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PubMed1993

Multiple coding and the evolutionary properties of RNA secondary structure.

This article evaluates evolutionary properties of the transition from RNA primary sequence to RNA secondary structure. It focuses on the restrictions that the conservation of a protein code in an RNA sequence puts on its potential to evolve towards a specific secondary structure. Restricting the mutations to those that do not affect the coding for a protein restricts both the accessibility and the connectivity of the sequence space. The accessibility is restricted because only certain point mutations are allowed. The connectivity is restricted because no insertions and deletions are allowed. Simulating an evolutionary search process for a specific secondary structure shows that (i) the reduction of allowable point mutations allows for adaptation to some large-scale topology, but strongly reduces the possibility of small-scale adaptations, (ii) the abolition of insertions and deletions has very little effect on the results of the search process. During the evolutionary search process for a secondary structure with a specific topology and a high frequency of base-pairing the quasispecies moves into a subspace in which the similarity between secondary structures of neighboring sequences is relatively high. Increased similarity between second structures of neighboring sequences is also found in the Rev responsive element (RRE) in the lentiviruses Caprine arthritis-encephalitis virus and Visna virus. In these viruses a biased nucleotide frequency in the RRE region suggests that selection for the RRE RNA secondary structure affects the amino acid sequence of the env gene. Our results show a variation in the ruggedness of fitness landscapes which are based on a high degree of epistatic interactions. Fitness landscapes play an essential role, not only in biotic evolution, but also in all kinds of optimization processes (Hill Climbing, Simulated Annealing, Genetic Algorithms, etc). Variation in their ruggedness should therefore be taken into account in the analysis of these processes.

Amino Acid Sequence↗

PubMed1991

Observations on maximum entropy processing of MR images.

A maximum entropy (MAXENT) criteria for MR image processing optimizations has previously shown poor performance, but this note observes that there are two entirely different kinds of "data transmission" applications which appear to have been intermixed. In the two cases, "image entropy" actually refers to different kinds of data variables. The previous literature formulations are for transfer of data in which pixel-locations are the transmitted variable, and these pixels may be neither uniform nor constant. The second application concerns the MRI data set for display. Its data variables are image pixel-values of magnetization intensity, and the data transfer mode has the sense of visual display. When MAXENT criteria are modified to address an array of pixel-value intensities, and use a pixel-value information entropy rather than pixel-locations entropy, then successful data processing results. Restoring display visualization from highly nonuniform surface coils for lumbar spine scans are demonstrated, as an example of MAXENT usefulness.

Image Processing, Computer-Assisted↗

PubMed2005

Evaluation of the performance of mechanisms for noise attenuation in a single-gene expression.

Experiments of synthetic gene regulatory modules and theoretical studies have clarified the stochastic nature of gene expression. The establishment of methods to control the fluctuation in gene expression is an indispensable step to the synthesis of robust and reliable genetic modules. In this study, we evaluate the performances of several major mechanisms to attenuate the fluctuation in a single-gene expression; noise attenuation through the control of the ratio of the transcription rate to the translation one, the interaction between synthesized proteins and background molecules, and an autoregulatory negative feedback. We analytically derive the dependence of the noise intensity on the parameter values related to elementary reaction processes, optimal conditions to attenuate the noise, and the limitation of the attenuation for those mechanisms. Our results can be an important basis for selecting the most efficient combination of the components in the design and synthesis of robust and reliable genetic modules. Furthermore, the knowledge on the performances that we obtain can also play a role in understanding the design principle of the intracellular gene regulatory networks.

Computational Biology↗

PubMed1979

[Nutritional optimization of thermal processing of canned food].

The model developed by Barreiro, Salas and Herrera (7) for the prediction of nutrient losses during the thermal processing of conduction heated foods was used in this work to optimize the thermal processing, maximizing nutrient retention in processes with equivalent sterilization values. The processes were stimulated in a digital computer (taking pea purée canned in cans 307 x 409 as the product analyzed). Aall of the processes had equivalent sterilization values with respect to Clostridium botulinum. The thiamine retention associated with each process was calculated by the model of Barreiro, Salas and Herrera (7). The maximum fraction of thiamine retained was of 0.688 for a process at 114.2 degrees C (237.5 degrees F) for 95 minutes. Also, the possibility of the existence of a can with optimum dimensions for maximum thiamine retention, with the same sterilization values, was studied. It was found that this optimum, with the same does not exist; on the contrary, the retention was at a minimum when the diameter approaches infinite and the height zero, and viceversa. For this reason, from the nutrient retention point of view, it is better to process the product in flat or slender cans for a given sterilization value.

Clostridium botulinum↗

PubMed2002

Scaling-up of a lactose wet granulation process in Mi-Pro high shear mixers.

The high shear wet granulation upscaling possibilities of a Pro-C-epT Mi-Pro 250 ml with a batch size of 40 g were investigated by down-scaling an alpha-lactose monohydrate wet granulation process from a Collette Gral 10 (8 l batch size) to a Pro-C-epT Mi-Pro with different bowl volumes of 5 l, and 1900, 900 and 250 ml. The wet granulation process was optimised in the Gral 10, next an octagonal design was build around the central point. Two process parameters, the impeller tip speed and the water content, were varied at three levels, which resulted in a two-factor three-level experimental design. alpha-Lactose monohydrate 200 M was granulated using a polyvinylpyrollidone K 30 (2.5% on dry material) binder solution. The granules were dried at 25 degrees C for 24 h, sieved and characterised. The granules were compressed to tablets. In all mixer volumes the used impeller tip speed range did not influence the granule or tablet properties. In all bowl volumes the influence of water concentration on actual yield, particle size distribution and granule friability was similar. All batch sizes resulted in tablets of similar quality. For the selected formulation the lab scale Mi-Pro high shear mixers with different bowl volumes could be used to determine the optimal process parameters and to scale up to the Collette Gral 10 pilot scale.

Lactose↗

PubMed2002

A photoacoustic technique for depth-resolved in situ monitoring of biofilms.

Biofilms occur in natural and engineered water systems. Biofouling in technical processes lowers the water quality and increases the frictional resistance in tubes. In wastewater treatment plants, biofilms are used for removal of organic an inorganic pollutants. For improvement of antifouling strategies and for process optimization in wastewater treatments plants, an analytical technique for online monitoring of biofilms is needed. In this article, a new setup for in situ monitoring of biofilms by photoacoustic spectroscopy is presented. To produce a biofilm, a mixture of microorganisms was grown in a nutrient solution inside a tube reactor. The content of the tube reactor was pumped through a flow channel, and biofilms were generated at the inner surfaces. Three photoacoustic sensor heads were integrated at different positions into the base plate of the flow channel. By photoacoustic spectroscopy, growth, thickness, and detachment of biofilms can be monitored on-line and nondestructively. Experiments presented in this article showed that the flow conditions influence the structure and thickness of biofilms. By changing the pH value, electrostatic interactions inside the biofilm matrix were influenced, and the subsequent detachment processes were observed online. The interaction of iron(III) oxide particles with biofilms led to particle adsorption on the outer and inner surfaces of the biofilm. Afterwards, biofilm flocs were sloughed off from the base biofilm.

Acoustics↗

PubMed2006

Current industrial practices of assessing permeability and P-glycoprotein interaction.

Combination of the in vitro models that are high throughput but less predictive and the in vivo models that are low throughput but more predictive is used effectively to evaluate the intestinal permeability and transport characteristics of a large number of drug candidates during lead selection and lead optimization processes. Parallel artificial membrane permeability assay and Caco-2 cells are the most frequently used in vitro models to assess intestinal permeability. The popularity of these models stems from their potential for high throughput, cost effectiveness, and adequate predictability of absorption potential in humans. However, several caveats associated with these models (eg, poor predictability for transporter-mediated and paracellularly absorbed compounds, significant nonspecific binding to cells/devices leading to poor recovery, variability associated with experimental factors) need to be considered carefully to realize their full potential. P-glycoprotein, among other pharmaceutically relevant transporters, has been well demonstrated to be the major determinant of drug disposition. The review article presents an objective analysis of the permeability and transporter models currently being used in the pharmaceutical industry and could help guide the discovery scientists in implementing these models in an optimal fashion.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMedDate not supplied

A triage system for processing fine needle aspiration cytology specimens.

Fine needle aspiration (FNA) cytology is increasingly used in the operating room, in radiology suites and in physicians' offices. A major cause of nondiagnostic FNA specimens is poor preparation techniques. To avoid this problem, we have developed a triage system for handling and preparing FNA specimens. (1) For aspirations performed without a cytotechnologist present, the aspirate is rinsed into 50% ethanol; Cytospin slides are then prepared and stained by the Papanicolaou method. Clinicians are disposed toward this indirect method since no special slide preparation techniques are necessary. The results are equal to those of direct smear preparations, and material so prepared may also be used for immunocytochemistry. (2) When a cytotechnologist is present, both direct and indirect preparations are made. (3) When an immediate interpretation is desired, to ensure adequacy and/or to make a diagnosis, alcohol-fixed direct smears are stained with a modified toluidine blue-eosin stain and read by the cytopathologist. This offers the advantage of a quick diagnosis, which may be made in less than 90 seconds, but with nuclear detail equal to that of the Papanicolaou stain and with good background staining. In summary, our three-tiered approach offers optimal processing for aspirates collected in various settings in our institution.

Biopsy, Needle↗

PubMed1991

Developing criteria for ordering common ancillary services.

This article describes the process utilized to develop criteria for appropriately ordering five ancillary services frequently performed in hospitals: 1) arterial blood gases, 2) electrocardiograms (ECGs), 3) serum electrolytes, 4) chest x-rays, and 5) complete blood counts (CBCs). The development of each set of criteria involved an initial consultant, a panel of six additional regional expert consultants, and three national reviewers. Each criteria set was developed through a process involving seven steps: 1) an initial working draft, 2) revisions at an initial meeting of the regional experts, 3) revisions at a second meeting of the regional experts, 4) written comments from the regional experts, 5) written comments from national reviewers, 6) additional written comments from regional experts, and 7) application of the criteria to cases in a community hospital. The change in item content was measured between steps and agreement with individual items was measured at steps 2, 3, and 4. The results indicate that appreciable change in content occurred with each step except step 4. Agreement started fairly high and was over 90% by step 4. The discussion considers the utility of each developmental step, factors affecting the utility of the criteria, the extent to which the results can be generalized, and the need for more research to identify optimal processes for the development of criteria to evaluate quality of care.

Ancillary Services, Hospital↗

PubMed2004

[A multidisciplinary mModule for oncological documentation within a hospital information system].

The follow-up documentation of oncological patients in Germany is inadequate in many cases: it is usually limited to a minimal dataset mandated by the epidemiological tumor registers; it is carried out in a paper-based fashion and rarely in a multi-disciplinary context. Parallel documentation efforts can result in redundant or erroneous data and excess work. The introduction of hospital information systems (HIS) allows the implementation of digital oncological documentation systems integrated in surrounding clinical workflows that can provide access to existing data sources as well as data entry and presentation across departmental boundaries. This concept enables the integration of tumor documentation, quality assurance and process optimization within HIS. Feasibility requirements include a high flexibility and adaptability of the underlying HIS to reach a seamless integration of oncological documentation forms within routine clinical workflows. This paper presents the conceptual design and implementation of a modular oncological documentation system at the Muenster University Hospital that is capable of integrating the documentation requirements of multiple departments within the hospital.

Computer Systems↗

PubMed2005

Delayed excitatory and inhibitory feedback shape neural information transmission.

Feedback circuitry with conduction and synaptic delays is ubiquitous in the nervous system. Yet the effects of delayed feedback on sensory processing of natural signals are poorly understood. This study explores the consequences of delayed excitatory and inhibitory feedback inputs on the processing of sensory information. We show, through numerical simulations and theory, that excitatory and inhibitory feedback can alter the firing frequency response of stochastic neurons in opposite ways by creating dynamical resonances, which in turn lead to information resonances (i.e., increased information transfer for specific ranges of input frequencies). The resonances are created at the expense of decreased information transfer in other frequency ranges. Using linear response theory for stochastically firing neurons, we explain how feedback signals shape the neural transfer function for a single neuron as a function of network size. We also find that balanced excitatory and inhibitory feedback can further enhance information tuning while maintaining a constant mean firing rate. Finally, we apply this theory to in vivo experimental data from weakly electric fish in which the feedback loop can be opened. We show that it qualitatively predicts the observed effects of inhibitory feedback. Our study of feedback excitation and inhibition reveals a possible mechanism by which optimal processing may be achieved over selected frequency ranges.

Action Potentials↗

PubMed2005

Adopting a practical statistical approach for evaluating assay agreement in drug discovery.

The authors assess the equivalence of 2 assays and put forward a general approach for assay agreement analysis that can be applied during drug discovery. Data sets generated by different assays are routinely compared to each other during the process of drug discovery. For a given target, the assays used for high-throughput screening and structure-activity relationship studies will most likely differ in their assay reagents, assay conditions, and/or detection technology, which makes the interpretation of data between assays difficult, particularly as most assays are used to measure quantitative changes in compound potency against the target. To better quantify the relationship of data sets from different assays for the same target, the authors evaluated the agreement between results generated by 2 different assays that measure the activity of compounds against the same protein, ALK5. The authors show that the agreement between data sets can be quantified using correlation and Bland-Altman plots, and the precision of the assays can be used to define the expectations of agreement between 2 assays. They propose a scheme for addressing issues of assay data equivalence, which can be applied to address questions of how data sets compare during the lead identification and lead optimization processes in which assays are frequently added and changed.

Activin Receptors, Type I↗

PubMed2001

Quantitative microbiological risk assessment.

The production of safe food is being increasingly based on the use of risk analysis, and this process is now in use to establish national and international food safety objectives. It is also being used more frequently to guarantee that safety objectives are met and that such guarantees are achieved in a cost-effective manner. One part of the overall risk analysis procedure-risk assessment-is the scientific process in which the hazards and risk factors are identified, and the risk estimate or risk profile is determined. Risk assessment is an especially important tool for governments when food safety objectives have to be developed in the case of 'new' contaminants in known products or known contaminants causing trouble in 'new' products. Risk assessment is also an important approach for food companies (i) during product development, (ii) during (hygienic) process optimalization, and (iii) as an extension (validation) of the more qualitative HACCP-plan. This paper discusses these two different types of risk assessment, and uses probability distribution functions to assess the risks posed by Escherichia coli O157:H7 in each case. Such approaches are essential elements of risk management, as they draw on all available information to derive accurate and realistic estimations of the risk posed. The paper also discusses the potential of scenario-analysis in simulating the impact of different or modified risk factors during the consideration of new or improved control measures.

Animals↗

PubMed2004

Structural elucidation of catechin and epicatechin in sorrel leaf extracts using liquid-chromatography coupled to diode array-, fluorescence-, and mass spectrometric detection.

Flavonoids are natural compounds in medicinal herbs and posses several biological activities important in plant drug design. Especially strong antioxidant effects play an important role against radical oxidative stress causing pathological processes, such as arteriosclerosis or cancer. The aim of this work was to investigate unknown analytes found in sorrel leaf (Rumex acetosa) extracts in order to discover new leading compounds to enable quality control in phytopharmaceuticals made thereof. Therefore compounds of interest were separated after methanolic extraction by reversed-phase liquid chromatography (RP-LC) employing silica-C18 as stationary phase using gradient elution with water (10 mM H3PO4) and acetonitrile as mobile phase. Structural elucidation was carried out by diode array, fluorescence, and mass spectroscopic detection. Photodiode-array detection allowed the extraction of UV-absorbance spectra from the peaks of interest. Absorbance maxima were found at 203 and 279 nm with a shoulder at 230 nm. Additionally fluorescence emission and excitation spectra were recorded from the analytes using a fluorescence detector (FLD) after stop flow (lambdaex = 279 nm, lambdaem = 307 nm). The chromatographic reversed-phase system was coupled to an ion-trap mass spectrometer (LC-MS) by using an electrospray ionization interface (ESI). After optimization processes the separation was carried out using an ammonium acetate buffer at pH 5.5. Mass spectrometric detection turned out to be more sensitive in negative mode. Collisionally induced dissociation (CID) was used to obtain fragment ions of structural relevance (LC-MS/MS). Finally, compounds of interest coming from sorrel leaf (Rumex acetosa) eluting at low acetonitrile concentrations were confirmed to be catechin and epicatechin.

Catechin↗

PubMed2006

Comparison of effects of high-pressure processing and heat treatment on immunoactivity of bovine milk immunoglobulin G in enriched soymilk under equivalent microbial inactivation levels.

Immunoglobulin-rich foods may provide health benefits to consumers. To extend the refrigerated shelf life of functional foods enriched with bovine immunoglobulin G (IgG), nonthermal alternatives such as high-pressure processing (HPP) may offer advantages to thermal processing for microbial reduction. To evaluate the effects of HPP on the immunoactivity of bovine IgG, a soymilk product enriched with milk protein concentrates, derived from dairy cows that were hyperimmunized with 26 human pathogens, was subjected to HPP or heat treatment. To achieve a 5 log reduction in inoculated Escherichia coli 8739, the HPP or heat treatment requirements were 345 MPa for 4 min at 30 degrees C or for 20 s at 70 degrees C, respectively. To achieve a 5 log reduction in natural flora in the enriched soymilk, the HPP or heat treatments needed were 552 MPa for 4 min at 30 degrees C or for 120 s at 78.2 degrees C, respectively. At equivalent levels for a 5 log reduction in E. coli, HPP and heat treatment caused 25% and no detectable loss in bovine IgG activity, respectively. However, at equivalent levels for a 5 log reduction in natural flora, HPP and heat resulted in 65 and 85% loss of bovine IgG activity, respectively. Results of combined pressure-thermal kinetic studies of bovine milk IgG activity were provided to determine the optimal process conditions to preserve product function.

Animals↗

PubMed2004

Temperature effect on Listeria monocytogenes growth in the event of contamination of cooked pork products.

The aim of this study was to describe the effect of temperature on the growth of Listeria monocytogenes in the event of postprocess contamination of packaged pork meats. This study was carried out in two steps. In the first step, the effect of temperature on L. monocytogenes growth rates was determined in duplicates at 13 temperatures between 2 and 43 degrees C by turbidimetric methods and adjusted by a quantitative secondary model. Then, seven sets of growth kinetics were collected by challenge testing in white pudding and roulade, both cooked pork products prepared according to an industrial process and stored at suboptimal temperatures ranging from 2 to 20 degrees C. In the second step, objectives were to (i) collect direct information on the temperature effect of L. monocytogenes on the two pork products, (ii) compare the two products regarding L. monocytogenes exposure, and (iii) compare results given by modeling (step i) with results obtained independently and then evaluate the model application domain. Each kinetic was built with at least 10 experimental data and two replicates. Comparison between L. monocytogenes behavior at 4 degrees C on white pudding and roulade indicated that both meat products were affected by food safety problems. Indeed, after contamination and storage for 10 days at 4 degrees C, the bacterial population increased by 2 log CFU/g in both products. Comparison between growth kinetic simulations and experimental data obtained separately gave satisfactory conclusions; the difference between observed and predicted bacterial population values was always less than 1 log CFU/g and a bias factor of 1.18 when growth rates were compared. These results applied to L. monocytogenes contamination of white pudding or roulade can now be used either in the management of optimal process and distribution networks or in risk assessment (exposure assessment).

Animals↗

PubMed2004

Effect of multislice scanners on patient dose from routine CT examinations in East Anglia.

As part of the dose optimization process, the Ionising Radiation (Medical Exposure) Regulations 2000 include requirements relating to the assessment of patient dose, and the setting and subsequent review of diagnostic reference levels. In East Anglia, audits of effective dose in CT have been carried out in 1996, 1999 and 2002. In the 2002 audit, nine of the 14 scanners assessed had been replaced since the previous audit. Eight of the new scanners were multislice scanners, acquiring up to 16 slices in a single rotation. The objective of the 2002 audit was to investigate the effect of the introduction of these multislice scanners on patient doses from routine CT examinations. Exposure parameters were collected for 10 different types of routine CT examination. In excess of 550 sets of patient data were obtained. For each of these, effective doses were calculated using the results of Monte Carlo simulations published by the National Radiological Protection Board. Averaged across all 10 examinations, regional mean effective doses are 34% higher than in 1999. The multislice scanners in the region give, on average, 35% more effective dose than the single-slice scanners. The effect of collimation in multislice scanners makes these effective dose differences most notable for examinations that use narrow slice widths. Further optimization of exposures on multislice scanners has the potential to reduce the differences observed between single-slice and multislice doses. However, when taken in combination with the increased use of CT in many hospitals, the effective dose increases observed are likely to result in a significant increase in the already substantial collective radiation dose from CT.

England↗

PubMed1992

Geostatistical and morphological methods applied to three-dimensional microscopy.

Three-dimensional (3-D) images of osteocyte lacunae were examined on a confocal microscope. Both geostatistical and morphological processing techniques were used to improve and to analyse them. By a geostastical approach, this study aims at improving 3-D confocal images before any further image processing. Optimized linear filters, which take account of the second-order statistics and the 3-D structure of the data, allow for the removal of imperfections such as noise and/or blur due to the axial convolution, and interpolate voxels on a face-centred cubic grid from an initial cubic grid. An application of this technique to 3-D biological images is demonstrated. In a second step, a 3-D binary image is digitized and cleaned with 3-D morphological filters. The standard 3-D measurements cannot be applied in this case, since all osteocytes cut the border of the field. For this reason a 3-D Boolean model has been adjusted, from which it is possible to derive all useful information on the repartition and the morphology of the osteocytes.

Humans↗