Phosphonate and quinoxaline cavitands for molecular recognition and sensing

In the last decade, phosphonate and quinoxaline cavitand have been extensively studied, highlighting their outstanding recognition properties. Their successful applications in material science and sensing open the way to new potential applications, such as border security, environmental monitoring and chiral recognition. The present thesis explores the recognition properties of phosphonate and quinoxaline cavitands towards new targets, for molecular recognition and sensing applications. Chapter 2 highlights the enantioselective behavior of phosphonate cavitands towards chiral guests in the solid state and in solution. Phosphonate cavitands were exploited for the molecular recognition of L-lactic acid (chapter 3), a widespread natural molecule which offer multiple potential applications, and a human sweat marker used for the detection of human presence (chapter 4). The second part is devoted to sensing applications of quinoxaline cavitands. Chapter 5 describes the use of QxCav for the preconcentration of drugs precursors, while chapter 6 reports the design, synthesis and grafting of a rigidified EtQxBox on a silicon wafer.

Towards Closed-loop Deep Brain Stimulation: Behavior Recognition from Human STN

Deep brain stimulation (DBS) provides significant therapeutic benefit for movement disorders such as Parkinson’s disease (PD). Current DBS devices lack real-time feedback (thus are open loop) and stimulation parameters are adjusted during scheduled visits with a clinician. A closed-loop DBS system may reduce power consumption and side effects by adjusting stimulation parameters based on patient’s behavior. Thus behavior detection is a major step in designing such systems. Various physiological signals can be used to recognize the behaviors. Subthalamic Nucleus (STN) Local field Potential (LFP) is a great candidate signal for the neural feedback, because it can be recorded from the stimulation lead and does not require additional sensors. This thesis proposes novel detection and classification techniques for behavior recognition based on deep brain LFP. Behavior detection from such signals is the vital step in developing the next generation of closed-loop DBS devices. LFP recordings from 13 subjects are utilized in this study to design and evaluate our method. Recordings were performed during the surgery and the subjects were asked to perform various behavioral tasks. Various techniques are used understand how the behaviors modulate the STN. One method studies the time-frequency patterns in the STN LFP during the tasks. Another method measures the temporal inter-hemispheric connectivity of the STN as well as the connectivity between STN and Pre-frontal Cortex (PFC). Experimental results demonstrate that different behaviors create different m odulation patterns in STN and it’s connectivity. We use these patterns as features to classify behaviors. A method for single trial recognition of the patient’s current task is proposed. This method uses wavelet coefficients as features and support vector machine (SVM) as the classifier for recognition of a selection of behaviors: speech, motor, and random. The proposed method is 82.4% accurate for the binary classification and 73.2% for classifying three tasks. As the next step, a practical behavior detection method which asynchronously detects behaviors is proposed. This method does not use any priori knowledge of behavior onsets and is capable of asynchronously detect the finger movements of PD patients. Our study indicates that there is a motor-modulated inter-hemispheric connectivity between LFP signals recorded bilaterally from STN. We utilize a non-linear regression method to measure this inter-hemispheric connectivity and to detect the finger movements. Our experimental results using STN LFP recorded from eight patients with PD demonstrate this is a promising approach for behavior detection and developing novel closed-loop DBS systems.

3D Visual Data-Driven Spatiotemporal Deformations for Non-Rigid Object Grasping Using Robot Hands

Sensing techniques are important for solving problems of uncertainty inherent to intelligent grasping tasks. The main goal here is to present a visual sensing system based on range imaging technology for robot manipulation of non-rigid objects. Our proposal provides a suitable visual perception system of complex grasping tasks to support a robot controller when other sensor systems, such as tactile and force, are not able to obtain useful data relevant to the grasping manipulation task. In particular, a new visual approach based on RGBD data was implemented to help a robot controller carry out intelligent manipulation tasks with flexible objects. The proposed method supervises the interaction between the grasped object and the robot hand in order to avoid poor contact between the fingertips and an object when there is neither force nor pressure data. This new approach is also used to measure changes to the shape of an object’s surfaces and so allows us to find deformations caused by inappropriate pressure being applied by the hand’s fingers. Test was carried out for grasping tasks involving several flexible household objects with a multi-fingered robot hand working in real time. Our approach generates pulses from the deformation detection method and sends an event message to the robot controller when surface deformation is detected. In comparison with other methods, the obtained results reveal that our visual pipeline does not use deformations models of objects and materials, as well as the approach works well both planar and 3D household objects in real time. In addition, our method does not depend on the pose of the robot hand because the location of the reference system is computed from a recognition process of a pattern located place at the robot forearm. The presented experiments demonstrate that the proposed method accomplishes a good monitoring of grasping task with several objects and different grasping configurations in indoor environments.

Mollusca Non-Grata: The influence of top-down control and residence time on the abundance, distribution, and behavior of non-native marine snails in Washington State

Thesis (Ph.D.)--University of Washington, 2016-06

On being loud and proud: Non-conformity and counter-conformity to group norms

Most experiments on conformity have been conducted in relation to judgments of physical reality; surprisingly few papers have experimentally examined the influence of group norms on social issues with a moral component. In response to this, participants were told that they were either in a minority or in a majority relative to their university group in terms of their attitudes toward recognition of gay couples in law (Expt 1: N = 205) and a government apology to Aborigines (Expt 2: N = 110). In both experiments, it was found that participants who had a weak moral basis for their attitude conformed to the group norm on private behaviours. In contrast, those who had a strong moral basis for their attitude showed non-conformity on private behaviours and counter-conformity on public behaviours. Incidences of nonconformity and counter-conformity are discussed with reference to theory and research on normative influence.

Role of flanking sequences and phosphorylation in the recognition of the simian-virus-40 large T-antigen nuclear localization sequences by importin-a

The nuclear import of simian-virus-40 large T-antigen (tumour antigen) is enhanced via phosphorylation by the protein kinase CK2 at Ser(112) in the vicinity of the NLS (nuclear localization sequence). To determine the structural basis of the effect of the sequences flanking the basic cluster KKKRK, and the effect of phosphorylation on the recognition of the NLS by the nuclear import factor importin-alpha (Impalpha), we co-crystallized non-autoinhibited Impalpha with peptides corresponding to the phosphorylated and non-phosphorylated forms of the NLS, and determined the crystal structures of the complexes. The structures show that the amino acids N-terminally flanking the basic cluster make specific contacts with the receptor that are distinct from the interactions between bipartite NLSs and Impalpha. We confirm the important role of flanking sequences using binding assays. Unexpectedly, the regions of the peptides containing the phosphorylation site do not make specific contacts with the receptor. Binding assays confirm that phosphorylation does not increase the affinity of the T-antigen NLS to Impalpha. We conclude that the sequences flanking the basic clusters in NLSs play a crucial role in nuclear import by modulating the recognition of the NLS by Impalpha, whereas phosphorylation of the T-antigen enhances nuclear import by a mechanism that does not involve a direct interaction of the phosphorylated residue with Impalpha.

Responses to neighbours and non-neighbours in the buff-banded rail (Gallirallus philippensis): no dear-enemy relationships

Territorial individuals often respond less aggressively to intrusions by their neighbours than to intrusions by unfamiliar individuals. This commonly observed strategy, the dear-enemy phenomenon, is thought to minimise the costs associated with territory defence. This study determined whether an insular population of territory-holding buff-banded rails (Gallirallus philippensis) exhibits dear-enemy relationships and whether males and females differ in their responses to neighbours and non-neighbours. Playback techniques were used to examine and compare the vocalisations and movements of focal individuals in response to the territorial advertisement calls of their neighbours and of unfamiliar individuals (non-neighbours). Results showed that focal birds did not respond differently to the calls of neighbours and non-neighbours; thus, no evidence for the dear-enemy phenomenon was found in this species. We suggest that this result is due to the significant threats posed by neighbours to territory owners in this territorial system, in addition to a high level of territorial instability in the population. Males and females were shown to differ qualitatively in their general territorial response to intruders but not in their relative responses to neighbours and non-neighbours, suggesting that the relative threats posed by neighbours and non-neighbours do not differ between the sexes.

Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli

Translational pausing may occur due to a number of mechanisms, including the presence of non-optimal codons, and it is thought to play a role in the folding of specific polypeptide domains during translation and in the facilitation of signal peptide recognition during see-dependent protein targeting. In this whole genome analysis of Escherichia coli we have found that non-optimal codons in the signal peptide-encoding sequences of secretory genes are overrepresented relative to the mature portions of these genes; this is in addition to their overrepresentation in the 5'-regions of genes encoding non-secretory proteins. We also find increased non-optimal codon usage at the 3' ends of most E. coli genes, in both non-secretory and secretory sequences. Whereas presumptive translational pausing at the 5' and 3' ends of E. coli messenger RNAs may clearly have a general role in translation, we suggest that it also has a specific role in sec-dependent protein export, possibly in facilitating signal peptide recognition. This finding may have important implications for our understanding of how the majority of non-cytoplasmic proteins are targeted, a process that is essential to all biological cells. (C) 2004 Elsevier Inc. All rights reserved.

Electrochemical anion recognition with ferrocene functionalised macrocycles

The syntheses and characterization of two new redox active cyclam ligands ferrocenylmethyl-(6-methyl-1,4,8,11-tetraazacyclotetradec-6-yl)-amine(L-3) and 1, 1'-ferrocenylmethyl-bis(6-methyl-1,4,8,11-tetraazacyclotetradec-6-yl)-amine (L-4) are reported. The compounds each possess a ferrocenyl group bearing one (L-3) or two (L-4) appended macrocycles linked by their exocyclic amino groups and the crystal structures of both compounds have been determined. Anion binding of L-3 and L-4 was investigated by electrochemical titrations where H-bonding to each macrocycle causing a shift in the Fc(+/0) redox potential was used as a reporter of guest binding. The Zn-II complex of L-3 has also been isolated and characterized structurally. These compounds were analysed for their capacity to electrochemically recognize anions in both aqueous and non-aqueous solution. We have found that L-3, L-4 and [ZnL3-](2+) sense Cl- and AcO- anions in MeCN-CH2Cl2, a function that is lost in aqueous solution.

Experimental hand pain delays recognition of the contralateral hand: Evidence that acute and chronic pain have opposite effects on information processing?

Recognising the laterality of a pictured hand involves making an initial decision and confirming that choice by mentally moving one's own hand to match the picture. This depends on an intact body schema. Because patients with complex regional pain syndrome type 1 (CRPS1) take longer to recognise a hand's laterality when it corresponds to their affected hand, it has been proposed that nociceptive input disrupts the body schema. However, chronic pain is associated with physiological and psychosocial complexities that may also explain the results. In three studies, we investigated whether the effect is simply due to nociceptive input. Study one evaluated the temporal and perceptual characteristics of acute hand pain elicited by intramuscular injection of hypertonic saline into the thenar eminence. In studies two and three, subjects performed a hand laterality recognition task before, during, and after acute experimental hand pain, and experimental elbow pain, respectively. During hand pain and during elbow pain, when the laterality of the pictured hand corresponded to the painful side, there was no effect on response time (RT). That suggests that nociceptive input alone is not sufficient to disrupt the working body schema. Conversely to patients with CRPS1, when the laterality of the pictured hand corresponded to the non-painful hand, RT increased similar to 380 ms (95% confidence interval 190 ms-590 ms). The results highlight the differences between acute and chronic pain and may reflect a bias in information processing in acute pain toward the affected part.

Recognition and inactivation of LPS by lipophorin particles

Lipophorin is the major lipid carrier in insects, but various observations indicate that lipophorin is also involved in immune reactions. To examine a possible role of lipophorin in defence reactions, we mixed hemolymph plasma from Galleria mellonella with LPS and noticed that lipophorin forms detergent-insoluble aggregates, while most other plasma proteins are not affected. Lipophorin particles isolated by low-density gradient centrifugation retained LPS-induced aggregation properties, which suggested to us that these immune-reactive particles are able to recognise LPS and respond by forming insoluble aggregates. Antibodies against LPS-binding proteins, such as immulectin-2 and beta-1,3-glucan binding protein, cross-reacted with proteins associated with purified lipophorin particles. To examine whether LPS-mediated aggregates inactivate LPS, we added LPS-lipophorin mixtures to purified lipophorin particles and monitored aggregate formation. Under these conditions lipophorin did not form insoluble aggregates, which indicates that lipophorin particles sequester LPS into non-toxic aggregates. (c) 2005 Elsevier Ltd. All rights reserved.

Surveying sexualities: Internet research with non-heterosexuals

In this article we describe and evaluate the process of conducting online survey research about the legal recognition of same-sex relationships (key findings from which we have reported elsewhere, see Harding and Peel, 2006). Our aim in so doing is to contribute to the growing generic literature on internet-based research methods (Nosek et al., 2002; Rhodes et al., 2003; Stern, 2003; Strickland et al., 2003; Thomas et al., 2000) to the research methods literature within lesbian, gay, bisexual, trans and queer (LGBTQ) psychologies (Fish, 2000; Morris and Rothblum, 1999; Meezan and Martin, 2003; Mustanski, 2001) and also to extend the germinal literature focusing on internet research with non-heterosexual groups (Elford et al., 2004; Ellis et al., 2003; Ross et al., 2000). We begin by discussing the process of developing the online survey tool, before outlining the experience of the survey ‘going live’ and providing details of who completed the survey. We conclude by exploring some of the positives and pitfalls of this type of research methodology.

Inhibitory effects of persistent apoptotic cells on monoclonal antibody production in vitro:simple removal of non-viable cells improves antibody productivity by hybridoma cells in culture

Cells undergoing apoptosis in vivo are rapidly detected and cleared by phagocytes. Swift recognition and removal of apoptotic cells is important for normal tissue homeostasis and failure in the underlying clearance mechanisms has pathological consequences associated with inflammatory and auto-immune diseases. Cell cultures in vitro usually lack the capacity for removal of non-viable cells because of the absence of phagocytes and, as such, fail to emulate the healthy in vivo micro-environment from which dead cells are absent. While a key objective in cell culture is to maintain viability at maximal levels, cell death is unavoidable and non-viable cells frequently contaminate cultures in significant numbers. Here we show that the presence of apoptotic cells in monoclonal antibody-producing hybridoma cultures has markedly detrimental effects on antibody productivity. Removal of apoptotic hybridoma cells by macrophages at the time of seeding resulted in 100% improved antibody productivity that was, surprisingly to us, most pronounced late on in the cultures. Furthermore, we were able to recapitulate this effect using novel super-paramagnetic Dead-Cert Nanoparticles to remove non-viable cells simply and effectively at culture seeding. These results (1) provide direct evidence that apoptotic cells have a profound influence on their non-phagocytic neighbors in culture and (2) demonstrate the effectiveness of a simple dead-cell removal strategy for improving antibody manufacture in vitro.

Non-rigid object tracking in complex scenes

A recently proposed colour based tracking algorithm has been established to track objects in real circumstances [Zivkovic, Z., Krose, B. 2004. An EM-like algorithm for color-histogram-based object tracking. In: Proc, IEEE Conf. on Computer Vision and Pattern Recognition, pp. 798-803]. To improve the performance of this technique in complex scenes, in this paper we propose a new algorithm for optimally adapting the ellipse outlining the objects of interest. This paper presents a Lagrangian based method to integrate a regularising component into the covariance matrix to be computed. Technically, we intend to reduce the residuals between the estimated probability distribution and the expected one. We argue that, by doing this, the shape of the ellipse can be properly adapted in the tracking stage. Experimental results show that the proposed method has favourable performance in shape adaption and object localisation.

Contrast- and illumination-invariant object recognition from active sensation

It has been suggested that the deleterious effect of contrast reversal on visual recognition is unique to faces, not objects. Here we show from priming, supervised category learning, and generalization that there is no such thing as general invariance of recognition of non-face objects against contrast reversal and, likewise, changes in direction of illumination. However, when recognition varies with rendering conditions, invariance may be restored, and effects of continuous learning may be reduced, by providing prior object knowledge from active sensation. Our findings suggest that the degree of contrast invariance achieved reflects functional characteristics of object representations learned in a task-dependent fashion.