Dans cette thèse, nous avons étudié le problème de cache codée en construisant la connexion entre le problème de cache codée avec placement non-codé et codage d'index, et en tirant parti des résultats de codage d'index pour caractériser les limites fondamentales du problème de cache codée. Nous avons principalement analysé le problème de cache codée dans le modèle de diffusion à liaison partagée et dans les réseaux combinés. Dans la première partie de cette thèse, pour les réseaux de diffusion de liens partagés, nous avons considéré la contrainte que le contenu placé dans les caches est non-codé. Lorsque le contenu du cache est non-codé et que les demandes de l'utilisateur sont révélées, le problème de cache peut être lié à un problème de codage d'index. Nous avons dérivé des limites fondamentales pour le problème de cache en utilisant des outils pour le problème de codage d'index. Nous avons dérivé un nouveau schéma réalisable de codage d'index en base d'un codage de source distribué. Cette borne interne est strictement meilleure que la borne interne du codage composite largement utilisée. Pour le problème de cache centralisée, une borne externe sous la contrainte de placement de cache non-codé est proposée en base de une borne externe “acyclic” de codage d’index. Il est prouvé que cette borne externe est atteinte par le schéma cMAN lorsque le nombre de fichiers n'est pas inférieur au nombre d'utilisateurs, et par le nouveau schéma proposé pour le codage d’index, sinon. Pour le problème de cache décentralisée, cette thèse propose une borne externe sous la contrainte que chaque utilisateur stocke des bits uniformément et indépendamment au hasard. Cette borne externe est atteinte par le schéma dMAN lorsque le nombre de fichiers n'est pas inférieur au nombre d'utilisateurs, et par notre codage d'index proposé autrement. Dans la deuxième partie de cette thèse, nous avons considéré le problème de cache dans les réseaux de relais, où le serveur communique avec les utilisateurs aidés par le cache via certains relais intermédiaires. En raison de la dureté de l'analyse sur les réseaux généraux, nous avons principalement considéré un réseau de relais symétrique bien connu, `réseaux de combinaison’, y compris H relais et binom {H} {r} utilisateurs où chaque utilisateur est connecté à un r-sous-ensemble de relais différent. Nous avons cherché à minimiser la charge de liaison maximale pour les cas les plus défavorables. Nous avons dérivé des bornes externes et internes dans cette thèse. Pour la borne externes, la méthode directe est que chaque fois que nous considérons une coupure de x relais et que la charge totale transmise à ces x relais peut être limitée à l'extérieur par la borne externes du modèle de lien partagé, y compris binom {x} {r} utilisateurs. Nous avons utilisé cette stratégie pour étendre les bornes externes du modèle de lien partagé et la borne externe “acyclic” aux réseaux de combinaison. Dans cette thèse, nous avons également resserré la borne externe “acyclic” dans les réseaux de combinaison en exploitant davantage la topologie du réseau et l'entropie conjointe des diverses variables aléatoires. Pour les schémas réalisables, il existe deux approches, la séparation et la non-séparation. De plus, nous avons étendu nos résultats à des modèles plus généraux, tels que des réseaux combinés où tous les relais et utilisateurs sont équipés par cache, et des systèmes de cache dans des réseaux relais plus généraux. Les résultats d'optimisation ont été donnés sous certaines contraintes et les évaluations numériques ont montré que nos schémas proposés surpassent l'état de l'art. / In this thesis, we investigated the coded caching problem by building the connection between coded caching with uncoded placement and index coding, and leveraging the index coding results to characterize the fundamental limits of coded caching problem. We mainly analysed the caching problem in shared-link broadcast model and in combination networks. In the first part of this thesis, for cache-aided shared-link broadcast networks, we considered the constraint that content is placed uncoded within the caches. When the cache contents are uncoded and the user demands are revealed, the caching problem can be connected to an index coding problem. We derived fundamental limits for the caching problem by using tools for the index coding problem. A novel index coding achievable scheme was first derived based on distributed source coding. This inner bound was proved to be strictly better than the widely used “composite (index) coding” inner bound by leveraging the ignored correlation among composites and the non-unique decoding. For the centralized caching problem, an outer bound under the constraint of uncoded cache placement is proposed based on the “acyclic index coding outer bound”. This outer bound is proved to be achieved by the cMAN scheme when the number of files is not less than the number of users, and by the proposed novel index coding achievable scheme otherwise. For the decentralized caching problem, this thesis proposes an outer bound under the constraint that each user stores bits uniformly and independently at random. This outer bound is achieved by dMAN when the number of files is not less than the number of users, and by our proposed novel index coding inner bound otherwise. In the second part of this thesis, we considered the centralized caching problem in two-hop relay networks, where the server communicates with cache-aided users through some intermediate relays. Because of the hardness of analysis on the general networks, we mainly considered a well-known symmetric relay networks, combination networks, including H relays and binom{H}{r} users where each user is connected to a different r-subset of relays. We aimed to minimize the max link-load for the worst cases. We derived outer and inner bounds in this thesis. For the outer bound, the straightforward way is that each time we consider a cut of x relays and the total load transmitted to these x relays could be outer bounded by the outer bound for the shared-link model including binom{x}{r} users. We used this strategy to extend the outer bounds for the shared-link model and the acyclic index coding outer bound to combination networks. In this thesis, we also tightened the extended acyclic index coding outer bound in combination networks by further leveraging the network topology and joint entropy of the various random variables. For the achievable schemes, there are two approaches, separation and non-separation. In the separation approach, we use cMAN cache placement and multicast message generation independent of the network topology. We then deliver cMAN multicast messages based on the network topology. In the non-separation approach, we design the placement and/or the multicast messages on the network topology. We proposed four delivery schemes on separation approach. On non-separation approach, firstly for any uncoded cache placement, we proposed a delivery scheme by generating multicast messages on network topology. Moreover, we also extended our results to more general models, such as combination networks with cache-aided relays and users, and caching systems in more general relay networks. Optimality results were given under some constraints and numerical evaluations showed that our proposed schemes outperform the state-of-the-art.

Mu-opioid receptor (MOR) agonists are effective agents for pain management, but are also limited by a number of undesirable effects. One approach to enhance the therapeutic effects and minimize the undesirable effects of MOR agonists may be to combine MOR agonists with an adjunct targeting a different receptor system. This targeted medical approach, known as “combination therapy”, aims to augment the desired effects of the MOR agonist (i.e. antinociception) and/or diminish the undesirable deleterious side effects of the MOR agonist. This dissertation investigated the utility of this approach in an assay of thermal nociception and schedule-controlled responding in male rhesus monkeys with three aims. One aim determined the utility of N-methyl D-aspartate (NMDA) receptor antagonists to selectively enhance MOR agonist antinociception. A second identified the pharmacological determinants of antinociceptive interactions between a nociceptin opioid peptide (NOP) receptor agonist and MOR agonists. A third aim investigated the potential for fixed-proportion mixtures of a competitive MOR antagonist and MOR agonist to manipulate antinociceptive efficacy. Experimental results did not support the utility of NMDA antagonists as adjuncts to selectively enhance MOR agonist antinociception. Furthermore, the antinociceptive interactions between a NOP agonist and MOR agonists were modest and occurred under a narrow range of conditions. Finally, fixed proportion MOR antagonist-agonist mixtures were effective in manipulating antinociceptive in vivo efficacy. In conclusion, this dissertation does not provide strong empirical evidence that a combination therapy approach will result in clinically effective and selective enhancement of MOR agonist analgesia. The dissertation concludes with proposed strategies and novel preclinical methods to enhance preclinical-to-clinical translation of effective candidate analgesics.

Introduction: Addition of a second drug used to be a strategy to achieve clinical stabilization of multiple sclerosis in many patients with on-going activity despite monotherapy. Modern immunosuppressive drugs used in monotherapy exert more specific mode of action. Methods: This retrospective observational study evaluated 5-year data from 85 patients with active multiple sclerosis despite monotherapy with either interferon beta or azathioprine, who received add-on azathioprine or interferon beta, respectively. In a subgroup of 23 patients 10- year data were analysed. In a second part of the study, a group of 126 patients switched either from interferon beta or glatiramer acetate to fingolimod was followed-up for one after the change of their treatment and a in a subgroup of 53 patients the 2-year data were assessed. Clinical (relapse frequency, disability) parameters were compared preceding and following the addition of second drug or the switch of treatment. Laboratory results and potential serious adverse events were evaluated in a group of patients with combination therapy. Results: The add-on treatment triggered a drop in annualised relapse rate by approximately 1.5 points sustained over 5 and 10 years. No effect on disability was observed. Simultaneously, white blood cell and lymphocyte counts...

>Magister Scientiae - MSc / Background and Aims Human Immunodeficiency Virus (HIV) type 1 group M subtype C (HIV-1C) accounts for nearly half of global HIV-1 infections, with South Africa (SA) being one of the countries with the highest infection burden. In recent years, SA has made great strides in tackling its HIV epidemic, resulting in the country being recognized globally as the one sub-Saharan country with the largest combination antiretroviral therapy (cART) programme. Regardless of the potency of cART, the efficacy of the treatment is limited and hampered by the emergence of drug resistance. The majority of research on HIV-1 infections, effect of antiretroviral (ARV) drugs and understanding resistance to ARV drugs has been extensively conducted, but mainly on HIV-1 subtype B (HIV-1B), with less information known about HIV-1C. HIV-1’s viral Integrase (IN) enzyme has become a viable target for highly specific cART, due to its importance in the infection and replication cycle of the virus. The lack of a complete HIV-1C IN protein structure has negatively impacted the progress on structural studies of nucleoprotein reaction intermediates. The mechanism of HIV-1 viral DNA’s integration has been studied extensively at biochemical and cellular levels, but not at a molecular level. This study aims to use in silico methods that involve molecular modeling and molecular dynamic (MD) simulations to prioritize mutations that could affect HIV-1C IN binding to DNA and the IN strand-transfer inhibitor (INSTI) dolutegravir (DTG). The purpose is to help tailor more effective personalized treatment options for patients living with HIV in SA. This study will in part use patient derived sequence data to identify mutations and model them into the protein structure to understand their impact on the HIV-1C IN protein structure folding and dynamics. Methods Our sample cohort consisted of 11 sample sequences derived from SA HIV-1 treatmentexperienced patients who were being treated with the INSTI raltegravir (RAL). The sequences were submitted to the Stanford HIV resistance database (HIVdb) to screen for any new/novel variants resulting from possible RAL failure. Some of these new variants were analyzed to analyse their effect, if any, on the binding of DTG to the HIV-1C IN protein. Additionally, an HIV-1C IN consensus sequence constructed from SA’s HIV-1 infected population was used to model a complete three-dimensional wild type (WT) HIV-1C IN homology model. All samples were sequenced by our collaborators at the Division of Medical Virology, Stellenbosch University together with the National Health Laboratory Services (NHLS), SA. The HIV-1CZA WT-IN protein enzyme was predicted using SWISS-MODEL, and the quality of the resulting model validated. Various analyses were conducted in order to study and assess the effect of the selected new variants on the protein structure and binding of DTG to the IN protein. The mutation Cutoff Scanning Matrix (mCSM) program was used to predict protein stability after mutation, while PyMol helped to study any changes in polar contact activity before and after mutation. PyMol was also used to generate four mutant HIV-1C IN complex structures and these structures together with the WT IN were subjected to production MD simulations for 150 nanoseconds (ns). Trajectory analyses of the MD simulations were also conducted and reported. Results A total of 21 new variants were detected in our sample cohort, from which only six were chosen for further analyses within the study. A homology model of HIV-1C IN was successfully constructed and validated. The structural quality assessment indicated high reliability of the HIV-1C IN tetrameric structure, with more than 90.0% confidence in modelled regions. Of the six selected variants, only one (S119P) was calculated to be slightly stabilizing to the protein structure, with the other five found to be destabilizing to the IN protein structure. Variant S119P showed a loss in polar contacts that could destabilize the protein structure, while variant Y143R, resulted in the gain of polar contacts which could reduce flexibility of the 140’s region affecting drug binding. Similarly, mutant systems P3 (S119P, Y143R) and P4 (V150A, M154I) showed reduced hydrogen bond formation and the weakest non-bonded pairwise interaction energy. These two systems, P3 and P4, also showed significantly reduced to none polar contacts between DTG, magnesium (MG) ions and the IN protein, compared to the WT IN and P2 mutant IN systems. Interestingly, the WT structure and systems P1 (I113V) and P2 (L63I, V75M, Y143R) showed the highest non-bonded interaction energy, compared to systems P3 and P4. This was further supported by the polar interaction analyses of simulation clusters from the WT IN and mutant IN system P2 (L63I, V75M, Y143R), which were the only protein structures that formed polar contacts with DTG, MG ions and DDE motif residues, while P1 only made contacts with DNA and IN residues. Conclusion Findings from this study leads to a conclusion that double mutants (S119P, Y143R) and (V150A, M154I) may result in a reduction in the efficacy of DTG, especially when in combination. Furthermore, variants identified in systems P1 and P2 may still allow for effective DTG binding to IN and outcompete viral DNA for host DNA to prevent strand transfer. To the best of our knowledge, this is the first study that uses the consensus WT HIV1C IN sequence to build an accurate 3D homology model to understand the effect of less frequently detected/reported variants on DTG binding in a South African context. https://etd.

Bakgrund: Crohns sjukdom är en form av inflammatorisk tarmsjukdom som kännetecknas av kronisk histologisk inflammation, en autoimmun sjukdom som inte är medicinskt botbar men det finns olika medicinska terapier som kan kontrollera symtomen. Det förekommer omväxlande perioder med skov och lugn, operation behövs ibland, medicineringen är konstant och alla dessa faktorer leder till försämrad livskvalitet. Crohns sjukdom skadar ofta ileum men det kan påverka vilket segment av mag-tarmkanalen som helst från mun till perianalt område, lesionerna kan ha formen av fläckar, med vissa delar påverkade medan andra förblir helt normala. Incidensen av Crohns sjukdom i Sverige är mellan 5 och 10 per 100 000 och prevalensen är cirka 200 per 100 000. Medan dödsfallet med Crohns sjukdom minskar, ökar de andra problemen som är förknippade med Crohns sjukdom och detta sätter press på sjukvården. För att hålla sjukdomen under kontroll behöver patienter farmakologisk induktionsbehandling i början av sjukdomen och underhållsbehandling under resten av livet. Just för att behandlingen behövs på lång sikt (livet ut) har det varit absolut nödvändigt att hitta den bästa behandlingsstrategin. Målet med behandlingen är att göra patienten symptomfri med hjälp av medicinering. Mål: Syftet med detta examensarbete var att ta reda på hur tillgängliga biologiska läkemedel ska användas för att få optimal effekt, närmare bestämt om de biologiska läkemedlen ska användas som monoterapi eller i kombination med andra läkemedel vid behandling av Crohns sjukdom. Metod: PubMed-databasen har använts för att söka, välja och analysera fem relevanta randomiserade kontrollerade kliniska prövningar om Crohns sjukdom. Nyckelordet som användes för att hitta alla dessa fem relevanta artiklar var ''Crohn's combination therapy''. Resultat: Resultaten i den första artikeln påpekar att kombinationsbehandling med infliximab + azatioprin hade bättre resultat jämfört med infliximab monoterapi och infliximab monoterapi hade bättre resultat jämfört med azatioprin monoterapi för att uppnå klinisk remission och slemhinneläkning. Den andra artikeln strider mot den första studien och säger att om tillräckliga läkemedelskoncentrationer uppnås och bibehålls genom terapeutisk läkemedelsövervakning med infliximab, kanske kombinationsterapi med tiopuriner inte behövs för att uppnå önskade kliniska resultat. Den tredje artikeln drog slutsatsen att adalimumab var överlägsen tiopuriner i att förhindra endoskopiskt återfall av Crohns sjukdom hos patienter med hög risk för återfall efter operation. Den fjärde artikeln identifierade ingen effektivitetsfördel med kombinationsbehandling med adalimumab + immunmodulatorer jämfört med adalimumab monoterapi. Den femte artikeln drog slutsatsen att vedolizumab i kombination med stabila doser av kortikosteroider inducerade mer effektivt klinisk remission än antingen placebo plus kortikosteroider eller enbart vedolizumab. Slutsatser: En universell slutsats kan inte dras om fördelen med kombinationsbehandling bestående av biologiska och immunsuppressiva läkemedel jämfört med biologisk monoterapi. Olika tillvägagångssätt är nödvändiga för varje enskild patient eftersom medicinen kan vara olika för induktions- och underhållsterapier, sjukdomsvaraktigheten påverkar hur patienten kommer att reagera på mediciner och medicineringen som Crohns sjukdoms-patienter fick tidigare kan också påverka hur patienten kommer att svara på medicinering. / Background: Crohn's disease is a form of inflammatory bowel disease characterized by chronic histological inflammation, an autoimmune disorder that is not medically curable but there are various medical therapies able to control the symptoms. It has periods of exacerbation and calmness, with surgery needed sometimes, the use of medication is constant and all these factors lead to an impaired quality of life. Crohn's disease often damages the ileum but it can affect any segment of the gastrointestinal tract from mouth to perianal area, the lesions may take the form of patches, with some sections affected while others remain perfectly normal. The incidence of Crohn's disease in Sweden is between 5 and 10 per 100,000 and the prevalence is around 200 per 100,000. While the fatal burden is declining, the non-fatal burden is increasing. In order to keep the disease under control, patients require pharmacological induction treatment at the beginning and maintenance treatment for the rest of their life. Because the treatment is needed long-term, finding the best treatment strategy has become imperative. The goal with the therapy is to make the patient symptom-free with the help of medication. Objective: The purpose of this degree project is to find out how biological drugs should be used in order to have optimal effect, more specifically, if the biological medicines should be used as monotherapy or in combination with other medicines in the treatment of Crohn's disease. Method: PubMed database has been used to search, select and analyze five relevant randomized controlled clinical trials about Crohn’s disease. The keyword used to find all these five relevant articles were ''Crohn's combination therapy''. Results: The results in the first article point out that Infliximab + Azathioprine combination therapy had better results compared to infliximab monotherapy and infliximab monotherapy had better results compared with Azathioprine monotherapy in achieving clinical remission and mucosal healing. The second article contradicts the first study and states that if adequate drug concentrations are achieved and maintained through therapeutic drug monitoring with infliximab, combination therapy with thiopurines may not be required to achieve desired clinical results. The third article concluded that adalimumab was superior to thiopurines in preventing endoscopic recurrence of Crohn's disease in patients with high risk of recurrence after surgery. The fourth article identified no efficacy benefit of adalimumab + immunomodulators combination therapy compared to adalimumab monotherapy. The fifth article concluded that vedolizumab in combination with stable doses of corticosteroids induced more efficient clinical remission than either placebo plus corticosteroids or vedolizumab alone. Conclusions: A universal conclusion cannot be drawn regarding the superiority of combination treatment consisting of biological and immunosuppressive medicines compared to biological monotherapy. Different approaches are necessary for every individual patient because the medication can be different for induction and maintenance therapies, the duration of the disease affects how the patient will respond to medication, and the medication that the Crohn’s disease patient took in the past may also affect how the patient will respond to medication.

DNA-damaging chemotherapeutics are a consistently employed for the treatment of cancer, and are regularly part of first-line combination therapeutic regimens. However, these regimens often display limited activity in cancers including of the lung and breast. Novel therapeutic strategies are urgently required. Understanding the molecular mechanisms regulating DNA-damaging chemotherapeutics activity will lead to such novel strategies. Activating transcription factor 3 (ATF3) is a stress inducible gene that plays a significant role in regulating cellular stress including DNA damage. This thesis investigates the role of ATF3 in mediating the cytotoxic effects of two commonly employed DNA-damaging chemotherapeutics, cisplatin and doxorubicin. This study also identifies other independent ATF3 inducing agents in potential novel combination therapeutic strategies. In this study, cell line models of cisplatin-resistance were generated independently from two non-small cell lung cancer (NSCLC) cell lines, Calu6 and H23. Full transcriptome RNA-sequencing analysis identified ATF3 as the most highly dysregulated apoptosis regulatory gene in the cisplatin-resistant compared to their respective parental cell lines following treatment with cisplatin. Further characterization identified cisplatin induced activation of JNK as the key regulator of ATF3 induction in these cell lines. Restoring JNK activity resulted in induced ATF3 expression and re-sensitization of the resistant cell lines to cisplatin treatment. FDA-approved 1200 compound library screens were employed to identify agents that can enhance cisplatin cytotoxicity as well as whose cytotoxicity was dependent on ATF3 expression. Vorinostat, an HDAC inhibitor, was identified in both screens and importantly displayed synergistic cytotoxicity in combination with cisplatin. In addition, ATF3 was also induced with treatments of the DNA damaging agent doxorubicin in these NSCLC cell lines including in the cisplatin resistant models. This work suggested a different mechanism of ATF3 induction by doxorubicin and the potential role of ATF3 in mediating doxorubicin cytotoxicity was further investigated in breast cancer cells. Doxorubicin robustly increased ATF3 expression in human breast cancer cell lines and tumor tissue ex-vivo. Loss of ATF3 in MEFs resulted in reduced sensitivity to doxorubicin treatment compared to wild-type MEFs. Employing the same library screen as above, compounds with ATF3 dependent mechanisms that could enhance doxorubicin cytotoxicity were identified. Vorinostat, as well as, the nucleoside analogues trifluridine and 6-mercaptopurine induced ATF3 expression and enhanced doxorubicin cytotoxicity. This study demonstrated that ATF3 plays an important role in mediating the cytotoxic effect of the DNA-damaging chemotherapeutics cisplatin and doxorubicin. It also provides rationale for ATF3 as a potential therapeutic target, and for the incorporation of ATF3 inducing agents in novel combination therapeutic strategies.

Magister Scientiae Dentium - MSc(Dent) / Candida glabrata (C. glabrata/ Cg) is a pathogenic organism that is increasingly developing frank innate and acquired resistance to the most commonly used antifungal agents, namely, azole group of antifungals. Furthermore, C. glabrata-associated oropharyngeal infections affecting immunocompromised patients, are more difficult to treat and the development of resistance worsen the prognosis. Molecular studies related the emergence of resistance in C. glabrata to the upregulation of ATP-binding cassette (ABC) transporter genes, which work by reducing drug concentration within the cell via drug efflux mechanism, and among these genes, CgCDR1 is considered to play a major role in resistance development. Thus, in order to overcome this problem, several combinations of antifungal agents are being studied. Aim: To evaluate the effect of a combination therapy of fluconazole and amphotericin B on the growth and CDR1 gene expression of C. glabrata. Research design and methodology: This in-vitro study evaluated the effect of a combination therapy of fluconazole and amphotericin B on the growth of C. glabrata and related it to the expression of CgCDR1 resistance gene. C. glabrata was revived in brain heart infusion (BHI) broth and later inoculated onto agar plates. Following overnight incubation, 5 colonies were transferred using a sterile loop into 2 ml of phosphate buffered saline (PBS) solution to establish McFarland (Mcf) standard. Later, the solution was diluted by transferring 200 μL to 400 ml of yeast peptone dextrose (YPD) agar (flask 1). From (flask 1), 90 ml, 99 ml and 89 ml of inoculum were allocated into 3 separate flasks, into which 10 ml fluconazole, 1 ml amphotericin B and 11 ml combination (10 ml fluconazole + 1 ml amphotericin B) were added, respectively. The inoculums were left to settle for 20 minutes, then incubated at 37oC with serial dilutions carried after 30 minutes, 2, 4, 6 and 24 hours. From the 96-microtiter plate, 10 μL for each treatment arm and time interval were transferred from selected wells and onto 30 Casein-peptone Soymeal-peptone (CASO) agar plates, and incubated for 24 hours. After incubation, the number of colonies were counted using an automated colony counter, to establish colony forming unit (CFU)/ml. CgCDR1 gene expression was analyzed using real time polymerase chain reaction. After 6 hours of incubation, a sample was taken from each treatment arm, transferred into CASO agar plates and incubated for 24 hours at 37oC. After establishing Mcf, gene extraction and gene expression were carried out according to manufacturer’s instructions. Results and discussion: No significant difference between the effect of the combination and amphotericin B was evident regarding C. glabrata growth. However, the combination therapy was more effective against C. glabrata than fluconazole, with a marked decrease in candidal growth at 30 minutes and 6 hours. Furthermore, the expression of CgCDR1 gene at 6 hours contact time was more pronounced in the samples of C. glabrata treated with the combination therapy, compared to that of the monotherapy. Conclusion: The combination therapy had better effect on the growth of C. glabrata than fluconazole monotherapy. On the other hand, the expression of CgCDR1 was detected in the samples of C. glabrata treated with the combination therapy, suggesting the ability of the yeast to adapt and develop resistance in such environment.

C-reactive protein (CRP) is a component of innate immunity. The concentration of CRP in serum increases in microbial infections including Streptococcus pneumoniae infection. Employing a mouse model of pneumococcal infection, it has been shown that passively administered human wild-type CRP protects mice against infection, provided that CRP is injected into mice within two hours of administering pneumococci. Engineered CRP (E-CRP) molecules have been reported recently; unlike wild-type CRP, passively administered E-CRP protected mice against infection even when E-CRP was injected into mice after twelve hours of administering pneumococci. The current study was aimed at comparing the protective capacity of E-CRP with that of an antibiotic clarithromycin. We established a mouse model of pneumococcal infection in which both E-CRP and clarithromycin, when used alone, provided minimal but equal protection against infection. In this model, the combination of E-CRP and clarithromycin drastically reduced bacteremia and increased survival of mice when compared to the protective effects of either E-CRP or clarithromycin alone. E-CRP was more effective in reducing bacteremia in mice treated with clarithromycin than in untreated mice. Also, there was 90% reduction in antibiotic dosing by including E-CRP in the antibiotic-treatment for maximal protection of infected mice. These findings provide an example of cooperation between the innate immune system and molecules that prevent multiplication of bacteria, and that should be exploited to develop novel combination therapies for infections against multidrug-resistant pneumococci. The reduction in antibiotic dosing by including E-CRP in the combination therapy might also resolve the problem of developing antibiotic resistance.

The purpose of this thesis is to examine the effects of inhaled corticosteroid drugs (ICs) on the voice due to their frequent use in treating an increasing prevalence of asthma disorders. As part of a larger five-year study, the focus of this thesis is specifically on whether 8 weeks of in vivo exposure to ICs will cause changes in the sustained subglottal pressure, sustained airflow, and visual-perceptual ratings of edema and erythema in excised rabbit larynges. Researchers administered either ICs or a control nebulized isotonic saline solution to 22 rabbits in vivo, sacrificed them, and harvested their larynges for benchtop research. While ensuring proper tissue preservation, researchers then finely dissected the larynges to expose the true vocal folds and run phonation trials. Dependent variables included continuous acoustic signals (Hz), subglottal pressure (cm H2O), and airflow (L/min) data for 15 phonation trials per rabbit larynx. Researchers also collected still image photographs at this time and subsequently normalized them for use in the visual-perceptual portion of this thesis. For visual-perceptual ratings, raters used a 0-3 equal appearing interval scale to rate aspects of edema and erythema on left and right vocal fold and arytenoid tissues. Results indicate that, when compared to control larynges exposed to nebulized isotonic saline, experimental larynges treated with ICs require significantly higher subglottal pressure to maintain phonation, p < .05. Mean sustained phonation for experimental larynges is 11.24 cm H2O compared to 8.92 cm H2O for that of control larynges. Phonation trials for experimental larynges have significantly higher sustained airflow with a mean of 0.09 L/min compared to 0.07 L/min for that of control larynges, p < .05. Surprisingly, experimental larynges have higher average fundamental frequencies with less variability (mean: 519 Hz, standard deviation: 66 Hz) than that of control larynges (mean: 446 Hz, standard deviation: 130 Hz). On visual-perceptual ratings, experimental larynges have significantly higher severity ratings on all eight items rated, p < .0001 - p = .0305. Based on these results, it is concluded that ICs cause significant damage to rabbit vocal folds, as evidenced by higher sustained pressure, higher airflow, and higher severity ratings for experimental versus control larynges. The dependent variables in this thesis are novel in benchtop model research and demonstrate a unique perspective on this research question. Thus, this thesis informs future phonation, benchtop, and visual-perceptual research.

The emergence of drug resistance is a serious threat to the long-term virologic success and durability of HIV-1 therapy. Adherence has been shown to be a major determinant of drug resistance; however, each pharmacologic class of antiretroviral drugs has a unique adherence–resistance relationship. We develop an immunological model of the HIV-1 infected human immune system that integrates the unique mechanisms of action of reverse transcriptase and protease inhibiting drugs. A system of impulsive differential equations is used to examine the drug kinetics within CD4⁺ T cells. Stability analysis was preformed to determine the long-term dynamics of the model. Using the endpoints of an impulsive periodic orbit in the drug levels, the maximal length of a drug holiday while avoiding drug resistance is theoretically determined; the minimum number of doses that must be subsequently taken to return to pre-interruption drug levels is also established. Heterogeneity in inter-individual differences on drug-holiday length is explored using sensitivity analysis based on Latin Hypercube Sampling and Partial Rank Correlation Coefficient analysis. Extremely short drug holidays are acceptable, as long as they are followed by a period of strict adherence. Numerical simulations demonstrate that if the drug holiday exceeds these recommendations, the cost in virologic rebound is unacceptably high. These theoretical predictions are in line with clinical results and may also help form the basis of future clinical trials.