No description available.

Abstract The hormonally active form of vitamin D, 1,25(OH)2D3, is involved in many biological functions throughout the body, such as regulation of calcium and phosphate homeostasis, bone remodeling and controlling cell proliferation and differentiation. Vitamin D receptor (VDR), a member of the nuclear hormone receptor (NHR) super family, mediates those genomic actions of 1,25 (OH)2D3 by actively repressing or activating its target genes. In the present study recombinant human nuclear VDR and its ligand binding domain (LBD) were expressed in Spodoptera frugiperda (Sf9) insect cells and in E.coli. Recombinant proteins were purified and their biochemical and biophysical properties were characterized. Recombinant VDR was shown to bind to the vitamin D response element (VDRE) of osteopontin and osteocalcin genes as a homodimer or as a heterodimer with the retinoid X receptor (RXR)-αΔAB. Full-length VDR and its LBD were demonstrated to bind natural ligand 1,25 (OH)2D3 with high affinity. The binding affinities of several vitamin D analogs were also determined. Ligand binding induced conformational change within the receptor was studied using several methods such as partial proteolytic digestion, small angle neutron scattering (SANS), native gel electrophoresis and circular dichroism (CD) spectroscopy. Results indicate that ligand binding induces conformational change within VDR and different 1,25(OH)2D3 analogs might induce a somewhat different conformation within the receptor. This is seen as an unequal capacity of analogs to stabilize receptor against proteases or heat and as differences in the promotion of receptor homodimerization. Compared to other nuclear hormone receptors, VDR presents a large insertion region at the N-terminal part of the LBD between helices H1 and H3, encoded by an additional exon. In the present study this additional exon was deleted and the properties of mutated LBD were compared to the wild type LBD. Biochemical analyses indicated that the mutant protein exhibits the same ligand binding, dimerization with RXR and transactivation properties as the wild-type VDR, suggesting that the insertion region does not affect these main functions. Furthermore, solution studies by small angle X-ray scattering indicated that the insertion region in the VDR locates on the surface of molecule and it is not structurally well ordered.

Receptores nucleares formam uma superfamília de proteínas responsáveis pela regulação da expressão de genes. Estruturalmente, são formados por três domínios: um domínio N-terminal bastante variável, um domínio altamente conservado de ligação com o DNA e um domínio C-terminal, menos conservado, denominado domínio de ligação com o ligante (LDB). Diversos experimentos mostram que a interação com o ligante afeta a estrutura e a mobilidade da hélice C-terminal dos receptores nucleares (hélice 12 do domínio de ligação com o ligante), sendo o principal mecanismo de ativação e repressão da transcrição. As primeiras estruturas de LBDs de receptores nucleares revelaram importantes diferenças entre estruturas contendo ligantes (holo) e estruturas apo, principalmente no que diz respeito a posição da hélice 12: em estruturas apo, foi observada a H12 em uma conformação aberta, expondo o sítio de ligação com o ligante, enquanto que em estruturas holo, foi observada a H12 em uma conformação fechada, dobrada sobre o corpo do LBD e envolvendo completamente o ligante. Essa diferença sugeriu um mecanismo para a entrada e saída de ligantes do sítio de ligação denominado modelo da ratoeira, entretanto, esse modelo apresenta diversas inconsistências e tem sido desacreditado. Estudos experimentais e teóricos recentes mostram que a hélice 12 é mais móvel na ausência de ligantes, entretanto, esses estudos não fornecem evidencias de que o aumento da mobilidade da está associado com o deslocamento da H12 em relação ao corpo do LBD, como sugerido pelo modelo da ratoeira. Embora esteja claro que a hélice 12 é mais móvel na ausência de ligantes, a dimensão da variação conformacional sofrida pela hélice 12 ainda não está clara. Nesse trabalho buscamos a construção de um modelo capaz de dimensionar a mobilidade da hélice 12 através da comparação direta entre simulações de dinâmica molecular e experimentos de anisotropia de fluorescência resolvida no tempo. Utilizando simulações de dinâmica molecular reproduzimos experimentos de anisotropia de fluorescência acoplando a sonda cys-flúor a hélice 12 do PPARγ para estudar sua mobilidade. Mostramos que as observações experimentais só podem ser explicadas por conformações onde a sonda fluorescente permanece presa a superfície do LBD. Foi mostrado também que curvas de anisotropia com decaimentos comparáveis com os decaimentos experimentais estão associados a pequenas variações conformacionais de hélice 12. Simulações para dois modelos de apo-PPARγ com a H12 aberta em relação ao corpo do LBD e para as estruturas cristalográficas de apo-RXR e apo-ER, onde a H12 também adota uma conformação aberta, revelaram curvas de anisotropia com decaimentos mais rápidos que os experimentais. Esses resultados implicam em um modelo onde a H12 sofre alterações conformacionais locais, não apresentando variações tão dramáticas como o proposto pelo modelo da ratoeira. / Nuclear Hormone Receptors comprise a protein superfamily responsible for regulation of gene expression. Structurally, they are composed by three domains: a variable N-terminal domain, a highly conserved DNA-binding domain (DBD), and a less conserved C-terminal domain, known as ligand binding domain (LBD). Many experiments have shown that the interaction with ligands affects the structure and the mobility of nuclear receptors C-terminal helix (LBDs Helix 12), being the main mechanism of transcription activation and repression. The first nuclear receptor LBDs structures revealed important differences between ligand bound (holo) and apo-structures concerning the position of the H12: in apo structures, H12 adopted an open conformation, exposing the ligand binding pocket, whereas in holo structures, the H12 was closed, packed over the body of the LBD, burying completely the ligand. This difference suggested a mechanism for ligand entry and exit from the binding pocket called mouse-trap model, however this model has several inconsistencies and has been discredited. Recent experimental and theoretical studies have shown that H12 is more labile in the absence of ligand, but these studies dont provide evidences that the increase in the mobility is associated with the detachment of H12 from the body of the LBD as suggested by the mouse-trap model. Although its clear that H12 is more flexible in the absence of ligands, the size of the conformational changes undergone by H12 is not yet clear. In this work we seek to construct a definitive model for the range of motions that H12 may undergo in the presence or absence of ligand using molecular dynamics simulations. Through direct comparison between molecular dynamics simulations and time-resolved fluorescence anisotropy experiments, we show that experimental observation can only be explained by conformations where the fluorescent probe is interacting with the surface of the PPARγ surface. We also show that simulations with anisotropy decay rates comparable to the experimental decay are associated with small helix 12 conformational changes. Simulations with two models of apo-PPARγ with H12 detached from the body of the LBD and with crystallographic structures of apo-RXR and apo-ER, where the H12 also is in an open conformation, display anisotropy decay rates significantly faster than the experimental ones. These results imply a model for the molecular mobility of the LBD where H12 undergoes local conformational changes and should exhibit dynamic properties less dramatic than proposed by the mouse trap model.

Receptores nucleares formam uma superfamília de proteínas responsáveis pela regulação da expressão de genes. Estruturalmente, são formados por três domínios: um domínio N-terminal bastante variável, um domínio altamente conservado de ligação com o DNA e um domínio C-terminal, menos conservado, denominado domínio de ligação com o ligante (LDB). Diversos experimentos mostram que a interação com o ligante afeta a estrutura e a mobilidade da hélice C-terminal dos receptores nucleares (hélice 12 do domínio de ligação com o ligante), sendo o principal mecanismo de ativação e repressão da transcrição. As primeiras estruturas de LBDs de receptores nucleares revelaram importantes diferenças entre estruturas contendo ligantes (holo) e estruturas apo, principalmente no que diz respeito a posição da hélice 12: em estruturas apo, foi observada a H12 em uma conformação aberta, expondo o sítio de ligação com o ligante, enquanto que em estruturas holo, foi observada a H12 em uma conformação fechada, dobrada sobre o corpo do LBD e envolvendo completamente o ligante. Essa diferença sugeriu um mecanismo para a entrada e saída de ligantes do sítio de ligação denominado modelo da ratoeira, entretanto, esse modelo apresenta diversas inconsistências e tem sido desacreditado. Estudos experimentais e teóricos recentes mostram que a hélice 12 é mais móvel na ausência de ligantes, entretanto, esses estudos não fornecem evidencias de que o aumento da mobilidade da está associado com o deslocamento da H12 em relação ao corpo do LBD, como sugerido pelo modelo da ratoeira. Embora esteja claro que a hélice 12 é mais móvel na ausência de ligantes, a dimensão da variação conformacional sofrida pela hélice 12 ainda não está clara. Nesse trabalho buscamos a construção de um modelo capaz de dimensionar a mobilidade da hélice 12 através da comparação direta entre simulações de dinâmica molecular e experimentos de anisotropia de fluorescência resolvida no tempo. Utilizando simulações de dinâmica molecular reproduzimos experimentos de anisotropia de fluorescência acoplando a sonda cys-flúor a hélice 12 do PPARγ para estudar sua mobilidade. Mostramos que as observações experimentais só podem ser explicadas por conformações onde a sonda fluorescente permanece presa a superfície do LBD. Foi mostrado também que curvas de anisotropia com decaimentos comparáveis com os decaimentos experimentais estão associados a pequenas variações conformacionais de hélice 12. Simulações para dois modelos de apo-PPARγ com a H12 aberta em relação ao corpo do LBD e para as estruturas cristalográficas de apo-RXR e apo-ER, onde a H12 também adota uma conformação aberta, revelaram curvas de anisotropia com decaimentos mais rápidos que os experimentais. Esses resultados implicam em um modelo onde a H12 sofre alterações conformacionais locais, não apresentando variações tão dramáticas como o proposto pelo modelo da ratoeira. / Nuclear Hormone Receptors comprise a protein superfamily responsible for regulation of gene expression. Structurally, they are composed by three domains: a variable N-terminal domain, a highly conserved DNA-binding domain (DBD), and a less conserved C-terminal domain, known as ligand binding domain (LBD). Many experiments have shown that the interaction with ligands affects the structure and the mobility of nuclear receptors C-terminal helix (LBDs Helix 12), being the main mechanism of transcription activation and repression. The first nuclear receptor LBDs structures revealed important differences between ligand bound (holo) and apo-structures concerning the position of the H12: in apo structures, H12 adopted an open conformation, exposing the ligand binding pocket, whereas in holo structures, the H12 was closed, packed over the body of the LBD, burying completely the ligand. This difference suggested a mechanism for ligand entry and exit from the binding pocket called mouse-trap model, however this model has several inconsistencies and has been discredited. Recent experimental and theoretical studies have shown that H12 is more labile in the absence of ligand, but these studies dont provide evidences that the increase in the mobility is associated with the detachment of H12 from the body of the LBD as suggested by the mouse-trap model. Although its clear that H12 is more flexible in the absence of ligands, the size of the conformational changes undergone by H12 is not yet clear. In this work we seek to construct a definitive model for the range of motions that H12 may undergo in the presence or absence of ligand using molecular dynamics simulations. Through direct comparison between molecular dynamics simulations and time-resolved fluorescence anisotropy experiments, we show that experimental observation can only be explained by conformations where the fluorescent probe is interacting with the surface of the PPARγ surface. We also show that simulations with anisotropy decay rates comparable to the experimental decay are associated with small helix 12 conformational changes. Simulations with two models of apo-PPARγ with H12 detached from the body of the LBD and with crystallographic structures of apo-RXR and apo-ER, where the H12 also is in an open conformation, display anisotropy decay rates significantly faster than the experimental ones. These results imply a model for the molecular mobility of the LBD where H12 undergoes local conformational changes and should exhibit dynamic properties less dramatic than proposed by the mouse trap model.

The notion of staging in the neurodegenerative disorders is modulated by the constant and progressive loss of several aspects of brain structural integrity, circuitry, and neuronal processes. These destructive processes eventually remove individuals' abilities to perform at sufficient and necessary functional capacity at several levels of disease severity. The classification of (a) patients on the basis of diagnosis, risk prognosis, and intervention outcome, forms the basis of clinical staging, and (b) laboratory animals on the basis of animal model of brain disorder, extent of insult, and dysfunctional expression, provides the components for the clinical staging and preclinical staging, respectively, expressing associated epidemiological, biological, and genetic characteristics. The major focus of clinical staging in the present account stems from the fundamental notions of Braak staging as they describe the course and eventual prognosis for Alzheimer's disease, Lewy Body dementia, and Parkinson's disease. Mild cognitive impairment, which expresses the decline in episodic and semantic memory performance below the age-adjusted normal range without marked loss of global cognition or activities of daily living, and the applications of longitudinal magnetic resonance imaging, major instruments for the monitoring of either disease progression in dementia, present important challenges for staging concepts. Although Braak notions present the essential basis for further developments, current staging conceptualizations seem inadequate to comply with the massive influx of information dealing with neurodegenerative processes in brain, advanced both under clinical realities, and discoveries in the laboratory setting. The contributions of various biomarkers of disease progression, e.g., amyloid precursor protein, and neurotransmitter system imbalances, e.g., dopamine receptor supersensitivity and interactive propensities, await their incorporation into the existing staging models thereby underlining the ongoing, dynamic feature of the staging of brain disorders.

We are living within the age of information. The ever increasing flow of data and publications poses a monumental bottleneck to scientific progress as despite the amazing abilities of the human mind, it is woefully inadequate in processing such a vast quantity of multidimensional information. The small bits of flotsam and jetsam that we leverage belies the amount of useful information beneath the surface. It is imperative that automated tools exist to better search, retrieve, and summarize this content. Combinations of document indexing and search engines can quickly find you a document whose content best matches your query - if the information is all contained within a single document. But it doesn’t draw connections, make hypotheses, or find knowledge hidden across multiple documents. Literature-based discovery is an approach that can uncover hidden interrelationships between topics by extracting information from existing published scientific literature. The proposed study utilizes a semantic-based approach that builds a graph of related concepts between two user specified sets of topics using semantic predications. In addition, the study includes properties of bibliographically related documents and statistical properties of concepts to further enhance the quality of the proposed intermediate terms. Our results show an improvement in precision-recall when incorporating citations.

This body of work explores an emerging aspect of human-robot interaction, transparency. Socially guided machine learning has proven that highly immersive robotic behaviors have yielded better results than lesser interactive behaviors for performance and shorter training time. While other work explores this transparency in learning by demonstration using non-verbal cues to point out the importance or preference users may have towards behaviors, my work follows this argument and attempts to extend it by offering cues to the internal task representation. What I show is that task-transparency, or the ability to connect and discuss the task in a fluent way implores the user to shape and correct the learned goal in ways that may be impossible by other present day learning by demonstration methods. Additionally, some participants are shown to prefer task-transparent robots which appear to have the ability of "introspection" in which it can modify the learned goal by other methods than just demonstration.

No description available.

Είναι γνωστό ότι η άνοια σχετίζεται με την απώλεια μνήμης, έκπτωση γλωσσικών ικανοτήτων, έλλειψη αυτονομίας και απώλεια της προσωπικής ταυτότητας του ασθενούς. Στόχος της παρούσας εργασίας είναι να αναδείξει τη σχέση αμφισημίας- άνοιας και να διερευνηθεί η σκοπιμότητα ύπαρξης ενός μεθοδολογικού εργαλείου για την εκτίμηση και τη διερεύνηση της γλωσσικής έκπτωσης στη άνοια μέσα από την γλωσσική επεξεργασία των λεξικών σχέσεων (μεταφορών –ομωνυμίας- μετωνυμιών) και να παρουσιάζει το προφίλ των ασθενών αυτών. Στην πρώτη ενότητα παρουσιάζω γενικά στοιχεία για την νόσο της άνοιας αλλά και στοιχεία για τους κυριότερους τύπους της νόσου όσον αφορά την γλωσσική συμπεριφορά των ασθενών. Στην ενότητα αυτή αναφέρω επίσης βασικά διαγνωστικά εργαλεία που χρησιμοποιούνται ευρέως για τον προσδιορισμό της νόσου, ενώ αναλυτικότερα στοιχεία για τα εργαλεία που χρησιμοποιούνται και τις δομές που εξετάζουν παρατίθενται στο παράρτημα. Κλείνοντας την ενότητα καταλήγω στα οφέλη και την αναγκαιότητα ύπαρξης πρώιμης διάγνωσης. Στην δεύτερη ενότητα αναφέρομαι κυρίως στο νοητικό λεξικό και στην δυσκολία πρόσβασης των ασθενών με πιθανή άνοια σε αυτό. Επιπλέον υπάρχουν στοιχεία για την λεξική κατάκτηση, επιλογή και ανάκτηση των πληροφοριών και φαίνεται η σχέση νοητικού λεξικού – αμφισημίας. Στην τρίτη ενότητα παρουσιάζω το φαινόμενο της αμφισημίας από την θεωρητική άποψη αρχικά της γλωσσολογίας, πως κατακτώνται οι αμφίσημες λέξεις και επεξεργάζονται σε σχέση με την ηλικία και καταλήγω στην νευρική συσχέτιση των λεξικών αμφισημιών με συγκεκριμένες εγκεφαλικές περιοχές. Στο τέλος της παρούσας ενότητας παρουσιάζω ευρήματα/ συμπεράσματα από πλήθος ερευνών που αφορούν την λεξική αμφισημία με διαφορετικές μεθόδους για κάθε τύπο άνοιας. Στην τελευταία ενότητα παρουσιάζω τις βασικές υποθέσεις μου πως η χρήση των λεξικών σχέσεων θα μπορεί να αποτελέσει διαγνωστικό εργαλείο στην άνοια. Επίσης παρουσιάζω την κατασκευή και τα αποτελέσματα της πειραματικής διαδικασίας ανάμεσα σε τέσσερα διαφορετικά υποκείμενα (πασχόντων –υγειών) διαφορετικής παθολογίας και σοβαρότητας. Ακολουθεί τέλος το παράρτημα με στοιχεία που αφορούν την διαφοροδιάγνωση της νόσου βάσει αλγορίθμων με τα γνωστικά ελλείμματα όπως παρουσιάζονται από τους φροντιστές των ασθενών αλλά και παθολογικών συμπτωμάτων που παρουσιάζουν, ενώ σε πίνακα υπάρχουν τα γλωσσικά στοιχεία που βοηθούν επίσης στην διαφοροδιάγνωση των κυριότερων τύπων άνοιας και τα αποτελέσματα της πειραματικής διαδικασίας. / It is well known that dementia is associated with memory loss, impaired language skills, lack of autonomy and loss of patients’ independence. The aim of this paper is to highlight the connection between ambiguity and dementia, and to investigate the feasibility of a methodological tool to assess and investigate the linguistic deduction in dementia through the linguistic processing of lexical relations (metaphor-homonymy-metonymy) and present the profile of such patients. In the first section I present general information as well as the linguistic features of the main types of dementia. In this section there is also a report on the diagnostic tools which are widely used to identify the disease. More detailed information about the use of these diagnostic tools is listed in the Annex. At the end of this section there is evidence about the benefits and the importance of early diagnosis. The second section is mainly referred to the mental lexicon and the difficulty patients with probable dementia face in accessing it. Furthermore there is evidence for lexical acquisition, selection and retrieval of information which shows the mental lexicon – ambiguity connection. In the third section I present the phenomenon of ambiguity, starting from the theoretical linguistic view; how the ambiguous words are conquered and processed in relation to age and lead to neural correlation of lexical ambiguity with specific brain regions. At the end of this section I present findings / conclusions of several researches, using different methods, on the lexical ambiguity on each type of dementia. The last section presents my basic assumptions concerning how the use of lexical relations can be a diagnostic tool in dementia. Furthermore, I present the construction and the results of the experimental process between four different subjects (patient-healthy) with different pathology and severity of the disease. Finally, at the annex, I present data on the differential diagnosis of the disease based on algorithms with cognitive deficits reported by caregivers of patients as well as pathology features. Also there is a board with differential linguistic elements which help distinguish the main types of dementia, along with the experimental material used and the results of the procedure.