Micrographia of the twenty-first century: from camera obscura to 4D microscopy

In this paper, the evolutionary and revolutionary developments of microscopic imaging are overviewed with a perspective on origins. From Alhazen’s camera obscura, to Hooke and van Leeuwenhoek’s two-dimensional optical micrography, and on to three- and four-dimensional (4D) electron microscopy, these developments over a millennium have transformed humans’ scope of visualization. The changes in the length and time scales involved are unimaginable, beginning with the visible shadows of candles at the centimetre and second scales, and ending with invisible atoms with space and time dimensions of sub-nanometre and femtosecond. With these advances it has become possible to determine the structures of matter and to observe their elementary dynamics as they unfold in real time. Such observations provide the means for visualizing materials behaviour and biological function, with the aim of understanding emergent phenomena in complex systems

What do faculties specializing in brain and neural sciences think about, and how do they approach, brain-friendly teaching-learning in Iran?

Objective: to investigate the perspectives and experiences of the faculties specializing in brain and neural sciences regarding brain-friendly teaching-learning in Iran. Methods: 17 faculties from 5 universities were selected by purposive sampling (2018). In-depth semi-structured interviews with directed content analysis were used. Results: 31 sub-subcategories, 10 subcategories, and 4 categories were formed according to the “General teaching model”. “Mentorship” was a newly added category. Conclusions: A neuro-educational approach that consider the roles of the learner’s brain uniqueness, executive function facilitation, and the valence system are important to learning. Such learning can be facilitated through cognitive load considerations, repetition, deep questioning, visualization, feedback, and reflection. The contextualized, problem-oriented, social, multi-sensory, experiential, spaced learning, and brain-friendly evaluation must be considered. Mentorship is important for coaching and emotional facilitation

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should therefore be as reliable and versatile as possible. In this context, we examined five aspects of the organization and mining of malaria genomic and post-genomic data: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Progresses toward a grid-enabled chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa

From Maxout to Channel-Out: Encoding Information on Sparse Pathways

Motivated by an important insight from neural science, we propose a new framework for understanding the success of the recently proposed "maxout" networks. The framework is based on encoding information on sparse pathways and recognizing the correct pathway at inference time. Elaborating further on this insight, we propose a novel deep network architecture, called "channel-out" network, which takes a much better advantage of sparse pathway encoding. In channel-out networks, pathways are not only formed a posteriori, but they are also actively selected according to the inference outputs from the lower layers. From a mathematical perspective, channel-out networks can represent a wider class of piece-wise continuous functions, thereby endowing the network with more expressive power than that of maxout networks. We test our channel-out networks on several well-known image classification benchmarks, setting new state-of-the-art performance on CIFAR-100 and STL-10, which represent some of the "harder" image classification benchmarks.Comment: 10 pages including the appendix, 9 figure

Mapping Topographic Structure in White Matter Pathways with Level Set Trees

Fiber tractography on diffusion imaging data offers rich potential for describing white matter pathways in the human brain, but characterizing the spatial organization in these large and complex data sets remains a challenge. We show that level set trees---which provide a concise representation of the hierarchical mode structure of probability density functions---offer a statistically-principled framework for visualizing and analyzing topography in fiber streamlines. Using diffusion spectrum imaging data collected on neurologically healthy controls (N=30), we mapped white matter pathways from the cortex into the striatum using a deterministic tractography algorithm that estimates fiber bundles as dimensionless streamlines. Level set trees were used for interactive exploration of patterns in the endpoint distributions of the mapped fiber tracks and an efficient segmentation of the tracks that has empirical accuracy comparable to standard nonparametric clustering methods. We show that level set trees can also be generalized to model pseudo-density functions in order to analyze a broader array of data types, including entire fiber streamlines. Finally, resampling methods show the reliability of the level set tree as a descriptive measure of topographic structure, illustrating its potential as a statistical descriptor in brain imaging analysis. These results highlight the broad applicability of level set trees for visualizing and analyzing high-dimensional data like fiber tractography output

Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

Knowledge, understanding and the dynamics of medical innovation

This paper investigates the processes by which scientific knowledge is created and legitimized. It focuses on scientific developments in a branch of medicine and explores the pathways through which the growth of knowledge enables advances in medical science and in clinical practice. This work draws conceptually on evolutionary approaches to technological change. The empirical part presents a longitudinal analysis of a database of scientific publications in the field of ophthalmology over a period of 50 years. Such an exercise allows us to identify pathways of shared understanding on a disease area, and to map out distinctive trajectories followed by the ophthalmology research community. The paper also contributes to general understanding of the innovation process by supporting the notion that knowledge coordination is a distributed process that cuts across and connects complementary areas of expertise.