Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

BACKGROUND: Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M. bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). In addition, we compare gene expression profiles generated using RNA-seq with those previously generated by us using the high-density Affymetrix® GeneChip® Bovine Genome Array platform from the same MDM-extracted RNA. RESULTS: A mean of 7.2 million reads from each MDM sample mapped uniquely and unambiguously to single Bos taurus reference genome locations. Analysis of these mapped reads showed 2,584 genes (1,392 upregulated; 1,192 downregulated) and 757 putative natural antisense transcripts (558 upregulated; 119 downregulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value ≤ 0.05). Of the differentially expressed genes, 694 were common to both the sense and antisense data sets, with the direction of expression (i.e. up- or downregulation) positively correlated for 693 genes and negatively correlated for the remaining gene. Gene ontology analysis of the differentially expressed genes revealed an enrichment of immune, apoptotic and cell signalling genes. Notably, the number of differentially expressed genes identified from RNA-seq sense strand analysis was greater than the number of differentially expressed genes detected from microarray analysis (2,584 genes versus 2,015 genes). Furthermore, our data reveal a greater dynamic range in the detection and quantification of gene transcripts for RNA-seq compared to microarray technology. CONCLUSIONS: This study highlights the value of RNA-seq in identifying novel immunomodulatory mechanisms that underlie host-mycobacterial pathogen interactions during infection, including possible complex post-transcriptional regulation of host gene expression involving antisense RNA

Implementation research for the prevention of antimicrobial resistance and healthcare-associated infections; 2017 Geneva infection prevention and control (IPC)-think tank (part 1)

Background Around 5–15% of all hospital patients worldwide suffer from healthcare-associated infections (HAIs), and years of excessive antimicrobial use in human and animal medicine have created emerging antimicrobial resistance (AMR). A considerable amount of evidence-based measures have been published to address these challenges, but the largest challenge seems to be their implementation. Methods In June 2017, a total of 42 experts convened at the Geneva IPC-Think Tank to discuss four domains in implementation science: 1) teaching implementation skills; 2) fostering implementation of IPC and antimicrobial stewardship (AMS) by policy making; 3) national/international actions to foster implementation skills; and 4) translational research bridging social sciences and clinical research in infection prevention and control (IPC) and AMR. Results Although neglected in the past, implementation skills have become a priority in IPC and AMS. They should now be part of any curriculum in health care, and IPC career paths should be created. Guidelines and policies should be aligned with each other and evidence-based, each document providing a section on implementing elements of IPC and AMS in patient care. International organisations should be advocates for IPC and AMS, framing them as patient safety issues and emphasizing the importance of implementation skills. Healthcare authorities at the national level should adopt a similar approach and provide legal frameworks, guidelines, and resources to allow better implementation of patient safety measures in IPC and AMS. Rather than repeating effectiveness studies in every setting, we should invest in methods to improve the implementation of evidence-based measures in different healthcare contexts. For this, we need to encourage and financially support collaborations between social sciences and clinical IPC research. Conclusions Experts of the 2017 Geneva Think Tank on IPC and AMS, CDC, and WHO agreed that sustained efforts on implementation of IPC and AMS strategies are required at international, country, and hospital management levels, to provide an adequate multimodal framework that addresses (not exclusively) leadership, resources, education and training for implementing IPC and AMS. Future strategies can build on this agreement to make strategies on IPC and AMS more effective

Methods for determining the optimal arrangement of water deluge systems on offshore installations

Offshore installations are prone to fire and/or explosion accidents. Fires have particularly serious consequences due to their high temperatures and heat flux, which affect humans, structures and environments alike. Due to the hydrocarbon explosions caused by delayed ignition following gas dispersion, fires can be the result of immediate ignition after gas release. Accordingly, it can be difficult to decrease their frequency, which is an element of risk (risk=frequency×consequence), using an active protection system (APS) such as gas detectors capable of shutting down the operation. Thus, it is more efficient to reduce the consequence using a passive protection system (PSS) such as water spray. It is important to decide the number and location of water deluge systems, thus the aim of this study is to introduce a new procedure for optimising the locations of water deluge systems using the water deluge location index (WLI) proposed herein. The locations of water deluge systems are thus optimised based on the results of credible fire scenarios using a three-dimensional computational fluid dynamics (CFD) tool. The effects of water spray and the effectiveness of the WLI are investigated in comparison with uniformly distributed sprays

Preparation and characterization of bamboo-based activated carbons as electrode materials for electric double layer capacitors

ArticleCarbon. 44(8):1592-1595 (2006)journal articl

Porohyperelastic anatomical models for hydrocephalus and idiopathic intracranial hypertension

This is the accepted manuscript of a paper published in the Journal of Neurosurgery, Published online February 6, 2015; DOI: 10.3171/2014.12.JNS14516.OBJECT Brain deformation can be seen in hydrocephalus and idiopathic intracranial hypertension (IIH) via medical images. The phenomenology of local effects, brain shift, and raised intracranial pressure and herniation are textbook concepts. However, there are still uncertainties regarding the specific processes that occur when brain tissue is subject to the mechanical stress of different temporal and spatial profiles of the 2 neurological disorders. Moreover, recent studies suggest that IIH and hydrocephalus may be diseases with opposite pathogenesis. Nevertheless, the similarities and differences between the 2 subjects have not been thoroughly investigated. METHODS An anatomical porohyperelastic finite element model was used to assess the brain tissue responses associated with hydrocephalus and IIH. The same set of boundary conditions, with the exception of brain loading for development of the transmantle pressure gradient, was applied for the 2 models. The distribution of stress and strain during tissue distortion is described by the mechanical parameters. RESULTS The results of both the hydrocephalus and IIH models correlated with pathological characteristics. For the hydrocephalus model, periventricular edema was associated with the presence of positive volumetric strain and void ratio in the lateral ventricle horns. By contrast, the IIH model revealed edema across the cerebral mantle, including the centrum semiovale, with a positive void ratio and volumetric strain. CONCLUSIONS The model simulates all the clinical features in correlation with the MR images obtained in patients with hydrocephalus and IIH, thus providing support for the role of the transmantle pressure gradient and capillary CSF absorption in CSF-related brain deformation. The finite element methods can be used for a better understanding of the pathophysiological mechanisms of neurological disorders associated with parenchymal volumetric fluctuation.Dr. M. Czosnyka is a consultant for J&J (Codman), and has received payment for lectures from Integra Lifescience. This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRFK) funded by the Ministry of Science, ICT, & Future Planning (2013R1A1A1004827); and the International Research & Development Program of the NRFK funded by the Ministry of Education, Science, and Technology of Korea (Grant No. 2014K1A3A1A21001366)

Quantum interference and Klein tunneling in graphene heterojunctions

The observation of quantum conductance oscillations in mesoscopic systems has traditionally required the confinement of the carriers to a phase space of reduced dimensionality. While electron optics such as lensing and focusing have been demonstrated experimentally, building a collimated electron interferometer in two unconfined dimensions has remained a challenge due to the difficulty of creating electrostatic barriers that are sharp on the order of the electron wavelength. Here, we report the observation of conductance oscillations in extremely narrow graphene heterostructures where a resonant cavity is formed between two electrostatically created bipolar junctions. Analysis of the oscillations confirms that p-n junctions have a collimating effect on ballistically transmitted carriers. The phase shift observed in the conductance fringes at low magnetic fields is a signature of the perfect transmission of carriers normally incident on the junctions and thus constitutes a direct experimental observation of ``Klein Tunneling.''Comment: 13 pages and 6 figures including supplementary information. The paper has been modified in light of new theoretical results available at arXiv:0808.048

Prescription sequence symmetry analysis: assessing risk, temporality, and consistency for adverse drug reactions across datasets in five countries

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Ab initio study of magnetism at the TiO2/LaAlO3 interface

In this paper we study the possible relation between the electronic and magnetic structure of the TiO2/LaAlO3 interface and the unexpected magnetism found in undoped TiO2 films grown on LaAlO$_3$. We concentrate on the role played by structural relaxation and interfacial oxygen vacancies. LaAlO3 has a layered structure along the (001) direction with alternating LaO and AlO2 planes, with nominal charges of +1 and -1, respectively. As a consequence of that, an oxygen deficient TiO2 film with anatase structure will grow preferently on the AlO2 surface layer. We have therefore performed ab-initio calculations for superlattices with TiO2/AlO2 interfaces with interfacial oxygen vacancies. Our main results are that vacancies lead to a change in the valence state of neighbour Ti atoms but not necessarily to a magnetic solution and that the appearance of magnetism depends also on structural details, such as second neighbor positions. These results are obtained using both the LSDA and LSDA+U approximations.Comment: Accepted for publication in Journal of Materials Scienc

Use of a novel coaxial guide needle-wire (GNW) combination system for computed tomography guided radiofrequency tumor ablation

We developed a novel coaxial system using a fine guide needle wire (GNW) to safely and easily place the radiofrequency needle under CT-guidance. The GNW consists of a fine needle (diameter, 21-gauge; length, 150 mm) and a wire (0.018 inch, 250 mm). An exclusive radiofrequency cannula (14-gauge; 160 mm) was also used. This system was used for the treatment of six hepatocellular carcinomas in six patients. All lesions were located deeper than 10 cm from the needle entry site. This system was useful in performing CT-guided RF ablation for deeply or precariously located liver lesions particularly in patients who are unable to hold their breath

Design of a pulse power supply unit for micro-ECM

Electrochemical micro-machining (μECM) requires a particular pulse power supply unit (PSU) to be developed in order to achieve desired machining performance. This paper summarises the development of a pulse PSU meeting the requirements of μECM. The pulse power supply provides tens of nanosecond pulse duration, positive and negative bias voltages and a polarity switching functionality. It fulfils the needs for tool preparation with reversed pulsed ECM on the machine. Moreover, the PSU is equipped with an ultrafast overcurrent protection which prevents the tool electrode from being damaged in case of short circuits. The developed pulse PSU was used to fabricate micro-tools out of 170 μm WC-Co alloy shafts via micro-electrochemical turning and drill deep holes via μECM in a disk made of 18NiCr6. The electrolyte used for both processes was a mixture of sulphuric acid and NaNO3 aqueous solutions.The research reported in this paper is supported by the European Commission within the project “Minimizing Defects in Micro-Manufacturing Applications (MIDEMMA)” (FP7-2011-NMP-ICT-FoF-285614