Time-Series Clustering of Single-Cell Trajectories in Collective Cell Migration.

Collective invasion drives multicellular cancer cells to spread to surrounding normal tissues. To fully comprehend metastasis, the methodology of analysis of individual cell migration in tissue should be well developed. Extracting and classifying cells with similar migratory characteristics in a colony would facilitate an understanding of complex cell migration patterns. Here, we used electrospun fibers as the extracellular matrix for the in vitro modeling of collective cell migration, clustering of mesenchymal and epithelial cells based on trajectories, and analysis of collective migration patterns based on trajectory similarity. We normalized the trajectories to eliminate the effect of cell location on clustering and used uniform manifold approximation and projection to perform dimensionality reduction on the time-series data before clustering. When the clustering results were superimposed on the trajectories before normalization, the results still exhibited positional similarity, thereby demonstrating that this method can identify cells with similar migration patterns. The same cluster contained both mesenchymal and epithelial cells, and this result was related to cell location and cell division. These data highlight the reliability of this method in identifying consistent migration patterns during collective cell migration. This provides new insights into the epithelial-mesenchymal interactions that affect migration patterns.

Early dynamics of chronic myeloid leukemia on nilotinib predicts deep molecular response.

Chronic myeloid leukemia (CML) is a myeloproliferative disorder caused by the BCR-ABL1 tyrosine kinase. Although ABL1-specific tyrosine kinase inhibitors (TKIs) including nilotinib have dramatically improved the prognosis of patients with CML, the TKI efficacy depends on the individual patient. In this work, we found that the patients with different nilotinib responses can be classified by using the estimated parameters of our simple dynamical model with two common laboratory findings. Furthermore, our proposed method identified patients who failed to achieve a treatment goal with high fidelity according to the data collected only at three initial time points during nilotinib therapy. Since our model relies on the general properties of TKI response, our framework would be applicable to CML patients who receive frontline nilotinib or other TKIs.

The Missing Voices of Disabled People.

This paper presents the development process of a graph database that connects statements posted by disabled people on various web-based platforms with accessibility requirements in the Danish Building Regulations (BR18). The aim is to bring the lived experience of disabled people into a vocabulary of space-making for architects. By elevating the missing voices of disabled people - describing what matters, how and why - the project supports the decision-making processes of architects to make the built environment more inclusive. The developed database relates statements posted by disabled people with sentences from paragraphs of BR18 through specific architectural features of room, element, and object. Using the architectural features as point of reference, the database not only highlights some of the most common building situations encountered by disabled people, but also allows anyone interested to explore their relationship to the real lives of disabled users and the statutory requirements.

Intermitochondrial signaling regulates the uniform distribution of stationary mitochondria in axons.

In the central nervous system (CNS), many neurons develop axonal arbors that are crucial for information processing. Previous studies have demonstrated that premature axons contain motile and stationary mitochondria, and their balance is important for axonal arborization. However, the mechanisms by which neurons determine the positions of stationary mitochondria as well as their turnover remain to be elucidated. We observed that the distribution of stationary mitochondrial spots along the unmyelinated and nonsynaptic axons is not random but rather relatively uniform both in primary cultured neurons and in tissues. Intriguingly, whereas the positions of each mitochondrial spot changed over time, the overall distribution remained uniform. In addition, local inactivation of mitochondria by KillerRed mediated chromophore-assisted light inactivation (CALI) inhibited the translocation of mitochondrial spots in adjacent axonal regions, suggesting that functional mitochondria enhance the motility of other mitochondria in the vicinity. Signals of ATP:ADP sensor, PercevalHR indicated that the ATP:ADP ratio was relatively high around mitochondria, and treating axons with phosphocreatine (PCr), which supplies ATP, reduced the immobile mitochondria induced by the local mitochondrial inactivation. In a mathematical model, we found that the ATP gradient generated by mitochondria, and ATP dependent regulation of mitochondrial motility could establish uniform mitochondrial distribution. These observations suggest that axons in the CNS possess the system that distributes mitochondria uniformly, and intermitochondrial signaling contribute to the regulation. In addition, our results suggest the possibility that ATP might be one of the molecules mediating the signaling.

User-Environment Interaction: The Usability Model for Universal Design Assessment.

Universal Design (UD) aims to provide designed environments that allow users to fully participate in all kinds of activities. Especially, the design of Sport and Leisure buildings should support and encourage the participation of mobility and sensory impaired people in any physical and social activity. Yet, the variety of physical and social users' needs calls for different approaches to investigate, analyze and assess how the environment fulfills users' needs and expectations. This paper presents a new analytical model that: a) investigates how people with mobility, visual, and hearing impairments interact with specific architectural features; b) links the examined user-environment interaction with the user's personal assessment of the spatial experience. The study employs the literature review of the existing analytical models, which are based on the concept of user-environment interaction and framed around empirically deducted basic human needs. These models address the issue of user-environment fit by focusing on the identification of environmental barriers. Also, some of these models are too descriptive and cannot inform the practice in creative design processes. The proposed analytical model, which is built upon the theoretical concepts of affordances and usability, aims to develop a qualitative evaluation method for identifying environmental facilitators by linking the design of architectural characteristics with the influenced perception of users of the physical and social aspects of the built environment. The model consists of three groups of elements: (1) users' physical abilities; (2) architectural features and (3) usability criteria. The inter-relations of each element across the groups develop the narrating scenarios that can be investigated from the user's perspective. This new model does not only advance the understanding of the spatial experiences of persons with mobility and sensory impairments but also offers new insights for exploring UD solutions by identifying the architectural features that enlarge the spectrum of possible user-environment interactions.

Users' Experience in Digital Architectural Design: Combining Qualitative Research Methods with a Generative Model.

This paper presents the development of a digital generative design tool for residential building that integrates qualitative data from potential users of buildings. The central aim is to understand and challenge the inherent biases in the design process of architecture for mobility impaired users, whose experiences might be difficult to understand for designers who often move around and use buildings without any difficulty. Although Universal Design promotes designed environments that are more sensitized with the diverse difference of individuals, the most of design generating tools are based on empirically deducted human needs, objectifying the people or seeing them as useful in simply validating design ideas. There is a clear distance in between the real needs and wishes of wheelchair users and what architects imagine when designing. Mixed-methods - expert interview, literature review and data analysis of disability blogs - are used to collect and analyse wheelchair users' experience. Accumulated qualitative data is, then, used as guiding input for the development of an explorative generative model that effectively produces large number of floor plans for residential architecture. The developed generative model effectively selects floor plans that correspond with challenges described by the wheelchair users. The selected floor plans become informed starting points for spatial planning, which can guide architects to produce new and unexpected design solutions that are more sensitised to wheelchair users' experience. The application of generative design tools in early stages of design tasks can help architects to understand users' needs and wishes, and thus challenge biased assumptions about wheelchair users' experiences. And yet, further research needs to be conducted in order to progress the system: additional user data and new design objectives can give rise to new hypothesis and allow the system to be more precise, responding to the complex reality of disabled people in their everyday lives.

Reliable target ligand detection by noise-induced receptor cluster formation.

Intracellular reactions are intrinsically stochastic. Nonetheless, cells can reliably respond to the changing environment by sensing their target molecules sensitively and specifically, even with the existence of abundant structurally-similar non-target molecules. The mechanism of how the cells can balance and achieve such different characteristics is not yet fully understood. In this work, we demonstrate that these characteristics can be attained by a ligand-induced stochastic cluster formation of receptors via the noise-induced symmetry breaking, in which the intrinsic stochasticity works to enhance sensitivity and specificity. We also show that the noise-induced cluster formation enables cells to detect the target ligand reliably by compensating the abundant non-target ligands in the environment. The proposed mechanism may lead to a deeper understanding of a biological function of the receptor clustering and provide an alternative candidate for the reliable ligand detection to the kinetic proofreading.

Balancing specificity, sensitivity, and speed of ligand discrimination by zero-order ultraspecificity.

Specific interactions between receptors and their target ligands in the presence of nontarget ligands are crucial for biological processes such as T cell ligand discrimination. To discriminate between the target and nontarget ligands, cells have to increase specificity to the target ligands by amplifying the small differences in affinity among ligands. In addition, sensitivity to the ligand concentration and quick discrimination are also important to detect low amounts of target ligands and facilitate fast cellular decision making after ligand recognition. In this work we propose a mechanism for nonlinear specificity amplification (ultraspecificity) based on zero-order saturating reactions, which was originally proposed to explain nonlinear sensitivity amplification (ultrasensitivity) to the ligand concentration. In contrast to the previously proposed proofreading mechanisms that amplify the specificity by a multistep reaction, our model can produce an optimal balance of specificity, sensitivity, and quick discrimination. Furthermore, we show that a model for insensitivity to a large number of nontarget ligands can be naturally derived from a model with the zero-order ultraspecificity. The zero-order ultraspecificity, therefore, may provide an alternative way to understand ligand discrimination from the viewpoint of nonlinear properties in biochemical reactions.

Qualitative Description of Spatial Quality in Inclusive Architecture.

Universal design (UD) has gained global significance and is in the process of institutionalisation in the Nordic Region. This is despite an urgent necessity for developing the theoretical basis and practical applicability of UD. Reflecting this need for furthering the comprehensive understanding of spatial implication of UD, this paper aims to contribute for articulating a means to assess the quality of UD in architecture. Drawing upon numerous cases from research conducted at the Danish Building Research Institute, the paper focuses on sensory aspects of spatial quality, and discusses as well as reflects an applied method for producing the qualitative description of selected buildings that embody UD through creative solutions. The qualitative description of collected examples appears to be effective in delineating sensory aspects of spatial experience; however the systematic development of assessment criteria is essential in order to support students and designers to make responsible decisions in shaping built environments that are accessible and inclusive but also enjoyable.

Characterization of Interfacial Charge-Transfer Photoexcitation of Polychromium-Oxo-Electrodeposited TiO2 as an Earth-Abundant Photoanode for Water Oxidation Driven by Visible Light.

Polychromium-oxo-deposited TiO2 (CrIII x Oy /TiO2 ) electrodes were fabricated by a simple electrochemical technique by using different TiO2 basal electrodes (anatase, rutile, and mixed polymorphic phases P25) as earth-abundant photoanodes for visible-light-driven water oxidation. The high-resolution transmission electron microscopy (HR-TEM) observation illustrated that an CrIII x Oy layer with approximately 2-3 nm thickness was formed on the surface of the crystalline TiO2 particles. Upon visible-light irradiation of the electrodes, the photoanodic current based on water oxidation was generated at the CrIII x Oy /TiO2 electrodes. However, the wavelength (below 620 nm) for photocurrent generation at CrIII x Oy /TiO2 -rutile was longer than that (below 560 nm) at CrIII x Oy /TiO2 -P25 by 60 nm, which is in agreement with the difference (0.2 eV) in the conduction band (CB) edge energy between rutile and anatase TiO2 . This gives a quantitative account for the photocurrent generation based on interfacial charge transfer (IFCT) from Cr 3d of the deposited CrIII x Oy layer to the TiO2 CB. The photocurrent generated for CrIII x Oy /TiO2 -rutile was higher than that for CrIII x Oy /TiO2 -anatase, which is ascribed to 1) more effective CrIII x Oy deposition on the rutile particles, 2) a larger electrolyte/CrIII x Oy interface for water oxidation as a result of smaller rutile particles (ca. 30-40 nm) compared with larger P25 particles (ca. 40-80 nm), and 3) more effective use of visible light owing to the low energy IFCT transition of rutile.

Experimental and theoretical bases for mechanisms of antigen discrimination by T cells.

Interaction only within specific molecules is a requisite for accurate operations of a biochemical reaction in a cell where bulk of background molecules exist. While structural specificity is a well-established mechanism for specific interaction, biophysical and biochemical experiments indicate that the mechanism is not sufficient for accounting for the antigen discrimination by T cells. In addition, the antigen discrimination by T cells also accompanies three intriguing properties other than the specificity: sensitivity, speed, and concentration compensation. In this work, we review experimental and theoretical works on the antigen discrimination by focusing on these four properties and show future directions towards understanding of the fundamental principle for molecular discrimination.

Visible-light-driven water oxidation at a polychromium-oxo-electrodeposited TiO2 electrode as a new type of earth-abundant photoanode.

A polychromium-oxo-deposited TiO2 electrode was fabricated as an earth-abundant photoanode for visible-light-driven water oxidation by a simple electrochemical technique. The photoelectrocatalytic water oxidation could occur based on a specific interfacial charge transfer (IFCT) from a Cr(III) to the TiO2 conduction band.

In vitro free radical scavenging activity of platinum nanoparticles.

A polyacrylic acid (PAA)-protected platinum nanoparticle species (PAA-Pt) was prepared by alcohol reduction of hexachloroplatinate. The PAA-Pt nanoparticles were well dispersed and homogeneous in size with an average diameter of 2.0 +/- 0.4 nm (n = 200). We used electron spin resonance to quantify the residual peroxyl radical ([Formula: see text]) generated from 2,2-azobis (2-aminopropane) dihydrochloride (AAPH) by thermal decomposition in the presence of O(2) and a spectrophotometric method to quantify the residual 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical. PAA-Pt scavenged these two radicals in a dose-dependent manner. Platinum was the functional component. PAA-Pt reduced the rate of oxygen consumption required for linoleic acid peroxidation initiated by [Formula: see text] generated from AAPH, indicating inhibition of the propagation of linolate peroxidation. A thiobarbituric acid test also revealed dose-dependent inhibition of the linolate peroxidation by PAA-Pt. Fifty micromolar platinum, as PAA-Pt, completely quenched 250 microM DPPH radical for 5 min. Even when twice diluted in half, the PAA-Pt still quenched 100% of the 250 microM DPPH radical. The scavenging activity of PAA-Pt is durable. These observations suggest that PAA-Pt is an efficient scavenger of free radicals.

Platinum nanoparticle antioxidants inhibit pulmonary inflammation in mice exposed to cigarette smoke.

Recent evidence implicates increased oxidative stress as an important mechanism of the pulmonary inflammation that occurs in cigarette smokers. Since cigarette smoke (CS) contains and generates a large amount of reactive oxygen species (ROS) that elicit pulmonary inflammation, antioxidants may become effective therapeutic agents for CS-related inflammatory lung diseases, such as chronic obstructive pulmonary disease. Platinum nanoparticles stabilized with polyacrylate to form a stable colloid solution (PAA-Pt) are a new class of antioxidants that has been shown to efficiently quench ROS. In the present study we investigated the therapeutic effects of PAA-Pt on pulmonary inflammation in smoking mice. PAA-Pt or saline was administered intranasally to DBA/2 mice, which were then exposed to CS or control air daily for 3 days. Mice were sacrificed 4h after their final exposure to CS or control air. CS exposure caused depletion of antioxidant capacity, NFkappaB activation, and neutrophilic inflammation in the lungs of mice, and intranasal administration of PAA-Pt prior to CS exposure was found to inhibit these changes. Intranasal administration of PAA-Pt alone did not elicit pulmonary inflammation or toxicity. In in vitro experiments, treatment of alveolar-type-II-like A549 cells with PAA-Pt inhibited cell death after exposure to a CS extract. These results suggest that platinum nanoparticles act as antioxidants that inhibit pulmonary inflammation induced by acute cigarette smoking.

Platinum nanoparticles have an activity similar to mitochondrial NADH:ubiquinone oxidoreductase.

This study was designed to examine if platinum nanoparticles have an activity similar to mitochondrial complex I, NADH:ubiquinone oxidoreductase. Platinum nanoparticles were prepared by a citrate reduction of H(2)PtCl(6) and protected by citrate itself and pectin (CP-Pt). Time- and dose-dependent decreases in NADH and a time-dependent increase in NAD(+) were observed in the presence of 50 microM CP-Pt; these observations were made using a spectrophotometric method in which the maximum absorption spectra at 340 and 260 nm were used for NADH and NAD(+), respectively. The required platinum concentration in CP-Pt to achieve a 50% oxidation of NADH for 3h was approximately 20 microM, and this NADH oxidation did not require oxygen as an electron acceptor. We also verified NAD(+) formation using an NAD(+)/NADH quantification kit. The absorption peak shift from 278 to 284 nm of 2,3-dimethoxy-5-methyl-6-(3-methyl-2-butenyl)-1,4-benzoquinone (CoQ(1)) was observed by incubating CoQ(1) with CP-Pt in an aqueous buffer. A further analysis with HPLC revealed the reduction of CoQ(1) to CoQ(1)H(2) by CP-Pt. As a whole, platinum nanoparticles have an NADH:ubiquinone oxidoreductase-like activity. This suggests that platinum nanoparticles are a potential medicinal substance for oxidative stress diseases with suppressed mitochondrial complex I.

Effects of a potent antioxidant, platinum nanoparticle, on the lifespan of Caenorhabditis elegans.

We have shown that platinum nanoparticles (nano-Pt) are a superoxide dismutase (SOD)/catalase mimetic. Various data have shown extension of the Caenorhabditis elegans lifespan by antioxidant treatment. The present study was designed to elucidate the survival benefit conferred by nano-Pt, as compared to the well-known SOD/catalase mimetic EUK-8. At 0.5mM, nano-Pt significantly extended the lifespan of wild-type N2 nematodes and at 0.25 and 0.5mM, nano-Pt recovered the shortened lifespan of the mev-1(kn1) mutant, which is due to excessive oxidative stress. In both instances, EUK-8 at 0.05, 0.5, and 5mM did not extend nematode lifespan. Even when 0.4M paraquat was loaded exogenously, nano-Pt (0.1 and 0.5mM) and EUK-8 (0.5 and 5mM) were effective in rescuing worms. Moreover, 0.5mM nano-Pt significantly reduced the accumulation of lipofuscin and ROS induced by paraquat. We measured the in vitro dose-dependent quenching of O(2)(-) and H(2)O(2), indicating that nano-Pt is a more potent SOD/catalase mimetic than EUK-8. Nano-Pt prolonged the worm lifespan, regardless of thermotolerance or dietary restriction. Taken together, nano-Pt has interesting anti-ageing properties.

Platinum nanoparticle is a useful scavenger of superoxide anion and hydrogen peroxide.

Bimetallic nanoparticles consisting of gold and platinum were prepared by a citrate reduction method and complementarily stabilized with pectin (CP-Au/Pt). The percent mole ratio of platinum was varied from 0 to 100%. The CP-Au/Pt were alloy-structured. They were well dispersed in water. The average diameter of platinum nanoparticles (CP-Pt) was 4.7 +/- 1.5 nm. Hydrogen peroxide (H(2)O(2)) was quenched by CP-Au/Pt consisting of more than 50% platinum whereas superoxide anion radical (O(2)(-)) was quenched by any CP-Au/Pt. The CP-Au/Pt quenched these two reactive oxygen species in dose-dependent manners. The CP-Pt is the strongest quencher. The CP-Pt decomposed H(2)O(2) and consequently generated O(2) like catalase. The CP-Pt actually quenched O(2)(-) which was verified by a superoxide dismutase (SOD) assay kit. This quenching activity against O(2)(-) persisted like SOD. Taken together, CP-Pt may be a SOD/catalase mimetic which is useful for medical treatment of oxidative stress diseases.