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PubMed2006

Optimal sum-of-pairs multiple sequence alignment using incremental Carrillo and Lipman bounds.

Alignment of sequences is an important routine in various areas of science, notably molecular biology. Multiple sequence alignment is a computationally hard optimization problem which involves the consideration of different possible alignments in order to find an optimal one, given a measure of goodness of alignments. Dynamic programming algorithms are generally well suited for the search of optimal alignments, but are constrained by unwieldy space requirements for large numbers of sequences. Carrillo and Lipman devised a method that helps to reduce the search space for an optimal alignment under a sum-of-pairs measure using bounds on the scores of its pairwise projections. In this paper, we generalize Carrillo and Lipman bounds and demonstrate a novel approach for finding optimal sum-of-pairs multiple alignments that allows incremental pruning of the optimal alignment search space. This approach can result in a drastic pruning of the final search space polytope (where we search for the optimal alignment) when compared to Carrillo and Lipman's approach and hence allows many runs that are not feasible with the original method.

Algorithms↗

PubMed2004

ANDI-03: a genetic algorithm tool for the analysis of activation detector data to unfold high-energy neutron spectra.

The thresholds of (n,xn) reactions in various activation detectors are commonly used to unfold the neutron spectra covering a broad energy span, i.e. from thermal to several hundreds of MeV. The saturation activities of the daughter nuclides (i.e. reaction products) serve as the input data of specific spectra unfolding codes, such as SAND-II and LOUHI-83. However, most spectra unfolding codes, including the above, require an a priori (guess) spectrum to starting up the unfolding procedure of an unknown spectrum. The accuracy and exactness of the resulting spectrum primarily depends on the subjectively chosen guess spectrum. On the other hand, the Genetic Algorithm (GA)-based spectra unfolding technique ANDI-03 (Activation-detector Neutron DIfferentiation) presented in this report does not require a specific starting parameter. The GA is a robust problem-solving tool, which emulates the Darwinian Theory of Evolution prevailing in the realm of biological world and is ideally suited to optimise complex objective functions globally in a large multidimensional solution space. The activation data of the 27Al(n,alpha)24Na, 116In(n,gamma)116mIn, 12C(n,2n)11C and 209Bi(n,xn)(210-x)Bi reactions recorded at the high-energy neutron field of the ISIS Spallation source (Rutherford Appleton Laboratory, UK) was obtained from literature and by applying the ANDI-03 GA tool, these data were used to unfold the neutron spectra. The total neutron fluence derived from the neutron spectrum unfolded using GA technique (ANDI-03) agreed within +/-6.9% (at shield top level) and +/-27.2% (behind a 60 cm thick concrete shield) with the same unfolded with the SAND-II code.

Algorithms↗

PubMed1996

Inwardly rectifying K+ channels that may participate in K+ buffering are localized in microvilli of Schwann cells.

The presence of K+ channels on the Schwann cell plasma membrane suggests that Schwann cells may participate actively during action potential propagation in the peripheral nervous system. One such role for Schwann cells may be to maintain a constant extracellular concentration of K+ in the face of K+ efflux from a repolarizing axon. This buffering is likely to involve the influx of K+ through inward rectifying K+ channels. The molecular cloning of these genes allowed us to examine their expression and localization in Schwann cells in detail. In this study, we demonstrate the expression of two inward rectifying K+ channels, IRK1 and IRK3, in adult rat sciatic nerve. Immunocytochemistry using a polyclonal antibody against these proteins showed that the channels were highly localized at nodes in sciatic nerve. By immunoelectron microscopy, the nodal staining was shown to be concentrated in the microvilli of Schwann cells (also called nodal processes). The large surface area of the microvilli and their presence in the nodal space suggest involvement with ionic buffering. Thus, IRK1 and IRK3 are well suited to K+ buffering by virtue of both their biophysical properties and their localization. The restricted distribution of the inward rectifying K+ channels also provides an example of the highly regulated localization of ion channels to their specialized membrane domains. In the Schwann cell, where the nodal processes are a minute fraction of the total cell membrane, a potent mechanism must be present to concentrate the channels in this structure.

Amino Acid Sequence↗

PubMed1995

MR imaging of the retroperitoneum.

The multiplanar and soft-tissue capabilities of MR imaging make it a valuable diagnostic tool for the retroperitoneal space and its organs. In addition, by virtue of its location, the retroperitoneum is well suited for study by this modality. Appropriate techniques, including the use of contrast, are discussed as are the normal and pathologic appearances of the organs and areas of the retroperitoneum.

Contrast Media↗

PubMed2003

Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.

Anticipating a continuing increase in the number of structures solved by molecular replacement in high-throughput crystallography and drug-discovery programs, a user-friendly web service for automated molecular replacement, map improvement, bias removal and real-space correlation structure validation has been implemented. The service is based on an efficient bias-removal protocol, Shake&wARP, and implemented using EPMR and the CCP4 suite of programs, combined with various shell scripts and Fortran90 routines. The service returns improved maps, converted data files and real-space correlation and B-factor plots. User data are uploaded through a web interface and the CPU-intensive iteration cycles are executed on a low-cost Linux multi-CPU cluster using the Condor job-queuing package. Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures.

Apolipoproteins E↗

PubMed1991

Evaluation of the disposable absorption containment trunk for female U-2 and TR-1 pilots.

Female U-2 and TR-1 pilots needed a urine collection device as part of their high flight pressure suit ensembles. The Disposable Absorption Containment Trunk (DACT) had been designed for short term use with the NASA Space Shuttle Program. This study evaluated the DACT for the extended and repetitive use required for integration into the U-2 and TR-1 aircraft. Six female subjects were tested wearing a custom-fit DACT and the 1030 full pressure suit ensemble with torso harness. They were strapped into the U-2 ejection seat with parachute and seat kit for 10 h and 45 min every 3 d for a total of 5 sessions. The DACT was evaluated for absorptive capability and comfort. Subjects were monitored for dermatitis, vaginitis, and urinary tract infections. The DACT reliably absorbed menstrual flow and urinary outputs to 950 cc. Higher urinary outputs resulted in minimal leakage. Dermatitis in the form of mild erythema and chafing was present, but cleared between sessions without medical intervention. Complaints concerning comfort were minor and limited to fit problems. One case of vaginitis developed. There were no cases of urinary tract infection. The DACT was found to be an acceptable method of urine collection for female U-2 and TR-1 pilots. Minor changes in design will enhance the comfort and performance of the DACT.

Adult↗

PubMed1989

Sustaining humans in space.

One goal of NASA's Ames Research Center is to extend the presence of humans in space. Biomedical research, human performance, and life-support systems form the core of the Ames program. Major questions highlight how the effects of microgravity on living systems are modified by exercise, artificial gravity, autogenic feedback training, and nutrition. Bioengineering and life science studies include humans, animals, and plants. Ames investigators collaborate extensively with outside university and commercial scientists, both within the United States and internationally.

Bone Density↗

PubMed2005

Multisensory space representations in the macaque ventral intraparietal area.

Animals can use different sensory signals to localize objects in the environment. Depending on the situation, the brain either integrates information from multiple sensory sources or it chooses the modality conveying the most reliable information to direct behavior. This suggests that somehow, the brain has access to a modality-invariant representation of external space. Accordingly, neural structures encoding signals from more than one sensory modality are best suited for spatial information processing. In primates, the posterior parietal cortex (PPC) is a key structure for spatial representations. One substructure within human and macaque PPC is the ventral intraparietal area (VIP), known to represent visual, vestibular, and tactile signals. In the present study, we show for the first time that macaque area VIP neurons also respond to auditory stimulation. Interestingly, the strength of the responses to the acoustic stimuli greatly depended on the spatial location of the stimuli [i.e., most of the auditory responsive neurons had surprisingly small spatially restricted auditory receptive fields (RFs)]. Given this finding, we compared the auditory RF locations with the respective visual RF locations of individual area VIP neurons. In the vast majority of neurons, the auditory and visual RFs largely overlapped. Additionally, neurons with well aligned visual and auditory receptive fields tended to encode multisensory space in a common reference frame. This suggests that area VIP constitutes a part of a neuronal circuit involved in the computation of a modality-invariant representation of external space.

Acoustic Stimulation↗

PubMed1997

VDAC channels mediate and gate the flow of ATP: implications for the regulation of mitochondrial function.

The mitochondrial channel, VDAC, forms large (3 nm in diameter) aqueous pores through membranes. We measured ATP flow (using the luciferin/luciferase method) through these channels after reconstitution into planar phospholipid membranes. In the open state of VDAC, as many as 2 x 10(6) ATP molecules can flow through one channel per second. The half-maximum rate occurs at approximately 75 mM ATP. The permeability of a single channel for ATP is 1.1 x 10(-14) cm3/s (about 1 cm/s after correcting for cross-sectional area), which is 100 times less than the permeability for chloride and 10 times less than that for succinate. Channel closure results in a 50% reduction in conductance, showing that monovalent ions are still quite permeable, yet ATP flux is almost totally blocked. This is consistent with an electrostatic barrier that results in inversion of the selectivity of the channel and could be an example of how large channels selectively control the flow of charged metabolites. Thus VDAC is ideally suited to controlling the flow of ATP between the cytosol and the mitochondrial spaces.

Adenosine Triphosphate↗

PubMed2002

Off-resonance correction using an estimated linear time map.

Images acquired in the presence of magnetic field deviations and reconstructed without taking into account the off-resonance, are distorted and corrupted with artifacts. Several post-processing algorithms have been developed for correcting the distortion when it is not possible to fix the field inhomogeneities. These off-resonance correction methods are, in general, slow and computing intensive. To make them faster they are usually adapted to a particular situation or approximated. One of these approximations is to assume that the field map is linear. Although this assumption makes the algorithm fast and robust it is not well suited for arbitrary field maps. On the other hand, there are k-space trajectories with an almost linear time map (time at which each k-space value is acquired), such as 2DFT and EPI. This paper presents an algorithm for off-resonance correction based on a linear time map approximation. This approximation allows a fast algorithm that takes advantage of the almost linearity of the time map and uses the whole field map to correct the images. The proposed correction algorithm reduces the off-resonance induced artifacts while being fast. The linear approximation of the time map needs to be done only once for each trajectory because it does not depend on the acquired image or field map data. The method can also be extended to a multi-plane approximation for sequences with more complex time maps.

Algorithms↗

PubMed1978

Detection of alcohols and volatile fatty acids by head-space gas chromatography in identification of anaerobic bacteria.

A head-space gas chromatographic technique for the analysis of volatile bacterial metabolites is described. Bacteroides fragilis, Clostridium perfringens, and Propionibacterium acnes, cultured in a glucose-containing peptone yeast extract medium, were studied. The head-space technique was compared with the injection of the complete liquid culture medium, and solvent extracts thereof, into the gas chromatograph. Volatile fatty acids could be detected by all three methods, whereas alcohols produced by C. perfringens and P. acnes were detectable only in the head-space chromatograms. Both FFAP and Porapak Q were used as gas chromatography stationary phase. Porapak Q was found more suitable than FFAP for the separation of alcohols. The head-space technique requires a minimum of preparation before the analysis and is well suited to automation.

Alcohols↗

PubMed2004

The different strategies for designing GPCR and kinase targeted libraries.

In recent years the trend in combinatorial library design has shifted to include target class focusing along with diversity and drug-likeness criteria. In this manuscript we review the computational tools available for target class library design and highlight the areas where they have proven useful in our work. The protein kinase family is used to illustrated structure-based target class focused library design, and the G-protein coupled receptor (GPCR) family is used to illustrate ligand-based target class focused library design. Most of the tools discussed are those designed for libraries targeted to a single protein and are simply applied "brute-force" to a large number of targets within the family. The tools that have proven to be the most useful in our work are those that can extract trends from the computational data such as docking and clustering or data mining large amounts of structure activity or high throughput screening data. Finally, areas where improvements are needed in the computational tools available for target class focusing are highlighted. These areas include tools to extract the relevant patterns from all available information for a family of targets, tools to efficiently apply models for all targets in the family rather than just a small subset, mining tools to extract the relevant information from the computational absorption, distribution, metabolism, excretion and toxicity (ADMET) and targeting data, and tools to allow interactive exploration of the virtual space around a library to facilitate the selection of the library that best suits the needs of the design team.

Animals↗

PubMed2002

Highly integrated system solutions for air conditioning.

Starting with the air handling unit, new features concerning energy efficient air treatment in combination with optimisation of required space were presented. Strategic concepts for the supply of one or more operating suites with a modular based air handling system were discussed. The operating theatre ceiling itself, as a major part of the whole integrated system, is no longer a simple air outlet: additional functions have been added in so-called media-bridges, so that it has changed towards a medical apparatus serving as a daily tool for the physicians and the operating staff. Last and not least, the servicing of the whole system has become an integral part of the facility management with remote access to the main functions and controls. The results are understood to be the basis for a discussion with specialists from medical and hygienic disciplines as well as with technically orientated people representing the hospital and building-engineering.

Air Conditioning↗

PubMed2003

Optimizing nitrogen removal in the BioDenitro process.

The potential and limits of different configurations of the BioDenitro-alternating process to suit the various design cases that can arise depending on the wastewater characteristics, space necessary and effluent nitrogen requirements were analysed through simulations of the activated sludge model No. 2. The first analysis involved the combination in one cycle of the main phase in the alternating reactors with an aerated phase having the two reactors in aerobic conditions and/or a hydraulic phase using the flow only in the anoxic reactor. This option has been found to have a very high potential for cases with strict requirements concerning effluent total nitrogen, but limited when the requirements are low effluent NH4-N, relatively high effluent total nitrogen and minimum solids and hydraulic retention times. When the latter conditions have to be fulfilled the incorporation of a post-aeration reactor to the alternating reactor was found to be very effective. In addition the configuration is very flexible because multiple combinations of post-aeration reactor volumes and in the duration of the different phases in the alternating reactors can be selected to achieve effluent nitrogen requirements. This flexibility is limited to the use of moderate values in the post-aeration reactor volumes and in the duration of the aerated phase. An experimental trial of the latter configuration was carried out and demonstrated its operational simplicity by achieving the desired nitrogen requirements in the effluent simply by changing the duration of the aerated phase for a given post-aeration reactor volume. From the experimental results an enhanced simultaneous nitrification-denitrification at the start of aeration in the alternating reactors was found and the ASM2 model was shown to have a satisfactory predictive capacity.

Bioreactors↗

PubMed2004

Contemporary conception of anti-G protection of cosmonauts in flights aboard "Soyuz" space vehicles.

To ensure safety of cosmonauts impacted by +Gx loads during insertion into orbit of a Soyuz-type space vehicle, it is critical to conduct appropriate medical selection of candidates to space flights, to give them proper complete physical and specialized centrifuge training, and to make it sure that at the moment of actual injection the cosmonaut's posture is optimal relative to the g-vector and that the body is tight fitting the custom-molded couch. No AGS is needed. For the purposes of protection of cosmonauts descending in the Soyuz vehicles, vital are countermeasures applied in the course of flight, water-salt supplements on the descent day, and the optimal posture, an anti-g suit, and a custom-molded couch with an additional body-restraint system and dampers used on the phase of reentry.

Acceleration↗

PubMed2003

Sexual selection in female perceptual space: how female túngara frogs perceive and respond to complex population variation in acoustic mating signals.

Female preferences for male mating signals are often evaluated on single parameters in isolation or small suites of characters. Most signals, however, are composites of many individual parameters. In this study we quantified multivariate traits in the advertisement call of the túngara frog, Physalaemus pustulosus. We represented the calls in multidimensional scaling space and chose nine test calls to represent the range of population variation. We then tested females for phonotactic preference between calls in each pair of the nine test calls. We used statistics developed for paired comparisons in such "round robin" competitions to evaluate the null hypothesis of equal attractiveness, and to examine the degree to which females responded to calls as being different from or similar to one another in attractiveness. We then examined the attractiveness of each test call relative to all other test calls as a function of their location in multivariate acoustic space (the acoustic landscape) to visualize sexual selection on calls. Finally, we used methods from cognitive psychology to illustrate the females' perception of call attractiveness in multivariate space, and compared this perceptual landscape to the acoustic landscape of quantitative call variation. We show that correlations between individual call characters are not strong and thus there are few biomechanical constraints on their independent evolution. Most call variables differed among males, and there was high repeatability of call characters within males. Females often discriminated between pairs of calls from the population, and there were significant differences among calls in their attractiveness. Female preferences for calls were not stabilizing. The region of the acoustic landscape that was most attractive to females included the mean call but was not centered around it. The females' perceptual or preference landscape did not correlate with the call's acoustic landscape, and female perception of calls decreased rather than enhanced call differences.

Animal Communication↗

PubMed2006

From genomics to chemical genomics: new developments in KEGG.

The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource (http://www.genome.jp/kegg/) provides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space (KEGG GENES) and the chemical space (KEGG LIGAND), and wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY). A fourth component, KEGG BRITE, has been formally added to the KEGG suite of databases. This reflects our attempt to computerize functional interpretations as part of the pathway reconstruction process based on the hierarchically structured knowledge about the genomic, chemical and network spaces. In accordance with the new chemical genomics initiatives, the scope of KEGG LIGAND has been significantly expanded to cover both endogenous and exogenous molecules. Specifically, RPAIR contains curated chemical structure transformation patterns extracted from known enzymatic reactions, which would enable analysis of genome-environment interactions, such as the prediction of new reactions and new enzyme genes that would degrade new environmental compounds. Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps.

Biotransformation↗

PubMed1981

Use of military antishock trouser in a child.

Angiographic localization and embolization has emerged as the preferred mode of therapy for arterial bleeding associated with pelvic fractures but is not always definitive. Our experience demonstrates the use of an external counter pressure device (MAST) as an essential part of the pediatric surgeon's armamentarium and suggests the need for concurrent venography during angiographic localization of pelvic bleeding sites.

Child↗