Developing an index of dietary estimation of fermentable carbohydrate to allow dietary analysis for epidemiological studies

It has been proposed that long-term consumption of diets rich in non-digestible carbohydrates (NDCs), such as cereals, fruit and vegetables might protect against several chronic diseases, however, it has been difficult to fully establish their impact on health in epidemiology studies. The wide range properties of the different NDCs may dilution their impact when they are combined in one category for statistical comparisons in correlations or multivariate analysis. Several mechanisms have been suggested to explain the protective effects of NDCs, including increased stool bulk, dilution of carcinogens in the colonic lumen, reduced transit time, lowering pH, and bacterial fermentation to short chain fatty acids (SCFA) in the colon. However, it is very difficult to measure SCFA in humans in vivo with any accuracy, so epidemiological studies on the impact of SCFA are not feasible. Most studies use dietary fibre (DF) or Non-Starch Polysaccharides (NSP) intake to estimate the levels, but not all fibres or NSP are equally fermentable. It has been proposed that long-term consumption of diets rich in non-digestible carbohydrates (NDCs), such as cereals, fruit and vegetables might protect against several chronic diseases, however, it has been difficult to fully establish their impact on health in epidemiology studies. The wide range properties of the different NDCs may dilution their impact when they are combined in one category for statistical comparisons in correlations or multivariate analysis. Several mechanisms have been suggested to explain the protective effects of NDCs, including increased stool bulk, dilution of carcinogens in the colonic lumen, reduced transit time, lowering pH, and bacterial fermentation to short chain fatty acids (SCFA) in the colon. However, it is very difficult to measure SCFA in humans in vivo with any accuracy, so epidemiological studies on the impact of SCFA are not feasible. Most studies use dietary fibre (DF) or Non-Starch Polysaccharides (NSP) intake to estimate the levels, but not all fibres or NSP are equally fermentable. The first aim of this thesis was the development of the equations used to estimate the amount of FC that reaches the human colon and is fermented fully to SCFA by the colonic bacteria. Therefore, several studies were examined for evidence to determine the different percentages of each type of NDCs that should be included in the final model, based on how much NDCs entered the colon intact and also to what extent they were fermented to SCFA in vivo. Our model equations are FC-DF or NSP$ 1: 100 % Soluble + 10 % insoluble + 100 % NDOs¥ + 5 % TS** FC-DF or NSP 2: 100 % Soluble + 50 % insoluble + 100 % NDOs + 5 % TS FC-DF* or NSP 3: 100 % Soluble + 10 % insoluble + 100 % NDOs + 10 % TS FC-DF or NSP 4: 100 % Soluble + 50 % insoluble + 100 % NDOs + 10 % TS *DF: Dietary fibre; **TS: Total starch; $NSP: non-starch polysaccharide; ¥NDOs: non-digestible oligosaccharide The second study of this thesis aimed to examine all four predicted FC-DF and FC-NSP equations developed, to estimate FC from dietary records against urinary colonic NDCs fermentation biomarkers. The main finding of a cross-sectional comparison of habitual diet with urinary excretion of SCFA products, showed weak but significant correlation between the 24 h urinary excretion of SCFA and acetate with the estimated FC-DF 4 and FC-NSP 4 when considering all of the study participants (n = 122). Similar correlations were observed with the data for valid participants (n = 78). It was also observed that FC-DF and FC-NSP had positive correlations with 24 h urinary acetate and SCFA compared with DF and NSP alone. Hence, it could be hypothesised that using the developed index to estimate FC in the diet form dietary records, might predict SCFA production in the colon in vivo in humans. The next study in this thesis aimed to validate the FC equations developed using in vitro models of small intestinal digestion and human colon fermentation. The main findings in these in vitro studies were that there were several strong agreements between the amounts of SCFA produced after actual in vitro fermentation of single fibre and different mixtures of NDCs, and those predicted by the estimated FC from our developed equation FC-DF 4. These results which demonstrated a strong relationship between SCFA production in vitro from a range of fermentations of single fibres and mixtures of NDCs and that from the predicted FC equation, support the use of the FC equation for estimation of FC from dietary records. Therefore, we can conclude that the newly developed predicted equations have been deemed a valid and practical tool to assess SCFA productions for in vitro fermentation.

Endoluminal calprotectin measurement in assessment of pouchitis and a new index of disease activity: a pilot study

Pouchitis is the most common complication following proctocolectomy with ileal pouch-anal anastomosis for ulcerative colitis (UC). To provide a standardized definition of pouchitis clinical, endoscopic and histological markers were grouped and weighted in the pouch disease activity index (PDAI). However, the delay in the assessment of the final score due to the time requested for histological analysis remains the main obstacle to the index implementation in clinical practice so that the use of modified-PDAI (mPDAI) with exclusion of histologic subscore has been proposed. We tested the ability of calprotectin measurement in the pouch endoluminal content to mimic the histologic score as defined in the PDAI, the index that we adopted as gold standard for pouchitis diagnosis. Calprotectin was measured by ELISA in the pouch endoluminal content collected during endoscopy in 40 consecutive patients with J-pouch. In each patient PDAI and mPDAI were calculated and 15% of patients were erroneously classified by mPDAI. ROC analysis of calprotectin values vs. acute histological subscore ≥ 3 identified different calprotectin cut-off values with corresponding sensitivity and specificity allowing the definition and scoring of different range of calprotectin subscores. We incorporated the calprotectin score in the mPDAI obtaining a new score that shows the same specificity as PDAI for diagnosis of pouchitis and higher sensitivity when compared with mPDAI. The use of the proposed new score, once validated in a larger series of patients, might be useful in the early management of patients with symptoms of pouchitis.

Improving the use of G-CSF during chemotherapy using physiological mathematical modelling : a quantitative systems pharmacology approach

La diminution des doses administrées ou même la cessation complète d'un traitement chimiothérapeutique est souvent la conséquence de la réduction du nombre de neutrophiles, qui sont les globules blancs les plus fréquents dans le sang. Cette réduction dans le nombre absolu des neutrophiles, aussi connue sous le nom de myélosuppression, est précipitée par les effets létaux non spécifiques des médicaments anti-cancéreux, qui, parallèlement à leur effet thérapeutique, produisent aussi des effets toxiques sur les cellules saines. Dans le but d'atténuer cet impact myélosuppresseur, on administre aux patients un facteur de stimulation des colonies de granulocytes recombinant humain (rhG-CSF), une forme exogène du G-CSF, l'hormone responsable de la stimulation de la production des neutrophiles et de leurs libération dans la circulation sanguine. Bien que les bienfaits d'un traitement prophylactique avec le G-CSF pendant la chimiothérapie soient bien établis, les protocoles d'administration demeurent mal définis et sont fréquemment déterminés ad libitum par les cliniciens. Avec l'optique d'améliorer le dosage thérapeutique et rationaliser l'utilisation du rhG-CSF pendant le traitement chimiothérapeutique, nous avons développé un modèle physiologique du processus de granulopoïèse, qui incorpore les connaissances actuelles de pointe relatives à la production des neutrophiles des cellules souches hématopoïétiques dans la moelle osseuse. À ce modèle physiologique, nous avons intégré des modèles pharmacocinétiques/pharmacodynamiques (PK/PD) de deux médicaments: le PM00104 (Zalypsis®), un médicament anti-cancéreux, et le rhG-CSF (filgrastim). En se servant des principes fondamentaux sous-jacents à la physiologie, nous avons estimé les paramètres de manière exhaustive sans devoir recourir à l'ajustement des données, ce qui nous a permis de prédire des données cliniques provenant de 172 patients soumis au protocol CHOP14 (6 cycles de chimiothérapie avec une période de 14 jours où l'administration du rhG-CSF se fait du jour 4 au jour 13 post-chimiothérapie). En utilisant ce modèle physio-PK/PD, nous avons démontré que le nombre d'administrations du rhG-CSF pourrait être réduit de dix (pratique actuelle) à quatre ou même trois administrations, à condition de retarder le début du traitement prophylactique par le rhG-CSF. Dans un souci d'applicabilité clinique de notre approche de modélisation, nous avons investigué l'impact de la variabilité PK présente dans une population de patients, sur les prédictions du modèle, en intégrant des modèles PK de population (Pop-PK) des deux médicaments. En considérant des cohortes de 500 patients in silico pour chacun des cinq scénarios de variabilité plausibles et en utilisant trois marqueurs cliniques, soient le temps au nadir des neutrophiles, la valeur du nadir, ainsi que l'aire sous la courbe concentration-effet, nous avons établi qu'il n'y avait aucune différence significative dans les prédictions du modèle entre le patient-type et la population. Ceci démontre la robustesse de l'approche que nous avons développée et qui s'apparente à une approche de pharmacologie quantitative des systèmes (QSP). Motivés par l'utilisation du rhG-CSF dans le traitement d'autres maladies, comme des pathologies périodiques telles que la neutropénie cyclique, nous avons ensuite soumis l'étude du modèle au contexte des maladies dynamiques. En mettant en évidence la non validité du paradigme de la rétroaction des cytokines pour l'administration exogène des mimétiques du G-CSF, nous avons développé un modèle physiologique PK/PD novateur comprenant les concentrations libres et liées du G-CSF. Ce nouveau modèle PK a aussi nécessité des changements dans le modèle PD puisqu’il nous a permis de retracer les concentrations du G-CSF lié aux neutrophiles. Nous avons démontré que l'hypothèse sous-jacente de l'équilibre entre la concentration libre et liée, selon la loi d'action de masse, n'est plus valide pour le G-CSF aux concentrations endogènes et mènerait en fait à la surestimation de la clairance rénale du médicament. En procédant ainsi, nous avons réussi à reproduire des données cliniques obtenues dans diverses conditions (l'administration exogène du G-CSF, l'administration du PM00104, CHOP14). Nous avons aussi fourni une explication logique des mécanismes responsables de la réponse physiologique aux deux médicaments. Finalement, afin de mettre en exergue l’approche intégrative en pharmacologie adoptée dans cette thèse, nous avons démontré sa valeur inestimable pour la mise en lumière et la reconstruction des systèmes vivants complexes, en faisant le parallèle avec d’autres disciplines scientifiques telles que la paléontologie et la forensique, où une approche semblable a largement fait ses preuves. Nous avons aussi discuté du potentiel de la pharmacologie quantitative des systèmes appliquées au développement du médicament et à la médecine translationnelle, en se servant du modèle physio-PK/PD que nous avons mis au point.

THE ASSOCIATION OF DEMOGRAPHIC VARIABLES AND DIETARY HABITS ON BODY MASS INDEX OF FOREIGN-BORN POPULATION IN SOUTH KOREA

The Republic of Korea (Korea) has been composed of a single ethnic group and, until very recently, has had little or no experience with large-volume of immigrants. The country, once known for its large-scale emigration, has emerged as a popular destination. As the foreign-born populations continue to grow, they experience dietary pattern changes. Dietary changes of immigrants are often associated with weight increase and consequently the risk of non-communicable diseases such as diabetes. This study examined the association of demographic variables and dietary habits on Body Mass Index (BMI) of foreign nationals living in Korea, based on a cross-sectional sample of 193 foreign-born men (120) and women (73). A web-based survey program, Zoho survey, was used to capture self-reported region of origin, socio-demographic variables, weight, height, frequency of physical activity, and food frequencies. For the entire sample (n=193), the World Health Organization (WHO) classification and the Korean Society for the Study of Obesity cut-off points of BMI were used. The average BMI was 24.6 (SD=3.6) kg/m2. Significant associations were observed between BMI and age (χ² (8, N=193) =26.22, p<.01), gender (χ² (2, N=193) =11.45, p<.01), and religious affiliation (χ² (4, N=191) =9.53, p<.05). On average, participants had meat and carbonated drinks 2.2 times a week; high calorie foods 1.5 times a week; and, dairy products 2.4 times a week. A significant correlation (r=.14, p<.05) between BMI and eating meat was also observed. This study showed that the BMI varied with age, gender and religion. Frequent consumption of meat was associated with a significant increase in BMI. This increase in BMI could be associated with the dietary changes experienced by the newcomers or absence of more familiar products. Consequently, as the volume of immigrants continues to increase in Korea, it is imperative to consider designing and implementing public health policies specifically in relation to a healthy diet that can impact the prevalence of preventable chronic diseases. Thus, health education among foreign-born population in Korea should focus on reducing the intake of meat and high energy foods.

Effect on the disability index of adult patients with benign paroxysmal positional vertigo using vestibular rehabilitation and human movement

Objective: determine the effect on the disability index of adult patients with benign paroxysmal positional vertigo (BPPV) using vestibular rehabilitation therapy (VRT) and human movement. Subjects: six subjects with an average age of 49.5 ± 14.22 years who have been diagnosed with benign paroxysmal positional vertigo by an otolaryngologist. Instruments: the Dizziness Handicap Inventory and a questionnaire to determine impact on the quality of life of patients with this pathology (Ceballos and Vargas, 2004). Procedure: subjects underwent vestibular therapy for four weeks together with habituation and balance exercises in a semi-supervised manner. Two measurements were performed, one before and one after the vestibular therapy and researchers determined if there was any improvement in the physical, functional, and emotional dimensions. Statistical analysis: descriptive statistics and Student’s t-test of repeated measures were applied to analyze results obtained. Results: significant statistical differences were found in the physical dimension between the pre-test (19.33 ± 4.67 points) and post-test (13 ± 7.24 points) (t = 2.65; p < 0.05).  In contrast, no significant statistical differences were found in the functional (t = 2.44; p>0.05), emotional (t = 2.37; p>0.05) or general dimensions (t = 2.55; p>0.05). Conclusion: vestibular therapy with a semi-supervised human movement program improved the index of disability due to vertigo (physical dimension) in BPPV subjects.

Origin discrimination and quality evaluation of Gastrodiae rhizoma (Orchidaceae) by high-performance liquid chromatographic fingerprint

Purpose: To develop a high-performance liquid chromatography (HPLC) fingerprint method for the quality control and origin discrimination of Gastrodiae rhizoma . Methods: Twelve batches of G. rhizoma collected from Sichuan, Guizhou and Shanxi provinces in china were used to establish the fingerprint. The chromatographic peak (gastrodin) was taken as the reference peak, and all sample separation was performed on a Agilent C18 (250 mm×4.6 mmx5 μm) column with a column temperature of 25 °C. The mobile phase was acetonitrile/0.8 % phosphate water solution (in a gradient elution mode) and the flow rate of 1 mL/min. The detection wavelength was 270 nm. The method was validated as per the guidelines of Chinese Pharmacopoeia. Results: The chromatograms of the samples showed 11 common peaks, of which no. 4 was identified as that of Gastrodin. Data for the samples were analyzed statistically using similarity analysis and hierarchical cluster analysis (HCA). The similarity index between reference chromatogram and samples’ chromatograms were all > 0.80. The similarity index of G. rhizoma from Guizhou, Shanxi and Sichuan is evident as follows: 0.854 - 0.885, 0.915 - 0.930 and 0.820 - 0.848, respectively. The samples could be divided into three clusters at a rescaled distance of 7.5: S1 - S4 as cluster 1; S5 - S8 cluster 2, and others grouped into cluster 3. Conclusion: The findings indicate that HPLC fingerprinting technology is appropriate for quality control and origin discrimination of G. rhizoma.

WEAK ISOMETRIES OF HAMMING SPACES

In this thesis we study weak isometries of Hamming spaces. These are permutations of a Hamming space that preserve some but not necessarily all distances. We wish to find conditions under which a weak isometry is in fact an isometry. This type of problem was first posed by Beckman and Quarles for Rn. In chapter 2 we give definitions pertinent to our research. The 3rd chapter focuses on some known results in this area with special emphasis on papers by V. Krasin as well as S. De Winter and M. Korb who solved this problem for the Boolean cube, that is, the binary Hamming space. We attempted to generalize some of their methods to the non-boolean case. The 4th chapter has our new results and is split into two major contributions. Our first contribution shows if n=p or p < n2, then every weak isometry of Hnq that preserves distance p is an isometry. Our second contribution gives a possible method to check if a weak isometry is an isometry using linear algebra and graph theory.

Prediction of G protein coupled receptors from plant genomes.

2016

Genome-wide analysis of G-type lectin genes in Fragaria vesca and functional characterization of FaMBL1 gene in defense response of F. × ananassa to fungal pathogens

Strawberry (Fragaria × ananassa) is an important soft fruit but easily to be infected by pathogens. Anthracnose and gray mold are two of the most destructive diseases of strawberry which lead to serious fruit rot. The first chapter introduced strawberry anthracnose caused by Colletotrichum acutatum. The infection strategy, disease cycle and management of C. acutatum on strawberry were reported. Likewise, the second chapter summarized the infection strategy of Botrytis cinerea and the defense responses of strawberry. As we already know white unripe strawberry fruits are more resistant to C. acutatum than red ripe fruits. During the interaction between strawberry white/red fruit and C. acutaum, a mannose binding lectin gene, FaMBL1, was found to be the most up-regulated gene and induced exclusively in white fruit. FaMBL1 belongs to the G-type lectin family which has important roles in plant development and defense process. To get insight into the role of FaMBL1, genome-wide identification was carried out on G-type lectin gene family in Fragaria vesca and the results were showed in chapter 3. G-type lectin genes make up a large family in F. vesca. Active expression upon biotic/abiotic stresses suggested a potential role of G-lectin genes in strawberry defenses. Hence, stable transgenic strawberry plants with FaMBL1 gene overexpressed were generated. Transformed strawberry plants were screened and identified. The results were showed in chapter 4, content of disease-related phytohormone, jasmonic acid, was found decreased in overexpressing lines compared with wild type (WT). Petioles inoculated by C. fioriniae of overexpressing lines had lower disease incidence than WT. Leaves of overexpressing lines challenged by B. cinerea showed remarkably smaller lesion diameters compared with WT. The chitinase 2-1 (FaChi2-1) showed higher expression in overexpressing lines than in WT during the interaction with B. cinerea, which could be related with the lower susceptibility of overexpressing lines.

The impact of cyclin D1 mRNA isoforms, morphology and p53 in mantle cell lymphoma: p53 alterations and blastoid morphology are strong predictors of a high proliferation index.

BACKGROUND: Mantle cell lymphoma is a clinically heterogeneous disease characterized by overexpression of cyclin D1 protein. Blastoid morphology, high proliferation, and secondary genetic aberrations are markers of aggressive behavior. Expression profiling of mantle cell lymphoma revealed that predominance of the 3'UTR-deficient, short cyclin D1 mRNA isoform was associated with high cyclin D1 levels, a high "proliferation signature" and poor prognosis. DESIGN AND METHODS: Sixty-two cases of mantle cell lymphoma were analyzed for cyclin D1 mRNA isoforms and total cyclin D1 levels by real-time reverse transcriptase polymerase chain reaction, and TP53 alterations were assessed by immunohistochemistry and molecular analysis. Results were correlated with proliferation index and clinical outcome. RESULTS: Predominance of the short cyclin D1 mRNA was found in 14 (23%) samples, including four with complete loss of the standard transcript. TP53 alterations were found in 15 (24%) cases. Predominance of 3'UTR-deficient mRNA was significantly associated with high cyclin D1 mRNA levels (P=0.009) and more commonly found in blastoid mantle cell lymphoma (5/11, P=0.060) and cases with a proliferation index of >20% (P=0.026). Both blastoid morphology (11/11, P<0.001) and TP53 alterations (15/15, P<0.001) were significantly correlated with a high proliferation index. A proliferation index of 10% was determined to be a significant threshold for survival in multivariate analysis (P=0.01). CONCLUSIONS: TP53 alterations are strongly associated with a high proliferation index and aggressive behavior in mantle cell lymphoma. Predominance of the 3'UTR-deficient transcript correlates with higher cyclin D1 levels and may be a secondary contributing factor to high proliferation, but failed to reach prognostic significance in this study.

Fecal calprotectin more accurately reflects endoscopic activity of ulcerative colitis than the Lichtiger Index, CRP, and blood leukocytes

Background: Thus far, the correlation of noninvasive markers with endoscopic activity in ulcerative colitis (UC) according to the modified Baron Index is unknown. We aimed to evaluate the correlation between endoscopic activity and fecal calprotectin (FC), C-reactive protein (CRP), blood leukocytes, and the Lichtiger Index (clinical score). Methods: UC patients undergoing complete colonoscopy were prospectively enrolled and scored clinically and endoscopically in an independent fashion. Fecal and blood samples were analyzed in UC patients and controls. Results: We enrolled 228 UC patients and 52 controls. Endoscopic disease activity correlated best with FC (Spearman's rank correlation coefficient r = 0.821), followed by the Lichtiger Index (r = 0.682), CRP (r = 0.556), and leukocytes (r = 0.401). FC was the only marker discriminating between different grades of endoscopic activity (grade 0, 20}11 mg/g; grade 1, 44}34 mg/g; grade 2, 111}74 mg/g; grade 3, 330}332 mg/g; grade 4, 659}319 mg/g; P = 0.0018 for discriminating grade 0 vs. 1 and P < 0.001 for discriminating all other grades). FC had the highest overall accuracy (91%) to detect endoscopically active disease (modified Baron Index _2), followed by the Lichtiger Index of _4 (77%), CRP larger than 5 mg/L (69%) and blood leukocytosis (58%). Conclusions: FC better correlated with the endoscopic disease activity than clinical activity, CRP, and blood leukocytes. The strong correlation with endoscopic disease activity suggests that FC represents a useful biomarker for noninvasive monitoring of disease activity in UC patients.

A note on the Fredholm properties of Toeplitz operators on weighted Bergman spaces with matrix-valued symbols

We characterize the essential spectra of Toeplitz operators Ta on weighted Bergman spaces with matrix-valued symbols; in particular we deal with two classes of symbols, the Douglas algebra C+H∞ and the Zhu class Q := L∞ ∩VMO∂ . In addition, for symbols in C+H∞ , we derive a formula for the index of Ta in terms of its symbol a in the scalar-valued case, while in the matrix-valued case we indicate that the standard reduction to the scalar-valued case fails to work analogously to the Hardy space case. Mathematics subject classification (2010): 47B35,

NIELSEN COINCIDENCE THEORY OF FIBRE-PRESERVING MAPS AND DOLD`S FIXED POINT INDEX

Let M -> B, N -> B be fibrations and f(1), f(2): M -> N be a pair of fibre-preserving maps. Using normal bordism techniques we define an invariant which is an obstruction to deforming the pair f(1), f(2) over B to a coincidence free pair of maps. In the special case where the two fibrations axe the same and one of the maps is the identity, a weak version of our omega-invariant turns out to equal Dold`s fixed point index of fibre-preserving maps. The concepts of Reidemeister classes and Nielsen coincidence classes over B are developed. As an illustration we compute e.g. the minimal number of coincidence components for all homotopy classes of maps between S(1)-bundles over S(1) as well as their Nielsen and Reidemeister numbers.

The first group (co)homology of a group G with coefficients in some G-modules

Let G be a group. We give some formulas for the first group homology and cohomology of a group G with coefficients in an arbitrary G-module (Z) over tilde. More explicit calculations are done in the special cases of free groups, abelian groups and nilpotent groups. We also perform calculations for certain G-module M, by reducing it to the case where the coefficient is a G-module (Z) over tilde. As a result of the well known equalities H-1(X, M) = H-1(pi(1)(X), M) and H-1(X, M) = H-1(pi(1) (X), M), for any G-module M, we are able to calculate the first homology and cohomology groups of topological spaces with certain local system of coefficients.

Reversibility properties of semigroup actions on homogeneous spaces

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)