Predictive optimality criterion for idealization of ion channel data and exact Akaike's criterion

Different statistical or low-pass filters may be used for the idealization of ion channel data. We address the problem of predicting optimal filter parameters, represented by a threshold test-value for statistical filters and by a cut-off frequency for low-pass filters. Optimal idealization is understood in the sense of maximal similarity between recovered and real signals. Special procedures are suggested to quantitatively characterize the difference between the recovered and the real signals, the latter being known for simulated data. These procedures, called objective criteria, play the role of referees in estimating the performance of different predictive optimality criteria. We have tested standard Akaike's AIC and its modification by Rissanen, MDL. Both gave unsatisfactory results. We have shown analytically, that the Akaike-type criterion, based on the use of a certain penalty for the log likelihood function per transition, indicates the correct optimum point only if the penalty is set equal to half the optimal threshold. As the latter varies significantly for different data sets, this criterion is not particularly helpful. A new universal predictive optimality criterion, valid for real data and any idealization method, is suggested. It is formally similar to AIC, but instead of log likelihood it uses the doubled number of false transitions. The predictive power of the new criterion is demonstrated with different types of data for Hinkley and 50% amplitude methods. Received: 23 July 1996 / Accepted: 9 May 1997     

DNA HOMO as a new landmark for nucleic acid properties. ab initio calculations and experimental mapping.

Of the non-covalent binding forces in DNA-drug or DNA-protein interaction, electrostatic interaction, stacking interaction, hydrogen bonds and hydrophobic effect have been well established. However, only a few HOMO-LUMO interaction in DNA have been reported. We examined the ab initio calculations of B-DNA duplex 5-mers. Based on the calculated results, we investigated the mapping of HOMO experimentally and found that DNA cleavage patterns with Co(II) and BPO (Benzoyl peroxide) were in good agreement with the ab initio calculation results.     

Genomic mapping by single copy landmark detection: a predictive model with a discrete mathematical approach

One of the goals of the Human Genome Project is to produce libraries of largely contiguous, ordered sets of molecular clones for use in sequencing and gene mapping projects. This is planned to be done for human and many model organisms. Theory and practice have shown that long-range contiguity and the degree to which the entire genome is covered by ordered clones can be affected by many biological variables. Many laboratories are currently experimenting with different experimental strategies and theoretical models to help plan strategies for accomplishing longrange molecular mapping of genomes. Here we describe a new mathematical model and formulas for helping to plan genome mapping projects, using various single-copy landmark (SCL) detection, or anchoring, strategies. We derive formulas that allow us to examine the effects of interactions among the following variables: average insert size of the cloning vector, average size of SCL, the number of SCL, and the redundancy in coverage of the clone library. We also examine and compare three different ways in which anchoring can be implemented: (1) anchors are selected independently of the library to be ordered (random anchoring); (2) anchors are made from end probes from both ends of clones in the library to be ordered (nonrandom anchoring); and (3) anchors are made from one end or the other, randomly, from clones in the library to be ordered (nonrandom anchoring). Our results show that, for biologically realistic conditions, nonrandom anchoring is always more effective than random anchoring for contig building, and there is little to be gained from making SCL from both ends of clones vs. only one end of clones. We compare and contrast our results with other similar mathematical models.     

Association mapping and fine mapping with TreeLD

SUMMARY: The program package TreeLD implements a unified approach to association mapping and fine mapping of complex trait loci and a novel approach to visualizing association data, based on an inferred ancestry of the sample. Fundamentally, the TreeLD approach is based on the idea that the evidence for association at a particular position is contained in the ancestral tree relating the sampled chromosomes at that position. TreeLD provides an easy-to-use interface and can be applied to case-control, TDT trio and quantitative trait data.     

Phylogenetic analysis ofIridaceae with parsimony and distance methods using the plastid generps4

A molecular phylogeny of the familyIridaceae based on the plastid generps4 was obtained using both parsimony and distance methods. Thirty-four species were examined together with eight outgroup species. Results show that theIridaceae are monophyletic, and thatIsophysis is likely to be the earliest emerging genus. SubfamilyIxioideae plus the generaAristea andNivenia form a strongly supported clade. Within subfam.Iridoideae, the tribeIrideae includes the genusBobartia (of disputed position), and the tribeMariceae includesCypella. The division ofIridoideae into tribes is consistent with their geographical distribution.     

Some advantages and limitations of mitosis as a phylogenetic criterion

The advantages and disadvantages of mitosis as a phylogenetic character are discussed. Mitosis is suggested to be a good character on the grounds that it is universally applicable and that it reflects features of the basic organism since it is unlikely to have arisen through multiple endosymbiotic events. Since mitosis is an absolutely essential feature of the cell cycle it is subject to a great deal of evolutionary pressure and one would not expect a priori that relatively inefficient mitotic apparatuses would persist. It is suggested that supposedly primitive mitotic apparatuses are not inefficient and that the evidence that they are functionally different from those of higher organisms is largely negative electron microscopic evidence. This type of evidence is not very satisfactory since it can result from poor preservation and consequently it should be continually retested. Another weakness of mitosis as a phylogenetic criterion (shared with other essentially morphological criteria) is that there is no easy way to relate structural change with genetic change. Thus, while mitosis is a useful phylogenetic character, its usefulness is limited.     

Plasma myeloperoxidase activity as a criterion of therapeutic effectiveness for patients with cardiovascular diseases

A significant increase in the myeloperoxidase (MPO) activity has been found in plasma of patients with stable angina and with acute coronary syndrome (ACS) in comparison with the control group. MPO concentration was significantly increased in plasma of ACS patients. Reduced MPO activity in the treated ACS patients correlated with a favorable outcome of the disease. Generally, changes in plasma MPO concentration coincided with changes in lactoferrin concentration thus confirming the role of neutrophil degranulation in the increase of plasma concentrations of these proteins. The increase in MPO activity was obviously determined by modification of the MPO protein caused by reactive oxygen species and halogen in the molar ratio of 1: 25 and 1: 50. The decrease in plasma MPO activity may be associated with increased plasma concentrations of the physiological inhibitor of its activity, ceruloplasmin, and also with modification of the MPO protein with reactive oxygen species and halogen at their molar ratio of 1: 100 and higher. Thus, MPO activity may be used for evaluation of effectiveness of the treatment of cardiovascular diseases.     

Ultrasound-Assisted Extraction of Arabinogalactan and Dihydroquercetin Simultaneously from Larix gmelinii as a Pretreatment for Pulping and Papermaking

An ultrasound-assisted extraction (UAE) method using ethanol was applied for extracting arabinogalactan (AG) and dihydroquercetin (DHQ) simultaneously from larch wood, as a pretreatment for pulping and papermaking. The extraction parameters were optimized by a Box-Behnken experimental design with the yields of AG and DHQ as the response values. Under optimum conditions (three extractions, each using 40% ethanol, for 50 min, 200 W ultrasound power and 1∶18 solid-liquid ratio), the yields of AG and DHQ were 183.4 and 36.76 mg/g, respectively. After UAE pretreated, the wood chips were used for Kraft pulping (KP) and high boiling solvent pulping (HBSP). The pulping yield after pretreatment was higher than that of untreated (the pulping yields of untreated HBSP and KP were 42.37% and 39.60%, and the pulping yields of HBSP and KP after UAE-pretreated were 44.23% and 41.50% respectively), as indicated by a lower kappa number (77.91 and 27.30 for untreated HBSP and KP; 77.01 and 26.83 for UAE-pretreated HBSP and KP). Furthermore, the characteristics of paper produced from pretreated wood chips were superior to those from the untreated chips: the basis weight was lower (85.67 and 82.48 g·cm⁻² for paper from untreated KP and HBSP; 79.94 and 80.25 g·cm⁻² for paper from UAE-pretreated KP and HBSP), and the tensile strengths, tearing strengths, bursting strengths, and folding strengths were higher than these of paper after UAE-pretreated, respectively.     

Assessing the robustness and optimality of alternative decision rules with varying assumptions

Several alternative decision rules have been proposed for how individuals assess and choose options, such as mates and territories. Three of these rules are the threshold rule, where individuals choose the first option that exceeds a preset level of quality, the best-of- n rule, where individuals assess a fixed number of options and then choose the best of those options, and the comparative Bayes rule, where individuals use estimates of options to selectively assess and choose options. It has been previously concluded that the threshold rule produces higher average fitness than the best-of- n rule when assessment costs are not trivial. However, previous comparisons assumed that time and options are infinite, individuals can estimate the distribution of option quality without uncertainty or mistakes, and individuals receive perfect information about the quality of assessed options. I found that the best-of- n rule produces higher average fitness than the threshold rule despite significant assessment costs, when time for choosing an option is limited, when individuals are choosing from a small pool of options, when estimates of the distribution of option quality are error-prone, and when there is uncertainty about the distribution of option quality. I also found that the comparative Bayes rule produces higher average fitness than the threshold and best-of-n rules when time or options are limited and when individuals receive imperfect information about the quality of assessed options. Therefore, the optimality of alternative decision rules depends on more than the size of assessment costs and the previous conclusions of empirical studies that have assumed such need to be re-examined. Copyright 2002 The Association for the Study of Animal Behaviour. Published by Elsevier Science Ltd. All rights reserved.     

Relation Between Calcium and Strontium Transport Rates as Determined Simultaneously in the Primary Root of Zea mays

Root segments of Zea mays 55 mm long, were exposed to nutrient containing ⁸⁵Sr and ⁴⁵Ca tracers. Translocation rather than uptake was measured, using a newly-designed glass compartmentation system and validated tracer analytic model. Ca transport from solutions containing between 0.25 and 5.0 mm Ca was only slightly affected by concentration, but translocation from 0.25 to 0.05 mm solutions was markedly reduced. Maximum transport of strontium from nutrient containing 0.05 mm Ca was twice that from 2.5 mm Ca, and also twice the maximum calcium transported. Thus, under the condition simulating calcium depletion, i.e., 0.05 mm Ca, greater amounts of strontium were transported. In these cases the solutions also contained stable strontium at concentrations between 0.25 and 5.0 mm. In simultaneous determinations, the ratio of Sr to Ca moved was exactly equal to the ratio of their concentrations in nutrient solution, and there was no evidence of discrimination. Dinitrophenol reduced transport of Sr and Ca to an equivalent extent, amounting to between 2 and 9% of non-treated control levels.     

QTL mapping using a memetic algorithm with modifications of BIC as fitness function

The problem of locating quantitative trait loci (QTL) for experimental populations can be approached by multiple regression analysis. In this context variable selection using a modification of the Bayesian Information Criterion (mBIC) has been well established in the past. In this article a memetic algorithm (MA) is introduced to find the model which minimizes the selection criterion. Apart from mBIC also a second modification (mBIC2) is considered, which has the property of controlling the false discovery rate. Given the Bayesian nature of our selection criteria, we are not only interested in finding the best model, but also in computing marker posterior probabilities using all models visited by MA. In a simulation study MA (with mBIC and mBIC2) is compared with a parallel genetic algorithm (PGA) which has been previously suggested for QTL mapping. It turns out that MA in combination with mBIC2 performs best, where determining QTL positions based on marker posterior probabilities yields even better results than using the best model selected by MA. Finally we consider a real data set from the literature and show that MA can also be extended to multiple interval mapping, which potentially increases the precision with which the exact location of QTLs can be estimated.     

Respiratory sinus arrhythmia as an objective criterion for studying and optimizing speech breathing parameters

It was established that the use of respiratory sinus arrhythmia as an objective physiological criterion of intersystem integration is effective and justifiable for the study, optimization, diagnosis, and correction of human speech breathing, speech, and speech behavior.