HIV screening of tuberculosis patients in Portugal: what are we missing?

BACKGROUND: Knowledge of human immunodeficiency virus (HIV) status is essential to effectively manage both tuberculosis (TB) and HIV infection. This is why the World Health Organization (WHO) recommends routine HIV testing in all TB patients. OBJECTIVE: To determine the number of TB patients with unknown HIV status in Portugal and to identify the factors associated with unknown HIV status. METHODS: A retrospective study of all TB notifications from 2008 to 2014 in Portugal was conducted. A multiple logistic regression model was used to evaluate the association of sociodemographic and clinical factors with unknown HIV status. RESULTS: We examined the records of 18 445 patients with TB notification, 2402 of whom (13%) had unknown HIV status. Unknown HIV status was positively associated with age >= 65 years (adjusted odds ratio [aOR] 1.208, 95%CI 1.037-1.408) and extra-pulmonary TB (aOR 1.381, 95%CI 1.252-1.523), but negatively associated with unemployment (aOR 0.755, 95%CI 0.637-0.895), alcohol dependence (aOR 0.809, 95%CI 0.682-0.959) and drug dependence (aOR 0.566, 95%CI 0.449-0.713). CONCLUSION: Risk perception is the most important barrier to complete knowledge of HIV status in TB patients in Portugal. Given the importance of HIV screening in TB patients, every effort should be made to ensure that all TB patients undergo HIV screening.RG was supported in part by the Centre for Mathematics of the University of Porto, Porto (UID/MAT/00144/2013), which is funded by Fundacao para a Ciencia e a Tecnologia, Lisbon, Portugal, with national (Ministerio da Educacao e Ciencia) and European structural funds (Fonds europeen de developpement regional) under the PT2020 partnership agreement

Is time the real line?

This paper is devoted to discussing the topological structure of the arrow of time. In the literature, it is often accepted that its algebraic and topological structures are that of a one-dimensional Euclidean space $\mathbb{E}^1$, although a critical review on the subject is not easy to be found. Hence, leveraging on an operational approach, we collect evidences to identify it structurally as a normed vector space $(\mathbb{Q}, |\cdot|)$, and take a leap of abstraction to complete it, up to isometries, to the real line. During the development of the paper, the space-time is recognized as a fibration, with the fibers being the sets of simultaneous events. The corresponding topology is also exposed: open sets naturally arise within our construction, showing that the classical space-time is non-Hausdorff. The transition from relativistic to classical regimes is explored too.Comment: 26 pages, 9 figures. Misprints corrected and minor adjustments according to the review proces

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

Peripheral arterial tonometry as a method of measuring reactive hyperaemia correlates with organ dysfunction and prognosis in the critically ill patient: a prospective observational study

Predictions of mortality may help in the selection of patients who benefit from intensive care. Endothelial dysfunction is partially responsible for many of the organic dysfunctions in critical illness. Reactive hyperaemia is a vascular response of the endothelium that can be measured by peripheral arterial tonometry (RH-PAT). We aimed to assess if reactive hyperaemia is affected by critical illness and if it correlates with outcomes. Prospective study with a cohort of consecutive patients admitted to an Intensive Care Unit. RH-PAT was accessed on admission and on the 7th day after admission. Early and late survivors were compared to non-survivors. The effect of RH-PAT variation on late mortality was studied by a logistic regression model. The association between RH-PAT and severity scores and biomarkers of organic dysfunction was investigated by multivariate analysis. 86 patients were enrolled. Mean ln(RHI) on admission was 0.580 and was significantly lower in patients with higher severity scores (p < 0.01) and early non-survivors (0.388; p = 0.027). The model for prediction of early-mortality estimated that each 0.1 decrease in ln(RHI) increased the odds for mortality by 13%. In 39 patients, a 2nd RH-PAT measurement was performed on the 7th day. The variation of ln(RHI) was significantly different between non-survivors and survivors (− 24.2% vs. 63.9%, p = 0.026). Ln(RHI) was significantly lower in patients with renal and cardiovascular dysfunction (p < 0.01). RH-PAT is correlated with disease severity and seems to be an independent marker of early mortality, cardiovascular and renal dysfunctions. RH-PAT variation predicts late mortality. There appears to be an RH-PAT impairment in the acute phase of severe diseases that may be reversible and associated with better outcomes.Professor Rita Gaio was partially supported by CMUP (UID/MAT/00144/2013), which is funded by FCT (Portugal) with national (MEC) and European structural funds (FEDER), under the partnership agreement PT2020

Relationship between body mass index and mean arterial pressure in normotensive and chronic hypertensive pregnant women: a prospective, longitudinal study

Being overweight is associated with both higher systolic blood pressure (SBP) and diastolic blood pressure (DBP) during pregnancy and increased risk of gestational hypertensive disorders. The objective of this study was to determine and quantify the effect of body mass index (BMI) on mean arterial pressure (MAP) at several time points throughout pregnancy in normotensive (NT) and chronic hypertensive pregnant (HT) women

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

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

Start of SPIDER operation towards ITER neutral beams

Heating Neutral Beam (HNB) Injectors will constitute the main plasma heating and current drive tool both in ITER and JT60-SA, which are the next major experimental steps for demonstrating nuclear fusion as viable energy source. In ITER, in order to achieve the required thermonuclear fusion power gain Q=10 for short pulse operation and Q=5 for long pulse operation (up to 3600s), two HNB injectors will be needed [1], each delivering a total power of about 16.5 MW into the magnetically-confined plasma, by means of neutral hydrogen or deuterium particles having a specific energy of about 1 MeV. Since only negatively charged particles can be efficiently neutralized at such energy, the ITER HNB injectors [2] will be based on negative ions, generated by caesium-catalysed surface conversion of atoms in a radio-frequency driven plasma source. A negative deuterium ion current of more than 40 A will be extracted, accelerated and focused in a multi-aperture, multi-stage electrostatic accelerator, having 1280 apertures (~ 14 mm diam.) and 5 acceleration stages (~200 kV each) [3]. After passing through a narrow gas-cell neutralizer, the residual ions will be deflected and discarded, whereas the neutralized particles will continue their trajectory through a duct into the tokamak vessels to deliver the required heating power to the ITER plasma for a pulse duration of about 3600 s. Although the operating principles and the implementation of the most critical parts of the injector have been tested in different experiments, the ITER NBI requirements have never been simultaneously attained. In order to reduce the risks and to optimize the design and operating procedures of the HNB for ITER, a dedicated Neutral Beam Test Facility (NBTF) [4] has been promoted by the ITER Organization with the contribution of the European Union\u2019s Joint Undertaking for ITER and of the Italian Government, with the participation of the Japanese and Indian Domestic Agencies (JADA and INDA) and of several European laboratories, such as IPP-Garching, KIT-Karlsruhe, CCFE-Culham, CEA-Cadarache. The NBTF, nicknamed PRIMA, has been set up at Consorzio RFX in Padova, Italy [5]. The planned experiments will verify continuous HNB operation for one hour, under stringent requirements for beam divergence (< 7 mrad) and aiming (within 2 mrad). To study and optimise HNB performances, the NBTF includes two experiments: MITICA, full-scale NBI prototype with 1 MeV particle energy and SPIDER, with 100 keV particle energy and 40 A current, aiming at testing and optimizing the full-scale ion source. SPIDER will focus on source uniformity, negative ion current density and beam optics. In June 2018 the experimental operation of SPIDER has started