Solutions to linear problems in aberrated optical systems

Linear problems are possibly the kindest problems in physics and mathematics. Given sufficient information, the linear equations describing such problems are intrinsically solvable. The solution can be written as a vector having undergone a linear transformation in a vector space; extracting the solution is simply a matter of inverting the transformation. In an ideal optical system, the problem of extracting the object under investigation would be well defined, and the solution trivial to implement. However, real optical systems are all aberrated in some way, and these aberrations obfuscate the information, scrambling it and rendering it inextricable. The process of detangling the object from the aberrated system is no longer a trivial problem or even a uniquely solvable one, and represents one of the great challenges in optics today. This thesis provides a review of the theory behind optical microscopy in the presence of absent information, an architecture for the modern physical and computational methods used to solve the linear inversion problem, and three distinct application spaces of relevance. I hope you find it useful

A Deep Learning Approach to Analyzing Continuous-Time Systems

Scientists often use observational time series data to study complex natural processes, but regression analyses often assume simplistic dynamics. Recent advances in deep learning have yielded startling improvements to the performance of models of complex processes, but deep learning is generally not used for scientific analysis. Here we show that deep learning can be used to analyze complex processes, providing flexible function approximation while preserving interpretability. Our approach relaxes standard simplifying assumptions (e.g., linearity, stationarity, and homoscedasticity) that are implausible for many natural systems and may critically affect the interpretation of data. We evaluate our model on incremental human language processing, a domain with complex continuous dynamics. We demonstrate substantial improvements on behavioral and neuroimaging data, and we show that our model enables discovery of novel patterns in exploratory analyses, controls for diverse confounds in confirmatory analyses, and opens up research questions that are otherwise hard to study.Comment: Main article: 12 pages, 1 table, 3 figures; Supplementary Information: 54 pages, 6 tables, 30 figure

Complex impedance spectroscopy for monitoring tissue responses to inserted neural implants

A series of animal experiments was conducted to characterize changes in the complex impedance of chronically implanted electrodes in neural tissue. Consistent trends in impedance changes were observed across all animals, characterized as a general increase in the measured impedance magnitude at 1 kHz. Impedance changes reach a peak approximately 7 days post-implant. Reactive responses around individual electrodes were described using immuno- and histo-chemistry and confocal microscopy. These observations were compared to measured impedance changes. Several features of impedance changes were able to differentiate between confined and extensive histological reactions. In general, impedance magnitude at 1 kHz was significantly increased in extensive reactions, starting about 4 days post-implant. Electrodes with extensive reactions also displayed impedance spectra with a characteristic change at high frequencies. This change was manifested in the formation of a semi-circular arc in the Nyquist space, suggestive of increased cellular density in close proximity to the electrode site. These results suggest that changes in impedance spectra are directly influenced by cellular distributions around implanted electrodes over time and that impedance measurements may provide an online assessment of cellular reactions to implanted devices.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/58178/2/jne7_4_007.pd

Fabrication and Imaging of Protein Crossover Structures

ABSTRACT Proteins often deform, dehydrate or otherwise denature when adsorbed or patterned directly onto an inorganic substrate, thus losing specificity and biofunctionality. One method used to maintain function is to pattern the protein of interest directly onto another underlying protein or polypeptide that acts as a buffer layer between the substrate and the desired protein. We have used microcontact printing (µcp) to cross-stamp orthogonal linear arrays of two different proteins (e.g., IgG, poly-lysine, protein A) onto glass substrates. This created three separate types of protein-substrate microenvironments, including crossover structures of protein one on protein two. We report preliminary fluorescent microscopy and scanning force microscopy characterization of these structures, including commonly encountered structural defects

Scientists' Warning to Humanity on Threats to Indigenous and Local Knowledge Systems

The knowledge systems and practices of Indigenous Peoples and local communities play critical roles in safeguarding the biological and cultural diversity of our planet. Globalization, government policies, capitalism, colonialism, and other rapid social-ecological changes threaten the relationships between Indigenous Peoples and local communities and their environments, thereby challenging the continuity and dynamism of Indigenous and Local Knowledge (ILK). In this article, we contribute to the “World Scientists' Warning to Humanity,” issued by the Alliance of World Scientists, by exploring opportunities for sustaining ILK systems on behalf of the future stewardship of our planet. Our warning raises the alarm about the pervasive and ubiquitous erosion of knowledge and practice and the social and ecological consequences of this erosion. While ILK systems can be adaptable and resilient, the foundations of these knowledge systems are compromised by ongoing suppression, misrepresentation, appropriation, assimilation, disconnection, and destruction of biocultural heritage. Three case studies illustrate these processes and how protecting ILK is central to biocultural conservation. We conclude with 15 recommendations that call for the recognition and support of Indigenous Peoples and local communities and their knowledge systems. Enacting these recommendations will entail a transformative and sustained shift in how ILK systems, their knowledge holders, and their multiple expressions in lands and waters are recognized, affirmed, and valued. We appeal for urgent action to support the efforts of Indigenous Peoples and local communities around the world to maintain their knowledge systems, languages, stewardship rights, ties to lands and waters, and the biocultural integrity of their territories—on which we all depend.Peer reviewe

Magna Carta, the Rule of Law and the Limits on Government

This paper surveys the legal tradition that links Magna Carta with the modern concepts of the rule of law and the limits on government. It documents that the original understanding of the rule of law included substantive commitments to individual freedom and limited government. Then, it attempts at explaining how and why such commitments were lost to a formalist interpretation of the rule of law from 1848 to 1939. The paper concludes by arguing how a revival of the substantive commitments of the rule of law is central in a project of reshaping modern states