’s curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional sampling. Traditional applications have focused on ecological populations but emerging large-scale applications, for example in DNA sequencing, are orders of magnitude larger and present new challenges. We developed a method to estimate accumulation curves for predicting the complexity of DNA sequencing libraries. This method uses rational function approximations to a classical non-parametric empirical Bayes estimator due to Good and Toulmin [Biometrika, 1956, 43, 45–63]. Here we demonstrate how the same approach can be highly effective in other large-scale applications involving biological data sets. These include estimating microbial species richness, immune repertoire size, and k-mer diversity for genome assembly applications. We show how the method can be modified to address populations containing an effectively infinite number of species where saturation cannot practically be attained. We also introduce a flexible suite of tools implemented as an R package that make these methods broadly accessible.     

Anticipating clinical resistance to target-directed agents : the BCR-ABL paradigm

The deregulated tyrosine kinase activity of BCR-ABL is necessary and sufficient to induce chronic myelogenous leukemia (CML). This observation has paved the way for the development of small-molecule inhibitors specifically targeting the kinase activity of the BCR-ABL protein. Indeed, the amazing success of imatinib has revolutionized the whole area of targeted cancer therapeutics. However, enthusiasm for the striking efficacy of imatinib has been tempered by the development of clinical resistance. In essentially all cases, resistance results from kinase domain mutations and/or overexpression of the BCR-ABL gene. To overcome resistance, several novel BCR-ABL inhibitors have been developed and are in clinical trials, though it is inevitable that resistance to second-generation inhibitors will occur as well. Nonetheless, kinases represent an attractive target for therapeutic intervention in several diseases and, at present, some 50 different kinase inhibitors are in clinical trials. We anticipate that resistance to these compounds will follow mechanisms similar to those observed with imatinib. Resistance mutations cause their effect either by direct steric hindrance to drug binding or by allosterically modulating kinase dynamics. This review highlights the principal mechanisms underlying point mutations from these two different classes to confer drug resistance.     

Apparent opposing effects of cyclic AMP and dibutyryl cyclic GMP on the neuronal firing of the blowfly chemo-receptors.

Cyclic AMP and its dibutyryl derivative inhibit neuronal firing of the labellar sugar sensitive receptor of the blowfly when applied in conjunction with the stimulant sucrose. Furthermore, simultaneous application of aminophylline (phosphodieterase inhibitor) and sucrose or in combination with cyclic AMP caused a similar depression of the sugar receptors response. In contrast, dibutyryl cyclic GMP elicited an increase in sugar receptor firing when applied with sucrose to sugar receptor. Either 5'-AMP or 5'-GMP in combination with sucrose had no discernable effect on the sugar receptors response. Different ratio combinations of cyclic AMP and dibutyryl cyyclic GMP showed the striking inhibitory effect of cyclic AMP upon the dibutyryl cyclic GMP elicited increases in receptor firing frequency. Therefore, it is suggested that these two nucleotides may be mediating different but complimentary aspects of sugar receptor function in a push-pull manner.     

Human thymocyte maturation in vitro: a flow cytometric analysis

Using an in vitro culture system, light scatter analyses, and two-color flow cytometry, we provide evidence that the interleukin-2 (IL-2) and transferrin receptors can be induced within 48 hr on nonproliferating immature thymocytes. The thymocytes (greater than 35%) that expressed the transferrin and IL-2 receptors demonstrated nuclear activation as measured by log 90 degrees light scatter analysis. Increases in antigen-receptor-associated T3-antigen expression followed transferrin and IL-2-receptor induction and occurred on maximally activated T4+T8+ thymocytes on Day 3 of culture. Maximal T3 expression did not occur until Days 5-7 and paralleled loss of T4, T8 coexpression, suggesting an association between a mature T3-Ti antigen receptor complex and a mature T4, T8 phenotype.     

Human kallikrein 6 expression in salivary gland tumors.

Human kallikrein 6 (hK6), also known as zyme/protease M/neurosin), is expressed in many normal glandular tissues. The aim of this study was to determine whether hK6 is expressed in salivary gland tissues and salivary gland tumors (both benign and malignant), using an immunohistochemical method. Pleomorphic adenomas (PA), adenoid cystic carcinomas, polymorphous low-grade adenocarcinomas, acinic cell carcinomas, mucoepidermoid carcinomas, and adenocarcinomas not otherwise specified of both minor and major salivary glands were examined. Cells lining duct-like structures and non-duct-like cells were scored. Only in PA of minor salivary gland origin was overall staining higher in duct-like than in non-duct-like cells. In all other tumors exhibiting both types of cells, hK6 staining was similar in both duct-like and non-duct-like cells. Tumors that exhibited non-duct-like cells only also exhibited cytoplasmic staining. Results of this study show that salivary gland tumors express hK6, apparently downregulated in comparison with normal salivary gland tissue, and that this expression is not specific for any of the tumors studied.