BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis

Amyloids and prion proteins are clinically and biologically important beta-structures, whose supersecondary structures are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Recent work has indicated the utility of pairwise probabilistic statistics in beta-structure prediction. We develop here a new strategy for beta-structure prediction, emphasizing the determination of beta-strands and pairs of beta-strands as fundamental units of beta-structure. Our program, BETASCAN, calculates likelihood scores for potential beta-strands and strand-pairs based on correlations observed in parallel beta-sheets. The program then determines the strands and pairs with the greatest local likelihood for all of the sequence's potential beta-structures. BETASCAN suggests multiple alternate folding patterns and assigns relative a priori probabilities based solely on amino acid sequence, probability tables, and pre-chosen parameters. The algorithm compares favorably with the results of previous algorithms (BETAPRO, PASTA, SALSA, TANGO, and Zyggregator) in beta-structure prediction and amyloid propensity prediction. Accurate prediction is demonstrated for experimentally determined amyloid beta-structures, for a set of known beta-aggregates, and for the parallel beta-strands of beta-helices, amyloid-like globular proteins. BETASCAN is able both to detect beta-strands with higher sensitivity and to detect the edges of beta-strands in a richly beta-like sequence. For two proteins (Abeta and Het-s), there exist multiple sets of experimental data implying contradictory structures; BETASCAN is able to detect each competing structure as a potential structure variant. The ability to correlate multiple alternate beta-structures to experiment opens the possibility of computational investigation of prion strains and structural heterogeneity of amyloid. BETASCAN is publicly accessible on the Web at http://betascan.csail.mit.edu.

Removal of enamel caries with an air abrasion powder

This study compared the efficiency of air abrasion on enamel caries with selective enamel powder (SEP) or with alumina powder and a negative and positive control group. Ninety-three extracted molars with non-cavitated incipient enamel lesions were selected. After embedding the roots in resin, each lesion was sectioned perpendicular to the surface and photographed. Each lesion was classified microscopically as having or not having dentin involvement. The lesions were distributed into four groups with an equal number of enamel caries with or without dentin involvement. Each group was treated differently: Group 1 had SEP abrasion, Group 2 had alumina abrasion, Group 3 had sodium bicarbonate abrasion (negative control) and Group 4 had bur treatment (positive control). The surface was rephotographed after treatment. Superimposition of the photographs identified areas of "correct-excavation," "under-excavation" and "over-excavation." There were no statistical differences between lesions treated with or without dentin involvement for Groups 2 through 4. However, in the SEP group, all measured areas were significantly influenced by dentin involvement. In pairwise comparisons, no statistical differences were found between the alumina and bur groups. The SEP group, however, showed statistically significant differences for each area compared to the alumina group in enamel caries without dentin involvement. SEP performed as well as alumina and bur in lesions with dentin involvement. SEP is different in its ablative properties toward caries with dentin involvement or no dentin involvement. In terms of dental treatment, SEP seems to have a diagnostic potential for enamel lesions before operative intervention in patients with high caries risk.

Performance of different polishing techniques for direct CAD/CAM ceramic restorations

This in vitro study evaluated the performance of three ceramic and two commonly used polishing methods on two CAD/CAM ceramics. Surface roughness and quality were compared. A glazed group (GLGR) of each ceramic material served as reference. One-hundred and twenty specimens of VITABLOCS Mark II (VITA) and 120 specimens of IPS Empress CAD (IPS) were roughened in a standardized manner. Twenty VITA and 20 IPS specimens were glazed (VITA Akzent Glaze/Empress Universal Glaze). Five polishing methods were investigated (n=20/group): 1) EVE Diacera W11DC-Set (EVE), 2) JOTA 9812-Set (JOTA), 3) OptraFine-System (OFI), 4) Sof-Lex 2382 discs (SOF) and 5) Brownie/Greenie/Occlubrush (BGO). Polishing quality was measured with a surface roughness meter (Ra and Rz values). The significance level was set at alpha=0.05. Kruskal Wallis tests and pairwise Wilcoxon rank sum tests with Bonferroni-Holm adjustment were used. Qualitative surface evaluation of representative specimens was done with SEM. On VITA ceramics, SOF produced lower Ra (p<0.00001) but higher Rz values than GLGR (p=0.003); EVE, JOTA, OFI and BGO yielded significantly higher Ra and Rz values than GLGR. On IPS ceramics, SOF and JOTA exhibited lower Ra values than GLGR (p<0.0001). Equivalent Ra but significantly higher Rz values occurred between GLGR and EVE, OFI or BGO. VITA and IPS exhibited the smoothest surfaces when polished with SOF. Nevertheless, ceramic polishing systems are still of interest to clinicians using CAD/CAM, as these methods are universally applicable and showed an increased durability compared to the investigated silicon polishers.

Push-out bond strength of CAD/CAM-ceramic luted to dentin with self-adhesive resin cements

OBJECTIVES: This study evaluated the initial and the artificially aged push-out bond strength between ceramic and dentin produced by one of five resin cements. METHODS: Two-hundred direct ceramic restorations (IPS Empress CAD) were luted to standardized Class I cavities in extracted human molars using one of four self-adhesive cements (SpeedCEM, RelyX Unicem Aplicap, SmartCem2 and iCEM) or a reference etch-and-rinse resin cement (Syntac/Variolink II) (n=40/cement). Push-out bond strength (PBS) was measured (1) after 24h water storage (non-aged group; n=20/cement) or (2) after artificial ageing with 5000 thermal cycles followed by 6 months humid storage (aged group; n=20/cement). Nonparametrical ANOVA and pairwise Wilcoxon rank-sum tests with Bonferroni-Holm adjustment were applied for statistical analysis. The significance level was set at alpha=0.05. In addition, failure mode and fracture pattern were analyzed by stereomicroscope and scanning electron microscopy. RESULTS: Whereas no statistically significant effect of storage condition was found (p=0.441), there was a significant effect of resin cement (p<0.0001): RelyX Unicem showed significantly higher PBS than the other cements. Syntac/Variolink II showed significantly higher PBS than SmartCEM2 (p<0.001). No significant differences were found between SpeedCEM, SmartCem2, and iCEM. The predominant failure mode was adhesive failure of cements at the dentin interface except for RelyX Unicem which in most cases showed cohesive failure in ceramic. SIGNIFICANCE: The resin cements showed marked differences in push-out bond strength when used for luting ceramic restorations to dentin. Variolink II with the etch-and-rinse adhesive Syntac did not perform better than three of the four self-adhesive resin cements tested.

Operator variability using different polishing methods and surface geometry of a nanohybrid composite

This study evaluated the operator variability of different finishing and polishing techniques. After placing 120 composite restorations (Tetric EvoCeram) in plexiglassmolds, the surface of the specimens was roughened in a standardized manner. Twelve operators with different experience levels polished the specimens using the following finishing/polishing procedures: method 1 (40 ?m diamond [40D], 15 ?m diamond [15D], 42 ?m silicon carbide polisher [42S], 6 ?m silicon carbide polisher [6S] and Occlubrush [O]); method 2 (40D, 42S, 6S and O); method 3 (40D, 42S, 6S and PoGo); method 4 (40D, 42S and PoGo) and method 5 (40D, 42S and O). The mean surface roughness (Ra) was measured with a profilometer. Differences between the methods were analyzed with non-parametric ANOVA and pairwise Wilcoxon signed rank tests (?=0.05). All the restorations were qualitatively assessed using SEM. Methods 3 and 4 showed the best polishing results and method 5 demonstrated the poorest. Method 5 was also most dependent on the skills of the operator. Except for method 5, all of the tested procedures reached a clinically acceptable surface polish of Ra?0.2 ?m. Polishing procedures can be simplified without increasing variability between operators and without jeopardizing polishing results.

Factor analysis of responses to thermal, electrical, and mechanical painful stimuli supports the importance of multi-modal pain assessment

During the last decade, a multi-modal approach has been established in human experimental pain research for assessing pain thresholds and responses to various experimental pain modalities. Studies have concluded that differences in responses to pain stimuli are mainly related to variation between individuals rather than variation in response to different stimulus modalities. In a factor analysis of 272 consecutive volunteers (137 men and 135 women) who underwent tests with different experimental pain modalities, it was determined whether responses to different pain modalities represent distinct individual uncorrelated dimensions of pain perception. Volunteers underwent single painful electrical stimulation, repeated painful electrical stimulation (temporal summation), test for reflex receptive field, pressure pain stimulation, heat pain stimulation, cold pain stimulation, and a cold pressor test (ice water test). Five distinct factors were found representing responses to 5 distinct experimental pain modalities: pressure, heat, cold, electrical stimulation, and reflex-receptive fields. Each of the factors explained approximately 8% to 35% of the observed variance, and the 5 factors cumulatively explained 94% of the variance. The correlation between the 5 factors was near null (median ρ=0.00, range -0.03 to 0.05), with 95% confidence intervals for pairwise correlations between 2 factors excluding any relevant correlation. Results were almost similar for analyses stratified according to gender and age. Responses to different experimental pain modalities represent different specific dimensions and should be assessed in combination in future pharmacological and clinical studies to represent the complexity of nociception and pain experience.

Detecting and resolving position-dependent temperature effects in real-time quantitative polymerase chain reaction

Real-time quantitative polymerase chain reaction (qPCR) depends on precise temperature control of the sample during cycling. In the current study, we investigated how temperature variation in plate-based qPCR instruments influences qPCR results. Temperature variation was measured by amplicon melting analysis as a convenient means to assess well-to-well differences. Multiple technical replicates of several SYBR Green I-based qPCR assays allowed correlation of relative well temperature to quantification cycle. We found that inadequate template denaturation results in an inverse correlation and requires increasing the denaturation temperature, adding a DNA destabilizing agent, or pretreating with a restriction enzyme. In contrast, inadequate primer annealing results in a direct correlation and requires lowering the annealing temperature. Significant correlations were found in 18 of 25 assays. The critical nature of temperature-dependent effects was shown in a blinded study of 29 patients for the diagnosis of Prader-Willy and Angelman syndromes, where eight diagnoses were incorrect unless temperature-dependent effects were controlled. A method to detect temperature-dependent effects by pairwise comparisons of replicates in routine experiments is presented and applied. Systematic temperature errors in qPCR instruments can be recognized and their effects eliminated when high precision is required in quantitative genetic diagnostics and critical complementary DNA analyses.

Phylogenetic and virulence analysis of tick-borne encephalitis virus field isolates from Switzerland

Tick-borne encephalitis (TBE) is an endemic disease in Switzerland, with about 110-120 reported human cases each year. Endemic areas are found throughout the country. However, the viruses circulating in Switzerland have not been characterized so far. In this study, the complete envelope (E) protein sequences and phylogenetic classification of 72 TBE viruses found in Ixodes ricinus ticks sampled at 39 foci throughout Switzerland were analyzed. All isolates belonged to the European subtype and were highly related (mean pairwise sequence identity of 97.8% at the nucleotide and 99.6% at the amino acid level of the E protein). Sixty-four isolates were characterized in vitro with respect to their plaque phenotype. More than half (57.8%) of isolates produced a mixture of plaques of different sizes, reflecting a heterogeneous population of virus variants. Isolates consistently forming plaques of small size were associated with recently detected endemic foci with no or only sporadic reports of clinical cases. All of six virus isolates investigated in an in vivo mouse model were highly neurovirulent (100% mortality) but exhibited a relatively low level of neuroinvasiveness, with mouse survival rates ranging from 50% to 100%. Therefore, TBE viruses circulating in Switzerland belong to the European subtype and are closely related. In vitro and in vivo surrogates suggest a high proportion of isolates with a relatively low level of virulence, which is in agreement with a hypothesized high proportion of subclinical or mild TBE infections.

Enamel loss and adhesive remnants following bracket removal and various clean-up procedures in vitro

This study evaluated the enamel loss and composite remnants after debonding and clean-up. The tested null hypothesis is that there are no differences between different polishing systems regarding removing composite remnants without damaging the tooth surface. Brackets were bonded to 75 extracted human molars and removed after a storage period of 100 hours. The adhesive remnant index (ARI) was evaluated. The clean-up was carried out with five different procedures: 1. carbide bur; 2. carbide bur and Brownie and Greenie silicone polishers; 3. carbide bur and Astropol polishers; 4. carbide bur and Renew polishers; and 5. carbide bur, Brownie, Greenie and PoGo polishers. Silicone impressions were made at baseline (T0) and after debonding (T1) and polishing (T2) to produce plaster replicas. The replicas were analysed with a three-dimensional laser scanner and measured with analytical software. Statistical analysis was performed with the Kruskal-Wallis test and pairwise Wilcoxon tests with Bonferroni-Holm adjustment (α = 0.05). Enamel breakouts after debonding were detectable in 27 per cent of all cases, with a mean volume loss of 0.02 mm(3) (±0.03 mm(3)) and depth of 44.9 μm (±48.3 μm). The overall ARI scores was 3 with a few scores of 1 and 2. The composite remnants after debonding had a mean volume of 2.48 mm(3) (±0.92 mm(3)). Mean volume loss due to polishing was 0.05 mm(3) (±0.26 mm(3)) and the composite remnants had a mean volume of 0.22 mm(3) (±0.32 mm(3)). There were no statistically significant differences in volumetric changes after polishing (P = 0.054) between the different clean-up methods. However, sufficient clean-up without enamel loss was difficult to achieve.

Molecular characterization and phylogenetic analysis of small ruminant lentiviruses isolated from Canadian sheep and goats

Background: Small Ruminant Lentiviruses (SRLV) are widespread in Canadian sheep and goats and represent an important health issue in these animals. There is however no data about the genetic diversity of Caprine Arthritis Encephalitis Virus (CAEV) or Maedi Visna Virus (MVV) in this country. Findings: We performed a molecular and phylogenetic analysis of sheep and goat lentiviruses from a small geographic area in Canada using long sequences from the gag region of 30 infected sheep and 36 infected goats originating from 14 different flocks. Pairwise DNA distance and phylogenetic analyses revealed that all SRLV sequences obtained from sheep clustered tightly with prototypical Maedi visna sequences from America. Similarly, all SRLV strains obtained from goats clustered tightly with prototypical US CAEV-Cork strain. Conclusions: The data reported in this study suggests that Canadian and US SRLV strains share common origins. In addition, the molecular data failed to bring to light any evidence of past cross species transmission between sheep and goats, which is consistent with the type of farming practiced in this part of the country where single species flocks predominate and where opportunities of cross species transmissions are proportionately low.

Simply a nest? Effects of different enrichments on stereotypic and anxiety-related behaviour in mice

Improving the home cages of laboratory mice by environmental enrichment has been widely used to reduce cage stereotypies and anxiety-related behaviour in behavioural tests. However, enrichment studies differ substantially in type, complexity and variation of enrichments. Therefore, it is unclear whether success depends on specific enrichment items, environmental complexity, or novelty associated with enrichment. The aim of this study was therefore to dissociate the effects of environmental complexity and novelty on stereotypy development and compare these effects with the provision of nesting material alone. Thus, 54 freshly weaned male ICR (CD-1) mice were pairwise allocated to standard laboratory cages enriched in three different ways (n = 18 per group). Treatment 1 consisted of cotton wool as nesting material. Treatments 2 and 3 were structurally more complex, including a shelter and a climbing structure as additional resources. To render complexity and novelty independent of the specific enrichment items, three shelters (cardboard house, plastic tunnel, red plastic house) and three climbing structures (ladder, rope, wooden bars) were used to create nine different combinations of enrichment. In treatment 2 (complexity), each pair of mice was assigned to a different combination that remained constant throughout 9 weeks, whereas in treatment 3 (novelty), each pair of mice was exposed to all 9 combinations in turn by changing them weekly in a pseudorandom order. After 9 weeks, stereotypic behaviour in the home cage was assessed from video recordings, and anxiety-related behaviour was assessed in two behavioural tests (elevated zero-maze, open-field). However, no significant differences in stereotypy scores and no consistent differences in anxiety-related behaviours were found between the three groups. These findings indicate that within standard laboratory cages neither complexity nor novelty of simple enrichments have additional effects on stereotypic and anxiety-related behaviour beyond those of adequate nesting material. (C) 2011 Elsevier B.V. All rights reserved.

The Schizophrenia Proneness Instrument, Child and Youth version (SPI-CY): Practicability and discriminative validity

Background Basic symptom (BS) criteria have been suggested to complement ultra-high risk (UHR) criteria in the early detection of psychosis in adults and in children and adolescents. To account for potential developmental particularities and a different clustering of BS in children and adolescents, the Schizophrenia Proneness Instrument, Child and Youth version (SPI-CY) was developed. Aims The SPI-CY was evaluated for its practicability and discriminative validity. Method The SPI-CY was administered to 3 groups of children and adolescents (mean age 16; range=8–18; 61% male): 23 at-risk patients meeting UHR and/or BS criteria (AtRisk), 22 clinical controls (CC), and 19 children and adolescents from the general population (GPS) matched to AtRisk in age, gender, and education. We expected AtRisk to score highest on the SPI-CY, and GPS lowest. Results The groups differed significantly on all 4 SPI-CY subscales. Pairwise post-hoc comparisons confirmed our expectations for all subscales and, at least on a descriptive level, most items. Pairwise subscale differences indicated at least moderate group effects (r≥0.37) which were largest for Adynamia (0.52≤r≥0.70). Adynamia also performed excellent to outstanding in ROC analyses (0.813≤AUC≥0.981). Conclusion The SPI-CY could be a helpful tool for detecting and assessing BS in the psychosis spectrum in children and adolescents, by whom it was well received. Furthermore, its subscales possess good discriminative validity. However, these results require validation in a larger sample, and the psychosis-predictive ability of the subscales in different age groups, especially the role of Adynamia, will have to be explored in longitudinal studies.

Distinct DNA methylation patterns in cirrhotic liver and hepatocellular carcinoma

Abberrant DNA methylation is one of the hallmarks of cancerogenesis. Our study aims to delineate differential DNA methylation in cirrhosis and hepatic cancerogenesis. Patterns of methylation of 27,578 individual CpG loci in 12 hepatocellular carcinomas (HCCs), 15 cirrhotic controls and 12 normal liver samples were investigated using an array-based technology. A supervised principal component analysis (PCA) revealed 167 hypomethylated loci and 100 hypermethylated loci in cirrhosis and HCC as compared to normal controls. Thus, these loci show a "cirrhotic" methylation pattern that is maintained in HCC. In pairwise supervised PCAs between normal liver, cirrhosis and HCC, eight loci were significantly changed in all analyses differentiating the three groups (p < 0.0001). Of these, five loci showed highest methylation levels in HCC and lowest in control tissue (LOC55908, CELSR1, CRMP1, GNRH2, ALOX12 and ANGPTL7), whereas two loci showed the opposite direction of change (SPRR3 and TNFSF15). Genes hypermethylated between normal liver to cirrhosis, which maintain this methylation pattern during the development of HCC, are depleted for CpG islands, high CpG content promoters and polycomb repressive complex 2 (PRC2) targets in embryonic stem cells. In contrast, genes selectively hypermethylated in HCC as compared to nonmalignant samples showed an enrichment of CpG islands, high CpG content promoters and PRC2 target genes (p < 0.0001). Cirrhosis and HCC show distinct patterns of differential methylation with regards to promoter structure, PRC2 targets and CpG islands.

Effects of a single administration of prostaglandin F2alpha, or a combination of prostaglandin F2alpha and prostaglandin E2, or placebo on fertility variables in dairy cows 3-5 weeks post partum, a randomized, double-blind clinical trial

BACKGROUND: Delayed uterine involution has negative effects on the fertility of cows; use of prostaglandin F2alpha alone as a single treatment has not been shown to consistently improve fertility. Combined administration of PGF2alpha and PGE2 increased uterine pressure in healthy cows. We hypothesized, that the combination of both prostaglandins would accelerate uterine involution and have, therefore, a positive effect on fertility variables. In commercial dairy farming, the benefit of a single post partum combined prostaglandin treatment should be demonstrated. METHODS: 383 cows from commercial dairy farms were included in this study. Uterine size and secretion were evaluated at treatment 21-35 days post partum and 14 days later. Cows were randomly allocated to one of three treatment groups: PGF2alpha and PGE2, PGF2alpha or placebo. For every animal participating in the study, the following reproduction variables were recorded: Interval from calving to first insemination, days open, number of artificial inseminations (AI) to conception; subsequent treatment of uterus, subsequent treatment of ovaries. Plasma progesterone level at time of treatment was used as a covariable. For continuous measurements, analysis of variance was performed. Fisher's exact test for categorical non-ordered data and exact Kruskal-Wallis test for ordered data were used; pairwise group comparisons with Bonferroni adjustment of significance level were performed. RESULTS: There was no significant difference among treatment groups in uterine size. Furthermore, there was no significant difference among treatments concerning days open, number of AI, and subsequent treatment of uterus and ovaries. Days from calving to first insemination tended to be shorter for cows with low progesterone level given PGF2alpha and PGE2 in combination than for the placebo-group (P = 0.024). CONCLUSION: The results of this study indicate that the administration of PGF2alpha or a combination of PGF2alpha and PGE2 21 to 35 days post partum had no beneficial effect upon measured fertility variables. The exception was a tendency for a shorter interval from calving to first insemination after administration of the combination of PGF2alpha and PGE2, as compared to the placebo group. Further research should be done in herds with reduced fertility and/or an increased incidence of postpartum vaginal discharge.

The effect of matrix bound parathyroid hormone on bone regeneration

INTRODUCTION: Autogenous bone is the most successful bone-grafting material; however, multiple disadvantages continue to drive developments of improved methods for bone regeneration. AIM: The aim of the present study was to test the hypothesis that an arginine-glycine-aspartic acid (RGD) modified polyethylene glycol-based matrix (PEG) containing covalently bound peptides of the parathyroid hormone (PTH(1-34)) enhances bone regeneration to a degree similar to autogenous bone. MATERIAL AND METHODS: Six American foxhounds received a total of 48 cylindrical titanium implants placed in the mandible between the first premolar and the second molar. Five, respectively, 7 months following tooth extraction, implants were placed into the center of surgically created defects. This resulted in a circumferential bone defect simulating an alveolar defect with a circular gap of 1.5 mm. Four treatment modalities were randomly allocated to the four defects per side: (1) PEG-matrix containing 20 microg/ml of PTH(1-34), and 350 microg/ml cys-RGD peptide, (2) PEG alone, (3) autogenous bone and (4) empty defects. Histomorphometric analysis was performed 4 and 12 weeks after implantation. The area fraction of newly formed bone was determined within the former defect and the degree of bone-to-implant contact (BIC) was evaluated both in the defect region and in the apical region of the implant. For statistical analysis ANOVA and subsequent pairwise Student's t-test were applied. RESULTS: Healing was uneventful and all implants were histologically integrated. Histomorphometric analysis after 4 weeks showed an average area fraction of newly formed bone of 41.7+/-1.8% for matrix-PTH, 26.6+/-4.1% for PEG alone, 43.9+/-4.5% for autogenous bone, and 28.9+/-1.5% for empty defects. After 12 weeks, the respective values were 49.4+/-7.0% for matrix-PTH, 39.3+/-5.7% for PEG alone, 50.5+/-3.4% for autogenous bone and 38.7+/-1.9% for empty defects. Statistical analysis after 4 and 12 weeks revealed significantly more newly formed bone in the PTH(1-34) group compared with PEG alone or empty defects, whereas no difference could be detected against autogenous bone. Regarding BIC no significant difference was observed between the four treatment groups neither at 4 nor at 12 weeks. CONCLUSION: It is concluded that an RGD-modified PEG hydrogel containing PTH(1-34) is an effective matrix system to obtain bone regeneration.