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PubMed1994

Easy adaptation of protein structure to sequence.

An investigation into the conservation of coarse, medium and fine grain structural properties has been performed over a data set of 175 protein tertiary structures in 34 different families, each characterized by a common core fold and a library of conserved sites formed for each family. It is shown that, while the conservation of coarse and medium grain properties correlates to the structural deviation between the proteins, fine grain properties are poorly conserved except in functional sites. This flexibility in fine grain properties suggests that folding can be viewed as an optimization process whereby side chains have freedom to position themselves as best as possible given environmental conformational constraints and that given a basic framework, the local structure is able to adapt easily to sequence variation. The conserved cores of the 34 families are used to estimate a minimal core size of 35% of the fold, consistent with buried residue considerations. Finally, conservation in side chain chi 1 torsion angles is combined with structural deviation, sequence deviation and resolution to suggest a set of example structure pairs suitable for testing automatic homology modelling programs.

Hydrogen Bonding↗

PubMed1999

Controlled atmosphere stunning of poultry.

For more than 20 yr Stork PMT has carried out a lot of research into stunning and killing of poultry with electrical and mechanical methods and by applying gas mixtures. For the past 3 yr, research was carried out under the European umbrellas (AIR and EUREKA) together with BOC, The Spelderholt, CIVO, and Bristol University. This research program involved tests on broiler stunning or killing with various gas mixtures. The effect on meat quality, bleeding, and plucking was studied, as well as the use of gas as a humane way of killing broilers. The study of meat quality was based on tenderness tests conducted on the shear force principle, meat color, and drip and cooking losses. The percentage of blood loss in bleeding, blood spots, and the amount of blood in the veins in relation to the gas mixtures and time of hanging were measured. The effect of gas killing on the plucking characteristics was studied by determining the feather release force and product handling. The behavior of the birds, reflexes, the onset of convulsions, electroencephalograms, and evoked responses were studied in relation to the humanness of gas killing. Anoxia generated through argon or a mixture of argon and carbon dioxide or hypercapnic hypoxia seems to be very promising. The tests revealed that meat tenderness and drip losses will improve. The blood spots, especially those on the thighs and breasts caused by stunning and hanging, disappear altogether. It also appeared that animal welfare will be drastically improved. From a technological point of view, broiler killing in a controlled gas atmosphere is considered to be the optimal process. However, successful introduction of the process requires legislative changes and poultry processors must be made aware of its economic benefits.

Abattoirs↗

PubMed2004

Epithelioid hemangioma of the penis: a clinicopathologic and immunohistochemical analysis of 19 cases, with special reference to exuberant examples often confused with epithelioid hemangioendothelioma and epithelioid angiosarcoma.

Epithelioid hemangiomas of the penis are very rare. To date, less than 10 examples have been reported in the English language literature. In this report, we describe the clinical, histopathologic, and immunohistochemical findings in 19 cases retrieved from our files. The patients ranged in age from 23 to 75 years (median age, 45 years) at the time of initial surgical resection. Seventeen patients presented with a solitary mass, and two presented with two separate, but closely approximated, lesions. The process involved the glans penis (n = 3), shaft (n = 11), base of the penis (n = 2), or penis, not otherwise specified (n = 3). The lesions ranged in size from <0.5 to 2.5 cm (median size, approximately 1.2 cm) in greatest dimension. Eleven examples were specifically noted to be dorsally located, and only one was stated to be ventral. Localized pain or tenderness was the most common complaint, documented in 12 cases. The preoperative duration of the lesions ranged from 5 days to 1 year (median 4.5 months). Microscopically, all examples contained a tumefactive proliferation of epithelioid endothelial cells, often in a nodular or lobular configuration and associated with an inflammatory infiltrate containing lymphocytes and eosinophils. In 14 cases, the vascular proliferation was associated with a small arterial segment, sometimes with mural damage and frequently (n = 13) with intraluminal epithelioid endothelial cells. Based on the growth pattern of the epithelioid endothelial cells, 13 cases were considered "typical," and six were considered exuberant or "atypical." The latter examples had a prominent centrally located zone where nests or sheet-like aggregates of epithelioid endothelial cells did not form discrete vessels. Immunohistochemical data are available for 15 tumors. The epithelioid endothelial cells usually had strong reactivity for CD31, lesser reactivity for factor VIIIrAg, and minimal reactivity for CD34. In 9 of 12 cases, a small number of epithelioid endothelial cells expressed keratins. In all cases tested, at least focal muscle-specific actin-positive myopericytic cells were present bordering the endothelial cells, and this was especially notable peripherally. Initial surgical intervention consisted of either a shave biopsy (n = 1), excisional biopsy (n = 2), or local excision (n = 16). A complete follow-up history is available for 12 patients, and incomplete follow-up information is available for an additional four patients. One patient developed a new epithelioid hemangioma at a site within the penis separate from the initial lesion, but no patient is known to have experienced a true metastasis or to have died of complications of this process. Optimal management appears to be complete local excision with periodic follow-up visits to monitor for local recurrence.

Adult↗

PubMed2001

Determination and use of the monetary values of the averted person-sievert for use in radiation protection decisions in Hungary.

The monetary value of the averted dose is a key element in the implementation of the optimization principle both in radiation praxis and intervention. The main concept of this principle is to select options so as to maintain exposures at a reasonable level. The feature of this concept is to look for the minimal total cost, i.e., the sum of the costs of protection and health detriment. In its publications, ICRP emphasized the need for developing models which also take into account the "subjective" aspects of health detriment in the optimization process, such as the perception of risk by individuals and the need to put more emphasis on equity in the distribution of individual doses. This paper proposes a modified alpha-value model based on CEPN's model (Centre d'Etude sur L'Evaluation de la Protection dans le Domaine Nucleaire) to put more emphasis on recently published considerations about the smaller effects of the portion of collective dose derived from small doses. The parameters of the monetary value of unit collective dose averted, which is a key element of this type of model, can be estimated by means of approaches like human capital (HC) and willingness to pay (WTP) from the point of view of economic theories. The present study summarizes the results achieved by WTP among the radiation specialists mainly from the Paks Nuclear Power Plant, Hungary. The aim of the effort was to determine the value of a statistical life and the monetary value of a unit person-sievert associated with averted occupational exposure due to ionizing radiation. To apply the WTP method, a questionnaire has been prepared on the basis of the one introduced by CEPN in the late 1990's. The investigations show that the value of US$6,200 person-Sv(-1) seems to be acceptable for the alphabase-value for the occupational situation in Hungary in 1999. WTP assessments should be applied with caution since the economic level of the country, the workplace surveyed, and the computational methods affect the results. In addition, achieving a high level safety culture must rely on international cooperation both from the theoretical and practical viewpoints, and international markets affect the associated costs. Therefore the monetary requirements cannot always be assessed solely on a national basis.

Cost-Benefit Analysis↗

PubMed2005

Communication in palliative care: a review of recent literature.

PURPOSE OF REVIEW: The quality of communication with patients, family, and team members is an extremely important element in palliative cancer care. The current paper reviews the literature on these topics as published in 2004. RECENT FINDINGS: Trust was found to be a major factor for relationship building. Information gathered by patient self-report is the method of choice, given improved insight in symptom prevalence, duration, frequency, and interference. Cultural factors in information giving, the optimal process and content, and the difficulty of conveying hope were addressed. Decision making in palliative care requires a complex integration of conceptual knowledge, ethical and legal implications, and communication skills. Aspects of manageability are explored. Although health care providers must communicate about emotions, the existential distress of cancer patients and carers often goes overlooked in the last phases of life. SUMMARY: Themes included the education of health care providers, the need to care for carers, and interdisciplinary communication. Little attention was given to the growing population of elderly patients. Observer-based studies are unfortunately scarce, making the practice of palliative communication unseen. Finally, few studies report the cost-effectiveness of palliative care interventions though such studies may enhance palliative care and convince policy makers of the need to support such care. More empirical work is needed to improve the level of quality needed to ensure a good remaining lifetime for cancer patients whose disease cannot be cured.

Communication↗

PubMed1995

Intrahospital transport of neuro ICU patients.

Neuroscience intensive care unit (NICU) patients are frequently transported out of the critical care environment for diagnostic and interventional procedures. Four hundred and seventy-one such transports from seventeen clinical centers were studied to identify the characteristics of intrahospital transport. Data collected included the destination and duration of transport, number and type of personnel involved, changes in monitoring and treatment during transport, adverse patient responses and the impact on patients left in the unit. Differences between transports characterized as elective or emergent in nature were noted. Results validate that intrahospital transport of NICU patients is both time and labor intensive. The study also suggests that the optimal process for safe and efficient transport is yet to be designed.

Central Nervous System Diseases↗

PubMed1989

Biochemical engineering challenges of purifying useful proteins.

Some of the biochemical engineering issues that arise when the purification of proteins is scaled up are examined. The first question addressed is the quantity of various proteins likely to be required. Consideration is given to the order in which isolation procedures may be applied and to the selective removal on a large scale of non-proteinaceous materials. Some general problems such as the effect of mechanical forces on proteins and their complexes and aggregates are examined, together with ways of enhancing the properties of these aggregates and the methods of recovering them. The manner in which on-line process optimization can be achieved during pilot plant trials is discussed and the paper concludes with a summary of new scientific developments to which the biochemical engineer will need to respond.

Biotechnology↗

PubMed1993

Use of PCR-mediated amplification of Mycobacterium leprae DNA in different types of clinical samples for the diagnosis of leprosy.

DNA of Mycobacterium leprae, obtained by a highly efficient nucleic acid extraction procedure, was used for standardisation of the amplification of an M. leprae-specific repetitive sequence by use of the polymerase chain reaction (PCR). With pure DNA, M. leprae-specific amplification was obtained with as low as 100 ag (1 ag = 10(-18) g) of target DNA, a quantity equal to about one-tenth of the bacterial genome. Optimal processing of different types of clinical samples such as biopsy material, blood and lymph fluid, from multibacillary leprosy patients, was studied. Simple freezing-boiling cycles in the presence of Triton X100, with some additional sample-specific modifications such as pre-treatment with NaOH to eliminate PCR inhibitors, was found to be sufficient to yield amplification of bacterial DNA in samples from paucibacillary patients. Clinical samples from 27 untreated leprosy patients, covering the various clinical forms of the disease, and with a bacterial index ranging from 5+ to 0, were collected and processed for PCR analysis. After hybridisation of the amplified material with a specific sequence, 25 of 27 patients analysed gave positive results for M. leprae in at least one of the samples. The potential of PCR for the diagnosis of leprosy is discussed.

Base Sequence↗

PubMed2002

Optimization of congested traffic by controlling stop-and-go waves.

We propose a new optimization strategy based on inducing stop-and-go waves on the main road and controlling their wavelength. Using numerical simulations of a recent stochastic car-following model we show that this strategy yields optimization of traffic flow when implemented in systems with a localized periodic inhomogeneity, such as signalized intersections and entry ramps. The optimization process is explained by our finding of a generalized fundamental diagram (GFD) for traffic, namely a flux-density-wavelength relation. Projecting the GFD on the density-flux plane yields a two-dimensional region of stable states, qualitatively similar to that found empirically [Kerner, Phys. Rev. Lett. 81, 3797 (1998)] in synchronized traffic.

Journal Article↗

PubMed2003

Direct excess entropy calculation for a Lennard-Jones fluid by the integral equation method.

The present work is devoted to the calculation of excess entropy by means of correlation functions, in the framework of integral equation theory. The tangent linear method is set up to get exact thermodynamic derivatives of the pair-correlation function, essential for the calculation of the physical quantities, as well as to carry out an optimization process for the achievement of thermodynamic consistency. The two-body entropy of the Lennard-Jones fluid is in very good agreement with the available molecular dynamics results, attesting the high degree of accuracy of the integral equation scheme. It is shown that an accurate prediction of the excess entropy and the resulting residual multiparticle entropy relies on the correct evaluation of the excess chemical potential, especially at high density. Two independent routes to calculate the latter are compared, and the consequences are discussed.

Journal Article↗

PubMed2005

Linear embedding via Green's operators: a modeling technique for finite electromagnetic band-gap structures.

We propose a modular electromagnetic modeling procedure for large finite electromagnetic band-gap (EBG) structures, called linear embedding via Green's operators. It is a diakoptic method based on the Huygens-Schelkunoff principle involving equivalent boundary current sources that electromagnetically characterize the enclosed domain of arbitrary shapes, as if it were a multiport system. In a cascade of embedding steps, separate reusable domains are combined to form larger domains. Device design often involves tuning local medium properties in a compact designated domain with a large environment. Through an additional embedding step the equivalent sources describing the environment can be transferred to the boundary of the designated domain, rendering subsequent design steps very fast. This two-stage optimization process is applied in the design of an EBG power splitter.

Journal Article↗

PubMed2006

Generation of long-range correlations in large systems as an optimization problem.

We propose an efficient method of generating long-range correlations in large systems. The development of this method was motivated by the problem of constructing an optimal model for a large-scale porous medium. There are typically long-range correlations in the properties of such porous media, such as their permeability and porosity, for which there are usually only limited data. The optimal model must not only honor (preserve) the available data and their correlation function, but also accurately predict the future behavior of fluid flow in the media. We formulate the problem of generating the long-range correlations as one of optimization, and utilize simulated annealing to generate a d-dimensional array which contains the correlations and honors the existing data. The optimization process is based on the data's correlation function. The method is, therefore, free of the many numerical difficulties and/or limitations that most previous techniques suffer from. It is completely general and may be used for generating long-range correlations with any type of correlation function, in both isotropic and anisotropic media. Representative examples are presented, and the method's efficiency and accuracy are discussed.

Journal Article↗

PubMed1986

Relationship between Photosynthesis and Protein Synthesis in Maize: II. Interconversions of the Photoassimilated Carbon in the Ear Leaf and in the Intermediary Organs to Synthesize the Seed Storage Proteins and Starch.

The mechanisms priming the production, the movement, and the transient and final storage of the photoassimilated carbon in the maize plant were examined at the metabolic level during the formation of the seed, with the ultimate aim to identify metabolic steps restricting grain yield and explaining the delay of formation of the reserve molecules. Under normal field conditions, we show that maize directly supplies the developing seed with the photoassimilated carbon which undergoes numerous interconversions from the ear leaf to the grain. The proteins, either in the leaf or in the seed, are primarily synthesized from incoming amino acids. Nevertheless, a secondary in situ synthesis of amino acids provides the proteins with new amino acids. The amino acids of this second set, slowly synthesized in the seed from the photosynthetic carbon skeletons, are not detected in their free form but immediately and regularly incorporated into the seed proteins, in such a way that, after 4 days of chase, the proportion of the radioactive labeling of the amino acids of the different storage protein groups corresponds to their amino acid composition. In the leaf, the labeling of proteins also arises from different metabolisms, but mainly from the photosynthetic metabolism. Contrary to the seed proteins, the time course of the labeled leaf proteins implies a rapid turnover. The second labeling of starch and proteins in the ear leaf involves a reassimilation of CO(2), a process optimizing the carbon uptake in maize.

Journal Article↗

PubMed1997

Applications of high-energy synchrotron radiation for structural studies of polycrystalline materials.

The large penetration power of high-energy X-rays (>60 keV) raises interesting prospects for new types of structural characterizations of polycrystalline materials. It becomes possible in a non-destructive manner to perform local studies, within the bulk of the material, of the fundamental materials physics properties: grain orientations, strain, dislocation densities etc. In favourable cases these properties may be mapped in three dimensions with a spatial resolution that matches the dimensions of the individual grains. Imbedded volumes and interfaces become accessible. Moreover, the high energies allow better in-situ studies of samples in complicated environments (industrial process optimization). General techniques for research in this energy range have been developed using broad-band angle-dispersive methods, on-line two-dimensional detectors and conical slits. Characterizations have been made at the level of the individual grains and grain boundaries as well as on ensembles of grains. The spatial resolution is presently of the order of 10-100 micom. Four examples of applications are presented along with an outlook.

Journal Article↗

PubMed1989

Paraplegic standing controlled by functional neuromuscular stimulation: Part II--Computer simulation studies.

We simulated two types of body motion. First, the body position is assumed to be initially perturbed from the upright position, and all muscles are assumed inactive at the initial position. The control law developed in the preceding paper drives the body segments to the standing position. Arm movements are then applied to the body to investigate how performance is affected by an external disturbance. Simulated body motion indicated that the current output-feedback control law functions well. The body can recover upright posture from a highly flexed position, and the controller can then maintain the body near the vertical during arm movements. The simulation results showed three consistent activation patterns based on energy minimization: 1) no antagonistic muscle pairs are coactivated, 2) strong muscles are recruited before weak ones, and 3) fast muscles are recruited before slow ones. The reason for the second and third observations is that energy liberation rate depends heavily on the relative amount of muscle activation. Since the current control law requires muscles to generate specific joint torques at a prescribed time, strong muscles do not have to be activated as much as weak ones, and recruiting a fast muscle at low activation level consumes less energy than recruiting a slow one at high activation level. Although the output-feedback control law functions well according to our simulation results, the static optimization process would, in practice, take too much computational time to make it practical. Based on the consistent activation patterns found in our simulations, we therefore developed a simpler (suboptimal) activation-distribution scheme that takes much less time and still gives nearly identical performance.

Biomechanical Phenomena↗

PubMed2000

Genetic algorithms for a robust 3-D MR-CT registration.

The aim of this paper is to present an original usage of genetic algorithms as a robust search space sampler in application to 3-D medical image elastic registration. An overview of the standard steps of a registration algorithm is given. We focus on the genetic algorithms use and particularly on the problem of extraction of the optimal solution among the final genetic population. We provide an original encoding scheme relying on a structural approach of point matching and then point out the need for a local optimization process. We then illustrate the algorithm with a concrete registration example and assert the results with a direct multivolume rendering tool. Finally, the algorithm is applied on the vanderbilt medical image database to assert the robustness and in order to compare it with other techniques.

Algorithms↗

PubMed2005

Simulating pathological gait using the enhanced linear inverted pendulum model.

In this paper, we propose a new method to simulate human gait motion when muscles are weakened. The method is based on the enhanced version of three-dimensional linear inverted pendulum model that is used for generation of gait in robotics. After the normal gait motion is generated by setting the initial posture and the parameters that decide the trajectories of the center of mass and angular momentum, the muscle to be weakened is specified. By minimizing an objective function based on the force exerted by the specified muscle during the motion, the set of parameters that represent the pathological gait was calculated. Since the number of parameters to describe the motion is small in our method, the optimization process converges much more quickly than in previous methods. The effects of weakening the gluteus medialis, the gluteus maximus, and vastus were analyzed. Important similarities were noted when comparing the predicted pendulum motion with data obtained from an actual patient.

Acceleration↗

PubMed2006

Motor unit conduction velocity distribution estimation from evoked motor responses.

Action potentials travel along the muscle fibers with a specific conduction velocity that depends on their structural and functional properties. Only the estimation of muscle conduction velocity distribution (MCVD) may be able to depict this propagation heterogeneity. Based on the method proposed by Cummins et al. (Electroenceph Clin Neurophysiol, 46:647-658, 1979) to estimate nerve conduction velocity distribution (NCVD), the present paper proposes a method that modifies the Cummins' approach to make it suitable for MCVD estimation from electrically evoked motor responses. The MCVD estimation algorithm was first assessed by means of simulated signals in order to control all signal features during the optimization process. Simulations showed that estimated distributions were very close to the true ones when taking into account the specificities of the muscle action potential, due to its generation and extinction (MSE divided by 5 on distribution standard deviation). This method was then applied to real signals. Elicited motor responses were recorded on the biceps brachii of healthy subjects either during repeated maximal stimulations at 20 Hz or during increasing intensity stimulations at 1 Hz. MCVD estimates were used to analyze fatigue and motor unit recruitment processes, respectively.

Action Potentials↗