Principal component analysis and assessment of language network activation patterns in pediatric epilepsy

This dissertation establishes a novel data-driven method to identify language network activation patterns in pediatric epilepsy through the use of the Principal Component Analysis (PCA) on functional magnetic resonance imaging (fMRI). A total of 122 subjects’ data sets from five different hospitals were included in the study through a web-based repository site designed here at FIU. Research was conducted to evaluate different classification and clustering techniques in identifying hidden activation patterns and their associations with meaningful clinical variables. The results were assessed through agreement analysis with the conventional methods of lateralization index (LI) and visual rating. What is unique in this approach is the new mechanism designed for projecting language network patterns in the PCA-based decisional space. Synthetic activation maps were randomly generated from real data sets to uniquely establish nonlinear decision functions (NDF) which are then used to classify any new fMRI activation map into typical or atypical. The best nonlinear classifier was obtained on a 4D space with a complexity (nonlinearity) degree of 7. Based on the significant association of language dominance and intensities with the top eigenvectors of the PCA decisional space, a new algorithm was deployed to delineate primary cluster members without intensity normalization. In this case, three distinct activations patterns (groups) were identified (averaged kappa with rating 0.65, with LI 0.76) and were characterized by the regions of: (1) the left inferior frontal Gyrus (IFG) and left superior temporal gyrus (STG), considered typical for the language task; (2) the IFG, left mesial frontal lobe, right cerebellum regions, representing a variant left dominant pattern by higher activation; and (3) the right homologues of the first pattern in Broca's and Wernicke's language areas. Interestingly, group 2 was found to reflect a different language compensation mechanism than reorganization. Its high intensity activation suggests a possible remote effect on the right hemisphere focus on traditionally left-lateralized functions. In retrospect, this data-driven method provides new insights into mechanisms for brain compensation/reorganization and neural plasticity in pediatric epilepsy.

Motion Correction Algorithm of Lung Tumors for Respiratory Gated PET Images

Respiratory gating in lung PET imaging to compensate for respiratory motion artifacts is a current research issue with broad potential impact on quantitation, diagnosis and clinical management of lung tumors. However, PET images collected at discrete bins can be significantly affected by noise as there are lower activity counts in each gated bin unless the total PET acquisition time is prolonged, so that gating methods should be combined with imaging-based motion correction and registration methods. The aim of this study was to develop and validate a fast and practical solution to the problem of respiratory motion for the detection and accurate quantitation of lung tumors in PET images. This included: (1) developing a computer-assisted algorithm for PET/CT images that automatically segments lung regions in CT images, identifies and localizes lung tumors of PET images; (2) developing and comparing different registration algorithms which processes all the information within the entire respiratory cycle and integrate all the tumor in different gated bins into a single reference bin. Four registration/integration algorithms: Centroid Based, Intensity Based, Rigid Body and Optical Flow registration were compared as well as two registration schemes: Direct Scheme and Successive Scheme. Validation was demonstrated by conducting experiments with the computerized 4D NCAT phantom and with a dynamic lung-chest phantom imaged using a GE PET/CT System. Iterations were conducted on different size simulated tumors and different noise levels. Static tumors without respiratory motion were used as gold standard; quantitative results were compared with respect to tumor activity concentration, cross-correlation coefficient, relative noise level and computation time. Comparing the results of the tumors before and after correction, the tumor activity values and tumor volumes were closer to the static tumors (gold standard). Higher correlation values and lower noise were also achieved after applying the correction algorithms. With this method the compromise between short PET scan time and reduced image noise can be achieved, while quantification and clinical analysis become fast and precise.

Principal Component Analysis and Assessment of Language Network Activation Patterns in Pediatric Epilepsy

This dissertation establishes a novel data-driven method to identify language network activation patterns in pediatric epilepsy through the use of the Principal Component Analysis (PCA) on functional magnetic resonance imaging (fMRI). A total of 122 subjects’ data sets from five different hospitals were included in the study through a web-based repository site designed here at FIU. Research was conducted to evaluate different classification and clustering techniques in identifying hidden activation patterns and their associations with meaningful clinical variables. The results were assessed through agreement analysis with the conventional methods of lateralization index (LI) and visual rating. What is unique in this approach is the new mechanism designed for projecting language network patterns in the PCA-based decisional space. Synthetic activation maps were randomly generated from real data sets to uniquely establish nonlinear decision functions (NDF) which are then used to classify any new fMRI activation map into typical or atypical. The best nonlinear classifier was obtained on a 4D space with a complexity (nonlinearity) degree of 7. Based on the significant association of language dominance and intensities with the top eigenvectors of the PCA decisional space, a new algorithm was deployed to delineate primary cluster members without intensity normalization. In this case, three distinct activations patterns (groups) were identified (averaged kappa with rating 0.65, with LI 0.76) and were characterized by the regions of: 1) the left inferior frontal Gyrus (IFG) and left superior temporal gyrus (STG), considered typical for the language task; 2) the IFG, left mesial frontal lobe, right cerebellum regions, representing a variant left dominant pattern by higher activation; and 3) the right homologues of the first pattern in Broca's and Wernicke's language areas. Interestingly, group 2 was found to reflect a different language compensation mechanism than reorganization. Its high intensity activation suggests a possible remote effect on the right hemisphere focus on traditionally left-lateralized functions. In retrospect, this data-driven method provides new insights into mechanisms for brain compensation/reorganization and neural plasticity in pediatric epilepsy.

Annotated record of the detailed examination of Mn deposits from the R/V Thomas Washington ROUNDABOUT Cruise stations

The cores described are taken during the R/V Thomas Washington ROUNDABOUT Cruise from May 1988 until March 1989 by the Scripps Institute of Oceanography. A total of 159 cores and dredges were recovered and are available at Scripps Institute of Oceanography for sampling and study.

Annotated record of the detailed examination of Mn deposits from the QUEBRADA (1969) and SIQUEIROS (1974) expeditions around the East Pacific Rise

Basalt samples obtained from the Siqueiros transform fault/fracture zone and the adjacent East Pacific Rise are mostly very fresh oceanic tholeiite and fractionated oceanic tholeiite with Fe+3/ Fe+2 ? 0.25; however, alkali basalts occur in the area as well. The rocks of the tholeiitic suite are ol + pl phyric and ol + pl + cpx phyric basalts, while the alkali basalts are ol and ol + pl phyric. Microprobe analyses of the tholeiitic suite phenocrysts indicate that they are Fo68-Fo86, An58-An75, and augite (Ca34Mg50Fe16). The range of olivine and plagioclase compositions represents the chemical variation of the phenocryst compositions with fractionation. The phenocyrsts in the alkali basalts are Fo81 and An69. The suite of tholeiites comprises a fractionation series characterized by relative enrichment of Fe, Ti, Mn, V, Na, K, and P and depletion of Ca, Al, Mg, Ni, and Cr. The fractionated tholeiites occur on the median ridge (which is a sliver of normal oceanic crust) of the double Siqueiros transform fault, on the western Siqueiros fracture zone, and on the adjoining East Pacific Rise, while the two transform fault troughs contain mostly unfractionated or only slightly fractionated tholeiite. We suggest that the fractionated tholeiites are produced by fractional crystallization of more 'primitive' tholeiitic liquid in a crustal magma chamber below the crest of the East Pacific Rise. This magma chamber may be disrupted by the transform fault troughs, thus explaining the paucity of fractionated tholeiites in the troughs. The alkali basalts are found only on the flanks of a topographic high near the intersection of the northern transform trough with the East Pacific Rise.

Annotated record of the detailed examination of Mn deposits from STYX expedition stations

The cores described in this paper were taken in the tropical central Pacific Ocean by Scripps Institution of Oceanography's R/V Alexander Agassiz on the STYX Expedition of April-September 1968. A total of 132 cores were attempted of which 97 were successful. These cores are available at Scripps for sampling and study.

Analisi preliminare dei risultati di TC perfusionale effettuata su tessuto polmonare sano

Le ultime ricerche in campo oncologico sulle cure antitumorali sono indirizzate verso una categoria definita target therapy. In particolare tra le più promettenti, le terapie antiangiogenetiche, il cui scopo primario è quello di limitare l’apporto di sangue al tumore. In questo contesto la Tomografia Computerizzata (TC) perfusionale rappresenta un’importante tecnica di imaging radiologico in grado, teoricamente, di fornire misure quantitative, che permettano una valutazione, anche precoce, della risposta alle terapie antiangiogenetiche. I principali problemi aperti in questo campo riguardano la standardizzazione dei protocolli di acquisizione e di elaborazione delle sequenze perfusionali, che determinano la scarsa riproducibilità dei risultati intra- ed inter-paziente, non consentendone l’uso nella pratica clinica. In letteratura sono presenti diversi studi riguardanti la perfusione dei tumori polmonari, ma vi sono pochi studi sull’affidabilità dei parametri perfusionali calcolati. Questa Tesi si propone di analizzare, quantificare e confrontare gli errori e l’affidabilità dei parametri perfusionali calcolati attraverso la TC perfusionale. In particolare, vengono generate delle mappe di errore ed effettuati dei confronti di diverse regioni del polmone sano. I risultati ottenuti dall’analisi dei casi reali sono discussi al fine di poter definire dei livelli di affidabilità dei parametri perfusionali e di quantificare gli errori che si commettono nella valutazione dei parametri stessi. Questo studio preliminare consentirà, quindi, un’analisi di riproducibilità, permettendo, inoltre, una normalizzazione dei valori perfusionali calcolati nella lesione, al fine di effettuare analisi intra- ed inter-paziente.

Mean dynamic topography of the North Indian Ocean

A satellite-only Mean Dynamic Topography (MDT) of the North Indian Ocean is estimated from the DIRR5 geoid and CNES_CLS11 mean sea surface (Schaffer et al. 2012). DIRR5 geoid is estimated from the latest release (Release 5) of GOCE gravity data according to previous studies (e.g., Johannessen et al. 2003; Raj, 2014). Note that this MDT estimated is referenced to a time period of 7 years (1993-1999). A correction data obtained from AVISO is later used to convert the MDT to a time reference of 20 years (1993-2012). More details are given in Raj (2016).

Circumarctic wetland dataset based on ENVISAT ASAR Global Monitoring Mode with links to geotiff image and NetCDF files (2005-01 to 2011-12)

A circumpolar representative and consistent wetland map is required for a range of applications ranging from upscaling of carbon fluxes and pools to climate modelling and wildlife habitat assessment. Currently available data sets lack sufficient accuracy and/or thematic detail in many regions of the Arctic. Synthetic aperture radar (SAR) data from satellites have already been shown to be suitable for wetland mapping. Envisat Advanced SAR (ASAR) provides global medium-resolution data which are examined with particular focus on spatial wetness patterns in this study. It was found that winter minimum backscatter values as well as their differences to summer minimum values reflect vegetation physiognomy units of certain wetness regimes. Low winter backscatter values are mostly found in areas vegetated by plant communities typically for wet regions in the tundra biome, due to low roughness and low volume scattering caused by the predominant vegetation. Summer to winter difference backscatter values, which in contrast to the winter values depend almost solely on soil moisture content, show expected higher values for wet regions. While the approach using difference values would seem more reasonable in order to delineate wetness patterns considering its direct link to soil moisture, it was found that a classification of winter minimum backscatter values is more applicable in tundra regions due to its better separability into wetness classes. Previous approaches for wetland detection have investigated the impact of liquid water in the soil on backscatter conditions. In this study the absence of liquid water is utilized. Owing to a lack of comparable regional to circumpolar data with respect to thematic detail, a potential wetland map cannot directly be validated; however, one might claim the validity of such a product by comparison with vegetation maps, which hold some information on the wetness status of certain classes. It was shown that the Envisat ASAR-derived classes are related to wetland classes of conventional vegetation maps, indicating its applicability; 30% of the land area north of the treeline was identified as wetland while conventional maps recorded 1-7%.

Circumpolar Landscape Units, links to GeoTIFFs

Requirements for space based monitoring of permafrost features had been already defined within the IGOS Cryosphere Theme Report at the start of the IPY in 2007 (IGOS, 2007). The WMO Polar Space Task Group (PSTG, http://www.wmo.int/pages/prog/sat/pstg_en.php) identified the need to review the requirements for permafrost monitoring and to update these requirements in 2013. Relevant surveys with focus on satellite data are already available from the ESA DUE Permafrost User requirements survey (2009), the United States National Research Council (2014) and the ESA - CliC - IPA - GTN -P workshop in February 2014. These reports have been reviewed and specific needs discussed within the community and a white paper submitted to the WMO PSTG. Acquisition requirements for monitoring of especially terrain changes (incl. rock glaciers and coastal erosion) and lakes (extent, ice properties etc.) with respect to current satellite missions have been specified. About 50 locations ('cold spots') where permafrost (Arctic and Antarctic) in situ monitoring has been taking place for many years or where field stations are currently established have been identified. These sites have been proposed to the WMO Polar Space Task Group as focus areas for future monitoring by high resolution satellite data. The specifications of these sites including meta-data on site instrumentation have been published as supplement to the white paper (Bartsch et al. 2014, doi:10.1594/PANGAEA.847003). The representativity of the 'cold spots' around the arctic has been in the following assessed based on a landscape units product which has been developed as part of the FP7 project PAGE21. The ESA DUE Permafrost service has been utilized to produce a pan-arctic database (25km, 2000-2014) comprising Mean Annual Surface Temperature, Annual and summer Amplitude of Surface Temperature, Mean Summer (July-August) Surface Temperature. Surface status (frozen/unfrozen) related products have been also derived from the ESA DUE Permafrost service. This includes the length of unfrozen period, first unfrozen day and first frozen day. In addition, SAR (ENVISAT ASAR GM) statistics as well as topographic parameters have been considered. The circumpolar datasets have been assessed for their redundancy in information content. 12 distinct units could be derived. The landscape units reveal similarities between North Slope Alaska and the region from the Yamal Peninsula to the Yenisei estuary. Northern Canada is characterized by the same landscape units like western Siberia. North-eastern Canada shows similarities to the Laptev coast region. This paper presents the result of this assessment and formulates recommendations for extensions of the in situ monitoring networks and categorizes the sites by satellite data requirements (specifically Sentinels) with respect to the landscape type and related processes.

Using Bird Distributions to Assess Extinction Risk and Identify Conservation Priorities in Biodiversity Hotspots

Habitat loss, fragmentation, and degradation threaten the World’s ecosystems and species. These, and other threats, will likely be exacerbated by climate change. Due to a limited budget for conservation, we are forced to prioritize a few areas over others. These places are selected based on their uniqueness and vulnerability. One of the most famous examples is the biodiversity hotspots: areas where large quantities of endemic species meet alarming rates of habitat loss. Most of these places are in the tropics, where species have smaller ranges, diversity is higher, and ecosystems are most threatened.

Species distributions are useful to understand ecological theory and evaluate extinction risk. Small-ranged species, or those endemic to one place, are more vulnerable to extinction than widely distributed species. However, current range maps often overestimate the distribution of species, including areas that are not within the suitable elevation or habitat for a species. Consequently, assessment of extinction risk using these maps could underestimate vulnerability.

In order to be effective in our quest to conserve the World’s most important places we must: 1) Translate global and national priorities into practical local actions, 2) Find synergies between biodiversity conservation and human welfare, 3) Evaluate the different dimensions of threats, in order to design effective conservation measures and prepare for future threats, and 4) Improve the methods used to evaluate species’ extinction risk and prioritize areas for conservation. The purpose of this dissertation is to address these points in Colombia and other global biodiversity hotspots.

In Chapter 2, I identified the global, strategic conservation priorities and then downscaled to practical local actions within the selected priorities in Colombia. I used existing range maps of 171 bird species to identify priority conservation areas that would protect the greatest number of species at risk in Colombia (endemic and small-ranged species). The Western Andes had the highest concentrations of such species—100 in total—but the lowest densities of national parks. I then adjusted the priorities for this region by refining these species ranges by selecting only areas of suitable elevation and remaining habitat. The estimated ranges of these species shrank by 18–100% after accounting for habitat and suitable elevation. Setting conservation priorities on the basis of currently available range maps excluded priority areas in the Western Andes and, by extension, likely elsewhere and for other taxa. By incorporating detailed maps of remaining natural habitats, I made practical recommendations for conservation actions. One recommendation was to restore forest connections to a patch of cloud forest about to become isolated from the main Andes.

For Chapter 3, I identified areas where bird conservation met ecosystem service protection in the Central Andes of Colombia. Inspired by the November 11th (2011) landslide event near Manizales, and the current poor results of Colombia’s Article 111 of Law 99 of 1993 as a conservation measure in this country, I set out to prioritize conservation and restoration areas where landslide prevention would complement bird conservation in the Central Andes. This area is one of the most biodiverse places on Earth, but also one of the most threatened. Using the case of the Rio Blanco Reserve, near Manizales, I identified areas for conservation where endemic and small-range bird diversity was high, and where landslide risk was also high. I further prioritized restoration areas by overlapping these conservation priorities with a forest cover map. Restoring forests in bare areas of high landslide risk and important bird diversity yields benefits for both biodiversity and people. I developed a simple landslide susceptibility model using slope, forest cover, aspect, and stream proximity. Using publicly available bird range maps, refined by elevation, I mapped concentrations of endemic and small-range bird species. I identified 1.54 km2 of potential restoration areas in the Rio Blanco Reserve, and 886 km2 in the Central Andes region. By prioritizing these areas, I facilitate the application of Article 111 which requires local and regional governments to invest in land purchases for the conservation of watersheds.

Chapter 4 dealt with elevational ranges of montane birds and the impact of lowland deforestation on their ranges in the Western Andes of Colombia, an important biodiversity hotspot. Using point counts and mist-nets, I surveyed six altitudinal transects spanning 2200 to 2800m. Three transects were forested from 2200 to 2800m, and three were partially deforested with forest cover only above 2400m. I compared abundance-weighted mean elevation, minimum elevation, and elevational range width. In addition to analyzing the effect of deforestation on 134 species, I tested its impact within trophic guilds and habitat preference groups. Abundance-weighted mean and minimum elevations were not significantly different between forested and partially deforested transects. Range width was marginally different: as expected, ranges were larger in forested transects. Species in different trophic guilds and habitat preference categories showed different trends. These results suggest that deforestation may affect species’ elevational ranges, even within the forest that remains. Climate change will likely exacerbate harmful impacts of deforestation on species’ elevational distributions. Future conservation strategies need to account for this by protecting connected forest tracts across a wide range of elevations.

In Chapter 5, I refine the ranges of 726 species from six biodiversity hotspots by suitable elevation and habitat. This set of 172 bird species for the Atlantic Forest, 138 for Central America, 100 for the Western Andes of Colombia, 57 for Madagascar, 102 for Sumatra, and 157 for Southeast Asia met the criteria for range size, endemism, threat, and forest use. Of these 586 species, the Red List deems 108 to be threatened: 15 critically endangered, 29 endangered, and 64 vulnerable. When ranges are refined by elevational limits and remaining forest cover, 10 of those critically endangered species have ranges < 100km2, but then so do 2 endangered species, seven vulnerable, and eight non-threatened ones. Similarly, 4 critically endangered species, 20 endangered, and 12 vulnerable species have refined ranges < 5000km2, but so do 66 non-threatened species. A striking 89% of these species I have classified in higher threat categories have <50% of their refined ranges inside protected areas. I find that for 43% of the species I assessed, refined range sizes fall within thresholds that typically have higher threat categories than their current assignments. I recommend these species for closer inspection by those who assess risk. These assessments are not only important on a species-by-species basis, but by combining distributions of threatened species, I create maps of conservation priorities. They differ significantly from those created from unrefined ranges.

Using GIS and Remote Sensing Technologies to Identify Environmental Variables of Malaria Vector Breeding Sites in Western Kenya

This study used Landsat 8 satellite imagery to identify environmental variables of households with malaria vector breeding sites in a malaria endemic rural district in Western Kenya. Understanding the influence of environmental variables on the distribution of malaria has been critical in the strengthening of malaria control programs. Using remote sensing and GIS technologies, this study performed a land classification, NDVI, Tasseled Cap Wetness Index, and derived land surface temperature values of the study area and examined the significance of each variable in predicting the probability of a household with a mosquito breeding site with and without larvae. The findings of this study revealed that households with any potential breeding sites were characterized by higher moisture, higher vegetation density (NDVI) and in urban areas or roads. The results of this study also confirmed that land surface temperature was significant in explaining the presence of active mosquito breeding sites (P< 0.000). The present study showed that freely available Landsat 8 imagery has limited use in deriving environmental characteristics of malaria vector habitats at the scale of the Bungoma East District in Western Kenya.

Fermion Mass Generation without Spontaneous Symmetry Breaking

The conventional mechanism of fermion mass generation in the Standard Model involves Spontaneous Symmetry Breaking (SSB). In this thesis, we study an alternate mechanism for the generation of fermion masses that does not require SSB, in the context of lattice field theories. Being inherently strongly coupled, this mechanism requires a non-perturbative approach like the lattice approach.

In order to explore this mechanism, we study a simple lattice model with a four-fermion interaction that has massless fermions at weak couplings and massive fermions at strong couplings, but without any spontaneous symmetry breaking. Prior work on this type of mass generation mechanism in 4D, was done long ago using either mean-field theory or Monte-Carlo calculations on small lattices. In this thesis, we have developed a new computational approach that enables us to perform large scale quantum Monte-Carlo calculations to study the phase structure of this theory. In 4D, our results confirm prior results, but differ in some quantitative details of the phase diagram. In contrast, in 3D, we discover a new second order critical point using calculations on lattices up to size $ 60^3$. Such large scale calculations are unprecedented. The presence of the critical point implies the existence of an alternate mechanism of fermion mass generation without any SSB, that could be of interest in continuum quantum field theory.

Monthly Arctic sea ice lead fraction in 0.5° x 0.5° resolution from SARAL/Altika altimeter, link to datasets in NetCDF 4 format

Sea ice leads play an essential role in ocean-ice-atmosphere exchange, in ocean circulation, geochemistry, and in ice dynamics. Their precise detection is crucial for altimetric estimations of sea ice thickness and volume. This study evaluates the performance of the SARAL/AltiKa (Satellite with ARgos and ALtiKa) altimeter to detect leads and to monitor their spatio-temporal dynamics. We show that a pulse peakiness parameter (PP) used to detect leads by Envisat RA-2 and ERS-1,-2 altimeters is not suitable because of saturation of AltiKa return echoes over the leads. The signal saturation results in loss of 6-10% of PP data over sea ice. We propose a different parameter-maximal power of waveform-and define the threshold to discriminate the leads. Our algorithm can be applied from December until May. It detects well the leads of small and medium size from 200 m to 3-4 km. So the combination of the high-resolution altimetric estimates with low-resolution thermal infra-red or radiometric lead fraction products could enhance the capability of remote sensing to monitor sea ice fracturing.