Methods to temporally align gait cycle data

The need for the temporal alignment of gait cycle data is well known; however, there is little consensus concerning which alignment method to use. In this paper, we discuss the pros and cons of some methods commonly applied to temporally align gait cycle data (normalization to percent gait cycle, dynamic time warping, derivative dynamic time warping, and piecewise alignment methods). In addition, we empirically evaluate these different methods' abilities to produce successful temporal alignment when mapping a test gait cycle trajectory to a target trajectory. We demonstrate that piecewise temporal alignment techniques outperform other commonly used alignment methods (normalization to percent gait cycle, dynamic time warping, and derivative dynamic time warping) in typical biomechanical and clinical alignment tasks. Lastly, we present an example of how these piecewise alignment techniques make it possible to separately examine intensity and temporal differences between gait cycle data throughout the entire gait cycle, which can provide greater insight into the complexities of movement patterns.     

Impact of stress, gender and menstrual cycle on immune system: possible role of nitric oxide

Stress is a factor found to be involved in the etiology of many diseases. Gender and menstrual cycle phases are other factors affecting the predisposition of individuals for certain diseases. Results from animal and human studies suggest that the distribution of immune system cells may change at different phases of the menstrual cycle. Acute mental stress in humans alters immune variables, too. The increase in the number of natural killer (NK) cells is the most consistent finding among the immune variables, though there are controversies for the other lymphocyte groups. Nitric oxide (NO) as an immune mediator has an unsettled role whether it causes the redistribution of the immune cells, or is an end product of lymphocyte activation. This study was planned to investigate the effect of mental stress on lymphocyte subtypes and the role of NO, for men and women at different phases of the cycle. For this purpose, healthy men (n = 10) and women (n = 10), during the follicular and luteal phases underwent Stroop colour-word interference and cold pressor tests. The immune system responses before and after the tests were determined by cell counts with the flowcytometer. Menstrual cycle phase was ascertained by plasma estrogen and progesterone measurements. Stress response was evaluated by blood pressure (BP) and heart rate (HR) measurements throughout the tests and plasma cortisol and urinary metanephrine and vanillylmandelic acid (VMA) measurements before and after the tests. Plasma and urinary NO determinations were performed before and after the test was completed. All the results were analysed with the appropriate statistical methods. The luteal phase differed from the other groups due to the presence of suppressed immune response to acute stress, including decreased CD4/CD8 ratio and NK cell percentage. On the other hand, acute stress caused a shift from cellular to humoral immunity in men. As indicated by these results, individual reaction towards stress is affected by gender and menstrual cycle phase. NO appears to be a possible effector molecule for these differences.     

PCNA等5种基因在小鼠睾丸发育过程中的表达

以出生1日、30日和成年昆明小鼠睾丸组织为实验材料,利用地高辛标记的基因探针在组织切片上进行DNA－mRNA分子原位杂交,研究了PCNA、cyclinD1、cdc2、P21和P16基因共5种细胞周期调控基因在小鼠睾丸发育中的表达变化。结果发现：PCNA基因在30日龄和成年鼠睾丸中都有强的表达;而cyclin D1基因只在30日龄的小鼠睾丸组织中有表达;P21、P16和cdc2基因在3个不同的发育阶段都没有表达。这些结果表明：(1)细胞周期调控基因cyclin D1、cdc2、P16和P21与小鼠睾丸发育和精子发生过程的细胞增殖控制关系不大,可能小鼠睾丸和精子发育过程中的细胞增殖调控与其他细胞的增殖调控有不同的机制;(2)cyclin D1基因在小鼠睾丸中的表达模式表明,cyclin D1基因在睾丸发育中有不同于细胞增殖促进的作用;(3)小鼠睾丸发育中,精子发生开始时期可能晚于30日龄。 Abstracts：Using in situ hybridization technique with Dig Labeled DNA probe, we studied the expression of PCNA,cyclin D1, cdc2, P21 and P16 gene in the test of one day old,30 days old and adult Kunming mouse.The results shows that the expression of PCNA gene was strong in the test of 30 days old and adult mouse; cyclin D1 gene only expressed in the test of 30 days old mouse; cdc2,P21 and P16 gene did not express in the test of all three groups of mouse.These results suggest that:(1)cyclin D1,cdc2,P16 and P21 genes are not related to the regulaton of cell cycle during test development and germ genaration, and possibly the machanism of cell cycle regulation during test development and germ genaration is different from other kind of cells;(2)cyclin D1 has other founctions except promoting cell profilation;and (3)the germ genaration during test development may start after 30 days old.     

Mutations Affecting Embryonic F-Actin Reorganization also Affect Separation of Nuclei from their Sisters and from the Cortex in Drosophila Cleavage Embryos

We showed in Drosophila that nuclear migration was reduced all through cleavage stages in embryos with any one of the maternal-effect mutations, gs(1)N441 and gs(1)N26 , in which F-actin reorganization in cleavage embryos is disordered. Moreover, we determined nuclear positions in embryos at cycle 1 and 2 in the wild type and two mutants, gs(1)N441 and gs(1)N26 , in order to test if the nuclear migration is regulated within a nuclear cycle. At cycle 1, there was no difference in nuclear position among the strains that we observed. At cycle 2 the two sister nuclei had already migrated posteriorly in the wild type. However, migration was not detectable at cycle 2 in the mutants. Besides, the two sister nuclei were less-separated from each other, and orientation of the two nuclei with regard to the anteroposterior axis was random, different from the wild type. These results support the hypothesis that F-actin is involved in the regulation to separate cleavage nuclei from each other and from the egg cortex. This regulation is apparently required for posteriorward nuclear migration, and for synchronous nuclear arrival in the whole egg cortex.     

Coral spawn timing is a direct response to solar light cycles and is not an entrained circadian response

Broadcast spawning corals release gametes into the oceans with extraordinarily accurate timing. While the date of spawning is set by the lunar cycle, the hour/minute of spawning is set by the solar cycle. In this report, we describe experiments that test whether the time of spawning is regulated by an entrained biological clock or whether it is directly controlled by the solar cycle. Montastraea franksi samples were collected on the morning of the predicted spawning. Fragments from colonies were kept under three different lighting conditions and spawning monitored. The three conditions were sunset times of 0, 1 or 2 h earlier than normal. Fragments from the same colony spawned differently under these three conditions, with an early sunset causing a corresponding early shift in spawning. These results indicate that spawn timing is not controlled by a circadian rhythm and that it is directly controlled by local solar light cycle.     

军标菌株生活史中各阶段生长发育时间的研究

为了更好地研究军标菌在其应用中的实验周期问题 ,采用插片培养法和载片培养法对军标中 5株实验菌的生活史中各阶段生长发育所需时间进行了研究。结果表明 ,5株菌的各时期生长发育所需时间有所不同。整个生活史最长的 4940min ,如AS 3 .42 5 4。最短的 3 888min ,如AS 3 .3 95 0。孢子萌发阶段所需时间也各不相同 ,最长的需 1 5 2 0min ,如AS 3 .3 885。最短的需 640min ,如AS 3 .3 95 0。这一研究为军标中霉菌试验周期 ,即 2 8d过长而且完全可缩短试验周期的观点 ,提供了有力的证据。     

Isolation of a dinoflagellate mitotic cyclin by functional complementation in yeast

Dinoflagellates are protists with permanently condensed chromosomes that lack histones and whose nuclear membrane remains intact during mitosis. These unusual nuclear characters have suggested that the typical cell cycle regulators might be slightly different than those in more typical eukaryotes. To test this, a cyclin has been isolated from the dinoflagellate Gonyaulax polyedra by functional complementation in cln123 mutant yeast. This GpCyc1 sequence contains two cyclin domains in its C-terminal region and a degradation box typical of mitotic cyclins. Similar to other dinoflagellate genes, GpCyc1 has a high copy number, with approximately 5000 copies found in the Gonyaulax genome. An antibody raised against the N-terminal region of the GpCYC1 reacts with a 68kDa protein on Western blots that is more abundant in cell cultures enriched for G2-phase cells than in those containing primarily G1-phase cells, indicating its cellular level follows a pattern expected for a mitotic cyclin. This is the first report of a cell cycle regulator cloned and sequenced from a dinoflagellate, and our results suggest control of the dinoflagellate cell cycle will be very similar to that of other organisms.     

Cluster analysis of dynamic parameters of gene expression

Cluster analysis has proven to be a valuable statistical method for analyzing whole genome expression data. Although clustering methods have great utility, they do represent a lower level statistical analysis that is not directly tied to a specific model. To extend such methods and to allow for more sophisticated lines of inference, we use cluster analysis in conjunction with a specific model of gene expression dynamics. This model provides phenomenological dynamic parameters on both linear and non-linear responses of the system. This analysis determines the parameters of two different transition matrices (linear and nonlinear) that describe the influence of one gene expression level on another. Using yeast cell cycle microarray data as test set, we calculated the transition matrices and used these dynamic parameters as a metric for cluster analysis. Hierarchical cluster analysis of this transition matrix reveals how a set of genes influence the expression of other genes activated during different cell cycle phases. Most strikingly, genes in different stages of cell cycle preferentially activate or inactivate genes in other stages of cell cycle, and this relationship can be readily visualized in a two-way clustering image. The observation is prior to any knowledge of the chronological characteristics of the cell cycle process. This method shows the utility of using model parameters as a metric in cluster analysis.     

Life cycle replacement by gene introduction under an allee effect in periodical cicadas

Periodical cicadas (Magicicada spp.) in the USA are divided into three species groups (-decim, -cassini, -decula) of similar but distinct morphology and behavior. Each group contains at least one species with a 17-year life cycle and one with a 13-year cycle; each species is most closely related to one with the other cycle. One explanation for the apparent polyphyly of 13- and 17-year life cycles is that populations switch between the two cycles. Using a numerical model, we test the general feasibility of life cycle switching by the introduction of alleles for one cycle into populations of the other cycle. Our results suggest that fitness reductions at low population densities of mating individuals (the Allee effect) could play a role in life cycle switching. In our model, if the 13-year cycle is genetically dominant, a 17-year cycle population will switch to a 13-year cycle given the introduction of a few 13-year cycle alleles under a moderate Allee effect. We also show that under a weak Allee effect, different year-classes ("broods") with 17-year life cycles can be generated. Remarkably, the outcomes of our models depend only on the dominance relationships of the cycle alleles, irrespective of any fitness advantages.     

CycD1, a putative G1 cyclin from Antirrhinum majus, accelerates the cell cycle in cultured tobacco BY-2 cells by enhancing both G1/S entry and progression through S and G2 phases

A putative G1 cyclin gene, Antma;CycD1;1 (CycD1), from Antirrhinum majus is known to be expressed throughout the cell cycle in the meristem and other actively proliferating cells. To test its role in cell cycle progression, we examined the effect of CycD1 expression in the tobacco (Nicotiana tabacum) cell suspension culture BY-2. Green fluorescent protein:CycD1 is located in the nucleus throughout interphase. Using epitope-tagged CycD1, we show that it interacts in vivo with CDKA, a cyclin dependent protein kinase that acts at both the G1/S and the G2/M boundaries. We examined the effect of induced expression at different stages of the cell cycle. Expression in G0 cells accelerated entry into both S-phase and mitosis, whereas expression during S-phase accelerated entry into mitosis. Consistent with acceleration of both transitions, the CycD1-associated cyclin dependent kinase can phosphorylate both histone H1 and Rb proteins. The expression of cyclinD1 led to the early activation of total CDK activity, consistent with accelerated cell cycle progression. Continuous expression of CycD1 led to moderate increases in growth rate. Therefore, in contrast with animal D cyclins, CycD1 can promote both G0/G1/S and S/G2/M progression. This indicates that D cyclin function may have diverged between plants and animals.     

A new Hybrid Monte Carlo algorithm for protein potential function test and structure refinement

A new Hybrid Monte Carlo (HMC) algorithm has been developed to test protein potential functions and, ultimately, refine protein structures. The main principle of this algorithm is, in each cycle, a new trial conformation is generated by carrying out a short period of molecular dynamics (MD) iterations with a set of random parameters (including the MD time step, the number of MD steps, the MD temperature, and the seed for initial MD velocity assignment); then to accept or reject the new conformation on the basis of the Metropolis criterion. The novelty in this paper is that the potential in MD iterations is different from that in the MC step. In the former, it is a molecular mechanics potential, in the latter it is a knowledge-based potential (KBP). Directed by the KBP, the MD iteration is used to search conformational space for realistic conformations with low KBP energy. It circumvents the difficulty in using KBP functions directly in MD simulation, as KBP functions are typically incomplete, and do not always have continuous derivatives required for the calculation of the forces. The new algorithm has been tested in explorations of conformational space. In these test calculations the KBP energy was found to drop below the value for the native conformation, and the correlation between the root mean square deviation (RMSD) and the KBP energy was shown to be different from the test results in other references. At the present time, the algorithm is useful for testing new KBP functions. Furthermore, if a KBP function can be found for which the native conformation has the lowest energy and the energy/RMSD correlation is good, then this new algorithm also will be a tool for refinement of the theory-based structural models.     

Analysis of the cell cycle in the root meristem of Allium cepa under the influence of ledakrin

The influence of a polish anticancer drug on the cell cycle using Allium test was studied. Methods of aceto-orcein squash slides, curve of labelled mitoses after 3H-thymidine incubation and cytophotometrics after Feulgen's reaction were employed. Ledakrin acts strongly antimitotically, but it does not block the cell cycle completely. The cytostatic activity of ledakrin results from its action on the interphase. The phases G1 and S are prolonged while M is unchanged after 6h incubation with ledakrin. During postincubation in water without ledakrin it was noted, at the beginning, that the mitotic activity decreases and it is brought about the lengthening of S and G2 phases. The duration of the cell cycle phases returns to the control level during further postincubation. The results of analysis of chromatin aberrations and the micronucleus test point to a mutagenic effect of ledakrin.     

Linkers of Cell Polarity and Cell Cycle Regulation in the Fission Yeast Protein Interaction Network

The study of gene and protein interaction networks has improved our understanding of the multiple, systemic levels of regulation found in eukaryotic and prokaryotic organisms. Here we carry out a large-scale analysis of the protein-protein interaction (PPI) network of fission yeast (Schizosaccharomyces pombe) and establish a method to identify ‘linker’ proteins that bridge diverse cellular processes - integrating Gene Ontology and PPI data with network theory measures. We test the method on a highly characterized subset of the genome consisting of proteins controlling the cell cycle, cell polarity and cytokinesis and identify proteins likely to play a key role in controlling the temporal changes in the localization of the polarity machinery. Experimental inspection of one such factor, the polarity-regulating RNB protein Sts5, confirms the prediction that it has a cell cycle dependent regulation. Detailed bibliographic inspection of other predicted ‘linkers’ also confirms the predictive power of the method. As the method is robust to network perturbations and can successfully predict linker proteins, it provides a powerful tool to study the interplay between different cellular processes.     

Correlation between cell size and position within the division cycle in suspension cultures of Chang liver cells

Chang liver cells from exponentially growing suspension cultures have been separated by sedimentation at unit gravity. Determinations of the protein content per cell showed that the fractionation procedure resulted in good separation of cells of different size. On the other hand, the DNA content of individual cells from the fractions, as determined cytofluorimetrically, indicated considerable heterogeneity in the size of cells from the same stage of the division cycle. On the basis of earlier results on intermitotic growth and the variation in the length of the cell cycle in homogeneous cell populations, a mathematical model has been constructed and tested using a computer program. The present results on the size distribution of cells from the different stages of the mitotic cycle are consistent with a regeneration of size heterogeneity in each cell generation, as a result of the dispersion of intermitotic times. The variation in cell cycle times may be related to a probabilistic event in the G1 period. In the mathematical model it was necessary to include a mechanism by which the regeneration of abnormally large cells is prevented. The experimental data are compatible with a gradually increasing inhibition of growth in cells larger than a certain size (circa 400 pg protein per cell).     

Chromosome radiosensitivity in 2 successive mitotic cycles of human lymphocytes

A culture of human lymphocytes was irradiated with gamma-quanta (0.5 Gy) after incubation during different time intervals, i.e. at different relative frequencies of cells in the first and second mitotic cycle. The frequency of aberrations produced in the G2 stage was analysed. The total yield of aberrations gradually increased with the increase of time lapse between the onset of cultivation and irradiation. If, however, the relative frequencies of the first and second mitoses are taken into account, it could be concluded that radiosensitivity of chromosomes remains constant in each cycle and independent from its duration. Besides, radiosensitivity of chromosomes during the second cycle is one and half times stronger, as compared to the first cycle. In accordance with the data of other authors, 5-bromodeoxyuridine has been found to significantly increase radiosensitivity.     

The different breeding strategies of penguins: A review

The 18 penguin species are exclusively and widely distributed in the Southern hemisphere, from the Equator to the Antarctic continent, and are thus submitted to various ecological constraints in their reproductive strategy. This results in a high variability in all aspects of the breeding biology of the different species. Although penguins appear primarily adapted for a marine existence, they remain dependent on land for breeding, rearing young, and moulting. Here we describe and compare the breeding cycle of all the penguin species, highlighting the characteristics of each species in terms of breeding range, population status, threats induced by environmental changes, duration of the different phases of the breeding cycle, mate fidelity, body mass, body height, egg mass and duration of egg formation. We also focus on the breeding cycle of the genus Aptenodytes, since it largely differs from the breeding cycle of most of the other penguin species.     

Pathogen disgust,but not moral disgust,changes across the menstrual cycle

The Compensatory Prophylaxis Hypothesis (CPH) proposes that during periods of increased susceptibility to infections, e.g., during the luteal phase of the menstrual cycle when progesterone suppresses immune function, women should feel more disgust toward pathogen cues and behave prophylactically. We investigate differences in disgust sensitivity and contamination sensitivity during different phases of the menstrual cycle in regularly cycling, healthy 93 rural and urban Polish women using the within-subject design. Disgust sensitivity was measured during two different phases of a menstrual cycle: 1) the follicular phase (the 5th or 6th day of the cycle) and 2) the luteal phase (on the 5th day after a positive ovulatory test or on 20th day of a cycle if the result of the ovulatory test was not positive). In the luteal phase, women scored higher on the Pathogen Disgust of the Three-Domain Disgust Scale, the Contamination Obsessions and Washing Compulsions Subscale of Padua Inventory, and on ratings of photographs showing sources of potential infections than in the follicular phase. Moral Disgust of the Three-Domain Disgust Scale did not differ between cycle phases. Hence, results suggest that women feel more disgusted toward cues to pathogens during the luteal phase, when susceptibility to infection is greater. We suggest that it is necessary to incorporate ovulatory testing as well as to conduct repeated measurements of disgust sensitivity in future tests of the CPH. Moreover, we believe that understanding how the feeling of pathogen disgust varies across the menstrual cycle and in relation to progesterone levels could be useful in designing effective infectious diseases prevention strategies for women.     

The evolution of life cycle complexity in aphids: Ecological optimization or historical constraint?

For decades, biologists have debated why many parasites have obligate multihost life cycles. Here, we use comparative phylogenetic analyses of aphids to evaluate the roles of ecological optimization and historical constraint in the evolution of life cycle complexity. If life cycle complexity is adaptive, it should be evolutionarily labile, that is, change in response to selection. We provide evidence that this is true in some aphids (aphidines), but not others (nonaphidines)—groups that differ in the intensity of their relationships with primary hosts. Next, we test specific mechanisms by which life cycle complexity could be adaptive or a constraint. We find that among aphidines there is a strong association between complex life cycles and polyphagy but only a weak correlation between life cycle complexity and reproductive mode. In contrast, among nonaphidines the relationship between life cycle complexity and host breadth is weak but the association between complex life cycles and sexual reproduction is strong. Thus, although the adaptiveness of life cycle complexity appears to be lineage specific, across aphids, life cycle evolution appears to be tightly linked with the evolution of other important natural history traits.     

New method for the analysis of flow cytometric data

A numerical method for deriving the fractions of cells in different phases of the cell cycle from a single observed DNA histogram is presented. The observed histogram is regarded as a polluted version (containing allocation errors) of the true histogram. A mathematical model is used to describe the pollution process. A theoretical histogram, representing the true histogram, is constructed so that G1 cells are put into one channel and G2M cells into another; the distribution of S cells in between is approximated with a set of harmonic functions. This theoretical histogram is subsequently disturbed with Gaussian dispersion functions to stimulate the pollution, yielding a predicted histogram. Using a maximum likelihood estimation technique, the model parameters are adjusted iteratively, matching the predicted histogram to the actually observed one. With the final parameter values substituted, the corresponding final theoretical histogram is regarded as a reliable reconstruction of the true histogram. From the latter, the required percentages can be read directly. The advantage of this approach over other mathematical analysis methods is that it allows a wide range of different, continuous distributions for relatively few model parameters (thus featuring flexibility and realism and a diminished risk of encountering computational problems). In addition, estimation errors providing a measure of accuracy can be obtained. To test the method, it was used to analyze various observed histograms from the literature that have been obtained by either simulation or actual flow cytometric measurements. The method appeared to perform well, as compared to the reported results of several other methods of analysis applied to the same data.     

A support vector machine based test for incongruence between sets of trees in tree space

ABSTRACT: BACKGROUND: The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene trees may have been influenced by other evolutionary processes such as selection, gene duplication, or horizontal gene transfer. RESULTS: Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributions of gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approach maps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) to measure the separation between two sets of pre-defined trees. We use a permutation test to assess the significance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to the comparison of gene trees simulated within different species trees across a range of species tree depths. Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect very small differences between two set of gene trees generated under different species trees. Our statistical test can also include tree reconstruction into its test framework through a variety of phylogenetic optimality criteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the form of receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detection of differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, it controlled false positive and false negative rates very well, indicating a high degree of accuracy. CONCLUSIONS: The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it an applicable test for any scenario where evolutionary or other factors can lead to trees with different multi-dimensional distributions. The software GeneOut is freely available under the GNU public license.