Bioinformatic methods in applied genomic research

Here I will focus on three main topics that best address and include the projects I have been working in during my three year PhD period that I have spent in different research laboratories addressing both computationally and practically important problems all related to modern molecular genomics. The first topic is the use of livestock species (pigs) as a model of obesity, a complex human dysfunction. My efforts here concern the detection and annotation of Single Nucleotide Polymorphisms. I developed a pipeline for mining human and porcine sequences. Starting from a set of human genes related with obesity the platform returns a list of annotated porcine SNPs extracted from a new set of potential obesity-genes. 565 of these SNPs were analyzed on an Illumina chip to test the involvement in obesity on a population composed by more than 500 pigs. Results will be discussed. All the computational analysis and experiments were done in collaboration with the Biocomputing group and Dr.Luca Fontanesi, respectively, under the direction of prof. Rita Casadio at the Bologna University, Italy. The second topic concerns developing a methodology, based on Factor Analysis, to simultaneously mine information from different levels of biological organization. With specific test cases we develop models of the complexity of the mRNA-miRNA molecular interaction in brain tumors measured indirectly by microarray and quantitative PCR. This work was done under the supervision of Prof. Christine Nardini, at the “CAS-MPG Partner Institute for Computational Biology” of Shangai, China (co-founded by the Max Planck Society and the Chinese Academy of Sciences jointly) The third topic concerns the development of a new method to overcome the variety of PCR technologies routinely adopted to characterize unknown flanking DNA regions of a viral integration locus of the human genome after clinical gene therapy. This new method is entirely based on next generation sequencing and it reduces the time required to detect insertion sites, decreasing the complexity of the procedure. This work was done in collaboration with the group of Dr. Manfred Schmidt at the Nationales Centrum für Tumorerkrankungen (Heidelberg, Germany) supervised by Dr. Annette Deichmann and Dr. Ali Nowrouzi. Furthermore I add as an Appendix the description of a R package for gene network reconstruction that I helped to develop for scientific usage (http://www.bioconductor.org/help/bioc-views/release/bioc/html/BUS.html).

Operating System Contribution to Composable Timing Behaviour in High-Integrity Real-Time Systems

The development of High-Integrity Real-Time Systems has a high footprint in terms of human, material and schedule costs. Factoring functional, reusable logic in the application favors incremental development and contains costs. Yet, achieving incrementality in the timing behavior is a much harder problem. Complex features at all levels of the execution stack, aimed to boost average-case performance, exhibit timing behavior highly dependent on execution history, which wrecks time composability and incrementaility with it. Our goal here is to restitute time composability to the execution stack, working bottom up across it. We first characterize time composability without making assumptions on the system architecture or the software deployment to it. Later, we focus on the role played by the real-time operating system in our pursuit. Initially we consider single-core processors and, becoming less permissive on the admissible hardware features, we devise solutions that restore a convincing degree of time composability. To show what can be done for real, we developed TiCOS, an ARINC-compliant kernel, and re-designed ORK+, a kernel for Ada Ravenscar runtimes. In that work, we added support for limited-preemption to ORK+, an absolute premiere in the landscape of real-word kernels. Our implementation allows resource sharing to co-exist with limited-preemptive scheduling, which extends state of the art. We then turn our attention to multicore architectures, first considering partitioned systems, for which we achieve results close to those obtained for single-core processors. Subsequently, we shy away from the over-provision of those systems and consider less restrictive uses of homogeneous multiprocessors, where the scheduling algorithm is key to high schedulable utilization. To that end we single out RUN, a promising baseline, and extend it to SPRINT, which supports sporadic task sets, hence matches real-world industrial needs better. To corroborate our results we present findings from real-world case studies from avionic industry.

Multicentre study for a robust protocol in single-voxel spectroscopy: quantification of MRS signals by time-domain fitting algorithms

Magnetic Resonance Spectroscopy (MRS) is an advanced clinical and research application which guarantees a specific biochemical and metabolic characterization of tissues by the detection and quantification of key metabolites for diagnosis and disease staging. The "Associazione Italiana di Fisica Medica (AIFM)" has promoted the activity of the "Interconfronto di spettroscopia in RM" working group. The purpose of the study is to compare and analyze results obtained by perfoming MRS on scanners of different manufacturing in order to compile a robust protocol for spectroscopic examinations in clinical routines. This thesis takes part into this project by using the GE Signa HDxt 1.5 T at the Pavillion no. 11 of the S.Orsola-Malpighi hospital in Bologna. The spectral analyses have been performed with the jMRUI package, which includes a wide range of preprocessing and quantification algorithms for signal analysis in the time domain. After the quality assurance on the scanner with standard and innovative methods, both spectra with and without suppression of the water peak have been acquired on the GE test phantom. The comparison of the ratios of the metabolite amplitudes over Creatine computed by the workstation software, which works on the frequencies, and jMRUI shows good agreement, suggesting that quantifications in both domains may lead to consistent results. The characterization of an in-house phantom provided by the working group has achieved its goal of assessing the solution content and the metabolite concentrations with good accuracy. The goodness of the experimental procedure and data analysis has been demonstrated by the correct estimation of the T2 of water, the observed biexponential relaxation curve of Creatine and the correct TE value at which the modulation by J coupling causes the Lactate doublet to be inverted in the spectrum. The work of this thesis has demonstrated that it is possible to perform measurements and establish protocols for data analysis, based on the physical principles of NMR, which are able to provide robust values for the spectral parameters of clinical use.

Neurological outcome, working capacity and prognostic factors of patients with SCIWORA

STUDY DESIGN: Retrospective case review. OBJECTIVES: In the present study, the neurological outcome, retirement and prognostic factors of patients with spinal cord injury without radiographic abnormality (SCIWORA) were evaluated. SETTING: Swiss national work accident insurance database. METHODS: The medical histories of 32 patients who were insured by the Swiss Accident Insurance Fund (SUVA) and had SCIWORA between 1995 and 2004 were evaluated thoroughly. Moreover, all available magnetic resonance imaging (MRI) scans were evaluated. RESULTS: At the last follow-up, none of the patients had complete spinal cord injury, only 4 patients had severe deficits and 12 patients had normal motor and sensory function in the neurological examination. However, only 7 out of 32 patients had returned to full-time work and 10 out of 32 patients were fully retired. Both the presence of spinal cord change (ρ=0.51) and higher maximum spinal cord compression (ρ=0.57) in MRI scan correlated with the likelihood for retirement; older age (ρ=0.38) and physical load of work (ρ=0.4) correlated with retirement to a lesser extent. CONCLUSION: Although the neurological outcome of SCIWORA is mostly good, the retirement rate is high. Presence of spinal cord change and severity of cord compression are the best predictors for the degree of retirement.

Predictive ability of a modified Örebro Musculoskeletal Pain Questionnaire in an acute/subacute low back pain working population

The original 'Örebro Musculoskeletal Pain Questionnaire' (original-ÖMPQ) has been shown to have limitations in practicality, factor structure, face and content validity. This study addressed these concerns by modifying its content producing the 'Örebro Musculoskeletal Screening Questionnaire' (ÖMSQ). The ÖMSQ and original-ÖMPQ were tested concurrently in acute/subacute low back pain working populations (pilot n = 44, main n = 106). The ÖMSQ showed improved face and content validity, which broadened potential application, and improved practicality with two-thirds less missing responses. High reliability (0.975, p < 0.05, ICC: 2.1), criterion validity (Spearman's r = 0.97) and internal consistency (α = 0.84) were achieved, as were predictive ability cut-off scores from ROC curves (112-120 ÖMSQ-points), statistically different ÖMSQ scores (p < 0.001) for each outcome trait, and a strong correlation with recovery time (Spearman's, r = 0.71). The six-component factor structure reflected the constructs originally proposed. The ÖMSQ can be substituted for the original-ÖMPQ in this population. Further research will assess its applicability in broader populations.

Developmental changes of BOLD signal correlations with global human EEG power and synchronization during working memory

In humans, theta band (5-7 Hz) power typically increases when performing cognitively demanding working memory (WM) tasks, and simultaneous EEG-fMRI recordings have revealed an inverse relationship between theta power and the BOLD (blood oxygen level dependent) signal in the default mode network during WM. However, synchronization also plays a fundamental role in cognitive processing, and the level of theta and higher frequency band synchronization is modulated during WM. Yet, little is known about the link between BOLD, EEG power, and EEG synchronization during WM, and how these measures develop with human brain maturation or relate to behavioral changes. We examined EEG-BOLD signal correlations from 18 young adults and 15 school-aged children for age-dependent effects during a load-modulated Sternberg WM task. Frontal load (in-)dependent EEG theta power was significantly enhanced in children compared to adults, while adults showed stronger fMRI load effects. Children demonstrated a stronger negative correlation between global theta power and the BOLD signal in the default mode network relative to adults. Therefore, we conclude that theta power mediates the suppression of a task-irrelevant network. We further conclude that children suppress this network even more than adults, probably from an increased level of task-preparedness to compensate for not fully mature cognitive functions, reflected in lower response accuracy and increased reaction time. In contrast to power, correlations between instantaneous theta global field synchronization and the BOLD signal were exclusively positive in both age groups but only significant in adults in the frontal-parietal and posterior cingulate cortices. Furthermore, theta synchronization was weaker in children and was--in contrast to EEG power--positively correlated with response accuracy in both age groups. In summary we conclude that theta EEG-BOLD signal correlations differ between spectral power and synchronization and that these opposite correlations with different distributions undergo similar and significant neuronal developments with brain maturation.

Language Construction of Reality in the German Tabloid Press/on Materials of BILD Newspaper/

From the moment of their birth, a person's life is determined by their sex. Goroshko wanted to find out why this difference is so striking, why society is so determined to sustain it, and how it can persist even when certain national or behavioural stereotypes are erased. She believes there are both social and biological differences between men and women, and set out to analyse these distinctions as they are manifested in language. Certain general characteristics can be identified. Males tend to write with less fluency, to refer to events in a verb phrase, to be time-oriented, to involve themselves more in their references to events, to locate events in their personal sphere of activity, and to refer less to others. Goroshko therefore concludes that the male is more active, more ego-involved in what he does and less concerned about others. Women were more fluent, referred to events in a noun-phrase, were less time-oriented, tended to be less involved in their event references, located events within their interactive community, and referred more to others. They spent much more time discussing personal and domestic subjects, relationship problems, family, health and reproductive matters, weight, food and clothing, men, and other women. Computer analysis showed that female speech was substantially more emotional, using hyperbole, metaphor, comparisons, epithets, ways of enumeration, interjections, rhetorical questions and exclamations. The level of literacy was higher in female speech, and women made fewer grammatical and spelling mistakes in written texts. Goroshko believes that her findings have relevance beyond the linguistic field. When working on anonymous texts she has been able to decide on the sex of the author and so believes that her research may even be of benefit to forensic science.

Changes in Psychological Characteristics of Working Adults in Different Stages of Economic Transition in Lithuania

Global economic changes have psychological consequences and Mr. Lepeska set out to assess these changes in working adults in Lithuania between 1993 and 1997. He surveyed two groups of working adults, with a total of 200 people, randomly selected and representing different organisations and professions. In both groups around 30% of participants were managers, with the remainder working in non-managerial positions. The participants were surveyed twice, once in 1993 and the second time in 1997,using various psychodiagnostic tools to measure their psychological characteristics. The results showed that strategies for coping with stress have changed, with problem solving strategies being used more often, and avoidance behaviour or seeking social support less. Men tended to have rejected these strategy more radically than women. Attitudes towards work had become more positive, with managers' attitudes having changed more significantly than those of employees from lower levels of organisations. Younger people were more positive towards work-related changes, while situational anxiety tended to increase with age, although overall it remained low. Mr. Lepeska found that while there were some indications of an increasing individualist in relation to peers, the traditional collective orientation of Lithuanian adults had if anything increased. People have become more accepting of an unequal distribution of power, making it difficult to increase the participation of subordinates in decision making. He also noted a tendency for Lithuanians to see their organisations as traditional families, expecting them to take care of them physically and economically in return for loyalty. The strong feminine orientation with its stress on interpersonal relations and overall quality of life has also strengthened, but the ability of Lithuanians to take initiative and control their environment was relatively low. Mr. Lepeska concludes that organisations should seek to recruit people who are able to adjust more easily to changes and consider measuring dominance, individualism, and attitudes to work-related change and situational anxiety in the process of professional selection. There should also be more emphasis on team building and on training managers to maintain closer relationships with their subordinates so as to increase the latter's participation in decision making. Good interpersonal relations can be a strong work motivator, as may be special attention to the security needs of older employees.

[Evaluation of the quality of husbandry of Franches-Montagnes horses in their breeding farms]

The quality of husbandry of Franches-Montagnes horses (FM) in Switzerland is evaluated on the basis of an investigation carried out in 2002 by the Swiss FM breeding federation. Questionnaires were sent to 3500 of its members and the results include data from 968 breeding enterprises, housing a total of 3965 FM: 46.1% were breeding mares (61.0% with foal at foot), 26.5% young stock, 1.3% stallions and 26.0% non breeding stock (74.6% of which were pleasure horses and 25.4% working horses). 57.6% of the FM were housed in individual boxes with or without permanent outdoor access, 25.4% were hold in groups with or without permanent outdoor access, the remaining 17.0% were kept in standing stalls. 95.0% of the FM had at least visual contact with other equines and 99.2% had sufficient light in their stable. 88.1% were stabled on long stalk straw, while only 4.3% were bedded on other materials other than straw. The average time spent at pasture per horse and per week ranged from 96.5 +/- 51.6 hours in summer to 27.2 +/- 26.7 hours in winter. On average, a FM is used for 8.3 +/- 6.5 hours per week. Horses with an paddock at their disposal spend an average of 39.8 +/- 45.9 hours there per week.

Haematopoietic stem cell transplantation in Switzerland. Report from the Swiss Transplant Working Group Blood and Marrow Transplantation (STABMT) Registry 1997-2003

In 1997, the Swiss Transplant Working Group Blood and Marrow Transplantation (STABMT) initiated a mandatory national registry for all haematopoietic stem cell transplants (HSCT) in Switzerland. As of 2003, information was collected of 2010 patients with a first HSCT (577 allogeneic (29%) and 1433 autologous (71%) HSCT) and 616 additional re-transplants. This included 1167 male and 843 female patients with a median age of 42.4 years (range 0.2-76.6 years). Main indications were leukaemias (592; 29%) lymphoproliferative disorders (1,061; 53%), solid tumours (295; 15%) and non-malignant disorders (62; 3%). At the time of analysis 1,263 patients were alive (63%), 747 had died (37%). Probability of survival, transplant related mortality or relapse at 5 years was 52%, 21%, 36% for allogeneic and 54%, 5%, 60% for autologous HSCT. Outcome depended on indication, donor type, stem cell source and age of patient. HSCT is an established therapy in Switzerland. These data describe current practice and outcome.

Quantifying and Comparing the Accuracy of Binary Biomarkers When Predicting a Failure Time Outcome

The positive and negative predictive value are standard measures used to quantify the predictive accuracy of binary biomarkers when the outcome being predicted is also binary. When the biomarkers are instead being used to predict a failure time outcome, there is no standard way of quantifying predictive accuracy. We propose a natural extension of the traditional predictive values to accommodate censored survival data. We discuss not only quantifying predictive accuracy using these extended predictive values, but also rigorously comparing the accuracy of two biomarkers in terms of their predictive values. Using a marginal regression framework, we describe how to estimate differences in predictive accuracy and how to test whether the observed difference is statistically significant.

Smooth Hazard Function Estimation for Interval Censored Data with Time Varying Covariates

In this paper we propose methods for smooth hazard estimation of a time variable where that variable is interval censored. These methods allow one to model the transformed hazard in terms of either smooth (smoothing splines) or linear functions of time and other relevant time varying predictor variables. We illustrate the use of this method on a dataset of hemophiliacs where the outcome, time to seroconversion for HIV, is interval censored and left-truncated.