Differential toxicity of amorphous silica nanoparticles toward phagocytic and epithelial cells

The objective of this study was to evaluate the influence of size and surface functionality of amorphous silica nanoparticles (SNPs) on their interaction with cultured cells. The intracellular uptake, phagocytic activity, and possible mechanisms of toxicity induced by SNPs were studied on murine alveolar macrophages and two epithelial cancer cell lines. It was found that phagocytic cells are more susceptible to amorphous SNPs than epithelial cells. SNPs with functionalized surfaces were capable to induce the formation of apoptotic cells to a higher extent than plain particles. Plain SNPs induced plasma membrane damage in phagocytic cells to a higher extent and caused cell death in a shorter period of time than surface-functionalized SNPs. The prevalence of necrotic mode of cell death was observed after treatment with plain SNPs. In the range studied surface functionality played an important role in SNPs toxicity.     

A Teacher’s Conception of Definition and Use of Examples When Doing and Teaching Mathematics

To contribute to an understanding of the nature of teachers’ mathematical knowledge and its role in teaching, the case study reported in this article investigated a teacher’s conception of a metamathematical concept, definition, and her use of examples in doing and teaching mathematics. Using an enactivist perspective on mathematical knowledge, the authors give an account of the case of Lily, a prospective, then beginning, teacher who conceived of mathematical definition as an object with particular form and function and engaged in purposeful, specialized use of examples when doing and teaching mathematics. Lily’s case illustrates how a teacher’s interpretation of examples (as exemplifications or single instances) and conception of the form and function of definitions can influence her doing and teaching mathematics. An implication is that teacher preparation should foster teachers’ abilities to use examples purposefully to provide students with rich opportunities to engage in mathematical processes such as defining.     

Counting singular plane curves via Hilbert schemes

We give a method of counting the number of curves with a given type of singularity in a suitably ample linear series on a smooth surface using punctual Hilbert schemes. The types of singularities for which our results suffice include the topological type with local equation x^a+y^b with ?a?3b. We work out the example of curves with the analytic type of singularity with local equation x²+yⁿ for 1<n<9.     

Influence of Data Acquisition Environment on Accuracy of Acoustic Voice Quality Measurements

Accuracy of acoustic voice analysis is influenced by the quality of recording. Lately, articles have suggested that soundcards perform equivalently to specialized professional-grade data acquisition (DA) systems. The purpose of this study was to investigate the influence of DA environment (DA system and microphone) on acoustic voice quality measurement (VQM) while balancing for gender, age, intersubject and intrasubject variability, and analysis software. More specifically, the relative performance of different hardware environments and the relationship between their technical characteristics and VQM performance was investigated. The discretization error and the effective dynamic range of the different DA environments were measured. We used 3 software systems to record and measure separately 2000 acoustic samples of sustained phonation for fundamental frequency, jitter, and shimmer. Analyses of variance (ANOVA) were performed with these parameters as the dependent variables. The results of the study suggested that professional-grade DA hardware is strongly recommended to provide accurate and valid voice assessment. The fundamental frequency measurement differences across DA environments were highly correlated to the discretization error (r=1.00), whereas jitter and shimmer were highly correlated to the effective dynamic range of the DA environments (r=-0.68 and r=-0.86, respectively).     

Comparing pharmacophore models derived from crystallography and NMR ensembles

NMR and X-ray crystallography are the two most widely used methods for determining protein structures. Our previous study examining NMR versus X-Ray sources of protein conformations showed improved performance with NMR structures when used in our Multiple Protein Structures (MPS) method for receptor-based pharmacophores (Damm, Carlson, J Am Chem Soc 129:8225–8235, 2007). However, that work was based on a single test case, HIV-1 protease, because of the rich data available for that system. New data for more systems are available now, which calls for further examination of the effect of different sources of protein conformations. The MPS technique was applied to Growth factor receptor bound protein 2 (Grb2), Src SH2 homology domain (Src-SH2), FK506-binding protein 1A (FKBP12), and Peroxisome proliferator-activated receptor-γ (PPAR-γ). Pharmacophore models from both crystal and NMR ensembles were able to discriminate between high-affinity, low-affinity, and decoy molecules. As we found in our original study, NMR models showed optimal performance when all elements were used. The crystal models had more pharmacophore elements compared to their NMR counterparts. The crystal-based models exhibited optimum performance only when pharmacophore elements were dropped. This supports our assertion that the higher flexibility in NMR ensembles helps focus the models on the most essential interactions with the protein. Our studies suggest that the “extra” pharmacophore elements seen at the periphery in X-ray models arise as a result of decreased protein flexibility and make very little contribution to model performance.     

Characteristics of Second Graders' Mathematical Writing

This study compared the characteristics of second graders' mathematical writing between an intervention and comparison group. Two six‐week Project M2 units were implemented with students in the intervention group. The units position students to communicate in ways similar to mathematicians, including engaging in verbal discourse where they themselves make sense of the mathematics through discussion and debate, writing about their reasoning on an ongoing basis, and utilizing mathematical vocabulary while communicating in any medium. Students in the comparison group learned from the regular school curriculum. Students in both the intervention and comparison groups conveyed high and low levels of content knowledge as indicated in archived data from an open‐response end‐of‐the‐year assessment. A multivariate analysis of variance indicated several differences favoring the intervention group. Both the high‐ and low‐level intervention subgroups outperformed the comparison group in their ability to (a) provide reasoning, (b) attempt to use formal mathematical vocabulary, and (c) correctly use formal mathematical vocabulary in their writing. The low‐level intervention subgroup also outperformed the respective comparison subgroup in their use of (a) complete sentences and (b) linking words. There were no differences between groups in their attempt at writing and attempts at and usage of informal mathematical vocabulary.     

Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins

Understanding how glycosylation affects protein structure, dynamics, and function is an emerging and challenging problem in biology. As a first step toward glycan modeling in the context of structural glycobiology, we have developed Glycan Reader and integrated it into the CHARMM-GUI, http://www.charmm-gui.org/input/glycan. Glycan Reader greatly simplifies the reading of PDB structure files containing glycans through (i) detection of carbohydrate molecules, (ii) automatic annotation of carbohydrates based on their three-dimensional structures, (iii) recognition of glycosidic linkages between carbohydrates as well as N-/O-glycosidic linkages to proteins, and (iv) generation of inputs for the biomolecular simulation program CHARMM with the proper glycosidic linkage setup. In addition, Glycan Reader is linked to other functional modules in CHARMM-GUI, allowing users to easily generate carbohydrate or glycoprotein molecular simulation systems in solution or membrane environments and visualize the electrostatic potential on glycoprotein surfaces. These tools are useful for studying the impact of glycosylation on protein structure and dynamics.