Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) allows a fast and reliable bacterial identification from culture plates. Direct analysis of clinical ...samples may increase its usefulness in samples in which a fast identification of microorganisms can guide empirical treatment, such as blood cultures (BC). Three hundred and thirty BC, reported as positive by the automated BC incubation device, were processed by conventional methods for BC processing, and by a fast method based on direct MALDI-TOF MS. Three hundred and eighteen of them yield growth on culture plates, and 12 were false positive. The MALDI-TOF MS-based method reported that no peaks were found, or the absence of a reliable identification profile, in all these false positive BC. No mixed cultures were found. Among these 318 BC, we isolated 61 Gram-negatives (GN), 239 Gram-positives (GP) and 18 fungi. Microorganism identifications in GN were coincident with conventional identification, at the species level, in 83.3% of BC and, at the genus level, in 96.6%. In GP, identifications were coincident with conventional identification in 31.8% of BC at the species level, and in 64.8% at the genus level. Fungaemia was not reliably detected by MALDI-TOF. In 18 BC positive for Candida species (eight C. albicans, nine C. parapsilosis and one C. tropicalis), no microorganisms were identified at the species level, and only one (5.6%) was detected at the genus level. The results of the present study show that this fast, MALDI-TOF MS-based method allows bacterial identification directly from presumptively positive BC in a short time (<30 min), with a high accuracy, especially when GN bacteria are involved.
Abstract
Motivation
Molecular profiling techniques have evolved to single-cell assays, where dense molecular profiles are screened simultaneously for each cell in a population. High-throughput ...single-cell experiments from a heterogeneous population of cells can be experimentally and computationally sorted as a sequence of samples pseudo-temporally ordered samples. The analysis of these datasets, comprising a large number of samples, has the potential to uncover the dynamics of the underlying regulatory programmes.
Results
We present a novel approach for modelling and inferring gene regulatory networks from high-throughput time series and pseudo-temporally sorted single-cell data. Our method is based on a first-order autoregressive moving-average model and it infers the gene regulatory network within a variational Bayesian framework. We validate our method with synthetic data and we apply it to single cell qPCR and RNA-Seq data for mouse embryonic cells and hematopoietic cells in zebra fish.
Availability and implementation
The method presented in this article is available at https://github.com/mscastillo/GRNVBEM.
Summary
Background
There is some evidence that, despite attempts to classify them separately, functional bowel disorders are not distinct entities and that such divisions are artificial.
Aim
To ...examine this issue in a large cohort of secondary care patients.
Methods
Consecutive, unselected adults with gastrointestinal (GI) symptoms attending out‐patient clinics at two hospitals in Hamilton, Ontario were recruited. Demographic data, symptoms and presence of anxiety, depression or somatisation were collected prospectively. We used validated questionnaires, including the Rome III questionnaire, with patients categorised as having irritable bowel syndrome (IBS), functional diarrhoea or chronic idiopathic constipation (CIC). We compared data between these disorders, and measured degree of overlap between them by suspending their mutual exclusivity.
Results
Of 3656 patients providing complete lower GI symptom data, 1551 (42.4%) met criteria for a functional bowel disorder. Diarrhoea‐predominant IBS (IBS‐D) patients were younger, and more were female, met criteria for anxiety, and reported somatisation‐type behaviour, compared with functional diarrhoea. Only loose, mushy or watery stools were more common in functional diarrhoea. When mutual exclusivity was suspended, overlap occurred in 27.6%. Constipation‐predominant IBS (IBS‐C) patients were younger, and more were female, had never married, reported anxiety type symptoms and exhibited somatisation‐type behaviour. One in five CIC patients reported abdominal pain or discomfort. All constipation symptoms were more common in IBS‐C. When the mutual exclusivity was suspended, overlap occurred in 18.1%.
Conclusions
There were significant differences in demographics between individuals with functional bowel disorders. Despite this, the Rome III classification system falls short of describing unique entities.
The formation of secondary organic aerosol (SOA) from the oxidation ofβ-pinene via nitrate radicals is investigated in the Georgia Tech Environmental Chamber (GTEC) facility. Aerosol yields are ...determined for experiments performed under both dry (relative humidity (RH) < 2 %) and humid (RH = 50 % and RH = 70 %) conditions. To probe the effects of peroxy radical (RO2) fate on aerosol formation, “RO2+NO3 dominant” and “RO2+HO2 dominant” experiments are performed. Gas-phase organic nitrate species (with molecular weights of 215, 229, 231, and 245 amu, which likely correspond to molecular formulas of C10H17NO4, C10H15NO5, C10H17NO5, and C10H15NO6, respectively) are detected by chemical ionization mass spectrometry (CIMS) and their formation mechanisms are proposed. The NO+ (at m/z 30) and NO2+ (atm/z 46) ions contribute about 11 % to the combined organics and nitrate signals in the typical aerosol mass spectrum, with the NO+ : NO2+ ratio ranging from 4.8 to 10.2 in all experiments conducted. The SOA yields in the “RO2+NO3 dominant” and “RO2+HO2 dominant” experiments are comparable. For a wide range of organic mass loadings (5.1–216.1 µg m-3), the aerosol mass yield is calculated to be 27.0–104.1 %. Although humidity does not appear to affect SOA yields, there is evidence of particle-phase hydrolysis of organic nitrates, which are estimated to compose 45–74 % of the organic aerosol. The extent of organic nitrate hydrolysis is significantly lower than that observed in previous studies on photooxidation of volatile organic compounds in the presence of NOx. It is estimated that about 90 and 10 % of the organic nitrates formed from the β-pinene+NO3 reaction are primary organic nitrates and tertiary organic nitrates, respectively. While the primary organic nitrates do not appear to hydrolyze, the tertiary organic nitrates undergo hydrolysis with a lifetime of 3–4.5 h. Results from this laboratory chamber study provide the fundamental data to evaluate the contributions of monoterpene+NO3 reaction to ambient organic aerosol measured in the southeastern United States, including the Southern Oxidant and Aerosol Study (SOAS) and the Southeastern Center for Air Pollution and Epidemiology (SCAPE) study.
Authentication of extra virgin olive oil (EVOO) is an important topic for olive oil industry. The fraudulent practices in this sector are a major problem affecting both producers and consumers. This ...study analyzes the capability of FT-Raman combined with chemometric treatments of prediction of the fatty acid contents (quantitative information), using gas chromatography as the reference technique, and classification of diverse EVOOs as a function of the harvest year, olive variety, geographical origin and Andalusian PDO (qualitative information). The optimal number of PLS components that summarizes the spectral information was introduced progressively. For the estimation of the fatty acid composition, the lowest error (both in fitting and prediction) corresponded to MUFA, followed by SAFA and PUFA though such errors were close to zero in all cases. As regards the qualitative variables, discriminant analysis allowed a correct classification of 94.3%, 84.0%, 89.0% and 86.6% of samples for harvest year, olive variety, geographical origin and PDO, respectively.
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•412 samples of Andalusian Extra virgin olive oils were studied by Raman spectroscopy.•Harvest year was included as a qualification variable.•PLS factors were progressively increased to analyze the evolution in the goodness of the statistical models.•New dimensionless calibration and prediction error measures were proposed.
•The relationships between the durability indicators are not modified in the new concretes.•The chloride penetration was slightly deeper in recycled concretes.•The electrical resistivity was higher ...in the recycled concretes than reference concrete.•The recycled concrete would exhibit satisfactory durability throughout their service life.
Effective industrial waste management is one of the challenges facing modern society. One possible solution, the inclusion of different proportions of waste of varying nature in concrete, calls for a thorough study of the durability of the resulting materials. Direct and indirect durability indices can be used to ensure that such concrete is able to withstand the actions to which it will be exposed throughout its service life to design safety, functionality and aesthetics and with no unexpected maintenance costs. In the present study, 20% and 25% of the natural coarse aggregate in concrete was replaced with recycled aggregate from the sanitary ware industry to explore the effect on chloride penetration and electrical resistivity, as well as the relationship among the durability indicators that predict concrete performance during its service life. The findings showed that chloride penetration was slightly deeper in recycled concretes, while no alterations were observed in the relationship among durability indicators. Electrical resistivity, in turn, was observed to rise with the use of recycled aggregate due to the intrinsic characteristics of this material. The new concretes proved to be as durable as the conventional material, performing satisfactorily throughout their service life.
The utility of cancer whole genome and transcriptome sequencing (cWGTS) in oncology is increasingly recognized. However, implementation of cWGTS is challenged by the need to deliver results within ...clinically relevant timeframes, concerns about assay sensitivity, reporting and prioritization of findings. In a prospective research study we develop a workflow that reports comprehensive cWGTS results in 9 days. Comparison of cWGTS to diagnostic panel assays demonstrates the potential of cWGTS to capture all clinically reported mutations with comparable sensitivity in a single workflow. Benchmarking identifies a minimum of 80× as optimal depth for clinical WGS sequencing. Integration of germline, somatic DNA and RNA-seq data enable data-driven variant prioritization and reporting, with oncogenic findings reported in 54% more patients than standard of care. These results establish key technical considerations for the implementation of cWGTS as an integrated test in clinical oncology.
The disclosure of information on the exercise of corporate social responsibility (CSR) is the mean most frequently used by companies to facilitate understanding of the social and environmental ...performance of an organisation and to improve relationships with stakeholders. The purpose of this paper is to analyse the role that the board of directors plays in relation to the disclosure of socially responsible information, with a focus on the application of the Global Reporting Initiative guidelines related to CSR. The composition and characteristics of the board of directors is crucial to corporate transparency, especially in an institutional environment where other corporate control mechanisms that guarantee rights for different participants are less developed. We analyse a sample of 98 non-financial Spanish companies quoted on the Madrid Stock Exchange for the period 2004–2010, which provide a data panel with 686 observations. In contrast to previous evidence for other institutional settings, our results show that corporate transparency regarding sustainability is directly linked to the independence and diversity of the directors and to the specialisation of functions through the creation of a specific CSR committee.
PURPOSE OF REVIEWWe performed a literature review of the latest studies on the interactions between the host immune system and microbes in chronic intestinal inflammatory conditions.
RECENT ...FINDINGSThe mechanisms leading to celiac disease (CeD) and inflammatory bowel disease (IBD), the most common chronic inflammatory gastrointestinal conditions, are complex. The intestinal homeostasis depends on the interactions between the microbiota, the intestinal mucosa and the host immune system. Failure to achieve or maintain equilibrium between a host and its microbiota has the potential to induce chronic conditions with an underlying inflammatory component. Mechanisms by which intestinal microbes trigger inflammation include the alteration of intestinal permeability, activation of the host immune system and digestion of dietary antigens with a consequent repercussion on tolerance to food. Therefore, therapies modulating gut microbiota, including diet, antibiotics, probiotics and faecal transplantation have a potential in CeD and IBD. Probiotics are effective to treat pouchitis and faecal transplant for ulcerative colitis, but the evidence is less clear in Crohnʼs disease or CeD.
SUMMARYDiverse regulatory mechanisms cooperate to maintain intestinal homeostasis, and a breakdown in these pathways may precipitate inflammation. The role of microbiota inducing immune dysfunction and inflammation supports the therapeutic rationale of manipulating microbiota to treat chronic inflammatory conditions.
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