Can current force fields reproduce ring puckering in 2-O-sulfo-α-l-iduronic acid? A molecular dynamics simulation study

The monosaccharide 2-O-sulfo-α-l-iduronic acid (IdoA2S) is one of the major components of glycosaminoglycans. The ability of molecular mechanics force fields to reproduce ring-puckering conformational equilibrium is important for the successful prediction of the free energies of interaction of these carbohydrates with proteins. Here we report unconstrained molecular dynamics simulations of IdoA2S monosaccharide that were carried out to investigate the ability of commonly used force fields to reproduce its ring conformational flexibility in aqueous solution. In particular, the distribution of ring conformer populations of IdoA2S was determined. The GROMOS96 force field with the SPC/E water potential can predict successfully the dominant skew-boat to chair conformational transition of the IdoA2S monosaccharide in aqueous solution. On the other hand, the GLYCAM06 force field with the TIP3P water potential sampled transitional conformations between the boat and chair forms. Simulations using the GROMOS96 force field showed no pseudorotational equilibrium fluctuations and hence no inter-conversion between the boat and twist boat ring conformers. Calculations of theoretical proton NMR coupling constants showed that the GROMOS96 force field can predict the skew-boat to chair conformational ratio in good agreement with the experiment, whereas GLYCAM06 shows worse agreement. The omega rotamer distribution about the C5–C6 bond was predicted by both force fields to have torsions around 10°, 190°, and 360°.

The reproducibility of acquiring three dimensional gait and plantar pressure data using established protocols in participants with and without type 2 diabetes and foot ulcers

Background Several prospective studies have suggested that gait and plantar pressure abnormalities secondary to diabetic peripheral neuropathy contributes to foot ulceration. There are many different methods by which gait and plantar pressures are assessed and currently there is no agreed standardised approach. This study aimed to describe the methods and reproducibility of three-dimensional gait and plantar pressure assessments in a small subset of participants using pre-existing protocols. Methods Fourteen participants were conveniently sampled prior to a planned longitudinal study; four patients with diabetes and plantar foot ulcers, five patients with diabetes but no foot ulcers and five healthy controls. The repeatability of measuring key biomechanical data was assessed including the identification of 16 key anatomical landmarks, the measurement of seven leg dimensions, the processing of 22 three-dimensional gait parameters and the analysis of four different plantar pressures measures at 20 foot regions. Results The mean inter-observer differences were within the pre-defined acceptable level (<7 mm) for 100 % (16 of 16) of key anatomical landmarks measured for gait analysis. The intra-observer assessment concordance correlation coefficients were > 0.9 for 100 % (7 of 7) of leg dimensions. The coefficients of variations (CVs) were within the pre-defined acceptable level (<10 %) for 100 % (22 of 22) of gait parameters. The CVs were within the pre-defined acceptable level (<30 %) for 95 % (19 of 20) of the contact area measures, 85 % (17 of 20) of mean plantar pressures, 70 % (14 of 20) of pressure time integrals and 55 % (11 of 20) of maximum sensor plantar pressure measures. Conclusion Overall, the findings of this study suggest that important gait and plantar pressure measurements can be reliably acquired. Nearly all measures contributing to three-dimensional gait parameter assessments were within predefined acceptable limits. Most plantar pressure measurements were also within predefined acceptable limits; however, reproducibility was not as good for assessment of the maximum sensor pressure. To our knowledge, this is the first study to investigate the reproducibility of several biomechanical methods in a heterogeneous cohort.

Neck length and mean arterial pressure in the sauropod dinosaurs

How blood was able to reach the heads of the long-necked sauropod dinosaurs has long been a matter of debate and several hypotheses have been presented. For example, it has been proposed that sauropods had exceptionally large hearts, multiple ‘normal’ sized hearts spaced at regular intervals up the neck or held their necks horizontal, or that the siphon effect was in operation. By means of an experimental model, we demonstrate that the siphon principle is able to explain how blood was able to adequately perfuse the sauropod brain. The return venous circulation may have been protected from complete collapse by a structure akin to the vertebral venous plexus. We derive an equation relating neck height and mean arterial pressure, which indicates that with a mean arterial pressure similar to that of the giraffe, the maximum safe vertical distance between heart and head would have been about 12 m. A hypothesis is presented that the maximum neck length in the fossil record is due to the siphon height limit. The equation indicates that to migrate over high ground, sauropods would have had to either significantly increase their mean arterial pressure or keep their necks below a certain height dependent on altitude.

Fluorescent Fields: electric lighting and the rationalization of the modern corporate workplace

This study investigates the implications of the introduction of electric lighting systems, building technologies, and theories of worker efficiency on the deep spatial and environmental transformations that occurred within the corporate workplace during the twentieth century. Examining the shift from daylighting strategies to largely artificially lit workplace environments, this paper argues that electric lighting significantly contributed to the architectural rationalization of both office work and the modern office environment. Contesting the historical and critical marginalization of lighting within the discourse of the modern built environment, this study calls for a reassessment of the role of artificial lighting in the development of the modern corporate workplace. Keywords: daylighting, fluorescent lighting, rationalization, workplace design

The effect of pressure and W-doping on the properties of ZnO thin films for NO2 gas sensing

Pure and W-doped ZnO thin films were obtained using magnetron sputtering at working pressures of 0.4 Pa and 1.33 Pa. The films were deposited on glass and alumina substrates at room temperature and subsequently annealed at 400oC for 1 hour in air. The effects of pressure and W-doping on the structure, chemical, optical and electronic properties of the ZnO films for gas sensing were examined. From AFM, the doped film deposited at higher pressure (1.33 Pa) has spiky morphology with much lower grain density and porosity compared to the doped film deposited at 0.4 Pa. The average gain size and roughness of the annealed films were estimated to be 65 nm and 2.2 nm, respectively with slightly larger grain size and roughness appeared in the doped films. From XPS the films deposited at 1.33 Pa favored the formation of adsorbed oxygen on the film surface and this has been more pronounced in the doped film which created active sites for OH adsorption. As a consequence the W-doped film deposited at 1.33 Pa was found to have lower oxidation state of W (35.1 eV) than the doped film deposited at 0.4 Pa (35.9 eV). Raman spectra indicated that doping modified the properties of the ZnO film and induced free-carrier defects. The transmittance of the samples also reveals an enhanced free-carrier density in the W-doped films. The refractive index of the pure film was also found to increase from 1.7 to 2.2 after W-doping whereas the optical band gap only slightly increased. The W-doped ZnO film deposited at 0.4 Pa appeared to have favorable properties for enhanced gas sensing. This film showed significantly higher sensing performance towards 5-10 ppm NO2 at lower operating temperature of 150oC most dominantly due to increased free-carrier defects achieved by W-doping.

Deeper and wider fully convolutional network coupled with conditional random fields for scene labeling

Deep convolutional neural networks (DCNNs) have been employed in many computer vision tasks with great success due to their robustness in feature learning. One of the advantages of DCNNs is their representation robustness to object locations, which is useful for object recognition tasks. However, this also discards spatial information, which is useful when dealing with topological information of the image (e.g. scene labeling, face recognition). In this paper, we propose a deeper and wider network architecture to tackle the scene labeling task. The depth is achieved by incorporating predictions from multiple early layers of the DCNN. The width is achieved by combining multiple outputs of the network. We then further refine the parsing task by adopting graphical models (GMs) as a post-processing step to incorporate spatial and contextual information into the network. The new strategy for a deeper, wider convolutional network coupled with graphical models has shown promising results on the PASCAL-Context dataset.

Context-based assessment: Creating opportunities for resonance between classroom fields and societal fields

There is on-going international interest in the relationships between assessment instruments, students’ understanding of science concepts and context-based curriculum approaches. This study extends earlier research showing that students can develop connections between contexts and concepts – called fluid transitions – when studying context-based courses. We provide an in-depth investigation of one student’s experiences with multiple contextual assessment instruments that were associated with a context-based course. We analyzed the student’s responses to context-based assessment instruments to determine the extent to which contextual tests, reports of field investigations, and extended experimental investigations afforded her opportunities to make connections between contexts and concepts. A system of categorizing student responses was developed that can inform other educators when analyzing student responses to contextual assessment. We also refine the theoretical construct of fluid transitions that informed the study initially. Implications for curriculum and assessment design are provided in light of the findings.