Digital filters for firing rate estimation

When a rate histogram is used to represent the firing pattern of a neuron there is the potential for serious error due to aliasing, and because of this the rate histogram is a very poor way to represent neural activity. It is theoretically possible to encode a signal in a spike train and decode it without error by filtering and sampling. There is no natural optimal filter design for this problem, but it is possible to specify the characteristics of a good rate estimating filter heuristically and design a filter with these characteristics. Two rate estimating filters are described here. Their performance has been tested, and compared to the rate histogram and the French-Holden rate estimating algorithm, by measuring their ability to recover signals encoded as impulse sequences by Integral Pulse Frequency Modulation (IPFM). These filters are simple to implement and perform well. They should be used in preference to the rate histogram.     

Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation

The oligonucleotide specificity for microarray hybridization can be predicted by its sequence identity to non-targets, continuous stretch to non-targets, and/or binding free energy to non-targets. Most currently available programs only use one or two of these criteria, which may choose ‘false’ specific oligonucleotides or miss ‘true’ optimal probes in a considerable proportion. We have developed a software tool, called CommOligo using new algorithms and all three criteria for selection of optimal oligonucleotide probes. A series of filters, including sequence identity, free energy, continuous stretch, GC content, self-annealing, distance to the 3′-untranslated region (3′-UTR) and melting temperature (T_m), are used to check each possible oligonucleotide. A sequence identity is calculated based on gapped global alignments. A traversal algorithm is used to generate alignments for free energy calculation. The optimal T_m interval is determined based on probe candidates that have passed all other filters. Final probes are picked using a combination of user-configurable piece-wise linear functions and an iterative process. The thresholds for identity, stretch and free energy filters are automatically determined from experimental data by an accessory software tool, CommOligo_PE (CommOligo Parameter Estimator). The program was used to design probes for both whole-genome and highly homologous sequence data. CommOligo and CommOligo_PE are freely available to academic users upon request.     

Electropositively charged filters for the recovery of yeasts and bacteria from beverages

The ability of electropositively charged filters to recover yeasts and lactic acid bacteria from a variety of beverages was evaluated. Filtration through 'Zeta plus', grade OSS, filters recovered nearly all of the yeast contaminants from table wines, sherry and port. Recovery of yeasts from cream liqueurs and egg-based beverages was also good but it was not possible to filter drinks containing orange juice, even through filters with nominal pore sizes of 2 to 10 μm. Lactic acid bacteria proved more difficult to recover than yeasts, even though smaller pore-sized filters (1 to 4 μm) were employed. However, a sufficiently high percentage of bacteria were recovered to justify use of these filters for quality assurance. The advantage of concentrating contaminants by using charged filters, and the influence of product composition on the efficiency of microbial adsorption are discussed. The growth of wine-spoiling yeasts and lactic acid bacteria were not inhibited by water- or ethanol-soluble extracts of the filter material.     

Rapid fractionation of wheat leaf protoplasts using membrane filtration : the determination of metabolite levels in the chloroplasts, cytosol, and mitochondria

A technique is presented for measuring the in vivo metabolite levels in the chloroplast stroma, the cytosol, and the mitochondrial matrix of wheat (Triticum aestivum, var `Timmo') leaf protoplasts, in which membrane filtration is used to prepare fractions enriched in the different subcellular fractions within 0.1 seconds after disruption of the protoplasts. By closing a syringe, protoplasts are forced through a net and disrupted, diluting the cytosol into the medium and also releasing intact chloroplasts and mitochondria which can then be immediately removed on membrane filters placed behind the nylon net. By varying the membrane filters, different filtrates are obtained corresponding to (a) mainly cytosol, or (b) cytosol and mitochondria with only low levels of chloroplasts; alternatively, (c) the entire protoplast contents are obtained by omitting the filters. The filtrates are immediately split, half flowing into HClO₄ where they are immediately quenched for subsequent metabolite analyses; the other half flows into detergent and is used to monitor the exact distribution of marker enzymes in each individual fractionation. Using the measured distributions of metabolite and of marker enzymes in the three filtrates, the subcellular distribution of the metabolite can be algebraically calculated. The method is presented using ATP as an example.

The quench time (0.1 second) made possible by membrane filtration is considerably faster than has been possible in the previously developed techniques using silicone oil centrifugation for chloroplasts (1 second) or mitochondria (1 minute). This rapid quench makes it possible to investigate subcellular pools which have a rapid turnover, like the adenine nucleotides.

     

Recurrent fracture of a recovery inferior vena cava filter with pulmonary migration

Inferior vena cava (IVC) filters are indicated in patients with venous thromboembolic disease in whom standard anticoagulation therapy is contraindicated or ineffective. A 32-year-old female presented to our hospital with chest pain 5 years after IVC filter placement. Imaging revealed sequential fracturing and embolization of two of the IVC filter arms to the pulmonary arteries. IVC filter fracture and subsequent migration to the lung is a rare complication. Systematic long-term follow-up in patients with IVC filters and, if possible, filter removal should be considered to prevent possible complications.     

Attrition-free pyrolysis to produce bio-oil and char

Experiments are performed on a laboratory scale setup where beech wood chips are heated by gas convection and walls radiation. This study shows that it is possible to obtain high bio-oil and char yields with relatively low external heat transfer coefficients. The main advantage of this convection/radiation heat transfer mode compared to solid–solid collisions, applied in fluidized bed or twin screw reactors, is the reduction of solid attrition (char and sand). Thus tricky gas–solid separation through hot cyclones and/or hot filters could be avoided or reduced. It should be possible to recover directly bio-oil with less char particles and char free of sand dust. These qualities would allow easier use of these bio-products in different applications.     

Development of simple fitness landscapes for peptides by artificial neural filter systems

The applicability of artificial neural filter systems as fitness functions for sequence-oriented peptide design was evaluated. Two example applications were selected: classification of dipeptides according to their hydrophobicity and classification of proteolytic cleavage-sites of protein precursor sequences according to their mean hydrophobicities and mean side-chain volumes. The cleavage-sites covered 12 residues. In the dipeptide experiments the objective was to separate a selected set of molecules from all other possible dipeptide sequences. Perceptrons, feedforward networks with one hidden layer, and a hybrid network were applied. The filters were trained by a (1,) evolution strategy. Two types of network units employing either a sigmoidal or a unimodal transfer function were used in the feedforward filters, and their influence on classification was investigated. The two-layer hybrid network employed gaussian activation functions. To analyze classification of the different filter systems, their output was plotted in the two-dimensional sequence space. The diagrams were interpreted as fitness landscapes qualifying the markedness of a characteristic peptide feature which can be used as a guide through sequence space for rational peptide design. It is demonstrated that the applicability of neural filter systems as a heuristic method for sequence optimization depends on both the appropriate network architecture and selection of representative sequence data. The networks with unimodal activation functions and the hybrid networks both led to a number of local optima. However, the hybrid networks produced the best prediction results. In contrast, the filters with sigmoidal activation produced good reclassification results leading to fitness landscapes lacking unreasonable local optima. Similar results were obtained for classification of both dipeptides and cleavage-site sequences.     

Electropositively charged filters for the recovery of yeasts and bacteria from beverages

The ability of electropositively charged filters to recover yeasts and lactic acid bacteria from a variety of beverages was evaluated. Filtration through 'Zeta plus', grade O5S, filters recovered nearly all of the yeast contaminants from table wines, sherry and port. Recovery of yeasts from cream liqueurs and egg-based beverages was also good but it was not possible to filter drinks containing orange juice, even through filters with nominal pore sizes of 2 to 10 micron. Lactic acid bacteria proved more difficult to recover than yeasts, even though smaller pore-sized filters (1 to 4 micron) were employed. However, a sufficiently high percentage of bacteria were recovered to justify use of these filters for quality assurance. The advantage of concentrating contaminants by using charged filters, and the influence of product composition on the efficiency of microbial adsorption are discussed. The growth of wine-spoiling yeasts and lactic acid bacteria were not inhibited by water- or ethanol-soluble extracts of the filter material.     

Spectral bandwidth in automated leukocyte classification

Investigators have repeatedly pointed out the importance of spectral information in the automated classification of white blood cells. In general, monochromatic images recorded through two or three color filters are used to extract this information. Although it has generally been thought that the use of narrow band filters provides "cleaner" color information than is obtainable through wide band filters, the choice has not been fully investigated and the question is far from being settled. The use of wide band filters has the clear practical advantage of increased light levels at the detector, resulting in higher signal-to-noise ratio with less demand on light source design. In order to investigate this issue, a series of 681 leukocytes of the most frequently occurring types were digitized by the use of both narrow (10 nm) and wide (90 nm) band filters. Parameters were extracted independently from both sets of images. These parameters were then used to develop a classifier for each set of images. The choice of features and classifier results indicate that there are no major performance differences between the two types of filters.     

The Dissociation Rate of Unlabelled Drugs from Receptor Sites: A Poorly Investigated,Yet Important Aspect in Receptor Research. Studies on the Serotonin-S2 Receptor

Abstract

The labelling by ³H-spiperone of serotonin-S₂ receptors in rat frontal cortex tissue adsorbed to glass fibre filters was investigated. For 12 unlabelled serotonin antagonists the dissociation time from serotonin-S₂ receptors was measured using rat frontal cortex tissue preparations adsorbed to glass fibre filters. The dissociation half-time varied from 4.8 min for pipamperone to 160 min for ritanserin. The drug-receptor dissociation time was not related to a particular class of chemical structure, or to the lipophilicity or the acid dissociation constant of the drugs. The essential requirement of experimental determination of the drug-receptor dissociation time for each drug individually is illustrated. The possible applications of the knowledge of the drug-receptor dissociation time in in vitro and in vivo receptor studies, in pharmacological and pharmaco-kinetic studies and in drug design and receptor modelling is discussed. For various serotonin-S₂ antagonists, the type of inhibition produced by the drug on ³H-ketanserin binding to serotonin-S₂ receptors was determined using suspensions of rat frontal cortical tissue. The observed patterns of inhibition were clearly related to the drug-receptor dissociation times: rapidly dissociating drugs produced competitive inhibition, drugs with dissociation half-times between 15-30 min produced mixed type inhibition, and the very slowly dissociating ritanserin produced non-competitive inhibition.     

Designing Patterns and Profiles for Faster HMM Search

Profile HMMs are powerful tools for modeling conserved motifs in proteins. They are widely used by search tools to classify new protein sequences into families based on domain architecture. However, the proliferation of known motifs and new proteomic sequence data poses a computational challenge for search, requiring days of CPU time to annotate an organism's proteome. It is highly desirable to speed up HMM search in large databases. We design PROSITE-like patterns and short profiles that are used as filters to rapidly eliminate protein-motif pairs for which a full profile HMM comparison does not yield a significant match. The design of the pattern-based filters is formulated as a multichoice knapsack problem. Profile-based filters with high sensitivity are extracted from a profile HMM based on their theoretical sensitivity and false positive rate. Experiments show that our profile-based filters achieve high sensitivity (near 100 percent) while keeping around 20times speedup with respect to the unfiltered search program. Pattern-based filters typically retain at least 90 percent of the sensitivity of the source HMM with 30-40times speedup. The profile-based filters have sensitivity comparable to the multistage filtering strategy HMMERHEAD and are faster in most of our experiments.     

Measuring sunscreen protection against solar-simulated radiation-induced structural radical damage to skin using ESR/spin trapping: development of an ex vivo test method

The in vitro star system used for sunscreen UVA-testing is not an absolute measure of skin protection being a ratio of the total integrated UVA/UVB absorption. The in vivo persistent-pigment-darkening method requires human volunteers. We investigated the use of the ESR-detectable DMPO protein radical-adduct in solar-simulator-irradiated skin substitutes for sunscreen testing. Sunscreens SPF rated 20+ with UVA protection, reduced this adduct by 40-65% when applied at 2 mg/cm(2). SPF 15 Organic UVA-UVB (BMDBM-OMC) and TiO(2)-UVB filters and a novel UVA-TiO(2) filter reduced it by 21, 31 and 70% respectively. Conventional broad-spectrum sunscreens do not fully protect against protein radical-damage in skin due to possible visible-light contributions to damage or UVA-filter degradation. Anisotropic spectra of DMPO-trapped oxygen-centred radicals, proposed intermediates of lipid-oxidation, were detected in irradiated sunscreen and DMPO. Sunscreen protection might be improved by the consideration of visible-light protection and the design of filters to minimise radical leakage and lipid-oxidation.     

Variables Influencing Extraction of Nucleic Acids from Microbial Plankton (Viruses,Bacteria, and Protists) Collected on Nanoporous Aluminum Oxide Filters

Anodic aluminum oxide (AAO) filters have high porosity and can be manufactured with a pore size that is small enough to quantitatively capture viruses. These properties make the filters potentially useful for harvesting total microbial communities from water samples for molecular analyses, but their performance for nucleic acid extraction has not been systematically or quantitatively evaluated. In this study, we characterized the flux of water through commercially produced nanoporous (0.02 μm) AAO filters (Anotop; Whatman) and used isolates (a virus, a bacterium, and a protist) and natural seawater samples to test variables that we expected would influence the efficiency with which nucleic acids are recovered from the filters. Extraction chemistry had a significant effect on DNA yield, and back flushing the filters during extraction was found to improve yields of high-molecular-weight DNA. Using the back-flush protocol, the mass of DNA recovered from microorganisms collected on AAO filters was ≥100% of that extracted from pellets of cells and viruses and 94% ± 9% of that obtained by direct extraction of a liquid bacterial culture. The latter is a minimum estimate of the relative recovery of microbial DNA, since liquid cultures include dissolved nucleic acids that are retained inefficiently by the filter. In conclusion, we demonstrate that nucleic acids can be extracted from microorganisms on AAO filters with an efficiency similar to that achievable by direct extraction of microbes in suspension or in pellets. These filters are therefore a convenient means by which to harvest total microbial communities from multiple aqueous samples in parallel for subsequent molecular analyses.     

Protein folding: evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as an example

A computer program designed to fold a peptide chain consisting solely of helical segments and connecting links of known length is described and evaluated. This study is a detailed extension of certain aspects of the earlier work of Ptitsyn &; Rashin (1975). Possible interaction sites on the helices are sequence dependent and are calculated as described by Richmond &; Richards (1978) using probable changes in solvent contact area as a guide. The helices are then paired according to the list of potential sites, with each helix being paired at least once. The lists of pairings are then examined geometrically, each site having a defined dihedral helix axis angle, a specified inter-helix axis distance, and defined rotations, when required, about each helix axis. Two simplified filters are used: (1) lengths of connecting links must be equal to or greater than the end-to-end distances of the helices; and (2) non-paired helices must not collide. With myoglobin as a test example and only six of the eight helices being considered, a conformation space consisting of more than 3 × 10⁸ structures was surveyed. The two filters reduced the acceptable structure list to 121. Slight readjustment of the parameters in the filters would have reduced this to 20 structures. Of these 20, one closely resembles the actual distribution of helices in myoglobin. The possible utility and pitfalls of this approach as part of an overall protein folding program are discussed.     

DIGITAL FILTERS IN AUDITORY PHYSIOLOGY

ABSTRACT

In auditory research, the manipulation of signals by filtering with analog electronic filters plays an important role. Recently, digital filters that compute signal modifications in realtime became available. They can mimic all functions of analog filters, and additionally make possible new experimental concepts.

This tutorial paper introduces the concept of digital filters by using analogies from acoustics. Even complex acoustical environments can be simulated with digital filters, as they allow the programming of almost arbitrary frequency and phase responses.     

Concentration of enteroviruses from estuarine water.

Pleated cartridge filters readily adsorb viruses in estuarine water at low pH containing aluminum chloride. Adsorbed viruses are efficiently recovered by treating filters with glycine buffer at high pH. By using these procedures, it was possible to recover approximately 70% of the poliovirus added to 400 liters of estuarine water in 3 liters of filter eluate. Reconcentration of virus in the filter eluate in small volumes that are convenient for viral assays was more difficult. Reconcentration methods described previously for eluates from filters that process tap water or treated wastewater were inadequate when applied to eluates from filters used to process estuarine water containing large amounts of organic compounds. Two methods were found to permit efficient concentration of virus in filter eluates in small volumes. In both methods, virus in 3 liters of filter eluate was adsorbed to aluminum hydroxide flocs and then recovered in approximately 150 ml of buffered fetal calf serum. Additional reductions in volume were achieved by ultrafiltration or hydroextraction. By using these procedures 60 to 80% of the virus in 3 liters of filter eluate could be recovered in a final volume of 10 to 40 ml.     

Concentration of enteroviruses from estuarine water.

Pleated cartridge filters readily adsorb viruses in estuarine water at low pH containing aluminum chloride. Adsorbed viruses are efficiently recovered by treating filters with glycine buffer at high pH. By using these procedures, it was possible to recover approximately 70% of the poliovirus added to 400 liters of estuarine water in 3 liters of filter eluate. Reconcentration of virus in the filter eluate in small volumes that are convenient for viral assays was more difficult. Reconcentration methods described previously for eluates from filters that process tap water or treated wastewater were inadequate when applied to eluates from filters used to process estuarine water containing large amounts of organic compounds. Two methods were found to permit efficient concentration of virus in filter eluates in small volumes. In both methods, virus in 3 liters of filter eluate was adsorbed to aluminum hydroxide flocs and then recovered in approximately 150 ml of buffered fetal calf serum. Additional reductions in volume were achieved by ultrafiltration or hydroextraction. By using these procedures 60 to 80% of the virus in 3 liters of filter eluate could be recovered in a final volume of 10 to 40 ml.     

Independent component analysis of natural image sequences yields spatio-temporal filters similar to simple cells in primary visual cortex.

Simple cells in the primary visual cortex process incoming visual information with receptive fields localized in space and time, bandpass in spatial and temporal frequency, tuned in orientation, and commonly selective for the direction of movement. It is shown that performing independent component analysis (ICA) on video sequences of natural scenes produces results with qualitatively similar spatio-temporal properties. Whereas the independent components of video resemble moving edges or bars, the independent component filters, i.e. the analogues of receptive fields, resemble moving sinusoids windowed by steady Gaussian envelopes. Contrary to earlier ICA results on static images, which gave only filters at the finest possible spatial scale, the spatio-temporal analysis yields filters at a range of spatial and temporal scales. Filters centred at low spatial frequencies are generally tuned to faster movement than those at high spatial frequencies.     

Emergence of invariant-feature detectors in the adaptive-subspace self-organizing map

 A new self-organizing map (SOM) architecture called the ASSOM (adaptive-subspace SOM) is shown to create sets of translation-invariant filters when randomly displaced or moving input patterns are used as training data. No analytical functional forms for these filters are thereby postulated. Different kinds of filters are formed by the ASSOM when pictures are rotated during learning, or when they are zoomed. The ASSOM can thus act as a learning feature-extraction stage for pattern recognizers, being able to adapt to many sensory environments and to many different transformation groups of patterns. Received: 14 September 1995 / Accepted in revised form: 8 May 1996     

Is Tillandsia capillaris an efficient bioindicator of atmospheric metal and metalloid deposition? Insights from five months of monitoring in an urban mining area

Atmospheric pollution in megacities has a major impact on human health and environmental quality. Air quality bioindicators may have some advantages over standard devices such as impactors or filters. In this study we evaluated the reliability of Tillandsia sp. versus passive filters for monitoring the atmospheric deposition of metal(loid)s in an area affected by anthropogenic activities. We aimed to gain insight into the composition and origin of atmospheric particles and their fate after deposition on the plant. Three zones with different contamination levels were monitored for five months in 2012. For the highly contaminated area, a linear increase in metal(loïd) accumulation was found in passive filters, whereas for transplanted Tillandsia capillaris the increase was almost linear for As, Cd, Hg, and Sn, but not for Ag, Pb, Sb, and Zn. For the moderately contaminated zone, the results showed that the exposure time was not sufficient for metal(loid) concentrations to increase in either the plants or filters. However, natural specimens provided some indications of the levels of metal contamination. Metal particles were observed on the plant surface and also in the central disc underneath tillandsia trichomes, suggesting that this is a possible pathway for metals to enter the plant. X-ray absorption spectroscopy demonstrated chemical transformation for Pb and As, both in filters and plants. For Pb, sorbed Pb and/or cell wall complexes were identified in the plants. No As^III-S species, indicative of As detoxification, were identified in the plant. Arsenic was oxidized from As^III to As^V in both plants and filters. Thus, in the present study, passive filters proved more reliable than T. capillaris transplants, although natural specimens provided some insights into local contamination. Particulate contaminants underwent chemical transformation after being trapped in the plant, but there was no clear evidence of internalization and detoxification.