Consistency from the perspective of an experimental systems approach to the sciences and their epistemic objects

It is generally accepted that the development of the modern sciences is rooted in experiment. Yet for a long time, experimentation did not occupy a prominent role, neither in philosophy nor in history of science. With the 'practical turn' in studying the sciences and their history, this has begun to change. This paper is concerned with systems and cultures of experimentation and the consistencies that are generated within such systems and cultures. The first part of the paper exposes the forms of historical and structural coherence that characterize the experimental exploration of epistemic objects. In the second part, a particular experimental culture in the life sciences is briefly described as an example. A survey will be given of what it means and what it takes to analyze biological functions in the test tube.

The Influence of Diet and Microbes on Colonic Immune Regulation and their Implications on Type 1 Diabetes

Dietary and microbial factors are thought to contribute to the rapidly increasing prevalence of T1D in many countries worldwide. The impact of these factors on immune regulation and diabetes development in non-obese diabetic (NOD) mice are investigated in this thesis. Diabetes can be prevented in NOD mice through dietary manipulation. Diet affects the composition of intestinal microbiota, which may subsequently influence intestinal immune homeostasis. However, the specific effects of anti-diabetogenic diets on gut immunity and the explicit associations between intestinal immune disruption and type 1 diabetes onset remain unclear. The research presented herein demonstrates that newly weaned NOD mice suffer from a mild level of colitis, which shifts the colonic immune cell balance towards a proinflammatory status. Several aberrations can also be observed in the peritoneal B cells of NOD mice; an increase in activation marker expression, increased trafficking to the pancreatic lymph nodes and significantly higher antigen presenting cell (APC) efficiency towards insulin-specific T cells. A shift towards inflammation is likewise observed in the colon of germ-free NOD mice, but signs of peritoneal B cell activation are lacking in these mice. Remarkably, most of the abnormalities in the colon, peritoneal macrophages and the peritoneal B cell APC activity of NOD mice are abrogated when NOD mice are maintained on a diabetes-preventive, soy-based diet (ProSobee) from the time of weaning. Dietary and microbial factors hence have a significant impact on colonic immune regulation and peritoneal B cell activation and it is suggested that these factors influence diabetes development in NOD mice.

Conventional and novel cardiovascular risk factors in young Finns and their associations with structural and functional vascular changes of subclinical atherosclerosis. The Cardiovascular Risk in Young Finns Study

Background: Atherosclerosis begins in early life progressing from asymptomatic to symptomatic as we age. Although substantial progress has been made in identifying the determinants of atherosclerosis in middle to older age adults at increased cardiovascular risk, there is lack of data examining determinants and prediction of atherosclerosis in young adults. Aims: The current study was designed to investigate levels of cardiovascular risk factors in young adults, subclinical measures of atherosclerosis, and prediction of subclinical arterial changes with conventional risk factor measures and novel metabolic profiling of serum samples. Subjects and Methods: This thesis utilised data from the follow-ups performed in 2001 and 2007 in the Cardiovascular Risk in Young Finns study, a Finnish population-based prospective cohort study that examined 2,204 subjects who were aged 30-45 years in 2007. Subclinical atherosclerosis was studied using noninvasive ultrasound measurements of carotid intima-media thickness (IMT), carotid arterial distensibility (CDist) and brachial flow-mediated dilation (FMD). Measurements included conventional risk factors and metabolic profiling using highthroughput nuclear magnetic resonance (NMR) methods that provided data on 42 lipid markers and 16 circulating metabolites. Results: Trends in lipids were favourable between 2001 and 2007, whereas waist circumference, fasting glucose, and blood pressure levels increased. To study the stability of noninvasive ultrasound markers, 6-year tracking (the likelihood to maintain the original fractile over time) in 6 years was examined. IMT tracked more strongly than CDist and FMD. Cardiovascular risk scores (Framingham, SCORE, Finrisk, Reynolds and PROCAM) predicted subclinical atherosclerosis equally. Lipoprotein subclass testing did not improve the prediction of subclinical atherosclerosis over and above conventional risk factors. However, circulating metabolites improved risk stratification. Tyrosine and docosahexaenoic acid were found to be novel biomarkers of high IMT. Conclusions: Prediction of cardiovascular risk in young Finnish adults can be performed with any of the existing risk scores. The addition of metabonomics to risk stratification improves prediction of subclinical changes and enables more accurate targeting of prevention at an early stage.

Astringent Food Compounds and Their Interactions with Taste Properties

Astringency is traditionally thought to be induced by plant tannins in foods. Because of this current research concerning the mechanism of astringency is focused on tannin‐protein interactions and thus on precipitation, which may be perceived by mechanoreceptors. However, astringency is elicited by a wide range of different phenolic compounds, as well as, some non‐phenolic compounds in various foods. Many ellagitannins or smaller compounds that contribute to astringent properties do not interact with salivary proteins and may be directly perceived through some receptors. Generally, the higher degree of polymerization of proanthocyanidins can be associated with more intense astringency. However, the astringent properties of smaller phenolic compounds may not be directly predicted from the structure of a compound, although glycosylation has a significant role. The astringency of organic acids may be directly linked to the perception of sourness, and this increases along with decreasing pH. Astringency can be divided into different sub‐qualities, including even other qualities than traditional mouth‐drying, puckering or roughing sensations. Astringency is often accompanied by bitter or sour or both taste properties. The different sub‐qualities can be influenced by different astringent compounds. In general, the glycolysation of the phenolic compound results in more velvety and smooth mouthdrying astringency. Flavonol glycosides and other flavonoid compounds and ellagitannins contribute to this velvety mouthdrying astringency. Additionally, they often lack the bitter properties. Proanthocyanidins and phenolic acids elicit more puckering and roughing astringency with some additional bitter properties. Quercetin 3‐O‐rutinoside, along with other quercetin glycosides, is among the key astringent compounds in black tea and red currants. In foods, there are always various other additional attributes that are perceived at the same with astringency. Astringent compounds themselves may have other sensory characteristics, such as bitter or sour properties, or they may enhance or suppress other sensory properties. Components contributing to these other properties, such as sugars, may also have similar effects on astringent sensations. Food components eliciting sweetness or fattiness or some polymeric polysaccharides can be used to mask astringent subqualities. Astringency can generally be referred to as a negative contributor to the liking of various foods. On the other hand, perceptions of astringent properties can vary among individuals. Many genetic factors that influence perceptions of taste properties, such as variations in perceiving a bitter taste or variations in saliva, may also effect the perception of astringency. Individuals who are more sensitive to different sensations may notice the differences between astringent properties more clearly. This may not have effects on the overall perception of astringency. However, in many cases, the liking of astringent foods may need to be learned by repetitive exposure. Astringency is often among the key sensory properties forming the unique overall flavour of certain foods, and therefore it also influences whether or not a food is liked. In many cases, astringency may be an important sub‐property suppressed by other more abundant sensory properties, but it may still have a significant contribution to the overall flavour and thus consumer preferences. The results of the practical work of this thesis show that the astringent phenolic compounds are mostly located in the skin fractions of black currants, crowberries and bilberries (publications I–III). The skin fractions themselves are rather tasteless. However, the astringent phenolic compounds can be efficiently removed from these skin fractions by consecutive ethanol extractions. Berries contain a wide range of different flavonol glycosides, hydroxycinnamic acid derivatives and anthocyanins and some of them strongly contribute to the different astringent and bitterness properties. Sweetness and sourness are located in the juice fractions along with the majority of sugars and fruit acids. The sweet and sour properties of the juice may be used to mask the astringent and bitterness properties of the extracts. Enzymatic treatments increase the astringent properties and fermented flavour of the black currant juice and decrease sweetness and freshness due to the effects on chemical compositions (IV). Sourness and sweetness are positive contributors to the liking of crowberry and bilberry fractions, whereas bitterness is more negative (V). Some astringent properties in berries are clearly negative factors, whereas some may be more positive. The liking of berries is strongly influenced by various consumer background factors, such as motives and health concerns. The liking of berries and berry fractions may also be affected by genetic factors, such as variations in the gene hTAS2R38, which codes bitter taste receptors (V).

SOIL ORGANIC CARBON, CARBON STOCK AND THEIR RELATIONSHIPS TO PHYSICAL ATTRIBUTES UNDER FOREST SOILS IN CENTRAL AMAZONIA

ABSTRACT The soil carbon under Amazonian forests has an important roles in global changing, making information on the soil content and depths of these stocks are considerable interest in efforts to quantify soil carbon emissions to the atmosphere.This study quantified the content and soil organic carbon stock under primary forest up to 2 m depth, at different topographic positions, at Cuieiras Biological Reserve, Manaus/ ZF2, km 34, in the Central Amazon, evaluating the soil attributes that may influence the permanence of soil carbon. Soil samples were collected along a transect of 850 m on topographic gradient Oxisol (plateau), Ultisol (slope) and Spodosol (valley). The stocks of soil carbon were obtained by multiplying the carbon content, soil bulk density and trickiness of soil layers. The watershed was delimited by using STRM and IKONOS images and the carbon contend obtained in the transects was extrapolated as a way to evaluate the potential for carbon stocks in an area of 2678.68 ha. The total SOC was greater in Oxisol followed by Spodosol and Ultisol. It was found direct correlations between the SOC and soil physical attributes. Among the clay soils (Oxisol and Ultisol), the largest stocks of carbon were observed in Oxisol at both the transect (90 to 175.5 Mg C ha-1) as the level of watershed (100.2 to 195.2 Mg C ha-1). The carbon stocks under sandy soil (Spodosol) was greater to clay soils along the transect (160-241 Mg C ha-1) and near them in the Watershed (96.90 to 146.01 Mg C ha-1).

New perspectives on the melanocortins and their cardiovascular effects: Potential implications for the treatment of cardiovascular diseases with melanocortin analogues

The melanocortin peptides, including melanocyte-stimulating hormones, α-, β- and γ-MSH, are derived from the precursor peptide proopiomelanocortin and mediate their biological actions via five different melanocortin receptors, named from MC1 to MC5. Melanocortins have been implicated in the central regulation of energy balance and cardiovascular functions, but their local effects, via yet unidentified sites of action, in the vasculature, and their therapeutic potential in major vascular pathologies remain unclear. Therefore, the main aim of this thesis was to characterise the role of melanocortins in circulatory regulation, and to investigate whether targeting of the melanocortin system by pharmacological means could translate into therapeutic benefits in the treatment of cardiovascular diseases such as hypertension. In experiments designed to elucidate the local effects of α-MSH on vascular tone, it was found that α-MSH improved blood vessel relaxation via a nitric oxide (NO)-dependent mechanism without directly contracting or relaxing blood vessels. Furthermore, α-MSH was shown to regulate the expression and function of endothelial NO synthase in cultured human endothelial cells via melanocortin 1 receptors. In keeping with the vascular protective role, pharmacological treatment of mice with α-MSH analogues displayed therapeutic efficacy in conditions associated with vascular dysfunction such as obesity. Furthermore, α-MSH analogues elicited marked diuretic and natriuretic responses, which together with their vascular effects, seemed to provide protection against sodium retention and blood pressure elevation in experimental models of hypertension. In conclusion, the present results identify novel effects for melanocortins in the local control of vascular function, pointing to the potential future use of melanocortin analogues in the treatment of cardiovascular pathologies.

Expression of the Immunohistochemical Markers p16 and Ki-67 and Their Usefulness in the Diagnosis of Cervical Intraepithelial Neoplasms

Objective The aim of this study was to determine the expression of the immunohistochemical markers p16 and Ki-67 in cervical intraepithelial neoplasms and their influence on the level of agreement among different observers and for the same observer. Methods The study included 184 patients with cervical intraepithelial neoplasms previously confirmed through biopsies performed between 2005 and 2006. Three pathologists reviewed the biopsies by using hematoxylin-eosin staining to reach a consensus on the diagnosis. Subsequently, an immunohistochemical study analyzed the expression of p16 and Ki-67 in such cases. Results The comparison among the reviewing pathologists revealed only moderate agreement (kappa = 0.44). The agreement improved when the differentiation of highgrade lesions (cervical intraepithelial neoplasm - CIN - 3) was analyzed (kappa = 0.59). p16 staining exhibited a high negative predictive value and sensitivity; however, the specificity was low. Overall, both qualitative and quantitative analyses of p16 and a quantitative analysis Ki-67 exhibited low accuracy. The agreement among diagnoses before immunohistochemistry was 0.47. The use of immunohistochemistry increased the agreement to 0.68. Conclusion Our study showed that the agreement among observers using traditional diagnostic criteria of cervical intraepithelial lesions can improve with the use of immunohistochemistry.

Character transformations and their functional significance as a key to the evolution of hystricognath Rodentia

Hystricognathi represent a monophyletic taxon within Rodentia. Since phylogenetically analyzed morphological systems are essential for revealing evolutionary processes, this study identifies evolutionary character transformations on the stem lineage of Hystricognathi as derived from the author's own work and the literature. Data so far indicate that evolutionary transformations in the rostral head region, the loss of tactile ability in the outer nasal skin and the mobile arrangement of the associated cartilage, were allied with a switch from omnivorous to herbivorous and fiber-rich nutrition. Additional character transformations in the skull assist in digesting such food. Structures associated with reproduction and placentation show a remarkable pro portion of derived character conditions: the chorioallantoic placenta has a ring-shaped organization and growth structure which optimizes the capacity for passive diffusion, a subplacenta occurred as a specialized region responsible for placental invasion and the inverted yolk sac facilitates substance exchange with the main placenta. Finally, precocial newborns evolved as a derived condition within Rodentia. All things considered, a mode of reproduction is indicated, which does not demand excessive additional energy intake by the mother and is in accordance with her low energetic diet. Hystricognathi possess major character transformations that represent prerequisites for their successful radiation at the time when more open ecosystems and grasslands evolved during Earth history. The analysis resulted in the reconstruction of a life-near picture of the hystricognath stem species pattern with high explanatory power in terms of changes in space and time and their interdependence with biodiversity.

Different pathways in the larval development of the crab Ucides cordatus (Decapoda, Ocypodidae) and their relation with high mortality rates by the end of massive larvicultures

One of the most limiting factors affecting the larval rearing of Ucides cordatus in the laboratory is a period of high mortality, which usually occurs late in the course of the larviculture during the metamorphosis from the zoeal to the megalopal phase. The objective of the present research was to analyze the post-embryonic development of U. cordatus on an individual basis and, in particular, to search for patterns linking disturbances in the molting process to the high larval death rates observed in massive larvicultures. A total of 50 larvae were individually reared from hatching to metamorphosis into the megalopal phase under controlled conditions, fed a combination of microalgae and rotifers. The survivorship rate was 70% until zoea V. The 35 surviving zoea V larvae followed two different pathways. Eleven underwent metamorphosis directly to megalopa, eighteen molted to zoea VI and six died as zoea V. In the last molting event, only two zoea VI larvae reached the megalopal stage, while the remaining sixteen died. In further observation under microscope, 13 of the dead zoea VI showed characteristics of the pre-molt stage and pereiopods disproportionably large in relation to the carapace. The observed pattern resembles the Molt Death Syndrome (MDS) described for other decapod species, in which larvae die in the late pre-molt phase of the molting cycle. We suggest that U. cordatus larvae develop disturbances in the molting process similar to the MDS described for other species and that these disturbances are related to a more complex pathway involving the emergence of larval stage zoea VI.

Spatialization of climate, physical and socioeconomic factors that affect the dairy goat production in Brazil and their impact on animal breeding decisions

Brazil has high climate, soil and environmental diversity, as well as distinct socioeconomic and political realities, what results in differences among the political administrative regions of the country. The objective of this study was to determine spatial distribution of the physical, climatic and socioeconomic aspects that best characterize the production of dairy goats in Brazil. Production indices of milk per goat, goat production, milk production, as well as temperature range, mean temperature, precipitation, normalized difference vegetation index, relative humidity, altitude, agricultural farms; farms with native pasture, farms with good quality pasture, farms with water resources, farms that receive technical guidance, family farming properties, non-familiar farms and the human development index were evaluated. The multivariate analyses were carried out to spatialize climatic, physical and socioeconomic variables and so differenciate the Brazilian States and Regions. The highest yields of milk and goat production were observed in the Northeast. The Southeast Region had the second highest production of milk, followed by the South, Midwest and North. Multivariate analysis revealed distinctions between clusters of political-administrative regions of Brazil. The climatic variables were most important to discriminate between regions of Brazil. Therefore, it is necessary to implement animal breeding programs to meet the needs of each region.

Biodegradable packaging materials in 2013 and their feasibility in chocolate industry

The development of biopolymers has been rapid in recent years and the range of available bioplastics is increasing continuously, driven by a growing demand for sustainable solutions. There are several key drivers behind this growth. The oil reservoirs are decreasing which is causing a price increase for the traditional plastic materials and therefore the gap to bioplastics’ price is getting smaller. In addition, other environmental topics, such as waste disposal and green production, have become more and more important factors for institutes, companies and consumers. Legislation and directives have to be taken into account as well in decision making concerning different packaging materials. The new environmental law with waste disposal responsibility will also have an effect on the packaging business. Therefore a need has risen to study closer the current offering closer of bio-based materials that could be used in chocolate packaging. In this Master’s Thesis the bioplastics’, and especially biodegradable materials’ technical properties and their development, availability, possible existing products in the markets, waste disposal possibilities and consumers attitude towards environmental friendly packaging is studied. This is a case study where the offering of biodegradable materials was investigated during March 2013 for Fazer Confectionary.

Partial budget analysis of prepartum antimicrobial therapy and Escherichia coli J5 vaccination of dairy heifers and their effect on milk production and milk quality parameters

Abstract: This study aimed to determine whether prepartum antimicrobial and/or Escherichia coli J5 vaccination in dairy heifers influence the milk production, milk quality, and estimate their economic benefit. Thus, 33 dairy heifers were enrolled in four groups using a split-splot design. Groups were: (G1) prepartum antimicrobial infusion and vaccination with an E. coli J5 bacterin, (G2) prepartum antimicrobial infusion, (G3) vaccination with an E. coli J5 bacterin, and (G4) control heifers. Composite milk samples for somatic cell count, total bacteria count and milk composition were collected 15 days after calving and every 15 days until the end of the experiment. Bacteriological analysis was carried out at the end of study. The milk production and the incidence of clinical cases of mastitis, as well as the costs associated with them were recorded. The results demonstrate a reduction on clinical mastitis rates by preventive strategies, which implicated in lower volume of discarded milk (0.99, 1.01, 1.04 and 3.98% for G1, G2, G3 and G4, respectively) and higher economic benefit. Thus, in well-managed dairy herds the prevention of heifer mastitis by vaccination or antimicrobial therapy can reduce the amount of antimicrobials needed to treat clinical mastitis cases and the days of discarded milk.