The Bacterial DNA Profiling of Chorionic Villi and Amniotic Fluids Reveals Overlaps with Maternal Oral, Vaginal, and Gut Microbiomes

The in utero microbiome hypothesis has been long debated. This hypothesis will change our comprehension of the pioneer human microbiome if proved correct. In 60 uncomplicated pregnancies, we profiled the microbiome of chorionic villi (CV) and amniotic fluids (AF) in relation to maternal saliva, rectum, and vagina and the soluble cytokines cascade in the vagina, CV and AF. In our series, 12/37 (32%) AF and 10/23 (44%) CV tested positive for bacterial DNA. CV and AF harbored bacterial DNA of Streptococcus and Lactobacillus, overlapping that of the matched oral and vaginal niches, which showed a dysbiotic microbiome. In these pregnant women, the immune profiling revealed an immune hyporesponsiveness in the vagina and a high intraamniotic concentration of inflammatory cytokines. To understand the eventual role of bacterial colonization of the CV and AF and the associated immune response in the pregnancy outcome, further appropriate studies are needed. In this context, further studies should highlight if the hematogenous route could justify the spread of bacterial DNA from the oral microbiome to the placenta and if vaginal dysbiosis could favor the likelihood of identifying CV and AF positive for bacterial DNA

Comments on selected fundamental aspects of microarray analysis

International audienceMicroarrays are becoming a ubiquitous tool of research in life sciences. However, the working principles of microarray-based methodologies are often misunderstood or apparently ignored by the researchers who actually perform and interpret experiments. This in turn seems to lead to a common over-expectation regarding the explanatory and/or knowledge-generating power of microarray analyses.In this note we intend to explain basic principles of five (5) major groups of analytical techniques used in studies of microarray data and their interpretation: the principal component analysis (PCA), the independent component analysis (ICA), the t-test, the analysis of variance (ANOVA), and self organizing maps (SOM). We discuss answers to selected practical questions related to the analysis of microarray data. We also take a closer look at the experimental setup and the rules, which have to be observed in order to exploit microarrays efficiently. Finally, we discuss in detail the scope and limitations of microarray-based methods. We emphasize the fact that no amount of statistical analysis can compensate for (or replace) a well thought through experimental setup. We conclude that microarrays are indeed useful tools in life sciences but by no means should they be expected to generate complete answers to complex biological questions. We argue that even well posed questions, formulated within a microarray-specific terminology, cannot be completely answered with the use of microarray analyses alone

The Bacterial DNA Profiling of Chorionic Villi and Amniotic Fluids Reveals Overlaps with Maternal Oral, Vaginal, and Gut Microbiomes

The in utero microbiome hypothesis has been long debated. This hypothesis will change our comprehension of the pioneer human microbiome if proved correct. In 60 uncomplicated pregnancies, we profiled the microbiome of chorionic villi (CV) and amniotic fluids (AF) in relation to maternal saliva, rectum, and vagina and the soluble cytokines cascade in the vagina, CV and AF. In our series, 12/37 (32%) AF and 10/23 (44%) CV tested positive for bacterial DNA. CV and AF harbored bacterial DNA of Streptococcus and Lactobacillus, overlapping that of the matched oral and vaginal niches, which showed a dysbiotic microbiome. In these pregnant women, the immune profiling revealed an immune hyporesponsiveness in the vagina and a high intraamniotic concentration of inflammatory cytokines. To understand the eventual role of bacterial colonization of the CV and AF and the associated immune response in the pregnancy outcome, further appropriate studies are needed. In this context, further studies should highlight if the hematogenous route could justify the spread of bacterial DNA from the oral microbiome to the placenta and if vaginal dysbiosis could favor the likelihood of identifying CV and AF positive for bacterial DNA

Vitamin D Receptor Polymorphisms in Sex-Frailty Paradox

The “male-female health-survival paradox” evidences that the survival advantage observed in women is linked to higher rates of disability and poor health status compared to men, a phenomenon also called the “sex-frailty paradox”. The depletion of vitamin D seems to play a role in the fragilization of old persons, and genetic polymorphisms of the vitamin D receptor (VDR) gene seem to be involved in regulating the vitamin D pathway. This study correlated the VDR gene polymorphisms (FokI, ApaI, BsmiI, and TaqI) with frailty, computed by frailty index (FI), in 202 persons (127 women and 75 men, aged from 60 to 116 years), aiming to capture the involvement of vitamin D in the sex-frailty paradox. The results showed slightly higher FI (p = 0.05), lower levels of 25(OH)D (p = 0.04), and higher levels of parathyroid hormone PTH (p = 0.002) and phosphorus (p < 0.001) in women than in men. Interestingly, the ApaI minor allele (Aa + aa) showed a significant positive association with FI (p = 0.03) and a negative association with inorganic phosphorus values (p = 0.04) compared to AA genotype only in women, regardless of age. The exact mechanism and the causal role that, in old women, links ApaI polymorphism with frailty are still unclear. However, we could speculate that a specific genetic profiling, other than 25(OH)D levels, play a role in the sex-frailty paradox

rasterdiv-An Information Theory tailored R package for measuring ecosystem heterogeneity from space : To the origin and back

Ecosystem heterogeneity has been widely recognized as a key ecological indicator of several ecological functions, diversity patterns and change, metapopulation dynamics, population connectivity or gene flow. In this paper, we present a new R package-rasterdiv-to calculate heterogeneity indices based on remotely sensed data. We also provide an ecological application at the landscape scale and demonstrate its power in revealing potentially hidden heterogeneity patterns. The rasterdiv package allows calculating multiple indices, robustly rooted in Information Theory, and based on reproducible open-source algorithms.Peer reviewe

Energy content and carbon emission audit of building materials

The main thesis examined in this research is that "the embedded energy of construction is much more significant than the operational energy for buildings in a tropical country such as Sri Lanka". All building elements (e.g. brickwall), materials (e.g. bricks) and "primitive" raw materials (e.g. clay) are placed in an aggregation-decomposition hierarchy. The process analysis carried out here basically captures most of the energy inputs associated with levels 1 and 2 in the IFIAS (1974) scheme, and accounts for around 90% of the embedded energy in a product. These calculations are based on Tonnes of Oil Equivalent (TOE). The data required to estimate these embedded energies were collected from building materials manufacturers. A computerised database was implemented using a relational database management system. This can be used to represent and calculate the embedded energies and carbon coefficients of building materials and elements that are hierarchically arranged. It can also handle multiple sources of data and perform calculations to give the average, maximum and minimum embedded energies, which are also classified according to fuel type and process stage. Though the analysis was done assuming that the final building is located in the City of Colombo, these database values can be used, with some caution, for buildings even outside the Colombo City or District. The embedded energy requirements were also calculated on the basis of the lowest quality energy (bio-equivalent energy), in addition to the more conventional basis of TOE. According to energy quality calculations carried out (based on efficiency considerations), 1GJ of energy from electricity is equivalent to 5 GJ of biomass energy, 1 GJ of fossil fuel energy is equivalent to 1.8 GJ of biomass energy and 1 GJ of electrical energy is equivalent to 2.78 GJ of fossil fuel energy. It is seen that the price per unit of biomass energy based on the actual prices of products is around one third of the actual price per unit of biomass energy. For fossil fuel and electricity on the other hand, the actual prices of products are much higher than the actual prices of the energy sources used for their production. In order to minimise adverse energy effects and to give a beneficial effect to halting global warming, policy measures to promote timber products are desirable. It is also seen that though materials which use timber fuels (e.g. bricks and tiles) consume more energy, the use of timber fuels is more competitive when compared on a bio-equivalent unit basis. Furthermore, with respect to carbon emissions, wood fuels are considered to be self sustaining. The use of timber, whether as a construction material or a fuel, will require properly planned re-forestation strategies. The energy contribution from walls for a typical two storey house is from 10 - 44%; for a single storey house it is from 29 - 49%. The contribution from roofs for the two storey house is from 4 - 7%, whereas it is 8 - 16% for the single storey house. The contribution from windows is 0.6 - 3% for the single storey house and 0.2 - 4.5% for the two storey. house. The contribution from the floor slab for the two storey house is 6 - 7%. The above ranges are a result of the difference of the between the use of low and high energy materials. The ratio between total embedded energy and annual operational energy for the buildings selected lies between 14 to 35 for the houses while for an office building with air conditioning loading it is 5. Though air conditioning has a large contribution towards the annual operational energy of a building, the total number of air conditioned buildings are small for a developing country such as Sri Lanka. Nevertheless, the results of the analysis show that the focus of energy efficient designs for buildings with air conditioning has to be on the operational energy. On the other hand, for houses, which are largely not air conditioned, the way to promote efficiency is by reducing the embedded energy through the appropriate choice of building materials. This is borne out not only by the high ratio of construction to operational energy ratio obtained, but also by the fact that the ratios for houses with low energy materials is almost half those for the houses with high energy materials. Key Words : Embedded Energy, Process Analysis, Building Materials, Carbon Emissions, Energy Databas

A multi-element psychosocial intervention for early psychosis (GET UP PIANO TRIAL) conducted in a catchment area of 10 million inhabitants: study protocol for a pragmatic cluster randomized controlled trial

Multi-element interventions for first-episode psychosis (FEP) are promising, but have mostly been conducted in non-epidemiologically representative samples, thereby raising the risk of underestimating the complexities involved in treating FEP in 'real-world' services

Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 to January 2022

The SARS-CoV-2 variant of concern Omicron was first detected in Italy in November 2021.AimTo comprehensively describe Omicron spread in Italy in the 2 subsequent months and its impact on the overall SARS-CoV-2 circulation at population level.MethodsWe analyse data from four genomic surveys conducted across the country between December 2021 and January 2022. Combining genomic sequencing results with epidemiological records collated by the National Integrated Surveillance System, the Omicron reproductive number and exponential growth rate are estimated, as well as SARS-CoV-2 transmissibility.ResultsOmicron became dominant in Italy less than 1 month after its first detection, representing on 3 January 76.9-80.2% of notified SARS-CoV-2 infections, with a doubling time of 2.7-3.3 days. As of 17 January 2022, Delta variant represented < 6% of cases. During the Omicron expansion in December 2021, the estimated mean net reproduction numbers respectively rose from 1.15 to a maximum of 1.83 for symptomatic cases and from 1.14 to 1.36 for hospitalised cases, while remaining relatively stable, between 0.93 and 1.21, for cases needing intensive care. Despite a reduction in relative proportion, Delta infections increased in absolute terms throughout December contributing to an increase in hospitalisations. A significant reproduction numbers' decline was found after mid-January, with average estimates dropping below 1 between 10 and 16 January 2022.ConclusionEstimates suggest a marked growth advantage of Omicron compared with Delta variant, but lower disease severity at population level possibly due to residual immunity against severe outcomes acquired from vaccination and prior infection