A general solution for the time delay introduced by a low-pass Butterworth digital filter: An application to musculoskeletal modeling

Low-pass Butterworth digital filters are commonly used in biomechanics-related research. In general, the input signal is filtered in the forward and reverse directions so that a temporal shift in the output signal does not occur. There are times, however, when introducing a specific time delay is an important consideration when modeling a physiological event. Filtering the data in the forward direction only can be used as an efficient method to account for a specific time delay. Specific delays are possible by carefully selecting the filter order and cut-off frequency. The purpose of this paper is to present the analytical formulation of a general solution for the time delay introduced by a low-pass Butterworth digital filter.     

Adaptive filter model of the cerebellum

The Marr-Albus model of the cerebellum has been reformulated with linear system analysis. This adaptive linear filter model of the cerebellum performs a filtering action of a phase lead-lag compensator with learning capability, and will give an account for the phenomena which have been termed cerebellar compensation. It is postulated that a Golgi cell may act as a phase lag element; for example, as a leaky integrator with time constant about several seconds. Under this assumption, a mossy fiber-granule cell-Golgi cell input network functions as a phase lead-lag compensator. Output signals from Golgi-granule cell systems, namely, parallel fiber signals, are gathered together through variable synaptic connections to form a Purkinje cell output. From a general theory of adaptive linear filters, learning principles for these modifiable connections are derived. By these learning principles, a Purkinje cell output converges to the desired response to minimize the mean square error of the performance. In a more general sense, a Purkinje cell acquires a filtering function on the basis of multiple pairs of input signals and corresponding desired output signals. The mode of convergence of the output signal is described when the input signal is sinusoidal.     

Adaptive filter mechanisms in human vision

As a result of our experiments we find that the absolute visibility of simple edge and bar patterns is determined by a cooperation between the maximum amplitude and the difference between the maximum gradients occurring in the patterns. Proceeding from the assumption that the second spatial derivative represents a basic mechanism in our visual system (Mach-bands, effects of masking between narrow lines and sharp edges, existence of even-symmetrical receptive fields in the retina and the LGN), we suggest a nonlinear summation device which produces the difference between gradients as a sum over the second derivative. Expressed in a slightly different manner we assume that the sum over the excitation embodied in a Mach-band acts as criterion during the absolute visibility of edge and bar patterns.     

Adaptive basis of codon usage in the haploid moss Physcomitrella patens

Patterns of codon usage bias were studied in the moss model species Physcomitrella patens. A total of 92 nuclear, protein coding genes were employed, and estimated levels of gene expression were tested for association with two measures of codon usage bias and other variables hypothesized to be associated with gene expression. Codon bias was found to be positively associated both with estimated levels of gene expression and GC content in the coding parts of studied genes. However, GC content in noncoding parts, that is, introns and 5' and 3' untranslated regions (UTRs), was not associated with estimated levels of gene expression. It is argued that codon bias is not shaped by mutational bias, but rather by weak natural selection for translational efficiency in P. patens. The possible role of life history characteristics in shaping patterns of codon usage in this species is discussed.     

Spectral analysis of flow cytometric data: design of a special-purpose low-pass digital filter

Spectral decomposition of flow cytometric datafiles of arbitrary dimension reveal information of both the signal and the noise components that constitute the histograms. This spectral information is used to construct a low-pass digital filter, which removes the high-frequency noise from the actual data. It is shown that this procedure guarantees non-trivial smoothing of the flow cytometric data in accordance with the local experimental situation. As a consequence optimal reconstruction of the signal is possible, which facilitates unambiguous interpretation of the data files and mathematical estimation of the statistical parameters.     

Codon usage divergence of homologous vertebrate genes and codon usage clock

Summary This paper is concerned with the divergence of synonymous codon usage and its bias in three homologous genes within vertebrate species. Genetic distances among species are described in terms of synonymous codon usage divergence and the correlation is found between the genetic distances and taxonomic distances among species under study. A codon usage clock is reported in alphaglobin and beta-globin. A method is developed to define the synonymous codon preference bias and it is observed that the bias changes considerably among species.     

Adaptation of the tendon to mechanical usage

Tendons primarily function as contractile force transmitters, but their mechanical properties may change dependent upon their level of mechanical usage. Using an ultrasound-based technique we have assessed tendon mechanical properties in vivo in a number of conditions representing different levels of mechanical usage. Ageing alters tendon mechanical properties; stiffness and modulus were lower in older adults by 10 and 14%, respectively, compared to young adults. Increased levels of exercise loading in old age can however partly reverse this process, as tendon stiffness and modulus were found to increase by 65 and 69%, respectively. Complete unloading due to bed rest or spinal cord injury both reduce tendon stiffness and modulus, however, only chronic unloading due to spinal cord injury seems to cause tendon atrophy. Alterations in tendon mechanical properties due to changes in the levels loading have implications for the speed of force transmission, the muscle's operating range and the likelihood of tendon strain injury.     

On the usage and measurement of landscape connectivity

This paper examines the usage and measurement of "landscape connectivity" in 33 recent studies. Connectivity is defined as the degree to which a landscape facilitates or impedes movement of organisms among resource patches. However, connectivity is actually used in a variety of ways in the literature. This has led to confusion and lack of clarity related to (1) function vs structure, (2) patch isolation vs landscape connectivity and, (3) corridors vs connectivity. We suggest the term connectivity should be reserved for its original purpose. We highlight nine studies; these include modeling studies that actually measured connectivity in accordance with the definition, and empirical studies that measured key components of connectivity. We found that measurements of connectivity provide results that can be interpreted as recommending habitat fragmentation to enhance landscape connectivity. We discuss reasons for this misleading conclusion, and suggest a new way of quantifying connectivity, which avoids this problem. We also recommend a method for reducing sampling intensity in landscape-scale empirical studies of connectivity.     

流式细胞仪在生物学中的应用

简要论述了流式细胞仪（flow cytometry,FCM）的工作原理,并对其在生物学基础科学研究中的应用进行阐述,包括对细胞凋亡、细胞周期、免疫细胞、细胞受体的研究应用。     

Synonymous codon usage in Thermosynechococcus elongatus (cyanobacteria) identifies the factors shaping codon usage variation

Analysis of synonymous codon usage pattern in the genome of a thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1 using multivariate statistical analysis revealed a single major explanatory axis accounting for codon usage variation in the organism. This axis is correlated with the GC content at third base of synonymous codons (GC3s) in correspondence analysis taking T. elongatus genes. A negative correlation was observed between effective number of codons i.e. Nc and GC3s. Results suggested a mutational bias as the major factor in shaping codon usage in this cyanobacterium. In comparison to the lowly expressed genes, highly expressed genes of this organism possess significantly higher proportion of pyrimidine-ending codons suggesting that besides, mutational bias, translational selection also influenced codon usage variation in T. elongatus. Correspondence analysis of relative synonymous codon usage (RSCU) with A, T, G, C at third positions (A3s, T3s, G3s, C3s, respectively) also supported this fact and expression levels of genes and gene length also influenced codon usage. A role of translational accuracy was identified in dictating the codon usage variation of this genome. Results indicated that although mutational bias is the major factor in shaping codon usage in T. elongatus, factors like translational selection, translational accuracy and gene expression level also influenced codon usage variation.     

Another usage of autotomized penis

Journal of Ethology - We described and compared the mating behavior and morphology of the reproductive system in chromodorid nudibranchs, then, examined how extensively the unique usage of the...     

Different usage of the glycosaminoglycan attachment sites of biglycan

Biglycan is a member of the small leucine-rich proteoglycan family. Its core protein comprises two chondroitin/dermatan sulfate attachment sites on serine 42 and serine 47, respectively, which are the fifth and tenth amino acid residues, respectively, after removal of the prepro peptide. Because the regulation of glycosaminoglycan chain assembly is not fully understood and because of the in vivo existence of monoglycanated biglycan, mutant core proteins were stably expressed in human 293 and Chinese hamster ovary cells in which i) either one or both serine residues were converted into alanine or threonine residues, ii) the number of acidic amino acids N-terminal of the respective serine residues was altered, and iii) a hexapeptide was inserted between the mutated site 1 and the unaltered site 2. Labeling experiments with [(35)S]sulfate and [(35)S]methionine indicated that serine 42 was almost fully used as the glycosaminoglycan attachment site regardless of whether site 2 was available or not for chain assembly. In contrast, substitution of site 2 was greatly influenced by the presence or absence of serine 42, although additional mutations demonstrated a direct influence of the amino acid sequence between the two sites. When site 2 was not substituted with a glycosaminoglycan chain, there was also no assembly of the linkage region. These results indicate that xylosyltransferase is the rate-limiting enzyme in glycosaminoglycan chain assembly and implicate a cooperative effect on the xylosyl transfer to site 2 by xylosylation of site 1, which probably becomes manifest before the removal of the propeptide. It is shown additionally that biglycan expressed in 293 cells may still contain the propeptide sequence and may carry heparan sulfate chains as well as sulfated N-linked oligosaccharides.     

Alternative promoter usage of the membrane glycoprotein CD36

Background  

The premature aging and cancer-prone Werner and Bloom syndromes are caused by defects in the RecQ helicase enzymes WRN and BLM, respectively. Recently, both WRN and BLM (as well as several other RecQ members) have been shown to possess a strand annealing activity in addition to the requisite DNA unwinding activity. Since an annealing function would appear to directly oppose the action of a helicase, we have examined in this study the dynamic equilibrium between unwinding and annealing mediated by either WRN or BLM.     

Species-specific differences in the usage of several caspase substrates

The activation of caspases cleaving a plethora of specific substrates is pivotal for initiation as well as execution of apoptosis. The recognition motif for caspases is a tetrapeptide sequence containing an essential aspartic acid residue at the fourth position (often DXXD). Here, we report that the caspase cleavage sites of most identified substrates show a high degree of conservation between different species. However, we have identified differences in the cleavage sites of five substrates between murine and human proteins leading to either select processing in only one species or to different cleavage patterns. Finally, we provide evidence that murine c-Abl but not its human homolog serves as efficient substrate during apoptosis.     

Alternative promoter usage of the membrane glycoprotein CD36

Background  

CD36 is a membrane glycoprotein involved in a variety of cellular processes such as lipid transport, immune regulation, hemostasis, adhesion, angiogenesis and atherosclerosis. It is expressed in many tissues and cell types, with a tissue specific expression pattern that is a result of a complex regulation for which the molecular mechanisms are not yet fully understood. There are several alternative mRNA isoforms described for the gene. We have investigated the expression patterns of five alternative first exons of the CD36 gene in several human tissues and cell types, to better understand the molecular details behind its regulation.     

Model-supervised kernel smoothing for the estimation of spatial usage

The analysis of telemetry data obtained from tagged animals often requires that a smooth surface of spatial usage is fitted to the observations. Well‐established statistical techniques for doing this, such as kernel smoothing (KS), are based on asymptotic arguments that guarantee the convergence of their estimates to the truth with increasing sample size. Often, in addition to telemetry data, ecologists have access to a wealth of information relating to the animals’ distribution and movement. This additional information is potentially useful for the estimation of spatial usage but currently remains unused by existing methods. In this paper, I outline and begin the validation of model‐supervised kernel smoothing (MSKS), a modification of KS that uses such information to supervise surface‐fitting to telemetry data. MSKS initially requires an ad‐hoc synthesis of all the available information, excluding telemetry, into an auxiliary usage surface (the model). This is then combined with the kernel‐smoothed telemetry data into a hybrid surface that is the weighted average of the two. Automatic selection of the smoothing coefficient and the weight associated with the model is done by means of likelihood cross‐validation. I examine the performance of MSKS first, by extensive, numerical exploration on simulated data in one‐dimensional space and second, on two‐dimensional data obtained from an individual‐based simulation of a central‐place forager. The results for different models and sample sizes indicate that MSKS has three important properties. Firstly, it generally outperforms KS by an extent that depends on the quality of the auxiliary model. Secondly, when the auxiliary model is not informative, MSKS automatically reverts to a similar output as KS. Finally, in practical terms, MSKS is easy to implement and adds little to the computational requirements already made by KS methods. I illustrate the application of MSKS and further validate its performance on satellite telemetry data collected from a grey seal on the east coast of Scotland.