Nutrition systems for pressure suits.
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Aerospace Medicine↗
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Acute and prolonged effects of G suit inflation on cardiovascular dynamics.
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Adolescent↗
H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences.
In order to create an alternative to the customary letter-series representation of nucleotide sequences a novel method was developed based on computer graphics. In this new method, the information content of a nucleotide sequence is mapped into a three-dimensional space function (H curve) which can be displayed and manipulated conveniently. Even very long nucleotide sequences can be represented by compact H curves. Such curves are not only characteristic "fingerprints" of complex genetic messages but also embody important parameters concerning the distribution of nucleotides. H curves appear to be particularly suitable for the visual analysis and comprehension of both the local and the global features of long DNA sequences.
Base Sequence↗
A model of hippocampally dependent navigation, using the temporal difference learning rule.
This paper presents a model of how hippocampal place cells might be used for spatial navigation in two watermaze tasks: the standard reference memory task and a delayed matching-to-place task. In the reference memory task, the escape platform occupies a single location and rats gradually learn relatively direct paths to the goal over the course of days, in each of which they perform a fixed number of trials. In the delayed matching-to-place task, the escape platform occupies a novel location on each day, and rats gradually acquire one-trial learning, i.e., direct paths on the second trial of each day. The model uses a local, incremental, and statistically efficient connectionist algorithm called temporal difference learning in two distinct components. The first is a reinforcement-based "actor-critic" network that is a general model of classical and instrumental conditioning. In this case, it is applied to navigation, using place cells to provide information about state. By itself, the actor-critic can learn the reference memory task, but this learning is inflexible to changes to the platform location. We argue that one-trial learning in the delayed matching-to-place task demands a goal-independent representation of space. This is provided by the second component of the model: a network that uses temporal difference learning and self-motion information to acquire consistent spatial coordinates in the environment. Each component of the model is necessary at a different stage of the task; the actor-critic provides a way of transferring control to the component that performs best. The model successfully captures gradual acquisition in both tasks, and, in particular, the ultimate development of one-trial learning in the delayed matching-to-place task. Place cells report a form of stable, allocentric information that is well-suited to the various kinds of learning in the model.
Animals↗
Preliminary crystallographic studies of urease from jack bean and from Klebsiella aerogenes.
Ureases from both jack bean (Canavalia ensiformis) seeds and Klebsiella aerogenes have been crystallized by the hanging drop method. The plant-derived urease crystals are regular octahedra analogous to those obtained by Sumner. Preliminary X-ray diffraction studies show that the crystals belong to the cubic space group F4(1)32, with a = 364 A, and appear to contain one or two subunits in the asymmetric unit. Using a synchrotron source, the crystals diffract to near 3.5 A resolution. Crystals of urease from K. aerogenes belong to the cubic space group I23 or I2(1)3, with a = 170.8 A and appear to contain a single catalytic unit per asymmetric unit. The crystals diffract to better than 2.0 A resolution and are well suited for structural analysis.
Bacterial Proteins↗
A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.
Graphical dot-matrix plots can provide the most complete and detailed comparison of two sequences. Presented here is DOTTER2, a dot-plot program for X-windows which can compare DNA or protein sequences, and also DNA versus protein. The main novel feature of DOTTER is that the user can vary the stringency cutoffs interactively, so that the dot-matrix only needs to be calculated once. This is possible thanks to a 'Greyramp tool' that was developed to change the displayed stringency of the matrix by dynamically changing the greyscale rendering of the dots. The Greyramp tool allows the user to interactively change the lower and upper score limit for the greyscale rendering. This allows exploration of the separation between signal and noise, and fine-grained visualisation of different score levels in the dot-matrix. Other useful features are dot-matrix compression, mouse-controlled zooming, sequence alignment display and saving/loading of dot-matrices. Since the matrix only has to be calculated once and since the algorithm is fast and linear in space, DOTTER is practical to use even for sequences as long as cosmids. DOTTER was integrated in the gene-modelling module of the genomic database system ACEDB3. This was done via the homology viewer BLIXEM in a way that also allows segments from the BLAST suite of searching programs to be superimposed on top of the full dot-matrix. This feature can also be used for very quick finding of the strongest matches. As examples, we analyse a Caenorhabditis elegans cosmid with several tandem repeat families, and illustrate how DOTTER can improve gene modelling.
Amino Acid Sequence↗
Neurosurgical suite of the future. I.
Although the past 10 years have seen a huge influx of technology into the operating room, the environment within which this technology is used has not been greatly modified. The result is a poorly integrated collection of machines and an overcrowded situation in the floor space around the operating room table. Clearly, many areas are open for improvement in the process of surgery, from booking a case to carrying out the operation. Newer operating room designs need to incorporate the flexibility to handle the ever-increasing digital information load that is being generated and that is necessary for the surgical environment to be efficient in time and cost. Room for expansion without major reconstruction should also be incorporated in these designs. In addition, because one operating room design cannot be all things to all specialties, specialized room designs for surgical services would be practical and necessary. The next 10 years will offer the opportunity to make some of these changes, and many groups are working toward making them a reality.
Humans↗
Determination of optimal angles for variable nutation proton magnetic spin-lattice, T1, and spin-spin, T2, relaxation times measurement.
T1 and T2 can be rapidly determined with a combination of multiangle spoiled gradient recalled echo (SPGR) and steady-state free precession (SSFP) imaging. Previously, we demonstrated a simple method for determining the set of SPGR and SSFP angles that provided greater T1 and T2 precision than a set of uniformly spaced angles. In this article a more rigorous approach for determining angles is described. Weighted least-squares is also introduced for T1 and T2 estimation and a novel weighting function described. This new approach, suited for imaging applications where large T1 and T2 ranges are anticipated, provides high and uniform precision over a wide range of T1 and T2 values.
Algorithms↗
A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique.
While there are a number of structurally non-redundant datasets of protein monomers, there is none of protein-protein interfaces. Yet, the availability of such a dataset is expected to provide an added insight into a number of investigations. First and foremost among these is analyzing the interfaces to obtain their prevailing architectures, the forces that account for the protein-protein associations and their packing considerations. Their comparisons with those of the monomers are likely to shed additional light on protein-protein recognition on the one hand and on the folding of the polypeptide chain on the other. Docking simulations are also expected to benefit from the existence of such a dataset. A major stumbling block to the generation of a dataset of interfaces has been that the interface is composed of at least two chains. Furthermore, in the interfaces, each of the chains might be represented by non-contiguous pieces. Their order in the interfaces being compared might be different as well. This discontinuity stems from the definition of an interface. An interface consists of interacting residues between the chains, and those that are in their vicinity in the supporting scaffold, within a certain distance threshold. This necessarily yields unordered fragments, as well as isolated residues. Our novel, efficient, sequence-order-independent structural comparison technique is ideally suited to handle the task of the generation of a library of structurally non-redundant protein-protein interfaces. As it is computer-vision based, it views atoms as collections of points in space, disregarding their chain connectivity. In this work, 351 interface-families are created. Comparisons of the interfaces, and separately, of the chains which contribute to them, yield some interesting cases. In one of the cases, while two interfaces are similar, the structure of only one of the two chains is similar between the two complexes. The structure of the second chain of the first complex differs from that of the second chain of the second complex. Here the structure of the cleft in the first chain dictates the specific binding interactions. In another case, while the interfaces in the two complexes are similar, both chains composing them differ between the complexes. Lastly, the chains composing the complexes are similar, but the interfaces are dissimilar, providing a set of data for investigations of the favorable orientations of protein-protein associations.
Algorithms↗
The epidermal permeability barrier.
The permeability barrier of the skin which prevents transcutaneous water loss and penetration of harmful drugs from the environment is localized in the horny layer of the epidermis. Multiple lipid bilayers obstructing the intercellular space of the stratum corneum fulfill this function. In contrast to cellular membranes consisting predominantly of phospholipids, these lamellae contain mostly ceramides, cholesterol and free fatty acids. The lamellae are derived from the contents of lamellar granules (LGs) which are synthesized in the viable epidermal layers by the keratinocytes. LGs display stacks of small disks each of which represents a flattened vesicle or liposome. Prior to terminal differentiation, the disks are exocytosed into the intercellular space and fused to form uninterrupted sheetlike lamellae. The singular lipid composition of LG-disks and of stratum corneum-lamellae reflects the multistage process of barrier formation. It also renders these structures well suited to provide for a barrier function.
Animals↗
Bimodal signal requisite for agonistic behavior in a dart-poison frog, Epipedobates femoralis.
Animal acoustic signals play seminal roles in mate attraction and regulation of male spacing, maintenance of pairbonds, localization of hosts by parasites, and feeding behavior. Among vertebrate signals, it is becoming clear that no single stereotyped signal feature reliably elicits species-specific behavior, but rather, that a suite of characters is involved. Within the largely nocturnal clade of anuran amphibians, the dart-poison frog, Epipedobates femoralis, is a diurnal species that physically and vigorously defends its calling territory against conspecific intruders. Here we report that physical attacks by a territorial male are provoked only in response to dynamic bimodal stimuli in which the acoustic playback of vocalizations is coupled with vocal sac pulsations, but not by either unimodal cues presented in isolation or static bimodal stimuli. These results suggest that integration of dynamic bimodal cues is necessary to elicit aggression in this species.
Agonistic Behavior↗
Comprehensive two-dimensional gas chromatography for fast screening of wash oils.
Fast screening of wash oils is demonstrated using comprehensive two-dimensional gas chromatography (GCxGC). Wash oils are used in ethylene production plants to minimize compressor fouling. The composition of a wash oil determines its effectiveness in solubilizing heavy hydrocarbons. In particular, the relative amount of 1- and 2-ring aromatics is important. The presence of oxygenates is undesirable because of adverse effects to the process. It is shown that GCxGC is well suited for this application. Species in wash oils are separated and grouped into three bands: a nonpolar aliphatics band, 1- and 2-ring aromatics band, and polyaromatics band. For a given polar secondary column, the spacing between bands in the second dimension can be adjusted in a broad range by selecting a primary column and an oven-temperature-programming rate. Integration of GCxGC peaks is evaluated using a standard GC integration program and a new GCxGC integration program. Consistent results are obtained using both programs for well-separated GCxGC peaks with relative differences for individual peak ranging from 0.04% to 1.6%. Peak responses are integrated by the GCxGC software, and the relative amounts of aromatics content and aliphatics content are estimated by peak response percent with relative standard deviations ranging from 0.15% to 2.8% (n = 3).
Journal Article↗
Poincare Husimi representation of eigenstates in quantum billiards.
For the representation of eigenstates on a Poincare section at the boundary of a billiard different variants have been proposed. We compare these Poincare Husimi functions, discuss their properties, and based on this select one particularly suited definition. For the mean behavior of these Poincare Husimi functions an asymptotic expression is derived, including a uniform approximation. We establish the relation between the Poincare Husimi functions and the Husimi function in phase space from which a direct physical interpretation follows. Using this, a quantum ergodicity theorem for the Poincare Husimi functions in the case of ergodic systems is shown.
Journal Article↗
Three-dimensional portal image-based dose reconstruction in a virtual phantom for rapid evaluation of IMRT plans.
A new method for rapid evaluation of intensity modulated radiation therapy (IMRT) plans has been developed, using portal images for reconstruction of the dose delivered to a virtual three-dimensional (3D) phantom. This technique can replace an array of less complete but more time-consuming measurements. A reference dose calculation is first created by transferring an IMRT plan to a cylindrical phantom, retaining the treatment gantry angles. The isocenter of the fields is placed on or near the phantom axis. This geometry preserves the relative locations of high and low dose regions and has the required symmetry for the dose reconstruction. An electronic portal image (EPI) is acquired for each field, representing the dose in the midplane of a virtual phantom. The image is convolved with a kernel to correct for the lack of scatter, replicating the effect of the cylindrical phantom surrounding the dose plane. This avoids the need to calculate fluence. Images are calibrated to a reference field that delivers a known dose to the isocenter of this phantom. The 3D dose matrix is reconstructed by attenuation and divergence corrections and summed to create a dose matrix (PI-dose) on the same grid spacing as the reference calculation. Comparison of the two distributions is performed with a gradient-weighted 3D dose difference based on dose and position tolerances. Because of its inherent simplicity, the technique is optimally suited for detecting clinically significant variances from a planned dose distribution, rather than for use in the validation of IMRT algorithms. An analysis of differences between PI-dose and calculation, delta PI, compared to differences between conventional quality assurance (QA) and calculation, delta CQ, was performed retrospectively for 20 clinical IMRT cases. PI-dose differences at the isocenter were in good agreement with ionization chamber differences (mean delta PI = -0.8%, standard deviation sigma = 1.5%, against delta CQ = 0.3%, sigma = 1.0%, respectively). PI-dose plane differences had significantly less variance than film plane differences (sigma = 1.1 and 2.1%, respectively). Twenty-two further cases were evaluated using 3D EPI-dosimetry alone. The mean difference delta over volumes with doses above 80% of the isocenter value was delta = -0.3%, sigma(delta) = 0.7%, and standard deviations of the distributions ranged from 1.0 to 2.0%. Verification time per plan, from initial calculation, delivery, dose reconstruction to evaluation, takes less than 1.5 h and is more than four times faster than conventional QA.
Algorithms↗
Parameters to consider in the selection and purchase of a freeze-drying system.
When considering the purchase of a freeze-dryer, the user must establish his own performance standards and particular requirements for the following reasons: 1. Large monetary investment required for the purchase, operation and maintenance of the equipment. 2. The expense and stability of the products to be freeze-dried. Some of the basic parameters that must be considered: 1. Product requirements, such as volumes, optimum temperature, and vacuum limits. 2. Facility restraints relating to the availability of space, and utilities. 3. Return on the capital investment (ROI) 4. Technical competence of operating and maintenance personnel. When the parameters are established, the buyer is prepared to purchase a freeze-dryer to best suit his needs. Precise cycle development, reliable hardware and personnel training, assure productivity and product quality.
Costs and Cost Analysis↗
A method for repeated CSF sampling in the freely moving rat.
With the use of a holder mounted on the skull of rats, a cannula can be implanted so that one end rests on the atlanto-occipital membrane overlying the cisterna magna. Needles introduced through the cannula allow repeated access to the cisterna magna in the freely moving animal. This system is stable for periods of up to 4 weeks and is suited for repeated sampling of the cerebrospinal fluid.
Animals↗
Regularized reconstruction in electrical impedance tomography using a variance uniformization constraint.
This paper describes a new approach to reconstruction of the conductivity field in electrical impedance tomography. Our goal is to improve the tradeoff between the quality of the images and the numerical complexity of the reconstruction method. In order to reduce the computational load, we adopt a linearized approximation to the forward problem that describes the relationship between the unknown conductivity and the measurements. In this framework, we focus on finding a proper way to cope with the ill-posed nature of the problem, mainly caused by strong attenuation phenomena; this is done by devising regularization techniques well suited to this particular problem. First, we propose a solution which is based on Tikhonov regularization of the problem. Second, we introduce an original regularized reconstruction method in which the regularization matrix is determined by space-uniformization of the variance of the reconstructed condictivities. Both methods are nonsupervised, i.e., all tuning parameters are automatically determined from the measured data. Tests performed on simulated and real data indicate that Tikhonov regularization provides results similar to those obtained with iterative methods, but with a much smaller amount of computations. Regularization using a variance uniformization constraint yields further improvements, particularly in the central region of the unknown object where attenuation is most severe. We anticipate that the variance uniformization approach could be adapted to iterative methods that preserve the nonlinearity of the forward problem. More generally, it appears as a useful tool for solving other severely ill-posed reconstruction problems such as eddy current tomography.
Algorithms↗
A conjugated infinite element method for half-space acoustic problems.
Many acoustic problems (especially in environmental acoustics) involve half-space domains bounded by a plane subjected to normal admittance boundary conditions. In the "low" frequency domain, the numerical treatment of such problems usually relies on boundary element methods based on a particular Green's function suited for the half-(admittance) plane. In the present paper, an alternative hybrid finite/infinite element scheme is proposed. The method relies on a direct treatment of nonhomogeneous boundary conditions along infinite element edges (or faces). The procedure is validated through comparisons with an available reference solution.
Acoustics↗