Different approaches to identify markers for meat quality and production traits in pigs: analysis of the transcriptome in post mortem skeletal muscle and investigation of candidate genes

Due to the growing attention of consumers towards their food, improvement of quality of animal products has become one of the main focus of research. To this aim, the application of modern molecular genetics approaches has been proved extremely useful and effective. This innovative drive includes all livestock species productions, including pork. The Italian pig breeding industry is unique because needs heavy pigs slaughtered at about 160 kg for the production of high quality processed products. For this reason, it requires precise meat quality and carcass characteristics. Two aspects have been considered in this thesis: the application of the transcriptome analysis in post mortem pig muscles as a possible method to evaluate meat quality parameters related to the pre mortem status of the animals, including health, nutrition, welfare, and with potential applications for product traceability (chapters 3 and 4); the study of candidate genes for obesity related traits in order to identify markers associated with fatness in pigs that could be applied to improve carcass quality (chapters 5, 6, and 7). Chapter three addresses the first issue from a methodological point of view. When we considered this issue, it was not obvious that post mortem skeletal muscle could be useful for transcriptomic analysis. Therefore we demonstrated that the quality of RNA extracted from skeletal muscle of pigs sampled at different post mortem intervals (20 minutes, 2 hours, 6 hours, and 24 hours) is good for downstream applications. Degradation occurred starting from 48 h post mortem even if at this time it is still possible to use some RNA products. In the fourth chapter, in order to demonstrate the potential use of RNA obtained up to 24 hours post mortem, we present the results of RNA analysis with the Affymetrix microarray platform that made it possible to assess the level of expression of more of 24000 mRNAs. We did not identify any significant differences between the different post mortem times suggesting that this technique could be applied to retrieve information coming from the transcriptome of skeletal muscle samples not collected just after slaughtering. This study represents the first contribution of this kind applied to pork. In the fifth chapter, we investigated as candidate for fat deposition the TBC1D1 [TBC1 (tre-2/USP6, BUB2, cdc16) gene. This gene is involved in mechanisms regulating energy homeostasis in skeletal muscle and is associated with predisposition to obesity in humans. By resequencing a fragment of the TBC1D1 gene we identified three synonymous mutations localized in exon 2 (g.40A>G, g.151C>T, and g.172T>C) and 2 polymorphisms localized in intron 2 (g.219G>A and g.252G>A). One of these polymorphisms (g.219G>A) was genotyped by high resolution melting (HRM) analysis and PCR-RFLP. Moreover, this gene sequence was mapped by radiation hybrid analysis on porcine chromosome 8. The association study was conducted in 756 performance tested pigs of Italian Large White and Italian Duroc breeds. Significant results were obtained for lean meat content, back fat thickness, visible intermuscular fat and ham weight. In chapter six, a second candidate gene (tribbles homolog 3, TRIB3) is analyzed in a study of association with carcass and meat quality traits. The TRIB3 gene is involved in energy metabolism of skeletal muscle and plays a role as suppressor of adipocyte differentiation. We identified two polymorphisms in the first coding exon of the porcine TRIB3 gene, one is a synonymous SNP (c.132T> C), a second is a missense mutation (c.146C> T, p.P49L). The two polymorphisms appear to be in complete linkage disequilibrium between and within breeds. The in silico analysis of the p.P49L substitution suggests that it might have a functional effect. The association study in about 650 pigs indicates that this marker is associated with back fat thickness in Italian Large White and Italian Duroc breeds in two different experimental designs. This polymorphisms is also associated with lactate content of muscle semimembranosus in Italian Large White pigs. Expression analysis indicated that this gene is transcribed in skeletal muscle and adipose tissue as well as in other tissues. In the seventh chapter, we reported the genotyping results for of 677 SNPs in extreme divergent groups of pigs chosen according to the extreme estimated breeding values for back fat thickness. SNPs were identified by resequencing, literature mining and in silico database mining. analysis, data reported in the literature of 60 candidates genes for obesity. Genotyping was carried out using the GoldenGate (Illumina) platform. Of the analyzed SNPs more that 300 were polymorphic in the genotyped population and had minor allele frequency (MAF) >0.05. Of these SNPs, 65 were associated (P<0.10) with back fat thickness. One of the most significant gene marker was the same TBC1D1 SNPs reported in chapter 5, confirming the role of this gene in fat deposition in pig. These results could be important to better define the pig as a model for human obesity other than for marker assisted selection to improve carcass characteristics.

Procedures of quality control and data analysis of multi-site ground-based observations for the absolute flux calibration of Gaia

The Gaia space mission is a major project for the European astronomical community. As challenging as it is, the processing and analysis of the huge data-flow incoming from Gaia is the subject of thorough study and preparatory work by the DPAC (Data Processing and Analysis Consortium), in charge of all aspects of the Gaia data reduction. This PhD Thesis was carried out in the framework of the DPAC, within the team based in Bologna. The task of the Bologna team is to define the calibration model and to build a grid of spectro-photometric standard stars (SPSS) suitable for the absolute flux calibration of the Gaia G-band photometry and the BP/RP spectrophotometry. Such a flux calibration can be performed by repeatedly observing each SPSS during the life-time of the Gaia mission and by comparing the observed Gaia spectra to the spectra obtained by our ground-based observations. Due to both the different observing sites involved and the huge amount of frames expected (≃100000), it is essential to maintain the maximum homogeneity in data quality, acquisition and treatment, and a particular care has to be used to test the capabilities of each telescope/instrument combination (through the “instrument familiarization plan”), to devise methods to keep under control, and eventually to correct for, the typical instrumental effects that can affect the high precision required for the Gaia SPSS grid (a few % with respect to Vega). I contributed to the ground-based survey of Gaia SPSS in many respects: with the observations, the instrument familiarization plan, the data reduction and analysis activities (both photometry and spectroscopy), and to the maintenance of the data archives. However, the field I was personally responsible for was photometry and in particular relative photometry for the production of short-term light curves. In this context I defined and tested a semi-automated pipeline which allows for the pre-reduction of imaging SPSS data and the production of aperture photometry catalogues ready to be used for further analysis. A series of semi-automated quality control criteria are included in the pipeline at various levels, from pre-reduction, to aperture photometry, to light curves production and analysis.

Longitudinal analysis of quality of life in patients receiving conformal radiation therapy for prostate cancer

To prospectively assess quality of life (QoL) in patients receiving conformal radiation therapy (CRT) for prostate cancer.

High-quality lung fixation by controlled closed loop perfusion for stereological analysis in a large animal model

Stereology is an essential method for quantitative analysis of lung structure. Adequate fixation is a prerequisite for stereological analysis to avoid bias in pulmonary tissue, dimensions and structural details. We present a technique for in situ fixation of large animal lungs for stereological analysis, based on closed loop perfusion fixation.

Quality Control in the Healthcare Industry: An Analysis of Surgery Turnover Times

For virtually all hospitals, utilization rates are a critical managerial indicator of efficiency and are determined in part by turnover time. Turnover time is defined as the time elapsed between surgeries, during which the operating room is cleaned and preparedfor the next surgery. Lengthier turnover times result in lower utilization rates, thereby hindering hospitals’ ability to maximize the numbers of patients that can be attended to. In this thesis, we analyze operating room data from a two year period provided byEvangelical Community Hospital in Lewisburg, Pennsylvania, to understand the variability of the turnover process. From the recorded data provided, we derive our best estimation of turnover time. Recognizing the importance of being able to properly modelturnover times in order to improve the accuracy of scheduling, we seek to fit distributions to the set of turnover times. We find that log-normal and log-logistic distributions are well-suited to turnover times, although further research must validate this finding. Wepropose that the choice of distribution depends on the hospital and, as a result, a hospital must choose whether to use the log-normal or the log-logistic distribution. Next, we use statistical tests to identify variables that may potentially influence turnover time. We find that there does not appear to be a correlation between surgerytime and turnover time across doctors. However, there are statistically significant differences between the mean turnover times across doctors. The final component of our research entails analyzing and explaining the benefits of introducing control charts as a quality control mechanism for monitoring turnover times in hospitals. Although widely instituted in other industries, control charts are notwidely adopted in healthcare environments, despite their potential benefits. A major component of our work is the development of control charts to monitor the stability of turnover times. These charts can be easily instituted in hospitals to reduce the variabilityof turnover times. Overall, our analysis uses operations research techniques to analyze turnover times and identify manners for improvement in lowering the mean turnover time and thevariability in turnover times. We provide valuable insight into a component of the surgery process that has received little attention, but can significantly affect utilization rates in hospitals. Most critically, an ability to more accurately predict turnover timesand a better understanding of the sources of variability can result in improved scheduling and heightened hospital staff and patient satisfaction. We hope that our findings can apply to many other hospital settings.

A cross-sectional analysis of the prevalence of dental anxiety and its relation to the oral health-related quality of life in patients with dental treatment needs at a university clinic in Switzerland

The aim of this observational, cross-sectional study was to analyse the relationship between dental anxiety (DA) and health-related quality of life aspects associated with oral conditions of a population with dental treatment needs in Switzerland.

Association between symptoms and quality of life in patients with schizophrenia: a pooled analysis of changes over time

Quality of life is an important outcome in the treatment of patients with schizophrenia. It has been suggested that patients' quality of life ratings (referred to as subjective quality of life, SQOL) might be too heavily influenced by symptomatology to be a valid independent outcome criterion. There has been only limited evidence on the association of symptom change and changes in SQOL over time. This study aimed to examine the association between changes in symptoms and in SQOL among patients with schizophrenia. A pooled data set was obtained from eight longitudinal studies that had used the Brief Psychiatric Rating Scale (BPRS) for measuring psychiatric symptoms and either the Lancashire Quality of Life Profile or the Manchester Short Assessment of Quality of Life for assessing SQOL. The sample comprised 886 patients with schizophrenia. After controlling for heterogeneity of findings across studies using linear mixed models, a reduction in psychiatric symptoms was associated with improvements in SQOL scores. In univariate analyses, changes in all BPRS subscales were associated with changes in SQOL scores. In a multivariate model, only associations between changes in the BPRS depression/anxiety and hostility subscales and changes in SQOL remained significant, with 5% and 0.5% of the variance in SQOL changes being attributable to changes in depression/anxiety and hostility respectively. All BPRS subscales together explained 8.5% of variance. The findings indicate that SQOL changes are influenced by symptom change, in particular in depression/anxiety. The level of influence is limited and may not compromise using SQOL as an independent outcome measure.

Factors influencing subjective quality of life in patients with schizophrenia and other mental disorders: a pooled analysis

Subjective quality of life (SQOL) is an important outcome in the treatment of patients with schizophrenia. However, there is only limited evidence on factors influencing SQOL, and little is known about whether the same factors influence SQOL in patients with schizophrenia and other mental disorders. This study aimed to identify the factors associated with SQOL and test whether these factors are equally important in schizophrenia and other disorders. For this we used a pooled data set obtained from 16 studies that had used either the Lancashire Quality of Life Profile or the Manchester Short Assessment of Quality of Life for assessing SQOL. The sample comprised 3936 patients with schizophrenia, mood disorders, and neurotic disorders. After controlling for confounding factors, within-subject clustering, and heterogeneity of findings across studies in linear mixed models, patients with schizophrenia had more favourable SQOL scores than those with mood and neurotic disorders. In all diagnostic groups, older patients, those in employment, and those with lower symptom scores had higher SQOL scores. Whilst the strength of the association between age and SQOL did not differ across diagnostic groups, symptom levels were more strongly associated with SQOL in neurotic than in mood disorders and schizophrenia. The association of employment and SQOL was stronger in mood and neurotic disorders than in schizophrenia. The findings may inform the use and interpretation of SQOL data for patients with schizophrenia.

Analysis of in-cylinder pressure transducer data quality utilizing a SIDI turbocharged engine

In-cylinder pressure transducers have been used for decades to record combustion pressure inside a running engine. However, due to the extreme operating environment, transducer design and installation must be considered in order to minimize measurement error. One such error is caused by thermal shock, where the pressure transducer experiences a high heat flux that can distort the pressure transducer diaphragm and also change the crystal sensitivity. This research focused on investigating the effects of thermal shock on in-cylinder pressure transducer data quality using a 2.0L, four-cylinder, spark-ignited, direct-injected, turbo-charged GM engine. Cylinder four was modified with five ports to accommodate pressure transducers of different manufacturers. They included an AVL GH14D, an AVL GH15D, a Kistler 6125C, and a Kistler 6054AR. The GH14D, GH15D, and 6054AR were M5 size transducers. The 6125C was a larger, 6.2mm transducer. Note that both of the AVL pressure transducers utilized a PH03 flame arrestor. Sweeps of ignition timing (spark sweep), engine speed, and engine load were performed to study the effects of thermal shock on each pressure transducer. The project consisted of two distinct phases which included experimental engine testing as well as simulation using a commercially available software package. A comparison was performed to characterize the quality of the data between the actual cylinder pressure and the simulated results. This comparison was valuable because the simulation results did not include thermal shock effects. All three sets of tests showed the peak cylinder pressure was basically unaffected by thermal shock. Comparison of the experimental data with the simulated results showed very good correlation. The spark sweep was performed at 1300 RPM and 3.3 bar NMEP and showed that the differences between the simulated results (no thermal shock) and the experimental data for the indicated mean effective pressure (IMEP) and the pumping mean effective pressure (PMEP) were significantly less than the published accuracies. All transducers had an IMEP percent difference less than 0.038% and less than 0.32% for PMEP. Kistler and AVL publish that the accuracy of their pressure transducers are within plus or minus 1% for the IMEP (AVL 2011; Kistler 2011). In addition, the difference in average exhaust absolute pressure between the simulated results and experimental data was the greatest for the two Kistler pressure transducers. The location and lack of flame arrestor are believed to be the cause of the increased error. For the engine speed sweep, the torque output was held constant at 203 Nm (150 ft-lbf) from 1500 to 4000 RPM. The difference in IMEP was less than 0.01% and the PMEP was less than 1%, except for the AVL GH14D which was 5% and the AVL GH15DK which was 2.25%. A noticeable error in PMEP appeared as the load increased during the engine speed sweeps, as expected. The load sweep was conducted at 2000 RPM over a range of NMEP from 1.1 to 14 bar. The difference in IMEP values were less 0.08% while the PMEP values were below 1% except for the AVL GH14D which was 1.8% and the AVL GH15DK which was at 1.25%. In-cylinder pressure transducer data quality was effectively analyzed using a combination of experimental data and simulation results. Several criteria can be used to investigate the impact of thermal shock on data quality as well as determine the best location and thermal protection for various transducers.

Age and gender differences in health-related quality of life of children and adolescents in Europe: a multilevel analysis

OBJECTIVES: To determine age and gender differences in health-related quality of life (HRQOL) in children and adolescents across 12 European countries using a newly developed HRQOL measure (KIDSCREEN). METHODS: The KIDSCREEN-52 questionnaire was filled in by 21,590 children and adolescents aged 8-18 from 12 countries. We used multilevel regression analyses to model the hierarchical structure of the data. In addition, effect sizes were computed to test for gender differences within each age group. RESULTS: Children generally showed better HRQOL than adolescents (P < 0.001). While boys and girls had similar HRQOL at young age, girls' HRQOL declined more than boys' (P < 0.001) with increasing age, depending on the HRQOL scale. There was significant variation between countries both at the youngest age and for age trajectories. CONCLUSIONS: For the first time, gender and age differences in children's and adolescents' HRQOL across Europe were assessed using a comprehensive and standardised instrument. Gender and age differences exist for most HRQOL scales. Differences in HRQOL across Europe point to the importance of national contexts for youth's well-being.

Is body weight the most appropriate criterion to select patients eligible for low-dose pulmonary CT angiography? Analysis of objective and subjective image quality at 80 kVp in 100 patients

The objective of this retrospective study was to assess image quality with pulmonary CT angiography (CTA) using 80 kVp and to find anthropomorphic parameters other than body weight (BW) to serve as selection criteria for low-dose CTA. Attenuation in the pulmonary arteries, anteroposterior and lateral diameters, cross-sectional area and soft-tissue thickness of the chest were measured in 100 consecutive patients weighing less than 100 kg with 80 kVp pulmonary CTA. Body surface area (BSA) and contrast-to-noise ratios (CNR) were calculated. Three radiologists analyzed arterial enhancement, noise, and image quality. Image parameters between patients grouped by BW (group 1: 0-50 kg; groups 2-6: 51-100 kg, decadally increasing) were compared. CNR was higher in patients weighing less than 60 kg than in the BW groups 71-99 kg (P between 0.025 and <0.001). Subjective ranking of enhancement (P = 0.165-0.605), noise (P = 0.063), and image quality (P = 0.079) did not differ significantly across all patient groups. CNR correlated moderately strongly with weight (R = -0.585), BSA (R = -0.582), cross-sectional area (R = -0.544), and anteroposterior diameter of the chest (R = -0.457; P < 0.001 all parameters). We conclude that 80 kVp pulmonary CTA permits diagnostic image quality in patients weighing up to 100 kg. Body weight is a suitable criterion to select patients for low-dose pulmonary CTA.

A multi-center retrospective analysis of treatment effects and quality of life in adult patients with cranial ependymomas

Long term quality of life data of adult patients harboring intracranial ependymomas have not been reported. The role of adjuvant radiation therapy in Grade II ependymomas is unclear and differs from study to study. We therefore sought to retrospectively analyze outcome and quality of life of adult patients that were operated on intracranial ependymomas at four different surgical centers in two countries. All patients were attempted to be contacted via telephone to assess quality of life (QoL) at the time of the telephone interview. The standard EORTC QoL Questionnaire C30 (EORTC QLQ-C30) and the EORTC QLQ-Brain Cancer Module (QLQ-BN20) were used. 64 adult patients with intracranial ependymomas were included in the study. The only factor that was associated with increased survival was age <55 years (p < 0.001). Supratentorial location was correlated with shorter progression free survival than infratentorial location (PFS; p = 0.048). In WHO Grade II tumors local irradiation did not lead to increased PFS (p = 0.888) or overall survival (p = 0.801). Even for incompletely resected Grade II tumors local irradiation did not lead to a benefit in PFS (p = 0.911). In a multivariate analysis of QoL, irradiated patients had significantly worse scores in the item "fatigue" (p = 0.037) than non-irradiated patients. Here we present QoL data of adult patients with intracranial ependymomas. Our data show that local radiation therapy may have long-term effects on patients' QoL. Since in the incompletely resected Grade II tumors local irradiation did not lead to a benefit in PFS in this retrospective study, prospective randomized studies are necessary. In addition to age, supratentorial tumor location is associated with a worse prognosis in adult ependymoma patients.