Miracle-dz/UniFAR-FTUs huggingface dataset:
INFLUENCE OF DIETARY FIBERS AND WHOLE GRAINS ON FECAL MICROBIOTA DURING IN VITRO FERMENTATION

There has been a dramatic increase in obesity, which presents a risk of many chronic health problems. Recent studies have shown that obese individuals harbor an abnormal gut microbiota (dysbiosis), which has sparked interest in the gut microbiota as a target for weight management. Dietary fiber and whole grains that can be metabolized by gut microbiota have been shown to promote the growth of beneficial bacteria in the gut. Increased consumption of dietary fiber and whole grains may improve host / gut microbiota interactions in obesity and other metabolic diseases by normalizing gut dysbiosis. The present thesis describes two research projects to assess the impact of dietary fibers and whole grain on gut microbiota. In the first study, six dietary fibers [pectin, guar gum, inulin, arabinoxylan, β-glucan, and resistant starch type 2 (RS-2)] were subjected to in vitro digestion and fermentation using fecal samples from obese and normal weight individuals. Pyrosequencing was used to assess the impact of each dietary fiber on the gut microbiota community. Short/branched chain fatty acids (SCFA/BCFA) and carbohydrate utilization were correlated with proportions of bacterial taxa. The data showed that RS-2 caused the most dynamic change of the whole microbiota community and Bifidobacterium increased almost 10-fold on pectin substrate compared with the control. Certain taxa may be targeted to increase SCFA production or increase dietary fiber utilization. For instance, Ruminococcaceae and Faecalibacterium displayed positive correlations with butyrate production and while a strong positive relationship was shown between β-glucan utilization and Firmicutes. In the second study, since SCFA can influence hormones involved in energy absorption, utilization, and storage, the SCFA profile from five whole grains (wheat, rye, corn, rice, and oats) using an in vitro method was evaluated. There were large differences in fermentation profiles among individuals, even when supplied with the same dietary fiber. The obese type microbiota was less efficient at butyrate production and less metabolically active than the normal weight type microbiota initially, but given sufficient whole grain substrates the bacteria quickly became metabolically active.
Texture characteristics and microstructure of skim milk mozzarella cheeses made using exopolysaccharide or non-exopolysaccharide producing starter cultures.

Three batches of mozzarella cheese were prepared using skim milk (< 0.1% fat), each with exopolysaccharide (EPS)-or non-exopolysaccharide (non-EPS)-producing starter cultures consisting of S. thermophilus and L. delbrueckii ssp. bulgaricus. The cheeses were analysed for moisture, protein and fat contents and for texture characteristics such as hardness, cohesiveness, adhesiveness, springiness, chewiness and gumminess. An Instron Universal Testing Machine was used to measure the texture characteristics while the microstructure of the cheeses was examined using a scanning electron microscope. The EPS cheeses showed 1.7% higher moisture content (on total cheese weight) than non-EPS cheeses. Both types of cheeses had similar protein content (-43%). Most of the texture measurements decreased during storage for both types of cheese; however, adhesiveness at 50% compression increased during storage. Both types of cheese showed similar hardness and springiness values during storage; the EPS cheeses showed lower values of cohesiveness and adhesiveness during storage. The microstructure of the cheeses showed large and small voids representing the location of the serum and fat phases. The starter bacteria were located in serum channels. The exopolysaccharide was in the form of filaments, which extended from the protein matrix, probably as a result of dehydration of the EPS during SEM sample preparation. The EPS was primarily produced by S. thermophilus which was found in abundance, but not L. delbrueckii ssp. bulgaricus. The EPS cheeses were more open and porous compared to the non-EPS cheeses which could have decreased the cohesiveness and adhesiveness of the product.
Conformations of MutS in DNA mismatch repair

markdownabstract__Abstract__ Prior to cell division, the DNA containing the genetic information of a cell has to be copied. During this process, errors are sometimes incorporated (so-called mismatches), which may cause genetic abnormalities in future cells. To prevent this, cells contain a DNA mismatch repair (MMR) system, which efficiently removes such errors. This is important, since a non-functional MMR system leads to cancer in humans. The activation of MMR requires several sequential steps which are initiated by the evolutionary conserved MutS- and MutL protein homologs. To better understand MMR, the Escherichia coli variants of these proteins were studied in this research. MutS goes through a series of conformational states to execute its role in MMR. This study describes several of these states. A structure of unbound MutS revealed how MutS uses the ability to kink its helical arms to allow embracing of the DNA helix. MutS forms tetramers and dimers, and this study shows that the tetrameric assembly of MutS releases slowly from DNA. Mismatches, however, are recognized by MutS dimers. The binding of the MutS dimer to different mismatches could be determined using a MutS mutant that can not form tetramers. After a mismatch is detected, MutS uses the nucleotide ATP to undergo a large conformational change. The crystal structure of this so-called ‘sliding clamp’ state could be visualized for the first time in this study. The structure explains how MutS needs this state to bind to the MutL protein through two surfaces, and how this loads MutL onto DNA. MutL can then initiate the repair process.
Biologia comparada de Tetranychus urticae em cultivares de algodoeiro I.Ciclo biológico

A laboratory study was carried out on the biology of Tetranychus urticae ( Koch 1836 ) ( Acari: Tetranychidae ) in cotton cultivars IAC-17, IAC-18 and IAC-19, with the objective of assessing the behavior of this spider mite. The study was carried out in leaf disks, under the following environmental conditions: temperature ranging from 24°C to 26°C, air relative humidity ranging from 52% to 62% and 14 hours photoperiod. Under these conditions, the cotton cultivars did not exert any influence on the duration of the immature phases and of the preovipositional period of T. urticae. as well as on its egg-laying capacity. Cultivar IAC-19 was the least adequate for the mite, since it provided the smaller values for viability in the egg to adult stage, duration of the egg-laying period and femals longevity. For all cultivars, the average duration of the quiescent period in the deutonymph phase was greater than that of the active period.
Perfil e evolução clínica do idoso hospitalizado atendido nas unidades de internação de um hospital de ensino

O envelhecimento acarreta varias alteracoes no organismo do idoso, que deixam esta populacao em situacao de fragilidade, aumentando assim os agravos a saude e consequente aumento no numero de hospitalizacoes. Alem disto, a hospitalizacao pode levar ao agravamento das alteracoes funcionais pre-existentes, sendo assim um fator de risco para o declinio funcional do idoso. Portanto, conhecer as causas e os fatores associados as hospitalizacoes e de grande interesse. Objetivos: Caracterizar os aspectos demograficos e clinicos dos idosos internados nas unidades de internacao de um hospital de ensino; identificar a evolucao clinica destes pacientes durante a hospitalizacao (alta, obito). Metodos: Foi realizada uma pesquisa de analise de prontuario eletronico, tipo transversal, dos pacientes idosos atendidos nas unidades de internacao no periodo de janeiro/2014 a dezembro/2014. A analise estatistica foi realizada atraves do teste de qui-quadrado, teste Analise de Variância (ANOVA), analise descritiva das variaveis de caracterizacao amostral, aplicacao do teste associativo pela estatistica qui-quadrado. Resultados: Os resultados mostram que a maioria dos pacientes avaliados e do sexo masculino (8014-53,8%), com grau de instrucao fundamental (9183-68,0%), com companheiro (8750-62,4%), do lar (4652-33,1%), seguido de trabalhadores do setor de servicos (3595-25,6%), de etnia branca (13902-93,5%) e catolica (11291-80,2%). A maioria dos pacientes apresentou doencas cardiovasculares (3689-24,8%), seguido de neoplasias (1953-13,1%) e doencas gastrointestinais (1733-11,64%). Apesar de a maioria das doencas serem prevalentes no sexo masculino, algumas apresentam um percentual maior de ocorrencia, como as neoplasias, as doencas hematologicas, doencas nefrourologicas e os traumas. A maior incidencia de obito ocorreu devido a infeccoes (817-60,0%), neoplasias (212-10,9%), doencas respiratorias (95-9,1%) e traumas (47-8,6%). As doencas respiratorias, infeccoes e traumas foram mais frequentes em pacientes com idades avancadas (>74 anos). Pacientes com infeccoes, doencas respiratorias e de pele apresentaram maior tempo de permanencia, (tempo medio de permanencia superior a 7,0 dias). Conclusao: Com o aumento da taxa de sobrevida ha tambem um aumento no numero de doencas cronicas, levando cada vez mais a hospitalizacao do idoso. Acoes voltadas para prevencao destas doencas no âmbito da Atencao Basica e de grande importância para que ocorra uma mudanca neste panorama no pais. A capacitacao dos cuidadores pela equipe multiprofissional e a realizacao de um plano de alta precoce contribuem para a diminuicao das reinternacoes destes idosos. As infeccoes apresentaram maior causa de obitos e de tempo de permanencia dessa populacao no hospital. Faz-se importante a educacao da populacao e profissionais da saude quanto aos cuidados para se evitar a disseminacao de infeccoes.
(Section A: Molecular, Structural, and Cellular Biology of Drug Transporters) Mammalian Nucleoside Transporters

Nucleoside transporters mediate cellular uptake of physiologic nucleosides for nucleic acid synthesis in the salvage pathways in many cell types. These transporters also play an important role in in vivo disposition and intracellular targeting of many nucleoside analogs used in anticancer and antiviral drug therapy. In mammalian cells, there are two major nucleoside transporter gene families: the equilibrative nucleoside transporters (ENTs) and the concentrative nucleoside transporters (CNTs). The ENTs are facilitated carrier proteins and the CNTs are Na+-dependent secondary active transporters. Recent molecular cloning of a number of ENT and CNT transporters has greatly advanced our understanding of the molecular and cellular mechanisms by which nucleosides and nucleoside analogs are transported across biological membranes. In this manuscript, we review the structure, function, tissue distribution, and cellular localization of various cloned mammalian nucleoside transporters. Information on transporter interaction with various nucleoside drugs and analogs is presented. Current knowledge on the regulation of nucleoside transporters in various cell types and tissues is reviewed. The therapeutic significance of nucleoside transporters is discussed along with emerging data from recent clinical studies.
Maize response to biodegradable polymer and urease inhibitor coated urea.

One possible approach to improve the nitrogen losses from the surface applied urea is to coat it with biodegradable materials and urease inhibitors. The pot experiment was carried out to compare the effects of newly developed urea on plant yield and nutrient uptake. Their relative residual effects were also investigated on plant and soil by repeating the same experiment without urea application. The treatments were prepared by using fluidized bed coating machine as urea alone, palm stearin +Cu coated urea, agar + Cu coated urea, gelatin +cu coated urea, Cu coated Urea, micronutrient coated urea. The treatments were added at a dose of 100 kg ha-1 by surface application on the pots filled by Munchong soil series. The soil was analyzed for physical and chemical properties and plant samples were analyzed for yield, nutrient uptake and total N. The outcome of the first pot experiment indicated that the application of coated urea increased dry matter yield from 60 to 20% pot-1 and enhanced N uptake up to77% as compare to urea alone. The results of the second experiment indicated improvement in N uptake (80%) of the plant, when it treated by coated urea. The investigation proved that the natural biodegradable polymer and Cu coated urea can reduce N loss; enhance the nutrient uptake and improve the plant production.
The patho-aetiology of hip osteoarthritis

Osteoarthritis of the hip frequently occurs in the absence of osteoarthritis in other large joints, suggesting that local factors are important in its pathogenesis. Hip morphology has been recognised as a potential local biomechanical risk factor for the development of hip osteoarthritis. There are no adequate studies examining osteoarthritis development in the hip. Historical cohorts are either limited by a short follow up or by small numbers. This thesis explores the natural history of hip osteoarthritis in a large population cohort with particular attention to hip morphology as a predictor of osteoarthritis development. Software was developed which allows objective measurements of hip morphology in a reproducible manner. Hip morphology was then measured in a 1000 subject cohort. A detailed description of hip morphology is presented in this thesis, with interesting observations of wide variation and a bimodal distribution for alpha angle (a measure of cam-type femoroacetabular impingement). This is suggestive of a discrete pathological entity, which was associated with osteoarthritis in the cross-sectional analysis. No signiﬁcant changes exist in terms of morphology during the course of the study and no signiﬁcant relationship exists between age and hip morphology. Longitudinal analysis of hip morphology with radiographic osteoarthritis and total hip replacement revealed a signiﬁcant association between cam-type femoroacetabular impingement and acetabular dysplasia with both outcome measures. Measurements of hip morphology were independently predictive of outcome when controlling for baseline age, BMI and joint space width, and signiﬁcantly increased our ability to predict osteoarthritis and total hip replacement. Similar associations were seen when considering hip pain and symptomatic osteoarthritis as the outcome measures of interest. Pincer-type femoroacetabular impingement was not signiﬁcantly associated with any of the outcome measures of interest and pain remains relatively poorly explained by both hip morphology and/or radiographic change. The understanding of hip morphology and its role in the natural history of osteoarthritis is signiﬁcantly improved by this research. Further research is now required to determine whether these morphological abnormalities represent modiﬁable risk factors for osteoarthritis progression.
Chromosomal evolution and phylogeny of golden moles and tenrecs (Mammalia : Afrosoricida)

Afrosoricida is a 65 million years old (my) eutherian order that together with the Tubulidentata (aardvark) and Macroscelidea (elephant shrews) form the Afroinsectiphillia, a subclade of Afrotheria. It includes two families – Chrysochloridae (nine genera of golden moles) and Tenrecidae (11 genera of tenrecs) – that collectively represent ~59% of the afrotherian generic diversity. This study presents the first comprehensive cytogenetic comparison between members of these two families (seven genera and 11 species/subspecies of golden moles, and two genera and 11 species of tenrecs) using Gand C-banding and chromosome painting. All detected rearrangements are interpreted in a strict cladistic framework. In the case of Chrysochloridae, this provides evidence for a sister relationship between Chrysochloris and Cryptochloris, the monophyly of the Amblysomus genus, and for the elevation of A. hottentotus meesteri to specific rank. The detection of telomeric-like repeats in the centromeres of all chromosomes of the Amblysomus species/subspecies but not in those of A. h. meesteri further strengthens its recognition as a distinct species. Parsimony analysis of chromosomal rearrangements within Tenrecidae, the second Afrotheria assemblage studied, showed that rearrangements which could be interpreted as Whole Arm Reciprocal Translocations (WARTs) were more likely to be the result of Robertsonian translocations. Four interspecific associations are recovered within Microgale that are consistent with morphological and molecular characters. It was also possible to infer ancestral karyotypes for the Chrysochloridae, Oryzorictinae and the two tenrecid genera, Oryzorictes and Microgale. Given the relatively high karyotypic diversity observed among some Microgale species and the prevailing debates on chromosomal evolution and regional palaeoenvironmental fluctuations, it is suggested that Microgale be added to the list of taxa where structural rearrangements are likely to have played a role in speciation. Using Genbank sequences and a relaxed Bayesian clock method, we estimate the age of the family Chrysochloridae at ~28.5 my and that of the genus Microgale at ~9.9 my. Based on these dates, it can be shown that most of the evolutionary branches are characterized by a slow rate of chromosomal change, but that markedly high rates are observed in some Microgale species and to a lesser extent in the lineage leading to A. robustus. The rates of chromosomal evolution and other cytogenetic features highlighted in this study are discussed in light of recent advances in understanding the molecular mechanims that underpin changes to genomic architecture.
Measuring the change in functional level of children rehabilitants with cerebral palsy: a brief report

To compare Gross Motor Function Measure (GMFM), Gross Motor Function Classification System (GMFCS), Functional Independence Measure (FIM®), Manual Ability Classification System (MACS), and Ashworth scale in their ability to discriminate larger and smaller benefits of rehabilitation. 248 children with cerebral palsy participated in an intensive rehabilitation intervention. Scores were assessed at admission and discharge. GMFCS and MACS scores did not change. Ashworth scale and FIM improved evenly in almost every rehabilitant. There were positive changes in GMFM scores of 233 rehabilitants with median pre/post difference 3.8 (range 0.4 to 29.2) points. While Ashworth scale, FIM, GMFCS, and MACS might be valuable tools to assess the level of functioning, they seemed to be too rough to describe mild changes observable during a short rehabilitation intervention. Comparing to them, GMFM scale seemed to be more sensitive in defining such changes.
Real-time in vivo imaging of human lymphatic system using an LED-based photoacoustic/ultrasound imaging system

Non-invasive in vivo imaging of lymphatic system is of paramount importance for analyzing the functions of lymphatic vessels, and for investigating their contribution to metastasis. Recently, we introduced a multi-wavelength real-time LED-based photoacoustic/ultrasound system (AcousticX). In this work, for the first time, we demonstrate that AcousticX is capable of real-time imaging of human lymphatic system. Results demonstrate the capability of this system to image vascular and lymphatic vessels simultaneously. This could potentially provide detailed information regarding the interconnected roles of lymphatic and vascular systems in various diseases, therefore fostering the growth of therapeutic interventions.
Caractérisation et conservation d'un nouveau système CUT associé à l'utilisation du xylane chez Xanthomonas campestris pv. campestris : implications en écologie microbienne

La degradation microbienne de la paroi vegetale n'est pas seulement un processus biologique important, elle presente egalement un interet scientifique grandissant pour de nombreuses applications biotechnologiques. Au cours de ces travaux, nous avons identifie le systeme de degradation et d'utilisation du xylane, un composant structural majeur des parois vegetales, chez les especes de Xanthomonas phytopathogenes. Ce systeme est requis pour la pathogenicite et nous avons montre qu'il est necessaire pour la croissance optimale des bacteries a la surface des feuilles des plantes hotes et non hotes. L'une de ses particularites est la presence de 2 transporteurs specifiques de la membrane externe (TBDT, TonB-dependent transporter) qui seraient impliques dans le transport actif de produits d'hydrolyse du xylane. Enfin, des analyses de genomique comparative ont permis de definir un ensemble de genes essentiel pour l'utilisation du xylane, conserve chez un grand nombre de bacteries phylogenetiquement tres distinctes et nichant dans le sol, les plantes, les systemes aquatiques ou les systemes digestifs des animaux. Nos travaux montrent que cet ensemble de genes est systematiquement associe avec des TBDTs, soulignant l'importance de ces proteines dans l'utilisation du xylane, le second polysaccharide vegetal le plus abondant dans la nature.
Integrating bioenergetics and conservation biology: thermal sensitivity of digestive performance in Eastern Collared Lizards (Crotaphytus collaris) may affect population persistence

Abstract Information on bioenergetics can provide valuable insight into the ecology, life history and population dynamics of organisms. For ectothermic animals, thermal sensitivity of digestion is an important determinant of net assimilated energy budgets. A recent study in the Ozark Mountains indicated that eastern collared lizards (Crotaphytus collaris) restricted to encroached glades (characterized by woody vegetation encroachment) experience reduced environmental heat loads and have reduced age-specific growth and reproductive rates compared to populations in intact glades. To assess the potential impact of reduced body temperatures on assimilation rates of C. collaris in encroached glades, we conducted feeding trials across four temperature treatments (28, 31, 34 and 37°C). We tested for temperature effects on voluntary feeding rates, passage times, apparent assimilated energy (AE) and metabolizable energy (ME). Passage times decreased and voluntary feeding rates increased significantly with increasing temperature. Consumption explained the majority of variance in AE and ME, followed by the effect of temperature treatments. Using data on voluntary feeding rates, passage times and ME as a function of temperature, we estimated over a 10-fold increase in predicted daily assimilated energy across temperature treatments (28°C = 0.58 kJ/day, 31°C = 1.20 kJ/day, 34°C = 4.30 kJ/day, 37°C = 7.95 kJ/day). Thus, lower heat loads in encroached glades may cause reduced body temperature and result in restricted energy assimilation rates. Our study provides a novel approach to the integration of bioenergetics and conservation and shows the efficacy of using information on digestive performance to investigate underlying mechanisms in a conservation context.
Update on neuroimaging in psychiatric disorders

Psychoradiology is a newly emerging filed describes the application of the neuroimaging techniques in analysing psychiatric conditions. Previously in psychiatry only gross structural abnormalities, that might cause psychosis, could be detected. Neuroimaging was used to detect and to differentiate depression from neurodegenerative disorders or brain tumours. Recently, functional neuroimaging, mostly in the form of functional magnetic resonance imaging, molecular neuroimaging with positron-emission tomography or single photon emission tomography, facilitates the identification of therapeutic targets, the determination of the dose of a new drug needed to occupy its target in the brain, following up the effect of the treatment and the selection of patients for clinical trials.