On Frequency Variation of Dynamic Resting-state Functional Brain Network Activation and Connectivity with Applications to both Healthy and Clinical Populations

One of the earliest and fundamental observation in scientific study of the brain was discovering the relation between activities in different local regions of brain and some core functions of the brain. This was later followed by observing that not only local activities of regions but also synchronous activities between distributed brain regions play a key role in high-level brain functions. Synchronous activity related to the functions of the brain is commonly referred to as functional connectivity (FC) and is studied in the form of connectivity states of the brain which measure degree of interactions between distributed parts of the brain. Functional connectivity has been studied with different imaging modalities such as electroencephalogram (EEG), magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI). The latter has the advantage of having relatively higher spatial resolution of the underlying functional regions and is our choice for the source of the data in this work. Functional connectivity analysis of the human brain in fMRI researches focuses on identifying meaningful brain networks that have coherent activity either during a task or in the resting state. These networks are generally identified either as collections of voxels whose time series correlate strongly with a pre-selected region or voxel, or using data-driven methodologies such as independent component analysis (ICA) that compute sets of maximally spatially independent voxel weightings (component spatial maps (SMs)), each associated with a single time course (TC). Recent studies of functional connectivity have shed light on new aspects of functional connectivity. For example, connectivity during a resting state (RS) of the brain had long been know to constitute a single state of connectivity and just recently it is argued that RS-connectivity, varies in time and has a dynamic nature. In this work, we investigate new aspects of RS-connectivity jointly with its dynamic aspect. As part of the new observations, we discuss that RS-connectivity is in fact frequency dependent in addition to be temporally dynamic. This discovery allows to capture RS-coonectivity at a given time as the superposition of multiple connectivity states along frequency dimension. Later, we also show that interaction between fMRI networks is not only frequency dependent and temporally dynamic but also may occur cross different frequency spectra which is the first evidennce of cross-frequency depenence between fMRI functional networks. We also discuss that all of these observations would enable us to design novel measures to explain RS-connectivity variation among different group of subjects such as healthy and diseased or males and females which would have clinical diagnosis applications and could possibly serve as new bio-markers to study underlying functions of the brain

The cost-effectiveness of alternative vaccination strategies for polyvalent meningococcal vaccines in Burkina Faso: A transmission dynamic modeling study.

BACKGROUND: The introduction of a conjugate vaccine for serogroup A Neisseria meningitidis has dramatically reduced disease in the African meningitis belt. In this context, important questions remain about the performance of different vaccine policies that target remaining serogroups. Here, we estimate the health impact and cost associated with several alternative vaccination policies in Burkina Faso. METHODS AND FINDINGS: We developed and calibrated a mathematical model of meningococcal transmission to project the disability-adjusted life years (DALYs) averted and costs associated with the current Base policy (serogroup A conjugate vaccination at 9 months, as part of the Expanded Program on Immunization [EPI], plus district-specific reactive vaccination campaigns using polyvalent meningococcal polysaccharide [PMP] vaccine in response to outbreaks) and three alternative policies: (1) Base Prime: novel polyvalent meningococcal conjugate (PMC) vaccine replaces the serogroup A conjugate in EPI and is also used in reactive campaigns; (2) Prevention 1: PMC used in EPI and in a nationwide catch-up campaign for 1-18-year-olds; and (3) Prevention 2: Prevention 1, except the nationwide campaign includes individuals up to 29 years old. Over a 30-year simulation period, Prevention 2 would avert 78% of the meningococcal cases (95% prediction interval: 63%-90%) expected under the Base policy if serogroup A is not replaced by remaining serogroups after elimination, and would avert 87% (77%-93%) of meningococcal cases if complete strain replacement occurs. Compared to the Base policy and at the PMC vaccine price of US$4 per dose, strategies that use PMC vaccine (i.e., Base Prime and Preventions 1 and 2) are expected to be cost saving if strain replacement occurs, and would cost US$51 (-US$236, US$490), US$188 (-US$97, US$626), and US$246 (-US$53, US$703) per DALY averted, respectively, if strain replacement does not occur. An important potential limitation of our study is the simplifying assumption that all circulating meningococcal serogroups can be aggregated into a single group; while this assumption is critical for model tractability, it would compromise the insights derived from our model if the effectiveness of the vaccine differs markedly between serogroups or if there are complex between-serogroup interactions that influence the frequency and magnitude of future meningitis epidemics. CONCLUSIONS: Our results suggest that a vaccination strategy that includes a catch-up nationwide immunization campaign in young adults with a PMC vaccine and the addition of this new vaccine into EPI is cost-effective and would avert a substantial portion of meningococcal cases expected under the current World Health Organization-recommended strategy of reactive vaccination. This analysis is limited to Burkina Faso and assumes that polyvalent vaccines offer equal protection against all meningococcal serogroups; further studies are needed to evaluate the robustness of this assumption and applicability for other countries in the meningitis belt

Machine Transcription Conversion Between Perso-Arabic and Romanized Writing Systems

Perso-Arabic script is the official writing system in Iran. Romanized transcriptions, based on phonology of Persian, have been extensively used in electronic communications especially on Internet. Dealing with the conversion between these two types of writing systems has been an interesting topic in Natural Language Processing. Similar to Machine Translation, these conversions can be applied at different grammatical layers; such as sentence, phrase or word layer. In this thesis, by choosing Dabire as a standard Romanized transcription, we introduce two approaches to achieve such conversions at word level. In Lexicon-based approach we use Finite State Technology for bi-directional conversion between Perso-Arabic and Dabire. The second approach uses association analysis for statistical conversion from Perso-Arabic to Dabire

Machine Transcription Conversion Between Perso-Arabic and Romanized Writing Systems

Perso-Arabic script is the official writing system in Iran. Romanized transcriptions, based on phonology of Persian, have been extensively used in electronic communications especially on Internet. Dealing with the conversion between these two types of writing systems has been an interesting topic in Natural Language Processing. Similar to Machine Translation, these conversions can be applied at different grammatical layers; such as sentence, phrase or word layer. In this thesis, by choosing Dabire as a standard Romanized transcription, we introduce two approaches to achieve such conversions at word level. In Lexicon-based approach we use Finite State Technology for bi-directional conversion between Perso-Arabic and Dabire. The second approach uses association analysis for statistical conversion from Perso-Arabic to Dabire

New draft item

The data consists of resting-state fMRI network time-courses of 405 subjects. Each time-course has 148 time-points (TR = 2seconds). 50 networks are estimated by Independent Components Analysis (ICA)

SubjectNetworkTimeCourses.mat

The data consists of resting-state fMRI network time-courses of 405 subjects. Each time-course has 148 time-points (TR = 2seconds). 50 networks are estimated by Independent Components Analysis (ICA)

Time-varying spectral power of resting-state fMRI networks reveal cross-frequency dependence in dynamic connectivity

<div><p>Brain oscillations and synchronicity among brain regions (brain connectivity) have been studied in resting-state (RS) and task-induced settings. RS-connectivity which captures brain functional integration during an unconstrained state is shown to vary with the frequency of oscillations. Indeed, high temporal resolution modalities have demonstrated both between and cross-frequency connectivity spanning across frequency bands such as theta and gamma. Despite high spatial resolution, functional magnetic resonance imaging (fMRI) suffers from low temporal resolution due to modulation with slow-varying hemodynamic response function (HRF) and also relatively low sampling rate. This limits the range of detectable frequency bands in fMRI and consequently there has been no evidence of cross-frequency dependence in fMRI data. In the present work we uncover recurring patterns of spectral power in network timecourses which provides new insight on the actual nature of frequency variation in fMRI network activations. Moreover, we introduce a new measure of dependence between pairs of rs-fMRI networks which reveals significant cross-frequency dependence between functional brain networks specifically default-mode, cerebellar and visual networks. This is the first strong evidence of cross-frequency dependence between functional networks in fMRI and our subject group analysis based on age and gender supports usefulness of this observation for future clinical applications.</p></div

The cost-effectiveness of alternative vaccination strategies for polyvalent meningococcal vaccines in Burkina Faso: A transmission dynamic modeling study.

BACKGROUND:The introduction of a conjugate vaccine for serogroup A Neisseria meningitidis has dramatically reduced disease in the African meningitis belt. In this context, important questions remain about the performance of different vaccine policies that target remaining serogroups. Here, we estimate the health impact and cost associated with several alternative vaccination policies in Burkina Faso. METHODS AND FINDINGS:We developed and calibrated a mathematical model of meningococcal transmission to project the disability-adjusted life years (DALYs) averted and costs associated with the current Base policy (serogroup A conjugate vaccination at 9 months, as part of the Expanded Program on Immunization [EPI], plus district-specific reactive vaccination campaigns using polyvalent meningococcal polysaccharide [PMP] vaccine in response to outbreaks) and three alternative policies: (1) Base Prime: novel polyvalent meningococcal conjugate (PMC) vaccine replaces the serogroup A conjugate in EPI and is also used in reactive campaigns; (2) Prevention 1: PMC used in EPI and in a nationwide catch-up campaign for 1-18-year-olds; and (3) Prevention 2: Prevention 1, except the nationwide campaign includes individuals up to 29 years old. Over a 30-year simulation period, Prevention 2 would avert 78% of the meningococcal cases (95% prediction interval: 63%-90%) expected under the Base policy if serogroup A is not replaced by remaining serogroups after elimination, and would avert 87% (77%-93%) of meningococcal cases if complete strain replacement occurs. Compared to the Base policy and at the PMC vaccine price of US$4 per dose, strategies that use PMC vaccine (i.e., Base Prime and Preventions 1 and 2) are expected to be cost saving if strain replacement occurs, and would cost US$51 (-US$236, US$490), US$188 (-US$97, US$626), and US$246 (-US$53, US$703) per DALY averted, respectively, if strain replacement does not occur. An important potential limitation of our study is the simplifying assumption that all circulating meningococcal serogroups can be aggregated into a single group; while this assumption is critical for model tractability, it would compromise the insights derived from our model if the effectiveness of the vaccine differs markedly between serogroups or if there are complex between-serogroup interactions that influence the frequency and magnitude of future meningitis epidemics. CONCLUSIONS:Our results suggest that a vaccination strategy that includes a catch-up nationwide immunization campaign in young adults with a PMC vaccine and the addition of this new vaccine into EPI is cost-effective and would avert a substantial portion of meningococcal cases expected under the current World Health Organization-recommended strategy of reactive vaccination. This analysis is limited to Burkina Faso and assumes that polyvalent vaccines offer equal protection against all meningococcal serogroups; further studies are needed to evaluate the robustness of this assumption and applicability for other countries in the meningitis belt

Analysis of co-occurrence rates of the modes.

<p>Cco-occurrence maps of frequency mode pairs. An entry (column <i>m</i>, row <i>n</i>)(1…50, 1…50) of a matrix at column <i>i</i> (1…4) and row <i>j</i> (1…4) of the figure shows cco-occurrence of frequency mode <i>i</i> in network <i>m</i>, given that frequency mode <i>j</i> is occurred at the same time-point in network <i>n</i>. Positive cc-occurrence (color coded as red) corresponds to <i>reinforcement effect</i> and negative cc-occurrence (color coded as blue) is corresponding to <i>suppression effect</i>.</p