Self-Assembly of Supramolecules Consisting of Octyl Gallate Hydrogen Bonded to Polyisoprene-block-poly(vinylpyridine) Diblock Copolymers

Synchrotron radiation was used to investigate the self-assembly in two comb-shaped supramolecules systems consisting of octyl gallate (OG), i.e., 1-octyl-3,4,5-trihydroxybenzoate, hydrogen bonded to the pyridine groups of polyisoprene-block-poly(vinylpyridine) diblock copolymers. In the case of the 1,2-polyisoprene-block-poly(4-vinylpyridine)(OG)x system, self-assembly was only observed for x ≥0.5, where x denotes the number of OG molecules per pyridine group. For x = 0.5, 0.75, 1.0, and 1.2 the system self-assembled in the form of hexagonally ordered cylinders of P4VP(OG) throughout the entire temperature range of 25-200 °C investigated. For the 1,4-polyisoprene-block-poly(2-vinylpyridine)(OG)x system, on the other hand, a considerably more complex phase behavior was found, including the formation of cubic, hexagonally ordered cylinders and lamellar morphologies. In this case several order-order transitions were observed as a function of temperature, including a lamellar to lamellar transition involving a collapse of the layer thickness. The absence of hydrogen bonding between the octyl gallate molecules and the pyridine groups at elevated temperatures is argued to be a key factor for many of the phenomena observed.

Converting Biomechanical Models from OpenSim to MuJoCo

OpenSim is a widely used biomechanics simulator with several anatomically accurate human musculo-skeletal models. While OpenSim provides useful tools to analyse human movement, it is not fast enough to be routinely used for emerging research directions, e.g., learning and simulating motor control through deep neural networks and Reinforcement Learning (RL). We propose a framework for converting OpenSim models to MuJoCo, the de facto simulator in machine learning research, which itself lacks accurate musculo-skeletal human models. We show that with a few simple approximations of anatomical details, an OpenSim model can be automatically converted to a MuJoCo version that runs up to 600 times faster. We also demonstrate an approach to computationally optimize MuJoCo model parameters so that forward simulations of both simulators produce similar results.Comment: Submitted to 5th International Conference on NeuroRehabilitation (ICNR2020

Unilateral zebrafish corneal injury induces bilateral cell plasticity supporting wound closure

The cornea, transparent and outermost structure of camera-type eyes, is prone to environmental challenges, but has remarkable wound healing capabilities which enables to preserve vision. The manner in which cell plasticity impacts wound healing remains to be determined. In this study, we report rapid wound closure after zebrafish corneal epithelium abrasion. Furthermore, by investigating the cellular and molecular events taking place during corneal epithelial closure, we show the induction of a bilateral response to a unilateral wound. Our transcriptomic results, together with our TGF-beta receptor inhibition experiments, demonstrate conclusively the crucial role of TGF-beta signaling in corneal wound healing. Finally, our results on Pax6 expression and bilateral wound healing, demonstrate the decisive impact of epithelial cell plasticity on the pace of healing. Altogether, our study describes terminally differentiated cell competencies in the healing of an injured cornea. These findings will enhance the translation of research on cell plasticity to organ regeneration.Peer reviewe

How to Maintain a Linked Data Cloud in a Deployed Semantic Portal

ISWC 2018 Posters & Demonstrations, Industry and Blue Sky Ideas TracksPeer reviewe

Creating the HISTO Ontology of Finnish History Events

Accepted, conference postponed to 202

Efficient light-induced phase transitions in halogen-bonded liquid crystals

Here, we present a new family of light-responsive, fluorinated supramolecular liquid crystals (LCs) showing efficient and reversible light-induced LC-to-isotropic phase transitions. Our materials design is based on fluorinated azobenzenes, where the fluorination serves to strengthen the noncovalent interaction with bond-accepting stilbazole molecules, and increase the lifetime of the cis-form of the azobenzene units. The halogen-bonded LCs were characterized by means of X-ray diffraction, hot-stage polarized optical microscopy, and differential scanning calorimetry. Simultaneous analysis of light-induced changes in birefringence, absorption, and optical scattering allowed us to estimate that <4% of the mesogenic units in the cis-form suffices to trigger the full LC-to-isotropic phase transition. We also report a light-induced and reversible crystal-to-isotropic phase transition, which has not been previously observed in supramolecular complexes. In addition to fundamental understanding of light-responsive supramolecular complexes, we foresee this study to be important in the development of bistable photonic devices and supramolecular actuators

Sampo-UI: A Full Stack JavaScript Framework for Developing Semantic Portal User Interfaces

This paper presents a new software framework, SAMPO-UI, for developing user interfaces for semantic portals. The goal is to provide the end-user with multiple application perspectives to Linked Data knowledge graphs, and a two-step usage cycle based on faceted search combined with ready-to-use tooling for data analysis. For the software developer, the SAMPO-UI framework makes it possible to create highly customizable, user-friendly, and responsive user interfaces using current state-of-the-art JavaScript libraries and data from SPARQL endpoints, while saving substantial coding effort. SAMPO-UI is published on GitHub under the open MIT License and has been utilized in several internal and external projects. The framework has been used thus far in creating six published and five forth-coming portals, mostly related to the Cultural Heritage domain, that have had tens of thousands of end-users on the Web.Peer reviewe

Zebrafish cornea formation and homeostasis reveal a slow maturation process, similarly to terrestrial vertebrates' corneas

Corneal blindness is the fourth leading cause of blindness worldwide. The superficial position of cornea on the eye makes this tissue prone to environmental aggressions, which can have a strong impact on sight. While most corneal pathology studies utilize terrestrial models, the knowledge on zebrafish cornea is too scarce to comprehend its strategy for the maintenance of a clear sight in aquatic environment. In this study, we deciphered the cellular and molecular events during corneal formation and maturation in zebrafish. After describing the morphological changes taking place from 3 days post fertilization (dpf) to adulthood, we analyzed cell proliferation. We showed that label retaining cells appear around 14 to 21dpf. Our cell proliferation study, combined to the study of Pax6a and krtt1c19e expression, demonstrate a long maturation process, ending after 45dpf. This maturation ends with a solid patterning of corneal innervation. Finally, we demonstrated that corneal wounding leads to an intense dedifferentiation, leading to the recapitulation of corneal formation and maturation, via a plasticity period. Altogether, our study deciphers the maturation steps of an aquatic cornea. These findings demonstrate the conservation of corneal formation, maturation and wound healing process in aquatic and terrestrial organisms, and they will enhance the use of zebrafish as model for corneal physiology studies.Peer reviewe

WarVictimSampo 1914–1922: a National War Memorial on the Semantic Web for Digital Humanities Research and Applications

AcceptedThis article presents the semantic portal and Linked Open Data service WARVICTIMSAMPO 1914-1922 about the war victims, battles, and prisoner camps in the Finnish Civil and other wars in 1914-1922. The system is based on a database of the National Archives of Finland and additional related data created, compiled, and linked during the project. The system contains detailed information about some 40,000 deaths extracted from several data sources and data about over 1,000 battles of the Civil War. A key novelty of WARVICTIMSAMPO 1914-1922 is the integration of ready-to-use Digital Humanities visualizations and data analysis tooling with semantic faceted search and data exploration, which allows, e.g., studying data about wider prosopographical groups in addition to individual war victims. The article focuses on demonstrating how the tools of the portal, as well as the underlying SPARQL endpoint openly available on the Web, can be used to explore and analyze war history in flexible and visual ways. WARVICTIMSAMPO 1914-1922 is a new member in the series of "Sampo" model-based semantic portals. The portal is in use and has had 23,000 users, including both war historians and the general public seeking information about their deceased relatives.Peer reviewe