176 research outputs found
Protein secondary structure: Entropy, correlations and prediction
Is protein secondary structure primarily determined by local interactions
between residues closely spaced along the amino acid backbone, or by non-local
tertiary interactions? To answer this question we have measured the entropy
densities of primary structure and secondary structure sequences, and the local
inter-sequence mutual information density. We find that the important
inter-sequence interactions are short ranged, that correlations between
neighboring amino acids are essentially uninformative, and that only 1/4 of the
total information needed to determine the secondary structure is available from
local inter-sequence correlations. Since the remaining information must come
from non-local interactions, this observation supports the view that the
majority of most proteins fold via a cooperative process where secondary and
tertiary structure form concurrently. To provide a more direct comparison to
existing secondary structure prediction methods, we construct a simple hidden
Markov model (HMM) of the sequences. This HMM achieves a prediction accuracy
comparable to other single sequence secondary structure prediction algorithms,
and can extract almost all of the inter-sequence mutual information. This
suggests that these algorithms are almost optimal, and that we should not
expect a dramatic improvement in prediction accuracy. However, local
correlations between secondary and primary structure are probably of
under-appreciated importance in many tertiary structure prediction methods,
such as threading.Comment: 8 pages, 5 figure
Detection of benzimidazole carbamates and amino metabolites in liver by surface plasmon resonance-biosensor
This research was funded by the Irish Department of Agriculture, Fisheries and Food under the Food Institutional Research Measure as part of the National Development Plan (Project 05/R&D/TN/355)peer-reviewedTwo surface plasmon resonance (SPR) biosensor screening assays were developed and validated to detect 11 benzimidazole carbamate (BZT) and four amino-benzimidazole veterinary drug residues in liver tissue. The assays used polyclonal antibodies, raised in sheep, to detect BZTs and amino-benzimidazoles. A modified Quick, Easy, Cheap, Effective, Rugged and Safe (QuEChERS) extraction method was developed to isolate benzimidazole carbamate residues. Liver samples were extracted using an acetonitrile extraction method. BZTs were purified by dispersive solid phase extraction (d-SPE) using C18 sorbent. Residues of amino-benzimidazoles were effectively cleaned-up using a simple cyclohexane defatting step. The assays were validated in accordance with the performance criteria described in 2002/657/EC. The BZT assay limit of detection was calculated to be 32 μg kg−1, the detection capability (CCβ) was determined to be 50 μg kg−1 and the mean recovery of analytes was in the range 77–132%. The amino-benzimidazole assay limit of detection was determined to be 41 μg kg−1, the CCβ was determined to be 75 μg kg−1 and analyte recovery was in the range 103–116%. Biosensor assay performance was tested by analysing liver tissue from animals treated with benzimidazole drugs and comparing the results with an ultra high performance liquid chromatography tandem mass spectrometry (UHPLC–MS/MS) confirmatory method. All non-compliant samples were identified using the biosensor assays.Department of Agriculture, Food and the Marin
Computer-Based Instruction and Cognitive Load
Following cognitive load theory, we used a computer-based software training paradigm to determining the optimal number of steps or information chunks to present before practice opportunities. Results demonstrating that the size of information chunks presented and the type of practice used individually influenced participants\u27 ability to effectively learn via computer-based instruction. These findings contribute to the literature by showing the importance of practice and optimal segment sizes for learning via a computer
Frequency and surface dependence of the mechanical loss in fused silica
We have compiled measurements of the mechanical loss in fused silica from
samples spanning a wide range of geometries and resonant frequency in order to
model the known variation of the loss with frequency and surface-to-volume
ratio. This improved understanding of the mechanical loss has contributed
significantly to the design of advanced interferometric gravitational wave
detectors, which require ultra-low loss materials for their test mass mirrors.Comment: 5 pages, 3 figure but 5 figure file
Examining the Effects of Gender and Presentation Mode on Learning from a Multimedia Presentation
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Visual presentation modes in multimedia learning include pictures, video, and animations. Research also reveals cognitive differences between males and females (Halpern, 2004). Which one of the presentation modes is more effective? Can one of these presentation modes be more effective for a specific gender? This study aimed to investigate the role of gender and presentation mode in multimedia learning. Participants were 72 university students randomly assigned to one of the two different versions of a computer-based multimedia program (narration with animation vs. narration with static images). A 2 × 2 factorial design is created by crossing gender and presentation mode (animation vs. static image). Dependent measures consisted of a transfer and a comprehension test. The results showed a significant modality by gender interaction on the comprehension test. Females performed better studying animations, whereas males performed better studying static pictures. The results are interpreted in light of multimedia learning principles and studies in the area of gender differences in learning. The important contribution of this study is the suggestion that individual differences such as gender should be considered in multimedia learning
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