An n-string tangle is a three dimensional ball with n-strings properly embedded in it. In late the 80's, C. Ernst and D. Sumners introduced a tangle model of protein-DNA complexes. This model assumes that the protein is a 3-dimensional ball and the protein-bound DNA are strings embedded inside the ball. Originally the tangle model was applied to proteins such as Cre recombinate which binds two DNA segments. The protein breaks and rejoins the DNA segments and then creatss knotted DNA. When this kind of protein complex bounds circular DNA, there will be two DNA loops outside of the DNA-protein complex. Hence we can use a 2-string tangle model for this complex. More recently, Pathania, Jayaram and Harshey predicted that the topological structure within the Mu protein complex consists of three DNA segments containing five crossigs. Since Mu binds DNA sequences at 3 sites, the Mu protein-DNA complex can be modeled by a 3-string tangle. Darcy, Leucke and Vazquez analyzed Pathania et al's experimental results by using 3-tangle analysis. Based on the 3-string tangle analysis of Mu protein-DNA complex, we addressed the possibility that a protein binds DNA sequences at four sites. Such a protein complex bound to a circular DNA molecule is modeled by a 4-string tangle with four loops outside of the tangle. In this thesis, we decided a biologically relevant 4-string tangle model. We also developed mathematics for solving tangle equations to predict the topology of DNA within the protein complex.

My research area is applications of topology to biology, especially DNA topology. DNA topology studies the shape and path of DNA in three dimensional space. My thesis relates to the study of DNA topology in a protein-DNA complex by solving tangle equations and calculating distances between DNA knots.

Small-molecule inhibitors of tau fibrillization are under investigation as tools for interrogating the tau aggregation pathway and as potential therapeutic agents for Alzheimer's disease. Established inhibitors include thiacarbocyanine dyes, which can inhibit recombinant tau fibrillization in the presence of anionic surfactant aggregation inducers. In an effort to increase inhibitory potency, a cyclic bis-thiacarbocyanine molecule containing two thiacarbocyanine moieties was synthesized and characterized with respect to tau fibrillization inhibitory activity by electron microscopy and ligand aggregation state by absorbance spectroscopy. Results showed that the inhibitory activity of the bis-thiacarbocyanine was qualitatively similar to a monomeric cyanine dye, but was more potent with 50% inhibition achieved at ∼80 nM concentration. At all concentrations tested in aqueous solution, the bis-thiacarbocyanine collapsed to form a closed clamshell structure. However, the presence of tau protein selectively stabilized the open conformation. These results suggest that the inhibitory activity of bis-thiacarbocyanine results from multivalency, and reveal a route to more potent tau aggregation inhibitors.

The hyperbolic volume of a knot complement is a topological knot invariant. Futer, Kalfagianni, and Purcell have estimated the volumes of Montesinos link complements for Montesinos links with at least three positive tangles. Here we extend their results to all hyperbolic Montesinos links.

This article analyses the impact of the IOTA distributed ledger technology (DLT) on smart cities. The world population is rapidly increasing while at the same time trends such as urbanization shape future demographics. Thus, fast-growing cities face the challenge of increasing demands in resources such as energy, water, transportation, while at the same time aiming to increase life quality by reducing burdens such as pollution and waste. The concept of a “Smart City” emerged with the ambition to solve a city’s issues by creating social and economic advantages while providing efficient resource allocation processes. Nevertheless, current information communication technologies tend to underperform a smartcities systems requirement since the quantity of connected devices increases which slows down the transition of a city becoming smart. The distributed ledger technology IOTA promises to enable automated, feeless transactions and processes with a high level of integrity, which may impact the development of smart cities. In this research the IOTA technology is introduced and investigated. The advantages of IOTA compared to conventional information communication technologies and the blockchain technology are highlighted. Thereafter, the current state of IOTA in smart cities is reviewed by analysing current research and use cases. To investigate the concept of a smart city the smart city initiative framework, including its subcategories is introduced. Additionally, different experts working on IOTA integrations related to smart city initiatives were interviewed giving insights into their field ofexpertise. Finally, an analysis and discussion of the IOTA technology use cases are put into relation with the multi-level perspective framework (Geels, 2006) highlighting the positive impact of IOTA on the development of smart cities. / I den här artikeln analyseras effekterna av IOTA:s teknik för distribuerade huvudböcker (DLT) på smarta städer. Världens befolkning ökar snabbt samtidigt som trender som urbanisering formar framtidens demografi. Snabbt växande städer står därför inför utmaningen att öka kraven på resurser som energi, vatten och transporter, samtidigt som de strävar efter att öka livskvaliteten genom att minska belastningar som föroreningar och avfall. Begreppet smart stad uppstod med ambitionen att lösa stadensproblem genom att skapa sociala och ekonomiska fördelar och samtidigt tillhandahålla effektiva processer för resursfördelning. Den nuvarande informations- och kommunikationstekniken tenderar dock att inte uppfylla kraven på system för smarta städer, eftersom mängden anslutna enheter ökar, vilket gör att övergången till en smart stad blir långsammare. Den distribuerade huvudbokstekniken IOTA lovar att möjliggöra automatiserade, felfria transaktioner och processer med en hög grad av integritet, vilket kan påverka utvecklingen av smarta städer. I den här forskningen introduceras och undersöks IOTA-tekniken. Fördelarna med IOTA jämfört med konventionell informationskommunikationsteknik och blockkedjetekniken lyfts fram. Därefter granskas det nuvarande läget för IOTA i smarta städer genom att analysera aktuell forskning och användningsfall. För att undersöka begreppet smart stad introduceras ramverket för initiativet för smarta städer, inklusive dess underkategorier. Dessutom intervjuades olika experter som arbetar med IOTA-integrationer isamband med initiativ för smarta städer för att ge en inblick i deras expertisområde. Slutligen analyseras och diskuteras IOTA-teknikens användningsområden i förhållande till ramverket för flernivåperspektivet (Geels, 2006), där IOTA:s positiva inverkan på utvecklingen av smarta städer lyfts fram.

This dissertation is an investigation into the classification of all hyperbolic manifolds which admit a reducible Dehn filling and a toroidal Dehn filling with distance 3. The first example was given by Boyer and Zhang. They used the Whitehead link. Eudave-Muñoz and Wu gave an infinite family of such hyperbolic manifolds using tangle arguments. I show in this dissertation that these are the only hyperbolic manifolds admitting a reducible Dehn filling and a toroidal Dehn filling with distance 3. The main tool to prove this is to use the intersection graphs on surfaces introduced and developed by Gordon and Luecke. / text

This is a sociological ethnography of nine people with dementia living in a private nursing home in central Scotland. It seeks to find an alternative way to view people in this situation, in a field that has been dominated by the medical modeL. By placing the people before the disease of dementia, they can be studied within the same framework as any people. For this study this framework is everyday life sociology with a focus on symbolic interactionism, ethnomethodology and dramaturgy. Additionally, by gaining the subjective perspective, we can get close to understanding meaning for these people. The ethnographic methods I use consist of participant observation and interviews. For analysis I employ NUDIST to structure the data and the thesis. The settng, Lavender Wing of Deer View Grange Nursing Home, provides context for the study. This is a culture of surveillance and routines, which can be restrictive, infantilizing and disabling for residents. Despite this culture research findings are of socially active participants. By examining relationships through an interactional framework three thematic areas developed concerned with emotions, interactions and classification. These thematic spheres demonstrate the emotional self, the interactional self and the generalized self of research informants. The emotional is concerned with the most inner and intimate self, often engaging in backstage intimacies and in thought. Significant others share with the interactional self, in frontstage performances, which are more ritualistic. The generalized self interacts with the generalized other, most often consisting of everyone in Lavender Wing and is concerned with classification and boundarydefinition. Within these spheres the described relationships are fluid and change according to the situation, and how participating actors define it. To engage in intimacies, rituals and form, and to shift between them requires social competence and active participation. People in this study demonstrate these. Despite restrictions they offer resistance to the environment and to dementia. They often make profound and metaphorical statements, to which this ethnography gives voice. Keywords Everyday life; interaction; nursing home culture; people with dementia; resistance; self and others; social competence; surveillance.

abstract: Alzheimer’s disease (AD) is characterized by the degeneration of cholinergic basal forebrain (CBF) neurons in the nucleus basalis of Meynert (nbM), which provides the majority of cholinergic input to the cortical mantle and together form the basocortical cholinergic system. Histone deacetylase (HDAC) dysregulation in the temporal lobe has been associated with neuronal degeneration during AD progression. However, whether HDAC alterations play a role in cortical and cortically-projecting cholinergic nbM neuronal degeneration during AD onset is unknown. In an effort to characterize alterations in the basocortical epigenome semi-quantitative western blotting and immunohistochemistry were utilized to evaluate HDAC and sirtuin (SIRT) levels in individuals that died with a premortem clinical diagnosis of no cognitive impairment (NCI), mild cognitive impairment (MCI), mild/moderate AD (mAD), or severe AD (sAD). In the frontal cortex, immunoblots revealed significant increases in HDAC1 and HDAC3 in MCI and mAD, followed by a decrease in sAD. Cortical HDAC2 levels remained stable across clinical groups. HDAC4 was significantly increased in prodromal and mild AD compared to aged cognitively normal controls. HDAC6 significantly increased during disease progression, while SIRT1 decreased in MCI, mAD, and sAD compared to controls. Basal forebrain levels of HDAC1, 3, 4, 6 and SIRT1 were stable across disease progression, while HDAC2 levels were significantly decreased in sAD. Quantitative immunohistochemistry was used to identify HDAC2 protein levels in individual cholinergic nbM nuclei immunoreactive for the early phosphorylated tau marker AT8, the late-stage apoptotic tau marker TauC3, and Thioflavin-S, a marker of mature neurofibrillary tangles (NFTs). HDAC2 nuclear immunoreactivity was reduced in individual cholinergic nbM neurons across disease stages, and was exacerbated in tangle-bearing cholinergic nbM neurons. HDAC2 nuclear reactivity correlated with multiple cognitive domains and with NFT formation. These findings identify global HDAC and SIRT alterations in the cortex while HDAC2 dysregulation contributes to cholinergic nbM neuronal dysfunction and NFT pathology during the progression of AD. / Dissertation/Thesis / Doctoral Dissertation Neuroscience 2018

This thesis has four chapters. After a brief introduction in Chapter 1, the $AJ$-conjecture is introduced in Chapter 2. The $AJ$-conjecture for a knot $K \subset S^3$ relates the $A$-polynomial and the colored Jones polynomial of $K$. If $K$ satisfies the $AJ$-conjecture, sufficient conditions on $K$ are given for the $(r,2)$-cable knot $C$ to also satisfy the $AJ$-conjecture. If a reduced alternating diagram of $K$ has $\eta_+$ positive crossings and $\eta_-$ negative crossings, then $C$ will satisfy the $AJ$-conjecture when $(r+4\eta_-)(r-4\eta_+)>0$ and the conditions of Theorem 2.2.1 are satisfied. Chapter 3 is about quantum curves and their relation to the $AJ$ conjecture. The variables $l$ and $m$ of the $A$-polynomial are quantized to operators that act on holomorphic functions. Motivated by a heuristic definition of the Jones polynomial from quantum physics, an annihilator of the Chern-Simons section of the Chern-Simons line bundle is found. For torus knots, it is shown that the annihilator matches with that of the colored Jones polynomial. In Chapter 4, a tangle functor is defined using semicyclic representations of the quantum group $U_q(sl_2)$. The semicyclic representations are deformations of the standard representation used to define Kashaev's invariant for a knot $K$ in $S^3$. It is shown that at certain roots of unity the semicyclic tangle functor recovers Kashaev's invariant.

This dissertation is on a study of 2-string free tangle decompositions of knots with tunnel number two. As an application, we construct infinitely many counter-examples to a conjecture in the literature stating that the tunnel number of the connected sum of prime knots doesn't degenerate by more than one: t(K_1#K_2)≥ t(K_1)+t(K_2)-1, for K_1 and K_2 prime knots. We also study 2-string free tangle decompositions of links with tunnel number two and obtain an equivalent statement to the one on knots. Further observations on tunnel number and essential tangle decompositions are also made. / text