High specificity of line-immunoassay based algorithms for recent HIV-1 infection independent of viral subtype and stage of disease.

ABSTRACT: BACKGROUND: Serologic testing algorithms for recent HIV seroconversion (STARHS) provide important information for HIV surveillance. We have shown that a patient's antibody reaction in a confirmatory line immunoassay (INNO-LIATM HIV I/II Score, Innogenetics) provides information on the duration of infection. Here, we sought to further investigate the diagnostic specificity of various Inno-Lia algorithms and to identify factors affecting it. METHODS: Plasma samples of 714 selected patients of the Swiss HIV Cohort Study infected for longer than 12 months and representing all viral clades and stages of chronic HIV-1 infection were tested blindly by Inno-Lia and classified as either incident (up to 12 m) or older infection by 24 different algorithms. Of the total, 524 patients received HAART, 308 had HIV-1 RNA below 50 copies/mL, and 620 were infected by a HIV-1 non-B clade. Using logistic regression analysis we evaluated factors that might affect the specificity of these algorithms. RESULTS: HIV-1 RNA <50 copies/mL was associated with significantly lower reactivity to all five HIV-1 antigens of the Inno-Lia and impaired specificity of most algorithms. Among 412 patients either untreated or with HIV-1 RNA ≥50 copies/mL despite HAART, the median specificity of the algorithms was 96.5% (range 92.0-100%). The only factor that significantly promoted false-incident results in this group was age, with false-incident results increasing by a few percent per additional year. HIV-1 clade, HIV-1 RNA, CD4 percentage, sex, disease stage, and testing modalities exhibited no significance. Results were similar among 190 untreated patients. CONCLUSIONS: The specificity of most Inno-Lia algorithms was high and not affected by HIV-1 variability, advanced disease and other factors promoting false-recent results in other STARHS. Specificity should be good in any group of untreated HIV-1 patients.

Sensitive and rapid detection of ganciclovir resistance by PCR based MALDI-TOF analysis.

BACKGROUND: Cytomegalovirus (CMV) infection is associated with significant morbidity and mortality in transplant recipients. Resistance against ganciclovir is increasingly observed. According to current guidelines, direct drug resistance testing is not always performed due to high costs and work effort, even when resistance is suspected. OBJECTIVES: To develop a more sensitive, easy applicable and cost-effective assay as proof of concept for direct drug resistance testing in CMV surveillance of post-transplant patients. STUDY DESIGN: Five consecutive plasma samples from a heart transplant patient with a primary CMV infection were analyzed by quantitative real-time polymerase chain reaction (rtPCR) as a surrogate marker for therapy failure, and by direct drug resistance detection assays such as Sanger sequencing and the novel primer extension (PEX) reaction matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) based method. RESULTS: This report demonstrates that PEX reaction followed by MALDI-TOF analysis detects the A594V mutation, encoding ganciclovir resistance, ten days earlier compared to Sanger sequencing and more than 30 days prior to an increase in viral load. CONCLUSION: The greatly increased sensitivity and rapid turnaround-time combined with easy handling and moderate costs indicate that this procedure could make a major contribution to improve transplantation outcomes.

Testing for hysteresis in unemployment in OECD countries: new evidence using stationarity panel tests with breaks

This paper tests hysteresis effects in unemployment using panel data for 19 OECD countries covering the period 1956-2001. The tests exploit the cross-section variations of the series, and additionally, allow for a diferent number of endogenous breakpoints in the unemployment series. The critical values are simulated based on our specific panel sizes and time periods. The findings stress the importance of accounting for exogenous shocks in the series and give support to the natural-rate hypothesis of unemployment for the majority of the countries analyzed

Testing for hysteresis in unemployment in OECD countries: new evidence using stationarity panel tests with breaks

This paper tests hysteresis effects in unemployment using panel data for 19 OECD countries covering the period 1956-2001. The tests exploit the cross-section variations of the series, and additionally, allow for a diferent number of endogenous breakpoints in the unemployment series. The critical values are simulated based on our specific panel sizes and time periods. The findings stress the importance of accounting for exogenous shocks in the series and give support to the natural-rate hypothesis of unemployment for the majority of the countries analyzed

Pseudoxanthoma elasticum : evaluation of diagnostic criteria based on molecular data

RÉSUMÉ EN FRANCAIS : Introduction: Le pseudoxanthome élastique (PXE) est une maladie génétique. Les mutations responsables ont été localisées au niveau du gène codant le transporteur transmembranaire ABC-C6. Des calcifications pathologiques des fibres élastiques de la peau, des yeux et du système cardiovasculaire en sont la conséquence. Buts: Evaluer les critères diagnostiques actuels du PXE en se basant sur les données moléculaires. Méthodes: 142 sujets provenant de 10 familles avec une anamnèse familiale positive pour le PXE ont été investiguées sur le plan clinique, histopathologique et génétique. Résultats: 25 sujets se sont avérés être homozygotes pour le gène PXE muté. 23 d'entre eux ont présenté les manifestations cliniques et histopathologique typiques. Les deux autres souffraient d'une élastose et d'une dégénérescence maculaire si importante qu'un diagnostic de PXE ne pouvait pas être confirmé cliniquement. 67 sujets se sont révélés être des porteurs hétérozygotes et 50 ne présentaient pas de mutation. De ces 117 sujets, 116 n'ont montré aucune lésion cutanée ou ophtalmique pouvant correspondre au PXE. Un seul des sujets sans mutation a présenté une importante élastose solaire ainsi qu'une cicatrisation de la rétine, imitant les lésions typiques du PXE. Quatre des 67 sujets hétérozygotes ont eu une biopsie de peau, dont les analyses histopathologique se sont avérées normales. Conclusion: Dans notre cohorte de patients, le PXE était transmis exclusivement de façoh autosomique récessive. La corrélation retrouvée entre le génotype et le phénotype a permis de confirmer les critères diagnostiques majeurs actuels. Le diagnostic clinique peut être difficile, voir impossible, chez des patients atteints d'une élastose solaire importante et/ou d'une dégénérescence maculaire étendue. Dans ces cas, un test moléculaire est nécessaire afin de confirmer le diagnostic de PXE. A notre connaissance, notre étude présentée ici est le premier travail comparant des données cliniques à des données moléculaires dans le domaine du PXE. ABSTRACT : Background: Pseudoxanthoma elasticum (PXE) is a genetic disorder due to mutations in the gene encoding the transmembrane transporter protein adenosine triphosphate binding cassette (ABC)-C6, resulting in calcifications of elastic fibers in the skin, eyes and cardiovascular system. Objectives: To evaluate the diagnostic criteria for PXE based on molecular data. Methods: Of 10 families with a positive history of PXE 142 subjects were investigated for clinical symptoms, histological findings and genetic haplotype analysis. Results: Of these, 25 subjects were haplotypic homozygous for PXE and 23 had typical clinical and histopathological manifestations. Two of the 25 patients showed such marked solar elastosis and macular degeneration that PXE could not be confirmed clinically. Sixty-seven subject were haplotypic heterozygous carriers and 50 haplotypic homozygous unaffected. Of these 117 subjects, 116 showed no cutaneous or ophthalmologic signs of PXE. In one of the 50 haplotypic homozygous unaffected patients important solar elastosis and scaring of the retina mimicked PXE lesions. Only four of the 67 haplotypic heterozygous carriers had biopsies of nonlesional skin; all were histopathologically normal. Conclusions: In our patients, PXE presents as an autosomal recessive genodermatosis. Correlation of haplotype and phenotype confirmed actual major diagnostic criteria. In patients with marked solar elastosis and/ or severe macular degeneration clinical diagnosis can be impossible and molecular testing is needed to confirm the presence of PXE. To the best of our knowledge our large study compares for the first time clinical findings with molecular data.

Testing Spatial Autocorrelation in Weighted Networks : the Modes Permutation Test

In a weighted spatial network, as specified by an exchange matrix, the variances of the spatial values are inversely proportional to the size of the regions. Spatial values are no more exchangeable under independence, thus weakening the rationale for ordinary permutation and bootstrap tests of spatial autocorrelation. We propose an alternative permutation test for spatial autocorrelation, based upon exchangeable spatial modes, constructed as linear orthogonal combinations of spatial values. The coefficients obtain as eigenvectors of the standardised exchange matrix appearing in spectral clustering, and generalise to the weighted case the concept of spatial filtering for connectivity matrices. Also, two proposals aimed at transforming an acessibility matrix into a exchange matrix with with a priori fixed margins are presented. Two examples (inter-regional migratory flows and binary adjacency networks) illustrate the formalism, rooted in the theory of spectral decomposition for reversible Markov chains.

Tricky and terrible T-cell tumors: these are thrilling times for testing: molecular pathology of peripheral T-cell lymphomas.

Peripheral T-cell lymphomas (PTCLs) encompass a group of rare and usually clinically aggressive diseases. The classification and diagnosis of these diseases are compounded by their marked pathological heterogeneity and complex clinical features. With the exception of ALK-positive anaplastic large cell lymphoma (ALCL), which is defined on the basis of ALK rearrangements, genetic features play little role in the definition of other disease entities. In recent years, hitherto unrecognized chromosomal translocations have been reported in small subsets of PTCLs, and genome-wide array-based profiling investigations have provided novel insights into their molecular characteristics. This article summarizes the current knowledge on the best-characterized genetic and molecular alterations underlying the pathogenesis of PTCLs, with a focus on recent discoveries, their relevance to disease classification, and their management implications from a diagnostical and therapeutical perspective.

Monitoring tumor antigen specific T-cell responses in cancer patients and phase I clinical trials of peptide-based vaccination.

Numerous phase I and II clinical trials testing the safety and immunogenicity of various peptide vaccine formulations based on CTL-defined tumor antigens in cancer patients have been reported during the last 7 years. While specific T-cell responses can be detected in a variable fraction of immunized patients, an even smaller but significant fraction of these patients have objective tumor responses. Efficient therapeutic vaccination should aim at boosting naturally occurring antitumor T- and B-cell responses and at sustaining a large number of tumor antigen specific and fully functional effector T cells at tumor sites. Recent progress in our ability to quantitatively and qualitatively monitor tumor antigen specific CD8 T-cell responses will greatly help in making rapid progress in this field.

A new technique for simultaneous validation of two manual nonmercury auscultatory sphygmomanometers (A&D UM-101 and Accoson Greenlight 300) based on the International protocol.

INTRODUCTION: Auscultatory nonmercury manual devices seem good alternatives for the mercury sphygmomanometers in the clinic and for research settings, but individual internal validation of each device is time-consuming. The aim of this study was to validate a new technique capable of testing two devices simultaneously, based on the International protocol of the European Society of Hypertension. METHODS: The concept of the new technique is to measure blood pressure alternatively by two observers using a mercury sphygmomanometer and by two observers using the A&D UM-101 and Accoson Greenlight 300 devices, connected by Y-tube to obtain simultaneous readings with both nonmercury devices. Thirty-three participants were enrolled (mean age 47.2±14.0 years). Nine sequential blood pressure measurements were performed for each participant. RESULTS: Both devices passed phase 1 using 15 participants. In phase 2.1 (n=33), on a maximum of 99 measurements, the Accoson device produced 81/95/99 measurements within 5/10/15 mmHg for systolic blood pressure (SBP) and 87/98/99 for diastolic blood pressure (DBP). The A&D device produced 86/96/99 for SBP and 94/99/99 for DBP. In phase 2.2 (n=33), 30 participants had at least 2 out of 3 SBP obtained with Accoson device within 5 mmHg of the mercury device, as compared with 29 of 33 participants with the A&D device. For DBP, this was 33 of 33 participants for both devices. CONCLUSION: Both the nonmercury devices passed the International protocol. The new technique of simultaneous device testing using a Y-tube represents a time saving application of the International protocol.

New perspectives in the use of ink evidence in forensic science: Part III: Operational applications and evaluation

The research reported in this series of article aimed at (1) automating the search of questioned ink specimens in ink reference collections and (2) at evaluating the strength of ink evidence in a transparent and balanced manner. These aims require that ink samples are analysed in an accurate and reproducible way and that they are compared in an objective and automated way. This latter requirement is due to the large number of comparisons that are necessary in both scenarios. A research programme was designed to (a) develop a standard methodology for analysing ink samples in a reproducible way, (b) comparing automatically and objectively ink samples and (c) evaluate the proposed methodology in forensic contexts. This report focuses on the last of the three stages of the research programme. The calibration and acquisition process and the mathematical comparison algorithms were described in previous papers [C. Neumann, P. Margot, New perspectives in the use of ink evidence in forensic science-Part I: Development of a quality assurance process for forensic ink analysis by HPTLC, Forensic Sci. Int. 185 (2009) 29-37; C. Neumann, P. Margot, New perspectives in the use of ink evidence in forensic science- Part II: Development and testing of mathematical algorithms for the automatic comparison of ink samples analysed by HPTLC, Forensic Sci. Int. 185 (2009) 38-50]. In this paper, the benefits and challenges of the proposed concepts are tested in two forensic contexts: (1) ink identification and (2) ink evidential value assessment. The results show that different algorithms are better suited for different tasks. This research shows that it is possible to build digital ink libraries using the most commonly used ink analytical technique, i.e. high-performance thin layer chromatography, despite its reputation of lacking reproducibility. More importantly, it is possible to assign evidential value to ink evidence in a transparent way using a probabilistic model. It is therefore possible to move away from the traditional subjective approach, which is entirely based on experts' opinion, and which is usually not very informative. While there is room for the improvement, this report demonstrates the significant gains obtained over the traditional subjective approach for the search of ink specimens in ink databases, and the interpretation of their evidential value.

Therapeutic cancer vaccines based on molecularly defined human tumor antigens.

The results of numerous phases I and II clinical trials testing the safety and immunogenicity of various cancer vaccine formulations based on cytolytic T lymphocytes (CTLs)-defined tumor antigens have been reported recently. Specific T cell responses can be detected in only a fraction of immunized patients. A smaller but significant fraction of these patients have objective tumor responses. Efficient therapeutic vaccination should aim at boosting naturally occurring anti-tumor responses and at sustaining a large contingent of tumor antigen-specific and fully functional effector T cells at tumor sites.

Refining abacavir hypersensitivity diagnoses using a structured clinical assessment and genetic testing in the Swiss HIV Cohort Study.

BACKGROUND: We aimed to assess the value of a structured clinical assessment and genetic testing for refining the diagnosis of abacavir hypersensitivity reactions (ABC-HSRs) in a routine clinical setting. METHODS: We performed a diagnostic reassessment using a structured patient chart review in individuals who had stopped ABC because of suspected HSR. Two HIV physicians blinded to the human leukocyte antigen (HLA) typing results independently classified these individuals on a scale between 3 (ABC-HSR highly likely) and -3 (ABC-HSR highly unlikely). Scoring was based on symptoms, onset of symptoms and comedication use. Patients were classified as clinically likely (mean score > or =2), uncertain (mean score > or = -1 and < or = 1) and unlikely (mean score < or = -2). HLA typing was performed using sequence-based methods. RESULTS: From 131 reassessed individuals, 27 (21%) were classified as likely, 43 (33%) as unlikely and 61 (47%) as uncertain ABC-HSR. Of the 131 individuals with suspected ABC-HSR, 31% were HLA-B*5701-positive compared with 1% of 140 ABC-tolerant controls (P < 0.001). HLA-B*5701 carriage rate was higher in individuals with likely ABC-HSR compared with those with uncertain or unlikely ABC-HSR (78%, 30% and 5%, respectively, P < 0.001). Only six (7%) HLA-B*5701-negative individuals were classified as likely HSR after reassessment. CONCLUSIONS: HLA-B*5701 carriage is highly predictive of clinically diagnosed ABC-HSR. The high proportion of HLA-B*5701-negative individuals with minor symptoms among individuals with suspected HSR indicates overdiagnosis of ABC-HSR in the era preceding genetic screening. A structured clinical assessment and genetic testing could reduce the rate of inappropriate ABC discontinuation and identify individuals at high risk for ABC-HSR.

FERTILIZER RECOMMENDATION SYSTEM FOR MELON BASED ON NUTRITIONAL BALANCE

Melon is one of the most demanding cucurbits regarding fertilization, requiring knowledge of soils, crop nutritional requirements, time of application, and nutrient use efficiency for proper fertilization. Developing support systems for decision-making for fertilization that considers these variables in nutrient requirement and supply is necessary. The objective of this study was parameterization of a fertilizer recommendation system for melon (Ferticalc-melon) based on nutritional balance. To estimate fertilizer recommendation, the system considers the requirement subsystem (REQ), which includes the demand for nutrients by the plant, and the supply subsystem (SUP), which corresponds to the supply of nutrients through the soil and irrigation water. After determining the REQtotal and SUPtotal, the system calculates the nutrient balances for N, P, K, Ca, Mg, and S, recommending fertilizer application if the balance is negative (SUP < REQ), but not if the balance is positive or zero (SUP ≥ REQ). Simulations were made for different melon types (Yellow, Cantaloupe, Galia and Piel-de-sapo), with expected yield of 45 t ha-1. The system estimated that Galia type was the least demanding in P, while Piel-de-sapo was the most demanding. Cantaloupe was the least demanding for N and Ca, while the Yellow type required less K, Mg, and S. As compared to other fertilizer recommendation methods adopted in Brazil, the Ferticalc system was more dynamic and flexible. Although the system has shown satisfactory results, it needs to be evaluated under field conditions to improve its recommendations.

Comparative sensitivity of tumor and non-tumor cell lines as reliable approach for in vitro cytotoxicity screening of lysine-based surfactants with potential pharmaceutical applications

Surfactants are used as additives in topical pharmaceuticals and drug delivery systems. The biocompatibility of amino acid-based surfactants makes them highly suitable for use in these fields, but tests are needed to evaluate their potential toxicity. Here we addressed the sensitivity of tumor (HeLa, MCF-7) and non-tumor (3T3, 3T6, HaCaT, NCTC 2544) cell lines to the toxic effects of lysine-based surfactants by means of two in vitro endpoints (MTT and NRU). This comparative assay may serve as a reliable approach for predictive toxicity screening of chemicals prior to pharmaceutical applications. After 24-h of cell exposure to surfactants, differing toxic responses were observed. NCTC 2544 and 3T6 cell lines were the most sensitive, while both tumor cells and 3T3 fibroblasts were more resistant to the cytotoxic effects of surfactants. IC50-values revealed that cytotoxicity was detected earlier by MTT assay than by NRU assay, regardless of the compound or cell line. The overall results showed that surfactants with organic counterions were less cytotoxic than those with inorganic counterions. Our findings highlight the relevance of the correct choice and combination of cell lines and bioassays in toxicity studies for a safe and reliable screen of chemicals with potential interest in pharmaceutical industry.

Task 4: Testing Iowa Portland Cement Concrete Mixtures for the AASHTO Mechanistic-Empirical Pavement Design Procedure, May 2008

The present research project was designed to identify the typical Iowa material input values that are required by the Mechanistic-Empirical Pavement Design Guide (MEPDG) for the Level 3 concrete pavement design. It was also designed to investigate the existing equations that might be used to predict Iowa pavement concrete for the Level 2 pavement design. In this project, over 20,000 data were collected from the Iowa Department of Transportation (DOT) and other sources. These data, most of which were concrete compressive strength, slump, air content, and unit weight data, were synthesized and their statistical parameters (such as the mean values and standard variations) were analyzed. Based on the analyses, the typical input values of Iowa pavement concrete, such as 28-day compressive strength (f’c), splitting tensile strength (fsp), elastic modulus (Ec), and modulus of rupture (MOR), were evaluated. The study indicates that the 28-day MOR of Iowa concrete is 646 + 51 psi, very close to the MEPDG default value (650 psi). The 28-day Ec of Iowa concrete (based only on two available data of the Iowa Curling and Warping project) is 4.82 + 0.28x106 psi, which is quite different from the MEPDG default value (3.93 x106 psi); therefore, the researchers recommend re-evaluating after more Iowa test data become available. The drying shrinkage (εc) of a typical Iowa concrete (C-3WR-C20 mix) was tested at Concrete Technology Laboratory (CTL). The test results show that the ultimate shrinkage of the concrete is about 454 microstrain and the time for the concrete to reach 50% of ultimate shrinkage is at 32 days; both of these values are very close to the MEPDG default values. The comparison of the Iowa test data and the MEPDG default values, as well as the recommendations on the input values to be used in MEPDG for Iowa PCC pavement design, are summarized in Table 20 of this report. The available equations for predicting the above-mentioned concrete properties were also assembled. The validity of these equations for Iowa concrete materials was examined. Multiple-parameters nonlinear regression analyses, along with the artificial neural network (ANN) method, were employed to investigate the relationships among Iowa concrete material properties and to modify the existing equations so as to be suitable for Iowa concrete materials. However, due to lack of necessary data sets, the relationships between Iowa concrete properties were established based on the limited data from CP Tech Center’s projects and ISU classes only. The researchers suggest that the resulting relationships be used by Iowa pavement design engineers as references only. The present study furthermore indicates that appropriately documenting concrete properties, including flexural strength, elastic modulus, and information on concrete mix design, is essential for updating the typical Iowa material input values and providing rational prediction equations for concrete pavement design in the future.