A benchmark test for a quantitative assessment of simple neuron models

Several methods and algorithms have recently been proposed that allow for the systematic evaluation of simple neuron models from intracellular or extracellular recordings. Models built in this way generate good quantitative predictions of the future activity of neurons under temporally structured current injection. It is, however, difficult to compare the advantages of various models and algorithms since each model is designed for a different set of data. Here, we report about one of the first attempts to establish a benchmark test that permits a systematic comparison of methods and performances in predicting the activity of rat cortical pyramidal neurons. We present early submissions to the benchmark test and discuss implications for the design of future tests and simple neurons models

Examination of Heterogeneous Crossing Sequences Between Toner and Rollerball Pen Strokes by Digital Microscopy and 3-D Laser Profilometry

The determination of line crossing sequences between rollerball pens and laser printers presents difficulties that may not be overcome using traditional techniques. This research aimed to study the potential of digital microscopy and 3-D laser profilometry to determine line crossing sequences between a toner and an aqueous ink line. Different paper types, rollerball pens, and writing pressure were tested. Correct opinions of the sequence were given for all case scenarios, using both techniques. When the toner was printed before the ink, a light reflection was observed in all crossing specimens, while this was never observed in the other sequence types. The 3-D laser profilometry, more time-consuming, presented the main advantage of providing quantitative results. The findings confirm the potential of the 3-D laser profilometry and demonstrate the efficiency of digital microscopy as a new technique for determining the sequence of line crossings involving rollerball pen ink and toner. With the mass marketing of laser printers and the popularity of rollerball pens, the determination of line crossing sequences between such instruments is encountered by forensic document examiners. This type of crossing presents difficulties with optical microscopic line crossing techniques involving ballpoint pens or gel pens and toner (1-4). Indeed, the rollerball's aqueous ink penetrates through the toner and is absorbed by the fibers of the paper, leaving the examiner with the impression that the toner is above the ink even when it is not (5). Novotny and Westwood (3) investigated the possibility of determining aqueous ink and toner crossing sequences by microscopic observation of the intersection before and after toner removal. A major disadvantage of their study resides in destruction of the sample by scraping off the toner line to see what was underneath. The aim of this research was to investigate the ways to overcome these difficulties through digital microscopy and three-dimensional (3-D) laser profilometry. The former was used as a technique for the determination of sequences between gel pen and toner printing strokes, but provided less conclusive results than that of an optical stereomicroscope (4). 3-D laser profilometry, which allows one to observe and measure the topography of a surface, has been the subject of a number of recent studies in this area. Berx and De Kinder (6) and Schirripa Spagnolo (7,8) have tested the application of laser profilometry to determine the sequence of intersections of several lines. The results obtained in these studies overcome disadvantages of other methods applied in this area, such as scanning electron microscope or the atomic force microscope. The main advantages of 3-D laser profilometry include the ease of implementation of the technique and its nondestructive nature, which does not require sample preparation (8-10). Moreover, the technique is reproducible and presents a high degree of freedom in the vertical axes (up to 1000 μm). However, when the paper surface presents a given roughness, if the pen impressions alter the paper with a depth similar to the roughness of medium, the results are not always conclusive (8). It becomes difficult in this case to distinguish which characteristics can be imputed to the pen impressions or the quality of the paper surface. This important limitation is assessed by testing different types of paper of variable quality (of different grammage and finishing) and the writing pressure. The authors will therefore assess the limits of 3-D laser profilometry technique and determine whether the method can overcome such constraints. Second, the authors will investigate the use of digital microscopy because it presents a number of advantages: it is efficient, user-friendly, and provides an objective evaluation and interpretation.

Field Demonstration and Laboratory Evaluation of Foamed Asphalts - Muscatine County, HR-233, 1985

In view of the energy, environmental, and economic advantages of the foamed asphalt process using local aggregates in cold mixes and the promising results from Research Project HR-212, a 4.2-mile section of county road in Muscatine County was built with foamed asphalt and local aggregates during August-September 1983. Extensive laboratory evaluation was carried out on five plant mixes representing foamed mixes used in the nine test sections, a laboratory prepared foamed mix, and a laboratory prepared hot mix similar to Plant Mix 1. The foamed mixes were compacted, cured under 15 curing conditions and tested for bulk specific gravity, Marshall stability at 77° F and at 140° F, cured moisture content, resilient modulus and effects of moisture damage due to freeze-thaw cycles, water soaking, and vacuum saturation. In addition, four sets of 83 core samples were taken at 1 to 15 months and tested for moisture content, specific gravity, Marshall stability, and resilient modulus. In summary, the test road has performed satisfactorily for almost two years. The few early construction problems encountered were to be expected for experimental projects dealing with new materials and technologies. Overall results to date are encouraging and foamed asphalt mixes have proved to have the potential as a viable base material in areas where marginal aggregates are available. It is hoped and expected that performance evaluation of the test sections will be continued and that more foamed asphalt trial projects will be constructed and monitored so that experiences and findings from this project can be verified and mix design criteria can be gradually established. For future foamed asphalt projects it is recommended that anti-stripping additives, such as hydrated lime, be added in view of the potential moisture susceptibility of foamed mixes observed in the laboratory evaluation.

Temporal quantification of MAPK induced expression in single yeast cells.

The quantification of gene expression at the single cell level uncovers novel regulatory mechanisms obscured in measurements performed at the population level. Two methods based on microscopy and flow cytometry are presented to demonstrate how such data can be acquired. The expression of a fluorescent reporter induced upon activation of the high osmolarity glycerol MAPK pathway in yeast is used as an example. The specific advantages of each method are highlighted. Flow cytometry measures a large number of cells (10,000) and provides a direct measure of the dynamics of protein expression independent of the slow maturation kinetics of the fluorescent protein. Imaging of living cells by microscopy is by contrast limited to the measurement of the matured form of the reporter in fewer cells. However, the data sets generated by this technique can be extremely rich thanks to the combinations of multiple reporters and to the spatial and temporal information obtained from individual cells. The combination of these two measurement methods can deliver new insights on the regulation of protein expression by signaling pathways.

Comparative modular analysis of gene expression in vertebrate development

The focus of my PhD research was the concept of modularity. In the last 15 years, modularity has become a classic term in different fields of biology. On the conceptual level, a module is a set of interacting elements that remain mostly independent from the elements outside of the module. I used modular analysis techniques to study gene expression evolution in vertebrates. In particular, I identified ``natural'' modules of gene expression in mouse and human, and I showed that expression of organ-specific and system-specific genes tends to be conserved between such distance vertebrates as mammals and fishes. Also with a modular approach, I studied patterns of developmental constraints on transcriptome evolution. I showed that none of the two commonly accepted models of the evolution of embryonic development (``evo-devo'') are exclusively valid. In particular, I found that the conservation of the sequences of regulatory regions is highest during mid-development of zebrafish, and thus it supports the ``hourglass model''. In contrast, events of gene duplication and new gene introduction are most rare in early development, which supports the ``early conservation model''. In addition to the biological insights on transcriptome evolution, I have also discussed in detail the advantages of modular approaches in large-scale data analysis. Moreover, I re-analyzed several studies (published in high-ranking journals), and showed that their conclusions do not hold out under a detailed analysis. This demonstrates that complex analysis of high-throughput data requires a co-operation between biologists, bioinformaticians, and statisticians.

Long-term in vivo regeneration of peripheral nerves through bioengineered nerve grafts.

Although autologous nerve graft is still the first choice strategy in nerve reconstruction, it has the severe disadvantage of the sacrifice of a functional nerve. Cell transplantation in a bioartificial conduit is an alternative strategy to improve nerve regeneration. Nerve fibrin conduits were seeded with various cell types: primary Schwann cells (SC), SC-like differentiated bone marrow-derived mesenchymal stem cells (dMSC), SC-like differentiated adipose-derived stem cells (dASC). Two further control groups were fibrin conduits without cells and autografts. Conduits were used to bridge a 1 cm rat sciatic nerve gap in a long term experiment (16 weeks). Functional and morphological properties of regenerated nerves were investigated. A reduction in muscle atrophy was observed in the autograft and in all cell-seeded groups, when compared with the empty fibrin conduits. SC showed significant improvement in axon myelination and average fiber diameter of the regenerated nerves. dASC were the most effective cell population in terms of improvement of axonal and fiber diameter, evoked potentials at the level of the gastrocnemius muscle and regeneration of motoneurons, similar to the autografts. Given these results and other advantages of adipose derived stem cells such as ease of harvest and relative abundance, dASC could be a clinically translatable route towards new methods to enhance peripheral nerve repair.

Analysis of variance of primary data on plant growth analysis

Plant growth analysis presents difficulties related to statistical comparison of growth rates, and the analysis of variance of primary data could guide the interpretation of results. The objective of this work was to evaluate the analysis of variance of data from distinct harvests of an experiment, focusing especially on the homogeneity of variances and the choice of an adequate ANOVA model. Data from five experiments covering different crops and growth conditions were used. From the total number of variables, 19% were originally homoscedastic, 60% became homoscedastic after logarithmic transformation, and 21% remained heteroscedastic after transformation. Data transformation did not affect the F test in one experiment, whereas in the other experiments transformation modified the F test usually reducing the number of significant effects. Even when transformation has not altered the F test, mean comparisons led to divergent interpretations. The mixed ANOVA model, considering harvest as a random effect, reduced the number of significant effects of every factor which had the F test modified by this model. Examples illustrated that analysis of variance of primary variables provides a tool for identifying significant differences in growth rates. The analysis of variance imposes restrictions to experimental design thereby eliminating some advantages of the functional growth analysis.

Development of Preliminary Load and Resistance Factor Design of Drilled Shafts in Iowa, RB03-012, 2014

The Federal Highway Administration (FHWA) mandated utilizing the Load and Resistance Factor Design (LRFD) approach for all new bridges initiated in the United States after October 1, 2007. To achieve part of this goal, a database for Drilled Shaft Foundation Testing (DSHAFT) was developed and reported on by Garder, Ng, Sritharan, and Roling in 2012. DSHAFT is aimed at assimilating high-quality drilled shaft test data from Iowa and the surrounding regions. DSHAFT is currently housed on a project website (http://srg.cce.iastate.edu/dshaft) and contains data for 41 drilled shaft tests. The objective of this research was to utilize the DSHAFT database and develop a regional LRFD procedure for drilled shafts in Iowa with preliminary resistance factors using a probability-based reliability theory. This was done by examining current design and construction practices used by the Iowa Department of Transportation (DOT) as well as recommendations given in the American Association of State Highway and Transportation Officials (AASHTO) LRFD Bridge Design Specifications and the FHWA drilled shaft guidelines. Various analytical methods were used to estimate side resistance and end bearing of drilled shafts in clay, sand, intermediate geomaterial (IGM), and rock. Since most of the load test results obtained from O-cell do not pass the 1-in. top displacement criterion used by the Iowa DOT and the 5% of shaft diameter for top displacement criterion recommended by AASHTO, three improved procedures are proposed to generate and extend equivalent top load-displacement curves that enable the quantification of measured resistances corresponding to the displacement criteria. Using the estimated and measured resistances, regional resistance factors were calibrated following the AASHTO LRFD framework and adjusted to resolve any anomalies observed among the factors. To illustrate the potential and successful use of drilled shafts in Iowa, the design procedures of drilled shaft foundations were demonstrated and the advantages of drilled shafts over driven piles were addressed in two case studies.

Parameterization of written signatures based on EFD

In this work we propose a method to quantify written signatures from digitalized images based on the use of Elliptical Fourier Descriptors (EFD). As usually signatures are not represented as a closed contour, and being that a necessary condition in order to apply EFD, we have developed a method that represents the signatures by means of a set of closed contours. One of the advantages of this method is that it can reconstruct the original shape from all the coefficients, or an approximated shape from a reduced set of them finding the appropriate number of EFD coefficients required for preserving the important information in each application. EFD provides accurate frequency information, thus the use of EFD opens many possibilities. The method can be extended to represent other kind of shapes.

Evaluation of Lightweight Profilers for Construction Smoothness Evaluation, MLR-02-02, 2004

High-speed non-contact laser profilers have become the standard testing equipment for pavement management ride quality testing. The same technology used in the high-speed profilers is now being used in lightweight profilers for construction smoothness testing. The lightweight profilers have many advantages over the California 25-ft profilograph. Despite the many advantages of the lightweight profilers, there is resistance from the contracting industry toward eliminating the 25-ft profilograph for construction ride testing. One way to reduce or overcome the resistance is to evaluate and demonstrate the advantages/disadvantages of the lightweight profiler in actual field use in Iowa. The objective of the study was to purchase a lightweight profiler and to evaluate its suitability for construction smoothness quality verification and quality acceptance on Iowa projects. A lightweight profiler, an Ames Engineering, Inc. LISA single laser unit, was received in February 2003 for the study. Based on the work done during the 2003 construction season, the following conclusions can be made: (1) For hot mix asphalt surfaces, the LISA correlated well with the contractors' profilographs; (2) LISA results are significantly affected by longitudinal tining on portland cement concrete pavements, requiring a laser system upgrade to give accurate results; (3) A significant timesaving was realized by using the LISA; (4) Increasing visibility and reducing time in the construction zone improved safety; (5) One person with limited lifting capabilities could set up and operate the LISA; and (6) With the current Iowa Department of Transportation specification, the LISA cannot totally replace the profilograph, since bridges and short segments with no adjoining pavement would still require a profilograph.

Selective ablation of photovoltaic materials with UV laser sources for monolithic interconnection of devices based on a-Si:H

Lasers are essential tools for cell isolation and monolithic interconnection in thin-film-silicon photovoltaic technologies. Laser ablation of transparent conductive oxides (TCOs), amorphous silicon structures and back contact removal are standard processes in industry for monolithic device interconnection. However, material ablation with minimum debris and small heat affected zone is one of the main difficulty is to achieve, to reduce costs and to improve device efficiency. In this paper we present recent results in laser ablation of photovoltaic materials using excimer and UV wavelengths of diode-pumped solid-state (DPSS) laser sources. We discuss results concerning UV ablation of different TCO and thin-film silicon (a-Si:H and nc-Si:H), focussing our study on ablation threshold measurements and process-quality assessment using advanced optical microscopy techniques. In that way we show the advantages of using UV wavelengths for minimizing the characteristic material thermal affection of laser irradiation in the ns regime at higher wavelengths. Additionally we include preliminary results of selective ablation of film on film structures irradiating from the film side (direct writing configuration) including the problem of selective ablation of ZnO films on a-Si:H layers. In that way we demonstrate the potential use of UV wavelengths of fully commercial laser sources as an alternative to standard backscribing process in device fabrication.

Comparison between a high-resolution single-stage Orbitrap and a triple quadrupole mass spectrometer for quantitative analyses of drugs.

The capabilities of a high-resolution (HR), accurate mass spectrometer (Exactive-MS) operating in full scan MS mode was investigated for the quantitative LC/MS analysis of drugs in patients' plasma samples. A mass resolution of 50,000 (FWHM) at m/z 200 and a mass extracted window of 5 ppm around the theoretical m/z of each analyte were used to construct chromatograms for quantitation. The quantitative performance of the Exactive-MS was compared with that of a triple quadrupole mass spectrometer (TQ-MS), TSQ Quantum Discovery or Quantum Ultra, operating in the conventional selected reaction monitoring (SRM) mode. The study consisted of 17 therapeutic drugs including 8 antifungal agents (anidulafungin, caspofungin, fluconazole, itraconazole, hydroxyitraconazole posaconazole, voriconazole and voriconazole-N-oxide), 4 immunosuppressants (ciclosporine, everolimus, sirolimus and tacrolimus) and 5 protein kinase inhibitors (dasatinib, imatinib, nilotinib, sorafenib and sunitinib). The quantitative results obtained with HR-MS acquisition show comparable detection specificity, assay precision, accuracy, linearity and sensitivity to SRM acquisition. Importantly, HR-MS offers several benefits over TQ-MS technology: absence of SRM optimization, time saving when changing the analysis from one MS to another, more complete information of what is in the samples and easier troubleshooting. Our work demonstrates that U/HPLC coupled to Exactive HR-MS delivers comparable results to TQ-MS in routine quantitative drug analyses. Considering the advantages of HR-MS, these results suggest that, in the near future, there should be a shift in how routine quantitative analyses of small molecules, particularly for therapeutic drugs, are performed.

Analysis of cannabinoids in oral fluid by liquid chromatography-tandem mass spectrometry

A sensitive method was developed for quantifying a wide range of cannabinoids in oral fluid (OF) by liquid chromatography-tandem mass spectrometry (LC-MS/MS). These cannabinoids include a dagger(9)-tetrahydrocannabinol (THC), 11-hydroxy-a dagger(9)-tetrahydrocannabinol (11-OH-THC), 11-nor-9-carboxy-a dagger(9)-tetrahydrocannabinol (THCCOOH), cannabinol (CBN), cannabidiol (CBD), a dagger(9)-tetrahydrocannabinolic acid A (THC-A), 11-nor-9-carboxy-a dagger(9)-tetrahydrocannabinol glucuronide (THCCOOH-gluc), and a dagger(9)-tetrahydrocannabinol glucuronide (THC-gluc). Samples were collected using a Quantisal (TM) device. The advantages of performing a liquid-liquid extraction (LLE) of KCl-saturated OF using heptane/ethyl acetate versus a solid-phase extraction (SPE) using HLB copolymer columns were determined. Chromatographic separation was achieved in 11.5 min on a Kinetex (TM) column packed with 2.6-mu m core-shell particles. Both positive (THC, 11-OH-THC, CBN, and CBD) and negative (THCCOOH, THC-gluc, THCCOOH-gluc, and THC-A) electrospray ionization modes were employed with multiple reaction monitoring using a high-end AB Sciex API 5000 (TM) triple quadrupole LC-MS/MS system. Unlike SPE, LLE failed to extract THC-gluc and THCCOOH-gluc. However, the LLE method was more sensitive for the detection of THCCOOH than the SPE method, wherein the limit of detection (LOD) and limit of quantification (LOQ) decreased from 100 to 50 pg/ml and from 500 to 80 pg/ml, respectively. The two extraction methods were successfully applied to OF samples collected from volunteers before and after they smoked a homemade cannabis joint. High levels of THC were measured soon after smoking, in addition to significant amounts of THC-A. Other cannabinoids were found in low concentrations. Glucuronide conjugate levels were lower than the method's LOD for most samples. Incubation studies suggest that glucuronides could be enzymatically degraded by glucuronidase prior to OF collection

Application of ultrasound in bone surgery: two case reports

The present study describes some of the applications of ultrasound in bone surgery, based on the presentation of two clinical cases. The Piezosurgery® ultrasound device was used (Tecnología Mectron Medical, Carasco, Italy). In one case the instrument was used to harvest a chin bone graft for placement in a bone defect at level 1.2, while in the other case a bony window osteotomy was made in the external wall of the maxillary sinus, in the context of a sinus membrane lift procedure. The Piezosurgery® device produces specific ultrasound frequency modulation (25-29 kHz), and has been designed to secure increased precision in application to bone surgery. This instrument produces selective sectioning of the mineralized bone structures, and causes less intra- and postoperative bleeding. One of the advantages of the Piezosurgery® device is that it can be used for maxillary sinus lift procedures in dental implant placement. In this context it considerably lessens the risk of sinus mucosa laceration by preparing the bony window in the external wall of the upper maxilla, and can be used to complete the lifting maneuver. The use of ultrasound in application to hard tissues can be regarded as a slow technique compared with the conventional rotary instruments, since it requires special surgical skill and involves a certain learning curve.

In vivo Structural Imaging of the Cerebellum, the Contribution of Ultra-High Fields.

This review covers some of the contributions to date from cerebellar imaging studies performed at ultra-high magnetic fields. A short overview of the general advantages and drawbacks of the use of such high field systems for imaging is given. One of the biggest advantages of imaging at high magnetic fields is the improved spatial resolution, achievable thanks to the increased available signal-to-noise ratio. This high spatial resolution better matches the dimensions of the cerebellar substructures, allowing a better definition of such structures in the images. The implications of the use of high field systems is discussed for several imaging sequences and image contrast mechanisms. This review covers studies which were performed in vivo in both rodents and humans, with a special focus on studies that were directed towards the observation of the different cerebellar layers.