Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of the immune system in the mammalian intestine as an alternate explanation for the action of antimicrobial growth promoters / Estela Costa

Terminal restriction fragment length polymorphism is a molecular technique used for comparative analysis of microbial community composition and dynamics. Three sampling methods for recovering bacterial community DNA associated with intestinal mucosa of mice were evaluated: mechanical agitation with PBS, hand washing with PBS containing Tween 80, and direct DNA extraction from mucosal plugs. In addition, the utility of two methods (i.e. Klenow fragment and mung bean nuclease) to reduce singlestranded DNA artifacts was tested. Based on T-RFLP analysis, there were diverse communities of bacteria associated with mucosa of the murine ileum, cecum, and descending colon. Although there was no significant difference in bacterial community composition between the mechanical agitation and direct DNA extraction methods regardless of intestinal location, community diversity was reduced for the wash method in the colon. The use of Klenow fragment and mung bean nuclease has been reported to eliminate single-stranded DNA artifacts (i.e. pseudo-T-restriction fragments); however, neither method was beneficial for characterizing mucosa-associated bacterial communities of the murine cecum. In conclusion, mechanical agitation and direct plug extraction yielded equivalent bacterial community DNA from the mucosa of the small 1 Chapter published as: Costa, E. , Puhl, N. J., Selinger, L. B. and Inglis, G. D. (2009). Characterization of mucosa-associated bacterial communities of the mouse intestine by terminal restriction fragment length polymorphism: Utility of sampling strategies and methods to reduce single-stranded DNA artifacts. Journal of Microbiological Methods, 78(2): 175-180.
OPTIMAL HEPATITIS B VIRUS PRIMER SEQUENCE DESIGN FOR ISOTHERMAL AMPLIFICATION

We have reported the successful use of the Loop Mediated Isothermal Amplification (LAMP) reaction for Hepatitis B Virus (HBV) DNA in a 25 μl micro-reactor for the development of a rapid diagnostic device recently. This method shows the successful amplification of HBV DNA with high specificity and sensitivity efficiently within one hour. Such a powerful method can be used for many other fast diagnostic applications with the help of optimal primer design and miniaturization of reactor. In this report, we will first summarize the general design rules for primer design from literature reviews and our experimental results. We will discuss the effects of HBV primers and concentrations of working buffers for optimal performance.
Inhaled insulin for diabetes mellitus.

A 52-year-old man with an 8-year history of type 2 diabetes mellitus visits his primary care provider for advice. His glucometer readings at home have been high despite treatment with a sulfonylurea, a thiazolidinedione, and metformin at maximal doses. He has never smoked. His glycated hemoglobin value is 8.6% and his fasting blood glucose concentration ranges between 170 and 220 mg per deciliter (9.4 and 12.2 mmol per liter). His blood pressure, weight, and lipid profile are within recommended target ranges. The patient and his physician discuss therapeutic options and agree that insulin treatment should be initiated. The physician wonders whether the patient might benefit from inhaled insulin and refers him to an endocrinologist for evaluation. T h e C l i nic a l Probl e m Diabetes mellitus, a major cause of illness and death across the globe, is responsible for a growing proportion of national health care expenditures. Insulin treatment is necessary for a substantial minority of patients with diabetes; more than 5 million Americans take insulin injections every day. 1-4 A wide range of subcutaneous insulins are available, many administered with penlike delivery devices and ultrafine needles that enhance the comfort and convenience of insulin treatment. 5 However, surveys indicate substantial resistance to insulin therapy on the part of both patients with type 2 diabetes who are not taking insulin and clinicians who care for such patients; the reasons for this resistance include anticipated pain, inconvenience, fear of hypoglycemia, and concern about weight gain. 6-8 True insulin and needle phobias are uncommon, although many patients appear to avoid insulin injections and blood glucose testing because of anxiety. 6,9-11 The youngest and oldest patients are least likely to accept injectable therapy and thus pose the greatest challenge for physicians who want to initiate insulin treatment. 12 Although resistance can be mitigated through education, efforts to develop oral, nasal, and inhaled formulations of insulin have been driven by the preference of patients to avoid subcutaneous injections. 13
Chemosensory context conditioning in Caenorhabditis elegans

ii TABLE OF CONTENTS iv LIST OF TABLES vi LIST OF FIGURES vii ABBREVIATIONS ix ACKNOWLEDGEMENTS x CHAPTER 1 1 1.1 General introduction 1 1.2 Context conditioning in Aplysia californica 3 1.3 Context conditioning in Hermissenda crassicornis 6 1.4 Context conditioning in the honeybee Apis Mellifera 10 1.5 Context conditioning in Lymnaea stagnalis 12 1.6 Context conditioning In Drosophila melanogaster 15 1.7 Context conditioning in Chasmagnathus granulatus 16 1.8 Context conditioning in Caenorhabditis elegans 20 1.9 Summary 23 CHAPTER 2 25 2.1 Short-term context conditioning introduction 25 2.2 General materials and methods for short-term context conditioning 26 2.3 Results 33 2.3. 1 Adult C. elegans show short-term context conditioning to taste and smell in a multiple worm assay 33 2.3. 2 Context conditioning for mechanosensory habituation is specific for taste and smell contexts 35 2.3. 3 GLR-1 and NMR-1 are important for context conditioning in C. elegans . 39 2.3. 4 AMPA receptors are important for short-term smell context conditioning in C. elegans 40 2.3. 5 NMDA receptors are not critical for short-term habituation but are important for short-term smell context conditioning in C. elegans 42 2.3. 6 Rescuing NMR-1 in transgenic nmr-1 mutant worms 44
Herpes Simplex Virus Type 1 Interactions with the Interferon System

The interferon (IFN) system is one of the first lines of defense activated against invading viral pathogens. Upon secretion, IFNs activate a signaling cascade resulting in the production of several interferon stimulated genes (ISGs), which work to limit viral replication and establish an overall anti-viral state. Herpes simplex virus type 1 is a ubiquitous human pathogen that has evolved to downregulate the IFN response and establish lifelong latent infection in sensory neurons of the host. This review will focus on the mechanisms by which the host innate immune system detects invading HSV-1 virions, the subsequent IFN response generated to limit viral infection, and the evasion strategies developed by HSV-1 to evade the immune system and establish latency in the host.
Bio-inspired Surface Texture Modification as a Viable Feature of Future Aquatic Antifouling Strategies: A Review

The imitation of natural systems to produce effective antifouling materials is often referred to as “biomimetics”. The world of biomimetics is a multidisciplinary one, needing careful understanding of “biological structures”, processes and principles of various organisms found in nature and based on this, designing nanodevices and nanomaterials that are of commercial interest to industry. Looking to the marine environment for bioinspired surfaces offers researchers a wealth of topographies to explore. Particular attention has been given to the evaluation of textures based on marine organisms tested in either the laboratory or the field. The findings of the review relate to the numbers of studies on textured surfaces demonstrating antifouling potential which are significant. However, many of these are only tested in the laboratory, where it is acknowledged a very different response to fouling is observed.
Comparing and analyzing the tripe gene block sequence of Barley stripe mosaic virus China strain.

The tripe gene block(TGB)genes of Barley stripe mosaic virus China strain(BSMV-CH)were amplified from cDNA of BSMV-CH RNAβ(GenBank accession No:AY789694)by PCR with special primer pairs,and cloned into pMD18-T vector for sequencing.Analysis of the sequences showed that the full length of BSMV-CH TGB1,TGB2 and TGB3 were 1 539,396 and 468 bp,with deduced 512,131 and 155 amino acids,respectively.BSMV-CH TGB1 shared 94.1%-95.4% nucleotide identities and 91.0%-94.5% amino acid identities with that of other BSMV strains,BSMV-CH TGB2 shared 96.5%-97.2% nucleotide identities and 98.5%-99.2% amino acid identities with that of other BSMV strains,and BSMV-CH TGB3 shared 95.7%-96.6% nucleotide identities and 94.2%-96.8% amino acid identities with that of other BSMV strains.Phylogenetic tree based on the amino acid of Hordeiviruses TGB genes showed that BSMV-CH was relatively closed to CV17 in genetic relationship.Therefore,BSMV-CH was deduced to be a recombined strain of CV17 and CV42.
TNF-Alfa is an Independent Serum Marker for Proliferative Retinopathy in Type 1 Diabetic Patients

Purpose: This study aimed to determine if there are any associations between serum levels of inflammatory markers and proliferative retinopathy (PDR) in type 1 diabetic patients. Design: A cross-sectional design was utilized for this study. Methods: One hundred twentyeight type 1 diabetic patients underwent stereo fundus photography according to the Early Treatment Diabetic Retinopathy Study and were divided into two retinopathy groups: no or nonproliferative retinopathy (NDR/NPDR; n=62) and PDR (n=66). Serum levels of tumor necrosis factor-a (TNF-a), interleukin (IL)-1h, IL-6, soluble vascular cellular adhesion molecule-1 (sVCAM-1), soluble intercellular adhesion molecule-1 (sICAM-1), P-selectin, and high-sensitivity C-reactive protein (hsCRP) were analyzed. Statistical analysis was performed using nonparametric Mann–Whitney U test and multivariate logistic regression analysis. Results: Patients with PDR had higher levels of TNF-a [7.0 pg/ml (b4–17) vs. 6.0 pg/ml (b4–25); P=. 009], sVCAM-1 [860 ng/ml (360–2120) vs. 700 ng/ml (310–1820); Pb.001], and P-selectin [180 ng/ml (39–400) vs. 150 ng/ml (42–440); P=. 017; figures are expressed as median (range)]. There were no differences in serum levels of sICAM-1 or hsCRP. IL-1h was not detectable in any patient, and IL-6 was detectable in only 22.7% of the patients. In multivariate logistic regression analysis, TNF-a was the single, persistent, independent determinant inflammatory marker for PDR. Conclusion: The association between TNF-a and PDR in type 1 diabetic patients suggests that inflammation might play a role in the pathogenesis of proliferative diabetic retinopathy.
Hosts of Amblyomma dissimile Koch, 1844 and Amblyomma rotundatum Koch, 1844 (Acari: Ixodidae)

Host records of Amblyomma dissimile Koch, 1844 and Amblyomma rotundatum Koch, 1844 from the literature were critically reviewed. A total of 417 records on 101 species of tetrapods, and 193 records in 74 species of tetrapods were determined for A. dissimile and A. rotundatum, respectively. Aves have been found only once infested with A. dissimile. This tick has been detected on four species of Bufonidae, while A. rotundatum has been recorded on 13 species from six families of Anura. Crocodilia has been recorded infested by A. rotundatum (captive host, one species) and A. dissimile (two species). Sixteen species of Mammalia from ten families and eight species from eight families have been found infested with A. dissimile and A. rotundatum, including humans, respectively. A total of 63 species of Squamata (10 families) were found infested with A. dissimile, while the corresponding numbers for A. rotundatum are 45 species in nine families. A total of 15 species of Testudines (four families) and nine species (three families) have been found infested with A. dissimile and A. rotundatum, respectively. When infestation on captive and laboratory hosts were excluded from the analysis the number of species naturally infested with A. dissimile diminished to 88 and 58 for A. rotundatum. However, natural hosts infested with larvae, nymphs and adults of A. dissimile are Bufo marinus (Linnaeus), Bufo peltocephalus Tschudi, Proechimys semispinosus (Tomes), Boa constrictor Linnaeus, Epicrates striatus (Fischer), Oxybelis aeneus (Wagler), Cyclura cychlura (Cuvier), Iguana iguana (Linnaeus), Tupinambis teguixin (Linnaeus) and Trachemys scripta (Thunberg), but the commonest hosts harbouring all parasitic stages are B. marinus, B. constrictor and I. iguana. Hosts for all parasitic stages of A. rotundatum are B. marinus, Bufo schneideri Werner and B. constrictor, although records on B. marinus are considerably higher than the records on the other two hosts. The contribution of sheep and Hydrochoerus hydrochaeris (Linnaeus) as hosts of A. dissimile, and Dasypus novemcinctus Linnaeus as host of A. rotundatum, were overestimated in previous studies. The ample host-range of these tick species may partly explain their wide distribution from southern U.S.A. to northern Argentina, but there are also chances that more than one species are represented under the names A. dissimile and A. rotundatum.
ATP-Sensitive K+ Channels in Pancreatic β-Cells: Spare-Channel Hypothesis

Since their discovery in pancreatic β-cells, ATP-sensitive K+ channels in the cell membrane have been thought to mediate glucose-induced β-cell depolarization, which is required for triggering the voltage-dependent Ca2+ uptake subserving insulin release. The theory is that metabolism of glucose (and other fuel molecules) increases intracellular ATP or possibly other metabolites that diffuse to the membrane and inhibit the opening of ATP-sensitive K+ channels. This slows the efflux of positively charged K+ and depolarizes the cell. A recurrent source of confusion regarding this idea stems from the early observation that these channels are so exquisitely sensitive to intracellular ATP that channel opening is predicted to be ∼99% inhibited under physiological conditions. To account for this apparent discrepancy, various mechanisms have been proposed that might render the channels less sensitive to intracellular ATP. We use a simple mathematical model to demonstrate that there is no major discrepancy and that, in fact, given the electrophysiological mechanisms existing in the β-cell, the extreme sensitivity of the channels to ATP is appropriate and even mandatory for their physiological function.
Ecotone shifts in southern Madagascar: first barcoding data and six new species of the endemic millipede genus Riotintobolus (Spirobolida, Pachybolidae)

Abstract Six new species of the Spirobolida millipede genus Riotintobolus Wesener, 2009, are described from the spiny forest in southern Madagascar utilising genetic barcoding, drawings and scanning electron microscopy: Riotintobolus tsimelahysp. nov., R. mangatsiakasp. nov., R. lavanonosp. nov., R. bovinussp. nov., R. antafokysp. nov. and R. makayisp. nov. One other Riotintobolus population from the spiny forest might represent an additional species based on genetic data, but it cannot be described as no male specimens were collected. At present, the genus Riotintobolus Wesener, 2009 has eight species from the spiny forest and two species from the littoral rainforest. A determination key to all ten species of the genus is provided. Molecular data reveal that the two critically endangered species from the humid littoral rainforest are not closely related to one another, but have their closest relative in the dry spiny forest ecosystem. Riotintobolus mandenensis Wesener, 2009, only known from the southern littoral rainforest of Mandena is related to R. tsimelahysp. nov. from the nearby spiny forest at Tsimelahy with a p-distance of 11%, while R. minutus Wesener, 2009 from the littoral forest of Sainte Luce is more distant to all other Riotintobolus species, but more closely related to R. bovinussp. nov. from the southwestern forest of the Makay.
On the Utility of Syllable-Based Acoustic Models for Pronunciation Variation Modelling

Recent research on the TIMIT corpus suggests that longer-length acoustic models are more appropriate for pronunciation variation modelling than the context-dependent phones that conventional automatic speech recognisers use. However, the impressive speech recognition results obtained with longer-length models on TIMIT remain to be reproduced on other corpora. To understand the conditions in which longer-length acoustic models result in considerable improvements in recognition performance, we carry out recognition experiments on both TIMIT and the Spoken Dutch Corpus and analyse the differences between the two sets of results. We establish that the details of the procedure used for initialising the longer-length models have a substantial effect on the speech recognition results. When initialised appropriately, longer-length acoustic models that borrow their topology from a sequence of triphones cannot capture the pronunciation variation phenomena that hinder recognition performance the most.
A conceptual framework for action on the social determinants of health.

When he announced his intention to create the Commission on Social Determinants of Health (CSDH), WHO Director-General Lee Jong-wook identified the Commission as part of a comprehensive effort to promote greater equity in global health, in a spirit of social justice1. The Commission’s goal, then, is to advance health equity, driving action to reduce health differences among social groups, within and between countries. Getting to grips with this mission requires finding answers to three fundamental problems: 1. Where do health differences among social groups originate, if we trace them back to their deepest roots? 2. What pathways lead from root causes to the stark differences in health status observed at the population level? 3. In light of the answers to the first two questions, where and how should we intervene to reduce health inequities? This paper seeks to make explicit a shared understanding of these issues that can orient the work of the CSDH.
Effect of Adding Exercise to a Diet Containing Glucomannan

The purpose of this study was to examine the effect of adding exercise to a diet containing glucomannan (GM) on body composition and blood parameters. 20 sedentary overweight (BMI>25) women (18–52 y, 33.4±12.1 y, 160.6±4.6 cm, 79.9±9.3 kg) completed an 8‐week diet 3000 mg GM (Natural Alternatives, San Diego, CA) daily combined with either no exercise (No‐Ex), or an exercise training program (Ex). The diet emphasized healthy food choices and portion size control. Ex group completed 3 weekly sessions of non‐linear periodized total‐body resistance exercise followed by 30 min of run‐walk. A blood draw, 1 repetition maximum squat and bench press, and shuttle‐run test were performed pre and post intervention. After 8‐weeks body mass (No‐Ex: −2.2±1.5 kg; Ex:−3.3±1.5 kg), fat mass, % fat mass, total cholesterol (TC) (No‐Ex: −9.3±20.0 mg·dL−1; Ex: −10.1±19.5 mg·dL−1), and low‐density lipoprotein cholesterol were reduced (p<0.05). Addition of exercise improved (p<0.05) high‐density lipoprotein cholesterol (HDL‐C) (No‐Ex: −2.3±4.5 mg·dL−1; Ex: 1.6±3.6 mg·dL−1), TC/HDL‐C, and physical performance and augmented reductions in fat mass (by 50%), and waist circumference. No changes were found for leptin, glucose, insulin, or homocysteine. Addition of resistance and endurance training to a GM diet regime significantly improves body composition, HDL‐C, and TC/HDL‐C.
Bitterness in enzymatically-produced hydrolysates of commercial shrimp (Pandalopsis dispar) processing waste

The shrimp processing industry produces a huge amount of waste which can potentially be converted into value-added products by enzymatic hydrolysis. Nevertheless, bitterness in hydro lysates is a common problem that needs to be addressed. In this study, 16 protein hydrolysate samples were produced from commercial shrimp (Pandalopsis dispar) processing wastes using Taguchi's L 1 6 (4) experimental design. Four factors, namely—water-to-substrate ratio, percent enzyme, time of hydrolysis and type of protease, were investigated. The properties of the shrimp waste hydrolysates were assessed by three responses: product yield, degree of hydrolysis and bitterness. It was found that the type of protease had the most significant impact on hydrolysate properties. Hydrolysates produced from the proteases had significantly higher soluble product yields compared to the controls incubated without added protease. Moreover, the yield from treatments with Alcalase or Protamex reached over 30 %, which was six times higher than the control samples. In terms of degree of hydrolysis (DH), Alcalase, Flavourzyme and Protamex gave higher DH than bromelain, which had a DH similar to the controls. Despite the high soluble yields and DH for Alcalase and Protamex hydrolysates, their bitterness was intense and the 10 % (w/v) solutions of these samples were evaluated to be greater than 2000 ppm caffeine. Bromelain and Flavourzyme samples had significantly lower bitterness close to 1500 ppm caffeine but these samples were still significantly more bitter than the controls, which contained nearly no bitterness. A sample (blended in 2:1 water-to-substrate ratio and hydrOlyzed with 4 % Alcalase for 4 hours) that gave a soluble yield of 37.64 %, a DH of 2.30 meq/g and bitterness of 2300 ppm was selected for further fractionation by size and hydrophobicity to study the characteristics of the bitter substances. Results showed that bitter substances were small having molecular weight under 3 kDa and contained a large amount of hydrophobic amino acid residues such as Tyr, Phe, Leu, He and Lys. Therefore, it was concluded that Flavourzyme had the best potential to be used to produce protein hydrolysates from shrimp processing discards and small hydrophobic peptides were the major contributors to the bitterness.
Principales caractéristiques epidémiologiques et impact économique de la fièvre aphteuse en afrique: Synthèse bibliographique

La fièvre aphteuse (fA) est la maladie transfrontalière la plus contagieuse des mammifères domestiques et sauvages (Organisation mondiale de la santé animale, 2009). Elle est causée par un virus non enveloppé à acide ribonucléique (ARN) de la famille des Picornaviridae appartenant au genre Aphthovirus. Ce virus présente une grande variabilité génétique. Il existe ainsi sept sérotypes immunologiquement distincts qui circulent dans le monde (O, A, C, SAT 1, SAT 2, SAT 3 et Asia 1) dont six en Afrique (tous les précédents à l’exception du sérotype Asia 1) et plus d’une soixantaine de sous-types au sein de ces sérotypes. La distribution de ces sérotypes est continuellement soumise à des modifications. En raison de sa distribution mondiale et des pertes économiques qu’elle occasionne au niveau du bétail dans les pays touchés, la FA est considérée par l’Organisation mondiale de la Santé animale (OIE) depuis l’éradication réussie de la peste bovine en 2011 (anonyme, 2011), comme l’une des plus importantes maladies animales. La maladie est rapportée dans les 2/3 des pays membres de l’OIE (Vosloo et al., 2002). Certains pays qui avaient un statut indemne de FA se sont retrouvés infectés à travers le commerce international d’animaux et de produits d’origine animale (gourreau et al., 2004). Au cours des dernières années et particulièrement en 2005-2006, on a assisté à une recrudescence de la maladie avec de nombreux foyers affectant des millions d’animaux et occasionnant d’importantes pertes économiques en Asie, en Amérique latine et en Afrique. Ceci a suscité une attention accrue des organisations internationales sur la maladie et son contrôle.