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.

Analysis of deep levels in a phenylenevinylene polymer by transient capacitance methods

Transient capacitance methods were applied to the depletion region of an abrupt asymmetric n(+) -p junction of silicon and unintentionally doped poly[2-methoxy, 5 ethyl (2' hexyloxy) paraphenylenevinylene] (MEH-PPV). Studies in the temperature range 100-300 K show the presence of a majority-carrier trap at 1.0 eV and two minority traps at 0.7 and 1.3 eV, respectively. There is an indication for more levels for which the activation energy could not be determined. Furthermore, admittance data reveal a bulk activation energy for conduction of 0.12 eV, suggesting the presence of an additional shallow acceptor state. (C) 1999 American Institute of Physics. [S0003-6951(99)02308-6].

Geochemical analysis at ODP Site 207-1259 from the Demerara Rise in the western equatorial Atlantic

Organic carbon-rich shales deposited during the Coniacian-Santonian Oceanic Anoxic Event 3 were drilled during ODP Leg 207 at Demerara Rise. We present integrated high-resolution geochemical records of core intervals from ODP Sites 1259 and 1261 both from nannofossil biozone CC14. Our results reveal systematic variations in marine and detrital sediment contribution, depositional processes, and bottom water redox conditions during black shale formation at two locations on Demerara Rise in different paleo-water depths. A combination of redox proxies (Fe/S, P/Al, C/P, redox-sensitive/sulfide-forming trace metals Mn, Cd, Mo, Ni, V, Zn) and other analytical approaches (bulk sediment composition, P speciation, electron microscopy, X-ray diffraction) evidence anoxic to sulfidic bottom water and sediment conditions throughout the deposition of black shale. These extreme redox conditions persisted and were periodically punctuated by short-termed periods with less reducing bottom waters irrespective of paleo-water depth. Sediment supply at both sites was generally dominated by marine material (carbonate, organic matter, opal) although relationships of detrital proxies as well as glauconitic horizons support some influence of turbidites, winnowing bottom currents and/or variable detritus sources, along with less reducing bottom water at the proposed shallower location (ODP Site 1259). At Site 1261, located at greater paleo-depth, redox fluctuations were more regular, and steady hemipelagic sedimentation sustained the development of mostly undisturbed lamination in the sedimentary record. Strong similarities of the studied deposits exist with the stratigraphic older Cenomanian-Turonian OAE2 black shale sections at Demerara Rise, suggesting that the primary mechanisms controlling continental supply and ocean redox state were time-invariant and kept the western equatorial Atlantic margin widely anoxic over millions of years.

Analysis of deep levels in a phenylenevinylene polymer by transient capacitance methods

Transient capacitance methods were applied to the depletion region of an abrupt asymmetric n(+) -p junction of silicon and unintentionally doped poly[2-methoxy, 5 ethyl (2' hexyloxy) paraphenylenevinylene] (MEH-PPV). Studies in the temperature range 100-300 K show the presence of a majority-carrier trap at 1.0 eV and two minority traps at 0.7 and 1.3 eV, respectively. There is an indication for more levels for which the activation energy could not be determined. Furthermore, admittance data reveal a bulk activation energy for conduction of 0.12 eV, suggesting the presence of an additional shallow acceptor state. (C) 1999 American Institute of Physics. [S0003-6951(99)02308-6].

Elemental Analysis and Forensic Comparison of Soils by Laser-Induced Breakdown Spectroscopy (LIBS) and Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS)

The elemental analysis of soil is useful in forensic and environmental sciences. Methods were developed and optimized for two laser-based multi-element analysis techniques: laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and laser-induced breakdown spectroscopy (LIBS). This work represents the first use of a 266 nm laser for forensic soil analysis by LIBS. Sample preparation methods were developed and optimized for a variety of sample types, including pellets for large bulk soil specimens (470 mg) and sediment-laden filters (47 mg), and tape-mounting for small transfer evidence specimens (10 mg). Analytical performance for sediment filter pellets and tape-mounted soils was similar to that achieved with bulk pellets. An inter-laboratory comparison exercise was designed to evaluate the performance of the LA-ICP-MS and LIBS methods, as well as for micro X-ray fluorescence (μXRF), across multiple laboratories. Limits of detection (LODs) were 0.01-23 ppm for LA-ICP-MS, 0.25-574 ppm for LIBS, 16-4400 ppm for µXRF, and well below the levels normally seen in soils. Good intra-laboratory precision (≤ 6 % relative standard deviation (RSD) for LA-ICP-MS; ≤ 8 % for µXRF; ≤ 17 % for LIBS) and inter-laboratory precision (≤ 19 % for LA-ICP-MS; ≤ 25 % for µXRF) were achieved for most elements, which is encouraging for a first inter-laboratory exercise. While LIBS generally has higher LODs and RSDs than LA-ICP-MS, both were capable of generating good quality multi-element data sufficient for discrimination purposes. Multivariate methods using principal components analysis (PCA) and linear discriminant analysis (LDA) were developed for discriminations of soils from different sources. Specimens from different sites that were indistinguishable by color alone were discriminated by elemental analysis. Correct classification rates of 94.5 % or better were achieved in a simulated forensic discrimination of three similar sites for both LIBS and LA-ICP-MS. Results for tape-mounted specimens were nearly identical to those achieved with pellets. Methods were tested on soils from USA, Canada and Tanzania. Within-site heterogeneity was site-specific. Elemental differences were greatest for specimens separated by large distances, even within the same lithology. Elemental profiles can be used to discriminate soils from different locations and narrow down locations even when mineralogy is similar.

Gwas analysis for the identification of molecular basis responsible for yield related traits and disease resistance in durum wheat

The PhD thesis was developed in the framework of Innovar H2020 project. This project aimed at using genomics, transcriptomics and phenotyping techniques to update varietal registration procedure used in Europe for Value of Cultivation and Use (VCU) and Distinctiness Uniformity and Stability (DUS) protocols. The phenotypic and genotypic diversity of a durum wheat panel were assessed for different agronomic traits, connected with wheat development, disease resistance and spike fertility. A panel of 253 durum wheat varieties was characterized for VCU and DUS traits and genotyped with Illumina 90K SNP Chip array (Wang et al., 2014). GWAS analysis was performed, detecting strong QTLs confirmed also by literature review. Candidate genes were identified for each trait and molecular markers will be developed to be used for marker assisted selection in breeding programs. As for disease resistance, the panel was evaluated for resistance to Soil-Borne-Cereal-Mosaic-Virus (SBCMV). A major QTL, sbm2, was detected on chromosome 2B responsible for durum wheat resistance (Maccaferri et al., 2011). The sbm2 interval was explored by fine mapping on segregant population using KASP markers and by RNASeq analysis, detecting candidate genes involved in plant-pathogen reaction. As regards yield related traits, detailed analysis was performed on the GNI-2A QTL (Milner et al., 2016), responsible for increased number spike fertility. Fine mapping analysis was performed on durum panel identifying hox2 a strong candidate gene, codifying for transcription factor protein. The gene is paralogue of GNI-1 (Sakuma et al., 2019), and it has a 4 kbp deletion responsible for increased number of florets per spikelet. To conclude, the herein reported thesis shows a complete characterization of agronomic and disease resistance traits in modern durum wheat varieties. The results obtained will augment available information for each variety, identifying informative molecular markers for breeding purposes and QTLs/candidate genes responsible for different agronomic traits.

Analysis Of The Dna Fourier Transform-infrared Microspectroscopic Signature Using An All-reflecting Objective.

The Fourier transform-infrared (FT-IR) signature of dry samples of DNA and DNA-polypeptide complexes, as studied by IR microspectroscopy using a diamond attenuated total reflection (ATR) objective, has revealed important discriminatory characteristics relative to the PO2(-) vibrational stretchings. However, DNA IR marks that provide information on the sample's richness in hydrogen bonds have not been resolved in the spectral profiles obtained with this objective. Here we investigated the performance of an all reflecting objective (ARO) for analysis of the FT-IR signal of hydrogen bonds in DNA samples differing in base richness types (salmon testis vs calf thymus). The results obtained using the ARO indicate prominent band peaks at the spectral region representative of the vibration of nitrogenous base hydrogen bonds and of NH and NH2 groups. The band areas at this spectral region differ in agreement with the DNA base richness type when using the ARO. A peak assigned to adenine was more evident in the AT-rich salmon DNA using either the ARO or the ATR objective. It is concluded that, for the discrimination of DNA IR hydrogen bond vibrations associated with varying base type proportions, the use of an ARO is recommended.

Effect Of Platform Connection And Abutment Material On Stress Distribution In Single Anterior Implant-supported Restorations: A Nonlinear 3-dimensional Finite Element Analysis.

Although various abutment connections and materials have recently been introduced, insufficient data exist regarding the effect of stress distribution on their mechanical performance. The purpose of this study was to investigate the effect of different abutment materials and platform connections on stress distribution in single anterior implant-supported restorations with the finite element method. Nine experimental groups were modeled from the combination of 3 platform connections (external hexagon, internal hexagon, and Morse tapered) and 3 abutment materials (titanium, zirconia, and hybrid) as follows: external hexagon-titanium, external hexagon-zirconia, external hexagon-hybrid, internal hexagon-titanium, internal hexagon-zirconia, internal hexagon-hybrid, Morse tapered-titanium, Morse tapered-zirconia, and Morse tapered-hybrid. Finite element models consisted of a 4×13-mm implant, anatomic abutment, and lithium disilicate central incisor crown cemented over the abutment. The 49 N occlusal loading was applied in 6 steps to simulate the incisal guidance. Equivalent von Mises stress (σvM) was used for both the qualitative and quantitative evaluation of the implant and abutment in all the groups and the maximum (σmax) and minimum (σmin) principal stresses for the numerical comparison of the zirconia parts. The highest abutment σvM occurred in the Morse-tapered groups and the lowest in the external hexagon-hybrid, internal hexagon-titanium, and internal hexagon-hybrid groups. The σmax and σmin values were lower in the hybrid groups than in the zirconia groups. The stress distribution concentrated in the abutment-implant interface in all the groups, regardless of the platform connection or abutment material. The platform connection influenced the stress on abutments more than the abutment material. The stress values for implants were similar among different platform connections, but greater stress concentrations were observed in internal connections.

Is Thyroid Stunning Clinically Relevant? A Retrospective Analysis Of 208 Patients.

Current guidelines have advised against the performance of (131)I-iodide diagnostic whole body scintigraphy (dxWBS) to minimize the occurrence of stunning, and to guarantee the efficiency of radioiodine therapy (RIT). The aim of the study was to evaluate the impact of stunning on the efficacy of RIT and disease outcome. This retrospective analysis included 208 patients with differentiated thyroid cancer managed according to a same protocol and followed up for 12-159 months (mean 30 ± 69 months). Patients received RIT in doses ranging from 3,700 to 11,100 MBq (100 mCi to 300 mCi). Post-RIT-whole body scintigraphy images were performed 10 days after RIT in all patients. In addition, images were also performed 24-48 hours after therapy in 22 patients. Outcome was classified as no evidence of disease (NED), stable disease (SD) and progressive disease (PD). Thyroid stunning occurred in 40 patients (19.2%), including 26 patients with NED and 14 patients with SD. A multivariate analysis showed no association between disease outcome and the occurrence of stunning (p = 0.3476). The efficacy of RIT and disease outcome do not seem to be related to thyroid stunning.

Combined Analysis Of νμ Disappearance And νμ→νe Appearance In Minos Using Accelerator And Atmospheric Neutrinos.

We report on a new analysis of neutrino oscillations in MINOS using the complete set of accelerator and atmospheric data. The analysis combines the ν(μ) disappearance and ν(e) appearance data using the three-flavor formalism. We measure |Δm(32)(2)| = [2.28-2.46] × 10(-3) eV(2) (68% C.L.) and sin(2)θ(23) = 0.35-0.65 (90% C.L.) in the normal hierarchy, and |Δm(32)(2)| = [2.32-2.53] × 10(-3) eV(2) (68% C.L.) and sin(2)θ(23) = 0.34-0.67 (90% C.L.) in the inverted hierarchy. The data also constrain δ(CP), the θ(23} octant degeneracy and the mass hierarchy; we disfavor 36% (11%) of this three-parameter space at 68% (90%) C.L.

Phylogenetic Analysis Of The Microbial Community In Hypersaline Petroleum Produced Water From The Campos Basin.

In this work the archaea and eubacteria community of a hypersaline produced water from the Campos Basin that had been transported and discharged to an onshore storage facility was evaluated by 16S recombinant RNA (rRNA) gene sequence analysis. The produced water had a hypersaline salt content of 10 (w/v), had a carbon oxygen demand (COD) of 4,300 mg/l and contains phenol and other aromatic compounds. The high salt and COD content and the presence of toxic phenolic compounds present a problem for conventional discharge to open seawater. In previous studies, we demonstrated that the COD and phenolic content could be largely removed under aerobic conditions, without dilution, by either addition of phenol degrading Haloarchaea or the addition of nutrients alone. In this study our goal was to characterize the microbial community to gain further insight into the persistence of reservoir community members in the produced water and the potential for bioremediation of COD and toxic contaminants. Members of the archaea community were consistent with previously identified communities from mesothermic reservoirs. All identified archaea were located within the phylum Euryarchaeota, with 98 % being identified as methanogens while 2 % could not be affiliated with any known genus. Of the identified archaea, 37 % were identified as members of the strictly carbon-dioxide-reducing genus Methanoplanus and 59 % as members of the acetoclastic genus Methanosaeta. No Haloarchaea were detected, consistent with the need to add these organisms for COD and aromatic removal. Marinobacter and Halomonas dominated the eubacterial community. The presence of these genera is consistent with the ability to stimulate COD and aromatic removal with nutrient addition. In addition, anaerobic members of the phyla Thermotogae, Firmicutes, and unclassified eubacteria were identified and may represent reservoir organisms associated with the conversion hydrocarbons to methane.

Longitudinal Analysis Of Hippocampal T2 Relaxometry In Fmtle.

To investigate the degree of T2 relaxometry changes over time in groups of patients with familial mesial temporal lobe epilepsy (FMTLE) and asymptomatic relatives. We conducted both cross-sectional and longitudinal analyses of T2 relaxometry with Aftervoxel, an in-house software for medical image visualization. The cross-sectional study included 35 subjects (26 with FMTLE and 9 asymptomatic relatives) and 40 controls; the longitudinal study was composed of 30 subjects (21 with FMTLE and 9 asymptomatic relatives; the mean time interval of MRIs was 4.4 ± 1.5 years) and 16 controls. To increase the size of our groups of patients and relatives, we combined data acquired in 2 scanners (2T and 3T) and obtained z-scores using their respective controls. General linear model on SPSS21® was used for statistical analysis. In the cross-sectional analysis, elevated T2 relaxometry was identified for subjects with seizures and intermediate values for asymptomatic relatives compared to controls. Subjects with MRI signs of hippocampal sclerosis presented elevated T2 relaxometry in the ipsilateral hippocampus, while patients and asymptomatic relatives with normal MRI presented elevated T2 values in the right hippocampus. The longitudinal analysis revealed a significant increase in T2 relaxometry for the ipsilateral hippocampus exclusively in patients with seizures. The longitudinal increase of T2 signal in patients with seizures suggests the existence of an interaction between ongoing seizures and the underlying pathology, causing progressive damage to the hippocampus. The identification of elevated T2 relaxometry in asymptomatic relatives and in patients with normal MRI suggests that genetic factors may be involved in the development of some mild hippocampal abnormalities in FMTLE.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

Quantitative Proteomic Analysis Reveals Metabolic Alterations, Calcium Dysregulation, And Increased Expression Of Extracellular Matrix Proteins In Laminin α2 Chain-deficient Muscle.

Congenital muscular dystrophy with laminin α2 chain deficiency (MDC1A) is one of the most severe forms of muscular disease and is characterized by severe muscle weakness and delayed motor milestones. The genetic basis of MDC1A is well known, yet the secondary mechanisms ultimately leading to muscle degeneration and subsequent connective tissue infiltration are not fully understood. In order to obtain new insights into the molecular mechanisms underlying MDC1A, we performed a comparative proteomic analysis of affected muscles (diaphragm and gastrocnemius) from laminin α2 chain-deficient dy(3K)/dy(3K) mice, using multidimensional protein identification technology combined with tandem mass tags. Out of the approximately 700 identified proteins, 113 and 101 proteins, respectively, were differentially expressed in the diseased gastrocnemius and diaphragm muscles compared with normal muscles. A large portion of these proteins are involved in different metabolic processes, bind calcium, or are expressed in the extracellular matrix. Our findings suggest that metabolic alterations and calcium dysregulation could be novel mechanisms that underlie MDC1A and might be targets that should be explored for therapy. Also, detailed knowledge of the composition of fibrotic tissue, rich in extracellular matrix proteins, in laminin α2 chain-deficient muscle might help in the design of future anti-fibrotic treatments. All MS data have been deposited in the ProteomeXchange with identifier PXD000978 (http://proteomecentral.proteomexchange.org/dataset/PXD000978).

De Novo Assembly And Transcriptome Analysis Of The Rubber Tree (hevea Brasiliensis) And Snp Markers Development For Rubber Biosynthesis Pathways.

Hevea brasiliensis (Willd. Ex Adr. Juss.) Muell.-Arg. is the primary source of natural rubber that is native to the Amazon rainforest. The singular properties of natural rubber make it superior to and competitive with synthetic rubber for use in several applications. Here, we performed RNA sequencing (RNA-seq) of H. brasiliensis bark on the Illumina GAIIx platform, which generated 179,326,804 raw reads on the Illumina GAIIx platform. A total of 50,384 contigs that were over 400 bp in size were obtained and subjected to further analyses. A similarity search against the non-redundant (nr) protein database returned 32,018 (63%) positive BLASTx hits. The transcriptome analysis was annotated using the clusters of orthologous groups (COG), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam databases. A search for putative molecular marker was performed to identify simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). In total, 17,927 SSRs and 404,114 SNPs were detected. Finally, we selected sequences that were identified as belonging to the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, which are involved in rubber biosynthesis, to validate the SNP markers. A total of 78 SNPs were validated in 36 genotypes of H. brasiliensis. This new dataset represents a powerful information source for rubber tree bark genes and will be an important tool for the development of microsatellites and SNP markers for use in future genetic analyses such as genetic linkage mapping, quantitative trait loci identification, investigations of linkage disequilibrium and marker-assisted selection.