VictorJuiz/thesis huggingface dataset:
Joint Power Control and User Association in Downlink Heterogeneous Networks

As 5G aims to provide 1000-fold network capacity to mobile networks, heterogeneous networks (HetNet) have become a promising technology to deliver this goal. This thesis proposes a novel algorithm to maximize network utility of a downlink SISO HetNet jointly over user association and BS power control. The proposed problem formulation allows for investigation of a trade-off between network utility and network power consumption in the HetNet. Through finding the appropriate balance in the trade-off, the proposed algorithm forms a non-greedy heuristic to determine the appropriate activation of BSs under arbitrary total network consumption constraints. Greedy heuristics as motivated by those in literature are further used to compare with the proposed heuristic. Furthermore, this thesis considers the division of the downlink spectrum into multiple sub-bands and optimizes user association and BS powers independently over each sub-band. This provides an interesting alternative to the existing "soft frequency reuse" (SFR) scheme widely employed to maintain high network capacity while ensuring coverage for cell-edge users. Rate performances under various sub-band divisions are compared with the SFR scheme to examine the impact on user rates by considering a two-tier HetNet in a regular hexagonal deployment, where pico BSs are placed at known locations near the edges of macro-cells.

Keywords: 5G
Communications
Heterogeneous
Mobile
Networking
Wireless
Advisor: Yu, Wei
Opportunistic Scheduling in Cluster Computing

Distributed computing frameworks have become popular in recent years because of their ability to easily scale computation to thousands of machines. Previous studies show that the popularity of data on these systems is highly skewed. A small set of files are responsible for a significant number of accesses. This data reuse should typically lead to performance improvements, but we find that cluster computing systems are unable to fully take advantage of this sharing. This is due to the fact that distributed systems schedule their work with no consideration of what is cached in the cluster. We have designed a system called Quartet that is aware of the data cached in memory and uses this information to opportunistically schedule work where the input data is cached. Our experimental results show that when workloads reuse data, Quartet can significantly increase the cluster cache hit rate and reduce the run times.

Keywords: cluster computing
Distributed systems
Advisor: Goel, Ashvin
Brown, Angela D
The Impact of Mindfulness-based Cognitive Therapy on Neural Processing of Sadness Provocation and Depressive Relapse in a High-risk Sample

The current study sought to investigate the neural mechanisms underlying Mindfulness-based Cognitive Therapy (MBCT). Eighty-one remitted patients with a lifetime history of depression were recruited and randomly assigned to either MBCT or Cognitive Behavioral Wellbeing Therapy. Participants underwent functional MRI while completing a sadness provocation task at pre- and post-treatment. MBCT participants evinced lower activation of the posterior insula, a region implicated in body awareness, whereas MBCT relapsers evinced further MPFC deactivation, a region implicated in ruminative thinking. Moreover, it appeared non-relapsers exhibited stable brain responsiveness across time points, whereas relapsers tended to fluctuate. Findings indicate MBCTâ s emphasis on stabilizing behavioral symptoms extends to functional brain profiles, and the activation pattern in relapsers may reflect dissociation from current sensory experiences when confronted by dysphoric cues. Implications pertain to clinical practice in terms of the importance of regularly monitoring client progress throughout treatment and addressing the misapplication of mindfulness skills.

Keywords: depressive relapse
fMRI
major depressive disorder
MBCT
mindfulness
therapy
Advisor: Segal, ZIndel
Farb, Norman
Development, Characterization and Evaluation of PLA Based Bio and Carbon Nanofiber Reinforced Composites for High Strength Applications

The current work presents the development and characterization of melt blended PLA based composites with a broad spectrum of filler reinforcements: Lignin/Tannin, PHA/TPU, and Carbon Nanofibers. PLA was kept as the major phase in the composites with the weight fraction being ≥ 85wt%. Lignin was shown to impart stiffness of the PLA matrix and Tannin can provide high interfacial damping. Lignin also inhibits crystallization with almost complete inhibition at a heating rate of 15 °C/min. TPU was shown to impart ductility to PLA and PHA imparted a large increase in the damping. PHA and TPU also imparted higher impact strength to PLA. Carbon nanofibers in PLA result in high strength and stiffness composites. The maximum momentum transfer during impact is also lowered which is believed to be due to large amount of fiber pullout. CNFs promote crystallization which is prominently seen in the cooling cycle.

Advisor: Naguib, Hani E
Identification of Novel Compounds That Inhibit HIV-1 Gene Expression by Targeting Viral RNA Processing

Novel strategies targeting different stages of the HIV lifecycle are vital for continued success in combating viral infection. Since HIV gene expression is dependent upon controlled splicing of the viral transcript, small molecule modulators of RNA processing hold tremendous promise as novel drugs. To this end, we screened splicing modulators for their effect on HIV-1 gene expression. We identified four compounds, 191, 791, 833 and 892, that strongly suppressed accumulation of HIV-1 incompletely spliced RNA and expression of viral structural/regulatory proteins. Furthermore, compound treatment had limited effects on alternative splicing of host RNA splicing events. Subsequent studies confirmed anti-HIV activity of two compounds in the context of peripheral blood mononuclear cells. The distinct effects of these compounds from previously characterized HIV-1 RNA processing inhibitors validate targeting this stage of the virus lifecycle. Elucidating the mechanism by which these compounds alter HIV-1 gene expression holds key insights for novel therapeutic strategies.

Keywords: anti-viral therapy
HIV
RNA processing
splicing
Advisor: Cochrane, Alan
Analysis of Yolk Cell Microtubule Network Dynamics and Organization during Zebrafish Epiboly

Epiboly, the first morphogenetic event in zebrafish development, is a coordinated process of the blastoderm and yolk syncytial layer spreading over the yolk cell. In the yolk cell, microtubule arrays extend longitudinally and their dynamics have been suggested to be important for normal epiboly. Despite these findings, the function of the yolk cell microtubules remains unclear. Live imaging of EB3-GFP, a microtubule plus-end tracking protein, revealed a change from active microtubule growth during early epiboly to a non-growing state during late epiboly. Antibody staining for tyrosinated and detyrosinated tubulin, markers of dynamic and stabilized microtubules respectively, revealed the presence of stable microtubules during late epiboly but not during early epiboly. The yolk microtubule network also appeared to be more resistant to the microtubule depolymerizing agent nocodazole at late epiboly stages. For the first time, I report a change in microtubule dynamics and suggest different roles of microtubules throughout epiboly phases.

Keywords: Danio rerio
Epiboly
Microtubules
Yolk cell
Zebrafish
Advisor: Bruce, Ashley
Hollow Core Bragg Waveguide Design and Fabrication for Enhanced Raman Spectroscopy

Raman spectroscopy is a widely used technique to unambiguously ascertain the chemical composition of a sample. The caveat with this technique is its extremely weak optical cross-section, making it difficult to measure Raman signal with standard optical setups. In this thesis, a novel hollow core Bragg Reflection Waveguide was designed to simultaneously increase the generation and collection of Raman scattered photons. A robust fabrication process of this waveguide was developed employing flip-chip bonding methods to securely seal the hollow core channel. The waveguide air-core propagation loss was experimentally measured to be 0.17 dB/cm, and the Raman sensitivity limit was measured to be 3 mmol/L for glycerol solution. The waveguide was also shown to enhance Raman modes of standard household aerosols that could not be seen with other devices.

Keywords: Bragg
Hollow core
Hollow core waveguide
Raman
Spectroscopy
Advisor: Helmy, Amr S
Model Order Reduction and Stability Enforcement of Finite-difference Time-domain Equations Beyond the CFL Limit

The Finite-Difference Time Domain (FDTD) method is a versatile and popular method for solving Maxwell's equations. As a consequence of the explicit time integration, the maximum stable time-step of FDTD is constrained by the Courant-Friedrichs-Lewy (CFL) limit. This thesis focuses on two interdependent topics: model order reduction (MOR) of explicit FDTD equations and stability enforcement above the CFL limit. The combination of these two topics leads to the proposed CFL extension technique which has been demonstrated for 2D and 3D simulations. In addition, the proposed method has also been applied to the FDTD sub-gridding application. Comparisons have been made with existing implicit and explicit CFL extension techniques with respect to versatility, computational efficiency, and numerical dispersion errors. While there exist computation and memory limitations, the proposed method has demonstrated excellent versatility and accuracy for all test cases while having significant speed-ups over standard FDTD.

Keywords: CFL Extension
FDTD Sub-gridding
Finite-Difference Time Domain
Model Order Reduction
Stability Enforcement
Advisor: Triverio, Piero
Sarris, Costas D
The Effects of the Novel Reproductive Peptide Phoenixin-20 Amide on GnRH and Kisspeptin Hypothalamic Cell Models

Reproductive function is coordinated by the actions of specific neuropeptides and hormones, which converge on GnRH neurons in the hypothalamus. Phoenixin-20 amide (PNX-20) is a recently described peptide that increases GnRH-stimulated LH secretion and upregulates GnRH receptor mRNA in the anterior pituitary. However, to date no studies have looked at the role of PNX-20 in the hypothalamus, where it is most highly expressed. Using cell lines representative of GnRH and kisspeptin neurons, the effects of PNX-20 in the hypothalamic cells were explored. PNX-20 increases GnRH mRNA expression, protein levels and secretion in a GnRH cell model and Kiss-1 mRNA in anteroventral periventricular and arcuate nuclei kisspeptin cell models. PNX-20 also activates the adenylyl cyclase and MAPK pathways. Furthermore, we report that kisspeptin increases gene expression of the PNX precursor protein, SMIM20. These results indicate that PNX-20 may be involved in the regulation of reproduction at the level of the hypothalamus.

Keywords: gonadotropin-releasing hormone
kisspeptin
phoenixin
Advisor: Belsham, Denise D
Contact Imager for Integrated Functional Assessment of Organs-on-a-chip

We describe a microfluidic platform for the assessment of small blood vessel function. The new, compact modular platform allows to reversibly host mouse mesenteric arteries on a microfluidic chip, without the need for any manual on-chip manipulation. The luminal and abluminal sides of chip-hosted vessels are exposed to well-defined chemical microenvironments, and physiological levels of transmural pressure and temperature are established. Vasoconstriction was induced by abluminal presentation of phenylephyrene and dose-response experiments were conducted. Vessel constriction was directly determined by direct projection of the chip-hosted artery via a fiber-optic faceplate onto a CMOS sensor, therefore removing the need for a microscope and an external camera. We believe the demonstrated approach will be broadly applicable for the routine functional assessment of different microtissues and organs-on-a-chip. In the context of intact arteries, the approach may ultimately enable the clinical assessment of patient microvascular status.

Keywords: Contact imaging
Lab on a chip
Lenless imaging
Microfluidic
organ on a chip
Reversible seal
Advisor: Dickie, Paige E
Cholesterol Plays a Crucial Role in High-fat-diet Induced ER stress and Non-alcoholic Fatty Liver Disease

By comparing C57 mice with two dyslipidemic models, LDL-receptor null (LDLR-/-) and LCAT/LDL-receptor null mice (LCAT-/-xLDLR-/-), our lab showed an observation of ER-membrane cholesterol being necessary to modulate ER-stress in a high-cholesterol-diet feeding paradigm. Here, we hypothesized that hepatic cholesterol biosynthesis plays an important role in mediating high-fat-diet-induced hepatic ER stress and NAFLD. In vivo, we fed C57, LDLR-/-, LCAT-/-xLDLR-/- mice a high-fat-diet for 16 weeks. Markers for hepatic ER-stress, cholesterol biosynthesis, ER-cholesterol, NAFLD and inflammasome were measured. High-fat-diet feeding induced ER-stress, NAFLD, cholesterol biosynthesis, NLRP3 activation and ER-membrane cholesterol accumulation in both C57 and LDLR-/- mice, while LCAT-/-xLDLR-/- mice were protected. In vitro, HepG2 cells were treated with palmitate overnight with/without zaragozic acid (ZA), to inhibit cholesterol biosynthesis. Treatment with palmitate induced ER-stress, cholesterol biosynthesis and NLRP3 activation, which were abrogated by ZA treatment. These findings implicate the role of cholesterol in nutritional excess-induced hepatic metabolic complications.

Keywords: Cholesterol
ER-stress
High fat diet
Murine
NAFLD/NASH
Obesity
Advisor: Ng, Dominic
Optical Detection of Interaction between Alzheimer's Disease Biomarkers and Carbon Nanotubes

Alzheimer's disease (AD) is a debilitating neurodegenerative disorder characterized by cognitive impairment. During AD, Amyloid Beta (A) is deposited extracellularly and forms plaques, disrupting neuronal communication. Acetylcholinesterase (AChE) and carbon nanotubes (CNTs) modulate amyloid fibrillation pathways. We explored effect of multi-walled CNTs (MWCNTs) and A

Keywords: acetylcholinesterase
Alzheimer's
amyloid-beta
butyrylcholinesterase
Carbon nanotubes
Ellman's method
Advisor: Kerman, Kagan
Large-Screen Displays: An Operating Experience Review and Team Cognitive Work Analysis

Large-screen displays are increasingly included in the human-machine interface of modern nuclear power plant main control rooms. The claimed benefits of these displays include: 1) support for operator situation awareness, and 2) support for teamwork. This thesis describes two activities of industry-standard Human Factors Engineering Program planning. First, an Operating Experience Review seeks evidence of the claimed benefits of large-screen displays through a literature review and series of subject-matter expert interviews. Second, a Team Cognitive Work Analysis examines a set of operational scenarios in a nuclear power plant and identifies collaboration requirements for a large-screen display. The application of Team Cognitive Work Analysis is novel for large-screen displays, and some of its techniques are novel to the nuclear domain. Methodological insights are discussed.

Advisor: Jamieson, Greg A
PKA Reduces the Rat and Human KCa3.1 Current, CaM Binding and Ca2+ Signaling, which Requires Ser332/ 334 in the CaM-binding C Terminus

The Ca2+-dependent K+ channel, KCa3.1 (KCNN4/IK/SK4), is a therapeutic target for several CNS disorders involving microglial activation. While PKA signaling is important in many cells that use KCa3.1, reports of channel regulation by PKA are inconsistent. Here, I found that in microglia, PKA activation with Sp-8-Br-cAMPS decreased the current, and this was prevented by the PKA inhibitor, PKI14-22. Mutating the single PKA site (S334A) in human KCa3.1 abolished the PKA-dependent regulation. CaM-affinity chromatography showed that CaM binding to KCa3.1 was decreased by PKA activation, and this regulation was absent in the S334A mutant. Single-channel analysis showed that PKA decreased the open probability in wild-type but not S334A mutant channels. The same decrease in current for native and wild-type (but not S334A) expressed KCa3.1 channels occurred when PKA was activated through the adenosine A2a receptor. Finally, PKA activation reduced Ca2+-release-activated Ca2+ (CRAC) entry following activation of metabotropic purinergic receptors.

Advisor: Schlichter, Lyanne C
The Role of Chirality in Self-assembly of Ferrocene Peptide Conjugates

In this report, the self-assembling behavior of four diastereomeric peptides has been investigated. A series of four Ferrocene tripeptides namely Fc-(L)Phe(L)Phe(L)Leu-OMe, Fc-(D)Phe(L)Phe(L)Leu-OMe, Fc-(L)Phe(D)Phe(L)Leu-OMe and Fc-(L)Phe(L)Phe(D)Leu-OMe have been synthesized and characterized. Next, the gelation performance has been thoroughly investigated and compared in different organic solvents. Interestingly, it has been found that only two peptides namely Fc-(L)Phe(L)Phe(L)Leu-OMe and Fc-(D)Phe(L)Phe(L)Leu-OMe form gel in toluene suggesting the potential effect of chirality in self-assembling process. The conformation and self-assembly have been investigated by variable concentration and variable temperature dependent NMR studies which suggest the involvement of multiple intermolecular hydrogen bonds for gelation. Gels have also been characterized by minimum gelation concentration, Fourier transform infrared spectroscopy and circular dichroism spectroscopy. The morphologies of their self-assembled states have been characterized by transmission electron microscopy. Interestingly, two of the Fc-peptides showed the presence of nanofibrillar network structure.

Keywords: Ferrocene-peptides
nanofibril
sellf-assembly
Advisor: Kraatz, Heinz-Bernhard
Proteomic Analyses of Human Fetal Atria and Ventricles

In this study we carried out a mass spectrometry-based proteome analysis of human fetal atria and ventricles. Heart protein lysates were analyzed on the Q-Exactive mass spectrometer in biological triplicates. Protein identification using MaxQuant yielded a total of 2,754 atrial (91%) and 2,825 ventricular protein groups (83%) in at least 2 of the 3 runs with 2 unique peptides. Statistical analyses using fold-enrichment (>2) and p-values (0.05) selected high confidence chamber enriched atrial (134) and ventricular (81) protein groups. Several previously characterised cardiac chamber-enriched proteins were identified in this study including atrial isoform of myosin light chain 2 (MYL7), atrial natriuretic peptide (NPPA), and connexin 40 (GJA5) for atria, and ventricular isoforms of myosin light chains (MYL2 and MYL3), myosin heavy chain 7 (MYH7), and connexin 43 (GJA1) for ventricle. Our data was compared to in-house generated and publicly available human microarrays, several human cardiac proteomes, and phenotype ontology databases.

Keywords: Bioinformatics
Chamber specificity
Fetal tissue
Mass spectrometry
Q-Exactive
Ventricle
Advisor: Gramolini, Anthony O
Targeting Clinically Viable Protein Tyrosine Phosphatases with Rationally Designed, Small Molecule Inhibitors and Artificially Induced Protein-Membrane Anchors

Protein tyrosine phosphatases (PTPs) regulate the phosphorylation state of many important signaling molecules and are increasingly viewed as integral components of signal transduction cascades. PTPs have been implicated in the development of type 2 diabetes, breast cancer and neurodegenerative disorders, and thus have been extensively explored as a potential therapeutic target. This thesis explores the functional components required for engineering novel modalities to successfully target protein tyrosine phosphatase 1B (PTP1B), the most well studied member of the large family of PTPs. In the first part of this thesis, a screen of a library of compounds identified potent salicylic acid inhibitors with promising single digit micromolar activity. In silico computational analysis drove the design and synthesis of a second generation of disalicylic acid inhibitors, and new, more selective and potent inhibitors have been identified. The second part of this thessis explores the first ever application of artificially induced protein-membrane anchors designed to target PTPs.

Advisor: Gunning, Patrick T
Investigating the Role of MicroRNAs in the Pathogenesis of Kidney Cancer Subtypes and their Clinical Utility as Cancer Biomarkers

Renal cell carcinoma (RCC) is the most common adult kidney neoplasm and constitutes a number of distinct subtypes. Papillary RCC (pRCC), a poorly characterized RCC subtype, can be subdivided into type 1 or 2. The objective of this study was to understand the pathogenesis of pRCC type 1. We identified genes and microRNAs (miRNAs) that are dysregulated in pRCC type 1. Pathway analysis showed enrichment of the focal adhesion pathway. We showed that miR-199a-3p, which is downregulated in pRCC type 1, regulates members of this pathway. Moreover, RCC subtypes may be difficult to differentiate by microscopy due to overlapping features. We demonstrated that miR-221 and -222 can discern chromophobe (chRCC) and renal oncocytoma, a benign neoplasm, from clear cell RCC (ccRCC) and pRCC. miR-126 can distinguish ccRCC from pRCC, whereas miR-15b and miR-22 had overlapping expression levels in chRCC and oncocytoma.

Keywords: Cancer biomarker
Focal adhesion pathway
MET
microRNA
miR-199a-3p
Renal cell carcinoma
Advisor: Yousef, George M
Elsholtz, Harry
New Kinematic and Geochronologic Evidence for the Quaternary Evolution of the Central Anatolian Fault Zone

In this study new structural, geomorphic and geochronologic data are provided for several key faults within the southern and central parts of the Central Anatolian Fault Zone, which suggest Quaternary left-lateral motion has been previously overstated. Our neotectonic mapping along the southern part of the CAFZ, coupled with 36Cl exposure dating, documents a left lateral slip rate of 0.77 ± 0.22 mm a-1 during the Late- Pleistocene, lower than rates of 3 mm a-1 originally proposed. To the north, the Erciyes fault is characterized by a linear array of monogenetic vents which suggest maximum horizontal extension in a WNW-ESE direction during the Late-Quaternary. Further north, mapping and structural analysis shows that the Erkilet and Gesi faults within the northern Erciyes basin are predominantly extensional. We re-characterize the CAFZ as one of an array of weakly active, highly segmented, transtensional fault systems in Central and Eastern Anatolia which have re-activated paleotectonic structures.

Keywords: Central Anatolia
Intracontinental Deformation
Neotectonics
Slip Rates
Advisor: Schoenbohm, Lindsay
Testing the Similarity Fit/Misfit Hypothesis in Adolescents and Parents with ADHD

Parents and adolescents with ADHD may engage in excessive conflict due to the nature of adolescent ADHD behaviours (impulsivity, inattention) and the difficulties associated with parenting them. This may be magnified when parents struggle with ADHD and when comorbid adolescent externalizing problems exist. Despite the logic of an exacerbative effect when adolescents and parents have ADHD, research suggests that parents with ADHD show more tolerance, empathy and less conflict with their children who share similar cognitive traits (i.e., similarity-fit hypothesis). This study tested the similarity-fit/misfit hypotheses in a sample of 156 adolescents (mean age = 15.25) and their parents. Results supported the similarity-fit process in fathers whereby fathers and adolescents with higher inattention levels engaged in fewer conflicts. In mothers, the similarity-misfit hypothesis was supported: frequency of conflict was highest when mothers and adolescents had highest levels of inattention. Results were interpreted in the context of gender and parental roles.

Keywords: Adolescent-parent conflict
Adolescents
Attention-Deficit/Hyperactivity Disorder
Parental ADHD
Similarity Fit hypothesis
Similarity Misfit hypothesis
Advisor: Wiener, Judith