A STUDY OF THE RELATIONSHIP BETWEEN SELF-ASSESSMENT AND CLINICAL EVALUATION OF HEARING STATUS

The relationship was explored between a subjective measure of hearing status, derived from a functional self-assessment expressed in terms of ability to hear and understand spoken words, and a comparable objective measure of hearing status, obtained from a speech reception test. The Augmentation Survey of the Health and Nutrition Examination Survey of the National Center for Health Statistics provided the necessary data for a sample of 3059 adults. Using chi-square tests for the subsample with the highest level of objectively assessed hearing status, favorable subjective assessments were found to be significantly associated with higher income, lower age group, higher level of educational attainment, greater psychological adjustment, fewer symptoms of depression, and higher self-ratings of overall health. In a linear regression with self-assessment of hearing status as the dependent variable, less than one-quarter of the variation could be explained by objective status and the six explanatory variables.^

Genetic variants in the mammalian target of rapamycin (mTOR) signaling pathway as predictors of survival and clinical response in women with ovarian cancer

Background. The mTOR pathway is commonly altered in human tumors and promotes cell survival and proliferation. Preliminary evidence suggests this pathway's involvement in chemoresistance to platinum and taxanes, first line therapy for epithelial ovarian cancer. A pathway-based approach was used to identify individual germline single nucleotide polymorphisms (SNPs) and cumulative effects of multiple genetic variants in mTOR pathway genes and their association with clinical outcome in women with ovarian cancer. ^ Methods. The case-series was restricted to 319 non-Hispanic white women with high grade ovarian cancer treated with surgery and platinum-based chemotherapy. 135 SNPs in 20 representative genes in the mTOR pathway were genotyped. Hazard ratios (HRs) for death and Odds ratios (ORs) for failure to respond to primary therapy were estimated for each SNP using the multivariate Cox proportional hazards model and multivariate logistic regression model, respectively, while adjusting for age, stage, histology and treatment sequence. A survival tree analysis of SNPs with a statistically significant association (p<0.05) was performed to identify higher order gene-gene interactions and their association with overall survival. ^ Results. There was no statistically significant difference in survival by tumor histology or treatment regimen. The median survival for the cohort was 48.3 months. Seven SNPs were significantly associated with decreased survival. Compared to those with no unfavorable genotypes, the HR for death increased significantly with the increasing number of unfavorable genotypes and women in the highest risk category had HR of 4.06 (95% CI 2.29–7.21). The survival tree analysis also identified patients with different survival patterns based on their genetic profiles. 13 SNPs on five different genes were found to be significantly associated with a treatment response, defined as no evidence of disease after completion of primary therapy. Rare homozygous genotype of SNP rs6973428 showed a 5.5-fold increased risk compared to the wild type carrying genotypes. In the cumulative effect analysis, the highest risk group (individuals with ≥8 unfavorable genotypes) was significantly less likely to respond to chemotherapy (OR=8.40, 95% CI 3.10–22.75) compared to the low risk group (≤4 unfavorable genotypes). ^ Conclusions. A pathway-based approach can demonstrate cumulative effects of multiple genetic variants on clinical response to chemotherapy and survival. Therapy targeting the mTOR pathway may modify outcome in select patients.^

TAZ AS A REGULATOR OF MESENCHYMAL TRANSFORMATION AND CLINICAL AGGRESSIVENESS IN GLIOMAS

Glioblastoma multiforme (GBM) is an aggressive, high grade brain tumor. Microarray studies have shown a subset of GBMs with a mesenchymal gene signature. This subset is associated with poor clinical outcome and resistance to treatment. To establish the molecular drivers of this mesenchymal transition, we correlated transcription factor expression to the mesenchymal signature and identified transcriptional co-activator with PDZ-binding motif (TAZ) to be highly associated with the mesenchymal shift. High TAZ expression correlated with worse clinical outcome and higher grade. These data led to the hypothesis that TAZ is critical to the mesenchymal transition and aggressive clinical behavior seen in GBM. We investigated the expression of TAZ, its binding partner TEAD, and the mesenchymal marker FN1 in human gliomas. Western analyses demonstrated increased expression of TAZ, TEAD4, and FN1 in GBM relative to lower grade gliomas. We also identified CpG islands in the TAZ promoter that are methylated in most lower grade gliomas, but not in GBMs. TAZ-methylated glioma stem cell (GSC) lines treated with a demethylation agent showed an increase in mRNA and protein TAZ expression; therefore, methylation may be another novel way TAZ is regulated since TAZ is epigenetically silenced in tumors with a better clinical outcome. To further characterize the role of TAZ in gliomagenesis, we stably silenced or over-expressed TAZ in GSCs. Silencing of TAZ decreased invasion, self-renewal, mesenchymal protein expression, and tumor-initiating capacity. Over-expression of TAZ led to an increase in invasion, mesenchymal protein expression, mesenchymal differentiation, and tumor-initiating ability. These actions are dependent on TAZ interacting with TEAD since all these effects were abrogated with TAZ could not bind to TEAD. We also show that TAZ and TEAD directly bind to mesenchymal gene promoters. Thus, TAZ-TEAD interaction is critically important in the mesenchymal shift and in the aggressive clinical behavior of GBM. We identified TAZ as a regulator of the mesenchymal transition in gliomas. TAZ could be used as a biomarker to both estimate prognosis and stratify patients into clinically relevant subgroups. Since mesenchymal transition is correlated to tumor aggressiveness, strategies to target and inhibit TAZ-TEAD and the downstream gene targets may be warranted in alternative treatment.

RNA-SEQUENCING APPLICATIONS: GENE EXPRESSION QUANTIFICATION AND METHYLATOR PHENOTYPE IDENTIFICATION

My dissertation focuses on two aspects of RNA sequencing technology. The first is the methodology for modeling the overdispersion inherent in RNA-seq data for differential expression analysis. This aspect is addressed in three sections. The second aspect is the application of RNA-seq data to identify the CpG island methylator phenotype (CIMP) by integrating datasets of mRNA expression level and DNA methylation status. Section 1: The cost of DNA sequencing has reduced dramatically in the past decade. Consequently, genomic research increasingly depends on sequencing technology. However it remains elusive how the sequencing capacity influences the accuracy of mRNA expression measurement. We observe that accuracy improves along with the increasing sequencing depth. To model the overdispersion, we use the beta-binomial distribution with a new parameter indicating the dependency between overdispersion and sequencing depth. Our modified beta-binomial model performs better than the binomial or the pure beta-binomial model with a lower false discovery rate. Section 2: Although a number of methods have been proposed in order to accurately analyze differential RNA expression on the gene level, modeling on the base pair level is required. Here, we find that the overdispersion rate decreases as the sequencing depth increases on the base pair level. Also, we propose four models and compare them with each other. As expected, our beta binomial model with a dynamic overdispersion rate is shown to be superior. Section 3: We investigate biases in RNA-seq by exploring the measurement of the external control, spike-in RNA. This study is based on two datasets with spike-in controls obtained from a recent study. We observe an undiscovered bias in the measurement of the spike-in transcripts that arises from the influence of the sample transcripts in RNA-seq. Also, we find that this influence is related to the local sequence of the random hexamer that is used in priming. We suggest a model of the inequality between samples and to correct this type of bias. Section 4: The expression of a gene can be turned off when its promoter is highly methylated. Several studies have reported that a clear threshold effect exists in gene silencing that is mediated by DNA methylation. It is reasonable to assume the thresholds are specific for each gene. It is also intriguing to investigate genes that are largely controlled by DNA methylation. These genes are called “L-shaped” genes. We develop a method to determine the DNA methylation threshold and identify a new CIMP of BRCA. In conclusion, we provide a detailed understanding of the relationship between the overdispersion rate and sequencing depth. And we reveal a new bias in RNA-seq and provide a detailed understanding of the relationship between this new bias and the local sequence. Also we develop a powerful method to dichotomize methylation status and consequently we identify a new CIMP of breast cancer with a distinct classification of molecular characteristics and clinical features.

Abortion and Clinical Practice. Abortion Review Papers from the bpas conference: London, 25 - 26 June 2008

The groundbreaking bpas conference The Future of Abortion: Controversies and Care brought together clinicians, academics, policymakers and advocates from the UK, Europe and the USA for a discussion about all aspects of abortion provision. Taking place during a critical Parliamentary debate about the UK abortion law, the conference generated great excitement and presented a number of important research findings and policy suggestions.In order to maximise the strides made by The Future of Abortion conference in taking forward an international, interdisciplinary discussion, Abortion Review is producing a series of special editions in which we have published edited transcripts of the presentations. In this third edition, Abortion and Clinical Practice, the presentations examine developments in abortion research and practice, and what these might indicate for the kind of abortion service that should be provided.

Tab. 1: Geographical, temperature and chemical features of sites on Bear Island and Spitsbergen

In arctic populations of Macrothrix hirsuticornis life cycles are mainly governed by temperature. This was found by using laboratory cultures in combination with the analysis of population samples from waters in Svalbard. In arctic waters ex-ephippio-++ usually produce gamogenetic F1-++ together with a high percentage of oo, which have to fertilize the resting eggs. Temperatures around 14°C, which are very rare in waters of Svalbard, will induce parthenogenetic oo in the F1 and even the F2-generation, a mode of reproduction normally found in Macrothrix-populations of Central Europe. This was found in laboratory cultures of M. hirsuticornis from Bear Island, and there was evidence, that a similar cycle occurs in warm wells in Spitsbergen. The arctic distribution of M. hirsuticornis mainly depends on temperature, which regulates the speed of individual development. But this can only be understood together with the length of time, during which suitable life conditions are given. Physiological adaptations to life in waters in high latitudes could not be found, in spite of the extreme northern occurrence of M. hirsuticornis.

The Japan-Peru FTA : antecedents, significance and main features

The Economic Partnership Agreement (EPA) between Japan and Peru came into effect on March 1, 2012. This paper provides background information about this agreement's significance, mostly from a Peruvian point of view. It focuses on the following subjects: the statistical trends showing Peru's declining shares in Japan's trade and investment flows with Latin American countries between the mid-1970s and mid-2000s, the main explanatory factors of such a deterioration in Peru's economic position over that period, the changes of trade policy strategy in both countries since the 2000s, and the EPA negotiation process and some of its key results as featured in the text of the agreement.

Gas discharges for continental Spain: geochemical and isotopic features

In this work the results of a geochemical and isotopic survey of 37 gas discharges was carried out in continental Spain are presented and discussed. On the basis of the gas chemical composition, four different areas can be distinguished, as follows: 1) Selva-Emborda (SE) region; 2) Guadalentin Valley (GV); 3) Campo de Calatrava (CC) and 3) the inner part of Spain (IS). The SE, GV and CC areas are characterized by CO2-rich gases, while IS has N2 as main gas compound. The CO2-rich gases can be distinguished at their turn on the basis on the helium and carbon isotopic composition. The SE and CC areas have a strong mantle signature (up to 3 Ra). Nevertheless, the carbon isotopic composition of CC is within the mantle range and that of SE is slightly more negative (down to -8‰ PDB). The GV gases have a lower mantle signature (61 Ra) with respect to SE and CC and more negative carbon isotopes (6-10‰ PDB). It is worth to mention that the SE, GV and CC areas are related to the youngest volcanic activity in continental Spain, for example the Garrotxa Volcanic Field in Catalonia records the latest event dated at 10,000 years, and the isotopic features, particularly those of helium, are suggesting the presence of magmatic bodies still cooling at depth. The N2-rich gases, i.e. those from the IS area, has an atmospheric origin, as highlighted by the N2/Ar ratio that ranges between those of air and ASW (Air Saturated Water). The isotopic composition of carbon is distinctly negative (down to -21‰ PDB) and that of helium is typically crustal (0.02-0.08 Ra), confirming that these gas discharges are related to a relatively shallow source.

Texture perception determined by doy protein isolate and inulin addition in potato puree: links with mechanical and microstructural features

This study evaluated the effect of adding soy protein isolate (SPI) and long-chain perception, trained and untrained panel inulin (INL) blends with 10 different SPI : INL ratios on the textural, rheological and 17 microstructural properties of freshly made and frozen/thawed potato puree. All the potato puree samples were subjected to a sensory texture pro?le analysis and a 21 trained panel rated the intensity of six descriptors, while an untrained panel did the same on six selected frozen/thawed products. The main SPI : INL ratio effect remained signi?cant for all the descriptors evaluated, when the analysis of variance was applied considering the untrained assessors as random effects. However, only trained panel scores for creaminess corresponded well with untrained assessor. Rheological ?ow index values were linked with variations in perceived consistency, and geometric and surface textural attributes were explained by structural features such as the presence of INL crystallites and SPI coarse strands.

Impact bruises in pomaceae fruits: Evaluation methods and structural features.

Using a laboratory impact tester, impacts were applied to fruits of different varieties of apples and pears. The response to impact was analized, and many parameters were recorded, to be correlated to bruise susceptibility and to ripeness changes. Different methods for the detection and evaluation of the bruised Area and its features were studied, using direct observation and various reactives. Different types of bruises were established.