Optical projection tomography implemented for accessibility and low cost ().

Optical projection tomography (OPT) is a three-dimensional mesoscopic imaging modality that can use absorption or fluorescence contrast, and is widely applied to fixed and live samples in the mm-cm scale. For fluorescence OPT, we present OPT implemented for accessibility and low cost, an open-source research-grade implementation of modular OPT hardware and software that has been designed to be widely accessible by using low-cost components, including light-emitting diode (LED) excitation and cooled complementary metal-oxide-semiconductor (CMOS) cameras. Both the hardware and software are modular and flexible in their implementation, enabling rapid switching between sample size scales and supporting compressive sensing to reconstruct images from undersampled sparse OPT data, e.

openFrame: A modular, sustainable, open microscopy platform with single-shot, dual-axis optical autofocus module providing high precision and long range of operation.

'openFrame' is a modular, low-cost, open-hardware microscopy platform that can be configured or adapted to most light microscopy techniques and is easily upgradeable or expandable to multiple modalities. The ability to freely mix and interchange both open-source and proprietary hardware components or software enables low-cost, yet research-grade instruments to be assembled and maintained. It also enables rapid prototyping of advanced or novel microscope systems.

Neuronal metabolism in learning and memory: The anticipatory activity perspective.

Current research on the molecular mechanisms of learning and memory is based on the "stimulus-response" paradigm, in which the neural circuits connecting environmental events with behavioral responses are strengthened. By contrast, cognitive and systems neuroscience emphasize the intrinsic activity of the brain that integrates information, establishes anticipatory actions, executes adaptive actions, and assesses the outcome via regulatory feedback mechanisms. We believe that the difference in the perspectives of systems and molecular studies is a major roadblock to further progress toward understanding the mechanisms of learning and memory.

Analytic and Holistic Thinkers: Differences in the Dynamics of Heart Rate Complexity When Solving a Cognitive Task in Field-Dependent and Field-Independent Conditions.

Analytic and holistic thinking styles are known to be associated with individual differences in various aspects of behavior and brain activity. In this study, we tested a hypothesis that differences in thinking styles may also be manifested at the level of neuro-visceral coordination. Heart rate variability (HRV) was compared between analytic and holistic thinkers at rest, during a simple motor choice reaction time task and when solving cognitive choice reaction time tasks in conditions with varying instructions contrasting the role of the field when evaluating objects.

Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways.

The transcriptional effector SMAD4 is a core component of the TGF-β family signaling pathways. However, its role in vertebrate embryo development remains unresolved. To address this, we deleted Smad4 in zebrafish and investigated the consequences of this on signaling by the TGF-β family morphogens, BMPs and Nodal.

Robust deep learning optical autofocus system applied to automated multiwell plate single molecule localization microscopy.

We presenta robust, long-range optical autofocus system for microscopy utilizing machine learning. This can be useful for experiments with long image data acquisition times that may be impacted by defocusing resulting from drift of components, for example due to changes in temperature or mechanical drift. It is also useful for automated slide scanning or multiwell plate imaging where the sample(s) to be imaged may not be in the same horizontal plane throughout the image data acquisition.

Application of direct stochastic optical reconstruction microscopy (dSTORM) to the histological analysis of human glomerular disease.

Electron microscopy (EM) following immunofluorescence (IF) imaging is a vital tool for the diagnosis of human glomerular diseases, but the implementation of EM is limited to specialised institutions and it is not available in many countries. Recent progress in fluorescence microscopy now enables conventional widefield fluorescence microscopes to be adapted at modest cost to provide resolution below 50 nm in biological specimens. We show that stochastically switched single-molecule localisation microscopy can be applied to clinical histological sections stained with standard IF techniques and that such super-resolved IF may provide an alternative means to resolve ultrastructure to aid the diagnosis of kidney disease where EM is not available.

Cell functioning in norm and pathology in terms of the activity paradigm: Oncogenesis.

Over the past years many theories of carcinogenesis have been developed. Nowadays, there are two prevalent theories of carcinogenesis - two-hit hypothesis, which considers mutations as the main factor in malignization and tissue hypothesis, which considers tissue homeostasis disruption for providing cells transformation. Both of these theories explain cancer origin basing on principles of the reactivity paradigm.

Complexity of heart rate variability during moral judgement of actions and omissions.

Recent research strongly supports the idea that cardiac activity is involved in the organisation of behaviour, including social behaviour and social cognition. The aim of this work was to explore the complexity of heart rate variability, as measured by permutation entropy, while individuals were making moral judgements about harmful actions and omissions. Participants (N = 58, 50% women, age 21-52 years old) were presented with a set of moral dilemmas describing situations when sacrificing one person resulted in saving five other people.

Reaction to norm transgressions and Islamization threat in culturally tight and loose contexts: a cross-cultural comparison of Germany versus Russia.

Prior research shows that North Americans and Western Europeans react to threats with defensive strategies based on behavioral approach vs. inhibition systems (BAS/BIS)-i.e.

Greater learning transfer effect for avoidance of loss than for achievement of gain in Finnish and Russian schoolchildren.

Classification of behavior into principal categories of approach and avoidance is grounded in evolutionary considerations and multiple results of behavioral, self-report, and brain-activity analyses. Contrasted via measures of cognitive processes, avoidance is accompanied by greater cognitive engagement than approach. Considering outcome as a key constituent of behavioral underpinnings, we interpret approach/avoidance distinction in terms of structure of experience: avoidance domain provides more detailed interaction with the environment, than approach domain.

Regression II. Development through regression.

As shown in our previous paper ('Regression I. Experimental approaches to regression', JAP, 65, 2, 345-65), the common mechanism of regression can be described as reversible dedifferentiation, which is understood as a relative increase of the proportion of low-differentiated (older) systems in actualized experience. Experimental data show that regression following disease (chronic tension headache) is followed by adaptation and an increase in system differentiation in that experience domain which contains systems responsible for that adaptation.

Regression I. Experimental approaches to regression.

The concept of regression is considered with an emphasis on the differences between the positions of Freud and Jung regarding its significance. The paper discusses the results of experimental analyses of individual experience dynamics (from gene expression changes and impulse neuronal activity in animals to prosocial behaviour in healthy humans at different ages, and humans in chronic pain) in those situations where regression occurs: stress, disease, learning, highly emotional states and alcohol intoxication. Common mechanisms of regression in all these situations are proposed.

DDR1 autophosphorylation is a result of aggregation into dense clusters.

The collagen receptor DDR1 is a receptor tyrosine kinase that promotes progression of a wide range of human disorders. Little is known about how ligand binding triggers DDR1 kinase activity. We previously reported that collagen induces DDR1 activation through lateral dimer association and phosphorylation between dimers, a process that requires specific transmembrane association.

Convolutional neural networks for reconstruction of undersampled optical projection tomography data applied to in vivo imaging of zebrafish.

Optical projection tomography (OPT) is a 3D mesoscopic imaging modality that can utilize absorption or fluorescence contrast. 3D images can be rapidly reconstructed from tomographic data sets sampled with sufficient numbers of projection angles using the Radon transform, as is typically implemented with optically cleared samples of the mm-to-cm scale. For in vivo imaging, considerations of phototoxicity and the need to maintain animals under anesthesia typically preclude the acquisition of OPT data at a sufficient number of angles to avoid artifacts in the reconstructed images.

Automated Fluorescence Lifetime Imaging High-Content Analysis of Förster Resonance Energy Transfer between Endogenously Labeled Kinetochore Proteins in Live Budding Yeast Cells.

We describe an open-source automated multiwell plate fluorescence lifetime imaging (FLIM) methodology to read out Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) labeling endogenous kinetochore proteins (KPs) in live budding yeast cells. The low copy number of many KPs and their small spatial extent present significant challenges for the quantification of donor fluorescence lifetime in the presence of significant cellular autofluorescence and photobleaching. Automated FLIM data acquisition was controlled by µManager and incorporated wide-field time-gated imaging with optical sectioning to reduce background fluorescence.

A drama movie activates brains of holistic and analytical thinkers differentially.

People socialized in different cultures differ in their thinking styles. Eastern-culture people view objects more holistically by taking context into account, whereas Western-culture people view objects more analytically by focusing on them at the expense of context. Here we studied whether participants, who have different thinking styles but live within the same culture, exhibit differential brain activity when viewing a drama movie.

Neuronal Bases of Systemic Organization of Behavior.

Despite the years of studies in the field of systems neuroscience, functions of neural circuits and behavior-related systems are still not entirely clear. The systems description of brain activity has recently been associated with cognitive concepts, e.g.

Sample Entropy of the Heart Rate Reflects Properties of the System Organization of Behaviour.

Cardiac activity is involved in the processes of organization of goal-directed behaviour. Each behavioural act is aimed at achieving an adaptive outcome and it is subserved by the actualization of functional systems consisting of elements distributed across the brain and the rest of the body. This paper proposes a system-evolutionary view on the activity of the heart and its variability.

Performance of a wearable acoustic system for fetal movement discrimination.

Fetal movements (FM) are a key factor in clinical management of high-risk pregnancies such as fetal growth restriction. While maternal perception of reduced FM can trigger self-referral to obstetric services, maternal sensation is highly subjective. Objective, reliable monitoring of fetal movement patterns outside clinical environs is not currently possible.

Quantitative time domain analysis of lifetime-based Förster resonant energy transfer measurements with fluorescent proteins: Static random isotropic fluorophore orientation distributions.

Förster resonant energy transfer (FRET) measurements are widely used to obtain information about molecular interactions and conformations through the dependence of FRET efficiency on the proximity of donor and acceptor fluorophores. Fluorescence lifetime measurements can provide quantitative analysis of FRET efficiency and interacting population fraction. Many FRET experiments exploit the highly specific labelling of genetically expressed fluorescent proteins, applicable in live cells and organisms.

Event-related potentials during individual, cooperative, and competitive task performance differ in subjects with analytic vs. holistic thinking.

It has been presented that Western cultures (USA, Western Europe) are mostly characterized by competitive forms of social interaction, whereas Eastern cultures (Japan, China, Russia) are mostly characterized by cooperative forms. It has also been stated that thinking in Eastern countries is predominantly holistic and in Western countries analytic. Based on this, we hypothesized that subjects with analytic vs.

Activity during Learning and the Nonlinear Differentiation of Experience.

Walter Freeman's work emphasises the role of individual activity and intentionality as opposed to the traditional stimulus-reaction view and the machine metaphor. The results of our computer modeling studies suggest the nonlinear dynamics of experience emerging from perception-action cycles. We consider the perception-action cycle as a behavioral continuum of anticipated outcomes of actions.