Long-Term Temporal Analysis of the Human Fecal Microbiota Revealed a Stable Core of Dominant Bacterial Species

Next-generation sequencing has greatly contributed to an improved ecological understanding of the human gut microbiota. Nevertheless, questions remain regarding the characteristics of this ecosystem and the ecological processes that shape it, and controversy has arisen regarding the stability of the bacterial populations and the existence of a temporal core. In this study, we have characterized the fecal microbial communities of three human individuals over a one-year period by 454 pyrosequencing of 16S rRNA tags in order to investigate the temporal characteristics of the bacterial communities. The findings revealed a temporal core of 33 to 40 species-level Operational Taxonomic Units (OTUs) within subjects. Although these OTUs accounted only for around 12% of the total OTUs detected, they added up to \u3e75% of the total sequences obtained for each individual. In order to determine the capacity of the sequencing and bioinformatic approaches applied during this study to accurately determine the proportion of a core microbiota, we analyzed the fecal microbiota of nine mice with a defined three-member community. This experiment revealed that the sequencing approach inflated the amount of rare OTUs, which introduced a significant degree of artificial variation across samples, and hence reduced the apparent fraction of shared OTUs. However, when assessing the data quantitatively by focusing on dominant lineages, the sequencing approaches deliver an accurate representation of the community. In conclusion, this study revealed that the human fecal microbiota is dominated by around 40 species that maintain persistent populations over the duration of one year. The findings allow conclusions about the ecological factors that shape the community and support the concept of a homeostatic ecosystem controlled largely by deterministic processes. Our analysis of a three-member community revealed that methodological artifacts of OTU-based approaches complicate core calculations, and these limitations have to be considered in the interpretation of microbiome studies

Three-body hadronic structure of low-lying 1/2+1/2^+ Σ\Sigma and Λ\Lambda resonances

We discuss the dynamical generation of some low-lying $1/2^+$ $\Sigma$'s and $\Lambda$'s in two-meson one-baryon systems. These systems have been constructed by adding a pion in $S$-wave to the $\bar{K} N$ pair and its coupled channels, where the $1/2^-$ $\Lambda$(1405)-resonance gets dynamically generated. We solve Faddeev equations in the coupled-channel approach to calculate the $T$-matrix for these systems as a function of the total energy and the invariant mass of one of the meson-baryon pairs. This squared $T$-matrix shows peaks at the energies very close to the masses of the strangeness -1, $1/2^+$ resonances listed in the particle data book.Comment: Contribution to the NSTAR07 conferenc

On semisimple algebra codes: generator theory

The class of affine variety codes is defined as the Fq linear subspaces of A a Fq-semisimple algebra, where Fq is the finite field with q=pr elements and characteristic p. It seems natural to impose to the code some extra structure such as been a subalgebra of A. In this case we will have codes that have a Mattson-Solomon transform treatment as the classical cyclic codes. Moreover, the results on the structure of semisimple finite dimensional algebras allow us to study those codes from the generator point of view

Halpha Kinematics of S4G Spiral Galaxies - III. Inner rotation curves

We present a detailed study of the shape of the innermost part of the rotation curves of a sample of 29 nearby spiral galaxies, based on high angular and spectral resolution kinematic Halpha Fabry-Perot observations. In particular, we quantify the steepness of the rotation curve by measuring its slope dRvc(0). We explore the relationship between the inner slope and several galaxy parameters, such as stellar mass, maximum rotational velocity, central surface brightness ({\mu}0), bar strength and bulge-to-total ratio. Even with our limited dynamical range, we find a trend for low-mass galaxies to exhibit shallower rotation curve inner slopes than high-mass galaxies, whereas steep inner slopes are found exclusively in high-mass galaxies. This trend may arise from the relationship between the total stellar mass and the mass of the bulge, which are correlated among them. We find a correlation between the inner slope of the rotation curve and the morphological T-type, complementary to the scaling relation between dRvc(0) and {\mu}0 previously reported in the literature. Although we find that the inner slope increases with the Fourier amplitude A2 and decreases with the bar torque Qb, this may arise from the presence of the bulge implicit in both A2 and Qb. As previously noted in the literature, the more compact the mass in the central parts of a galaxy (more concretely, the presence of a bulge), the steeper the inner slopes. We conclude that the baryonic matter dominates the dynamics in the central parts of our sample galaxies.Comment: 11 pages, 11 figures, accepted for publication in MNRA

Mapping of the human visual cortex using image-guided transcranial magnetic stimulation

We describe a protocol using transcranial magnetic stimulation (TMS) to systematically map the visual sensations induced by focal and non-invasive stimulation of the human occipital cortex. TMS is applied with a figure of eight coil to 28 positions arranged in a 232-cm grid over the occipital area. A digitizing tablet connected to a PC computer running customized software, and audio and video recording are used for detailed and accurate data collection and analysis of evoked phosphenes. A frameless image-guided neuronavigational device is used to describe the position of the actual sites of the stimulation coils relative to the cortical surface. Our results show that TMS is able to elicit phosphenes in almost all sighted subjects and in a proportion of blind subjects. Evoked phosphenes are topographically organized. Despite minor inter-individual variations, the mapping results are reproducible and show good congruence among different subjects. This procedure has potential to improve our understanding of physiologic organization and plastic changes in the human visual system and to establish the degree of remaining functional visual cortex in blind subjects. Such a non-invasive method is critical for selection of suitable subjects for a cortical visual prosthesis.This research has been carried out with financial support from the Commission of the European Communities, specific RTD programme ‘Quality of Life and Management of Living Resources’, QLK6-CT-2001-00279 and by the Ministerio de Ciencia y Tecnologıa(MAT2000-1049)Fondo de Investigaciones de la Seguridad Social (FISS 01-0674)National Institute of Mental Health (MH60734, MH57980)National Eye Institute (EYEY12091)Harvard-Thorndike General Clinical Research Center at Beth Israel Deaconess Medical Center (NCRR MO1 RR01032).Medicin

\u3ci\u3eIn Vivo\u3c/i\u3e Selection To Identify Bacterial Strains with Enhanced Ecological Performance in Synbiotic Applications

One strategy for enhancing the establishment of probiotic bacteria in the human intestinal tract is via the parallel administration of a prebiotic, which is referred to as a synbiotic. Here we present a novel method that allows a rational selection of putative probiotic strains to be used in synbiotic applications: in vivo selection (IVS). This method consists of isolating candidate probiotic strains from fecal samples following enrichment with the respective prebiotic. To test the potential of IVS, we isolated bifidobacteria from human subjects who consumed increasing doses of galactooligosaccharides (GOS) for 9 weeks. A retrospective analysis of the fecal microbiota of one subject revealed an 8-fold enrichment in Bifidobacterium adolescentis strain IVS-1 during GOS administration. The functionality of GOS to support the establishment of IVS-1 in the gastrointestinal tract was then evaluated in rats administered the bacterial strain alone, the prebiotic alone, or the synbiotic combination. Strain-specific quantitative real-time PCR showed that the addition of GOS increased B. adolescentis IVS-1 abundance in the distal intestine by nearly 2 logs compared to rats receiving only the probiotic. Illumina 16S rRNA sequencing not only confirmed the increased establishment of IVS-1 in the intestine but also revealed that the strain was able to outcompete the resident Bifidobacterium population when provided with GOS. In conclusion, this study demonstrated that IVS can be used to successfully formulate a synergistic synbiotic that can substantially enhance the establishment and competitiveness of a putative probiotic strain in the gastrointestinal tract

\u3ci\u3eIn Vivo\u3c/i\u3e Selection To Identify Bacterial Strains with Enhanced Ecological Performance in Synbiotic Applications

One strategy for enhancing the establishment of probiotic bacteria in the human intestinal tract is via the parallel administration of a prebiotic, which is referred to as a synbiotic. Here we present a novel method that allows a rational selection of putative probiotic strains to be used in synbiotic applications: in vivo selection (IVS). This method consists of isolating candidate probiotic strains from fecal samples following enrichment with the respective prebiotic. To test the potential of IVS, we isolated bifidobacteria from human subjects who consumed increasing doses of galactooligosaccharides (GOS) for 9 weeks. A retrospective analysis of the fecal microbiota of one subject revealed an 8-fold enrichment in Bifidobacterium adolescentis strain IVS-1 during GOS administration. The functionality of GOS to support the establishment of IVS-1 in the gastrointestinal tract was then evaluated in rats administered the bacterial strain alone, the prebiotic alone, or the synbiotic combination. Strain-specific quantitative real-time PCR showed that the addition of GOS increased B. adolescentis IVS-1 abundance in the distal intestine by nearly 2 logs compared to rats receiving only the probiotic. Illumina 16S rRNA sequencing not only confirmed the increased establishment of IVS-1 in the intestine but also revealed that the strain was able to outcompete the resident Bifidobacterium population when provided with GOS. In conclusion, this study demonstrated that IVS can be used to successfully formulate a synergistic synbiotic that can substantially enhance the establishment and competitiveness of a putative probiotic strain in the gastrointestinal tract

Set-optimization meets variational inequalities

We study necessary and sufficient conditions to attain solutions of set-optimization problems in therms of variational inequalities of Stampacchia and Minty type. The notion of a solution we deal with has been introduced Heyde and Loehne, for convex set-valued objective functions. To define the set-valued variational inequality, we introduce a set-valued directional derivative and we relate it to the Dini derivatives of a family of linearly scalarized problems. The optimality conditions are given by Stampacchia and Minty type Variational inequalities, defined both by the set valued directional derivative and by the Dini derivatives of the scalarizations. The main results allow to obtain known variational characterizations for vector valued optimization problems

Network meta‐analysis of post‐exposure prophylaxis randomized clinical trials

Objectives: We performed a network meta‐analysis of PEP randomized clinical trials to evaluate the best regimen. / Methods: After MEDLINE/Pubmed search, studies were included if: (1) were randomized, (2) comparing at least 2 PEP three‐drug regimens and, (3) reported completion rates or discontinuation at 28 days. Five studies with 1105 PEP initiations were included and compared ritonavir‐boosted lopinavir (LPV/r) vs. atazanavir (ATV) (one study), cobicistat‐boosted elvitegravir (EVG/c) (one study), raltegravir (RAL) (one study) or maraviroc (MVC) (two studies). We estimated the probability of each treatment of being the best based on the evaluation of five outcomes: PEP non‐completion at day 28, PEP discontinuation due to adverse events, PEP switching due to any cause, lost to follow‐up and adverse events. / Results: Participants were mostly men who have sex with men (n = 832, 75%) with non‐occupational exposure to HIV (89.86%). Four‐hundred fifty‐four (41%) participants failed to complete their PEP course for any reason. The Odds Ratio (OR) for PEP non‐completion at day 28 in each antiretroviral compared to LPV/r was: ATV 0.95 (95% CI 0.58–1.56; EVG/c: OR 0.65 95% CI 0.30–1.37; RAL: OR 0.68 95% CI 0.41–1.13; and MVC: OR 0.69 95% CI 0.47–1.01. In addition, the rankogram showed that EVG/c had the highest probability of being the best treatment for the lowest rates in PEP non‐completion at day 28, switching, lost to follow‐up or adverse events and MVC for PEP discontinuations due to adverse events. / Conclusions: Our study shows the advantages of integrase inhibitors when used as PEP, particularly EVG as a Single‐Tablet Regimen

Borehole water level response to barometric pressure as an indicator of aquifer vulnerability

The response of borehole water levels to barometric pressure changes in semiconfined aquifers can be used to determine barometric response functions from which aquifer and confining layer properties can be obtained. Following earlier work on barometric response functions and aquifer confinement, we explore the barometric response function as a tool to improve the assessment of groundwater vulnerability in semiconfined aquifers, illustrated through records from two contrasting boreholes in the semiconfined Chalk Aquifer, East Yorkshire, UK. After removal of recharge and Earth tide influences on the water level signal, barometric response functions were estimated and aquifer and confining layer properties determined through an analytical model of borehole water level response to barometric pressure. A link between the thickness and vertical diffusivity of the confining layer determined from the barometric response function, and groundwater vulnerability is proposed. The amplitude spectrum for barometric pressure and instrument resolution favor determination of the barometric response function at frequencies to which confining layer diffusivities are most sensitive. Numerical modeling indicates that while the high frequency response reflects confining layer properties in the immediate vicinity of the borehole, the low frequency response reflects vertical, high diffusivity pathways though the confining layer some hundreds of meters distant. A characteristic time scale parameter, based on vertical diffusivities and thicknesses of the saturated and unsaturated confining layer, is introduced as a measure of semiconfined aquifer vulnerability. The study demonstrates that the barometric response function has potential as a tool for quantitative aquifer vulnerability assessment in semiconfined aquifers