The dynamics of a family’s gut microbiota reveal variations on a theme

Abstract Background It is clear that the structure and function of the human microbiota has significant impact on maintenance of health and yet the factors that give rise to an adult microbiota are poorly understood. A combination of genetics, diet, environment, and life history are all thought to impact the development of the gut microbiome. Here we study a chronosequence of the gut microbiota found in eight individuals from a family consisting of two parents and six children ranging in age from two months to ten years old. Results Using 16S rRNA gene and metagenomic shotgun sequence data, it was possible to distinguish the family from a cohort of normal individuals living in the same geographic region and to differentiate each family member. Interestingly, there was a significant core membership to the family members’ microbiota where the abundance of this core accounted for the differences between individuals. It was clear that the introduction of solids represents a significant transition in the development of a mature microbiota. This transition was associated with increased diversity, decreased stability, and the colonization of significant abundances of Bacteroidetes and Clostridiales. Although the children and mother shared essentially the identical diet and environment, the children’s microbiotas were not significantly more similar to their mother than they were to their father. Conclusions This analysis underscores the complex interactions that give rise to a personalized microbiota and suggests the value of studying families as a surrogate for longitudinal studies.http://deepblue.lib.umich.edu/bitstream/2027.42/109502/1/40168_2014_Article_54.pd

Integrated stratigraphy for the Late Quaternary in the eastern Tyrrhenian Sea

A high-resolution integrated stratigraphy is presented for the Late Quaternary in the southern-eastern Tyrrhenian Sea. It is based on calcareous plankton taxa (planktonic foraminifera and nannoplankton) distribution, d18OGlobigerinoides ruber record, tephrostratigraphy and radiometric dating methods (210Pb and 137Cs, AMS 14C) for a composite sediment core (from the top to the bottom, C90-1m, C90 and C836) from the continental shelf of the Salerno Gulf. High sedimentation rates from ca 1 cm/100 y for the early Holocene, to 3.45 cm/100 y for the middle Holocene to 8.78 cm/100 y from late Holocene and to 20 cm/100 y for the last 600 AD, make this area an ideal marine archive of secular paleoclimate changes. Quantitative distributional trend in planktonic foraminifera identify seven known (1Fe7F) eco-biozones, and several auxiliary bioevents of high potential for Mediterranean biostratigraphic correlation. Recognised were: the acme distribution of Neogloboquadrina pachyderma r.c. between 10.800 0.400 ka BP and 5.500 0.347 ka BP, a strong increase in abundance of Globorotalia truncatulinoides r.c. and l.c. at 5.500 0.347 ka BP and at 4.571 0.96 ka BP, respectively, an acme interval of Globigerinoides quadrilobatus (between 3.702 0.048 ka BP and 2.70 0.048 ka BP) and the acme/paracme intervals of T. quinqueloba (acme between 3.350 0.054 ka BP and 1.492 0.016 ka BP; paracme between 1.492 0.016 ka BP and 0.657 0.025 ka BP; acme beginning 0.657 0.025 ka BP). These results, integrated with trends of selected calcareous nannofossil species (Florisphaera profunda, Brarudosphaera bigelowii, Gephyrocapsa oceanica and Emiliania huxleyi) and d18OG. ruber signature, are consistent with the most important pre-Holocene and early Holocene paleoclimatic and paleoceanographic phases i.e., the BöllingeAllerod, the Younger Dryas and the time interval of Sapropel S1 deposition in the eastern Mediterranean Sea. These features revealed the high potential of this shallow water environment for high-resolution stratigraphy and correlation for the western Mediterranean. In addition, the chemical characterization of seven tephra layers supplied further data about the age and the dispersal area of some well-known Campi Flegrei explosive events, inferring the possible occurrence of explosive activity at Vesuvius around the middle of the 6th century, and contributing to refine the tephrostratigraphic framework for the last 15 ka in the south-eastern Tyrrhenian Sea.Published71-852.2. Laboratorio di paleomagnetismoJCR Journalrestricte

Nonhuman gamblers: lessons from rodents, primates, and robots

The search for neuronal and psychological underpinnings of pathological gambling in humans would benefit from investigating related phenomena also outside of our species. In this paper, we present a survey of studies in three widely different populations of agents, namely rodents, non-human primates, and robots. Each of these populations offers valuable and complementary insights on the topic, as the literature demonstrates. In addition, we highlight the deep and complex connections between relevant results across these different areas of research (i.e., cognitive and computational neuroscience, neuroethology, cognitive primatology, neuropsychiatry, evolutionary robotics), to make the case for a greater degree of methodological integration in future studies on pathological gambling

Experimental study for evaluation of a suitable ground displacement monitoring system: Pilot hole Campi Flegrei Deep Drilling Project case

The paper presents an experimental study carried out in 2012 during the drilling activity for a pilot hole performed in the framework of the Campi Flegrei Deep Drilling Project. A monitoring network has been installed to test and choose a suitable ground deformation system for the subsequent deep drilling of about 3.5 km in the Campi Flegrei Caldera (Italy). We describe the seismic network installed to characterize the structure of the pilot hole area and the ground deformation monitoring system chosen for the small drilling area. Data analysis and results obtained indicate that Total Station is a suitable tool for this case.Published4V. Dinamica dei processi pre-eruttiviN/A or not JC

Murine norovirus infection does not cause major disruptions in the murine intestinal microbiota

Abstract Background Murine norovirus (MNV) is the most common gastrointestinal pathogen of research mice and can alter research outcomes in biomedical mouse models of inflammatory bowel disease (IBD). Despite indications that an altered microbiota is a risk factor for IBD, the response of the murine intestinal microbiota to MNV infection has not been examined. Microbiota disruption caused by MNV infection could introduce the confounding effects observed in research experiments. Therefore, this study investigated the effects of MNV infection on the intestinal microbiota of wild-type mice. Results The composition of the intestinal microbiota was assessed over time in both outbred Swiss Webster and inbred C57BL/6 mice following MNV infection. Mice were infected with both persistent and non-persistent MNV strains and tissue-associated or fecal-associated microbiota was analyzed by 16S rRNA-encoding gene pyrosequencing. Analysis of intestinal bacterial communities in infected mice at the phylum and family level showed no major differences to uninfected controls, both in tissue-associated samples and feces, and also over time following infection, demonstrating that the intestinal microbiota of wild-type mice is highly resistant to disruption following MNV infection. Conclusions This is the first study to describe the intestinal microbiota following MNV infection and demonstrates that acute or persistent MNV infection is not associated with major disruptions of microbial communities in Swiss Webster and C57BL/6 mice.http://deepblue.lib.umich.edu/bitstream/2027.42/112329/1/40168_2012_Article_7.pd

Climate fluctuations and human impact during the late Holocene in a multi-proxy marine record from the Gulf of Gaeta (Tyrrhenian Sea, central Italy)

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Murine norovirus infection does not cause major disruptions in the murine intestinal microbiota

BACKGROUND: Murine norovirus (MNV) is the most common gastrointestinal pathogen of research mice and can alter research outcomes in biomedical mouse models of inflammatory bowel disease (IBD). Despite indications that an altered microbiota is a risk factor for IBD, the response of the murine intestinal microbiota to MNV infection has not been examined. Microbiota disruption caused by MNV infection could introduce the confounding effects observed in research experiments. Therefore, this study investigated the effects of MNV infection on the intestinal microbiota of wild-type mice. RESULTS: The composition of the intestinal microbiota was assessed over time in both outbred Swiss Webster and inbred C57BL/6 mice following MNV infection. Mice were infected with both persistent and non-persistent MNV strains and tissue-associated or fecal-associated microbiota was analyzed by 16S rRNA-encoding gene pyrosequencing. Analysis of intestinal bacterial communities in infected mice at the phylum and family level showed no major differences to uninfected controls, both in tissue-associated samples and feces, and also over time following infection, demonstrating that the intestinal microbiota of wild-type mice is highly resistant to disruption following MNV infection. CONCLUSIONS: This is the first study to describe the intestinal microbiota following MNV infection and demonstrates that acute or persistent MNV infection is not associated with major disruptions of microbial communities in Swiss Webster and C57BL/6 mice

Within study comparisons and risk of bias in international development: Systematic review and critical appraisal

Background Many systematic reviews incorporate nonrandomised studies of effects, sometimes called quasi‐experiments or natural experiments. However, the extent to which nonrandomised studies produce unbiased effect estimates is unclear in expectation or in practice. The usual way that systematic reviews quantify bias is through “risk of bias assessment” and indirect comparison of findings across studies using meta‐analysis. A more direct, practical way to quantify the bias in nonrandomised studies is through “internal replication research”, which compares the findings from nonrandomised studies with estimates from a benchmark randomised controlled trial conducted in the same population. Despite the existence of many risks of bias tools, none are conceptualised to assess comprehensively nonrandomised approaches with selection on unobservables, such as regression discontinuity designs (RDDs). The few that are conceptualised with these studies in mind do not draw on the extensive literature on internal replications (within‐study comparisons) of randomised trials. Objectives Our research objectives were as follows: Objective 1: to undertake a systematic review of nonrandomised internal study replications of international development interventions. Objective 2: to develop a risk of bias tool for RDDs, an increasingly common method used in social and economic programme evaluation. Methods We used the following methods to achieve our objectives. Objective 1: we searched systematically for nonrandomised internal study replications of benchmark randomised experiments of social and economic interventions in low‐ and middle‐income countries (L&MICs). We assessed the risk of bias in benchmark randomised experiments and synthesised evidence on the relative bias effect sizes produced by benchmark and nonrandomised comparison arms. Objective 2: We used document review and expert consultation to develop further a risk of bias tool for quasi‐experimental studies of interventions (ROBINS‐I) for RDDs. Results Objective 1: we located 10 nonrandomised internal study replications of randomised trials in L&MICs, six of which are of RDDs and the remaining use a combination of statistical matching and regression techniques. We found that benchmark experiments used in internal replications in international development are in the main well‐conducted but have “some concerns” about threats to validity, usually arising due to the methods of outcomes data collection. Most internal replication studies report on a range of different specifications for both the benchmark estimate and the nonrandomised replication estimate. We extracted and standardised 604 bias coefficient effect sizes from these studies, and present average results narratively. Objective 2: RDDs are characterised by prospective assignment of participants based on a threshold variable. Our review of the literature indicated there are two main types of RDD. The most common type of RDD is designed retrospectively in which the researcher identifies post‐hoc the relationship between outcomes and a threshold variable which determines assignment to intervention at pretest. These designs usually draw on routine data collection such as administrative records or household surveys. The other, less common, type is a prospective design where the researcher is also involved in allocating participants to treatment groups from the outset. We developed a risk of bias tool for RDDs. Conclusions Internal study replications provide the grounds on which bias assessment tools can be evidenced. We conclude that existing risk of bias tools needs to be further developed for use by Campbell collaboration authors, and there is a wide range of risk of bias tools and internal study replications to draw on in better designing these tools. We have suggested the development of a promising approach for RDD. Further work is needed on common methodologies in programme evaluation, for example on statistical matching approaches. We also highlight that broader efforts to identify all existing internal replication studies should consider more specialised systematic search strategies within particular literatures; so as to overcome a lack of systematic indexing of this evidence