[Carta Real, 1613, 07, 20]

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Induction of inhibitory factor κBα mRNA in the central nervous system after peripheral lipopolysaccharide administration: An in situ hybridization histochemistry study in the rat

In this study we investigate the mRNA expression of inhibitory factor κBα (IκBα) in cells of the rat brain induced by an intraperitoneal (i.p.) injection of lipopolysaccharide (LPS). IκB controls the activity of nuclear factor κB, which regulates the transcription of many immune signal molecules. The detection of IκB induction, therefore, would reveal the extent and the cellular location of brain-derived immune molecules in response to peripheral immune challenges. Low levels of IκBα mRNA were found in the large blood vessels and in circumventricular organs (CVOs) of saline-injected control animals. After an i.p. LPS injection (2.5 mg/kg), dramatic induction of IκBα mRNA occurred in four spatio-temporal patterns. Induced signals were first detected at 0.5 hr in the lumen of large blood vessels and in blood vessels of the choroid plexus and CVOs. Second, at 1–2 hr, labeling dramatically increased in the CVOs and choroid plexus and spread to small vascular and glial cells throughout the entire brain; these responses peaked at 2 hr and declined thereafter. Third, cells of the meninges became activated at 2 hr and persisted until 12 hr after the LPS injection. Finally, only at 12 hr, induced signals were present in ventricular ependyma. Thus, IκBα mRNA is induced in brain after peripheral LPS injection, beginning in cells lining the blood side of the blood–brain barrier and progressing to cells inside brain. The spatiotemporal patterns suggest that cells of the blood–brain barrier synthesize immune signal molecules to activate cells inside the central nervous system in response to peripheral LPS. The cerebrospinal fluid appears to be a conduit for these signal molecules.

Formation of mnemonic neuronal responses to visual paired associates in inferotemporal cortex is impaired by perirhinal and entorhinal lesions.

Functional roles of the cortical backward signal in long-term memory formation were studied in monkeys performing a visual pair-association task. Before the monkeys learned the task, the anterior commissure was transected, disconnecting the anterior temporal cortex of each hemisphere. After training with 12 pairs of pictures, single units were recorded from the inferotemporal cortex of the monkeys as the control. By injecting a grid of ibotenic acid, we unilaterally lesioned the entorhinal and perirhinal cortex, which provides massive direct and indirect backward projections ipsilaterally to the inferotemporal cortex. After the lesion, the monkeys fixated the cue stimulus normally, relearned the preoperatively learned set (set A), and learned a new set (set B) of paired associates. Then, single units were recorded from the same area as for the prelesion control. We found that (i) in spite of the lesion, the sampled neurons responded strongly and selectively to both the set A and set B patterns and (ii) the paired associates elicited significantly correlated responses in the control neurons before the lesion but not in the cells tested after the lesion, either for set A or set B stimuli. We conclude that the ability of inferotemporal neurons to represent association between picture pairs was lost after the lesion of entorhinal and perirhinal cortex, most likely through disruption of backward neural signals to the inferotemporal neurons, while the ability of the neurons to respond to a particular visual stimulus was left intact.

Proactive and reactive inhibition during overt and covert actions. An electrical neuroimaging study.

Response inhibition is the ability to suppress inadequate but automatically activated, prepotent or ongoing response tendencies. In the framework of motor inhibition, two distinct operating strategies have been described: “proactive” and “reactive” control modes. In the proactive modality, inhibition is recruited in advance by predictive signals, and actively maintained before its enactment. Conversely, in the reactive control mode, inhibition is phasically enacted after the detection of the inhibitory signal. To date, ample evidence points to a core cerebral network for reactive inhibition comprising the right inferior frontal gyrus (rIFG), the presupplementary motor area (pre-SMA) and the basal ganglia (BG). Moreover, fMRI studies showed that cerebral activations during proactive and reactive inhibition largely overlap. These findings suggest that at least part of the neural network for reactive inhibition is recruited in advance, priming cortical regions in preparation for the upcoming inhibition. So far, proactive and reactive inhibitory mechanisms have been investigated during tasks in which the requested response to be stopped or withheld was an “overt” action execution (AE) (i.e., a movement effectively performed). Nevertheless, inhibitory mechanisms are also relevant for motor control during “covert actions” (i.e., potential motor acts not overtly performed), such as motor imagery (MI). MI is the conscious, voluntary mental rehearsal of action representations without any overt movement. Previous studies revealed a substantial overlap of activated motor-related brain networks in premotor, parietal and subcortical regions during overtly executed and imagined movements. Notwithstanding this evidence for a shared set of cerebral regions involved in encoding actions, whether or not those actions are effectively executed, the neural bases of motor inhibition during MI, preventing covert action from being overtly performed, in spite of the activation of the motor system, remain to be fully clarified. Taking into account this background, we performed a high density EEG study evaluating cerebral mechanisms and their related sources elicited during two types of cued Go/NoGo task, requiring the execution or withholding of an overt (Go) or a covert (MI) action, respectively. The EEG analyses were performed in two steps, with different aims: 1) Analysis of the “response phase” of the cued overt and covert Go/NoGo tasks, for the evaluation of reactive inhibitory control of overt and covert actions. 2) Analysis of the “preparatory phase” of the cued overt and covert Go/NoGo EEG datasets, focusing on cerebral activities time-locked to the preparatory signals, for the evaluation of proactive inhibitory mechanisms and their related neural sources. For these purposes, a spatiotemporal analysis of the scalp electric fields was applied on the EEG data recorded during the overt and covert Go/NoGo tasks. The spatiotemporal approach provide an objective definition of time windows for source analysis, relying on the statistical proof that the electric fields are different and thus generated by different neural sources. The analysis of the “response phase” revealed that key nodes of the inhibitory circuit, underpinning inhibition of the overt movement during the NoGo response, were also activated during the MI enactment. In both cases, inhibition relied on the activation of pre-SMA and rIFG, but with different temporal patterns of activation in accord with the intended “covert” or “overt” modality of motor performance. During the NoGo condition, the pre-SMA and rIFG were sequentially activated, pointing to an early decisional role of pre-SMA and to a later role of rIFG in the enactment of inhibitory control of the overt action. Conversely, a concomitant activation of pre-SMA and rIFG emerged during the imagined motor response. This latter finding suggested that an inhibitory mechanism (likely underpinned by the rIFG), could be prewired into a prepared “covert modality” of motor response, as an intrinsic component of the MI enactment. This mechanism would allow the rehearsal of the imagined motor representations, without any overt movement. The analyses of the “preparatory phase”, confirmed in both overt and covert Go/NoGo tasks the priming of cerebral regions pertaining to putative inhibitory network, reactively triggered in the following response phase. Nonetheless, differences in the preparatory strategies between the two tasks emerged, depending on the intended “overt” or “covert” modality of the possible incoming motor response. During the preparation of the overt Go/NoGo task, the cue primed the possible overt response programs in motor and premotor cortex. At the same time, through preactivation of a pre-SMA-related decisional mechanism, it triggered a parallel preparation for the successful response selection and/or inhibition during the subsequent response phase. Conversely, the preparatory strategy for the covert Go/NoGo task was centred on the goal-oriented priming of an inhibitory mechanism related to the rIFG that, being tuned to the instructed covert modality of the motor performance and instantiated during the subsequent MI enactment, allowed the imagined response to remain a potential motor act. Taken together, the results of the present study demonstrate a substantial overlap of cerebral networks activated during proactive recruitment and subsequent reactive enactment of motor inhibition in both overt and covert actions. At the same time, our data show that preparatory cues predisposed ab initio a different organization of the cerebral areas (in particular of the pre-SMA and rIFG) involved with sensorimotor transformations and motor inhibitory control for executed and imagined actions. During the preparatory phases of our cued overt and covert Go/NoGo tasks, the different adopted strategies were tuned to the “how” of the motor performance, reflecting the intended overt and covert modality of the possible incoming action.

Contribution à la validation du modèle cognitif du trouble obsessionnel- compulsif : le rôle des expériences de l’enfance et des états affectifs

Depuis une vingtaine d’années, le modèle cognitif basé sur les interprétations (Groupe de recherche sur la cognition dans le trouble obsessionnel compulsif [OCCWG], 1997, 2001, 2003, 2005) représente le modèle psychologique de l’étiologie et du maintien du TOC le plus étudié au plan empirique. Cependant, peu de recherches ont porté sur les deux postulats importants du modèle touchant respectivement le développement des croyances liées à l’obsessionnalité et la contribution des états affectifs au maintien des interprétations et des croyances (réactivité cognitive). L’objectif de cette thèse est de contribuer à la validation empirique de ces postulats. Fondé sur un devis corrélationnel dans un échantillon de participants mixte (participants troubles obsessionnels-compulsifs et participants non cliniques), le premier article étudie les liens entre les expériences de l’enfance et la présence de croyances obsessionnelles chez l’adulte. Deux modèles alternatifs sont comparés qui représentent d’une part un lien spécifique, et d’autre part un lien non spécifique entre les expériences de l’enfance et les croyances obsessionnelles adultes. Les résultats suggèrent la présence à la fois de relations spécifiques et non spécifiques entre les expériences de l’enfance et les croyances adultes. Les expériences de l’enfance et les domaines de croyance obsessionnels qui montrent des liens spécifiques sont ceux relatifs à la responsabilité, à la perception du danger, et au perfectionnisme. En contrepartie, les expériences de l’enfance relatives à la perception de danger et dans une moindre mesure la sociotropie, apparaissent étroitement liés à la plupart des domaines de croyances adultes (intolérance à l’incertitude, surestimation du danger, importance et contrôle des pensées). Dans la seconde étude, nous nous intéressons à la mesure et l’analyse longitudinales de la réactivité cognitive telle qu’elle s’exprime dans l’environnement naturel de huit participants troubles obsessionnels-compulsifs de type ruminateur. Par le biais de huit protocoles à cas uniques intensifs, l’analyse de contingence entre les scores quotidiens d’humeur (4 états émotionnels cotés par participant) et d’interprétations (une interprétation idiographique des intrusions par participant) permet d’établir une mesure de l’importance de la réactivité cognitive chez chaque participant. Ces résultats sont ensuite analysés du point de vue des postulats principaux de deux modèles spécifiques de la réactivité cognitive (modèle de l’Infusion de l’affect [Forgas, 2008] et modèle de l’Humeur comme intrant [Meeten & Davey, 2011]. Ainsi, les analyses intra-individuelles répétées trans-comportements) et interindividuelles (trans-participants) permettent d’illustrer le rôle proximal déterminant des stratégies de traitement de l’information (traitement systématique; traitement superficiel; traitement altéré) employées par les participants. En résumé, les résultats obtenus dans ces deux études fournissent des données utiles à la poursuite de la validation du modèle des interprétations du TOC. Dans la première étude, l’identification de liens spécifiques entre les EE et les croyances obsessionnelles soutient la séquence étiologique postulée, alors que l’identification de liens non spécifiques suggère que d’autres trajectoires étiologiques peuvent être pertinentes. Dans la seconde étude, l’analyse longitudinale et naturaliste des covariations humeur – interprétations se révèle d’abord féconde à identifier les phénomènes de réactivité cognitive postulés dans le modèle des interprétations. Ensuite, en conformité aux modèles intégrés de la réactivité cognitive, l’analyse des liens entre cette réactivité et les stratégies privilégiées de neutralisation des participants permet d’identifier le rôle clé des différentes stratégies de traitement de l’information dans la réactivité cognitive.

Worry activation impairs intelligence test performace only under ego depletion

Detrimental effects of anxiety on cognitive performance have been explained by the activation of worry, detracting attention away from the task at hand. However, recent research has shown that anxiety is only related to performance when self-control capacity is low (i.e., ego depletion). The aim of the present work has been to extend these findings by showing that activation of worry will interfere with cognitive performance more strongly when self-control capacity is momentarily depleted compared to intact. After manipulations of self-control capacity and worry activation, 70 undergraduates completed a standardized intelligence test. As expected, activation of worry was associated with lower performance when self-control capacity was depleted, but had no effect when self-control capacity was intact. The findings implicate that worry may play a causal role in the anxiety–performance relationship, but only when its regulation by self-control is momentarily hindered.

Contribution à la validation du modèle cognitif du trouble obsessionnel- compulsif : le rôle des expériences de l’enfance et des états affectifs

Depuis une vingtaine d’années, le modèle cognitif basé sur les interprétations (Groupe de recherche sur la cognition dans le trouble obsessionnel compulsif [OCCWG], 1997, 2001, 2003, 2005) représente le modèle psychologique de l’étiologie et du maintien du TOC le plus étudié au plan empirique. Cependant, peu de recherches ont porté sur les deux postulats importants du modèle touchant respectivement le développement des croyances liées à l’obsessionnalité et la contribution des états affectifs au maintien des interprétations et des croyances (réactivité cognitive). L’objectif de cette thèse est de contribuer à la validation empirique de ces postulats. Fondé sur un devis corrélationnel dans un échantillon de participants mixte (participants troubles obsessionnels-compulsifs et participants non cliniques), le premier article étudie les liens entre les expériences de l’enfance et la présence de croyances obsessionnelles chez l’adulte. Deux modèles alternatifs sont comparés qui représentent d’une part un lien spécifique, et d’autre part un lien non spécifique entre les expériences de l’enfance et les croyances obsessionnelles adultes. Les résultats suggèrent la présence à la fois de relations spécifiques et non spécifiques entre les expériences de l’enfance et les croyances adultes. Les expériences de l’enfance et les domaines de croyance obsessionnels qui montrent des liens spécifiques sont ceux relatifs à la responsabilité, à la perception du danger, et au perfectionnisme. En contrepartie, les expériences de l’enfance relatives à la perception de danger et dans une moindre mesure la sociotropie, apparaissent étroitement liés à la plupart des domaines de croyances adultes (intolérance à l’incertitude, surestimation du danger, importance et contrôle des pensées). Dans la seconde étude, nous nous intéressons à la mesure et l’analyse longitudinales de la réactivité cognitive telle qu’elle s’exprime dans l’environnement naturel de huit participants troubles obsessionnels-compulsifs de type ruminateur. Par le biais de huit protocoles à cas uniques intensifs, l’analyse de contingence entre les scores quotidiens d’humeur (4 états émotionnels cotés par participant) et d’interprétations (une interprétation idiographique des intrusions par participant) permet d’établir une mesure de l’importance de la réactivité cognitive chez chaque participant. Ces résultats sont ensuite analysés du point de vue des postulats principaux de deux modèles spécifiques de la réactivité cognitive (modèle de l’Infusion de l’affect [Forgas, 2008] et modèle de l’Humeur comme intrant [Meeten & Davey, 2011]. Ainsi, les analyses intra-individuelles répétées trans-comportements) et interindividuelles (trans-participants) permettent d’illustrer le rôle proximal déterminant des stratégies de traitement de l’information (traitement systématique; traitement superficiel; traitement altéré) employées par les participants. En résumé, les résultats obtenus dans ces deux études fournissent des données utiles à la poursuite de la validation du modèle des interprétations du TOC. Dans la première étude, l’identification de liens spécifiques entre les EE et les croyances obsessionnelles soutient la séquence étiologique postulée, alors que l’identification de liens non spécifiques suggère que d’autres trajectoires étiologiques peuvent être pertinentes. Dans la seconde étude, l’analyse longitudinale et naturaliste des covariations humeur – interprétations se révèle d’abord féconde à identifier les phénomènes de réactivité cognitive postulés dans le modèle des interprétations. Ensuite, en conformité aux modèles intégrés de la réactivité cognitive, l’analyse des liens entre cette réactivité et les stratégies privilégiées de neutralisation des participants permet d’identifier le rôle clé des différentes stratégies de traitement de l’information dans la réactivité cognitive.

Slow deterministic vector rogue waves

For an erbium-doped fiber laser mode-locked by carbon nanotubes, we demonstrate experimentally and theoretically a new type of the vector rogue waves emerging as a result of the chaotic evolution of the trajectories between two orthogonal states of polarization on the Poincare sphere. In terms of fluctuation induced phenomena, by tuning polarization controller for the pump wave and in-cavity polarization controller, we are able to control the Kramers time, i.e. the residence time of the trajectory in vicinity of each orthogonal state of polarization, and so can cause the rare events satisfying rogue wave criteria and having the form of transitions from the state with the long residence time to the state with a short residence time.

Advanced Techniques for Image Quality Assessment of Modern X-ray Computed Tomography Systems

X-ray computed tomography (CT) imaging constitutes one of the most widely used diagnostic tools in radiology today with nearly 85 million CT examinations performed in the U.S in 2011. CT imparts a relatively high amount of radiation dose to the patient compared to other x-ray imaging modalities and as a result of this fact, coupled with its popularity, CT is currently the single largest source of medical radiation exposure to the U.S. population. For this reason, there is a critical need to optimize CT examinations such that the dose is minimized while the quality of the CT images is not degraded. This optimization can be difficult to achieve due to the relationship between dose and image quality. All things being held equal, reducing the dose degrades image quality and can impact the diagnostic value of the CT examination.

A recent push from the medical and scientific community towards using lower doses has spawned new dose reduction technologies such as automatic exposure control (i.e., tube current modulation) and iterative reconstruction algorithms. In theory, these technologies could allow for scanning at reduced doses while maintaining the image quality of the exam at an acceptable level. Therefore, there is a scientific need to establish the dose reduction potential of these new technologies in an objective and rigorous manner. Establishing these dose reduction potentials requires precise and clinically relevant metrics of CT image quality, as well as practical and efficient methodologies to measure such metrics on real CT systems. The currently established methodologies for assessing CT image quality are not appropriate to assess modern CT scanners that have implemented those aforementioned dose reduction technologies.

Thus the purpose of this doctoral project was to develop, assess, and implement new phantoms, image quality metrics, analysis techniques, and modeling tools that are appropriate for image quality assessment of modern clinical CT systems. The project developed image quality assessment methods in the context of three distinct paradigms, (a) uniform phantoms, (b) textured phantoms, and (c) clinical images.

The work in this dissertation used the “task-based” definition of image quality. That is, image quality was broadly defined as the effectiveness by which an image can be used for its intended task. Under this definition, any assessment of image quality requires three components: (1) A well defined imaging task (e.g., detection of subtle lesions), (2) an “observer” to perform the task (e.g., a radiologists or a detection algorithm), and (3) a way to measure the observer’s performance in completing the task at hand (e.g., detection sensitivity/specificity).

First, this task-based image quality paradigm was implemented using a novel multi-sized phantom platform (with uniform background) developed specifically to assess modern CT systems (Mercury Phantom, v3.0, Duke University). A comprehensive evaluation was performed on a state-of-the-art CT system (SOMATOM Definition Force, Siemens Healthcare) in terms of noise, resolution, and detectability as a function of patient size, dose, tube energy (i.e., kVp), automatic exposure control, and reconstruction algorithm (i.e., Filtered Back-Projection– FPB vs Advanced Modeled Iterative Reconstruction– ADMIRE). A mathematical observer model (i.e., computer detection algorithm) was implemented and used as the basis of image quality comparisons. It was found that image quality increased with increasing dose and decreasing phantom size. The CT system exhibited nonlinear noise and resolution properties, especially at very low-doses, large phantom sizes, and for low-contrast objects. Objective image quality metrics generally increased with increasing dose and ADMIRE strength, and with decreasing phantom size. The ADMIRE algorithm could offer comparable image quality at reduced doses or improved image quality at the same dose (increase in detectability index by up to 163% depending on iterative strength). The use of automatic exposure control resulted in more consistent image quality with changing phantom size.

Based on those results, the dose reduction potential of ADMIRE was further assessed specifically for the task of detecting small (<=6 mm) low-contrast (<=20 HU) lesions. A new low-contrast detectability phantom (with uniform background) was designed and fabricated using a multi-material 3D printer. The phantom was imaged at multiple dose levels and images were reconstructed with FBP and ADMIRE. Human perception experiments were performed to measure the detection accuracy from FBP and ADMIRE images. It was found that ADMIRE had equivalent performance to FBP at 56% less dose.

Using the same image data as the previous study, a number of different mathematical observer models were implemented to assess which models would result in image quality metrics that best correlated with human detection performance. The models included naïve simple metrics of image quality such as contrast-to-noise ratio (CNR) and more sophisticated observer models such as the non-prewhitening matched filter observer model family and the channelized Hotelling observer model family. It was found that non-prewhitening matched filter observers and the channelized Hotelling observers both correlated strongly with human performance. Conversely, CNR was found to not correlate strongly with human performance, especially when comparing different reconstruction algorithms.

The uniform background phantoms used in the previous studies provided a good first-order approximation of image quality. However, due to their simplicity and due to the complexity of iterative reconstruction algorithms, it is possible that such phantoms are not fully adequate to assess the clinical impact of iterative algorithms because patient images obviously do not have smooth uniform backgrounds. To test this hypothesis, two textured phantoms (classified as gross texture and fine texture) and a uniform phantom of similar size were built and imaged on a SOMATOM Flash scanner (Siemens Healthcare). Images were reconstructed using FBP and a Sinogram Affirmed Iterative Reconstruction (SAFIRE). Using an image subtraction technique, quantum noise was measured in all images of each phantom. It was found that in FBP, the noise was independent of the background (textured vs uniform). However, for SAFIRE, noise increased by up to 44% in the textured phantoms compared to the uniform phantom. As a result, the noise reduction from SAFIRE was found to be up to 66% in the uniform phantom but as low as 29% in the textured phantoms. Based on this result, it clear that further investigation was needed into to understand the impact that background texture has on image quality when iterative reconstruction algorithms are used.

To further investigate this phenomenon with more realistic textures, two anthropomorphic textured phantoms were designed to mimic lung vasculature and fatty soft tissue texture. The phantoms (along with a corresponding uniform phantom) were fabricated with a multi-material 3D printer and imaged on the SOMATOM Flash scanner. Scans were repeated a total of 50 times in order to get ensemble statistics of the noise. A novel method of estimating the noise power spectrum (NPS) from irregularly shaped ROIs was developed. It was found that SAFIRE images had highly locally non-stationary noise patterns with pixels near edges having higher noise than pixels in more uniform regions. Compared to FBP, SAFIRE images had 60% less noise on average in uniform regions for edge pixels, noise was between 20% higher and 40% lower. The noise texture (i.e., NPS) was also highly dependent on the background texture for SAFIRE. Therefore, it was concluded that quantum noise properties in the uniform phantoms are not representative of those in patients for iterative reconstruction algorithms and texture should be considered when assessing image quality of iterative algorithms.

The move beyond just assessing noise properties in textured phantoms towards assessing detectability, a series of new phantoms were designed specifically to measure low-contrast detectability in the presence of background texture. The textures used were optimized to match the texture in the liver regions actual patient CT images using a genetic algorithm. The so called “Clustured Lumpy Background” texture synthesis framework was used to generate the modeled texture. Three textured phantoms and a corresponding uniform phantom were fabricated with a multi-material 3D printer and imaged on the SOMATOM Flash scanner. Images were reconstructed with FBP and SAFIRE and analyzed using a multi-slice channelized Hotelling observer to measure detectability and the dose reduction potential of SAFIRE based on the uniform and textured phantoms. It was found that at the same dose, the improvement in detectability from SAFIRE (compared to FBP) was higher when measured in a uniform phantom compared to textured phantoms.

The final trajectory of this project aimed at developing methods to mathematically model lesions, as a means to help assess image quality directly from patient images. The mathematical modeling framework is first presented. The models describe a lesion’s morphology in terms of size, shape, contrast, and edge profile as an analytical equation. The models can be voxelized and inserted into patient images to create so-called “hybrid” images. These hybrid images can then be used to assess detectability or estimability with the advantage that the ground truth of the lesion morphology and location is known exactly. Based on this framework, a series of liver lesions, lung nodules, and kidney stones were modeled based on images of real lesions. The lesion models were virtually inserted into patient images to create a database of hybrid images to go along with the original database of real lesion images. ROI images from each database were assessed by radiologists in a blinded fashion to determine the realism of the hybrid images. It was found that the radiologists could not readily distinguish between real and virtual lesion images (area under the ROC curve was 0.55). This study provided evidence that the proposed mathematical lesion modeling framework could produce reasonably realistic lesion images.

Based on that result, two studies were conducted which demonstrated the utility of the lesion models. The first study used the modeling framework as a measurement tool to determine how dose and reconstruction algorithm affected the quantitative analysis of liver lesions, lung nodules, and renal stones in terms of their size, shape, attenuation, edge profile, and texture features. The same database of real lesion images used in the previous study was used for this study. That database contained images of the same patient at 2 dose levels (50% and 100%) along with 3 reconstruction algorithms from a GE 750HD CT system (GE Healthcare). The algorithms in question were FBP, Adaptive Statistical Iterative Reconstruction (ASiR), and Model-Based Iterative Reconstruction (MBIR). A total of 23 quantitative features were extracted from the lesions under each condition. It was found that both dose and reconstruction algorithm had a statistically significant effect on the feature measurements. In particular, radiation dose affected five, three, and four of the 23 features (related to lesion size, conspicuity, and pixel-value distribution) for liver lesions, lung nodules, and renal stones, respectively. MBIR significantly affected 9, 11, and 15 of the 23 features (including size, attenuation, and texture features) for liver lesions, lung nodules, and renal stones, respectively. Lesion texture was not significantly affected by radiation dose.

The second study demonstrating the utility of the lesion modeling framework focused on assessing detectability of very low-contrast liver lesions in abdominal imaging. Specifically, detectability was assessed as a function of dose and reconstruction algorithm. As part of a parallel clinical trial, images from 21 patients were collected at 6 dose levels per patient on a SOMATOM Flash scanner. Subtle liver lesion models (contrast = -15 HU) were inserted into the raw projection data from the patient scans. The projections were then reconstructed with FBP and SAFIRE (strength 5). Also, lesion-less images were reconstructed. Noise, contrast, CNR, and detectability index of an observer model (non-prewhitening matched filter) were assessed. It was found that SAFIRE reduced noise by 52%, reduced contrast by 12%, increased CNR by 87%. and increased detectability index by 65% compared to FBP. Further, a 2AFC human perception experiment was performed to assess the dose reduction potential of SAFIRE, which was found to be 22% compared to the standard of care dose.

In conclusion, this dissertation provides to the scientific community a series of new methodologies, phantoms, analysis techniques, and modeling tools that can be used to rigorously assess image quality from modern CT systems. Specifically, methods to properly evaluate iterative reconstruction have been developed and are expected to aid in the safe clinical implementation of dose reduction technologies.

Nitrate metabolism in the dinoflagellate Lingulodinium polyedrum

Les dinoflagellés sont des eucaryotes unicellulaires retrouvés dans la plupart des écosystèmes aquatiques du globe. Ces organismes amènent une contribution substantielle à la production primaire des océans, soit en tant que membre du phytoplancton, soit en tant que symbiontes des anthozoaires formant les récifs coralliens. Malheureusement, ce rôle écologique majeur est souvent négligé face à la capacité de certaines espèces de dinoflagellés à former des fleurs d'eau, parfois d'étendue et de durée spectaculaires. Ces floraisons d'algues, communément appelées "marées rouges", peuvent avoir de graves conséquences sur les écosystèmes côtiers, sur les industries de la pêche et du tourisme, ainsi que sur la santé humaine. Un des facteurs souvent corrélé avec la formation des fleurs d'eau est une augmentation dans la concentration de nutriments, notamment l’azote et le phosphore. Le nitrate est un des composants principaux retrouvés dans les eaux de ruissellement agricoles, mais également la forme d'azote bioaccessible la plus abondante dans les écosystèmes marins. Ainsi, l'agriculture humaine a contribué à magnifier significativement les problèmes associés aux marées rouges au niveau mondial. Cependant, la pollution ne peut pas expliquer à elle seule la formation et la persistance des fleurs d'eau, qui impliquent plusieurs facteurs biotiques et abiotiques. Il est particulièrement difficile d'évaluer l'importance relative qu'ont les ajouts de nitrate par rapport à ces autres facteurs, parce que le métabolisme du nitrate chez les dinoflagellés est largement méconnu. Le but principal de cette thèse vise à remédier à cette lacune. J'ai choisi Lingulodinium polyedrum comme modèle pour l'étude du métabolisme du nitrate, parce que ce dinoflagellé est facilement cultivable en laboratoire et qu'une étude transcriptomique a récemment fourni une liste de gènes pratiquement complète pour cette espèce. Il est également intéressant que certaines composantes moléculaires de la voie du nitrate chez cet organisme soient sous contrôle circadien. Ainsi, dans ce projet, j'ai utilisé des analyses physiologiques, biochimiques, transcriptomiques et bioinformatiques pour enrichir nos connaissances sur le métabolisme du nitrate des dinoflagellés et nous permettre de mieux apprécier le rôle de l'horloge circadienne dans la régulation de cette importante voie métabolique primaire. Je me suis tout d'abord penché sur les cas particuliers où des floraisons de dinoflagellés sont observées dans des conditions de carence en azote. Cette idée peut sembler contreintuitive, parce que l'ajout de nitrate plutôt que son épuisement dans le milieu est généralement associé aux floraisons d'algues. Cependant, j’ai découvert que lorsque du nitrate était ajouté à des cultures initialement carencées ou enrichies en azote, celles qui s'étaient acclimatées au stress d'azote arrivaient à survivre près de deux mois à haute densité cellulaire, alors que les cellules qui n'étaient pas acclimatées mourraient après deux semaines. En condition de carence d'azote sévère, les cellules arrivaient à survivre un peu plus de deux semaines et ce, en arrêtant leur cycle cellulaire et en diminuant leur activité photosynthétique. L’incapacité pour ces cellules carencées à synthétiser de nouveaux acides aminés dans un contexte où la photosynthèse était toujours active a mené à l’accumulation de carbone réduit sous forme de granules d’amidon et corps lipidiques. Curieusement, ces deux réserves de carbone se trouvaient à des pôles opposés de la cellule, suggérant un rôle fonctionnel à cette polarisation. La deuxième contribution de ma thèse fut d’identifier et de caractériser les premiers transporteurs de nitrate chez les dinoflagellés. J'ai découvert que Lingulodinium ne possédait que très peu de transporteurs comparativement à ce qui est observé chez les plantes et j'ai suggéré que seuls les membres de la famille des transporteurs de nitrate de haute affinité 2 (NRT2) étaient réellement impliqués dans le transport du nitrate. Le principal transporteur chez Lingulodinium était exprimé constitutivement, suggérant que l’acquisition du nitrate chez ce dinoflagellé se fondait majoritairement sur un système constitutif plutôt qu’inductible. Enfin, j'ai démontré que l'acquisition du nitrate chez Lingulodinium était régulée par la lumière et non par l'horloge circadienne, tel qu'il avait été proposé dans une étude antérieure. Finalement, j’ai utilisé une approche RNA-seq pour vérifier si certains transcrits de composantes impliquées dans le métabolisme du nitrate de Lingulodinium étaient sous contrôle circadien. Non seulement ai-je découvert qu’il n’y avait aucune variation journalière dans les niveaux des transcrits impliqués dans le métabolisme du nitrate, j’ai aussi constaté qu’il n’y avait aucune variation journalière pour n’importe quel ARN du transcriptome de Lingulodinium. Cette découverte a démontré que l’horloge de ce dinoflagellé n'avait pas besoin de transcription rythmique pour générer des rythmes physiologiques comme observé chez les autres eukaryotes.

Image-Guided Precision Manipulation of Cells and Nanoparticles in Microfluidics

Manipulation of single cells and particles is important to biology and nanotechnology. Our electrokinetic (EK) tweezers manipulate objects in simple microfluidic devices using gentle fluid and electric forces under vision-based feedback control. In this dissertation, I detail a user-friendly implementation of EK tweezers that allows users to select, position, and assemble cells and nanoparticles. This EK system was used to measure attachment forces between living breast cancer cells, trap single quantum dots with 45 nm accuracy, build nanophotonic circuits, and scan optical properties of nanowires. With a novel multi-layer microfluidic device, EK was also used to guide single microspheres along complex 3D trajectories. The schemes, software, and methods developed here can be used in many settings to precisely manipulate most visible objects, assemble objects into useful structures, and improve the function of lab-on-a-chip microfluidic systems.

Reproducing Women: Female Bodily Narratives and English Patriarchies, 1600-1660

During the early Stuart period, England’s return to male monarchal rule resulted in the emergence of a political analogy that understood the authority of the monarch to be rooted in the “natural” authority of the father; consequently, the mother’s authoritative role within the family was repressed. As the literature of the period recognized, however, there would be no family unit for the father to lead without the words and bodies of women to make narratives of dynasty and legitimacy possible. Early modern discourse reveals that the reproductive roles of men and women, and the social hierarchies that grow out of them, are as much a matter of human design as of divine or natural law. Moreover, despite the attempts of James I and Charles I to strengthen royal patriarchal authority, the role of the monarch was repeatedly challenged on stage and in print even prior to the British Civil Wars and the 1649 beheading of Charles I. Texts produced at moments of political crisis reveal how women could uphold the legitimacy of familial and political hierarchies, but they also disclose patriarchy’s limits by representing “natural” male authority as depending in part on women’s discursive control over their bodies. Due to the epistemological instability of the female reproductive body, women play a privileged interpretive role in constructing patriarchal identities. The dearth of definitive knowledge about the female body during this period, and the consequent inability to fix or stabilize somatic meaning, led to the proliferation of differing, and frequently contradictory, depictions of women’s bodies. The female body became a site of contested meaning in early modern discourse, with men and women struggling for dominance, and competitors so diverse as to include kings, midwives, scholars of anatomy, and female religious sectarians. Essentially, this competition came down to a question of where to locate somatic meaning: In the opaque, uncertain bodies of women? In women’s equally uncertain and unreliable words? In the often contradictory claims of various male-authored medical treatises? In the whispered conversations that took place between women behind the closed doors of birthing rooms? My dissertation traces this representational instability through plays by William Shakespeare, John Ford, Thomas Middleton, and William Rowley, as well as in monstrous birth pamphlets, medical treatises, legal documents, histories, satires, and ballads. In these texts, the stories women tell about and through their bodies challenge and often supersede male epistemological control. These stories, which I term female bodily narratives, allow women to participate in defining patriarchal authority at the levels of both the family and the state. After laying out these controversies and instabilities surrounding early modern women’s bodies in my first chapter, my remaining chapters analyze the impact of women’s words on four distinct but overlapping reproductive issues: virginity, pregnancy, birthing room rituals, and paternity. In chapters 2 and 3, I reveal how women construct the inner, unseen “truths” of their reproductive bodies through speech and performance, and in doing so challenge the traditional forms of male authority that depend on these very constructions for coherence. Chapter 2 analyzes virginity in Thomas Middleton and William Rowley’s play The Changeling (1622) and in texts documenting the 1613 Essex divorce, during which Frances Howard, like Beatrice-Joanna in the play, was required to undergo a virginity test. These texts demonstrate that a woman’s ability to feign virginity could allow her to undermine patriarchal authority within the family and the state, even as they reveal how men relied on women to represent their reproductive bodies in socially stabilizing ways. During the British Civil Wars and Interregnum (1642-1660), Parliamentary writers used Howard as an example of how the unruly words and bodies of women could disrupt and transform state politics by influencing court faction; in doing so, they also revealed how female bodily narratives could help recast political historiography. In chapter 3, I investigate depictions of pregnancy in John Ford’s tragedy, ‘Tis Pity She’s a Whore (1633) and in early modern medical treatises from 1604 to 1651. Although medical texts claim to convey definitive knowledge about the female reproductive body, in actuality male knowledge frequently hinged on the ways women chose to interpret the unstable physical indicators of pregnancy. In Ford’s play, Annabella and Putana take advantage of male ignorance in order to conceal Annabella’s incestuous, illegitimate pregnancy from her father and husband, thus raising fears about women’s ability to misrepresent their bodies. Since medical treatises often frame the conception of healthy, legitimate offspring as a matter of national importance, women’s ability to conceal or even terminate their pregnancies could weaken both the patriarchal family and the patriarchal state that the family helped found. Chapters 4 and 5 broaden the socio-political ramifications of women’s words and bodies by demonstrating how female bodily narratives are required to establish paternity and legitimacy, and thus help shape patriarchal authority at multiple social levels. In chapter 4, I study representations of birthing room gossip in Thomas Middleton’s play, A Chaste Maid in Cheapside (1613), and in three Mistris Parliament pamphlets (1648) that satirize parliamentary power. Across these texts, women’s birthing room “gossip” comments on and critiques such issues as men’s behavior towards their wives and children, the proper use of household funds, the finer points of religious ritual, and even the limits of the authority of the monarch. The collective speech of the female-dominated birthing room thus proves central not only to attributing paternity to particular men, but also to the consequent definition and establishment of the political, socio-economic, and domestic roles of patriarchy. Chapter 5 examines anxieties about paternity in William Shakespeare’s The Winter’s Tale (1611) and in early modern monstrous birth pamphlets from 1600 to 1647, in which children born with congenital deformities are explained as God’s punishment for the sexual, religious, and/or political transgressions of their parents or communities. Both the play and the pamphlets explore the formative/deformative power of women’s words and bodies over their offspring, a power that could obscure a father’s connection to his children. However, although the pamphlets attempt to contain and discipline women’s unruly words and bodies with the force of male authority, the play reveals the dangers of male tyranny and the crucial role of maternal authority in reproducing and authenticating dynastic continuity and royal legitimacy. My emphasis on the socio-political impact of women’s self-representation distinguishes my work from that of scholars such as Mary Fissell and Julie Crawford, who claim that early modern beliefs about the female reproductive body influenced textual depictions of major religious and political events, but give little sustained attention to the role female speech plays in these representations. In contrast, my dissertation reveals that in such texts, patriarchal society relies precisely on the words women speak about their own and other women’s bodies. Ultimately, I argue that female bodily narratives were crucial in shaping early modern culture, and they are equally crucial to our critical understanding of sexual and state politics in the literature of the period.

Nitrate metabolism in the dinoflagellate Lingulodinium polyedrum

Les dinoflagellés sont des eucaryotes unicellulaires retrouvés dans la plupart des écosystèmes aquatiques du globe. Ces organismes amènent une contribution substantielle à la production primaire des océans, soit en tant que membre du phytoplancton, soit en tant que symbiontes des anthozoaires formant les récifs coralliens. Malheureusement, ce rôle écologique majeur est souvent négligé face à la capacité de certaines espèces de dinoflagellés à former des fleurs d'eau, parfois d'étendue et de durée spectaculaires. Ces floraisons d'algues, communément appelées "marées rouges", peuvent avoir de graves conséquences sur les écosystèmes côtiers, sur les industries de la pêche et du tourisme, ainsi que sur la santé humaine. Un des facteurs souvent corrélé avec la formation des fleurs d'eau est une augmentation dans la concentration de nutriments, notamment l’azote et le phosphore. Le nitrate est un des composants principaux retrouvés dans les eaux de ruissellement agricoles, mais également la forme d'azote bioaccessible la plus abondante dans les écosystèmes marins. Ainsi, l'agriculture humaine a contribué à magnifier significativement les problèmes associés aux marées rouges au niveau mondial. Cependant, la pollution ne peut pas expliquer à elle seule la formation et la persistance des fleurs d'eau, qui impliquent plusieurs facteurs biotiques et abiotiques. Il est particulièrement difficile d'évaluer l'importance relative qu'ont les ajouts de nitrate par rapport à ces autres facteurs, parce que le métabolisme du nitrate chez les dinoflagellés est largement méconnu. Le but principal de cette thèse vise à remédier à cette lacune. J'ai choisi Lingulodinium polyedrum comme modèle pour l'étude du métabolisme du nitrate, parce que ce dinoflagellé est facilement cultivable en laboratoire et qu'une étude transcriptomique a récemment fourni une liste de gènes pratiquement complète pour cette espèce. Il est également intéressant que certaines composantes moléculaires de la voie du nitrate chez cet organisme soient sous contrôle circadien. Ainsi, dans ce projet, j'ai utilisé des analyses physiologiques, biochimiques, transcriptomiques et bioinformatiques pour enrichir nos connaissances sur le métabolisme du nitrate des dinoflagellés et nous permettre de mieux apprécier le rôle de l'horloge circadienne dans la régulation de cette importante voie métabolique primaire. Je me suis tout d'abord penché sur les cas particuliers où des floraisons de dinoflagellés sont observées dans des conditions de carence en azote. Cette idée peut sembler contreintuitive, parce que l'ajout de nitrate plutôt que son épuisement dans le milieu est généralement associé aux floraisons d'algues. Cependant, j’ai découvert que lorsque du nitrate était ajouté à des cultures initialement carencées ou enrichies en azote, celles qui s'étaient acclimatées au stress d'azote arrivaient à survivre près de deux mois à haute densité cellulaire, alors que les cellules qui n'étaient pas acclimatées mourraient après deux semaines. En condition de carence d'azote sévère, les cellules arrivaient à survivre un peu plus de deux semaines et ce, en arrêtant leur cycle cellulaire et en diminuant leur activité photosynthétique. L’incapacité pour ces cellules carencées à synthétiser de nouveaux acides aminés dans un contexte où la photosynthèse était toujours active a mené à l’accumulation de carbone réduit sous forme de granules d’amidon et corps lipidiques. Curieusement, ces deux réserves de carbone se trouvaient à des pôles opposés de la cellule, suggérant un rôle fonctionnel à cette polarisation. La deuxième contribution de ma thèse fut d’identifier et de caractériser les premiers transporteurs de nitrate chez les dinoflagellés. J'ai découvert que Lingulodinium ne possédait que très peu de transporteurs comparativement à ce qui est observé chez les plantes et j'ai suggéré que seuls les membres de la famille des transporteurs de nitrate de haute affinité 2 (NRT2) étaient réellement impliqués dans le transport du nitrate. Le principal transporteur chez Lingulodinium était exprimé constitutivement, suggérant que l’acquisition du nitrate chez ce dinoflagellé se fondait majoritairement sur un système constitutif plutôt qu’inductible. Enfin, j'ai démontré que l'acquisition du nitrate chez Lingulodinium était régulée par la lumière et non par l'horloge circadienne, tel qu'il avait été proposé dans une étude antérieure. Finalement, j’ai utilisé une approche RNA-seq pour vérifier si certains transcrits de composantes impliquées dans le métabolisme du nitrate de Lingulodinium étaient sous contrôle circadien. Non seulement ai-je découvert qu’il n’y avait aucune variation journalière dans les niveaux des transcrits impliqués dans le métabolisme du nitrate, j’ai aussi constaté qu’il n’y avait aucune variation journalière pour n’importe quel ARN du transcriptome de Lingulodinium. Cette découverte a démontré que l’horloge de ce dinoflagellé n'avait pas besoin de transcription rythmique pour générer des rythmes physiologiques comme observé chez les autres eukaryotes.

Exercicis d’Estadística Aplicada a l’Administració Pública

Aquest material és un complement al quadern Estadística Aplicada a l’Administració Pública de la col·lecció Joan Fuster de materials docents en valencià, en el qual es desenvolupaven els continguts de l’assignatura Estadística Aplicada a l’Administració Pública del segon curs del grau de Gestió i Administració Pública de la Universitat d’Alacant. L’objectiu d’aquest quadern és tenir un material que reforce els coneixements adquirits de l’assignatura a classe i que l’alumnat els puga posar en pràctica de forma autònoma amb la resolució dels exercicis.

La transformación de la política antidrogas de Estados Unidos y su incidencia en la cooperación colombo-estadounidense en la lucha contra las drogas (2010-2014).

Con la llegada del demócrata Barack Obama a la presidencia de Estados Unidos, se inició un proceso de transformación de la política antidrogas estadounidense, lo cual, impactó en el ámbito doméstico y exterior, en ése último, especialmente en cuanto cooperación refiere. Considerando lo anterior, la investigación analiza cómo la transformación de la política antidrogas de Estados Unidos ha incidido en la cooperación colombo-estadounidense en materia de lucha contra las drogas. Para ello, se estudia la transformación del modelo estadounidense, se identifica la evolución de la cooperación contra el narcotráfico entre los dos Estados en el periodo 2009- 2014 y se examina la incidencia de la transformación de la política estadounidense antidrogas en la política antidrogas de Colombia.