Perturbed geodesics on the moduli space of flat connections and Yang-Mills theory

If we consider the moduli space of flat connections of a non trivial principal SO(3)-bundle over a surface, then we can define a map from the set of perturbed closed geodesics, below a given energy level, into families of perturbed Yang-Mills connections depending on a small parameter. In this paper we show that this map is a bijection and maps perturbed geodesics into perturbed Yang-Mills connections with the same Morse index.Comment: 58 pages, 3 figure

Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction.

We developed a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 14 times more libraries for high-throughput Illumina sequencing to be generated for the same cost. We call this new method Hackflex. The quality of library preparation was tested by constructing libraries from Escherichia coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex (recently renamed as Illumina DNA Prep) or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. In order to test the library quality for genomes with a higher and a lower G+C content, library construction methods were also tested on Pseudomonas aeruginosa PAO1 and Staphylococcus aureus ATCC 25923, respectively. We demonstrated that Hackflex can produce high-quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. We show that strongly size-selected libraries produce sufficient yield and complexity to support de novo microbial genome assembly, and that assemblies of the large-insert libraries can be much more contiguous than standard libraries without strong size selection. We introduce a new set of sample barcodes that are distinct from standard Illumina barcodes, enabling Hackflex samples to be multiplexed with samples barcoded using standard Illumina kits. Using Hackflex, we were able to achieve a per-sample reagent cost for library prep of A$7.22 (Australian dollars) (US$5.60; UK £3.87, £1=A$1.87), which is 9.87 times lower than the standard Nextera Flex protocol at advertised retail price. An additional simple modification and further simplification of the protocol by omitting the wash step enables a further price reduction to reach an overall 14-fold cost saving. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programmes where sequencing large numbers of libraries is beneficial

Hackflex: low cost Illumina sequencing library construction for high sample counts

ABSTRACT We developed Hackflex, a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 11 times more libraries for high-throughput Illumina sequencing to be generated at a fixed cost. We call this new method Hackflex. Quality of library preparation was tested by constructing libraries from E. coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. We demonstrated that Hackflex can produce high quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. Using Hackflex, we were able to achieve a per sample reagent cost of library prep of A$8.66, which is 8.23 times lower than the Standard Nextera Flex protocol at advertised retail price. An additional simple modification to the protocol enables a further price reduction of up to 11 fold or about A$6.50/sample. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programs where sequencing large numbers of libraries is beneficial

Whole Genome Sequencing Analysis of Porcine Faecal Commensal Escherichia coli Carrying Class 1 Integrons from Sows and Their Offspring.

Intensive pig production systems often rely on the use of antimicrobials and heavy metal feed additives to maintain animal health and welfare. To gain insight into the carriage of antimicrobial resistance genes (ARGs) in the faecal flora of commercially reared healthy swine, we characterised the genome sequences of 117 porcine commensal E. coli that carried the class 1 integrase gene (intI1+). Isolates were sourced from 42 healthy sows and 126 of their offspring from a commercial breeding operation in Australia in 2017. intI1+ E. coli was detected in 28/42 (67%) sows and 90/126 (71%) piglets. Phylogroup A, particularly clonal complex 10, and phylogroup B1 featured prominently in the study collection. ST10, ST20, ST48 and ST361 were the dominant sequence types. Notably, 113/117 isolates (96%) carried three or more ARGs. Genes encoding resistance to -lactams, aminoglycosides, trimethoprim, sulphonamides, tetracyclines and heavy metals were dominant. ARGs encoding resistance to last-line agents, such as carbapenems and third generation cephalosporins, were not detected. IS26, an insertion sequence noted for its ability to capture and mobilise ARGs, was present in 108/117 (92%) intI1+ isolates, and it played a role in determining class 1 integron structure. Our data shows that healthy Australian pig faeces are an important reservoir of multidrug resistant E. coli that carry genes encoding resistance to multiple first-generation antibiotics and virulence-associated genes

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig.

Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors

A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen

BackgroundEarly weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. As an alternative to antibiotic treatment, studies have previously investigated the potential of probiotics for the prevention of postweaning diarrhea. In order to describe the post-weaning gut microbiota, and to study the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we sampled and processed over 800 faecal time-series samples from 126 piglets and 42 sows.ResultsHere we report on the largest shotgun metagenomic dataset of the pig gut lumen microbiome to date, consisting of >8 Tbp of shotgun metagenomic sequencing data. The animal trial, the workflow from sample collection to sample processing, and the preparation of libraries for sequencing, are described in detail. We provide a preliminary analysis of the dataset, centered on a taxonomic profiling of the samples, and a 16S-based beta diversity analysis of the mothers and the piglets in the first 5 weeks after weaning.ConclusionsThis study was conducted to generate a publicly available databank of the faecal metagenome of weaner piglets aged between 3 and 9 weeks old, treated with different probiotic formulations and intramuscular antibiotic treatment. Besides investigating the effects of the probiotic and intramuscular antibiotic treatment, the dataset can be explored to assess a wide range of ecological questions with regards to antimicrobial resistance, host-associated microbial and phage communities, and their dynamics during the aging of the host

Dye Stabilization and Wavelength Tunability in Lasing Fibers Based on DNA

Lasers based on biological materials are attracting an increasing interest in view of their use in integrated and transient photonics. Deoxyribonucleic acid (DNA) as optical biopolymer in combination with highly emissive dyes has been reported to have excellent potential in this respect. However, achieving miniaturized lasing systems based on solid-state DNA shaped in different geometries to confine and enhance emission is still a challenge, and the physicochemical mechanisms originating fluorescence enhancement are not fully understood. Herein, a class of wavelength-tunable lasers based on DNA nanofibers is demonstrated, for which optical properties are highly controlled through the system morphology. A synergistic effect is highlighted at the basis of lasing action. Through a quantum chemical investigation, it is shown that the interaction of DNA with the encapsulated dye leads to hindered twisting and suppressed channels for the nonradiative decay. This is combined with effective waveguiding, optical gain, and tailored mode confinement to promote morphologically controlled lasing in DNA-based nanofibers. The results establish design rules for the development of bright and tunable nanolasers and optical networks based on DNA nanostructures

Longitudinal changes of cardiotocographic parameters throughout pregnancy: a prospective cohort study comparing small-for-gestational-age and normal fetuses from 24 to 40 weeks

Objective: To compare longitudinal trends of cardiotocographic (CTG) parameters between small-for-gestational-age (SGA) and normal fetuses, from 24 to 41 weeks of pregnancy. Methods: A prospective cohort study was carried out in singleton pregnancies without fetal malformations. At least one CTG was performed in each of the following intervals: 24-26 weeks+6 days, 27-29 weeks+6 days, 30-32 weeks+6 days, 33-35 weeks+6 days, 36-38 weeks+6 days and >= 39 weeks. Tracings were analyzed using the Omniview-SisPorto (R) 3.6 system. Cases with a normal - pregnancy outcome, including a birthweight >= 10th percentile for gestational age, were compared with two groups of SGA fetuses: with birthweight < 10th percentile (SGA < p10) and < 3rd percentile (SGA < p3; a subgroup of the latter). Generalized linear mixed-effects models were used for analysis. Results: A total of 176 fetuses (31 SGA) and 1256 tracings (207 from SGA fetuses) were evaluated. All CTG parameters changed significantly throughout pregnancy in the three groups, with a decreasing baseline and probability of decelerations, and an increasing average long-term variability (LTV), average short-term variability (STV) and accelerations. Baseline showed a more pronounced decrease (steeper slope) in SGA fetuses, being higher in these cases at earlier gestational ages and lower later in pregnancy. Average LTV was significantly lower in SGA < p3 fetuses, but a parallel increase occurred in all groups. There was a considerable inter-fetal variability within each group. Conclusion: A unique characterization of CTG trends throughout gestation in SGA fetuses was provided. A steeper descent of the baseline was reported for the first time. The findings raise the possibility of clinical application of computerized CTG analysis in screening and management of fetal growth restriction

COVID-19 Vaccines and Atrial Fibrillation: Analysis of the Post-Marketing Pharmacovigilance European Database

Atrial fibrillation (AF) has been described in COVID-19 patients. Recently, some case reports and US pharmacovigilance analyses described AF onset as a rare adverse event following COVID-19 vaccination. The possible correlation is unclear. We systematically analyzed the reports of AF related to COVID-19 vaccines collected in the European pharmacovigilance database, EudraVigilance (EV), from 2020 to November 2022. We carried out descriptive and disproportionality analyses. Moreover, we performed a sensitivity analysis, excluding the reports describing other possible alternative AF causes (pericarditis, myocarditis, COVID-19, or other drugs that may cause/exacerbate AF). Overall, we retrieved 6226 reports, which represented only 0.3% of all those related to COVID-19 vaccines collected in EV during our study period. AF reports mainly referred to adults (in particular, &gt;65 years old), with an equal distribution in sex. Reports were mainly related to tozinameran (54.04%), elasomeran (28.3%), and ChAdOx1-S (14.32%). The reported AF required patient hospitalization in 35% of cases and resulted in a life-threatening condition in 10% of cases. The AF duration (when reported) was highly variable, but the majority of the events had a short duration (moda = 24 h). Although an increased frequency of AF reporting with mRNA vaccines emerges from our study, other investigations are required to investigate the possible correlation between COVID-19 vaccination and the rare AF occurrence

Long-term Exposure to Ambient Air Pollution and its Association with Mental Well-Being, Depression and Anxiety: A Nationally Representative Study

"Introduction: Exposure to ambient air pollution may play a role in the onset of common mental disorders like depressive and anxiety disorders. The association of long-term exposure to particles smaller than 10 μm (PM10) with these diseases remains unclear. This study aimed to estimate the association of long-term exposure to PM10 with mental well-being and the frequency of probable diagnosis of common mental disorders. Methods: A nationally representative cross-sectional study was done in mainland Portugal. Long-term exposure was estimated through one-year average concentrations of PM10, calculated with data from the Portuguese Environment Agency, attributed individually considering individuals’ postal codes of residence. The mental well-being and the probable diagnosis of common mental disorders were ascertained through the five-item Mental Health Inventory scale. Linear and Robust Poisson regression models were computed to estimate change percentages, prevalence ratios (PR), and their 95% confidence intervals (95% CI). Results: The median (interquartile range) concentration of PM10 was 18.6 (15.3 - 19.3) μg/m3. The mental well-being score was 72 (56 - 84) points, on a scale from 0 to 100. A probable diagnosis of common mental disorders was found in 22.7% (95% CI: 20.0 to 25.6). Long-term exposure to PM10 was associated with a non-statistically significant decrease in the mental well-being score [for each 10 μg/m³ increment in one-year average PM10 concentrations, there was a 2% (95% CI: -8 to 4) decrease], and with a non-statistically significant increase in the common mental health frequency (PR = 1.012, 95% CI: 0.979 to 1.045). Conclusion: We did not find statistically significant associations between long-term exposure to PM10 and mental well-being or the frequency of probable diagnosis of common mental disorders. These results may be explained by the reduced variability in the exposure values, given the geographical distribution and functioning of the network of air quality monitoring stations. This study contributes with evidence for low levels of air pollutants, being one of the first to adjust for individual and aggregate-level variables. Moreover, to the best of our knowledge, this was the first nationally representative, population-based study conducted on the Portuguese population using real-life data. Maintaining a robust and nationwide air quality monitoring network is essential for obtaining quality exposure data."he Portuguese National Health Examination Survey was developed as part of a project financed under the Public Health Initiatives Programme (“Improvement of epidemiological health information to support public health decision and management in Portugal. Towards reduced inequalities, improved health and bilateral cooperation”) with a €1 500 000 grant from Iceland, Liechtenstein and Norway, the EEA Grants and the Portuguese Government. This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sec-tors