CLASSIFY: A group teaching exercise in microbial identification and numerical taxonomy using a Commodore 64 microcomputer

An exercise designed to teach the basic principles of numerical taxonomy is described. The exercise utilizes a computer program, CLASSIFY, written in BASIC for the Commodore 64 microcomputer, which will accept student data obtained from the identification of bacteria, calculate the similarity coefficients, and perform Single Linkage Cluster Analysis. Bacterial identification can be achieved using live cultures and rapid identification kits, or, alternatively, via the bacterial culture simulation program, BUG SIMULATOR, which would be useful for data generation by students inexperienced in handling microbes (e.g. secondary school students).     

Deterministic and stochastic features of rhythmic human movement

The dynamics of rhythmic movement has both deterministic and stochastic features. We advocate a recently established analysis method that allows for an unbiased identification of both types of system components. The deterministic components are revealed in terms of drift coefficients and vector fields, while the stochastic components are assessed in terms of diffusion coefficients and ellipse fields. The general principles of the procedure and its application are explained and illustrated using simulated data from known dynamical systems. Subsequently, we exemplify the method’s merits in extracting deterministic and stochastic aspects of various instances of rhythmic movement, including tapping, wrist cycling and forearm oscillations. In particular, it is shown how the extracted numerical forms can be analysed to gain insight into the dependence of dynamical properties on experimental conditions.     

A generic, object-oriented data model for life cycle analysis applications

Life Cycle Analysis (LCA) requires the manipulation of a large amount of both quantitative and qualitative data. It is also a continuous and iterative process in which the knowledge of previous steps is always necessary for the realization and understanding of subsequent stages. Current LCA data models are mostly organized as lists from which quantitative data can be extracted and manipulated, subsequently leading to lists of numerical results. Performing an LCA can benefit from more flexible structures that allow for complete or partial treatments and provides links between the successive transformations of various types of information. A generic, object-oriented model is presented, written in ISO/STEP EXPRESS, using the STEP principles.     

Resonance Raman spectroscopy

Resonance Raman spectroscopy may yield precise information on the conformation of, and on the interactions assumed by, the chromophores involved in the first steps of the photosynthetic process, whether isolated in solvents, embedded in soluble or membrane proteins, or, as shown recently, in vivo. By making use of this technique, it is possible, for instance, to relate the electronic properties of these molecules to their structure and/or the physical properties of their environment, or to determine subtle changes of their conformation associated with regulatory processes. After a short introduction to the physical principles that govern resonance Raman spectroscopy, the information content of resonance Raman spectra of chlorophyll and carotenoid molecules is described in this review, together with the experiments which helped in determining which structural parameter each Raman band is sensitive to. A selection of applications of this technique is then presented, in order to give a fair and precise idea of which type of information can be obtained from its use in the field of photosynthesis.     

Diagnostic testing revisited: pathways through uncertainty

To aid physicians who may be having difficulty applying the principles of decision analysis to diagnostic data according to the methods published in the past several years, the authors of this paper set out a few principles and schemes for using and interpreting diagnostic data obtained from dichotomous tests. They also present a simple BASIC program for calculating post-test probabilities from likelihood ratios and pretest probabilities that a particular disease is present in a particular patient; the program can be adapted for use on microcomputers.     

Whole-cell MALDI-TOF Mass Spectrometry is an Accurate and Rapid Method to Analyze Different Modes of Macrophage Activation

MALDI-TOF is an extensively used mass spectrometry technique in chemistry and biochemistry. It has been also applied in medicine to identify molecules and biomarkers. Recently, it has been used in microbiology for the routine identification of bacteria grown from clinical samples, without preparation or fractionation steps. We and others have applied this whole-cell MALDI-TOF mass spectrometry technique successfully to eukaryotic cells. Current applications range from cell type identification to quality control assessment of cell culture and diagnostic applications. Here, we describe its use to explore the various polarization phenotypes of macrophages in response to cytokines or heat-killed bacteria. It allowed the identification of macrophage-specific fingerprints that are representative of the diversity of proteomic responses of macrophages. This application illustrates the accuracy and simplicity of the method. The protocol we described here may be useful for studying the immune host response in pathological conditions or may be extended to wider diagnostic applications.     

X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers

The widespread use of mass spectrometry for protein identification has created a demand for computationally efficient methods of matching mass spectrometry data to protein databases. A search using X!Tandem, a popular and representative program, can require hours or days to complete, particularly when missed cleavages and post-translational modifications are considered. Existing techniques for accelerating X!Tandem by employing parallelism are unsatisfactory for a variety of reasons. The paper describes a parallelization of X!Tandem, called X!!Tandem, that shows excellent speedups on commodity hardware and produces the same results as the original program. Furthermore, the parallelization technique used is unusual and potentially useful for parallelizing other complex programs.     

A teaching exercise for the identification of bacteria using an interactive computer program

An interactive computer program written in Fortran is described which provides an exercise in the identification of bacteria. The program, IDEN, provides a novel way of enhancing a student's approach to systematic bacteriology and numerical identification procedures. An unknown bacterium is assigned to a student who is provided with a list of possible species and a list of tests which may be carried out. The student's objective is the correct identification of the unknown in the most economical manner. An indication is given concerning the way in which this program can be used to enhance theoretical instruction and practical investigation.     

Hemodynamics in the mouse aortic arch as assessed by MRI, ultrasound, and numerical modeling

Mice are widely used to study arterial disease in humans, and the pathogenesis of arterial diseases is known to be strongly influenced by hemodynamic factors. It is, therefore, of interest to characterize the hemodynamic environment in the mouse arterial tree. Previous measurements have suggested that many relevant hemodynamic variables are similar between the mouse and the human. Here we use a combination of Doppler ultrasound and MRI measurements, coupled with numerical modeling techniques, to characterize the hemodynamic environment in the mouse aortic arch at high spatial resolution. We find that the hemodynamically induced stresses on arterial endothelial cells are much larger in magnitude and more spatially uniform in the mouse than in the human, an effect that can be explained by fluid mechanical scaling principles. This surprising finding seems to be at variance with currently accepted models of the role of hemodynamics in atherogenesis and the known distribution of atheromatous lesions in mice.     

Co-construction of an assessment method of the environmental sustainability for cattle farms involved in a Protected Designation of Origin (PDO) cheese value chain,Cantal PDO

In France, numerous Protected Designation of Origin (PDO) cheese value chains have revised their specifications to address environmental protection, particularly at the farm level. In this stage, it is nevertheless impossible to state whether the proposed modifications may ensure the sustainability of environmental protection as no environmental sustainability diagnostic has been conducted. The aim of this study is to construct an assessment method for the Cantal PDO farms.A multi-criteria assessment approach was implemented in the following 5 steps: definition of the framework of the study, determination of the principles and criteria, definition of the indicators, aggregation of all elements of the assessment, and finally, test of the assessment method on farms. Focus groups meetings were organised for the first four steps. The panel discussions were based on data obtained from both the literature and surveys of stakeholders operating in the value chain and within the territory.The obtained assessment method comprises 4 principles characterised by 33 indicators. The most important principle (45%), management of grassland resources, is a key economic and environmental point of the studied farms. It reflects the necessary intensive use of grass by the animals in the PDO farms. Few existing methods addressed this principle that required the design of several new indicators. The second principle, impact of agricultural practices (25%), is often included in environmental sustainability assessment methods The adopted indicators are, thus, drawn from existing methods and adapted to the context of the farms studied. The management of the farm buildings and the landscape principle (18%) is often considered in social sustainability. Its role in environmental sustainability can be explained by its strong link with the image of PDO products. Primarily drawn from the literature, the used indicators have been extended to make the assessment method as objective as possible. Finally, the management of local, energy and water resources principle has the lowest weighting (12%). This can be explained by the limited number of indicators.This assessment method was constructed for the Cantal PDO farms by considering their environment and particularities. In consequence, the stakeholders have taken ownership of it. It could be used by other ruminant systems based on grassland. The development of numerous indicators enhanced the pool of existing indicators. This assessment method was sensitive and allowed for the discrimination between farms.     

widgetcon: A website and program for quick conversion among common population genetic data formats

One of the most tedious steps in genetic data analyses is the reformatting data generated with one program for use with other applications. This conversion is necessary because comprehensive evaluation of the data may be based on different algorithms included in diverse software, each requiring a distinct input format. A platform‐independent and freely available program or a web‐based tool dedicated to such reformatting can save time and efforts in data processing. Here, we report widgetcon , a website and a program which has been developed to quickly and easily convert among various molecular data formats commonly used in phylogenetic analysis, population genetics, and other fields. The web‐based service is available at https://www.widgetcon.net . The program and the website convert the major data formats in four basic steps in less than a minute. The resource will be a useful tool for the research community and can be updated to include more formats and features in the future.     

Bottom-up approaches in synthetic biology and biomaterials for tissue engineering applications

Synthetic biologists use engineering principles to design and construct genetic circuits for programming cells with novel functions. A bottom-up approach is commonly used to design and construct genetic circuits by piecing together functional modules that are capable of reprogramming cells with novel behavior. While genetic circuits control cell operations through the tight regulation of gene expression, a diverse array of environmental factors within the extracellular space also has a significant impact on cell behavior. This extracellular space offers an addition route for synthetic biologists to apply their engineering principles to program cell-responsive modules within the extracellular space using biomaterials. In this review, we discuss how taking a bottom-up approach to build genetic circuits using DNA modules can be applied to biomaterials for controlling cell behavior from the extracellular milieu. We suggest that, by collectively controlling intrinsic and extrinsic signals in synthetic biology and biomaterials, tissue engineering outcomes can be improved.     

Selection of proteins with desired properties from natural proteome libraries using mRNA display

mRNA display is a powerful yet challenging in vitro selection technique that can be used to identify proteins with desired properties from both natural proteome and combinatorial polypeptide libraries. The physical conjugation between a protein and its own RNA presents unique challenges in manipulating the displayed proteins at a low nanomolar scale in an RNase-free environment. The following protocol outlines the generation of cDNA libraries derived from natural organisms as well as the steps required for generation of mRNA-protein fusion molecules, in vitro functional selection and regeneration of the selected cDNA library. The selection procedures for the identification of protease substrates and Ca(2+)-dependent calmodulin-binding proteins from natural cDNA libraries are presented as examples. The method can be generally applied to the identification of protein sequences with desired properties from various natural proteome libraries. One round of mRNA display-based selection can be accomplished in ~7 d.     

A Monte Carlo approach to calculate dose distribution around the lineal brachytherapy sources.

Monte Carlo means the statistical methods used to solve stochastic or deterministic physical or mathematical problems. The use of this technique for solving deterministic problems is indicated whenever there is no analytical solution for the problem or when this solution is very difficult or when the use of numerical methods requires an excessive amount of CPU-time. This paper describes the application of Monte Carlo methods using a computer program, called ISODOSE, which calculates isodose curves around linear radioactive sources to be used in brachytherapy treatment-planning. Brachytherapy is a special form of cancer treatment in which the radioactive source is placed near or inside the tumor, in order to produce cancer tissue necrosis. The program is written in C language, and the results will be compared to similar data obtained from a commercially available program at Hospital do Cancer de Recife (Brazil), radiation therapy institute. The use of Monte Carlo techniques in the ISODOSE program allows for plotting isodose curves around linear sources, and it is especially more precise near the borders of the source (singularities), taking less time than it would be possible by using deterministic methods. The ISODOSE program can be used for brachytherapy planning in small clinics in Recife and adjacent areas.     

Crossed immuno-affinoelectrophoresis. An analytical method to predict the result of affinity chromatography

Crossed immuno-affinoelectrophoresis is described as an analytical technique in which the principles of electrophoresis and biospecific interaction are combined. By this method the results of affinity chromatographic experiments can be predicted. Human serum proteins were analyzed by crossed immuno-affinoelectrophoresis and affinity chromatography on concanavalin A bound to Sepharose and concordant results were obtained. Moreover crossed immuno-affinoelectrophoresis is suggested for identification of components with certain recognizable molecular structures.     

The difference among generations in evaluating interior lighting environment

This paper explores the difference among generations in evaluating interior lighting environment, and provides some knowledge for interior lighting design, which can accommodate all generations. Fifteen Computer Graphic pictures, which had the same dimensions (W3000 mmxH2800 mmxD6300 mm) but a different luminous environment are evaluated. Pictures are presented on a screen with a liquid crystal projector in a shaded dark room.A Semantic Differential technique with 12 subjective scales with 5 steps was used for the evaluation. Participants were chosen from 3 age groups: young, middle age, and elderly people.A difference among generations in evaluating interior lighting environment emerged. These tendencies could not be explained solely by visibility. It seems that the personal experience is closely related to the evaluation and preference of luminous environment.     

An automated program to find animals and crop photographs for individual recognition

Detailed data on individual animals are critical to ecological and evolutionary studies, but attaching identifying marks can alter individual fates and behavior leading to biases in parameter estimates and ethical issues. Individual-recognition software has been developed to assist in identifying many species from non-invasive photographic data. These programs utilize algorithms to find unique individual characteristics and compare images to a catalogue of known individuals. Currently, all applications for individual identification require manual processing to crop images so only the area of interest remains, or the area of interest must be manually delineated in each image. Thus, one of the main bottlenecks in processing data from photographic capture-recapture surveys is in cropping to an area of interest so that matching algorithms can identify the individual. Here, we describe the development and testing of an automated cropping program. The methods and techniques we describe are broadly applicable to any system where raw photos must be cropped down to a specific area of interest before pattern recognition software can be used for individual identification. We developed and tested the program for use with identification photos of wild giraffes.     

Registry of unrelated bone marrow donors.

Reports of successful transplantation of bone marrow obtained from unrelated donors who were histocompatibility leukocyte antigen (HLA) identical prompted the Canadian Red Cross Blood Transfusion Service in Ottawa to assess the possibility of developing a bone marrow donor registry in Canada. We sent a pamphlet that explained the program to 1568 people who had undergone apheresis and asked them to reply, stating their interest. At the same time the pamphlets and a poster were placed in the blood donor clinic. We received 1232 replies (78.6%) from the apheresis donors, 838 (68.0%) of which indicated a willingness to attend information sessions. Of the 7158 people who gave blood during the 3-month study period, 225 (3.1%) were interested. At the time this paper was written 47 information sessions had been held, and 721 people had attended, 624 (86.5%) of whom had signed a consent form. This indicates a clear interest in a bone marrow donation program. We believe that the ethical issues are overcome by requesting the donation before identification of any patient. From our experience a national registry of unrelated donors seems feasible, and steps are being taken to implement such a program.