VictorJuiz/thesis huggingface dataset:
The effective temperatures of gas-phase biological molecules stored in a quadrupole ion trap

The internal energy distribution undergoing collision-induced dissociation (CID) in the cell of a quadrupole ion trap (QIT) mass spectrometer can be characterized by the effective temperature, which would help determine the activation energy and entropy. Here, the relationship in a Bruker QIT has been reexamined based on kinetic measurements at two qz values. An observed linear relationship between ion effective temperatures and resonant activation amplitudes appears qualitatively different from simplified theoretical simulation, which is in agreement with previous results on Finnigan ion trap. However, the normalization process aiming to compensate for the m/z dependency of the required fragmentation energy that is used successfully in Finnigan-geometry traps is not entirely successful for use in Bruker-geometry trans. The calibration determined here roughly indicates the relationship between ion effective temperature, resonant excitation amplitude and ion m/z. However, Successful extraction of the dissociation energetics still requires a better accuracy of the calibration.
Dreaming the divine: Ritual and architecture at ancient Greek healing sanctuaries in Asklepios

This study examines the relationship between architecture and the ritual of incubation at the ancient Greek healing sanctuaries, especially those dedicated to Asklepios. By highlighting key features of specific sanctuaries, including those at Pergamon, Epidauros, Corinth, and Athens, the study traces the role of architecture in enhancing experience from the macro-level (location of the sanctuary in the environment) to the micro-level (location for incubation). It concludes with the construction of the epiphany of the deity in the patient's atopic dream. Unlike most ancient cults, epiphanic healing requires the patient to make contact with the divinity, an unfamiliar and mythically hazardous undertaking. The architectural and ritual elements of the cult function collectively to facilitate the experience and influence the incubants' thought processes. By creating a network of associations using symbols and architecture, the cult is able to address incubants who have different levels of comprehension and experiences, as well as channel negative cultural perceptions about epiphany into functional ones. The study takes a holistic approach, using both material and textual remains, as both are essential in recreating the complex environment.
Perceived learning needs of post secondary faculty of institutions moving towards online course delivery

This qualitative study sought to investigate the perceptions of faculty at small post secondary institutions as they learn to make the transition to online teaching. It also gathered information related to the types of learning strategies employed by faculty in meeting these needs and the kinds of institutional support mechanisms they believed to be important in supporting their efforts. The study involved semi-structured interviews with eight faculty members from two institutions. Analysis of the data showed that faculty moving into online teaching perceive that they need to learn about technology, about educational theory and teaching and about how to make best use of the technology to support student learning. What faculty members perceived they needed to know varied from individual to individual and seemed directly related to their educational backgrounds and experience with technology. All of the participants felt that institutional support was important in meeting their needs. The learning patterns described by faculty related to how they approached learning about online teaching were consistent with well-established principles of adult learning. Specifically, the data revealed strong themes of self-directedness, experiential learning and reliance on accumulated experience, preference for practical and timely application of new knowledge and motivation that is influenced by both internal and external factors. In addition, the faculty members in this study showed strong reliance on collaboration and working with others in support of their learning. They also described ongoing reflection on practice and experience as part of a constructive learning process. The findings of the study strongly indicate that post secondary institutions wishing to move towards online delivery models must assume responsibility for institutional support mechanisms in support of faculty attempting to become online teachers. Models need to be multi-faceted and designed around principles of adult learning. Based on study findings and the literature, specific recommendations regarding the design of institutional support for faculty are made in the thesis.

Keywords: Teaching
Learning
Online data processing
Teaching, Computer-assisted instruction
A CDKN1C mutation in Beckwith-Wiedemann syndrome patients reduces efficiency of RNA splicing

A G → T mutation in a run of 7 G's in intron 3 of the CDKN1C gene was found in a family with some members affected by the overgrowth syndrome Beckwith-Wiedemann syndrome (BWS). All affected members of the family carry the mutation and inherited the allele maternally, strongly suggesting a role in causing BWS. I transfected 293HEK cells with plasmid constructs containing CDKN1C intron 3 and parts of exon 3 and exon 4 and found that the mutation reduces RNA splicing efficiency. Mutation of all 7 G's further reduced splicing efficiency but only in the presence of the putative CDKN1C polyadenylation signal and not when the SV40 polyadenylation signal was present. Examination of CDKN1C expression by RT-PCR in one available patient fibroblast cell line showed that the reduction in splicing efficiency seen in transfected cells also occurred in vivo in these cells. Maternal monoallelic expression was verified in this cell line.
Rethinking rights: Equality, power, and oppression in the liberal state

Rethinking Rights examines pornography and hate speech as test cases in advancing an argument for the liberal state to engage in activism in the name of equality for women and minorities. Such cases expose a core tension within liberalism between neutrality and equality, since state neutrality in the face of a systemically sexist and racist culture only reinforces that culture and further silences the speech of women and minorities within it. I argue that, on the liberal's own terms, the commitment to equality has priority over the commitment to neutrality. Once that has been established, I address two issues commonly raised by liberals against state activism: the question of how to ensure that the state is acting in the name of equality, rather than in its own, or some other, interest; and the issue that censorship, in any form, is anathema to liberalism. Both discussions raise issues of state power, particularly as it intersects with feminist speech act theory and with the work of Foucault and Judith Butler. These theories, taken together, turn both state power and the notion of censorship on their heads---no longer is hate speech about the power of the speaker, but about the power of the state in permitting or regulating it; no longer is censorship about state suppression after an utterance, but about the very production of utterances at all. Taking these insights on board, the liberal should be in a position to embrace state activism in the service of equality, not as a compromise of liberal principles, but as an entailment of those very principles.
The constitution of community in legal sites: a study of law, crime and its control

This dissertation focuses on the concept of community in legal sites relating to crime and its control. It draws on three case studies: community notification of sex offenders, community policing strategies designed to address gang loitering in Chicago, and the proliferation of gated communities. While other work emphasizes the dominance of advanced liberal governance or the rise of a preventive state, these case studies draw out diverse translations of the concept of community in law, as it is deployed for achieving governmental ends relating to crime prevention. In so doing, this dissertation treats the documents produced within legal sites as empirical representations in the history of legal ideas, and as evidence of how social issues are imported, defined, translated, and negotiated within the legal field. The case studies demonstrate that the invocation of community in these sites operates in conjunction with other operative concepts, such as risk, harm, or the material form that community may be taking. This provides insights that are missed in more general accounts, including the interplay between community and risk management, the inflections of law and community implicated in the constitution of community harm, and the spatial vision of community motivating the adjudication of boundaries between gated communities and non-residents. This dissertation finds that governing through community is not as stable as theories of advanced liberalism suggest. Instead, invocations of “community” draw on and inform other visions alongside (or instead of) dominant political rationalities. This includes the “people's welfare” of police science, divergent visions of the “social,” and an array of expert, lay, and administrative knowledges that are authorized by law in constituting risk and its management. These hybridities, in turn, have practical effects for the legal programmes and rationalities developed in creating, implementing, and adjudicating crime prevention efforts.

Keywords: Crime prevention
Crime prevention, Citizen participation
Communities
Asymmetric desymmetrization of strained alkenes

We have extended the rhodium-catalyzed asymmetric ring-opening reaction of strained oxabicyclic alkenes to include sulfur nucleophiles. These products are obtained as a single diastereomer in high yield with excellent enantioselectivity (> 90%). During the course of our studies, we noted that the order of addition of reagents is important to the reaction outcome, providing subtle mechanistic insights that enhance our understanding of the working model developed in our group. Furthermore, halide effects proved to be crucial not only to the enantioselectivity of this reaction, but also in thwarting catalyst poisoning. Apart from oxabicyclic alkenes, we set forth to examine highly strained cyclopropenes as potential substrates in an asymmetric carbometalation reaction for the purpose of generating chiral cyclopropanes. By employing a palladium (II) catalyst in conjunction with functional group tolerant organozinc reagents, we obtained cyclopropanes with excellent enantioselectivity using simple diethylzinc (99% ee). One severe limitation of this methodology is the incompatibility of coordinating solvents, which underscores the utility of organozinc reagents. In an effort to ameliorate this deficiency, we have identified nickel (II) catalysts which may enable the use a diverse array of organozinc reagents, including those derived from ubiquitous organic iodides. To showcase the efficiency of the palladium-catalyzed asymmetric alkylative ring-opening (ARO) reaction developed in our group, we ventured into the total synthesis of ebelactone A, whose 7 stereocentres could arise from a single desymmetrization operation of a suitably adorned oxabicyclic alkene. The challenge of assembling this target molecule using an ARO strategy lies in the stereoselective preparation of a trisubstituted (E)-alkene. Our efforts to employ direct olefination, metathesis and aldol methods are discussed.
Characterization and mutant analysis of the Drosophila melanogaster homologues of amphiphysin and enthoprotin, two proteins implicated in vesicular trafficking

Vesicular trafficking is necessary in eukaryotic organisms to move proteins and membrane from organelle to organelle or plasma membrane. Budding and scission of vesicles requires the interplay of a number of cytoplasmic proteins, many of which also interact with membranes. The study of such molecules is frequently defined either in biochemical assays or through the expression of various constructs in a cell culture system. What is often missing is insight into function in an intact multicellular organism. Drosophila inelanogaster is an excellent model for studying such proteins as its development is well characterized and it has well-defined genetics to allow for the study of mutants. In this thesis, I have chosen to investigate amphiphysin and enthoprotin, two membrane-interacting proteins implicated in the formation of clathrin-coated vesicles. Amphiphysin contains multiple protein interaction domains and is thought to act as a scaffold during late steps of clathrin-mediated endocytosis particularly at synapses. Based on studies in yeast and vertebrate cell culture, enthoprotin is thought to help form clathrin-coated pits in the trans-Golgi network (TON) to endosome trafficking pathway. It is believed to act by promoting membrane curvature and by binding to both clathrin and clathrin adaptors. Drosophila amphiphysin (Amph) is not found at the pre-synaptic membrane, but rather at the post-synaptic membrane. Amph mutants are viable and have a locomotory defect. However, they show no defects in synaptic neurophysiology, suggesting a role for Amph in muscle development. Drosophila Enthoprotin (Enth) is localized to the TGN and endosome, consistent with its predicted function. Enth mutants are viable with slightly roughened eyes, but otherwise appear normal. However, oogenesis is disrupted at a late stage and females mutants are completely sterile. Analysis of germline clones shows that Enth is required only in the follicle cells for normal oogenesis. Additionally, Enth mutant clones show a cell growth phenotype that appears to be due to perturbation of the Akt pathway. Amph functions quite differently in Drosophila than work from vertebrate cell culture had suggested. Enth seems to function where expected, but mutant analysis revealed unexpected phenotypes. Together, this work highlights the value of studying proteins in vivo.
Effects of metabolizing enzyme modulators on chloral hydrate- and tribromoethanol-induced hepatotoxicity and analgesia

Chloral hydrate (CH) and tribromoethanol (TBOH) are anesthetics associated with hepatotoxicity. The metabolites and metabolizing enzymes responsible for anesthesia or toxicity are unknown. This thesis hypothesizes that trihaloethanols caused the anesthesia whereas trihaloacetaldehydes caused the toxicity. The effect of modulating metabolic enzymes in vitro (isolated rat hepatocytes) and in vivo (mice) were investigated. Ethanol reduced the hepatotoxicity of CH, trichloroethanol (TCOH), bromal and TBOH, and lengthened the anesthesia induced by CH and TCOH. This was prevented by inhibiting alcohol dehydydrogenase (ADH), indicating that the ADH-NADH-complex formed by ethanol reduced trihaloacetaldehydes to trihaloethanols. CYP3A induction increased hepatotoxicity and prevented anesthesia because CYP3A catalyzed the oxidation of trihaloethanols and trihaloacetaldehydes to form toxic free radicals. Cellular glutathione, the ferric chelator desferoxamine, and the antioxidant butylated hydroxyanisole prevented the lipid peroxidation, mitochondrial function disruption and hepatocytotoxicity. In conclusion, trihaloethanols caused anesthesia whereas trihaloacetaldehydes caused hepatotoxicity.
Novel optical properties of two-dimensional Silicon photonic crystals

Macroporous silicon two-dimensional photonic crystals with photonic band gaps in the near- and mid-infrared are investigated through a number of theoretical and experimental studies. The bulk properties of crystals with a triangular lattice of air pores in silicon (and a 1.5 μm lattice pitch) are measured via Fourier transform infrared spectroscopy and laser spectroscopy. Broadband measurements show deep band gaps in the mid-infrared, in agreement with band structure calculations. Calculations also predict the existence of many high-frequency band gaps in addition to the well-known fundamental band gap. Transmission measurements within the photonic band gap of thin crystals reveal a large attenuation of approximately 10 dB per crystal row, demonstrating that only a few crystal rows are needed to approximate a semi-infinite crystal. The transmission of orthogonally polarized beams through a thick crystal is used to measure birefringence within the first photonic band. The measured birefringence shows excellent agreement with band structure calculations and reaches a maximum value of 0.366 ± 0.002, significantly exceeding the birefringence of naturally anisotropic crystals. Single-mode transmission is demonstrated in photonic crystal waveguides formed by a missing row of air pores. Broadband transmission with novel Fabry-Perot oscillations is measured within the 3.3–5.5 μm bulk crystal band gap, in good agreement with band structure calculations and finite-difference time-domain transmission calculations. A tunable two-dimensional photonic crystal is demonstrated via the temperature dependence of a nematic liquid crystal infiltrated into the crystal pores. The 4.4 μm band edge is tuned over 70 nm and band structure calculations are used to infer the alignment of the liquid crystal within the pores. Finally, ultrafast all-optical switching is achieved using free-carriers to shift the 1.9 μm band edge of a photonic crystal with a 500 nm lattice pitch. Pump and probe spectroscopy is used to measure a band edge blueshift of 29 ± 1 nm (for a maximum pump fluence of 2.1 ± 0.4 mJ·cm−2) that occurs over a 400 fs timescale. The many new properties demonstrated in this thesis highlight the exciting possibility of using macroporous silicon photonic crystals to create a new generation of unique and highly-integrated photonic devices.
Osteopontin expression is required for myofibroblast differentiation

Osteopontin (OPN) is up-regulated during wound healing and is required for granulation tissue formation and fibrotic repair. Since ablation of OPN expression impacts fibroblast migration, adhesion and survival, myofibroblast differentiation was examined in OPN-null fibroblasts. Western blot analyses of TGFβ1-treated cardiac and dermal fibroblasts exhibited a ∼2-5-fold greater α-SMA and ED-a FN expression with no apparent change in OPN-null fibroblasts. OPN Silencing reduced α-SMA expression to levels of OPN-null fibroblasts. Immunostaining for F-actin, α-SMA and α-actinin, and TEM confirmed poor stress-fibre organization, reduced focal adhesion development and inhibited lamellopodia formation from OPN-null fibroblasts. OPN-null fibroblasts exhibited 40-60% less spreading, 50% less resistance to shear force and a ∼3-fold lesser collagen-gel contraction. These defects were partially rescued by transfection with OPN. Mass spectrometry of focal adhesion extracts identified absence of HMGB1 protein from OPN-null fibroblasts, despite being enriched in WT-extracts. OPN appears to regulate differentiation and activity of myofibroblasts in response to TGFβ1 stimulation.
Effects of analogue treatment on the control of JH biosynthesis during the reproductive cycle of Diploptera punctata

Cycling levels of juvenile hormone control reproduction in the cockroach Diploptera punctata; however, the mechanisms controlling JH have remained elusive. JH analogues help to understand these mechanisms. Here we use the aromatic analogues fenoxycarb, pyriproxifen and diofenolan to induce complete suppression of JH biosynthesis throughout the gonadotrophic cycle. Adult females treated with 30 mug of fenoxycarb and subsequently denervated displayed that suppression of JH by JH analogues was controlled, in part, by the NCAI. CA were removed and treated with 10 -7 M of Dippu AST7 in vitro. Maximal inhibition of JH biosynthesis by allatostatin requires intact nervous connections to the brain when females are topically treated with fenoxycarb, which was significant for specific days of the gonadotrophic cycle. Quantitative PCR displayed that levels of AST and ASTR2 in brains of females on day 3, 4 and 5 increase when treated with 30 mug fenoxycarb relative to controls.
Infants' understanding of object movement based on shape

This study explored 8- and 12-month-old infants' abilities to recognize how different shaped objects should move based on their physical properties. Using a violation-of-expectation preferential-looking paradigm, each infant was presented with 4 trials comprised of 2 video displays depicting an expected physical event (a ball rolling or a cube sliding) and an unexpected physical event (a ball sliding or a cube rolling). Eight-month-old infants did not show a preference for either expected or unexpected events---they simply showed a preference for rolling objects over sliding objects. Twelve-month-olds also showed a bias for rolling objects, but more notably they also responded to the expectedness of the event, showing a bias towards unexpected motion over expected motion. These findings are discussed in terms of theories and possible implications.
Allogeneic HLA immunization as an HIV-1 vaccine strategy

Xenovaccination of rhesus macaques with Human Leukocyte Antigen (HLA) Class I and II proteins has been demonstrated to elicit protective immunity against challenge with SIV grown in human cells. The analogous approach in humans of allovaccination may not be susceptible to the same pathogenic characteristics of HIV that have confounded virus-specific vaccine formulations. To determine if HLA allovaccination in humans could lead to protective immunity against HIV, we prospectively followed women receiving whole-cell allovaccination in the form of leukocyte immunotherapy for recurrent spontaneous abortion. Whole-cell vaccine recipients and their respective partners (referred to as donors) provided pre- and post-immune blood samples for analysis. Study participants were HLA-typed by sequence-specific PCR, and antibodies specific for HLA Class I and II antigens were measured in recipient plasma. To determine if anti-HLA antibody responses detected in recipient plasma samples were capable of neutralizing HIV-1 in vitro, we grew laboratory strain HIVIIIB and primary isolate HIV301660 in CD4 + T lymphocytes derived from each respective donor. The ability of purified whole IgG from responding patients to neutralize infectivity of the respective donor-derived virus was then assayed in vitro. Two of seven patients receiving the allovaccination made strong anti-HLA antibody responses specific to the HLA haplotype of the donor in response to the whole-cell vaccination. A recipient whole IgG sample with antibodies directed primarily against HLA Class I antigens did not neutralize HIVIIIB. In contrast, a recipient sample with antibodies against both HLA Class I and II antigens was able to neutralize HIVIIIB and primary isolate HIV301660 . Thus, using a human model of allovaccination, we have provided proof-of-principle data that indicate that allele specific anti-HLA antibodies elicited by a whole-cell immunogen are capable of neutralizing HIV-1 in vitro. This result supports the possibility that alloimmunization of humans with a mixture of purified HLA molecules could provide a new approach to vaccination against HIV-1.