Endpoint error in smoothing and differentiating raw kinematic data: An evaluation of four popular methods

‘Endpoint error’ describes the erratic behavior at the beginning and end of the computed acceleration data which is commonly observed after smoothing and differentiating raw displacement data. To evaluate endpoint error produced by four popular smoothing and differentiating techniques, Lanshammar's (1982, J. Biomechanics 15, 99–105) modification of the Pezzack et al. (1977, J. Biomechanics, 10, 377–382) raw angular displacement data set was truncated at three different locations corresponding to the major peaks in the criterion acceleration curve. Also, for each data subset, three padding conditions were applied. Each data subset was smoothed and differentiated using the Butterworth digital filter, cubic spline, quintic spline, and Fourier series to obtain acceleration values. RMS residual errors were calculated between the computed and criterion accelerations in the endpoint regions. Although no method completely eliminated endpoint error, the results demonstrated clear superiority of the quintic spline over the other three methods in producing accurate acceleration values close to the endpoints of the modified Pezzack et al. (1977) data set. In fact, the quintic spline performed best with non-padded data (cumulative error=48.0 rad s⁻²). Conversely, when applied to non-padded data, the Butterworth digital filter produced wildly deviating values beginning more than the 10 points from the terminal data point (cumulative error=226.6 rad s⁻²). Each of the four methods performed better when applied to data subsets padded by linear extrapolation (average cumulative error=68.8 rad s⁻²) than when applied to analogous subsets padded by reflection (average cumulative error=86.1 rad s⁻²).     

Problems with essential fatty acids: time for a new paradigm?

The term ‘essential fatty acid’ is ambiguous and inappropriately inclusive or exclusive of many polyunsaturated fatty acids. When applied most rigidly to linoleate and -linolenate, this term excludes the now well accepted but conditional dietary need for two long chain polyunsaturates (arachidonate and docosahexaenoate) during infancy. In addition, because of the concomitant absence of dietary -linolenate, essential fatty acid deficiency is a seriously flawed model that has probably led to significantly overestimating linoleate requirements. Linoleate and -linolenate are more rapidly β-oxidized and less easily replaced in tissue lipids than the common ‘non-essential’ fatty acids (palmitate, stearate, oleate). Carbon from linoleate and -linolenate is recycled into palmitate and cholesterol in amounts frequently exceeding that used to make long chain polyunsaturates. These observations represent several problems with the concept of ‘essential fatty acid’, a term that connotes a more protected and important fatty acid than those which can be made endogenously. The metabolism of essential and non-essential fatty acids is clearly much more interconnected than previously understood. Replacing the term ‘essential fatty acid’ by existing but less biased terminology, i.e. polyunsaturates, ω3 or ω6 polyunsaturates, or naming the individual fatty acid(s) in question, would improve clarity and would potentially promote broader exploration of the functional and health attributes of polyunsaturated fatty acids.     

Sequence dependent hydration of DNA

The transitions between the different helical conformations of DNA depend on the base sequence and the ambient conditions such as humidity and counter-ion concentration. In this study energy minimization techniques have been used to locate water molecule sites around nucleotides especially those which form hydrogen bonds between two or more nucleotide atoms and thus form solvent mediated bridges. We have studied several sequences and find that those which are known not to exist in the low hydration ‘A’ form have very similar number of bridging sites in both ‘A’ and ‘B’ conformations. Those sequences which are found in the ‘A’ conformation have considerably more bridging sites in this low hydration form than in the ‘B’ conformation. Sequence related solvent effects for a given conformation have also been analysed.     

Pharmacogenomics: out of the lab and into the community

Pharmacogenomics is the study of the inherited basis of differences in response to drugs. These interindividual differences are often more than tenfold; a ‘slow metabolizer’ or ‘low-responsive’ individual might therefore require ten times less than the recommended dose of a drug than a ‘rapid metabolizer’ or ‘high-responsive’ person, and the slow metabolizer is often more likely to experience drug toxicity than a rapid metabolizer. Our knowledge is developing rapidly to the point that the physician will soon use DNA-based tests to aid in decision-making with respect to the most appropriate drug and dosage given to each patient. If the patient's DNA is available, however, what boundaries should be placed on that DNA? If the patient's genotype becomes known to the physician (and presumably to the patient him- or herself), what ethical questions might arise and how will they be resolved? This article discusses these issues and outlines some of the possible solutions.     

Influence of gene-linkage and recombination of evolutionary algorithms on the rate of evolution, genetic diversity and the response of evolving populations to disturbance

Both biological populations and fault tolerant evolvable hardware systems need to respond rapidly to changes in their dynamic environmental niche. Such changes can be caused by a disturbance event or fault occurring. Here I examine evolutionary algorithms, based on eukaryote sexual selection, which allow different levels of recombination of ‘genes’. The differences in recombination are based on ‘genes’ related to the optimisation process being either linked on a single ‘chromosome’ or being present on separate ‘chromosomes’. When genes are present on separate chromosomes the initial rate of evolution of a randomly generated population is faster than if the genes are linked on the same chromosome. However, when the optimisation problem is changed during the optimisation period, indicating a disturbance or fault occurring, the initial fitness of the linked population is higher and the rate of optimisation immediately after the disturbance is more rapid than for the non-linked populations. The genotypic and phenotypic diversity of the linked populations are also significantly higher immediately prior to the disturbance event. I propose this diversity provides the necessary variation to allow more rapid evolution following a disturbance. The results demonstrate the importance of population diversity in response to change, supporting theory from conservation biology.     

Transitions between cooperative and non-cooperative responding in the 'Pigeon's Dilemma'

Two pigeons played Iterated Prisoner's Dilemma (IPD) against a simulated opponent pre-programmed to play ‘Tit-For-Tat’ (TFT) and ‘Random’ (RND) strategies. Each pigeon received differential amounts of access to food following choices of either ‘cooperate’ or ‘defect’ on a trial. After 1000 trials against TFT and 500 trials against RND, results indicated that choice allocation was optimal when the birds played against RND but was sub-optimal when the birds played against TFT. In order to determine why the pigeons responded suboptimally against TFT, a trial-by-trial analysis of the data was conducted. The analysis revealed that once a pigeon had received the ‘Sucker's’ payoff (S), it was more likely to defect and receive the ‘Temptation’ payoff (T) than to cooperate and receive the ‘Reward’ (R) payoff. Local reinforcement contingencies appear to determine suboptimal responding against TFT in the iterated Pigeon's Dilemma.     

The influence of digital filter type,amplitude normalisation method,and co-contraction algorithm on clinically relevant surface electromyography data during clinical movement assessments

There is a large and growing body of surface electromyography (sEMG) research using laboratory-specific signal processing procedures (i.e., digital filter type and amplitude normalisation protocols) and data analyses methods (i.e., co-contraction algorithms) to acquire practically meaningful information from these data. As a result, the ability to compare sEMG results between studies is, and continues to be challenging. The aim of this study was to determine if digital filter type, amplitude normalisation method, and co-contraction algorithm could influence the practical or clinical interpretation of processed sEMG data. Sixteen elite female athletes were recruited. During data collection, sEMG data was recorded from nine lower limb muscles while completing a series of calibration and clinical movement assessment trials (running and sidestepping). Three analyses were conducted: (1) signal processing with two different digital filter types (Butterworth or critically damped), (2) three amplitude normalisation methods, and (3) three co-contraction ratio algorithms. Results showed the choice of digital filter did not influence the clinical interpretation of sEMG; however, choice of amplitude normalisation method and co-contraction algorithm did influence the clinical interpretation of the running and sidestepping task. Care is recommended when choosing amplitude normalisation method and co-contraction algorithms if researchers/clinicians are interested in comparing sEMG data between studies.     

Allocation, plasticity and allometry in plants

Allocation is one of the central concepts in modern ecology, providing the basis for different strategies. Allocation in plants has been conceptualized as a proportional or ratio-driven process (‘partitioning’). In this view, a plant has a given amount of resources at any point in time and it allocates these resources to different structures. But many plant ecological processes are better understood in terms of growth and size than in terms of time. In an allometric perspective, allocation is seen as a size-dependent process: allometry is the quantitative relationship between growth and allocation. Therefore most questions of allocation should be posed allometrically, not as ratios or proportions. Plants evolve allometric patterns in response to numerous selection pressures and constraints, and these patterns explain many behaviours of plant populations.

In the allometric view, plasticity in allocation can be understood as a change in a plant's allometric trajectory in response to the environment. Some allocation patterns show relatively fixed allometric trajectories, varying in different environments primarily in the speed at which the trajectory is travelled, whereas other allocation patterns show great flexibility in their behaviour at a given size. Because plant growth is often indeterminate and its rate highly influenced by environmental conditions, ‘plasticity in size’ is not a meaningful concept. We need a new way to classify, describe and analyze plant allocation and plasticity because the concepts ‘trait’ and ‘plasticity’ are too broad. Three degrees of plasticity can be distinguished: (1) allometric growth (‘apparent plasticity’), (2) modular proliferation and local physiological adaptation, and (3) integrated plastic responses. Plasticity, which has evolved because it increases individual fitness, can be a disadvantage in plant production systems, where we want to optimize population, not individual, performance.     

Quantification of high-frequency sea-level fluctuations in shallow-water carbonates: an example from the Berriasian–Valanginian (French Jura)

When quantifying sedimentary processes on shallow carbonate platforms, it is important to know the high-frequency accommodation changes through time. Accommodation changes in cyclic successions are often analysed by simply converting cycle thickness to Fischer plots. This approach is not satisfactory, because it does not account for differential compaction, possible erosion, sea-level fall below the depositional surface, or subtidal cycles. An attempt is made here to reconstruct a realistic, high-frequency accommodation and sea-level curve based on a detailed facies and cyclostratigraphical analysis of Middle Berriasian to Lower Valanginian sections in the French Jura Mountains. The general depositional environment was a shallow-marine carbonate platform on a passive margin. Our approach includes the following steps: (1) facies interpretation; (2) cyclostratigraphical analysis and identification of Milankovitch parameters in a well-constrained chronostratigraphic framework; (3) differential decompaction according to facies; (4) estimation of depth ranges of erosion and vadose zone; (5) estimation of water-depth ranges at sequence boundaries and maximum flooding intervals; (6) estimation of mean subsidence rate; (7) classification of depositional sequences according to types of facies evolution: ‘catch-up’, ‘catch-down’, ‘give-up’, or ‘keep-up’; (8) classification of depositional sequences according to long-term sea-level evolution: ‘rising’, ‘stable’, ‘falling’; (9) calculation of ‘eustatic’ sea-level change for each depositional sequence using the parameters inferred from these scenarios, assuming that sea-level cycles were essentially symmetrical (which is probable in Early Cretaceous greenhouse conditions); (10) calculation of a sea-level curve for each studied section; (11) comparison of these curves among each other to filter out differential subsidence; (12) construction of a ‘composite eustatic’ sea-level curve for the entire studied platform; (13) spectral analysis of the calculated sea-level curves. Limitations of the method are those common to every stratigraphic analysis. However, the method has the potential to improve the original cyclostratigraphical interpretations and to better constrain the high-frequency sea-level changes that control carbonate production and sediment fluxes.     

Different architectures of the collagen fibril: morphological aspects and functional implications

Several tissues known to contain collagen fibrils with a ‘helical’ arrangement were studied by t.e.m. and freeze-fracture. In all the tissues examined, the diameter of the collagen fibrils appeared to be tissue-specific and fairly constant within the same tissue. No statistical differences, on the contrary, were detectable in the coiling angle which appeared similar in all the tissues and independent of both diameter and age of the fibril. Rat tail tendon was also examined under the same technical conditions and showed collagen fibrils of large and very heterogeneous diameter and with a consistent ‘straight’ arrangement. These data seem to suggest that the ‘helical’ and ‘straight’ arrangements may actually identify different types of collagen fibrils. The authors discuss the possible functional significance of these arrangements and present two hypotheses on the three-dimensional structure of the ‘helical’ fibril.     

Ultrastructure of meristematic cells of dormant and released buds in Tradescantia paludosa

The lateral bud meristems of Tradescantia paludosa show a characteristic cytohistological zonation during dormancy. The cells comprising this so called ‘zone of inhibition’, which is located at the extreme tip of the bud apex, rarely synthesize nuclear DNA or undergo mitotic division. These nuclei are as large as prophase nuclei, yet contain only telophase (2C) amounts of DNA and significantly lower amounts of histone as compared to the 2C nuclei of the actively dividing cells.Ultrastructural observations of the nuclei in the ‘zone of inhibition’ show that a large proportion of the chromatin is organized as less condensed, diffuse, euchromatin fibrils; however, the chromatin of the actively dividing nuclei of the cells outside the ‘zone of inhibition’ or in the released bud meristems is organized to a greater extent as condensed clumps of heterochromatin. When the dormancy is released, the nuclei in the ‘zone of inhibition’ synthesize DNA and histone and undergo cell division in approx. 4 days. Striking changes in the organization of chromatin fibrils take place during this transition period. The diffuse chromatin fibrils of the nuclei in the ‘zone of inhibition’ progressively become more and more condensed as the cell prepares to undergo the first mitotic division after the release of dormancy. This change which is coupled with the synthesis of histones in the nuclei of the ‘zone of inhibition’ suggests a prominent structural role of these basic proteins in the organization of the chromatin. The large volume of 2C nuclei of the ‘zone of inhibition’ seems, therefore, to result not from a great nuclear mass, but probably from a relatively small degree of condensation of chromatin.     

Structural correlation between lipophilicity and lipopolysaccharide-sequestering activity in spermine-sulfonamide analogs

Lipopolysaccharides (LPS), otherwise termed ‘endotoxins’, are outer-membrane constituents of Gram-negative bacteria, and play a key role in the pathogenesis of ‘Septic Shock’, a major cause of mortality in the critically ill patient. We had previously defined the pharmacophore necessary for small molecules to specifically bind and neutralize this complex carbohydrate. A series of aryl and aliphatic spermine-sulfonamide analogs were synthesized and tested in a series of binding and cell-based assays in order to probe the effect of lipophilicity on sequestration ability. A strong correlation was indeed found, supporting the hypothesis that endotoxin-neutralizing ability involves a lipophilic or membrane attachment event. The research discussed herein may be useful for the design of additional carbohydrate recognizing molecules and endotoxin-neutralizing drugs.     

Determination of the polymorphic composition of smooth pea starch

A method for estimating the proportions of ‘A’ and ‘B’ polymorphs comprising a sample of ‘C’ type starch is proposed which uses established experimental techniques with commercially available spreadsheet and X-ray analysis software. Waxy maize, potato and smooth pea starches were used to provide X-ray diffraction patterns characteristic of the ‘A’, ‘B’ and ‘C’ starch polymorphs. Samples of amorphous starches were also prepared. The method initially involved subtraction of the amorphous phase and instrumental background from the X-ray diffraction patterns of each starch sample using the spreadsheet program, Lotus 1-2-3. The remainder of the pattern, representing the crystalline portion of the starch sample, was then analysed by profile fitting to elucidate the positions and areas of individual diffraction peaks. The ratio of the total peak area to the areas under peaks characteristic of ‘A’ and ‘B’ type starches, respectively, were used to calculate the relative proportions of these polymorphs in smooth pea starch. These proportions were found to be 56±3% ‘A’ polymorph to 44±3% ‘B’ polymorph. A ‘C’ type pattern was constructed by using Lotus 1-2-3 to combine diffraction patterns from the crystalline portions of ‘A’ and ‘B’ type starches in the proportions given above. Polymorph patterns were obtained by manipulation of the diffraction patterns from the crystalline portions of starches using Lotus 1-2-3. An ‘A’ type pattern was obtained by subtraction of a ‘B’ type pattern from that of a ‘C’ type. Similarly, a ‘B’ type pattern was obtained by subtraction of an ‘A’ type pattern from that of a ‘C’ type.     

Protein turnover and cell-cycle initiation in yeast

The effects of short pulses of cycloheximide on the traversal of the G1 phase of the cell cycle of the yeast Saccharomyces cerevisiae were examined. Cells were released from a block at the regulatory stage of G1, termed ‘start’, and pulsed with cycloheximide. Delays in budding which were considerably longer than the length of the pulse were observed. During the delay the cells remained blocked at ‘start’. No delay in budding was observed after cycloheximide pulses, when cells were released from a cdc 24 block which arrests the budding process but not ‘start’. Overall protein synthesis did not show an additional delay after the pulse. The extra lag following cycloheximide pulses appears to reflect a unique feature of ‘start’. It may be accounted for by a requirement at ‘start’ for a labile protein with a half-life time of about 6 min.     

Spinach-thylakoid phosphorylation: Studies on the kinetics of changes in photosystem antenna size, spill-over and phosphorylation of light-harvesting chlorophyll a/b protein

The kinetics of LHCP phosphorylation and associated changes in photosystem cross-section and energy ‘spill-over’ from PS II to PS I have been examined in isolated spinach chloroplasts. During an initial phosphorylation period of 3–6 min, in the presence of saturating concentrations of Mg²⁺, the increase in PS I and decrease in PS II cross-section are largely completed, as judged by both measurements of the steady-state redox state of Q and fluorescence yield changes. This corresponds to a period of rapid ³²P incorporation into the low-molecular weight LHCP polypeptide. Subsequent to this initial 3–6-min period there is substantial further phosphorylation of both LHCP polypeptides, which is not accompanied by significant changes in photosystem cross-section, even after the chloroplasts had been unstacked with extensive mixing of PS I and PS II by Mg-removal. It is suggested that there exists a specific ‘mobile’ population of LHCP molecules which is rapidly phosphorylated and which may be enriched in the low-molecular-weight polypeptide. In addition, measurements of the kinetics of the ‘spill-over’ changes upon either Mg²⁺ addition or removal indicate that the continued phosphorylation of LHCP is able to increase the ‘spill-over’ process under favourable ionic conditions.     

Intracellular signalling proteins as ‘smart’ agents in parallel distributed processes

In eucaryotic organisms, responses to external signals are mediated by a repertoire of intracellular signalling pathways that ultimately bring about the activation/inactivation of protein kinases and/or protein phosphatases. Until relatively recently, little thought had been given to the intracellular distribution of the components of these signalling pathways. However, experimental evidence from a diverse range of organisms indicates that rather than being freely distributed, many of the protein components of signalling cascades show a significant degree of spatial organisation. Here, we briefly review the roles of ‘anchor’, ‘scaffold’ and ‘adaptor’ proteins in the organisation and functioning of intracellular signalling pathways. We then consider some of the parallel distributed processing capacities of these adaptive systems. We focus on signalling proteins-both as individual ‘devices’ (agents) and as ‘networks’ (ecologies) of parallel processes. Signalling proteins are described as ‘smart thermodynamic machines’ which satisfy ‘gluing’ (functorial) roles in the information economy of the cell. This combines two information-processing views of signalling proteins. Individually, they show ‘cognitive’ capacities and collectively they integrate (cohere) cellular processes. We exploit these views by drawing comparisons between signalling proteins and verbs. This text/dialogical metaphor also helps refine our view of signalling proteins as context-sensitive information processing agents.     

A characteristic pharmacological action of ‘Yang-invigorating’ Chinese tonifying herbs: Enhancement of myocardial ATP-generation capacity

In order to investigate the pharmacological basis of ‘Yang-invigorating’ action, the effect of oral treatment with the methanolic extract of ‘Yang-invigorating’ herbs on ATP-generation capacity was examined, using heart homogenates prepared from herb-pretreated mice. Tonifying (i.e., health-promoting) herbs of other functional categories were also included for comparison. The results indicated that ‘Yang-invigorating’ Chinese tonifying herbs could invariably enhance myocardial ATP-generation capacity, with the extent of stimulation varying among the herbs. In contrast, ‘Yin-nourishing’ herbs either did not stimulate or even decreased myocardial ATP-generation capacity. While ‘Qi-invigorating’ herbs produced variable effects on myocardial ATP-generation capacity, most of the ‘blood-enriching’ herbs did not cause any significant changes. The results obtained from studies using myocardial mitochondrial fractions isolated from herb-pretreated mice suggest that ‘Yang-invigorating’ herbs might speed up ATP generation by increasing mitochondrial electron transport. The ensemble of results has provided evidence for the first time to support the pharmacological basis of ‘Yang invigoration’ in Chinese medicine.     

Cues for apoptotic cell engulfment: eat-me, don't eat-me and come-get-me signals

Efficient elimination of cells undergoing programmed cell death is crucial for normal tissue homeostasis and for the regulation of immune responses. This review examines unique signals presented by apoptotic cells and the mechanisms by which phagocytes recognize and respond to these signals to orchestrate the selective and rapid removal of apoptotic cells. Such unique signals include direct and indirect ‘eat-me’ markers on the apoptotic cell surface, the absence of ‘don't eat-me’ markers normally found on living cells and soluble ‘come-get-me’ signals secreted by apoptotic cells to attract phagocytes to sites of apoptotic cell death. Once apoptotic cells are identified, their uptake by phagocytes further depends on the molecular machinery highly conserved from Caenorhabditis elegans to mammals.     

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.     

Double infection experiments with echinostomatids (Trematoda) in Lymnaea stagnalis by implantation of rediae and exposure to miracidia

1972. Double infection experiments with echinostomatids (Trematoda) in Lymnaea stagnalis by implantation of rediae and exposure to miracidia. International Journal for Parasitology, 2: 409–423. Echinostomatid species parasitizing Lymnaea stagnalis as first intermediate hosts in a South German Lake have been found present in natural double infections, but at frequencies lower than expected. Simultaneous double infection and superinfection experiments in Lymnaea stagnalis with Isthmiophora melis, Echinoparyphium aconiatum and Echinostoma revolutum were performed by redial implantation and by exposure to miracidia. All three combinations possible of these echinostomatids proved to be unstable, one species being eliminated by another ‘stronger’ one after an invariable suppression order. The degree of vigour of Isthmiophora melis in this suppression order is greater if mother rediae (macropharyngeate) are present, i.e. after miracidial invasion instead of daughter redial implantation. Snails parasitized by rediae of a ‘weak’ type could be superinfected by implantation of rediae of a ‘strong’ type, but not if the first (‘weak’) infection had reached the stage of shedding cercariae. Superinfection by implantation of Echinoparyphium aconiatum rediae (‘strong’ type) was not successful when the first infection consisted of sporocysts of plagiorchiids, or of Apatemon sp. (Strigeidae) that had reached the stage of shedding cercariae.