864 research outputs found

    Compartmentalization of androgen receptors at endogenous genes in living cells

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    A wide range of nuclear proteins are involved in the spatio-temporal organization of the genome through diverse biological processes such as gene transcription and DNA replication. Upon stimulation by testosterone and translocation to the nucleus, multiple androgen receptors (ARs) accumulate in microscopically discernable foci which are irregularly distributed in the nucleus. Here, we investigated the formation and physical nature of these foci, by combining novel fluorescent labeling techniques to visualize a defined chromatin locus of AR-regulated genes-PTPRN2 or BANP-simultaneously with either AR foci or individual AR molecules. Quantitative colocalization analysis showed evidence of AR foci formation induced by R1881 at both PTPRN2 and BANP loci. Furthermore, single-particle tracking (SPT) revealed three distinct subdiffusive fractional Brownian motion (fBm) states: immobilized ARs were observed near the labeled genes likely as a consequence of DNA-binding, while the intermediate confined state showed a similar spatial behavior but with larger displacements, suggesting compartmentalization by liquid-liquid phase separation (LLPS), while freely mobile ARs were diffusing in the nuclear environment. All together, we show for the first time in living cells the presence of AR-regulated genes in AR foci.</p

    A Data-Driven Approach for Modeling Agents

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    Agents are commonly created on a set of simple rules driven by theories, hypotheses, and assumptions. Such modeling premise has limited use of real-world data and is challenged when modeling real-world systems due to the lack of empirical grounding. Simultaneously, the last decade has witnessed the production and availability of large-scale data from various sensors that carry behavioral signals. These data sources have the potential to change the way we create agent-based models; from simple rules to driven by data. Despite this opportunity, the literature has neglected to offer a modeling approach to generate granular agent behaviors from data, creating a gap in the literature. This dissertation proposes a novel data-driven approach for modeling agents to bridge the research gap. The approach is composed of four detailed steps including data preparation, attribute model creation, behavior model creation, and integration. The connection between and within each step is established using data flow diagrams. The practicality of the approach is demonstrated with a human mobility model that uses millions of location footprints collected from social media. In this model, the generation of movement behavior is tested with five machine learning/statistical modeling techniques covering a large number of model/data configurations. Results show that Random Forest-based learning is the most effective for the mobility use case. Furthermore, agent attribute values are obtained/generated with machine learning and translational assignment techniques. The proposed approach is evaluated in two ways. First, the use case model is compared to another model which is developed using a state-of-the-art data-driven approach. The model’s prediction performance is comparable to the state-of-the-art model. The plausibility of behaviors and model structure in the use case model is found to be closer to real-world than the state-of-the-art model. This outcome indicates that the proposed approach produces realistic results. Second, a standard mobility dataset is used for driving the mobility model in place of social media data. Despite its small size, the data and model resembled the results gathered from the primary use case indicating the possibility of using different datasets with the proposed approach

    A map-matching algorithm dealing with sparse cellular fingerprint observations

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    The widespread availability of mobile communication makes mobile devices a resource for the collection of data about mobile infrastructures and user mobility. In these contexts, the problem of reconstructing the most likely trajectory of a device on the road network on the basis of the sequence of observed locations (map-matching problem) turns out to be particularly relevant. Different contributions have demonstrated that the reconstruction of the trajectory of a device with good accuracy is technically feasible even when only a sparse set of GNSS positions is available. In this paper, we face the problem of coping with sparse sequences of cellular fingerprints. Compared to GNSS positions, cellular fingerprints provide coarser spatial information, but they work even when a device is missing GNSS positions or is operating in an energy saving mode. We devise a new map-matching algorithm, that exploits the well-known Hidden Markov Model and Random Forests to successfully deal with noisy and sparse cellular observations. The performance of the proposed solution has been tested over a medium-sized Italian city urban environment by varying both the sampling of the observations and the density of the fingerprint map as well as by including some GPS positions into the sequence of fingerprint observations

    Reflecting Human Knowledge of Place and Route-Choice Behavior Using Big Data

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    Exploring human knowledge of geographical space and related behavior not only helps in understanding human-environment interactions and dynamic geographic processes, but also advances Geographic Information Systems (GIS) toward a human-centric paradigm to make daily life more efficient. Today’s relatively easy acquisition of various big data provides an unprecedented opportunity for geographers to answer research questions that previously could not be adequately addressed. However, new challenges also arise regarding data quality and bias as well as change in methodology for dealing with big data that are different from traditional data types. Representing people’s perception of place and studying driver’s route-choice behavior are two of the many applications of big data in answering research questions about human knowledge and behavior in the fields of GIS and transportation. Incorporating three papers, this dissertation focuses on these two different applications to achieve the following objectives: 1) examine the degree to which a geographic place’s spatial extent can be estimated from human-generated geotagged photos; 2) address the challenge of geotagged photos’ uneven spatial distribution in place estimation and explore an approach that can better derive a place’s spatial extent; 3) develop a method that can properly estimate the spatial extent of a place that has multiple disjoint regions while considering geotagged photos’ uneven distribution; 4) explore useful spatiotemporal patterns of taxi drivers’ route-choice behavior in a dynamic urban environment. This dissertation makes three major contributions to big data applications’ systematic theory: 1) proposes an effective approach to handling the uneven spatial distribution problem of geotagged photos as a type of volunteered geographic data by modeling their representativeness; 2) develops methods that can properly derive the vague spatial extent of a place with or without disjoint regions; and 3) explores taxi drivers’ route-choice patterns in different situations that can inform future transportation decisions and policy-making processes

    Advanced Map Matching Technologies and Techniques for Pedestrian/Wheelchair Navigation

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    Due to the constantly increasing technical advantages of mobile devices (such as smartphones), pedestrian/wheelchair navigation recently has achieved a high level of interest as one of smartphones’ potential mobile applications. While vehicle navigation systems have already reached a certain level of maturity, pedestrian/wheelchair navigation services are still in their infancy. By comparing vehicle navigation systems, a set of map matching requirements and challenges unique in pedestrian/wheelchair navigation is identified. To provide navigation assistance to pedestrians and wheelchair users, there is a need for the design and development of new map matching techniques. The main goal of this research is to investigate and develop advanced map matching technologies and techniques particular for pedestrian/wheelchair navigation services. As the first step in map matching, an adaptive candidate segment selection algorithm is developed to efficiently find candidate segments. Furthermore, to narrow down the search for the correct segment, advanced mathematical models are applied. GPS-based chain-code map matching, Hidden Markov Model (HMM) map matching, and fuzzy-logic map matching algorithms are developed to estimate real-time location of users in pedestrian/wheelchair navigation systems/services. Nevertheless, GPS signal is not always available in areas with high-rise buildings and even when there is a signal, the accuracy may not be high enough for localization of pedestrians and wheelchair users on sidewalks. To overcome these shortcomings of GPS, multi-sensor integrated map matching algorithms are investigated and developed in this research. These algorithms include a movement pattern recognition algorithm, using accelerometer and compass data, and a vision-based positioning algorithm to fill in signal gaps in GPS positioning. Experiments are conducted to evaluate the developed algorithms using real field test data (GPS coordinates and other sensors data). The experimental results show that the developed algorithms and the integrated sensors, i.e., a monocular visual odometry, a GPS, an accelerometer, and a compass, can provide high-quality and uninterrupted localization services in pedestrian/wheelchair navigation systems/services. The map matching techniques developed in this work can be applied to various pedestrian/wheelchair navigation applications, such as tracking senior citizens and children, or tourist service systems, and can be further utilized in building walking robots and automatic wheelchair navigation systems

    Exploring urban visitors' mobilities. A multi-method approach

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    Aquesta tesi doctoral sorgeix de la necessitat d’aprofundir en el coneixement de les mobilitats dels visitants, entendre les decisions que configuren el seu comportament espacio-temporal i identificar i explorar els efectes que les seves mobilitats tenen sobre les destinacions urbanes. La tesi es desenvolupa entorn a quatre objectius específics que s’emmarquen en l’àmbit de recerca relacionat amb el seguiment de l’activitat dels visitants en destinacions turístiques urbanes. Cadascun d’aquests objectius es desenvolupa en cadascun dels articles científics que conformen aquesta tesi doctoral, publicats tots ells en revistes de revisió per parells. El primer article es proposa com a objectiu identificar els factors, relacionats amb el perfil socioeconòmic dels turistes i amb les característiques de la seva estada, que determinen la selecció d’opcions de transport i mobilitat sostenible per moure’s per la destinació urbana. El segon article pretén analitzar i comprendre com afecta el comportament espacio-temporal dels turistes en els seus patrons de consum econòmic i, per tant, en la generació d’ingressos per a l’economia local. El tercer article es proposa analitzar la influència de l’espai urbà sobre la forma en què els visitants es desplacen per la destinació. I finalment, el quart article té per objectiu reconstruir trajectòries i/o fluxos espacio-temporals a partir de dades geolocalitzades de les xarxes socials per tal de detectar patrons de mobilitat dels visitants de destinacions urbanes. Les fonts de dades i els mètodes utilitzats per complir amb els objectius de partida són diverses. En aquest sentit, la tesi aporta també una àmplia radiografia dels pros i les contres de les diferents fonts de dades disponibles per a l’anàlisi de les mobilitats dels visitants en destinacions turístiques.Esta tesis doctoral surge de la necesidad de profundizar en el conocimiento de las movilidades de los visitantes,entender las decisiones que configuran su comportamiento espaciotemporal e identificar y explorar los efectos que sus movilidades tienen sobre los destinos urbanos. La tesis se desarrolla en torno a cuatro objetivos específicos que se enmarcan en el ámbito de investigación de seguimiento de visitantes, y que se desarrollan en cada uno de los artículos científicos, publicados todos ellos en revistas de revisión por pares, que conforman esta tesis. El primer artículo se propone como objetivo identificar los factores, relacionados con el perfil socioeconómicos de los turistas y con las características de su estancia, que determinan la selección de opciones de transporte y movilidad sostenible para moverse por el destino urbano. El segundo artículo pretende analizar y comprender cómo afecta el comportamiento espaciotemporal de los turistas en sus patrones de consumo económico y, por tanto, en la generación de ingresos para la economía local. El tercer artículo se propone analizar la influencia del espacio urbano sobre la forma en que los visitantes se desplazan por el destino. Y finalmente, el cuarto artículo tiene por objetivo reconstruir trayectorias y / o flujos espaciotemporales a partir de datos geolocalizados de las redes sociales para detectar patrones de movilidad de los visitantes de destinos urbanos. Las fuentes de datos y los métodos utilizados para cumplir con los objetivos de partida son diversos. En este sentido, la tesis aporta también una amplia radiografía de los pros y contras de las diferentes fuentes de datos disponibles para el análisis de las movilidades de los visitantes en destinos turísticos.This dissertation arises from the need to deepen the knowledge of the mobility of visitors, understand the decisions that shape their spatiotemporal behaviour and identify and explore the effects that their mobility has on urban destinations. The thesis is developed around four specific objectives that fall within the scope of visitor tracking research, and that are developed in each of the scientific articles, all of them published in peer-reviewed journals, that make up this thesis. The first article aims to identify the factors, related to the socioeconomic profile of tourists and the characteristics of their stay, that determine the selection of sustainable transport and mobility options to move within the urban destination. The second article aims to analyse and understand how the visitors’ spatiotemporal behaviour affects their patterns of economic consumption and, therefore, the generation of income for the local economy. The third article aims to analyse the influence of the built environment on the visitors’ mobilities at destination. And finally, the fourth article aims to reconstruct trajectories and / or spatiotemporal flows from geolocated data obtained from social networks in order to detect visitors’ mobility patterns at urban destinations. The data sources and methods used to meet the objectives are multiple. In this sense, the thesis also provides an extensive x-ray of the pros and cons of the different data sources available for the analysis of visitors’ mobilities in tourist destinations

    Human dynamics in the age of big data: a theory-data-driven approach

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    The revolution of information and communication technology (ICT) in the past two decades have transformed the world and people’s lives with the ways that knowledge is produced. With the advancements in location-aware technologies, a large volume of data so-called “big data” is now available through various sources to explore the world. This dissertation examines the potential use of such data in understanding human dynamics by focusing on both theory- and data-driven approaches. Specifically, human dynamics represented by communication and activities is linked to geographic concepts of space and place through social media data to set a research platform for effective use of social media as an information system. Three case studies covering these conceptual linkages are presented to (1) identify communication patterns on social media; (2) identify spatial patterns of activities in urban areas and detect events; and (3) explore urban mobility patterns. The first case study examines the use of and communication dynamics on Twitter during Hurricane Sandy utilizing survey and data analytics techniques. Twitter was identified as a valuable source of disaster-related information. Additionally, the results shed lights on the most significant information that can be derived from Twitter during disasters and the need for establishing bi-directional communications during such events to achieve an effective communication. The second case study examines the potential of Twitter in identifying activities and events and exploring movements during Hurricane Sandy utilizing both time-geographic information and qualitative social media text data. The study provides insights for enhancing situational awareness during natural disasters. The third case study examines the potential of Twitter in modeling commuting trip distribution in New York City. By integrating both traditional and social media data and utilizing machine learning techniques, the study identified Twitter as a valuable source for transportation modeling. Despite the limitations of social media such as the accuracy issue, there is tremendous opportunity for geographers to enrich their understanding of human dynamics in the world. However, we will need new research frameworks, which integrate geographic concepts with information systems theories to theorize the process. Furthermore, integrating various data sources is the key to future research and will need new computational approaches. Addressing these computational challenges, therefore, will be a crucial step to extend the frontier of big data knowledge from a geographic perspective. KEYWORDS: Big data, social media, Twitter, human dynamics, VGI, natural disasters, Hurricane Sandy, transportation modeling, machine learning, situational awareness, NYC, GI

    Filling the Gaps: On the Completion of Sparse Call Detail Records for Mobility Analysis

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    International audienceCall Detail Records (CDRs) have been widely used in the last decades for studying different aspects of human mobility. The accuracy of CDRs strongly depends on the user-network interaction frequency: hence, the temporal and spatial spar-sity that typically characterize CDR can introduce a bias in the mobility analysis. In this paper, we evaluate the bias induced by the use of CDRs for inferring important locations of mobile subscribers, as well as their complete trajectories. Besides, we propose a novel technique for estimating real human trajectories from sparse CDRs. Compared to previous solutions in the literature, our proposed technique reduces the error between real and estimated human trajectories and at the same time shortens the temporal period where users' locations remain undefined
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