New horizons in mouse immunoinformatics:reliable in silico prediction of mouse class I histocompatibility major complex peptide binding affinity

Quantitative structure–activity relationship (QSAR) analysis is a main cornerstone of modern informatic disciplines. Predictive computational models, based on QSAR technology, of peptide-major histocompatibility complex (MHC) binding affinity have now become a vital component of modern day computational immunovaccinology. Historically, such approaches have been built around semi-qualitative, classification methods, but these are now giving way to quantitative regression methods. The additive method, an established immunoinformatics technique for the quantitative prediction of peptide–protein affinity, was used here to identify the sequence dependence of peptide binding specificity for three mouse class I MHC alleles: H2–Db, H2–Kb and H2–Kk. As we show, in terms of reliability the resulting models represent a significant advance on existing methods. They can be used for the accurate prediction of T-cell epitopes and are freely available online (http://www.jenner.ac.uk/MHCPred).

Hydrogeophysical characterization of anisotropy in the Biscayne Aquifer using geophysical methods

The anisotropy of the Biscayne Aquifer which serves as the source of potable water for Miami-Dade County was investigated by applying geophysical methods. Electrical resistivity imaging, self potential and ground penetration radar techniques were employed in both regional and site specific studies. In the regional study, electrical anisotropy and resistivity variation with depth were investigated with azimuthal square array measurements at 13 sites. The observed coefficient of electrical anisotropy ranged from 1.01 to 1.36. The general direction of measured anisotropy is uniform for most sites and trends W-E or SE-NW irrespective of depth. Measured electrical properties were used to estimate anisotropic component of the secondary porosity and hydraulic anisotropy which ranged from 1 to 11% and 1.18 to 2.83 respectively. 1-D sounding analysis was used to models the variation of formation resistivity with depth. Resistivities decreased from NW (close to the margins of the everglades) to SE on the shores of Biscayne Bay. Porosity calculated from Archie's law, ranged from 18 to 61% with higher values found along the ridge. Higher anisotropy, porosities and hydraulic conductivities were on the Atlantic Coastal Ridge and lower values at low lying areas west of the ridge. The cause of higher anisotropy and porosity is attributed to higher dissolution rates of the oolitic facies of the Miami Formation composing the ridge. The direction of minimum resistivity from this study is similar to the predevelopment groundwater flow direction indicated in published modeling studies. Detailed investigations were carried out to evaluate higher anisotropy at West Perrine Park located on the ridge and Snapper Creek Municipal well field where the anisotropy trend changes with depth. The higher anisotropy is attributed to the presence of solution cavities oriented in the E-SE direction on the ridge. Similarly, the change in hydraulic anisotropy at the well field might be related to solution cavities, the surface canal and groundwater extraction wells.^

An overview on Human Leukocyte Antigen (HLA) region gene expression during Pseudomonas aeruginosa infection

The human leukocyte antigen (HLA) complex is an extensively studied cluster of genes with immunoregulatory function. Pseudomonas aeruginosa is capable of infecting individuals with weakened immune systems, and is associated with a high mortality rate. Previous genetic studies of the HLA region have found correlations between bacterial infection and its effect on regulating HLA gene expressions to establish their infection. This project analyzes the expression of classical HLA loci (A, B, C, DR, DQ, DP) in human B cells and macrophage cells during the infection of virulent strains of P. aeruginosa. Cells were cultured and infected with different virulent live, and heat-killed strains of P. aeruginosa for different time periods. The mRNA was extracted and converted into cDNA followed by real-time quantitative PCR and data analysis. The Western Blot technique was used to identify the targeted protein’s cell surface expression. Infection with P. aeruginosa was found to inhibit the expression of HLA proteins. The PA14 strain inhibited expression of all targeted genes in all experiments. Infections with PA01 and PA103 showed different patterns depending on the incubation time and the targeted gene. These differences suggest that the three strains use various mechanisms to inhibit HLA protein expression.

Determinação da energia de ativação e pureza de medicamentos de referência, genérico e similar utilizando técnicas termoanalíticas

In this work, the reference drugs, generic and similar to the active ingredients acetylsalicylic acid, paracetamol, captopril, hydrochlorothiazide and mebendazole were purchased from local pharmacies and studied by thermogravimetry (TG) and Differential Scanning Calorimetry (DSC). Thermal decomposition was assessed to obtain from the Ozawa method the activation energy in inert atmosphere (nitrogen), using three different heating ratios (5, 10 and 20 o C min-1). The pharmaceutical formulation of the AAS reference was the one who presented different from the others (generic and similar) Thermogravimetric profile indicating likely interaction between the active ingredient and excipients. Was observed at the heating rate of the inverse temperature that no linearity of the data, ie, there was no correlation between the percentage of mass loss and the activation energy involved in the thermal decomposition of the pharmaceutical formulation of the AAS reference log graph. The analysis by differential scanning calorimetry was performed in nitrogen atmosphere with a heating rate of 10 ° C min-1. In the analysis of these same drugs, the data curves found on the melting point were, except for hydrochlorothiazide, are consistent with the literature. Hydrochlorothiazide presented a melting point well below that found in the literature, which may be justified due to the interaction of the active ingredient with the excipient lactose. In the study of purity, using the Van't Hoff equation, the reference drugs hydrochlorothiazide and mebendazole reference generic and showed similar impurity content below the limit established that this equation must be greater than 2.5 mol%

Compressive strength of dental composites photo-activated with different light tips

The aim of this study was to evaluate the compressive strength of microhybrid (FiltekTM Z250) and nanofilled (FiltekTM Supreme XT) composite resins photo-activated with two different light guide tips, fiber optic and polymer, coupled with one LED. The power density was 653 mW cm−2 when using the fiber optic light tip and 596 mW cm−2 with the polymer. After storage in distilled water at 37 ± 2 "C for seven days, the samples were subjected to mechanical testing of compressive strength in an EMIC universal mechanical testing machine with a load cell of 5 kN and speed of 0.5 mm min−1. The statistical analysis was performed using ANOVA with a confidence interval of 95% and Tamhane’s test. The results showed that the mean values of compressive strength were not influenced by the different light tips (p > 0.05). However, a statistical difference was observed (p < 0.001) between the microhybrid composite resin photo-activated with the fiber optic light tip and the nanofilled composite resin. Based on these results, it can be concluded that microhybrid composite resin photo-activated with the fiber optic light tip showed better results than nanofilled, regardless of the tip used, and the type of the light tip did not influence the compressive strength of either composite. Thus, the presented results suggest that both the fiber optic and polymer light guide tips provide adequate compressive strength to be used to make restorations. However, the fiber optic light tip associated with microhybrid composite resin may be an interesting option for restorations mainly in posterior teeth.

On the mobility, membrane location and functionality of mechanosensitive channels in Escherichia coli

We thank Frans Bianchi and Franz Ho for assistance with molecular cloning, Tim Rasmussen for providing the pTRC-MscK plasmid, Andrew Robinson for providing the pBAD-mEos3.2 plasmid, Matthias Heinemann for assistance with the flow cytometry measurements, Paul Schavemaker for performing Smoldyn simulations and Michiel Punter for programming ImageJ plugins for PALM reconstructions and single-particle tracking. We thank Ian Booth for critical reading of the manuscript, and Christoffer Åberg and Matteo Gabba for valuable discussions. The authors would like to thank David Dryden and Marcel Reuter for performing preliminary experiments from which this work has been built. The work was funded by the EU FP7 ITN-network program NICHE.

Potential Shifts in Canadian High Arctic Sedimentary Organic Matter Composition With Permafrost Active Layer Detachments

Increased temperature and precipitation in Arctic regions have led to deeper thawing and structural instability in permafrost soil. The resulting localized disturbances, referred to as active layer detachments (ALDs), may transport organic matter (OM) to more biogeochemically active zones. To examine this further, solid state cross polarization magic angle spinning 13C nuclear magnetic resonance (CPMAS NMR) and biomarker analysis were used to evaluate potential shifts in riverine sediment OM composition due to nearby ALDs within the Cape Bounty Arctic Watershed Observatory, Nunavut, Canada. In sedimentary OM near ALDs, NMR analysis revealed signals indicative of unaltered plant-derived material, likely derived from permafrost. Long chain acyclic aliphatic lipids, steroids, cutin, suberin and lignin occurred in the sediments, consistent with a dominance of plant-derived compounds, some of which may have originated from permafrost-derived OM released by ALDs. OM degradation proxies for sediments near ALDs revealed less alteration in acyclic aliphatic lipids, while constituents such as steroids, cutin, suberin and lignin were found at a relatively advanced stage of degradation. Phospholipid fatty acid analysis indicated that microbial activity was higher near ALDs than downstream but microbial substrate limitation was prevalent within disturbed regions. Our study suggests that, as these systems recover from disturbance, ALDs likely provide permafrost-derived OM to sedimentary environments. This source of OM, which is enriched in labile OM, may alter biogeochemical patterns and enhance microbial respiration within these ecosystems.

Supporting Metacognitive Development in Early Science Education: Exploring Elementary Teachers' Beliefs and Practices in Metacognition

Metacognition is the understanding and control of cognitive processes. Students with high levels of metacognition achieve greater academic success. The purpose of this mixed-methods study was to examine elementary teachers’ beliefs about metacognition and integration of metacognitive practices in science. Forty-four teachers were recruited through professional networks to complete a questionnaire containing open-ended questions (n = 44) and Likert-type items (n = 41). Five respondents were selected to complete semi-structured interviews informed by the questionnaire. The selected interview participants had a minimum of three years teaching experience and demonstrated a conceptual understanding of metacognition. Statistical tests (Pearson correlation, t-tests, and multiple regression) on quantitative data and thematic analysis of qualitative data indicated that teachers largely understood metacognition but had some gaps in their understanding. Participants’ reported actions (teaching practices) and beliefs differed according to their years of experience but not gender. Hierarchical multiple regression demonstrated that the first block of gender and experience was not a significant predictor of teachers' metacognitive actions, although experience was a significant predictor by itself. Experience was not a significant predictor once teachers' beliefs were added. The majority of participants indicated that metacognition was indeed appropriate for elementary students. Participants consistently reiterated that students’ metacognition developed with practice, but required explicit instruction. A lack of consensus remained around the domain specificity of metacognition. More specifically, the majority of questionnaire respondents indicated that metacognitive strategies could not be used across subject domains, whereas all interviewees indicated that they used strategies across subjects. Metacognition was integrated frequently into Ontario elementary classrooms; however, metacognition was integrated less frequently in science lessons. Lastly, participants used a variety of techniques to integrate metacognition into their classrooms. Implications for practice include the need for more professional development aimed at integrating metacognition into science lessons at both the Primary and Junior levels. Further, teachers could benefit from additional clarification on the three main components of metacognition and the need to integrate all three to successfully develop students’ metacognition.

Molecular docking and geographical information systems as tools to assess the potential impact of veterinary medicines on non-target organisms and the environment

Veterinary medicines (VMs) from agricultural industry can enter the environment in a number of ways. This includes direct exposure through aquaculture, accidental spillage and disposal, and indirect entry by leaching from manure or runoff after treatment. Many compounds used in animal treatments have ecotoxic properties that may have chronic or sometimes lethal effects when they come into contact with non-target organisms. VMs enter the environment in mixtures, potentially having additive effects. Traditional ecotoxicology tests are used to determine the lethal and sometimes reproductive effects on freshwater and terrestrial organisms. However, organisms used in ecotoxicology tests can be unrepresentative of the populations that are likely to be exposed to the compound in the environment. Most often the tests are on single compound toxicity but mixture effects may be significant and should be included in ecotoxicology testing. This work investigates the use, measured environmental concentrations (MECs) and potential impact of sea lice treatments on salmon farms in Scotland. Alternative methods for ecotoxicology testing including mixture toxicity, and the use of in silico techniques to predict the chronic impact of VMs on different species of aquatic organisms were also investigated. The Scottish Environmental Protection Agency (SEPA) provided information on the use of five sea lice treatments from 2008-2011 on Scottish salmon farms. This information was combined with the recently available data on sediment MECs for the years 2009-2012 provided by SEPA using ArcGIS 10.1. In depth analysis of this data showed that from a total of 55 sites, 30 sites had a MEC higher than the maximum allowable concentration (MAC) as set out by SEPA for emamectin benzoate and 7 sites had a higher MEC than MAC for teflubenzuron. A number of sites that were up to 16 km away from the nearest salmon farm reported as using either emamectin benzoate or teflubenzuron measured positive for the two treatments. There was no relationship between current direction and the distribution of the sea lice treatments, nor was there any evidence for alternative sources of the compounds e.g. land treatments. The sites that had MECs higher than the MAC could pose a risk to non-target organisms and disrupt the species dynamics of the area. There was evidence that some marine protected sites might be at risk of exposure to these compounds. To complement this work, effects on acute mixture toxicity of the 5 sea lice treatments, plus one major metabolite 3-phenoxybenzoic acid (3PBA), were measured using an assay using the bioluminescent bacteria Aliivibrio fischeri. When exposed to the 5 sea lice treatments and 3PBA A. fischeri showed a response to 3PBA, emamectin benzoate and azamethiphos as well as combinations of the three. In order to establish any additive effect of the sea lice treatments, the efficacy of two mixture prediction equations, concentration addition (CA) and independent action ii(IA) were tested using the results from single compound dose response curves. In this instance IA was the more effective prediction method with a linear regression confidence interval of 82.6% compared with 22.6% of CA. In silico molecular docking was carried out to predict the chronic effects of 15 VMs (including the five used as sea lice control). Molecular docking has been proposed as an alternative screening method for the chronic effects of large animal treatments on non-target organisms. Oestrogen receptor alpha (ERα) of 7 non-target bony fish and the African clawed frog Xenopus laevis were modelled using SwissModel. These models were then ‘docked’ to oestradiol, the synthetic oestrogen ethinylestradiol, two known xenoestrogens dichlorodiphenyltrichloroethane (DDT) and bisphenol A (BPA), the antioestrogen breast cancer treatment tamoxifen and 15 VMs using Auto Dock 4. Based on the results of this work, four VMs were identified as being possible xenoestrogens or anti-oestrogens; these were cypermethrin, deltamethrin, fenbendazole and teflubenzuron. Further investigation, using in vitro assays, into these four VMs has been suggested as future work. A modified recombinant yeast oestrogen screen (YES) was attempted using the cDNA of the ERα of the zebrafish Danio rerio and the rainbow trout Oncorhynchus mykiss. Due to time and difficulties in cloning protocols this work was unable to be completed. Use of such in vitro assays would allow for further investigation of the highlighted VMs into their oestrogenic potential. In conclusion, VMs used as sea lice treatments, such as teflubenzuron and emamectin benzoate may be more persistent and have a wider range in the environment than previously thought. Mixtures of sea lice treatments have been found to persist together in the environment, and effects of these mixtures on the bacteria A. fischeri can be predicted using the IA equation. Finally, molecular docking may be a suitable tool to predict chronic endocrine disrupting effects and identify varying degrees of impact on the ERα of nine species of aquatic organisms.

An in vitro investigation on the cytotoxic and nuclear receptor transcriptional activity of the mycotoxins fumonisin B1 and beauvericin

Fumonisin B1 (FB1) and beauvericin (BEA) are secondary metabolites of filamentous fungi, which under appropriate temperature and humidity conditions may develop on various foods and feeds. To date few studies have been performed to evaluate the toxicological and endocrine disrupting effects of FB1 and BEA. The present study makes use of various in vitro bioassays including; oestrogen, androgen, progestagen and glucocorticoid reporter gene assays (RGAs) for the study of nuclear receptor transcriptional activity, the thiazolyl blue tetrazolium bromide (MTT) assay to monitor cytotoxicity and high content analysis (HCA) for the detection of pre-lethal toxicity in the RGA and Caco-2 human colon adenocarcinoma cells. At the receptor level, 0.001-10μM BEA or FB1 did not induce any agonist responses in the RGAs. However at non-cytotoxic concentrations, an antagonistic effect was exhibited by FB1 on the androgen nuclear receptor transcriptional activity at 10μM and BEA on the progestagen and glucocorticoid receptors at 1μM. MTT analysis showed no decrease in cell viability at any concentration of FB1, whereas BEA showed a significant decrease in viability at 10μM. HCA analysis confirmed that the reduction in the progestagen receptor transcriptional activity at 1μM BEA was not due to pre-lethal toxicity. In addition, BEA (10μM) induced significant toxicity in both the TM-Luc (progestagen responsive) and Caco-2 cells.

Two new 3' PML breakpoints in t(15;17)(q22;q21)-positive acute promyelocytic leukemia.

In the present article, two new types of PML/RARA junctions are described. Both were identified in diagnostic samples from two t(15;17)(q22;q21)-positive acute promyelocytic leukemia (APL) patients who failed to achieve complete remission. By using different sets of primers, reverse transcriptase polymerase chain reaction (RT-PCR) of PML/RARA junctions showed atypical larger bands compared with those generated from the three classical PML breakpoints already described. Sequence analysis of the fusion region of the amplified cDNAs allowed us to determine the specificity of these fragments in both patients. This analysis showed two new hybrid transcripts that were 53 and 306 base pairs (bp) longer than that expressed by the NB4 cell line (PML breakpoint within intron 6), and are the result of the direct joining of RARA exon 3 with PML exon 7a (patient 2) or the 5' portion of PML exon 7b (patient 1), respectively. In patient 1, RT-PCR analysis of the reciprocal RARA/PML junction showed a smaller transcript than that expected in bcr1 cases, while in patient 2 no amplified fragment was obtained. Cytogenetic analysis and/or fluorescence in situ hybridization (FISH) showed that both patients had the t(15;17) translocation. The clinical and hematological profiles expressed by the two patients carrying these unexpected types of PML/RARA rearrangement did not differ significantly from that commonly seen in other APLs with the exception of the poor outcome. Genes Chromosomes Cancer 27:35-43, 2000.

Pregnancy Planning and Diabetes:A Qualitative Exploration of Women's Attitudes Toward Preconception Care

Introduction: Seeking preconception care is recognized as an important health behavior for women with preexisting diabetes. Yet many women with diabetes do not seek care or advice until after they are pregnant, and many enter pregnancy with suboptimal glycemic control. This study explored the attitudes about pregnancy and preconception care seeking in a group of nonpregnant women with type 1 diabetes mellitus. Methods: In-depth semistructured interviews were completed with 14 nonpregnant women with type 1 diabetes. Results: Analysis of the interview data revealed 4 main themes: 1) the emotional complexity of childbearing decisions, 2) preferences for information related to pregnancy, 3) the importance of being known by your health professional, and 4) frustrations with the medical model of care. Discussion: These findings raise questions about how preconception care should be provided to women with diabetes and highlight the pivotal importance of supportive, familiar relationships between health professionals and women with diabetes in the provision of individualized care and advice. By improving the quality of relationships and communication between health care providers and patients, we will be better able to provide care and advice that is perceived as relevant to the individual, whatever her stage of family planning. © 2012 by the American College of Nurse-Midwives.

Avskaffandet av revisionsplikten : Ränteeffekter på företag inom fastighetsbranschen efter avskaffandet av revisionsplikten

Bakgrund: År 2010 avskaffades revisionsplikten för mindre aktiebolag i Sverige. Anledningen till avskaffandet var att minska kostnaderna för mindre företag. Tidigare forskning har kommit fram till att företag som valt bort revisor får en högre kreditkostnad när de till exempel tar lån. Den tidigare forskningen menar att detta kan bero på att banker och andra kreditinstitut anser att oreviderade finansiella rapporter har en sämre kvalitet än reviderade rapporter vilket leder till en högre risk för kreditgivarna. Denna uppsats kommer att undersöka om det finns någon skillnad på låneräntan mellan företag som valt att ha kvar revisor och företag som valt bort revisor. Syfte: Syftet med denna uppsats är att undersöka, jämföra samt analysera låneräntan hos mindre aktiebolag inom fastighetsbranschen som inte är revisionspliktiga. Metod: Kvantitativ metod, multipel regressionsanalys. Resultat: Resultaten i denna studie visar på att företag med revisor har en lägre ränta i genomsnitt jämfört med företag utan revisor. Vi har även fått fram att revision har en negativ påverkan på företags ränta, men detta resultat är inte signifikant. Därför kan vi inte uttala oss om att revision har en negativ påverkan på företags ränta, trots att tidigare forskning har visat det. Slutsats: Företags val av revisor eller ej är inte det viktigaste för kreditgivare när det kommer till vilken ränta företagen skall få på sina lån. Det finns andra faktorer som har en större påverkan på räntan. I denna studie är det företags storlek samt andelen materiella tillgångar i förhållande till totala tillgångar som har den största negativa påverkan på företags ränta. Detta indikerar att banker och andra kreditinstitut ser dessa företag som en lägre risk.

New Chinese Words in 2014 – A Study of Word-formation Processes

随着社会的发展，尤其是互联网的发展，很多语言每年都涌现出了不少新词汇。词语是每个语言最基本也是最重要的组成部分，因此分析这些新词汇的结构特点以及构词法是很有意义的。这篇文章分析了2014年出现在中文里的新词汇和它们的构词方式，论文的目的是为了更好地了解中文词汇的发展和特点。本文以《2014汉语新词语》中公布的2014年出现的新词汇作为语料进行分析，发现了以下两个主要特点：第一，合成法，派生法，缩略法是2014年产生的新词汇的主要构词方式；第二， 百分之七十二的新词汇是多音节词（包含三个或者三个以上音节），而百分之八十的是名词。这些特点说明中文词汇现阶段的特点和发展趋势，跟传统的中文词汇有不同之处。

"Reformpädagogik" als Systembegriff

„Reformpädagogik" diente bislang ausschließlich zur Kennzeichnung einer historischen Epoche. Eine kritische Analyse dieser Voraussetzung heutiger Debatten scheint gerade angesichts der neueren Publikationen zum Thema geboten. In einer Art Perspektivenwechsel wird die Verwendung von „Reformpädagogik" als ein für die Pädagogik in der Moderne notwendiger Systembegriff vorgeschlagen und begründet. Dabei wird bei der Struktur der Erziehungswissenschaft von der Polarität zwischen „Reform"/„Idealismus" auf der einen und „Erfahrung" auf der anderen Seite ausgegangen. Die Verwendung von „Reformpädagogik" als Systembegriff ermöglicht letztlich zweierlei: (1) eine veränderte Analyse des tradierten reformpädagogischen Erbes unter Einbezug von Johann Amos Comenius und Heinz-Joachim Heydorn sowie (2) die Einsicht in die Notwendigkeit einer permanenten Diskussion über Ziele und Wege gegenwärtiger pädagogischer Reform. (DIPF/Orig.)