Social Networks Analysis

This morning Dr. Risser will introduce you to the basic ideas of social network analysis. You will learn some history behind the study of social networks. Dr. Risser will introduce you to mathematical measures of social networks including centrality measures and measures of spread and cohesion. You will also learn how to use a computer program to analyze social network data

Long-Range Pollution Transport: Trans-Atlantic Mechanisms and Lagrangian Modeling Methods

Over the past several decades, it has become apparent that anthropogenic activities have resulted in the large-scale enhancement of the levels of many trace gases throughout the troposphere. More recently, attention has been given to the transport pathway taken by these emissions as they are dispersed throughout the atmosphere. The transport pathway determines the physical characteristics of emissions plumes and therefore plays an important role in the chemical transformations that can occur downwind of source regions. For example, the production of ozone (O3) is strongly dependent upon the transport its precursors undergo. O3 can initially be formed within air masses while still over polluted source regions. These polluted air masses can experience continued O3 production or O3 destruction downwind, depending on the air mass's chemical and transport characteristics. At present, however, there are a number of uncertainties in the relationships between transport and O3 production in the North Atlantic lower free troposphere. The first phase of the study presented here used measurements made at the Pico Mountain observatory and model simulations to determine transport pathways for US emissions to the observatory. The Pico Mountain observatory was established in the summer of 2001 in order to address the need to understand the relationships between transport and O3 production. Measurements from the observatory were analyzed in conjunction with model simulations from the Lagrangian particle dispersion model (LPDM), FLEX-PART, in order to determine the transport pathway for events observed at the Pico Mountain observatory during July 2003. A total of 16 events were observed, 4 of which were analyzed in detail. The transport time for these 16 events varied from 4.5 to 7 days, while the transport altitudes over the ocean ranged from 2-8 km, but were typically less than 3 km. In three of the case studies, eastward advection and transport in a weak warm conveyor belt (WCB) airflow was responsible for the export of North American emissions into the FT, while transport in the FT was governed by easterly winds driven by the Azores/Bermuda High (ABH) and transient northerly lows. In the fourth case study, North American emissions were lofted to 6-8 km in a WCB before being entrained in the same cyclone's dry airstream and transported down to the observatory. The results of this study show that the lower marine FT may provide an important transport environment where O3 production may continue, in contrast to transport in the marine boundary layer, where O3 destruction is believed to dominate. The second phase of the study presented here focused on improving the analysis methods that are available with LPDMs. While LPDMs are popular and useful for the analysis of atmospheric trace gas measurements, identifying the transport pathway of emissions from their source to a receptor (the Pico Mountain observatory in our case) using the standard gridded model output, particularly during complex meteorological scenarios can be difficult can be difficult or impossible. The transport study in phase 1 was limited to only 1 month out of more than 3 years of available data and included only 4 case studies out of the 16 events specifically due to this confounding factor. The second phase of this study addressed this difficulty by presenting a method to clearly and easily identify the pathway taken by only those emissions that arrive at a receptor at a particular time, by combining the standard gridded output from forward (i.e., concentrations) and backward (i.e., residence time) LPDM simulations, greatly simplifying similar analyses. The ability of the method to successfully determine the source-to-receptor pathway, restoring this Lagrangian information that is lost when the data are gridded, is proven by comparing the pathway determined from this method with the particle trajectories from both the forward and backward models. A sample analysis is also presented, demonstrating that this method is more accurate and easier to use than existing methods using standard LPDM products. Finally, we discuss potential future work that would be possible by combining the backward LPDM simulation with gridded data from other sources (e.g., chemical transport models) to obtain a Lagrangian sampling of the air that will eventually arrive at a receptor.

Sexual transmission of HIV according to viral load and antiretroviral therapy: systematic review and meta-analysis

OBJECTIVES: To synthesize the evidence on the risk of HIV transmission through unprotected sexual intercourse according to viral load and treatment with combination antiretroviral therapy (ART). DESIGN: Systematic review and meta-analysis. METHODS: We searched Medline, Embase and conference abstracts from 1996-2009. We included longitudinal studies of serodiscordant couples reporting on HIV transmission according to plasma viral load or use of ART and used random-effects Poisson regression models to obtain summary transmission rates [with 95% confidence intervals, (CI)]. If there were no transmission events we estimated an upper 97.5% confidence limit. RESULTS: We identified 11 cohorts reporting on 5021 heterosexual couples and 461 HIV-transmission events. The rate of transmission overall from ART-treated patients was 0.46 (95% CI 0.19-1.09) per 100 person-years, based on five events. The transmission rate from a seropositive partner with viral load below 400 copies/ml on ART, based on two studies, was zero with an upper 97.5% confidence limit of 1.27 per 100 person-years, and 0.16 (95% CI 0.02-1.13) per 100 person-years if not on ART, based on five studies and one event. There were insufficient data to calculate rates according to the presence or absence of sexually transmitted infections, condom use, or vaginal or anal intercourse. CONCLUSION: Studies of heterosexual discordant couples observed no transmission in patients treated with ART and with viral load below 400 copies/ml, but data were compatible with one transmission per 79 person-years. Further studies are needed to better define the risk of HIV transmission from patients on ART.

A social network-based approach to assess de facto independence of regulatory agencies

This article uses a policy network perspective to assess the independence of regulatory agencies (RAs) in liberalized public utility sectors. We focus on the de facto independence of RAs from elected politicians, regulatees and other co-regulators. We go further than previous studies, which only undertook a general analysis of the de jure independence of RAs from political authorities. Specifically, we apply a social network analysis (SNA), which concentrates on the attributes and relational profiles of all actors involved in new regulatory arrangements. The concept of de facto independence is applied to the Swiss telecommunications sector in order to provide initial empirical insights. Results clearly show that SNA indicators are an appropriate tool to identify the de facto independence of RAs and can improve knowledge about the issues arising from the emergence of the ‘regulatory State’.

Localization of Epileptogenic Zone on Pre-surgical Intracranial EEG Recordings: Toward a Validation of Quantitative Signal Analysis Approaches

In patients diagnosed with pharmaco-resistant epilepsy, cerebral areas responsible for seizure generation can be defined by performing implantation of intracranial electrodes. The identification of the epileptogenic zone (EZ) is based on visual inspection of the intracranial electroencephalogram (IEEG) performed by highly qualified neurophysiologists. New computer-based quantitative EEG analyses have been developed in collaboration with the signal analysis community to expedite EZ detection. The aim of the present report is to compare different signal analysis approaches developed in four different European laboratories working in close collaboration with four European Epilepsy Centers. Computer-based signal analysis methods were retrospectively applied to IEEG recordings performed in four patients undergoing pre-surgical exploration of pharmaco-resistant epilepsy. The four methods elaborated by the different teams to identify the EZ are based either on frequency analysis, on nonlinear signal analysis, on connectivity measures or on statistical parametric mapping of epileptogenicity indices. All methods converge on the identification of EZ in patients that present with fast activity at seizure onset. When traditional visual inspection was not successful in detecting EZ on IEEG, the different signal analysis methods produced highly discordant results. Quantitative analysis of IEEG recordings complement clinical evaluation by contributing to the study of epileptogenic networks during seizures. We demonstrate that the degree of sensitivity of different computer-based methods to detect the EZ in respect to visual EEG inspection depends on the specific seizure pattern.

Role of MicroRNA Modulation in the Interferon-α/Ribavirin Suppression of HIV-1 In Vivo.

BACKGROUND Interferon-α (IFN-α) treatment suppresses HIV-1 viremia and reduces the size of the HIV-1 latent reservoir. Therefore, investigation of the molecular and immunologic effects of IFN-α may provide insights that contribute to the development of novel prophylactic, therapeutic and curative strategies for HIV-1 infection. In this study, we hypothesized that microRNAs (miRNAs) contribute to the IFN-α-mediated suppression of HIV-1. To inform the development of novel miRNA-based antiretroviral strategies, we investigated the effects of exogenous IFN-α treatment on global miRNA expression profile, HIV-1 viremia, and potential regulatory networks between miRNAs and cell-intrinsic anti-HIV-1 host factors in vivo. METHODS Global miRNA expression was examined in longitudinal PBMC samples obtained from seven HIV/HCV-coinfected, antiretroviral therapy-naïve individuals before, during, and after pegylated interferon-α/ribavirin therapy (IFN-α/RBV). We implemented novel hybrid computational-empirical approaches to characterize regulatory networks between miRNAs and anti-HIV-1 host restriction factors. RESULTS miR-422a was the only miRNA significantly modulated by IFN-α/RBV in vivo (p<0.0001, paired t test; FDR<0.037). Our interactome mapping revealed extensive regulatory involvement of miR-422a in p53-dependent apoptotic and pyroptotic pathways. Based on sequence homology and inverse expression relationships, 29 unique miRNAs may regulate anti-HIV-1 restriction factor expression in vivo. CONCLUSIONS The specific reduction of miR-422a is associated with exogenous IFN-α treatment, and likely contributes to the IFN-α suppression of HIV-1 through the enhancement of anti-HIV-1 restriction factor expression and regulation of genes involved in programmed cell death. Moreover, our regulatory network analysis presents additional candidate miRNAs that may be targeted to enhance anti-HIV-1 restriction factor expression in vivo.

Comparison of theoretical fixation stability of three devices employed in medial opening wedge high tibial osteotomy: a finite element analysis.

BACKGROUND Medial open wedge high tibial osteotomy is a well-established procedure for the treatment of unicompartmental osteoarthritis and symptomatic varus malalignment. We hypothesized that different fixation devices generate different fixation stability profiles for the various wedge sizes in a finite element (FE) analysis. METHODS Four types of fixation were compared: 1) first and 2) second generation Puddu plates, and 3) TomoFix plate with and 4) without bone graft. Cortical and cancellous bone was modelled and five different opening wedge sizes were studied for each model. Outcome measures included: 1) stresses in bone, 2) relative displacement of the proximal and distal tibial fragments, 3) stresses in the plates, 4) stresses on the upper and lower screw surfaces in the screw channels. RESULTS The highest load for all fixation types occurred in the plate axis. For the vast majority of the wedge sizes and fixation types the shear stress (von Mises stress) was dominating in the bone independent of fixation type. The relative displacements of the tibial fragments were low (in μm range). With an increasing wedge size this displacement tended to increase for both Puddu plates and the TomoFix plate with bone graft. For the TomoFix plate without bone graft a rather opposite trend was observed.For all fixation types the occurring stresses at the screw-bone contact areas pulled at the screws and exceeded the allowable threshold of 1.2 MPa for at least one screw surface. Of the six screw surfaces that were studied, the TomoFix plate with bone graft showed a stress excess of one out of twelve and without bone graft, five out of twelve. With the Puddu plates, an excess stress occurred in the majority of screw surfaces. CONCLUSIONS The different fixation devices generate different fixation stability profiles for different opening wedge sizes. Based on the computational simulations, none of the studied osteosynthesis fixation types warranted an intransigent full weight bearing per se. The highest fixation stability was observed for the TomoFix plates and the lowest for the first generation Puddu plate. These findings were revealed in theoretical models and need to be validated in controlled clinical settings.

Rapid method to express and purify human membrane protein using the Xenopus oocyte system for functional and low-resolution structural analysis.

Progress toward elucidating the 3D structures of eukaryotic membrane proteins has been hampered by the lack of appropriate expression systems. Recent work using the Xenopus oocyte as a novel expression system for structural analysis demonstrates the capability of providing not only the significant amount of protein yields required for structural work but also the expression of eukaryotic membrane proteins in a more native and functional conformation. There is a long history using the oocyte expression system as an efficient tool for membrane transporter and channel expression in direct functional analysis, but improvements in robotic injection systems and protein yield optimization allow the rapid scalability of expressed proteins to be purified and characterized in physiologically relevant structural states. Traditional overexpression systems (yeast, bacteria, and insect cells) by comparison require chaotropic conditions over several steps for extraction, solubilization, and purification. By contrast, overexpressing within the oocyte system for subsequent negative-staining transmission electron microscopy studies provides a single system that can functionally assess and purify eukaryotic membrane proteins in fewer steps maintaining the physiological properties of the membrane protein.

Effectiveness of meticillin-resistant Staphylococcus aureus decolonization in long-term haemodialysis patients: a systematic review and meta-analysis.

BACKGROUND Chronic haemodialysis patients are a high-risk population for meticillin-resistant Staphylococcus aureus (MRSA) colonization, which is a precursor of infection. AIM To summarize the effect of nasal (± whole-body wash) MRSA decolonization in haemodialysis patients by means of a systematic review and meta-analysis. METHODS We identified eligible studies using Medline, Embase, the Cochrane database, clinicaltrials.org, and conference abstracts investigating the success of MRSA decolonization in haemodialysis patients. For the statistical analysis, we used Stata 13 to express study-specific proportions with 95% confidence intervals. A likelihood ratio test was used to assess inter-study heterogeneity. FINDINGS Six published prospective cohort studies and one study described in a conference abstract met our inclusion criteria. From 1150 haemodialysis patients enrolled in these studies, MRSA was isolated from nasal swabs of 147 (12.8%) patients. Six of the trials used mupirocin nasal ointment and combined it with chlorhexidine body washes for decolonization. The most widely used protocol was a five-day course of mupirocin nasal ointment application three times a day, and chlorhexidine body wash once daily. The pooled success rate of decolonization was 0.88 (95% confidence interval: 0.75-0.95). A likelihood ratio test of the fixed versus the random-effects model showed significant inter-study heterogeneity (P = 0.047). Four of seven studies determined subsequent MRSA infections in 94 carriers overall, two (2%) of which experienced infection. CONCLUSION The use of mupirocin together with whole-body decolonization is highly effective in eradicating MRSA carriage in haemodialysis patients. The current literature, however, is characterized by a lack of comparative effectiveness studies for this intervention.

Motivational interviewing and feedback for college drinkers: Handling missing values with complete case analysis and multiple imputation

Objective: In this secondary data analysis, three statistical methodologies were implemented to handle cases with missing data in a motivational interviewing and feedback study. The aim was to evaluate the impact that these methodologies have on the data analysis. ^ Methods: We first evaluated whether the assumption of missing completely at random held for this study. We then proceeded to conduct a secondary data analysis using a mixed linear model to handle missing data with three methodologies (a) complete case analysis, (b) multiple imputation with explicit model containing outcome variables, time, and the interaction of time and treatment, and (c) multiple imputation with explicit model containing outcome variables, time, the interaction of time and treatment, and additional covariates (e.g., age, gender, smoke, years in school, marital status, housing, race/ethnicity, and if participants play on athletic team). Several comparisons were conducted including the following ones: 1) the motivation interviewing with feedback group (MIF) vs. the assessment only group (AO), the motivation interviewing group (MIO) vs. AO, and the intervention of the feedback only group (FBO) vs. AO, 2) MIF vs. FBO, and 3) MIF vs. MIO.^ Results: We first evaluated the patterns of missingness in this study, which indicated that about 13% of participants showed monotone missing patterns, and about 3.5% showed non-monotone missing patterns. Then we evaluated the assumption of missing completely at random by Little's missing completely at random (MCAR) test, in which the Chi-Square test statistic was 167.8 with 125 degrees of freedom, and its associated p-value was p=0.006, which indicated that the data could not be assumed to be missing completely at random. After that, we compared if the three different strategies reached the same results. For the comparison between MIF and AO as well as the comparison between MIF and FBO, only the multiple imputation with additional covariates by uncongenial and congenial models reached different results. For the comparison between MIF and MIO, all the methodologies for handling missing values obtained different results. ^ Discussions: The study indicated that, first, missingness was crucial in this study. Second, to understand the assumptions of the model was important since we could not identify if the data were missing at random or missing not at random. Therefore, future researches should focus on exploring more sensitivity analyses under missing not at random assumption.^

Improved Techniques for Acquisition and Analysis of Dynamic Contrast-Enhanced Magnetic Resonance Imaging for Detecting Vascular Permeability in the Central Nervous System

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a noninvasive technique for quantitative assessment of the integrity of blood-brain barrier and blood-spinal cord barrier (BSCB) in the presence of central nervous system pathologies. However, the results of DCE-MRI show substantial variability. The high variability can be caused by a number of factors including inaccurate T1 estimation, insufficient temporal resolution and poor contrast-to-noise ratio. My thesis work is to develop improved methods to reduce the variability of DCE-MRI results. To obtain fast and accurate T1 map, the Look-Locker acquisition technique was implemented with a novel and truly centric k-space segmentation scheme. In addition, an original multi-step curve fitting procedure was developed to increase the accuracy of T1 estimation. A view sharing acquisition method was implemented to increase temporal resolution, and a novel normalization method was introduced to reduce image artifacts. Finally, a new clustering algorithm was developed to reduce apparent noise in the DCE-MRI data. The performance of these proposed methods was verified by simulations and phantom studies. As part of this work, the proposed techniques were applied to an in vivo DCE-MRI study of experimental spinal cord injury (SCI). These methods have shown robust results and allow quantitative assessment of regions with very low vascular permeability. In conclusion, applications of the improved DCE-MRI acquisition and analysis methods developed in this thesis work can improve the accuracy of the DCE-MRI results.

Científicos y políticas públicas : la incidencia de una red en el tratamiento de una Ley de Ordenamiento Territorial

Nuestro trabajo tiene como objetivo aplicar conceptos de la teoría de los sistemas complejos y herramientas del análisis de redes sociales para describir y analizar el surgimiento y la evolución de una red social conformada por científicos, docentes, graduados y funcionarios públicos de diferentes organismos científicos y académicos, que crearon y participaron de un equipo multidisciplinario que elaboró un informe sobre un proyecto de ley de Ordenamiento Territorial y Usos del Suelo de la provincia de Mendoza en el año 2006. Para la compresión de la evolución del proceso de elaboración del proyecto de ley de ordenamiento territorial y de usos del suelo, organizaremos la estructura del trabajo de la siguiente manera: - Primero aplicaremos aspectos teóricos y metodológicos, basados en la sistematización realizada por Rolando García en su libro “Sistemas Complejos. Conceptos, método y fundamentación epistemológica de la investigación interdisciplinaria", para realizar el recorte del sistema objeto de estudio. - En segundo lugar utilizaremos la Teoría de Análisis de Redes Sociales para describir la composición y estructura del sistema (nodos y vínculos) en cada momento. La estructura del sistema en cada momento significativo será graficada por medio el Software Ucinet 6 y NetDraw. - Por último, haremos referencia a las dificultades que tuvo el proceso desde el punto de vista de las condicionalidades que generaban los modelos mentales que portaban los participantes.

Aplicación de métodos bibliométricos a la evaluación de colecciones : El caso de la Biblioteca del Instituto Argentino de Radioastronomía

Con el objetivo de determinar el grupo de publicaciones nucleares a considerar en el desarrollo de la colección de la Biblioteca del IAR, se realiza un estudio bibliométrico de la producción y del consumo de literatura científica de los investigadores de la institución a la que la biblioteca pertenece. A partir del análisis de referencias de los trabajos publicados por los investigadores se determinan la obsolescencia y la utilidad de la literatura consultada. Mediante la extracción de palabras clave y de los autores se determinan también los frentes de investigación del instituto y los grupos de investigadores que trabajan en esos frentes, aplicando los métodos de análisis de co-ocurrencia de palabras, coautorías y análisis de redes sociales. Los resultados dan cuenta de una baja obsolescencia para la literatura consultada, de una elevada preferencia para consultar y publicar en dos o tres títulos de publicaciones periódicas de la disciplina, y demuestran finalmente la existencia de dos frentes de investigación dentro de la institución

Analysis and visualization of the dynamics of research groups in terms of projects and co-authored publications : A case study of library and information science in Argentina

Objective: The present study offers a novel methodological contribution to the study of the configuration and dynamics of research groups, through a comparative perspective of the projects funded (inputs) and publication co-authorships (output). Method: A combination of bibliometric techniques and social network analysis was applied to a case study: the Departmento de Bibliotecología (DHUBI), Universidad Nacional de La Plata, Argentina, for the period 2000-2009. The results were interpreted statistically and staff members of the department, were interviewed. Results: The method makes it possible to distinguish groups, identify their members and reflect group make-up through an analytical strategy that involves the categorization of actors and the interdisciplinary and national or international projection of the networks that they configure. The integration of these two aspects (input and output) at different points in time over the analyzed period leads to inferences about group profiles and the roles of actors. Conclusions: The methodology presented is conducive to micro-level interpretations in a given area of study, regarding individual researchers or research groups. Because the comparative input-output analysis broadens the base of information and makes it possible to follow up, over time, individual and group trends, it may prove very useful for the management, promotion and evaluation of science

Aplicación de métodos bibliométricos a la evaluación de colecciones : El caso de la Biblioteca del Instituto Argentino de Radioastronomía

Con el objetivo de determinar el grupo de publicaciones nucleares a considerar en el desarrollo de la colección de la Biblioteca del IAR, se realiza un estudio bibliométrico de la producción y del consumo de literatura científica de los investigadores de la institución a la que la biblioteca pertenece. A partir del análisis de referencias de los trabajos publicados por los investigadores se determinan la obsolescencia y la utilidad de la literatura consultada. Mediante la extracción de palabras clave y de los autores se determinan también los frentes de investigación del instituto y los grupos de investigadores que trabajan en esos frentes, aplicando los métodos de análisis de co-ocurrencia de palabras, coautorías y análisis de redes sociales. Los resultados dan cuenta de una baja obsolescencia para la literatura consultada, de una elevada preferencia para consultar y publicar en dos o tres títulos de publicaciones periódicas de la disciplina, y demuestran finalmente la existencia de dos frentes de investigación dentro de la institución