Isothermal microcalorimetry for antifungal susceptibility testing of Mucorales, Fusarium spp., and Scedosporium spp.

We evaluated isothermal microcalorimetry for real-time susceptibility testing of non-Aspergillus molds. MIC and minimal effective concentration (MEC) values of Mucorales (n = 4), Fusarium spp. (n = 4), and Scedosporium spp. (n = 4) were determined by microbroth dilution according to the Clinical Laboratory Standard Institute M38-A2 guidelines. Heat production of molds was measured at 37 °C in Sabouraud dextrose broth inoculated with 2.5 × 10(4) spores/mL in the presence of amphotericin B, voriconazole, posaconazole, caspofungin, and anidulafungin. As determined by microcalorimetry, amphotericin B was the most active agent against Mucorales (MHIC 0.06-0.125 μg/mL) and Fusarium spp. (MHIC 1-4 μg/mL), whereas voriconazole was the most active agent against Scedosporium spp. (MHIC 0.25 to 8 μg/mL). The percentage of agreement (within one 2-fold dilution) between the MHIC and MIC (or MEC) was 67%, 92%, 75%, and 83% for amphotericin B, voriconazole, posaconazole, and caspofungin, respectively. Microcalorimetry provides additional information on timing of antifungal activity, enabling further investigation of drug-mold and drug-drug interaction, and optimization of antifungal treatment.

An efficient algorithm to perform multiple testing in epistasis screening

Background: Research in epistasis or gene-gene interaction detection for human complex traits has grown over the last few years. It has been marked by promising methodological developments, improved translation efforts of statistical epistasis to biological epistasis and attempts to integrate different omics information sources into the epistasis screening to enhance power. The quest for gene-gene interactions poses severe multiple-testing problems. In this context, the maxT algorithm is one technique to control the false-positive rate. However, the memory needed by this algorithm rises linearly with the amount of hypothesis tests. Gene-gene interaction studies will require a memory proportional to the squared number of SNPs. A genome-wide epistasis search would therefore require terabytes of memory. Hence, cache problems are likely to occur, increasing the computation time. In this work we present a new version of maxT, requiring an amount of memory independent from the number of genetic effects to be investigated. This algorithm was implemented in C++ in our epistasis screening software MBMDR-3.0.3. We evaluate the new implementation in terms of memory efficiency and speed using simulated data. The software is illustrated on real-life data for Crohn’s disease. Results: In the case of a binary (affected/unaffected) trait, the parallel workflow of MBMDR-3.0.3 analyzes all gene-gene interactions with a dataset of 100,000 SNPs typed on 1000 individuals within 4 days and 9 hours, using 999 permutations of the trait to assess statistical significance, on a cluster composed of 10 blades, containing each four Quad-Core AMD Opteron(tm) Processor 2352 2.1 GHz. In the case of a continuous trait, a similar run takes 9 days. Our program found 14 SNP-SNP interactions with a multiple-testing corrected p-value of less than 0.05 on real-life Crohn’s disease (CD) data. Conclusions: Our software is the first implementation of the MB-MDR methodology able to solve large-scale SNP-SNP interactions problems within a few days, without using much memory, while adequately controlling the type I error rates. A new implementation to reach genome-wide epistasis screening is under construction. In the context of Crohn’s disease, MBMDR-3.0.3 could identify epistasis involving regions that are well known in the field and could be explained from a biological point of view. This demonstrates the power of our software to find relevant phenotype-genotype higher-order associations.

The Learning Affect Monitor (LAM) - A computer-based system integrating quantitative and qualitative assessment of affective states in daily life.

The Learning Affect Monitor (LAM) is a new computer-based assessment system integrating basic dimensional evaluation and discrete description of affective states in daily life, based on an autonomous adapting system. Subjects evaluate their affective states according to a tridimensional space (valence and activation circumplex as well as global intensity) and then qualify it using up to 30 adjective descriptors chosen from a list. The system gradually adapts to the user, enabling the affect descriptors it presents to be increasingly relevant. An initial study with 51 subjects, using a 1 week time-sampling with 8 to 10 randomized signals per day, produced n = 2,813 records with good reliability measures (e.g., response rate of 88.8%, mean split-half reliability of .86), user acceptance, and usability. Multilevel analyses show circadian and hebdomadal patterns, and significant individual and situational variance components of the basic dimension evaluations. Validity analyses indicate sound assignment of qualitative affect descriptors in the bidimensional semantic space according to the circumplex model of basic affect dimensions. The LAM assessment module can be implemented on different platforms (palm, desk, mobile phone) and provides very rapid and meaningful data collection, preserving complex and interindividually comparable information in the domain of emotion and well-being.

Assessment of Nondestructive Testing Technologies for Quality Control/Quality Assurance of Asphalt Mixtures, TR-653, 2015

Asphalt pavements suffer various failures due to insufficient quality within their design lives. The American Association of State Highway and Transportation Officials (AASHTO) Mechanistic-Empirical Pavement Design Guide (MEPDG) has been proposed to improve pavement quality through quantitative performance prediction. Evaluation of the actual performance (quality) of pavements requires in situ nondestructive testing (NDT) techniques that can accurately measure the most critical, objective, and sensitive properties of pavement systems. The purpose of this study is to assess existing as well as promising new NDT technologies for quality control/quality assurance (QC/QA) of asphalt mixtures. Specifically, this study examined field measurements of density via the PaveTracker electromagnetic gage, shear-wave velocity via surface-wave testing methods, and dynamic stiffness via the Humboldt GeoGauge for five representative paving projects covering a range of mixes and traffic loads. The in situ tests were compared against laboratory measurements of core density and dynamic modulus. The in situ PaveTracker density had a low correlation with laboratory density and was not sensitive to variations in temperature or asphalt mix type. The in situ shear-wave velocity measured by surface-wave methods was most sensitive to variations in temperature and asphalt mix type. The in situ density and in situ shear-wave velocity were combined to calculate an in situ dynamic modulus, which is a performance-based quality measurement. The in situ GeoGauge stiffness measured on hot asphalt mixtures several hours after paving had a high correlation with the in situ dynamic modulus and the laboratory density, whereas the stiffness measurement of asphalt mixtures cooled with dry ice or at ambient temperature one or more days after paving had a very low correlation with the other measurements. To transform the in situ moduli from surface-wave testing into quantitative quality measurements, a QC/QA procedure was developed to first correct the in situ moduli measured at different field temperatures to the moduli at a common reference temperature based on master curves from laboratory dynamic modulus tests. The corrected in situ moduli can then be compared against the design moduli for an assessment of the actual pavement performance. A preliminary study of microelectromechanical systems- (MEMS)-based sensors for QC/QA and health monitoring of asphalt pavements was also performed.

Pathogenic role of basic calcium phosphate crystals in destructive arthropathies.

BACKGROUND: basic calcium phosphate (BCP) crystals are commonly found in osteoarthritis (OA) and are associated with cartilage destruction. BCP crystals induce in vitro catabolic responses with the production of metalloproteases and inflammatory cytokines such as interleukin-1 (IL-1). In vivo, IL-1 production induced by BCP crystals is both dependant and independent of NLRP3 inflammasome. We aimed to clarify 1/ the role of BCP crystals in cartilage destruction and 2/ the role of IL-1 and NLRP3 inflammasome in cartilage degradation related to BCP crystals. METHODOLOGY PRINCIPAL FINDINGS: synovial membranes isolated from OA knees were analysed by alizarin Red and FTIR. Pyrogen free BCP crystals were injected into right knees of WT, NLRP3 -/-, ASC -/-, IL-1α -/- and IL-1β-/- mice and PBS was injected into left knees. To assess the role of IL-1, WT mice were treated by intra-peritoneal injections of anakinra, the IL-1Ra recombinant protein, or PBS. Articular destruction was studied at d4, d17 and d30 assessing synovial inflammation, proteoglycan loss and chondrocyte apoptosis. BCP crystals were frequently found in OA synovial membranes including low grade OA. BCP crystals injected into murine knee joints provoked synovial inflammation characterized by synovial macrophage infiltration that persisted at day 30, cartilage degradation as evidenced by loss of proteoglycan staining by Safranin-O and concomitant expression of VDIPEN epitopes, and increased chondrocyte apoptosis. BCP crystal-induced synovitis was totally independent of IL-1α and IL-1β signalling and no alterations of inflammation were observed in mice deficient for components of the NLRP3-inflammasome, IL-1α or IL-1β. Similarly, treatment with anakinra did not prevent BCP crystal effects. In vitro, BCP crystals elicited enhanced transcription of matrix degrading and pro-inflammatory genes in macrophages. CONCLUSIONS SIGNIFICANCE: intra-articular BCP crystals can elicit synovial inflammation and cartilage degradation suggesting that BCP crystals have a direct pathogenic role in OA. The effects are independent of IL-1 and NLRP3 inflammasome.

Basic calcium phosphate crystals induce IL-1B secretion in vitro through activation of the Nalp3 inflammasome

Objectives: We tested the effects of the three forms of basic calcium phosphate (BCP) crystals (octacalcium phosphate (OCP), carbonate-substituted apatite (CA) and hydroxyapatite (HA)) on monocytes and macrophages on IL-1β secretion. The requirement for the NALP3 inflammasome and TLR2 and TLR4 receptors in this acute response was analyzed.

Testing the effects of genetic crossing distance on embryo survival within a metapopulation of brown trout (Salmo trutta)

Predicting progeny performance from parental genetic divergence can potentially enhance the efficiency of supportive breeding programmes and facilitate risk assessment. Yet, experimental testing of the effects of breeding distance on offspring performance remains rare, especially in wild populations of vertebrates. Recent studies have demonstrated that embryos of salmonid fish are sensitive indicators of additive genetic variance for viability traits. We therefore used gametes of wild brown trout (Salmo trutta) from five genetically distinct populations of a river catchment in Switzerland, and used a full factorial design to produce over 2,000 embryos in 100 different crosses with varying genetic distances (FST range 0.005-0.035). Customized egg capsules allowed recording the survival of individual embryos until hatching under natural field conditions. Our breeding design enabled us to evaluate the role of the environment, of genetic and nongenetic parental contributions, and of interactions between these factors, on embryo viability. We found that embryo survival was strongly affected by maternal environmental (i.e. non-genetic) effects and by the microenvironment, i.e. by the location within the gravel. However, embryo survival was not predicted by population divergence, parental allelic dissimilarity, or heterozygosity, neither in the field nor under laboratory conditions. Our findings suggest that the genetic effects of inter-population hybridization within a genetically differentiated meta-population can be minor in comparison to environmental effects.

CD4+CD25+Foxp3+ regulatory T cells: from basic research to potential therapeutic use.

Regulatory T cells control immune responses to self- and foreign-antigens and play a major role in maintaining the balance between immunity and tolerance. This article reviews recent key developments in the field of CD4+CD25+Foxp3+ regulatory T (TREG) cells. It presents their characteristics and describes their range of activity and mechanisms of action. Some models of diseases triggered by the imbalance between TREG cells and effector pathogenic T cells are described and their potential therapeutic applications in humans are outlined.

Myelin basic protein content of aggregating rat brain cell cultures treated with cytokines and/or demyelinating antibody: effects of macrophage enrichment.

The demyelinative potential of the cytokines interleukin-1 alpha (IL-1 alpha), interferon-gamma (IFN-gamma), and tumor necrosis factor-alpha (TNF-alpha) has been investigated in myelinating aggregate brain cell cultures. Treatment of myelinated cultures with these cytokines resulted in a reduction in myelin basic protein (MBP) content. This effect was additively increased by anti-myelin/oligodendrocyte glycoprotein (alpha-MOG) in the presence of complement. Qualitative immunocytochemistry demonstrated that peritoneal macrophages, added to the fetal telencephalon cell suspensions at the start of the culture period, successfully integrated into aggregate cultures. Supplementing the macrophage component of the cultures in this fashion resulted in increased accumulation of MBP. The effect of IFN-gamma on MBP content of cultures was not affected by the presence of macrophages in increased numbers.

Alkali Content of Fly Ash – Measuring and Testing Strategies for Compliance, TR-628, 2015

Sodium and potassium are the common alkalis present in fly ash. Excessive amounts of fly ash alkalis can cause efflorescence problems in concrete products and raise concern about the effectiveness of the fly ash to mitigate alkali-silica reaction (ASR). The available alkali test, which is commonly used to measure fly ash alkali, takes approximately 35 days for execution and reporting. Hence, in many instances the fly ash has already been incorporated into concrete before the test results are available. This complicates the job of the fly ash marketing agencies and it leads to disputes with fly ash users who often are concerned with accepting projects that contain materials that fail to meet specification limits. The research project consisted of a lab study and a field study. The lab study focused on the available alkali test and how fly ash alkali content impacts common performance tests (mortar-bar expansion tests). Twenty-one fly ash samples were evaluated during the testing. The field study focused on the inspection and testing of selected, well documented pavement sites that contained moderately reactive fine aggregate and high-alkali fly ash. A total of nine pavement sites were evaluated. Two of the sites were control sites that did not contain fly ash. The results of the lab study indicated that the available alkali test is prone to experimental errors that cause poor agreement between testing labs. A strong (linear) relationship was observed between available alkali content and total alkali content of Class C fly ash. This relationship can be used to provide a quicker, more precise method of estimating the available alkali content. The results of the field study failed to link the use of high-alkali fly ash with the occurrence of ASR in the various concrete sites. Petrographic examination of the pavement cores indicated that Wayland sand is an ASR-sensitive aggregate. This was in good agreement with Iowa DOT field service records. It was recommended that preventative measures should be used when this source of sand is used in concrete mixtures.

Soluble MHC-peptide complexes: tools for the monitoring of T cell responses in clinical trials and basic research.

Soluble MHC-peptide complexes, commonly known as tetramers, allow the detection and isolation of antigen-specific T cells. Although other types of soluble MHC-peptide complexes have been introduced, the most commonly used MHC class I staining reagents are those originally described by Altman and Davis. As these reagents have become an essential tool for T cell analysis, it is important to have a large repertoire of such reagents to cover a broad range of applications in cancer research and clinical trials. Our tetramer collection currently comprises 228 human and 60 mouse tetramers and new reagents are continuously being added. For the MHC II tetramers, the list currently contains 21 human (HLA-DR, DQ and DP) and 5 mouse (I-A(b)) tetramers. Quantitative enumeration of antigen-specific T cells by tetramer staining, especially at low frequencies, critically depends on the quality of the tetramers and on the staining procedures. For conclusive longitudinal monitoring, standardized reagents and analysis protocols need to be used. This is especially true for the monitoring of antigen-specific CD4+ T cells, as there are large variations in the quality of MHC II tetramers and staining conditions. This commentary provides an overview of our tetramer collection and indications on how tetramers should be used to obtain optimal results.

Relating Creep Testing to Rutting of Asphalt Concrete Mixes, HR-311, Part 2, 1991

The Iowa Department of Transportation began creep and resilient modulus testing of asphalt concrete mixtures in 1989. Part 1 of this research reported in January 1990 was a laboratory study of hot mix asphalt (HMA) mixtures made with O, 30, 60, 85 and 100% crushed gravel, crushed limestone and crushed quartzite combined with uncrushed sand and gravel. Creep test results from Marshall specimens related well to the percent of crushed particles and the perceived resistance to rutting. The objective of this research, part 2, was to determine if there was a meaningful correlation between pavement rut depth and the resilient modulus or the creep resistance factor. Four and six inch diameter cores were drilled from rutted primary and interstate pavements and interstate pavements with design changes intended to resist rutting. The top 2 1/2 inches of each core, most of which was surface course, was used for creep and resilient modulus testing. There is a good correlation between the resilient modulus of four and six inch diameter cores. Creep resistance factors of four and six inch diameter cores also correlated well. There is a poor correlation between resilient modulus and the creep resistance factor. The rut depth per million 18,000 pound equivalent single axle loadings (ESAL) for these pavements did not correlate well with either the resilient modulus or the creep resistance factor.

Evaluation of Recycled Rubber in Asphalt Cement Concrete - Field Testing, Final Report for HR-330, 330A, 330B, 330C, 330D, 2002

Roughly 242 million used tires are generated annually in the United States. Many of these tires end up being landfilled or stockpiled. The stockpiles are unsightly, unsanitary, and also collect water which creates the perfect breeding ground for mosquitoes, some of which carry disease. In an effort to reduce the number of used tire stockpiles the federal government mandated the use of recycled rubber in federally funded, state implemented department of transportation (DOT) projects. This mandate required the use of recycled rubber in 5% of the asphalt cement concrete (ACC) tonnage used in federally funded projects in 1994, increasing that amount by 5% each year until 20% was reached, and remaining at 20% thereafter. The mandate was removed as part of the appropriations process in 1994, after the projects in this research had been completed. This report covers five separate projects that were constructed by the Iowa Department Of Transportation (DOT) in 1991 and 1992. These projects had all had some form of rubber incorporated into their construction and were evaluated for 5 years. The conclusion of the study is that the pavements with tire rubber added performed essentially the same as conventional ACC pavement. An exception was the use of rubber chips in a surface lift. This performed better at crack control and worse with friction values than conventional ACC. The cost of the pavement with rubber additive was significantly higher. As a result, the benefits do not outweigh the costs of using this recycled rubber process in pavements in Iowa.

A general theory of rank testing

This paper develops an approach to rank testing that nests all existing rank tests andsimplifies their asymptotics. The approach is based on the fact that implicit in every ranktest there are estimators of the null spaces of the matrix in question. The approach yieldsmany new insights about the behavior of rank testing statistics under the null as well as localand global alternatives in both the standard and the cointegration setting. The approach alsosuggests many new rank tests based on alternative estimates of the null spaces as well as thenew fixed-b theory. A brief Monte Carlo study illustrates the results.