Conservation Laws in Cellular Automata

Conservation laws in physics are numerical invariants of the dynamics of a system. In cellular automata (CA), a similar concept has already been defined and studied. To each local pattern of cell states a real value is associated, interpreted as the “energy” (or “mass”, or . . . ) of that pattern.The overall “energy” of a configuration is simply the sum of the energy of the local patterns appearing on different positions in the configuration. We have a conservation law for that energy, if the total energy of each configuration remains constant during the evolution of the CA. For a given conservation law, it is desirable to find microscopic explanations for the dynamics of the conserved energy in terms of flows of energy from one region toward another. Often, it happens that the energy values are from non-negative integers, and are interpreted as the number of “particles” distributed on a configuration. In such cases, it is conjectured that one can always provide a microscopic explanation for the conservation laws by prescribing rules for the local movement of the particles. The onedimensional case has already been solved by Fuk´s and Pivato. We extend this to two-dimensional cellular automata with radius-0,5 neighborhood on the square lattice. We then consider conservation laws in which the energy values are chosen from a commutative group or semigroup. In this case, the class of all conservation laws for a CA form a partially ordered hierarchy. We study the structure of this hierarchy and prove some basic facts about it. Although the local properties of this hierarchy (at least in the group-valued case) are tractable, its global properties turn out to be algorithmically inaccessible. In particular, we prove that it is undecidable whether this hierarchy is trivial (i.e., if the CA has any non-trivial conservation law at all) or unbounded. We point out some interconnections between the structure of this hierarchy and the dynamical properties of the CA. We show that positively expansive CA do not have non-trivial conservation laws. We also investigate a curious relationship between conservation laws and invariant Gibbs measures in reversible and surjective CA. Gibbs measures are known to coincide with the equilibrium states of a lattice system defined in terms of a Hamiltonian. For reversible cellular automata, each conserved quantity may play the role of a Hamiltonian, and provides a Gibbs measure (or a set of Gibbs measures, in case of phase multiplicity) that is invariant. Conversely, every invariant Gibbs measure provides a conservation law for the CA. For surjective CA, the former statement also follows (in a slightly different form) from the variational characterization of the Gibbs measures. For one-dimensional surjective CA, we show that each invariant Gibbs measure provides a conservation law. We also prove that surjective CA almost surely preserve the average information content per cell with respect to any probability measure.

The single principle of compositional data analysis, continuing fallacies, confusionsand misunderstandings and some suggested remedies

In any discipline, where uncertainty and variability are present, it is important to haveprinciples which are accepted as inviolate and which should therefore drive statisticalmodelling, statistical analysis of data and any inferences from such an analysis.Despite the fact that two such principles have existed over the last two decades andfrom these a sensible, meaningful methodology has been developed for the statisticalanalysis of compositional data, the application of inappropriate and/or meaninglessmethods persists in many areas of application. This paper identifies at least tencommon fallacies and confusions in compositional data analysis with illustrativeexamples and provides readers with necessary, and hopefully sufficient, arguments topersuade the culprits why and how they should amend their ways

Composição volátil dos defeitos intrínsecos do café por CG/EM-headspace

About 20% of Brazilian raw coffee production is considered inappropriate for exportation. Consequently, these beans are incorporated to good quality beans in the Brazilian market. This by-product of coffee industry is called PVA due to the presence of black (P), green (V) and sour (A) defective beans which are known to contribute considerably for cup quality decrease. Data on the volatile composition of Brazilian defective coffee beans are scarce. In this study, we evaluated the volatile composition of immature, black-immature, black defective beans and PVA compared to good quality beans. Potential defective beans markers were identified.

Biodiesel: visão crítica do status atual e perspectivas na academia e na indústria

This article presents a bibliographic review of research carried out on different alternative processes for biodiesel production. The supercritical and subcritical (non catalytic) reaction conditions, the use of solid basic, solid acid and other heterogeneous catalysts, including the use of immobilized enzymes and whole-cell catalysts are also critically compared with the traditional homogeneous alkaline or acid catalysts that are common on industrial applications. Advantages and limitations of all these processes for the transference from the laboratory to the industry are discussed. A correlation of the chemical composition with the quality parameters of the produced biodiesel is done with aim to stablish adequate procedures for the right selection of the raw-material. Castor bean oil is used as an example of inappropriate oil in order to produce a B100 that fulfill all the international physico-chemical quality standards. In this article are presented research results to adequate the values of viscosity, density and iodine number of the castor and soybean biodiesel to the international standard limits by means blending these both biodiesels at the right ratio.

Role of ErbB2 and ErbB4 in Cancer Growth, Prognosis and as Targets for Immunotherapy

ErbB receptors (EGFR, ErbB2, ErbB3 and ErbB4) are growth factor receptors that regulate signals of cell differentiation, proliferation, migration and survival. Inappropriate activation of these receptors is associated with the development and severity of many cancers and has prognostic and predictive value in cancer therapy. Drugs, such as therapeutic antibodies, targeted against EGFR and ErbB2, are currently used in therapy of breast, colorectal and head and neck cancers. The role of ErbB4 in tumorigenesis has remained relatively poorly understood. Alternative splicing produces four different isoforms of one ErbB4 gene. These isoforms (JM-a, JM-b, CYT-1 and CYT-2) are functionally dissimilar and proposed to have different roles in carcinogenesis. The juxtamembrane form JM-a undergoes regulated intramembrane proteolysis producing a soluble receptor ectodomain and an intracellular domain that translocates into the nucleus and regulates transcription. Nuclear signaling via JM-a isoform stimulates cancer cell proliferation. This study aimed to develop antibodies targeting the proposed oncogenic ErbB4 JM-a isoform that show potential in inhibiting ErbB4 dependent tumorigenesis. Also, the clinical relevance of ErbB4 shedding in cancer was studied. The currently used monoclonal antibody trastuzumab, targeting ErbB2, has shown efficacy in breast cancer therapy. In this study novel tissues with ErbB2 amplification and trastuzumab sensitivity were analyzed. The results of this study indicated that a subpopulation of breast cancer patients demonstrate increased shedding and cleavage of ErbB4. A JM-a isoform-specific antibody that inhibited ErbB4 shedding and consequent activation of ErbB4 had anti-tumor activity both in vitro and in vivo. Thus, ErbB4 shedding associates with tumor growth and specific targeting of the cleavable JM-a isoform could be considered as a strategy for developing novel ErbB-based cancer drugs. In addition, it was demonstrated that ErbB2 amplification is common in intestinal type gastric cancers with poor clinical outcome. Trastuzumab inhibited growth of gastric and breast cancer cells with equal efficacy. Thus, ErbB2 may be a useful target in gastric cancer.

Epidemiology of Cytochrome P450-mediated Drug-Drug Interactions

Drug-drug interactions (DDIs) comprise an important cause of adverse drug reactions leading to excess hospitalizations. Drug metabolism is catalyzed by 75% by cytochrome P450 (CYP) enzymes and thus they are often involved in pharmacokinetic DDIs. In general, DDIs are studied in randomized controlled clinical trials in selected study populations. The overall aim of the present studies was to perform observational pharmacoepidemiological surveys on CYP-mediated DDIs in diseases important at the population level. The prevalence of co-administrations of four prodrugs (losartan, codeine, tramadol, and clopidogrel), three sulphonylureas (glibenclamide, glimepiride, and glipizide), or two statins (lovastatin and simvastatin) with well established agents altering CYP activity, as well as of statins with fibrates, was studied in Finland utilizing data from a university hospital medication database (inpatients) and the National Prescription Register of the Social Insurance Institution of Finland, Kela (outpatients). Clinical consequences of potential DDIs were estimated by reviewing laboratory data, and information from hospital care and cause-of-death registers. Concomitant use of study substrates with interacting medication was detected in up to one fifth of patients in both hospital and community settings. Potential CYP3A4 interactions in statin users did not manifest in clear adverse laboratory values but pharmacodynamic DDIs between statins and fibrates predisposed patients to muscular toxicity. Sulphonylurea DDIs with CYP2C9 inhibitors increased the risk of hypoglycaemia. CYP3A4 inhibitor use with clopidogrel was not associated with significant changes in mortality but non-fatal thrombosis and haemorrhage complications were seen less often in this group. Concomitant administration of atorvastatin with clopidogrel moderately attenuated the antithrombotic effect by clopidogrel. The overall mortality was increased in CYP3A4 inducer and clopidogrel co-users. Atorvastatin used concomitantly with prodrug clopidogrel seems to be beneficial in terms of total and LDL cholesterol concentrations, and overall mortality compared with clopidogrel use without interacting medication. In conclusion, CYP-mediated DDIs are a common and often unrecognized consequence of irrational drug prescribing.

COMPARISON OF PROCEDURES FOR IMMEDIATE CHEMICAL ANALYSIS OF CHARCOAL

ABSTRACT The climate change, the quest for sustainability and the strong environmental pressures for alternatives to traditional fossil fuels have increased the interest in the search and use of renewable energy sources. Among them stands out the biomass of charcoal coming from renewable forests, widely used as a thermal reductant in the steel industry in the detriment of the use of mineral coal coke. This study aimed to compare different operating procedures of immediate chemical analysis of charcoal. Seven essays to immediate chemical analysis were compared, spread between procedures performed by Brazilian companies and laboratories, the test described by NBR 8112 and one realized with a thermogravimetric analyzer (TGA) using the parameters of the NBR 8112. There were significant differences in the volatiles matter content and consequently in the fixed carbon contents found. The differences between the procedures and the NBR 8112 were caused by an excess burning time, a mass sample above or below the standard or inappropriate container used for burning. It observed that the TGA appraisal of the volatiles content must be carried out with a burning time equal to 2 minutes to obtain results similar to those of the NBR 8112 norm. Moreover, the ash content values were statistically identical and the particles size did not influence the differences between means.

KNOWLEDGE ON ADJUVANT PROPERTIES, DISPOSAL OF PESTICIDERESIDUES AND SPRAY DRIFT OCCURRENCE IN THE STATE OF MATO GROSSO

ABSTRACT This paper aimed at investigating the knowledge level of people working on pesticide spraying activities concerning spray adjuvant properties, as well as collecting information on disposal locations for residues from internal spray tank cleaning, and finally the understanding of pesticide spray drift occurrence in the state of Mato Grosso, Brazil. The information was gathered through a questionnaire answered by participants of a rural extension program in application technology located in nineteen grain and fiber producing regions of Mato Grosso state. Among the mentioned adjuvants, 49.0% belonged to the mineral oil class and 17.9% of participants did not know the functions performed by such products. In addition, 58.5% of the participants discarded residues into the field. Among the participants who answered the question about spray drift occurrence causes, 54.1% indicated problems relating to inadequate weather conditions. In conclusion, there is a lack of knowledge on adjuvant functions, besides of inappropriate residue disposal in the state of Mato Grosso. Spray drift was referred as a problem; however, most of participants were not able to discuss the causes of these losses.

Improving Transportation and Warehousing Efficiency with Simulation-Based Decision Support Systems

Transportation and warehousing are large and growing sectors in the society, and their efficiency is of high importance. Transportation also has a large share of global carbondioxide emissions, which are one the leading causes of anthropogenic climate warming. Various countries have agreed to decrease their carbon emissions according to the Kyoto protocol. Transportation is the only sector where emissions have steadily increased since the 1990s, which highlights the importance of transportation efficiency. The efficiency of transportation and warehousing can be improved with the help of simulations, but models alone are not sufficient. This research concentrates on the use of simulations in decision support systems. Three main simulation approaches are used in logistics: discrete-event simulation, systems dynamics, and agent-based modeling. However, individual simulation approaches have weaknesses of their own. Hybridization (combining two or more approaches) can improve the quality of the models, as it allows using a different method to overcome the weakness of one method. It is important to choose the correct approach (or a combination of approaches) when modeling transportation and warehousing issues. If an inappropriate method is chosen (this can occur if the modeler is proficient in only one approach or the model specification is not conducted thoroughly), the simulation model will have an inaccurate structure, which in turn will lead to misleading results. This issue can further escalate, as the decision-maker may assume that the presented simulation model gives the most useful results available, even though the whole model can be based on a poorly chosen structure. In this research it is argued that simulation- based decision support systems need to take various issues into account to make a functioning decision support system. The actual simulation model can be constructed using any (or multiple) approach, it can be combined with different optimization modules, and there needs to be a proper interface between the model and the user. These issues are presented in a framework, which simulation modelers can use when creating decision support systems. In order for decision-makers to fully benefit from the simulations, the user interface needs to clearly separate the model and the user, but at the same time, the user needs to be able to run the appropriate runs in order to analyze the problems correctly. This study recommends that simulation modelers should start to transfer their tacit knowledge to explicit knowledge. This would greatly benefit the whole simulation community and improve the quality of simulation-based decision support systems as well. More studies should also be conducted by using hybrid models and integrating simulations with Graphical Information Systems.

Use of Medicinal Plants with Teratogenic and Abortive Effects by PregnantWomen in a City in Northeastern Brazil

Purpose The purpose of this study is to verify the use ofmedicinal plants by pregnant women treated at four Basic Health Units and at a public maternity facility in Brazil s northeast. Methods This is a cross-sectional, quantitative study, performed between February and April 2014. The subjects were 178 pregnant women, aged 18 to 42 years. To collect data, a structured questionnaire with dichotomous and multiple choice questions was used. To verify the correlation between the variables, Pearson s chi-square test was used. Results The study showed that 30.9% of the pregnant women used medicinal plants, and boldo was the most cited (35.4%). All the plants utilized, except lemongrass, have toxic effects in pregnancy, according to Resolution SES/RJ N° 1757. There was no statistically significant correlation between social class and use of medicinal plants. Conclusion The health of the study participants and their unborn children is at risk due to the inappropriate use of medicinal plants.

How (not) to interview children : interviews with young children in sexual abuse investigations in Finland

The present thesis had two main objectives: The first was to assess how child sexual abuse (CSA) interviews in Finland are conducted through analysing the interviewing techniques applied and the language used by the interviewers, as well as to suggest ways to improve interviews if they were found to have deficiencies. The second main aim was to contribute to the growing research corpus concerning CSA interviews, in particular, by addressing how interviewers follow up information provided by the child, by analysing whether child health care professionals would use childadapted language, and by studying the kind of modifications in the verbal behaviour of interviewers and children that were associated with a) repeated interviews, b) a support person’s presence at the interview, and c) the use of anatomically detailed dolls. Two complementary samples of CSA interviews were analysed. The first one was composed of child interviews with 3-12-year-old children (N = 27) that had been considered problematic by lawyers or other involved professionals (Studies I and IV). The second sample consisted of unselected interviews (N = 43) with children aged 3 to 8 years conducted in a number of hospitals in different parts of the country (Studies II and III). Study I: The verbal interaction between interviewer and child was analysed in a sample of interviews that had been considered to be problematic by involved professionals. Results showed that interviewers used inappropriate questioning techniques, relying on option-posing, specific suggestive and unspecific suggestive questions to a significant extent, these comprising around 50% of all interviewer utterances. The proportion of invitations, which the research community recommends interviewers to rely on, was strikingly low. Invitations and directive utterances were associated with an increase in informative responses by the child in terms of response type, number of new details reported, as well as length of response. The opposite was true for option-posing and suggestive utterances. Longer questions by the interviewer (in number of words) often rendered no reply from the child, whereas shorter questions were followed by descriptive answers. Even after the child had provided an informative answer, interviewers failed to follow up the information in an adequate way and instead continued to rely on focused and leading questions. Study II: Due to the possible bias of the sample analysed in Study I, the most important analyses were rerun with the unselected sample and reported separately. Results were quite similar between the two studies, indicating that the problems observed in Study I, with interviewers relying on option-posing and suggestive questions to a significant extent, are likely to be general and not specific for those interviews. Even if suggestive questions were slightly less and invitations slightly more common in this sample than in the previous study, almost half of the interviewer questions were still optionposing or suggestive, and also in this sample, interviewers failed to follow up information by the child in a facilitating manner. Differentiating between judicial and contextual details showed that while facilitators, invitations, and directive utterances elicited more contextual than judicial details, the opposite was true for specific suggestive utterances. These results might be explained by the reluctance of children to describe sexual details related to the abuse events. Alternatively, they may also be due to children describing incorrect sexual details as a result of suggestive interviewing techniques. Study III: This study examined features of the language used by the interviewers. Interviewer utterances included multiple questions, long statements, complicated grammar and concepts, as well as unclear references to persons and situations. More than a fifth of the interviewer utterances were coded as belonging to at least one of these categories. The results suggest that even professionals who are experienced in interacting with children may have difficulties in using a child-sensitive language, adding to the pool of studies showing similar problems to occur in legal hearings with children conducted by lawyers. As children rarely comment on, or even recognise, their lack of comprehension, the use of a language that is too complex can have detrimental consequences for the outcomes of investigative interviews. Interviewers used different approaches to introduce the topic of abuse. While 15% of the children spontaneously addressed the topic of abuse, probably indicating that they felt confident with the interviewer and the situation, in almost 50% of the cases, the interviewer introduced the topic of abuse in a way that can be considered leading. Interviews were characterised by a lack of structure, apparent in frequent rapid switches of topic by the interviewer. This manner was associated with a decrease in the number of new details provided by the children. Study IV: This study analysed possible changes in the interview dynamics associated with repeated interviewing, the presence of a support person (related to the child), and the use of anatomically detailed (AD) dolls. Repeated interviewing, in combination with suggestive questions, has previously been found to seriously contaminate children’s accounts. In the present material, interviewers used significantly more suggestive utterances in the repeated condition, thus endangering the reliability of the children’s reports. Few studies have investigated the effects of a support person’s presence at the interview. The results of the present study showed that interviewers talked more and children provided less information when a support person was present. Supporting some earlier findings regarding the use of AD dolls, the present results showed that using AD dolls was associated with longer interviewer utterances and shorter, less responsive, and less detailed child responses. Interviewers used up to five times more unspecific suggestive utterances when dolls were used, for instance through repeatedly asking the child to show “what really happened” with the dolls. Conclusion: The results indicate that CSA interviews in Finland are not conducted in a manner that follows best practice as defined by the research community and as stated in a number of guidelines. When comparing these questioning strategies with the recommendations, which have been predominant in the field for more than ten years now, it can be concluded that the interviews analysed were conducted in a manner that undermines the possibility to elicit an uncontaminated and accurate narrative from the children. A particularly worrying finding was the fact that interviewers did not follow up relevant information by the children in an adequate way. A number of clinical implications can be drawn from the results, particularly concerning the need for improvement in the quality of CSA interviews. There is convincing research regarding how to improve CSA interviews, notably through training forensic child interviewers to use a structured interviewing protocol, and providing them with continuous supervision and feedback. Allocating appropriate resources to improve the quality of forensic child interviews is a matter of protecting the rights of all persons involved in CSA investigations, in particular those of the children.

Effects of cytochrome P450 enzyme inhibitors and inducers on the metabolism of S-ketamine

The human body eliminates foreign compounds primarily by metabolizing them to hydrophilic forms to facilitate effective excretion through the kidneys. Cytochrome P450 (CYP) enzymes in the liver and intestine contribute to the metabolism of many drugs. Pharmacokinetic drugdrug interactions occur if the activity of CYPs are inhibited or induced by another drug. Prescribing multiple drugs to the improve effectiveness of therapy or to treat coexisting diseases is a common practice in clinical medicine. Polypharmacy predisposes patients to adverse effects because of the profound unpredictability in CYP enzymatic-mediated drug metabolism. S-ketamine is a phencyclidine derivative which functions as an antagonist of the N-methyl-Daspartate (NMDA) receptor in the central nervous system. It is a unique anaesthetic producing “dissociative anaesthesia” in high doses and analgesia in low doses. Studies with human liver microsomes suggest that ketamine is metabolized primarily via CYP3A4 and CYP2B6 enzymes. In this thesis, in healthy volunteers, randomized and controlled cross-over studies were conducted to investigate the effects of different CYP inducers and inhibitors on the pharmacokinetics and pharmacodynamics of oral and intravenous S-ketamine. The plasma concentrations of ketamine and its metabolite, norketamine, were determined at different timepoints over a 24 hour period. Other pharmacodynamic variables were examined for 12 hours. Results of these studies showed that the inhibition of the CYP3A4 pathway by clarithromycin or grapefruit juice increased the exposure to oral S-ketamine by 2.6- and 3.0-fold. Unexpectedly, CYP3A4 inhibition by itraconazole caused no significant alterations in the plasma concentrations of oral S-ketamine. CYP3A4 induction by St. John´s wort or rifampicin decreased profoundly the concentrations of oral S-ketamine. However, after rifampicin, there were no significant differences in the plasma concentrations of S-ketamine when it was administered intravenously. This demonstrated that rifampicin inhibited the metabolism of Sketamine at the intestinal level. When CYP2B6 was inhibited by ticlopidine, there was a 2.4- fold increase in the exposure of S-ketamine. These studies demonstrated that low dose oral Sketamine is metabolized both via CYP3A4 and CYP2B6 pathways. The concomitant use of drugs that affect CYP3A4 or CYP2B6, during oral S-ketamine treatment, may cause clinically significant drug-drug interactions.

Regulation of lymphocyte response in vitro and in vivo

CD4+ T helper (Th) cells have an important role in the defence against diverse pathogens. Th cells can differentiate into several functionally distinct subtypes including Th1 and Th2 cells. Th1 cells are important for eradicating intracellular pathogens, whereas Th2 cells pro¬tect our body against extracellular parasites. However if uncontrolled, Th cells can mediate immunopathology such as asthma or allergies, but inappropriate Th response can also lead to autoimmune diseases such as multiple sclerosis or type 1 diabetes. Deeper knowledge of the regulation of the lymphocyte response both in vitro and in vivo is important for un¬derstanding the pathogenesis of immune-mediated diseases and microbe-host interactions. In the work presented in this thesis, the first goal was to elucidate the role of novel factors, PIM kinases and c-FLIP in the regulation of human Th cell differentiation. The oncogenic serine-threonine kinases of the PIM family were shown to be preferentially expressed in Th1 cells and in addition, by using RNA interference, they were also shown to be positive regulators of Th1 differentiation. The PIM depletion experiments suggest that PIM kinases promote the expression of the hallmark cytokine of Th1 cells, IFNγ, and influence the IL12/STAT4 pathway during the early Th1 cell differentiation. In addition to cytokine and T cell receptor (TCR) induced pathways, caspase activity has been shown to regulate Th cell proliferation. In the work presented in this thesis, the two isoforms of the caspase regulator protein, c-FLIP, were shown to be differentially ex¬pressed in Th1 and Th2 cells. Both of the isoforms were up-regulated in response to TCR activation, but the expression of the short isoform was selectively induced by IL4, the Th2 inducing cytokine. Furthermore, the c-FLIP isoforms had distinct and opposite roles during the early differentiation of Th1 and Th2 cells. The knockdown of the long isoform of c-FLIP led to the induction of Th1 marker genes, such as IFNγ and TBET, whereas the depletion of c-FLIP short down-regulated Th2 marker genes IL-4 and GATA3. The third goal was to elucidate the gene expression profiles characterizing the T- and B-lymphocyte responses in vivo during experimental infection by intracellular bacte¬rium Chlamydia pneumoniae. Previously, it has been shown that CD8+ and CD4+ T cells are important for the protection against Chlamydia pneumoniae. In this study, the analysis revealed up-regulation of interferon induced genes during recurrent infection underlining the importance of IFNγ secreted by Th1 and CD8+ T cells in the protection against this pathogen. Taken together, in this study novel regulators of Th cell differ¬entiation were discovered and in addition the gene expression profiles of lymphocytes induced by Chlamydia pneumoniae infection were characterized.

Libyan breast cancer: Health services and biology. Diagnosis delay and prognostic value of DNA pploidy, S-phase fraction, and Ki-67 and Bcl-2 immunohistochemistry

The aim of this study was to investigate the diagnosis delay and its impact on the stage of disease. The study also evaluated a nuclear DNA content, immunohistochemical expression of Ki-67 and bcl-2, and the correlation of these biological features with the clinicopathological features and patient outcome. 200 Libyan women, diagnosed during 2008–2009 were interviewed about the period from the first symptoms to the final histological diagnosis of breast cancer. Also retrospective preclinical and clinical data were collected from medical records on a form (questionnaire) in association with the interview. Tumor material of the patients was collected and nuclear DNA content analysed using DNA image cytometry. The expression of Ki-67 and bcl-2 were assessed using immunohistochemistry (IHC). The studies described in this thesis show that the median of diagnosis time for women with breast cancer was 7.5 months and 56% of patients were diagnosed within a period longer than 6 months. Inappropriate reassurance that the lump was benign was an important reason for prolongation of the diagnosis time. Diagnosis delay was also associated with initial breast symptom(s) that did not include a lump, old age, illiteracy, and history of benign fibrocystic disease. The patients who showed diagnosis delay had bigger tumour size (p<0.0001), positive lymph nodes (p<0.0001), and high incidence of late clinical stages (p<0.0001). Biologically, 82.7% of tumors were aneuploid and 17.3% were diploid. The median SPF of tumors was 11% while the median positivity of Ki-67 was 27.5%. High Ki-67 expression was found in 76% of patients, and high SPF values in 56% of patients. Positive bcl-2 expression was found in 62.4% of tumors. 72.2% of the bcl-2 positive samples were ER-positive. Patients who had tumor with DNA aneuploidy, high proliferative activity and negative bcl-2 expression were associated with a high grade of malignancy and short survival. The SPF value is useful cell proliferation marker in assessing prognosis, and the decision cut point of 11% for SPF in the Libyan material was clearly significant (p<0.0001). Bcl-2 is a powerful prognosticator and an independent predictor of breast cancer outcome in the Libyan material (p<0.0001). Libyan breast cancer was investigated in these studies from two different aspects: health services and biology. The results show that diagnosis delay is a very serious problem in Libya and is associated with complex interactions between many factors leading to advanced stages, and potentially to high mortality. Cytometric DNA variables, proliferative markers (Ki-67 and SPF), and oncoprotein bcl-2 negativity reflect the aggressive behavior of Libyan breast cancer and could be used with traditional factors to predict the outcome of individual patients, and to select appropriate therapy.

Transcriptional and Epigenetic Regulation of Human CD4+ T Helper Lineage Specification

Activated T helper (Th) cells have ability to differentiate into functionally distinct Th1, Th2 and Th17 subsets through a series of overlapping networks that include signaling and transcriptional control and the epigenetic mechanisms to direct immune responses. However, inappropriate execution in the differentiation process and abnormal function of these Th cells can lead to the development of several immune mediated diseases. Therefore, the thesis aimed at identifying genes and gene regulatory mechanisms responsible for Th17 differentiation and to study epigenetic changes associated with early stage of Th1/Th2 cell differentiation. Genome wide transcriptional profiling during early stages of human Th17 cell differentiation demonstrated differential regulation of several novel and currently known genes associated with Th17 differentiation. Selected candidate genes were further validated at protein level and their specificity for Th17 as compared to other T helper subsets was analyzed. Moreover, combination of RNA interference-mediated downregulation of gene expression, genome-wide transcriptome profiling and chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq), combined with computational data integration lead to the identification of direct and indirect target genes of STAT3, which is a pivotal upstream transcription factor for Th17 cell polarization. Results indicated that STAT3 directly regulates the expression of several genes that are known to play a role in activation, differentiation, proliferation, and survival of Th17 cells. These results provide a basis for constructing a network regulating gene expression during early human Th17 differentiation. Th1 and Th2 lineage specific enhancers were identified from genome-wide maps of histone modifications generated from the cells differentiating towards Th1 and Th2 lineages at 72h. Further analysis of lineage-specific enhancers revealed known and novel transcription factors that potentially control lineage-specific gene expression. Finally, we found an overlap of a subset of enhancers with SNPs associated with autoimmune diseases through GWASs suggesting a potential role for enhancer elements in the disease development. In conclusion, the results obtained have extended our knowledge of Th differentiation and provided new mechanistic insights into dysregulation of Th cell differentiation in human immune mediated diseases.