Reliability and discriminatory power of methods for dental plaque quantification

This in situ study evaluated the discriminatory power and reliability of methods of dental plaque quantification and the relationship between visual indices (VI) and fluorescence camera (FC) to detect plaque.

A comparison of ground cover and frequency estimation methods for post-harvest soil monitoring

The amount and type of ground cover is an important characteristic to measure when collecting soil disturbance monitoring data after a timber harvest. Estimates of ground cover and bare soil can be used for tracking changes in invasive species, plant growth and regeneration, woody debris loadings, and the risk of surface water runoff and soil erosion. A new method of assessing ground cover and soil disturbance was recently published by the U.S. Forest Service, the Forest Soil Disturbance Monitoring Protocol (FSDMP). This protocol uses the frequency of cover types in small circular (15cm) plots to compare ground surface in pre- and post-harvest condition. While both frequency and percent cover are common methods of describing vegetation, frequency has rarely been used to measure ground surface cover. In this study, three methods for assessing ground cover percent (step-point, 15cm dia. circular and 1x5m visual plot estimates) were compared to the FSDMP frequency method. Results show that the FSDMP method provides significantly higher estimates of ground surface condition for most soil cover types, except coarse wood. The three cover methods had similar estimates for most cover values. The FSDMP method also produced the highest value when bare soil estimates were used to model erosion risk. In a person-hour analysis, estimating ground cover percent in 15cm dia. plots required the least sampling time, and provided standard errors similar to the other cover estimates even at low sampling intensities (n=18). If ground cover estimates are desired in soil monitoring, then a small plot size (15cm dia. circle), or a step-point method can provide a more accurate estimate in less time than the current FSDMP method.

Monitoring of Urinary Calcium and Phosphorus Excretion in Preterm Infants - Comparison of two Methods

OBJECTIVES: Premature babies require supplementation with calcium and phosphorus to prevent metabolic bone disease of prematurity. To guide mineral supplementation, two methods of monitoring urinary excretion of calcium and phosphorus are used: urinary calcium or phosphorus concentration and calcium/creatinine or phosphorus/creatinine ratios. We compare these two methods in regards to their agreement on the need for mineral supplementation. METHODS: Retrospective chart review of 230 premature babies with birthweight <1500 g, undergoing screening of urinary spot samples from day 21 of life and fortnightly thereafter. Hypothetical cut-off values for urine calcium or phosphorus concentration (1 mmol/l) and urine calcium/creatinine ratio (0.5 mol/mol) or phosphorus/creatinine ratio (4 mol/mol) were applied to the sample results. The agreement on whether or not to supplement the respective minerals based on the results with the two methods was compared. Multivariate general linear models sought to identify patient characteristic to predict disagreeing results. RESULTS: 24.8% of cases disagreed on the indication for calcium supplementation, 8.8% for phosphorus. Total daily calcium intake was the only patient characteristic associated with discordant results. CONCLUSIONS: With the intention to supplement the respective mineral, comparison of urinary mineral concentration with mineral/creatinine ratio is moderate for Calcium and good for Phosphorus. The results do not allow to identify superiority of either method on the decision which babies require calcium and/or phosphorus supplements.

Detection of Leishmania RNA virus in Leishmania parasites.

BACKGROUND Patients suffering from cutaneous leishmaniasis (CL) caused by New World Leishmania (Viannia) species are at high risk of developing mucosal (ML) or disseminated cutaneous leishmaniasis (DCL). After the formation of a primary skin lesion at the site of the bite by a Leishmania-infected sand fly, the infection can disseminate to form secondary lesions. This metastatic phenotype causes significant morbidity and is often associated with a hyper-inflammatory immune response leading to the destruction of nasopharyngeal tissues in ML, and appearance of nodules or numerous ulcerated skin lesions in DCL. Recently, we connected this aggressive phenotype to the presence of Leishmania RNA virus (LRV) in strains of L. guyanensis, showing that LRV is responsible for elevated parasitaemia, destructive hyper-inflammation and an overall exacerbation of the disease. Further studies of this relationship and the distribution of LRVs in other Leishmania strains and species would benefit from improved methods of viral detection and quantitation, especially ones not dependent on prior knowledge of the viral sequence as LRVs show significant evolutionary divergence. METHODOLOGY/PRINCIPAL FINDINGS This study reports various techniques, among which, the use of an anti-dsRNA monoclonal antibody (J2) stands out for its specific and quantitative recognition of dsRNA in a sequence-independent fashion. Applications of J2 include immunofluorescence, ELISA and dot blot: techniques complementing an arsenal of other detection tools, such as nucleic acid purification and quantitative real-time-PCR. We evaluate each method as well as demonstrate a successful LRV detection by the J2 antibody in several parasite strains, a freshly isolated patient sample and lesion biopsies of infected mice. CONCLUSIONS/SIGNIFICANCE We propose that refinements of these methods could be transferred to the field for use as a diagnostic tool in detecting the presence of LRV, and potentially assessing the LRV-related risk of complications in cutaneous leishmaniasis.

HLA-B⁎27 subtype specificity determines targeting and viral evolution of a hepatitis C virus-specific CD8+ T cell epitope

Background & Aims: HLA-B⁄27 is associated with spontaneous HCV genotype 1 clearance. HLA-B⁄27-restricted CD8+ T cells target three NS5B epitopes. Two of these epitopes are dominantly targeted in the majority of HLA-B⁄27+ patients. In chronic infection, viral escape occurs consistently in these two epitopes. The third epitope (NS5B2820) was dominantly targeted in an acutely infected patient. This was in contrast, however, to the lack of recognition and viral escape in the large majority of HLA-B⁄27+ patients. Here, we set out to determine the host factors contributing to selective targeting of this epitope. Methods: Four-digit HLA class I typing and viral sequence analyses were performed in 78 HLA-B⁄27+ patients with chronic HCV genotype 1 infection. CD8+ T cell analyses were performed in a subset of patients. In addition, HLA/peptide affinity was compared for HLA-B⁄27:02 and 05. Results: The NS5B2820 epitope is only restricted by the HLA-B⁄27 subtype HLA-B⁄27:02 (that is frequent in Mediterranean populations), but not by the prototype HLA-B⁄27 subtype B⁄27:05. Indeed, the epitope is very dominant in HLA-B⁄27:02+ patients and is associated with viral escape mutations at the anchor position for HLA-binding in 12 out of 13 HLA-B⁄27:02+ chronically infected patients. Conclusions: The NS5B2820 epitope is immunodominant in the context of HLA-B⁄27:02, but is not restricted by other HLA-B⁄27 subtypes. This finding suggests an important role of HLA subtypes in the restriction of HCV-specific CD8+ responses. With minor HLA subtypes covering up to 39% of specific populations, these findings may have important implications for the selection of epitopes for global vaccines.

Changes in emotion recognition relate to hypertension status

Background: Emotional processing in essential hypertension beyond self-report questionnaire has hardly been investigated. The aim of this study is to examine associations between hypertension status and recognition of facial affect. Methods: 25 healthy, non-smoking, medication-free men including 13 hypertensive subjects aged between 20 and 65 years completed a computer-based task in order to examine sensitivity of recognition of facial affect. Neutral faces gradually changed to a specific emotion in a pseudo-continuous manner. Slides of the six basic emotions (fear, sadness, disgust, happiness, anger, surprise) were chosen from the „NimStim Set“. Pictures of three female and three male faces were electronically morphed in 1% steps of intensity from 0% to 100% (36 sets of faces with 100 pictures each). Each picture of a set was presented for one second, ranging from 0% to 100% of intensity. Participants were instructed to press a stop button as soon as they recognized the expression of the face. After stopping a forced choice between the six basic emotions was required. As dependent variables, we recorded the emotion intensity at which the presentation was stopped and the number of errors (error rate). Recognition sensitivity was calculated as emotion intensity of correctly identified emotions. Results: Mean arterial pressure was associated with a significantly increased recognition sensitivity of facial affect for the emotion anger (ß = - .43, p = 0.03*, Δ R2= .110). There was no association with the emotions fear, sadness, disgust, happiness, and surprise (p’s > .0.41). Mean arterial pressure did not relate to the mean number of errors for any of the facial emotions. Conclusions: Our findings suggest that an increased blood pressure is associated with increased recognition sensitivity of facial affect for the emotion anger, if a face shows anger. Hypertensives perceive facial anger expression faster than normotensives, if anger is shown.

Recognition memory across the lifespan: the impact of word frequency and study-test interval on estimates of familiarity and recollection

The goal of this study was to investigate recognition memory performance across the lifespan and to determine how estimates of recollection and familiarity contribute to performance. In each of three experiments, participants from five groups from 14 up to 85 years of age (children, young adults, middle-aged adults, young-old adults, and old-old adults) were presented with high- and low-frequency words in a study phase and were tested immediately afterwards and/or after a one day retention interval. The results showed that word frequency and retention interval affected recognition memory performance as well as estimates of recollection and familiarity. Across the lifespan, the trajectory of recognition memory followed an inverse u-shape function that was neither affected by word frequency nor by retention interval. The trajectory of estimates of recollection also followed an inverse u-shape function, and was especially pronounced for low-frequency words. In contrast, estimates of familiarity did not differ across the lifespan. The results indicate that age differences in recognition memory are mainly due to differences in processes related to recollection while the contribution of familiarity-based processes seems to be age-invariant.

Evaluation of a solid phase microextraction method for community-based monitoring of 1,3-butadiene and benzene in Houston, Texas

The Houston region is home to arguably the largest petrochemical and refining complex anywhere. The effluent of this complex includes many potentially hazardous compounds. Study of some of these compounds has led to recognition that a number of known and probable carcinogens are at elevated levels in ambient air. Two of these, benzene and 1,3-butadiene, have been found in concentrations which may pose health risk for residents of Houston.^ Recent popular journalism and publications by local research institutions has increased the interest of the public in Houston's air quality. Much of the literature has been critical of local regulatory agencies' oversight of industrial pollution. A number of citizens in the region have begun to volunteer with air quality advocacy groups in the testing of community air. Inexpensive methods exist for monitoring of ozone, particulate matter and airborne toxic ambient concentrations. This study is an evaluation of a technique that has been successfully applied to airborne toxics.^ This technique, solid phase microextraction (SPME), has been used to measure airborne volatile organic hydrocarbons at community-level concentrations. It is has yielded accurate and rapid concentration estimates at a relatively low cost per sample. Examples of its application to measurement of airborne benzene exist in the literature. None have been found for airborne 1,3-butadiene. These compounds were selected for an evaluation of SPME as a community-deployed technique, to replicate previous application to benzene, to expand application to 1,3-butadiene and due to the salience of these compounds in this community. ^ This study demonstrates that SPME is a useful technique for quantification of 1,3-butadiene at concentrations observed in Houston. Laboratory background levels precluded recommendation of the technique for benzene. One type of SPME fiber, 85 μm Carboxen/PDMS, was found to be a sensitive sampling device for 1,3-butadiene under temperature and humidity conditions common in Houston. This study indicates that these variables affect instrument response. This suggests the necessity of calibration within specific conditions of these variables. While deployment of this technique was less expensive than other methods of quantification of 1,3-butadiene, the complexity of calibration may exclude an SPME method from broad deployment by community groups.^

A comparative review of water disinfection methods appropriate for developing countries and their efficacy, cost-efficiency, and usability

Developing countries are heavily burdened by limited access to safe drinking water and subsequent water-related diseases. Numerous water treatment interventions combat this public health crisis, encompassing both traditional and less-common methods. Of these, water disinfection serves as an important means to provide safe drinking water. Existing literature discusses a wide range of traditional treatment options and encourages the use of multi-barrier approaches including coagulation-flocculation, filtration, and disinfection. Most sources do not delve into approaches specifically appropriate for developing countries, nor do they exclusively examine water disinfection methods.^ The objective of this review is to focus on an extensive range of chemical, physio-chemical, and physical water disinfection techniques to provide a compilation, description and evaluation of options available. Such an objective provides further understanding and knowledge to better inform water treatment interventions and explores alternate means of water disinfection appropriate for developing countries. Appropriateness for developing countries corresponds to the effectiveness of an available, easy to use disinfection technique at providing safe drinking water at a low cost.^ Among chemical disinfectants, SWS sodium hypochlorite solution is preferred over sodium hypochlorite bleach due to consistent concentrations. Tablet forms are highly recommended chemical disinfectants because they are effective and very easy to use, but also because they are stable. Examples include sodium dichloroisocyanurate, calcium hypochlorite, and chlorine dioxide, which vary in cost depending on location and availability. Among physio-chemical disinfection options, electrolysis which produces mixed oxidants (MIOX) provides a highly effective disinfection option with a higher upfront cost but very low cost over the long term. Among physical disinfection options, solar disinfection (SODIS) applications are effective, but they treat only a fixed volume of water at a time. They come with higher initial costs but very low on-going costs. Additional effective disinfection techniques may be suitable depending on the location, availability and cost.^

Comparison of methods for downscaling runoff from regional climate models in Spanish basins

At present there is much literature that refers to the advantages and disadvantages of different methods of statistical and dynamical downscaling of climate variables projected by climate models. Less attention has been paid to other indirect variables, like runoff, which play a significant role in evaluating the impact of climate change on hydrological systems. Runoff presents a much greater bias in climate models than other climate variables, like temperature or precipitation. It is very important to identify the methods that minimize bias while downscaling runoff from the gridded results of climate models to the basin scale

A comparative analysis between FEM and Boundary Methods in bending of Plates

Two different methods of analysis of plate bending, FEM and BM are discussed in this paper. The plate behaviour is assumed to be represented by using the linear thin plate theory where the Poisson-Kirchoff assumption holds. The BM based in a weighted mean square error technique produced good results for the problem of plate bending. The computational effort demanded in the BM is smaller than the one needed in a FEM analysis for the same level of accuracy. The general application of the FEM cannot be matched by the BM. Particularly, different types of geometry (plates of arbitrary geometry) need a similar but not identical treatment in the BM. However, this loss of generality is counterbalanced by the computational efficiency gained in the BM in the solution achievement

Diversification, expression, and γδ T cell recognition of evolutionarily distant members of the MIC family of major histocompatibility complex class I-related molecules

Distant relatives of major histocompatibility complex (MHC) class I molecules, human MICA and MICB, function as stress-induced antigens that are broadly recognized by intestinal epithelial γδ T cells. They may thus play a central role in the immune surveillance of damaged, infected, or otherwise stressed intestinal epithelial cells. However, the generality of this system in evolution and the mode of recognition of MICA and MICB are undefined. Analysis of cDNA sequences from various primate species defined translation products that are homologous to MICA and MICB. All of the MIC polypeptides have common characteristics, although they are extraordinarily diverse. The most notable alterations are several deletions and frequent amino acid substitutions in the putative α-helical regions of the α1α2 domains. However, the primate MIC molecules were expressed on the surfaces of normal and transfected cells. Moreover, despite their sharing of relatively few identical amino acids in potentially accessible regions of their α1α2 domains, they were recognized by diverse human intestinal epithelial γδ T cells that are restricted by MICA and MICB. Thus, MIC molecules represent a family of MHC proteins that are structurally diverse yet appear to be functionally conserved. The promiscuous mode of γδ T cell recognition of these antigens may be explained by their sharing of a single conserved interaction site.

Four primordial modes of tRNA-synthetase recognition, determined by the (G,C) operational code

In distinction to single-stranded anticodons built of G, C, A, and U bases, their presumable double-stranded precursors at the first three positions of the acceptor stem are composed almost invariably of G-C and C-G base pairs. Thus, the “second” operational RNA code responsible for correct aminoacylation seems to be a (G,C) code preceding the classic genetic code. Although historically rooted, the two codes were destined to diverge quite early. However, closer inspection revealed that two complementary catalytic domains of class I and class II aminoacyl-tRNA synthetases (aaRSs) multiplied by two, also complementary, G2-C71 and C2-G71 targets in tRNA acceptors, yield four (2 × 2) different modes of recognition. It appears therefore that the core four-column organization of the genetic code, associated with the most conservative central base of anticodons and codons, was in essence predetermined by these four recognition modes of the (G,C) operational code. The general conclusion follows that the genetic code per se looks like a “frozen accident” but only beyond the “2 × 2 = 4” scope. The four primordial modes of tRNA–aaRS recognition are amenable to direct experimental verification.

Suppressor mutations in Escherichia coli methionyl-tRNA formyltransferase: Role of a 16-amino acid insertion module in initiator tRNA recognition

The specific formylation of initiator methionyl-tRNA by methionyl-tRNA formyltransferase (MTF; EC 2.1.2.9) is important for the initiation of protein synthesis in eubacteria and in eukaryotic organelles. The determinants for formylation in the tRNA are clustered mostly in the acceptor stem. As part of studies on the molecular mechanism of recognition of the initiator tRNA by MTF, we report here on the isolation and characterization of suppressor mutations in Escherichia coli MTF, which compensate for the formylation defect of a mutant initiator tRNA, lacking a critical determinant in the acceptor stem. We show that the suppressor mutant in MTF has a glycine-41 to arginine change within a 16-amino acid insertion found in MTF from many sources. A mutant with glycine-41 changed to lysine also acts as a suppressor, whereas mutants with changes to aspartic acid, glutamine, and leucine do not. The kinetic parameters of the purified wild-type and mutant Arg-41 and Lys-41 enzymes, determined by using the wild-type and mutant tRNAs as substrates, show that the Arg-41 and Lys-41 mutant enzymes compensate specifically for the strong negative effect of the acceptor stem mutation on formylation. These and other considerations suggest that the 16-amino acid insertion in MTF plays an important role in the specific recognition of the determinants for formylation in the acceptor stem of the initiator tRNA.

Distinct Modes of Macrophage Recognition for Apoptotic and Necrotic Cells Are Not Specified Exclusively by Phosphatidylserine Exposure

The distinction between physiological (apoptotic) and pathological (necrotic) cell deaths reflects mechanistic differences in cellular disintegration and is of functional significance with respect to the outcomes that are triggered by the cell corpses. Mechanistically, apoptotic cells die via an active and ordered pathway; necrotic deaths, conversely, are chaotic and passive. Macrophages and other phagocytic cells recognize and engulf these dead cells. This clearance is believed to reveal an innate immunity, associated with inflammation in cases of pathological but not physiological cell deaths. Using objective and quantitative measures to assess these processes, we find that macrophages bind and engulf native apoptotic and necrotic cells to similar extents and with similar kinetics. However, recognition of these two classes of dying cells occurs via distinct and noncompeting mechanisms. Phosphatidylserine, which is externalized on both apoptotic and necrotic cells, is not a specific ligand for the recognition of either one. The distinct modes of recognition for these different corpses are linked to opposing responses from engulfing macrophages. Necrotic cells, when recognized, enhance proinflammatory responses of activated macrophages, although they are not sufficient to trigger macrophage activation. In marked contrast, apoptotic cells profoundly inhibit phlogistic macrophage responses; this represents a cell-associated, dominant-acting anti-inflammatory signaling activity acquired posttranslationally during the process of physiological cell death.