Automatic analysis of composite physical signals using non-negative factorization and information criterion

In time-resolved spectroscopy, composite signal sequences representing energy transfer in fluorescence materials are measured, and the physical characteristics of the materials are analyzed. Each signal sequence is represented by a sum of non-negative signal components, which are expressed by model functions. For analyzing the physical characteristics of a measured signal sequence, the parameters of the model functions are estimated. Furthermore, in order to quantitatively analyze real measurement data and to reduce the risk of improper decisions, it is necessary to obtain the statistical characteristics from several sequences rather than just a single sequence. In the present paper, we propose an automatic method by which to analyze composite signals using non-negative factorization and an information criterion. The proposed method decomposes the composite signal sequences using non-negative factorization subjected to parametric base functions. The number of components (i.e., rank) is also estimated using Akaike's information criterion. Experiments using simulated and real data reveal that the proposed method automatically estimates the acceptable ranks and parameters.     

Porcine parvovirus removal using trimer and biased hexamer peptides

Assuring the microbiological safety of biological therapeutics remains an important concern. Our group has recently reported small trimeric peptides that have the ability to bind and remove a model nonenveloped virus, porcine parvovirus (PPV), from complex solutions containing human blood plasma. In an effort to improve the removal efficiency of these small peptides, we created a biased library of hexamer peptides that contains two previously reported trimeric peptides designated WRW and KYY. This library was screened and several hexamer peptides were discovered that also removed PPV from solution, but there was no marked improvement in removal efficiency when compared to the trimeric peptides. Based on simulated docking experiments, it appeared that hexamer peptide binding is dictated more by secondary structure, whereas the binding of trimeric peptides is dominated by charge and hydrophobicity. This study demonstrates that trimeric and hexameric peptides may have different, matrix-specific roles to play in virus removal applications. In general, the hexamer ligand may perform better for binding of specific viruses, whereas the trimer ligand may have more broadly reactive virus-binding properties.     

Contribution to the theory of random and biased nets

The probabilistic theory of random and biased nets is further developed by the “tracing” method treated previously. A number of biases expected to be operating in nets, particularly in sociograms, is described. Distribution of closed chain lengths is derived for random nets and for nets with a simple “reflexive” bias. The “island model” bias is treated for the case of two islands and a single axon tracing, resulting in a pair of linear difference equations with two indices. The reflexive bias is extended to multiple-axon tracing by an approximate method resulting in a modification of the random net recursion formula. Results previously obtained are compared with empirical findings and attempts are made to account for observed discrepancies.     

Fine structure and innervation of an annelid muscle with the longest recorded sarcomere

The fine structure of myoepithelial cells of the proventriculus of a marine annelid (Syllis spongiphila) is described. The contractile system of these muscle fibers includes a single medial Z band. The thick filaments possess a ~140 Å paramyosin-like periodicity, but the filament disposition in these cells corresponds to that of other striated muscles, and actin orbitals in the A band number up to 20. The distance between the centers of the two H bands in the largest cells is ca. 40 µ Dyads involving T-system invaginations and isolated vesicles of the sarcoplasmic reticulum are situated at all sarcomere levels. Insertions of the contractile material onto invaginations of the inner and outer cell surfaces are described. Presumed polyaxonal neuromuscular junctions are established across wide synaptic clefts and include terminals with spherical and non-spherical synaptic vesicles. Inclusions occupying the core of each muscle cell appear to be rich in magnesium.     

The design and analysis of case-control studies with biased sampling

A design is proposed for case-control studies in which selection of subjects for full variable ascertainment is based jointly on disease status and on easily obtained "screening" variables that may be related to the disease. Recruitment of subjects follows an independent Bernoulli sampling scheme, with recruitment probabilities set by the investigator in advance. In particular, the sampling can be set up to achieve, on average, frequency matching, provided prior estimates of the disease rates or odds ratios associated with screening variables such as age and sex are available. Alternatively--for example, when studying a rare exposure--one can enrich the sample with certain categories of subject. Following such a design, there are two valid approaches to logistic regression analysis, both of which allow for efficient estimation of effects associated with the screening variables that were allowed to bias the recruitment. The statistical properties of the estimators are compared, both for large samples, based on asymptotics, and for small samples, based on simulations.     

Estimating and interpreting secondary attack risk: Binomial considered biased

The household secondary attack risk (SAR), often called the secondary attack rate or secondary infection risk, is the probability of infectious contact from an infectious household member A to a given household member B, where we define infectious contact to be a contact sufficient to infect B if he or she is susceptible. Estimation of the SAR is an important part of understanding and controlling the transmission of infectious diseases. In practice, it is most often estimated using binomial models such as logistic regression, which implicitly attribute all secondary infections in a household to the primary case. In the simplest case, the number of secondary infections in a household with m susceptibles and a single primary case is modeled as a binomial(m, p) random variable where p is the SAR. Although it has long been understood that transmission within households is not binomial, it is thought that multiple generations of transmission can be neglected safely when p is small. We use probability generating functions and simulations to show that this is a mistake. The proportion of susceptible household members infected can be substantially larger than the SAR even when p is small. As a result, binomial estimates of the SAR are biased upward and their confidence intervals have poor coverage probabilities even if adjusted for clustering. Accurate point and interval estimates of the SAR can be obtained using longitudinal chain binomial models or pairwise survival analysis, which account for multiple generations of transmission within households, the ongoing risk of infection from outside the household, and incomplete follow-up. We illustrate the practical implications of these results in an analysis of household surveillance data collected by the Los Angeles County Department of Public Health during the 2009 influenza A (H1N1) pandemic.     

Analysis of energetically biased transcripts of viruses and transposable elements

RNA interference (RNAi) is a natural endogenous process by which double-stranded RNA molecules trigger potent and specific gene silencing in eukaryotic cells and is characterized by target RNA cleavage. In mammals, small interfering RNAs (siRNAs) are the trigger molecules of choice and constitute a new class of RNA-based antiviral agents. In an efficient RNAi response, the antisense strand of siRNAs must enter the RNA-induced silencing complex (RISC) in a process mediated by thermodynamic features. In this report, we hypothesize that silent mutations capable of inverting thermodynamic properties can promote resistance to siRNAs. Extensive computational analyses were used to assess whether continuous selective pressure that promotes such mutations could lead to the emergence of viral strains completely resistant to RNAi (i.e., prone to transfer only the sense strands to RISC). Based on our findings, we propose that, although synonymous mutations may produce functional resistance, this strategy cannot be systematically adopted by viruses since the longest RNAi-refractory sequence is only 10 nt long. This finding also suggests that all mRNAs display fluctuating thermodynamic landscapes and that, in terms of thermodynamic features, RNAi is a very efficient antiviral system since there will always be sites susceptible to siRNAs.     

A comparison of regression interval mapping and multiple interval mapping for linked QTL

Regression interval mapping and multiple interval mapping are compared with regard to mapping linked quantitative trait loci (QTL) in inbred-line cross experiments. For that purpose, a simulation study was performed using genetic models with two linked QTL. Data were simulated for F(2) populations of different sizes and with all QTL and marker alleles fixed for alternative alleles in the parental lines. The criteria for comparison are power of QTL identification and the accuracy of the QTL position and effect estimates. Further, the estimates of the relative QTL variance are assessed. There are distinct differences in the QTL position estimates between the two methods. Multiple interval mapping tends to be more powerful as compared to regression interval mapping. Multiple interval mapping further leads to more accurate QTL position and QTL effect estimates. The superiority increased with wider marker intervals and larger population sizes. If QTL are in repulsion, the differences between the two methods are very pronounced. For both methods, the reduction of the marker interval size from 10 to 5 cM increases power and greatly improves QTL parameter estimates. This contrasts with findings in the literature for single QTL scenarios, where a marker density of 10 cM is generally considered as sufficient. The use of standard (asymptotic) statistical theory for the computation of the standard errors of the QTL position and effect estimates proves to give much too optimistic standard errors for regression interval mapping as well as for multiple interval mapping.     

Spontaneous discharge patterns of mesencephalic neurons: interval histogram and mean interval relationship

Summary The spontaneous nerve impulse activity of 354 neurons of the mesencephalic reticular formation resp. the superior colliculus of unanesthetized curarized rats resp. cats has been recorded by microelectrodes and processed by means of a LINC computer. A relationship between the shape of interimpulse interval histogram (IH) and the mean interimpulse intervals (MI) of the same spike train has been found. Neurons with long MI's (low frequency of firing) are never characterized by symmetrical IH's, the exponential IH (characterizing random occurrence of impulses) being the most common in these cases. Neurons with symmetrical IH's are usually those with short MI's (fast firing rate). Longlasting recordings with changing MI show that the shape of IH's may not be considered in general a stable feature of certain neurons (in the majority of cases it changes together with the MI). Neurons with symmetrical IH's and short MI's may not be found in the superficial layers but in the depth of the superior colliculus only (having probably like the reticular formation integrative functions). A computer model is presented explaining the observed dependency of the IH shape on the MI duration in terms of the change in the mean frequency of common input process.     

Flow properties of high-molecular-weight DNA solutions: viscosity, recoil, and longest retardation time

Viscosity η, recoil Γ, and longest retardation time τ_1R were measured for buffered aqueous solution of T2 DNA (M = 1.3 × 10⁸) and cell lysattes of Bacillus subtiles W23 (DNA M = 2 × 10⁹) as a function of concetration, shear stress σ, and time of shear t, using a cartesian-diver-suspended couette flow system. For the T2 solution, η decreased with increasing σ, Γ(t) going through a maximum with t. For the B. subtiles lysates, the preponderant rheological component of which is chromatin DNA, above a critical σ, the η, Γ(t), and τ_1R increased t over 15 to 45 minutes duration to values up to several times larger, indicating the formation of intermolecular aggregates. The onset of such effects and their significance in th e measurement of molecular properties by hydrodynamic means is disscussed.