Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure (versión actualizada)

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage

Ribozymes of hepatitis delta virus have been proposed to use an active-site cytosine as an acid-base catalyst in the self-cleavage reaction. In this study, we have examined the role of cytosine in more detail with the antigenomic ribozyme. Evidence that proton transfer in the rate-determining step involved cytosine 76 (C76) was obtained from examining cleavage activity of the wild-type and imidazole buffer-rescued C76-deleted (C76Δ) ribozymes in D2O and H2O. In both reactions, a similar kinetic isotope effect and shift in the apparent pKa indicate that the buffer is functionally substituting for the side chain in proton transfer. Proton inventory of the wild-type reaction supported a mechanism of a single proton transfer at the transition state. This proton transfer step was further characterized by exogenous base rescue of a C76Δ mutant with cytosine and imidazole analogues. For the imidazole analogues that rescued activity, the apparent pKa of the rescue reaction, measured under kcat/KM conditions, correlated with the pKa of the base. From these data a Brønsted coefficient (β) of 0.51 was determined for the base-rescued reaction of C76Δ. This value is consistent with that expected for proton transfer in the transition state. Together, these data provide strong support for a mechanism where an RNA side chain participates directly in general acid or general base catalysis of the wild-type ribozyme to facilitate RNA cleavage.

The interferon-inducible double-stranded RNA-activated protein kinase self-associates in vitro and in vivo.

The interferon-inducible double-stranded (ds) RNA-activated protein kinase (PKR) exhibits antiviral, anticellular, and antitumor activities. The mechanisms of its enzymatic activation by autophosphorylation and of the observed transdominant inhibitory phenotype of enzymatically inactive mutants have invoked PKR dimerization. Here we present direct evidence in support of PKR-PKR interaction. We show that radiolabeled PKR can specifically interact with matrix-bound unlabeled PKR in the absence of dsRNA. The self-association activity resides, in part, in the N-terminal region of 170 residues, which also constitutes the dsRNA-binding domain (DRBD). DRBD can bind to matrix-bound PKR or to matrix-bound DRBD. Dimerization of DRBD was directly demonstrated by chemical crosslinking. Affinity chromatography and electrophoretic mobility supershift assays demonstrated that mutants that fail to bind dsRNA can still exhibit protein-protein interaction. The PKR-PKR interaction could also be observed in a two-hybrid transcriptional activation assay in mammalian cells and consequently is likely to be an important feature of PKR activity in vivo.

The Importance of the First Psychotherapy Case in the Development of the Therapist's Professional Self as Viewed Through the Lens of Self Psychology

This paper explores the gap in the literature between what is herein referred to as the "first psychotherapy case" and its impact on the development of the trainee psychotherapist's professional self. The self psychology concepts of identity development, selfobject needs and fulfillment, narcissism, shame, countertransference, and structuralization are incorporated into the theoretical framework from which this developmental milestone is viewed. The theory's emphasis on early experiences and the development of self highlight the distinctiveness of the first case for the therapist. The beginning psychotherapy case poses a unique context for selfobject experiences and the developing self, involving both the therapist's presumably mature needs (assuming an existing cohesive nuclear self) and more infantile needs as the professional, peripheral self develops. As a result, the potential and important implications for the psychotherapist, the patient, training implications for the supervisor, and the ensuing treatment through termination are identified. The intent is to shed light on an area that is understudied thus far, and to begin a conversation as to why and how the impact of the first case on the psychotherapist should be examined. Implications, limitations, and ideas for future exploratory and qualitative research are also discussed.

Understanding Mastectomy from a Self Psychology Perspective: The Breast as a Self Object

For many women, if not all, breasts are an important component of bodyself-image; a woman may love them or dislike them, but she is rarely neutral" (Young, 2003, p.152). Breast cancer may be one of the oldest forms of cancer known to humans (American Cancer Society, 2010), and in 2008 in the United States over 182,000 women and almost 2,000 men were diagnosed with some form of breast cancer (American Cancer Society, 2008). In that same year 40,480 women and 450 men died from the disease. While any type of cancer diagnosis can instill a fear of mortality and incapacitation in the recipient, breast cancer holds a special meaning for women because of the significance placed on the breast both personally and societally. Removal of the breast tissue and muscle, or mastectomy, remains one of the primary forms of treatment for this disease. The breast plays an important role in a woman's identity, and the loss of one or both breasts due to breast cancer can have a monumental impact on her sense of self. A mastectomy affectsnot only a woman's relationship with herself, but with her family, friends, and society. It changes her outlook on life, her perception of her roles in the world, and her interest in interacting with others. Exploring these issues is important to understanding how doctors, nurses, mental health professionals, family members and support networks can best assist patients in coping with their illness. This paper attempts to understand the psychological issues and injuriesassociated with mastectomy through the lens of Self Psychology. It postulates that the breast itself is a selfobject for most women, and that its loss results in the fragmentation of the self. I will focus particularly on women between the ages of 25 and 40 years of age, in the marital and parental phases of developmental (Wolf, 1988), as the effect of a mastectomy on body image, sexuality, and genderbased roles such as motherhood has been shown to differ according to the age of the patient, with younger patients experiencing more distress (Ashing-Giwa et al, 2004).

Effects of Temporal Self-Comparisons on the Pursuit of Improvement

Thesis (Ph.D.)--University of Washington, 2016-06

A longitudinal investigation of self-other discrimination and the emergence of mirror self-recognition

The aim in this study was to investigate the association between infants' developing interest in their self-image and the onset of mirror self-recognition (MSR). A longitudinal study was conducted with 98 infants who were seen at intervals of 3 months from 9-24 months of age. At each session, the infants were administered a preferential-looking test whereby they were presented with a video image of themselves alongside a video image of a same-aged peer in two conditions, unmarked and marked. From the 12-month session onwards, the infants were also administered a version of the standard mark test of MSR. The infants showed a significant preference for looking at images of themselves in both conditions coincident with the onset of MSR. This result indicates that developing an interest in the self-image is an important component in the development of MSR. (C) 2003 Elsevier Science Inc. All rights reserved.

The role of catastrophic misinterpretation of bodily sensations and panic self-efficacy in predicting panic severity

This study investigated the role of both negative and positive cognitions in predicting panic severity in an international sample of patients diagnosed with panic disorder (with and without agoraphobia). One hundred and fifty-nine patients were administered the Brief Bodily Sensations Interpretation Questionnaire (BBSIQ), the Self-efficacy to Control Panic Attacks Questionnaire, and the Panic and Agoraphobia Scale (PAS) prior to receiving treatment. Regression analyses indicated that both catastrophic misinterpretation of bodily sensations and panic self-efficacy independently predicted panic severity. The influence of panic self-efficacy upon panic severity remained significant even after controlling for the presence or absence of agoraphobia. There was no evidence to suggest a moderating relationship between the two cognitive factors. Results are discussed in terms of the need to consider both negative and positive cognitions in cognitive accounts of panic disorder. (C) 2002 Elsevier Science Inc. All rights reserved.

Woodrow Wilson's ''Rhetorical restructuring'': The transformation of the American self and the construction of the German enemy

From a comprehensive study of the public addresses of Woodrow Wilson in the period following the outbreak of the war in Europe in August 1914 to the war's conclusion in June 1919, this essay examines Wilson's transformation of the long-held vision of America as merely a great example of liberty to its embodiment as the self-sacrificing champion of liberty. It will demonstrate how this transformation of the American "self" was inextricably connected to a changing image of the war and the construction of an enemy image of the German government.

Effect of moisture content on the R-70 self-heating rate of Callide coal

Strip samples from the Boundary Hill pit at Callide have been tested in an adiabatic oven to assess the effect of moisture on the R-70 self-heating rate of coal. The two strip samples tested had R-70 self-heating rate values of 10.23 and 8.61 degrees C/h. As the moisture content of the coal was progressively increased, from the dry state of the test, the R-70 value decreased dramatically. At approximately 40-50% of the moisture holding capacity of the coal, the self-heating rate becomes measurable. Above this critical level of moisture content, the heat produced by oxidation is dissipated by moisture evaporation and coal self-heating is significantly delayed. (c) 2005 Elsevier B.V All rights reserved.

The parameterless self-organizing map algorithm

The parameterless self-organizing map (PLSOM) is a new neural network algorithm based on the self-organizing map (SOM). It eliminates the need for a learning rate and annealing schemes for learning rate and neighborhood size. We discuss the relative performance of the PLSOM and the SOM and demonstrate some tasks in which the SOM fails but the PLSOM performs satisfactory. Finally we discuss some example applications of the PLSOM and present a proof of ordering under certain limited conditions.

When group members admit to being conformist: The role of relative intragroup status in conformity self-reports

Five studies examined the hypothesis that people will strategically portray the self as being more g-roup influenced the more junior they feel within the group. Among social psychologists (Study 1), ratings of self-conformity by g-roup members were greater when the status of the participant was low than when it was high. These effects were replicated in Studies 2, 3, and 4 in which relative intragroup status was manipulated. In Study 3, the authors found junior group members described themselves as more conformist than senior members when they were addressing an ingroup audience, but when they were addressing an outgroup audience the effect disappeared. Furthermore, junior members (but not senior members) rated themselves as more conformist when they were led to believe their responses were public than when responses were private (Study 5). The discussion focuses on the strategic processes underlying low-status group members' self-reports of group influence and the functional role of conformity in groups.

Merton's true self and the psychology of the dialogical self

Thomas Merton pursued a life-long quest to grasp the nature of the “true self.” This is the self that lives in and through Christ. Opposed to this is the false self that is expressive of infidelity. It is argued that the interaction between the true and false selves constitutes a dialogical process. The thesis of the essay is that this interaction expresses the dynamics associated with what some psychologists refer to as the “dialogical self.” The dialogical self is a model of the inner life that draws attention to the interpretive process required to deal with the many voices that get internalized in an engagement with the world.

Laser beam self-focusing in the atmosphere

We propose to exploit a self-focusing effect in the atmosphere to assist delivering powerful laser beams from orbit to the ground. We demonstrate through numerical modeling that when the self-focusing length is comparable with the atmosphere height the spot size on the ground can be reduced well below the diffraction limits without beam quality degradation. The density variation suppresses beam filamentation and provides the self-focusing of the beam as a whole. The use of light self-focusing in the atmosphere can greatly relax the requirements for the orbital optics and ground receivers.