Regenerating cortical connections in a dish: the entorhino-hippocampal organotypic slice co-culture as tool for pharmacological screening of molecules promoting axon regeneration

We present a method for using long-term organotypic slice co-cultures of the entorhino-hippocampal formation to analyze the axon-regenerative properties of a determined compound. The culture method is based on the membrane interphase method, which is easy to perform and is generally reproducible. The degree of axonal regeneration after treatment in lesioned cultures can be seen directly using green fluorescent protein (GFP) transgenic mice or by axon tracing and histological methods. Possible changes in cell morphology after pharmacological treatment can be determined easily by focal in vitro electroporation. The well-preserved cytoarchitectonics in the co-culture facilitate the analysis of identified cells or regenerating axons. The protocol takes up to a month.

Evaluation of a clinical tool for early etiology identification in status epilepticus.

OBJECTIVES: Because early etiologic identification is critical to select appropriate specific status epilepticus (SE) management, we aim to validate a clinical tool we developed that uses history and readily available investigations to guide prompt etiologic assessment. METHODS: This prospective multicenter study included all adult patients treated for SE of all but anoxic causes from four academic centers. The proposed tool is designed as a checklist covering frequent precipitating factors for SE. The study team completed the checklist at the time the patient was identified by electroencephalography (EEG) request. Only information available in the emergency department or at the time of in-hospital SE identification was used. Concordance between the etiology indicated by the tool and the determined etiology at hospital discharge was analyzed, together with interrater agreement. RESULTS: Two hundred twelve patients were included. Concordance between the etiology hypothesis generated using the tool and the finally determined etiology was 88.7% (95% confidence interval (CI) 86.4-89.8) (κ = 0.88). Interrater agreement was 83.3% (95% CI 80.4-96) (κ = 0.81). SIGNIFICANCE: This tool is valid and reliable for identification early the etiology of an SE. Physicians managing patients in SE may benefit from using it to identify promptly the underlying etiology, thus facilitating selection of the appropriate treatment.

A Transportation Safety Planning Tool for the City of Ames, August 2011

The historically-reactive approach to identifying safety problems and mitigating them involves selecting black spots or hot spots by ranking locations based on crash frequency and severity. The approach focuses mainly on the corridor level without taking the exposure rate (vehicle miles traveled) and socio-demographics information of the study area, which are very important in the transportation planning process, into consideration. A larger study analysis unit at the Transportation Analysis Zone (TAZ) level or the network planning level should be used to address the needs of development of the community in the future and incorporate safety into the long-range transportation planning process. In this study, existing planning tools (such as the PLANSAFE models presented in NCHRP Report 546) were evaluated for forecasting safety in small and medium-sized communities, particularly as related to changes in socio-demographics characteristics, traffic demand, road network, and countermeasures. The research also evaluated the applicability of the Empirical Bayes (EB) method to network-level analysis. In addition, application of the United States Road Assessment Program (usRAP) protocols at the local urban road network level was investigated. This research evaluated the applicability of these three methods for the City of Ames, Iowa. The outcome of this research is a systematic process and framework for considering road safety issues explicitly in the small and medium-sized community transportation planning process and for quantifying the safety impacts of new developments and policy programs. More specifically, quantitative safety may be incorporated into the planning process, through effective visualization and increased awareness of safety issues (usRAP), the identification of high-risk locations with potential for improvement, (usRAP maps and EB), countermeasures for high-risk locations (EB before and after study and PLANSAFE), and socio-economic and demographic induced changes at the planning-level (PLANSAFE).

Controlled expression of recombinant proteins in Physcomitrella patens by a conditional heat-shock promoter: a tool for plant research and biotechnology.

The ability to express tightly controlled amounts of endogenous and recombinant proteins in plant cells is an essential tool for research and biotechnology. Here, the inducibility of the soybean heat-shock Gmhsp17.3B promoter was addressed in the moss Physcomitrella patens, using beta-glucuronidase (GUS) and an F-actin marker (GFP-talin) as reporter proteins. In stably transformed moss lines, Gmhsp17.3B-driven GUS expression was extremely low at 25 degrees C. In contrast, a short non-damaging heat-treatment at 38 degrees C rapidly induced reporter expression over three orders of magnitude, enabling GUS accumulation and the labelling of F-actin cytoskeleton in all cell types and tissues. Induction levels were tightly proportional to the temperature and duration of the heat treatment, allowing fine-tuning of protein expression. Repeated heating/cooling cycles led to the massive GUS accumulation, up to 2.3% of the total soluble proteins. The anti-inflammatory drug acetyl salicylic acid (ASA) and the membrane-fluidiser benzyl alcohol (BA) also induced GUS expression at 25 degrees C, allowing the production of recombinant proteins without heat-treatment. The Gmhsp17.3B promoter thus provides a reliable versatile conditional promoter for the controlled expression of recombinant proteins in the moss P. patens.

MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data.

A recurring task in the analysis of mass genome annotation data from high-throughput technologies is the identification of peaks or clusters in a noisy signal profile. Examples of such applications are the definition of promoters on the basis of transcription start site profiles, the mapping of transcription factor binding sites based on ChIP-chip data and the identification of quantitative trait loci (QTL) from whole genome SNP profiles. Input to such an analysis is a set of genome coordinates associated with counts or intensities. The output consists of a discrete number of peaks with respective volumes, extensions and center positions. We have developed for this purpose a flexible one-dimensional clustering tool, called MADAP, which we make available as a web server and as standalone program. A set of parameters enables the user to customize the procedure to a specific problem. The web server, which returns results in textual and graphical form, is useful for small to medium-scale applications, as well as for evaluation and parameter tuning in view of large-scale applications, requiring a local installation. The program written in C++ can be freely downloaded from ftp://ftp.epd.unil.ch/pub/software/unix/madap. The MADAP web server can be accessed at http://www.isrec.isb-sib.ch/madap/.

2 Iowa Safety Efforts: Analyst Tool & Location Aggregation Project, July 8, 2003

Report produced by the Iowa Department of Transportation about Iowa Safety with Tools and Aggregation.

The application of agricultural land rating and crop models to CO2 and climate change issues in Northern regions : the Mackenzie Basin case study

Selostus: Viljelyvyöhykkeiden ja kasvumallien soveltaminen ilmastonmuutoksen tutkimisessa: Mackenzien jokialue, Kanada

High-precision satellite positioning system as a new tool to study the biomechanics of human locomotion.

New Global Positioning System (GPS) receivers allow now to measure a location on earth at high frequency (5Hz) with a centimetric precision using phase differential positioning method. We studied whether such technique was accurate enough to retrieve basic parameters of human locomotion. Eight subjects walked on an athletics track at four different imposed step frequencies (70-130steps/min) plus a run at free pace. Differential carrier phase localization between a fixed base station and the mobile antenna mounted on the walking person was calculated. In parallel, a triaxial accelerometer, attached to the low back, recorded body accelerations. The different parameters were averaged for 150 consecutive steps of each run for each subject (total of 6000 steps analyzed). We observed a perfect correlation between average step duration measured by accelerometer and by GPS (r=0.9998, N=40). Two important parameters for the calculation of the external work of walking were also analyzed, namely the vertical lift of the trunk and the velocity variation per step. For an average walking speed of 4.0km/h, average vertical lift and velocity variation were, respectively, 4.8cm and 0.60km/h. The average intra-individual step-to-step variability at a constant speed, which includes GPS errors and the biological gait style variation, were found to be 24. 5% (coefficient of variation) for vertical lift and 44.5% for velocity variation. It is concluded that GPS technique can provide useful biomechanical parameters for the analysis of an unlimited number of strides in an unconstrained free-living environment.

Toxoplasma gondii: flat-mounting of retina as a new tool for the observation of ocular infection in mice.

Ocular toxoplasmosis is the principal cause of posterior uveitis and a leading cause of blindness. Animal models are required to improve our understanding of the pathogenesis of this disease. The method currently used for the detection of retinal cysts in animals involves the observation, under a microscope, of all the sections from infected eyes. However, this method is time-consuming and lacks sensitivity. We have developed a rapid, sensitive method for observing retinal cysts in mice infected with Toxoplasma gondii. This method involves combining the flat-mounting of retina - a compromise between macroscopic observation and global analysis of this tissue - and the use of an avirulent recombinant strain of T. gondii expressing the Escherichia coli beta-galactosidase gene, visually detectable at the submacroscopic level. Single cyst unilateral infection was found in six out of 17 mice killed within 28 days of infection, whereas a bilateral infection was found in only one mouse. There was no correlation between brain cysts number and ocular infection.

Automated Recording of Bridge Inspection Data in the Pontis Format Final Report, HR-364 April 1995

A large percentage of bridges in the state of Iowa are classified as structurally or fiinctionally deficient. These bridges annually compete for a share of Iowa's limited transportation budget. To avoid an increase in the number of deficient bridges, the state of Iowa decided to implement a comprehensive Bridge Management System (BMS) and selected the Pontis BMS software as a bridge management tool. This program will be used to provide a selection of maintenance, repair, and replacement strategies for the bridge networks to achieve an efficient and possibly optimal allocation of resources. The Pontis BMS software uses a new rating system to evaluate extensive and detailed inspection data gathered for all bridge elements. To manually collect these data would be a highly time-consuming job. The objective of this work was to develop an automated-computerized methodology for an integrated data base that includes the rating conditions as defined in the Pontis program. Several of the available techniques that can be used to capture inspection data were reviewed, and the most suitable method was selected. To accomplish the objectives of this work, two userfriendly programs were developed. One program is used in the field to collect inspection data following a step-by-step procedure without the need to refer to the Pontis user's manuals. The other program is used in the office to read the inspection data and prepare input files for the Pontis BMS software. These two programs require users to have very limited knowledge of computers. On-line help screens as well as options for preparing, viewing, and printing inspection reports are also available. The developed data collection software will improve and expedite the process of conducting bridge inspections and preparing the required input files for the Pontis program. In addition, it will eliminate the need for large storage areas and will simplify retrieval of inspection data. Furthermore, the approach developed herein will facilitate transferring these captured data electronically between offices within the Iowa DOT and across the state.

Calprotectine fécale: outil diagnostique dans les maladies inflammatoires chroniques de l'intestin [Fecal calprotectin: a diagnostic tool for inflammatory bowel disease].

Fecal calprotectin (FC) is a valid biomarker to discriminate with a good sensitivity and specificity the presence of mucosal lesions of the gastrointestinal tube (e.g. ulcers in the context of inflammatory bowel disease (IBD)) from functional disorders (e.g. irritable bowel syndrome). FC is not specific for IBD and can be elevated also in gastrointestinal infections, ischemic colitis or neoplasia. An elevated FC should stimulate further investigations, notably an endoscopic workup. The level of FC correlates with the endoscopic score in Crohn's disease and ulcerative colitis. The correlation of FC and the endoscopic severity is better than the one of CRP or blood leukocytes. Thus, FC can also be used in the follow-up of IBD patients.