No / A Collaborations for Leadership in Applied Health Research and Care (CLAHRC) funded study engaged health visitors in investigating the ways in which routinely collected data were captured, stored, transferred, analysed and then used to inform clinical practice. This report focuses on the establishment of a community of practice (CoP) to support these activities and then presents the outcome of the CoP's investigations into the collection and use of data on one key area of concern; maternal smoking behaviour. Evidence-based recommendations for clinical practice made by the CoP ranged from simple changes to the daily working practices of health visitors to ensure accurate data collection and dissemination of information, to major changes to processes and procedures relating to data quality and data sharing. The findings of the CoP emphasised the importance of cross-discipline communication and collaboration.

Adherence is considered a prerequisite for the success of exercise programs for musculoskeletal disorders. The negative effects of non-adherence to exercise recommendations impact the cost of care, and also treatment effectiveness, treatment duration, the therapeutic relationship, waiting times, the efficiency of personnel and use of equipment. Adherence to therapeutic exercise intervention is a multifaceted problem. The World Health Organization (WHO) established the multidimensional adherence model (MAM). The MAM describes five interactive dimensions (socioeconomic, healthcare team and system, condition-related, therapy-related, and patient-related factors) that have an effect on patient adherence. The first purpose of this dissertation was to explore the MAM dimension of condition-related factors to determine the Quick Disabilities of the Arm Shoulder and Hand (QDASH) minimal clinical important difference (MCID) for three distal upper extremity conditions. The second purpose was to explore the MAM dimension of personal factors to learn from individuals who expressed incongruence between their QDASH and GROC scores; how they described their perceived change in therapy. The third purpose was to explore the MAM dimension of therapy-related factors to examine the effect of patient-therapist collaborative goal setting on patient adherence to treatment and QDASH outcomes. Results demonstrated in the first study that diagnosis specific MCID’s differed from the global MCID using multiple diagnoses. In the second study results demonstrated that patients expect to have a dedicated therapist who they can trust to work collaboratively with them to establish goals and spend time with them to achieve these goals. In the third study, our first hypothesis was not supported for all three measures of adherence. The median for home exercise program diary adherence was found to trend towards significance by 8.7 percent favoring the experimental group Mann-Whitney U (p < .100). Our second hypothesis was not supported. The experimental group receiving collaborative goal setting intervention had similar QDASH mean change scores 45.9±27.6 compared to the control group 46.1±23.8, Mann-Whitney U (p < .859).

Combining effect sizes from individual studies using random-effects models are commonly applied in high-dimensional gene expression data. However, unknown study heterogeneity can arise from inconsistency of sample qualities and experimental conditions. High heterogeneity of effect sizes can reduce statistical power of the models. We proposed two new methods for random effects estimation and measurements for model variation and strength of the study heterogeneity. We then developed a statistical technique to test for significance of random effects and identify heterogeneous genes. We also proposed another meta-analytic approach that incorporates informative weights in the random effects meta-analysis models. We compared the proposed methods with the standard and existing meta-analytic techniques in the classical and Bayesian frameworks. We demonstrate our results through a series of simulations and application in gene expression neurodegenerative diseases.

Alcohol Dependence (AD) is a chronic substance use disorder with moderate heritability (60%). Linkage and genome-wide association studies (GWAS) have implicated a number of loci; however, the molecular mechanisms underlying AD are unclear. Advances in systems biology allow genome-wide expression data to be integrated with genetic data to detect expression quantitative trait loci (eQTL), polymorphisms that regulate gene expression levels, influence phenotypes and are significantly enriched among validated genetic signals for many commonly studied traits including AD. We integrated genome-wide mRNA and miRNA expression data with genotypic data from the nucleus accumbens (NAc), a major addiction-related brain region, of 36 subjects (18 AD cases, 18 matched controls). We applied weighted gene co-expression network analysis (WGCNA) to identify mRNA and miRNA gene co-expression modules significantly associated with AD. We identified six mRNA modules, two of which were downregulated in AD and were enriched for neuronal marker gene expression. The remaining four modules were upregulated in AD and enriched for astrocyte and microglial marker gene expressions. After performing gene set enrichment analysis (GSEA), we found that neuronal-specific modules enriched for oxidative phosphorylation, mitochondrial dysfunction and MAPK signaling pathways and glial-specific modules enriched for immune related processes, cell adhesion molecules and cell signaling pathways. WGCNA was also applied to miRNA data and identified two downregulated and one upregulated modules in AD. We intersected computationally predicted miRNA:mRNA interactions with miRNA and mRNA expression correlations to identify 481 significant (FDR<0.10) miRNA:mRNA targeting pairs. Over half (54%) of the mRNAs were targeted cooperatively by more than one miRNA suggesting a potentially important cellular mechanism relevant to AD. After integrating our expression and genetic data we identified 591 significant mRNA and 68 significant miRNA cis-eQTLs (<1 megabase) (FDR<0.10). After querying against GWAS data from the Colaborative Study on Genetics of Alcohol and Study of Addiction: Gentics and Environment, eQTLs for neuronatin (NNAT; rs1780705), proteosome subunit type 5 (PSMB5; rs10137082), long non-coding RNA (PKI55; rs13392737), adaptor related protein complex 1 sigma one subunit (AP1S1; rs12079545) and translocation associate membrane protein 1 (TRAM1; rs13277972) were associated with AD or alcohol related phenotypes at p<10-4.

INTRODUÇÃO: Recentemente, a classificação molecular do câncer gástrico (CG) emergiu como opção promissora para definir subgrupos prognósticos, distinguir o comportamento biológico, além de permitir a identificação de potenciais alvos terapêuticos para drogas específicas. Por meio de técnicas moleculares, o CG foi dividido em 4 subtipos: instabilidade de microssatélites (MSI), vírus Epstein-Barr (EBV)-positivo, genomicamente estável (GS) e instabilidade cromossômica (CIN). Os custos associados à complexidade técnica das metodologias moleculares são ainda um obstáculo para sua implantação na prática de rotina. OBJETIVOS: Determinar os grupos da classificação molecular por meio da expressão proteica de marcadores associados a cada subtipo. Comparar as diferentes classificações moleculares existentes e propor um novo modelo. MÉTODOS: Foram avaliados, retrospectivamente, 287 pacientes com CG submetidos à gastrectomia-D2 curativa, por meio da construção de tissue microarray. A expressão das proteínas de reparo do DNA, E-caderina e p53 foram avaliadas por imuno-histoquímica (IH), determinando os grupos MSI, GS e CIN, respectivamente. O EBV foi detectado por hibridização in situ (ISH). RESULTADOS: Após avaliação histopatológica, 179 (62,4%) pacientes foram classificados como CIN, 58 (20,2%) MSI, 30 (10,5%) EBV e 20 (7%) como GS. Os subtipos associaram-se com características distintas, tais como: gênero masculino (EBV, p=0.101); idade avançada (MSI, p=0,017), menor relação neutrófilo-linfócito (CIN, p=0,029), gastrectomia total (EBV, p < 0,001), localização distal (MSI, p=0,004), Laurén difuso (GS, p < 0,001), e estádio avançado (GS, p=0,014). O subtipo MSI apresentou melhor sobrevida livre de doença (SLD) (82,8%), seguido pelo EBV e CIN (ambos com 70%) e GS (50%) (p=0.005). A sobrevida global (SG) foi maior nos tumores MSI (75,9%), seguido pelo EBV (73,3%), CIN (65.4%) e GS (45%, mediana de 25 meses) (p=0.007). Em análise multivariada, gastrectomia total, pT, pN e os subtipos tumorais foram fatores significativos associados à SLD (MSI p=0,012; EBV p=0,037; CIN p=0,018; GS referência). Do mesmo modo, o tipo de cirurgia, pT, e os subtipos tumorais foram fatores independentes associados a SG (MSI p=0,010; EBV p=0,006; CIN p=0,025; GS referência). Com base no risco de recidiva dos pacientes do estudo, nova classificação, que inclui 5 subtipos, foi proposta. Evidenciou-se que a classificação por risco e cluster tiveram melhor acurácia para identificar recidivas e óbitos respectivamente. CONCLUSÃO: A análise IH/ISH foi capaz de determinar subtipos de CG com características clinicopatológicas e prognósticos distintos, reproduzindo os subtipos obtidos pela classificação molecular / BACKGROUND: Recently, the molecular classification of gastric cancer (CG) emerged as a promising option to define prognostic subgroups, to distinguish biological behavior, and to identify potential therapeutic targets for specific drugs. Through molecular techniques, GC was divided into 4 subtypes: microsatellite instability (MSI), Epstein-Barr virus (EBV) positive, genomically stable (GS) and chromosomal instability (CIN). The costs associated with the technical complexity of the molecular methodologies are still an obstacle to its implementation in routine practice. OBJECTIVES: To determine molecular classification groups by means of protein expression of markers associated with each subtype. To compare the different existing molecular classifications and propose a new model. METHODS: We retrospectively evaluated 287 CG patients submitted to curative D2-gastrectomy through the construction of tissue microarray. Expression of the DNA repair proteins, E-cadherin and p53 were evaluated by immunohistochemistry (IH), determining the MSI, GS and CIN subtypes, respectively. EBV was detected by in situ hybridization (ISH). RESULTS: After the histopathological evaluation, 179 (62.4%) patients were classified as CIN, 58 (20.2%) MSI, 30 (10.5%) EBV and 20 GS (7%) as GS. The subtypes presented associations with distinct characteristics, such as: male gender (EBV, p=0.101); advanced age (MSI, p=0.017), Laurén diffuse type (GS, p < 0.001), lower neutrophil-lymphocyte ratio (CIN, p=0.029), total gastrectomy (EBV, p < 0.001), distal location (MSI, p=0.004), and advanced stage (GS, p=0.014). The MSI subtype presented better disease-free survival (DFS) (82.8%), followed by the EBV and CIN subtypes (both with 70%) and GS (50%) (p=0.005). Overall survival (OS) was higher in MSI tumors (75.9%), followed by EBV (73.3%), CIN (65.4%) and GS (45%, median of 25 months) (p=0.007). In multivariate analysis, total gastrectomy, tumor invasion, lymph node metastasis, and tumor subtypes were significant factors associated with SLD (MSI p=0.012, EBV p=0.037, CIN p=0.018, GS reference). Likewise, type of surgery, pT, and tumor subtypes were independent factors associated with OS (p=0.010, p=0.010, EBV p=0.006, CIN p=0.025, GS reference). Based on the risk of recurrence, a new classification including 5 subtypes was proposed. It was evidenced that the risk classification and cluster had better accuracy to identify recurrences and deaths respectively. CONCLUSION: The IH / ISH analysis was able to determine CG groups with clinicopathological characteristics and distinct prognoses, reproducing the subtypes obtained by the molecular classification

O vínculo entre papilomavírus humano de alto risco e câncer cervical está bem estabelecido. Apesar da existência de vacinas profiláticas contra infecções pelos tipos mais comuns de HPV, para infecções e tumores causados por esses vírus as alternativas terapêuticas são restritas. Encontramos alguns motivos com homologias para proteínas do HPV de alto risco durante o imunoscreening de uma biblioteca de phage display com soros de participantes HPV-16-soropositivos da coorte Ludwig-McGill. Após enriquecimento das sequências, os bacteriófagos recombinantes foram purificados e amplificados para uso como imunógenos.Usando uma abordagem profilática, nós vacinamos experimentalmente camundongos imunocompetentes com um dos nossos bacteriófagos recombinantes, usando o bacteriófago sem inserto como controle. Estes camundongos foram então desafiados com células tumorais TC-1 (HPV-16 positivas), tendo-se avaliado as respostas imunes disparadas durante a progressão tumoral. Também usamos uma abordagem terapêutica, aonde os camundongos foram primeiro injetados com as células tumorais e imunizados com o bacteriófago após o estabelecimento do tumor. O crescimento tumoral foi monitorado e os tumores, baço e linfonodos foram avaliados quanto à quantidade e qualidade da resposta imunológica. Os testes de ELISA revelaram que todos os camundongos vacinados responderam à imunização com os diferentes bacteriófagos. O crescimento tumoral foi significativamente reduzido nas imunizações profiláticas e terapêuticas, embora a redução do tumor fosse mínima quando os camundongos foram tratados 9 dias após o enxerto. A redução no crescimento tumoral também se traduziu em uma sobrevivência significativamente maior para os camundongos imunizados. Estudos de infiltração celular não revelaram alterações em diversas sub-populações imunes, mas uma tendência de aumento de linfócitos T citotóxicos foi observada nos camundongos imunizados com PEP1 (bacteriófago contendo inserto). A importância deste aumento de CD8 na redução observada do crescimento tumoral foi confirmada utilizando camundongos CD8-knockout, onde a redução do crescimento tumoral previamente observada foi anulada. Foi observado um aumento de taxa CD8:CD4 nos camundongos imunizados e isto é uma indicação de ambiente tumoral citotóxico. Os ensaios de proliferação celular para testar a especificidade do antígeno dos linfócitos dos camundongos imunizados foram, no entanto, inconclusivos; da mesma forma, não pudemos alterar o padrão observado com o uso de adjuvante CpG. A utilidade da técnica de phage display também foi observada neste trabalho experimental. Trabalhos adicionais para entender o mecanismo de ação desses fagos recombinantes no controle do crescimento de tumores causados por HPV e seu potencial imuno-estimulador são necessários / The link between high-risk human papillomavirus and cervical cancer is well established. Despite the existence of prophylactic vaccines against infections by the most common types of HPV, therapeutic alternatives are limited for infections and tumors caused by these viruses. We found some homology motifs for high-risk HPV proteins during the immune-panning of a phage display library with sera from HPV-16- seropositive participants of the Ludwig-McGill cohort. After enrichment of the sequences, the recombinant bacteriophages were purified and amplified for use as immunogens. Using a prophylactic approach, we vaccinated experimentally immunocompetent mice with one of our recombinant bacteriophages using the insertless bacteriophage as a control. These mice were then challenged with TC-1 tumor cells (HPV-16 positive), and the immune responses triggered during tumor progression were evaluated. We also used a therapeutic approach where mice were first injected with tumor cells and immunized with the bacteriophage after tumor establishment. Tumor growth was monitored and tumors, spleen and lymph nodes were evaluated for the quantity and quality of the immune response. ELISA tests revealed that all vaccinated mice responded to immunization with the different bacteriophages. Tumor growth was significantly reduced in prophylactic and therapeutic immunizations, although tumor reduction was minimal when mice were treated 9 days after TC-1 cells grafting. The reduction in tumor growth also translated into a significantly greater survival for the immunized mice. Cell infiltration studies did not reveal changes in several immune subpopulations, but an upward trend in cytotoxic T lymphocytes was observed in mice immunized with PEP1 (insert-containing bacteriophage). The importance of this increase in CD8 in the observed reduction of tumor growth was confirmed using CD8-knockout mice, where the previously observed reduction of tumor growth was abolished. An increase in CD8:CD4 rate was observed in the immunized mice and this is an indication of a cytotoxic tumor environment. Cell proliferation assays to test the antigen specificity of lymphocytes from immunized mice were, however, inconclusive; likewise, we could not change the pattern observed with the use of CpG adjuvant. The usefulness of the phage display technique was also observed in this experimental work. Additional studies to understand the mechanism of action of these recombinant phages in the control of HPV tumor growth and its immunostimulatory potential are warranted

O vínculo entre papilomavírus humano de alto risco e câncer cervical está bem estabelecido. Apesar da existência de vacinas profiláticas contra infecções pelos tipos mais comuns de HPV, para infecções e tumores causados por esses vírus as alternativas terapêuticas são restritas. Encontramos alguns motivos com homologias para proteínas do HPV de alto risco durante o imunoscreening de uma biblioteca de phage display com soros de participantes HPV-16-soropositivos da coorte Ludwig-McGill. Após enriquecimento das sequências, os bacteriófagos recombinantes foram purificados e amplificados para uso como imunógenos.Usando uma abordagem profilática, nós vacinamos experimentalmente camundongos imunocompetentes com um dos nossos bacteriófagos recombinantes, usando o bacteriófago sem inserto como controle. Estes camundongos foram então desafiados com células tumorais TC-1 (HPV-16 positivas), tendo-se avaliado as respostas imunes disparadas durante a progressão tumoral. Também usamos uma abordagem terapêutica, aonde os camundongos foram primeiro injetados com as células tumorais e imunizados com o bacteriófago após o estabelecimento do tumor. O crescimento tumoral foi monitorado e os tumores, baço e linfonodos foram avaliados quanto à quantidade e qualidade da resposta imunológica. Os testes de ELISA revelaram que todos os camundongos vacinados responderam à imunização com os diferentes bacteriófagos. O crescimento tumoral foi significativamente reduzido nas imunizações profiláticas e terapêuticas, embora a redução do tumor fosse mínima quando os camundongos foram tratados 9 dias após o enxerto. A redução no crescimento tumoral também se traduziu em uma sobrevivência significativamente maior para os camundongos imunizados. Estudos de infiltração celular não revelaram alterações em diversas sub-populações imunes, mas uma tendência de aumento de linfócitos T citotóxicos foi observada nos camundongos imunizados com PEP1 (bacteriófago contendo inserto). A importância deste aumento de CD8 na redução observada do crescimento tumoral foi confirmada utilizando camundongos CD8-knockout, onde a redução do crescimento tumoral previamente observada foi anulada. Foi observado um aumento de taxa CD8:CD4 nos camundongos imunizados e isto é uma indicação de ambiente tumoral citotóxico. Os ensaios de proliferação celular para testar a especificidade do antígeno dos linfócitos dos camundongos imunizados foram, no entanto, inconclusivos; da mesma forma, não pudemos alterar o padrão observado com o uso de adjuvante CpG. A utilidade da técnica de phage display também foi observada neste trabalho experimental. Trabalhos adicionais para entender o mecanismo de ação desses fagos recombinantes no controle do crescimento de tumores causados por HPV e seu potencial imuno-estimulador são necessários / The link between high-risk human papillomavirus and cervical cancer is well established. Despite the existence of prophylactic vaccines against infections by the most common types of HPV, therapeutic alternatives are limited for infections and tumors caused by these viruses. We found some homology motifs for high-risk HPV proteins during the immune-panning of a phage display library with sera from HPV-16- seropositive participants of the Ludwig-McGill cohort. After enrichment of the sequences, the recombinant bacteriophages were purified and amplified for use as immunogens. Using a prophylactic approach, we vaccinated experimentally immunocompetent mice with one of our recombinant bacteriophages using the insertless bacteriophage as a control. These mice were then challenged with TC-1 tumor cells (HPV-16 positive), and the immune responses triggered during tumor progression were evaluated. We also used a therapeutic approach where mice were first injected with tumor cells and immunized with the bacteriophage after tumor establishment. Tumor growth was monitored and tumors, spleen and lymph nodes were evaluated for the quantity and quality of the immune response. ELISA tests revealed that all vaccinated mice responded to immunization with the different bacteriophages. Tumor growth was significantly reduced in prophylactic and therapeutic immunizations, although tumor reduction was minimal when mice were treated 9 days after TC-1 cells grafting. The reduction in tumor growth also translated into a significantly greater survival for the immunized mice. Cell infiltration studies did not reveal changes in several immune subpopulations, but an upward trend in cytotoxic T lymphocytes was observed in mice immunized with PEP1 (insert-containing bacteriophage). The importance of this increase in CD8 in the observed reduction of tumor growth was confirmed using CD8-knockout mice, where the previously observed reduction of tumor growth was abolished. An increase in CD8:CD4 rate was observed in the immunized mice and this is an indication of a cytotoxic tumor environment. Cell proliferation assays to test the antigen specificity of lymphocytes from immunized mice were, however, inconclusive; likewise, we could not change the pattern observed with the use of CpG adjuvant. The usefulness of the phage display technique was also observed in this experimental work. Additional studies to understand the mechanism of action of these recombinant phages in the control of HPV tumor growth and its immunostimulatory potential are warranted

Introduction: Chronic orofacial pain (COFP) is distressing and disabling to sufferers and can be costly to patients, health services and society. Frequently, no underlying medical pathology can be found to account for the condition. Despite this, patients are treated according to a biomedical model, often by mechanistic and invasive procedures, which tend to be unsuccessful and not evidence based. Evidence suggests that cognitive behavioural therapy (CBT) based management may produce improved outcomes for patients. However, published studies can tell us little about which intervention components are effective, or recommend an optimum way for these components to be applied. Aim: To develop an evidence based intervention for the management of COFP that is feasible and acceptable to patients and practitioners. Method: The Medical Research Council’s guidelines for developing complex interventions were used as a framework for the research. Evidence from multiple sources was synthesised to produce the draft components of an intervention to manage COFP. An exploratory trial investigated preliminary outcomes, acceptability, feasibility and explored parameters for a full scale randomised control trial. Results: The intervention was acceptable to participants and could be feasibly implemented. No conclusions could be drawn relating to the effectiveness of the intervention. Participants were not affected at baseline for a number of outcomes, which implies that cut off points should be introduced into the inclusion and exclusion criteria of any future studies. Conclusion: The study produced an intervention which is acceptable and feasible to participants, however it is not known if it is effective. A number of recommendations are made for progression to a larger, definitive trial.

Parkinson’s disease (PD) is a disorder of the nervous system that causes problems with movement (motor symptoms) as well as other problems such as mood disorders, cognitive changes, sleep disorders, constipation, pain, and other non-motor symptoms. The severity of PD symptoms worsens over time as the disease progresses, and while there are treatments for the motor and some non-motor symptoms there is no known cure for PD. Thus there is a high demand for therapies to slow the progressive neurodegeneration observed in PD. Two clinical trials at the University of Kentucky College of Medicine (NCT02369003, NCT01833364) are currently underway that aim to develop a disease-modifying therapy that slows the progression of PD. These clinical trials are evaluating the safety and feasibility of an autologous peripheral nerve graft to the substantia nigra in combination with Deep Brain Stimulation (DBS) for the treatment of PD. By grafting peripheral nerve tissue to the Substantia Nigra, the researchers aim to introduce peripheral nerve tissue, which is capable of functional regeneration after injury, to the degenerating Substantia Nigra of patients with PD. The central hypothesis of these clinical trials is that the grafted tissue will slow degeneration of the target brain region through neural repair actions of Schwann cells as well as other pro-regenerative features of the peripheral nerve tissue. This dissertation details analysis of the peripheral nerve tissue used in the above clinical trials with respect to tissue composition and gene expression, both of injury-naive human peripheral nerve as well as the post-conditioning injury nerve tissue used in the grafting procedure. RNA-seq analysis of sural nerve tissue pre and post-conditioning show significant changes in gene expression corresponding with transdifferentiation of Schwann cells from a myelinating to a repair phenotype, release of growth factors, activation of macrophages and other immune cells, and an increase in anti-apoptotic and neuroprotective gene transcripts. These results reveal in vivo gene expression changes involved in the human peripheral nerve injury repair process, which has relevance beyond this clinical trial to the fields of Schwann cell biology and peripheral nerve repair. To assess the neurobiology of the graft post-implantation we developed an animal model of the grafting procedure, termed Neuro-Avatars, which feature human graft tissue implanted into athymic nude rats. Survival and infiltration of human graft cells into the host brain were shown using immunohistochemistry of Human Nuclear Antigen. Surgical methods and outcomes from the ongoing development of this animal model are reported. To connect the results of these laboratory studies to the clinical trial we compared the severity of motor symptoms before surgery to one year post-surgery in patients who received the analyzed graft tissue. Motor symptom severity was assessed using the Unified Parkinson’s Disease Rating Scale Part III. Finally, the implications and future directions of this research is discussed. In summary, this dissertation advances the translational science cycle by using clinical trial findings and samples to answer basic science questions that will in turn guide future clinical trial design.

Normal movement execution requires proper coupling of motor and sensory activation. An increasing body of literature supports the idea that incorporation of sensory stimulation into motor rehabilitation practices increases its effectiveness. Paired associative stimulation (PAS) studies, in which afferent and efferent pathways are activated in tandem, have brought attention to the importance of well-timed stimulation rather than non-associative (i.e., open-loop) activation. In patients with tetraplegia resulting from spinal cord injury (SCI), varying degrees of upper limb function may remain and could be harnessed for rehabilitation. Incorporating associative sensory stimulation coupled with self-paced motor training would be a means for supplementing sensory deficits and improving functional outcomes. In a motor rehabilitation setting, it seems plausible that sensory feedback stimulation in response to volitional movement execution (to the extent possible), which is not utilized in most PAS protocols, would produce greater benefits. This capability is developed and tested in the present study by implementing a brain-computer interface (BCI) to apply sensory stimulation synchronized with movement execution through the detection of movement intent in real time from electroencephalography (EEG). The results demonstrate that accurate sensory stimulation application in response to movement intent is feasible in SCI patients with chronic motor deficit and often precedes the onset of movement, which is deemed optimal by PAS investigations that do not involve a volitional movement task.