Computational Methods for Reconstruction and Analysis of Genome-Scale Metabolic Networks

Metabolism is the cellular subsystem responsible for generation of energy from nutrients and production of building blocks for larger macromolecules. Computational and statistical modeling of metabolism is vital to many disciplines including bioengineering, the study of diseases, drug target identification, and understanding the evolution of metabolism. In this thesis, we propose efficient computational methods for metabolic modeling. The techniques presented are targeted particularly at the analysis of large metabolic models encompassing the whole metabolism of one or several organisms. We concentrate on three major themes of metabolic modeling: metabolic pathway analysis, metabolic reconstruction and the study of evolution of metabolism. In the first part of this thesis, we study metabolic pathway analysis. We propose a novel modeling framework called gapless modeling to study biochemically viable metabolic networks and pathways. In addition, we investigate the utilization of atom-level information on metabolism to improve the quality of pathway analyses. We describe efficient algorithms for discovering both gapless and atom-level metabolic pathways, and conduct experiments with large-scale metabolic networks. The presented gapless approach offers a compromise in terms of complexity and feasibility between the previous graph-theoretic and stoichiometric approaches to metabolic modeling. Gapless pathway analysis shows that microbial metabolic networks are not as robust to random damage as suggested by previous studies. Furthermore the amino acid biosynthesis pathways of the fungal species Trichoderma reesei discovered from atom-level data are shown to closely correspond to those of Saccharomyces cerevisiae. In the second part, we propose computational methods for metabolic reconstruction in the gapless modeling framework. We study the task of reconstructing a metabolic network that does not suffer from connectivity problems. Such problems often limit the usability of reconstructed models, and typically require a significant amount of manual postprocessing. We formulate gapless metabolic reconstruction as an optimization problem and propose an efficient divide-and-conquer strategy to solve it with real-world instances. We also describe computational techniques for solving problems stemming from ambiguities in metabolite naming. These techniques have been implemented in a web-based sofware ReMatch intended for reconstruction of models for 13C metabolic flux analysis. In the third part, we extend our scope from single to multiple metabolic networks and propose an algorithm for inferring gapless metabolic networks of ancestral species from phylogenetic data. Experimenting with 16 fungal species, we show that the method is able to generate results that are easily interpretable and that provide hypotheses about the evolution of metabolism.

Patriarkkana ikuisuuden performanssissa : Maskuliinisuuden ja miehen ruumiillisuuden rakentuminen mormonien Duties and Blessings of the Priesthood -opetuskäsikirjassa

The material I analyze for my master's thesis is a teaching manual used by the Mormons (the Church of Jesus Christ of Latter-day Saints), called "Duties and Blessings of the Priesthood". This work includes numerous lesson plans, each one with a separate topic. The manual is intended especially for teaches, but can also be used for individual study. The main target of my research is to find out how men and their bodies are constructed in the manual. Prescriptive texts together with narrative stories and illustrations create a multifaceted picture of Mormon notions of masculinity and corporeality. I approach my research material from a constructivist perspective. I build my interpretative reading upon Critical Discourse Analysis. I am especially interested in how the manual interprets and understands connections between gender, embodiment and religion. I understand gender in Judith Butler's terms, as a performance of styled and repeated gestures. Some of the discussions I raise in my work draw upon the disciplines of Critical Men's Studies and Sociology of Religion. In Mormonism, gender is thought to be an elementary part of human ontology. It is an eternal trait inherited from God the Father (and God the Mother). The place of men in Mormon cosmology is determined by their double role as patriarchs, fathers and priests. The main objective of mortal life is to gain salvation together with one's family. The personal goal of a Mormon man is to one day become a god. Patriarchs are responsible for the spiritual and material well-being of their family. The head of a household should be gentle and loving, but still an unconditional authority. In the manual, a Mormon man is depicted as a successor of mythical and exemplary men of sacred history. The perfect and sinless body of Jesus Christ serves as an ideal for the male body. Mormon masculinity is also defined by priesthood - the holy power of God - which is given to practically all male Mormons. Through the priesthood, a Mormon man serves as the governor of God on Earth. The Mormon priest has the authority to bind the immanent and the transcendent worlds together with gestures, poses and motions performed with his body. In Mormonism, the body also symbolizes a temple or a space where the sacred meets the profane. Because the priesthood borne by a man is holy, he has to treat his body accordingly. The body is valuable in itself, without it one cannot be saved. Men are forbidden of polluting their bodies by using stimulants or by having sexual relations out of wedlock. A priesthood holder must uphold healthy habits, dress neatly, and conduct himself in a temperate manner. He must also be outgoing and attentive. The manual suggests that a man's goodness or wickedness can be perceived from his external appearance. The Church of Jesus Christ of Latter-day Saints is a hierarchical and man-led organisation. The ideals of gender and corporeality are set by a homogenous priesthood leadership that consists mainly of white heterosexual American men. The larger Mormon community can control individual men by sanctioning. Growing as a Mormon man happens under the guidance of one's reference group.

Meltdown - a tool for classification and analysis of DSF data

An application that translates raw thermal melt curve data into more easily assimilated knowledge is described. This program, called ‘Meltdown’, performs a number of data remediation steps before classifying melt curves and estimating melting temperatures. The final output is a report that summarizes the results of a differential scanning fluorimetry experiment. Meltdown uses a Bayesian classification scheme, enabling reproducible identification of various trends commonly found in DSF datasets. The goal of Meltdown is not to replace human analysis of the raw data, but to provide a sensible interpretation of the data to make this useful experimental technique accessible to naïve users, as well as providing a starting point for detailed analyses by more experienced users.

Application of molecular orbital theory to the interpretation of x-ray absorption spectra of platinum complexes

X-ray LIII-absorption edges of platinum in nine octahedral complexes have been recorded using a bent crystal spectrograph. The edge features of the discontinuities have been interpreted with the help of qualitative molecular orbital diagrams. A correlation between the energy separation of the first two absorption maxima and the spectrochemical series of the ligands has been arrived at.

Malaria burden and costs of intensified control in Bhutan, 2006-2014: A situational analysis

- Introduction Malaria cases have dwindled in Bhutan with aim of malaria elimination by 2016. The aims of this study are to determine the trends and burden of malaria, the costs of intensified control activities, the main donors of the control activities and the costs of different preventive measures in the pre-elimination phase (2006-2014). - Methods A descriptive analysis of malaria surveillance data from 2006-2014 was carried out, using data from the Vector-borne Disease Control Programme (VDCP), Bhutan. Malaria morbidity and mortality among local Bhutanese and foreign nationals were analysed. The cost of different control and preventive measures, and estimation of the average numbers of long-lasting insecticidal nests (LLINs) per person were calculated. - Findings There were 5,491 confirmed malaria cases from 2006 to 2014. By 2013, there was an average of one LLIN for every 1·51 individuals. The Global Fund was the main international donor accounting for > 80% of the total funds. The cost of procuring LLINs accounted for > 90% of the total cost of prevention measures. - Interpretation The malaria burden reduced significantly over the study period with high coverage of LLINs in Bhutan. This foreseeable challenges that require national attention to maintain malaria-free status after elimination are importation of malaria, particularly from India; continued protection of the population in endemic districts through complete coverage with LLINs and IRS; and exploration of local funding modalities post elimination in the event there is a reduction in international funding.

Computational methods for the prediction of the structure and interactions of coiled-coil peptides

The past several years have seen significant advances in the development of computational methods for the prediction of the structure and interactions of coiled-coil peptides. These methods are generally based on pairwise correlations of amino acids, helical propensity, thermal melts and the energetics of sidechain interactions, as well as statistical patterns based on Hidden Markov Model (HMM) and Support Vector Machine (SVM) techniques. These methods are complemented by a number of public databases that contain sequences, motifs, domains and other details of coiled-coil structures identified by various algorithms. Some of these computational methods have been developed to make predictions of coiled-coil structure on the basis of sequence information; however, structural predictions of the oligomerisation state of these peptides still remains largely an open question due to the dynamic behaviour of these molecules. This review focuses on existing in silico methods for the prediction of coiled-coil peptides of functional importance using sequence and/or three-dimensional structural data.

Depression, Anxiety, Psychiatric Comorbidity and Dimensions of Temperament and Personality

This study is part of the Mood Disorders Project conducted by the Department of Mental Health and Alcohol Research, National Public Health Institute, and consists of a general population survey sample and a major depressive disorder (MDD) patient cohort from Vantaa Depression Study (VDS). The general population survey study was conducted in 2003 in the cities of Espoo and Vantaa. The VDS is a collaborative depression research project between the Department of Mental Health and Alcohol Research of the National Public Health Institute and the Department of Psychiatry of the Peijas Medical Care District (PMCD) beginning in 1997. It is a prospective, naturalistic cohort study of 269 secondary-level care psychiatric out- and inpatients with a new episode of Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV) MDD. In the general population survey study, a total of 900 participants (300 from Espoo, 600 from Vantaa) aged 20 70 years were randomly drawn from the Population Register Centre in Finland. A self-report booklet, including the Eysenck Personality Inventory (EPI), the Temperament and Character Inventory Revised (TCI-R), the Beck Depression Inventory and the Beck Anxiety Inventory was mailed to all subjects. Altogether 441 participants responded (94 returned only the shortened version without TCI-R) and gave their informed consent. VDS involved screening all patients aged 20-60 years (n=806) in the PMCD for a possible new episode of DSM-IV MDD. 542 consenting patients were interviewed with a semi-structured interview (the WHO Schedules for Clinical Assessment in Neuropsychiatry, version 2.0). 269 patients with a current DSM-IV MDD were included in the study and further interviewed with semi-structured interviews to assess all other axis I and II psychiatric diagnoses. Exclusion criteria were DSM-IV bipolar I and II, schizoaffective disorder, schizophrenia or another psychosis, organic and substance-induced mood disorders. In the present study are included those 193 (139 females, 54 males) individuals who could be followed up at both 6 and 18 months, and their depression had remained unipolar. Personality was investigated with the EPI. Personality dimensions associated not only to the symptoms of depression, but also to the symptoms of anxiety among general population and in depressive patients, as well as to comorbid disorders in MDD patients, supporting the dimensional view of depression and anxiety. Among the general population High Harm Avoidance and low Self-Directedness associated moderately, whereas low extraversion and high neuroticism strongly with the depressive and anxiety symptoms. The personality dimensions, especially high Harm Avoidance, low Self-Directedness and high neuroticism were also somewhat predictive of self-reported use of health care services for psychiatric reasons, and lifetime mental disorder. Moreover, high Harm Avoidance associated with a family history of mental disorder. In depressive patients, neuroticism scores were found to decline markedly and extraversion scores to increase somewhat with recovery. The predictive value of the changes in symptoms of depression and anxiety in explaining follow-up neuroticism was about 1/3 of that of baseline neuroticism. In contrast to neuroticism, the scores of extraversion showed no dependence on the symptoms of anxiety, and the change in the symptoms of depression explained only 1/20 of the follow-up extraversion compared with baseline extraversion. No evidence was found of the scar effect during a one-year follow-up period. Finally, even after controlling for symptoms of both depression and anxiety, depressive patients had a somewhat higher level of neuroticism (odds ratio 1.11, p=0.001) and a slightly lower level of extraversion (odds ratio 0.92, p=0.003) than subjects in the general population. Among MDD patients, a positive dose-exposure relationship appeared to exist between neuroticism and prevalence and number of comorbid axis I and II disorders. A negative relationship existed between level of extraversion and prevalence of comorbid social phobia and cluster C personality disorders. Personality dimensions are associated with the symptoms of depression and anxiety. Futhermore these findings support the hypothesis that high neuroticism and somewhat low extraversion might be vulnerability factors for MDD, and that high neuroticism and low extraversion predispose to comorbid axis I and II disorders among patients with MDD.

Spirometric studies on the adult general population of Helsinki : bronchodilation responses, determinants, and intrasession repeatability of FEV1, FEV6, FVC, and forced expiratory time

Spirometry is the most widely used lung function test in the world. It is fundamental in diagnostic and functional evaluation of various pulmonary diseases. In the studies described in this thesis, the spirometric assessment of reversibility of bronchial obstruction, its determinants, and variation features are described in a general population sample from Helsinki, Finland. This study is a part of the FinEsS study, which is a collaborative study of clinical epidemiology of respiratory health between Finland (Fin), Estonia (Es), and Sweden (S). Asthma and chronic obstructive pulmonary disease (COPD) constitute the two major obstructive airways diseases. The prevalence of asthma has increased, with around 6% of the population in Helsinki reporting physician-diagnosed asthma. The main cause of COPD is smoking with changes in smoking habits in the population affecting its prevalence with a delay. Whereas airway obstruction in asthma is by definition reversible, COPD is characterized by fixed obstruction. Cough and sputum production, the first symptoms of COPD, are often misinterpreted for smokers cough and not recognized as first signs of a chronic illness. Therefore COPD is widely underdiagnosed. More extensive use of spirometry in primary care is advocated to focus smoking cessation interventions on populations at risk. The use of forced expiratory volume in six seconds (FEV6) instead of forced vital capacity (FVC) has been suggested to enable office spirometry to be used in earlier detection of airflow limitation. Despite being a widely accepted standard method of assessment of lung function, the methodology and interpretation of spirometry are constantly developing. In 2005, the ATS/ERS Task Force issued a joint statement which endorsed the 12% and 200 ml thresholds for significant change in forced expiratory volume in one second (FEV1) or FVC during bronchodilation testing, but included the notion that in cases where only FVC improves it should be verified that this is not caused by a longer exhalation time in post-bronchodilator spirometry. This elicited new interest in the assessment of forced expiratory time (FET), a spirometric variable not usually reported or used in assessment. In this population sample, we examined FET and found it to be on average 10.7 (SD 4.3) s and to increase with ageing and airflow limitation in spirometry. The intrasession repeatability of FET was the poorest of the spirometric variables assessed. Based on the intrasession repeatability, a limit for significant change of 3 s was suggested for FET during bronchodilation testing. FEV6 was found to perform equally well as FVC in the population and in a subgroup of subjects with airways obstruction. In the bronchodilation test, decreases were frequently observed in FEV1 and particularly in FVC. The limit of significant increase based on the 95th percentile of the population sample was 9% for FEV1 and 6% for FEV6 and FVC; these are slightly lower than the current limits for single bronchodilation tests (ATS/ERS guidelines). FEV6 was proven as a valid alternative to FVC also in the bronchodilation test and would remove the need to control duration of exhalation during the spirometric bronchodilation test.

Acyclic edge coloring of subcubic graphs

An acyclic edge coloring of a graph is a proper edge coloring such that there are no bichromatic cycles. The acyclic chromatic index of a graph is the minimum number k such that there is an acyclic edge coloring using k colors and it is denoted by a′(G). From a result of Burnstein it follows that all subcubic graphs are acyclically edge colorable using five colors. This result is tight since there are 3-regular graphs which require five colors. In this paper we prove that any non-regular connected graph of maximum degree 3 is acyclically edge colorable using at most four colors. This result is tight since all edge maximal non-regular connected graphs of maximum degree 3 require four colors.

Dynamic nature of proteins - interpretation of residual dipolar couplings

Protein conformations and dynamics can be studied by nuclear magnetic resonance spectroscopy using dilute liquid crystalline samples. This work clarifies the interpretation of residual dipolar coupling data yielded by the experiments. It was discovered that unfolded proteins without any additional structure beyond that of a mere polypeptide chain exhibit residual dipolar couplings. Also, it was found that molecular dynamics induce fluctuations in the molecular alignment and doing so affect residual dipolar couplings. The finding clarified the origins of low order parameter values observed earlier. The work required the development of new analytical and computational methods for the prediction of intrinsic residual dipolar coupling profiles for unfolded proteins. The presented characteristic chain model is able to reproduce the general trend of experimental residual dipolar couplings for denatured proteins. The details of experimental residual dipolar coupling profiles are beyond the analytical model, but improvements are proposed to achieve greater accuracy. A computational method for rapid prediction of unfolded protein residual dipolar couplings was also developed. Protein dynamics were shown to modulate the effective molecular alignment in a dilute liquid crystalline medium. The effects were investigated from experimental and molecular dynamics generated conformational ensembles of folded proteins. It was noted that dynamics induced alignment is significant especially for the interpretation of molecular dynamics in small, globular proteins. A method of correction was presented. Residual dipolar couplings offer an attractive possibility for the direct observation of protein conformational preferences and dynamics. The presented models and methods of analysis provide significant advances in the interpretation of residual dipolar coupling data from proteins.

Knowledge through Discussion : An Interpretation of Epistemology in Plato's Meno

According to Meno s paradox we cannot inquire into what we do not know because we do not know what we are inquiring into. There are many ways to interpret the paradox but the central issue about our ability to reach truth is a profound one. In the dialogue Meno, Plato presents the paradox and an outline of a solution which enables us to reach knowledge (epistēmē) through philosophical discussion. During the last century Meno has often been considered transitional between Socratic thinking and Plato s own philosophy, and thus the dialogue has not been adequately interpreted as an integrated whole. Therefore the distinctive epistemology of the dialogue has not gained due notice. In this thesis the dialogue is analysed as an integrated whole and the philosophical interpretation also takes into account its dramatic features. The thesis emphasises the role of language and definitions in acquiring knowledge. Among the results concerning these subjects is a new interpretation of Socrates s defintion of shape (schēma). The theory of anamnēsis all learning is recollection in the Meno is argued to answer the paradox philosophically although Plato s presentation also contains playful and ironic elements. The background of the way Plato presents his case is that he appreciated the fact that no argument can plausibly demonstrate that argumentation is able to reach truth. In the Meno, Plato makes the earliest explicit distinction between knowledge and true belief in the history of Western philosophy. He also gives a definition of knowledge which is the basis of the so called classical definition of knowledge as justified true belief. In the Meno, true beliefs become knowledge when someone ties them down by reasoning about the explanation. The analysis of the epistemology of the dialogue from this perspective gives an interpretation which integrates the central concepts of the epistemology in the dialogue elenchos, anamnēsis and hypothetical inquiry into a unified whole which contains a plausible argument according to which the ignorant can reach knowledge through discussion. The conception that emerges by such an analysis is interesting both from the point of view of current interests and that of the history of philosophy. The method of knowledge acquisition in the Meno can, for example, be seen as a predecessor of modern scientific methods. The Meno is the earliest Greek mathematical text that has survived in its original form. The analysis presented in the thesis of the geometric passages in the dialogue provides new results both concerning Socrates s geometry lesson with the slave and the example presenting the hypothetical method. Concerning the latter, a new interpretation is presented. Keywords: anamnēsis, epistēmē, knowledge, Meno s paradox, Plato

Applicability of Statistical Learning Algorithms for Spatial Variability of Rock Depth

Two algorithms are outlined, each of which has interesting features for modeling of spatial variability of rock depth. In this paper, reduced level of rock at Bangalore, India, is arrived from the 652 boreholes data in the area covering 220 sqa <.km. Support vector machine (SVM) and relevance vector machine (RVM) have been utilized to predict the reduced level of rock in the subsurface of Bangalore and to study the spatial variability of the rock depth. The support vector machine (SVM) that is firmly based on the theory of statistical learning theory uses regression technique by introducing epsilon-insensitive loss function has been adopted. RVM is a probabilistic model similar to the widespread SVM, but where the training takes place in a Bayesian framework. Prediction results show the ability of learning machine to build accurate models for spatial variability of rock depth with strong predictive capabilities. The paper also highlights the capability ofRVM over the SVM model.

First observation of the decay Bs --> Ds K and measurement of the ratio of branching fractions Br(Bs --> DsK)/Br(Bs --> Ds pi)

A combined mass and particle identification fit is used to make the first observation of the decay Bs --> Ds K and measure the branching fraction of Bs --> Ds K relative to Bs --> Ds pi. This analysis uses 1.2 fb^-1 integrated luminosity of pbar-p collisions at sqrt(s) = 1.96 TeV collected with the CDF II detector at the Fermilab Tevatron collider. We observe a Bs --> Ds K signal with a statistical significance of 8.1 sigma and measure Br(Bs --> Ds K)/Br(Bs --> Ds pi) = 0.097 +- 0.018(stat) +- 0.009(sys).

First Observation of B̅ s0→Ds±K∓ and Measurement of the Ratio of Branching Fractions B(B̅ s0→Ds±K∓)/B(B̅ s0→Ds+π-)

A combined mass and particle identification fit is used to make the first observation of the decay B̅ s0→Ds±K∓ and measure the branching fraction of B̅ s0→Ds±K∓ relative to B̅ s0→Ds+π-. This analysis uses 1.2  fb-1 integrated luminosity of pp̅ collisions at √s=1.96  TeV collected with the CDF II detector at the Fermilab Tevatron collider. We observe a B̅ s0→Ds±K∓ signal with a statistical significance of 8.1σ and measure B(B̅ s0→Ds±K∓)/B(B̅ s0→Ds+π-)=0.097±0.018(stat)±0.009(syst).

First Observation of B̅ s0→Ds±K∓ and Measurement of the Ratio of Branching Fractions B(B̅ s0→Ds±K∓)/B(B̅ s0→Ds+π-)

A combined mass and particle identification fit is used to make the first observation of the decay Bs --> Ds K and measure the branching fraction of Bs --> Ds K relative to Bs --> Ds pi. This analysis uses 1.2 fb^-1 integrated luminosity of pbar-p collisions at sqrt(s) = 1.96 TeV collected with the CDF II detector at the Fermilab Tevatron collider. We observe a Bs --> Ds K signal with a statistical significance of 8.1 sigma and measure Br(Bs --> Ds K)/Br(Bs --> Ds pi) = 0.097 +- 0.018(stat) +- 0.009(sys).