Molecular epidemiology of multi- and extensively-drug-resistant Mycobacterium tuberculosis in Ireland, 2001-2014.

OBJECTIVES: The primary objective of this work was to examine the acquisition and spread of multi-drug resistant (MDR) tuberculosis (TB) in Ireland. METHODS: All available Mycobacterium tuberculosis complex (MTBC) isolates (n = 42), from MDR-TB cases diagnosed in Ireland between 2001 and 2014, were analysed using phenotypic drug-susceptibility testing, Mycobacterial-Interspersed-Repetitive-Units Variable-Number Tandem-Repeat (MIRU-VNTR) genotyping, and whole-genome sequencing (WGS). RESULTS: The lineage distribution of the MDR-TB isolates comprised 54.7% Euro-American, 33.3% East Asian, 7.2% East African Indian, and 4.8% Indo-Oceanic. A significant association was identified between the East Asian Beijing sub-lineage and the relative risk of an isolate being MDR. Over 75% of MDR-TB cases were confirmed in non-Irish born individuals and 7 MIRU-VNTR genotypes were identical to clusters in other European countries indicating cross-border spread of MDR-TB to Ireland. WGS data provided the first evidence in Ireland of in vivo microevolution of MTBC isolates from drug-susceptible to MDR, and from MDR to extensively-drug resistant (XDR). In addition, they found that the katG S315T isoniazid and rpoB S450L rifampicin resistance mutations were dominant across the different MTBC lineages. CONCLUSIONS: Our molecular epidemiological analyses identified the spread of MDR-TB to Ireland from other jurisdictions and its potential to evolve to XDR-TB.

Monte Carlo simulation and patient dosimetry for a kilovoltage cone-beam CT unit.

PURPOSE: The purpose of this work is to characterize the x-ray volume imager (XVI), the cone-beam computed tomography (CBCT) unit mounted on the Elekta Synergy linac, with F1 bowtie filter and to calculate the three-dimensional dose delivered to patients using volumetric acquisition. METHODS: The XVI is modeled in detail using a new Monte Carlo (MC) code, BEAMPP, under development at the National Research Council Canada. In this investigation, a new component module is developed to accurately model the unit's bowtie filter used in conjunction with the available beam collimators at the clinical energy of 120 kV. The modeling is compared against percentage depth dose (PDD) and profile measurements. Kilovoltage radiation beams' phase space files are also analyzed. The authors also describe a method for the absolute dose calibration of the MC model of the CBCT unit when used in a clinical volumetric acquisition mode. Finally, they calculate three-dimensional patient dose from CBCT image acquisition in three clinical cases of interest: Pelvis, lung, and head and neck. RESULTS: The agreement between measurement and MC is shown to be very good: Within +/- 2% for the PDD and within +/- 3.5% inside the radiation field for all the collimators with the F1 bowtie filter. A full account of the absolute calibration method is given and dose calculation is validated against ion chamber measurements in different locations of a plastic phantom. Calculations and experiments agree within +/- 2% or better in both at the center and the periphery of the phantom, with worst agreement of 4.5% at the surface of the phantom and for one specific combination of collimator and filter. Patient dose from CBCT scan reveals that dose to tissue is between 2 and 2.5 cGy for a pelvis or a lung full acquisition. For H&N dose to tissue is 5 cGy, with the unit presets used in this work. Dose to bony structures can be two to three times higher than dose to tissue. CONCLUSIONS: The XVI CBCT unit has been fully modeled including the F1 bowtie filter. Absolute dose distribution from the unit has been successfully validated. Full MC patient dose calculation has shown that the three-dimensional dose distribution from CBCT is complex. Patient dose from CBCT exposure cannot be completely accounted for by using a numerical factor as an estimate of the dose at the center of the body. Furthermore, additional dose to bone should be taken into account when adopting any IGRT strategy and weighed vs the unquestionable benefits of the technique in order to optimize treatment. Full three-dimensional dose calculation is recommended if patient dose from CBCT is to be integrated in any adaptive planning strategy.

High-performance computing for Monte Carlo radiotherapy calculations.

We report on the RTGrid project, which investigates approaches for using high-performance computing infrastructures, such as the grid, in order to reduce the turnaround time of Monte Carlo (MC) simulation-based radiotherapy treatment planning. The main aim of this project is to render accurate dose calculations using MC simulations clinically feasible. To this end, we have successfully implemented and deployed the RTGrid distributed simulation framework for MC dose calculations. In this paper, we present the main experimental findings.

Simulating oblique incident irradiation using the BEAMnrc Monte Carlo code.

A new source for the simulation of oblique incident irradiation has been developed for the BEAMnrc Monte Carlo code. In this work, we describe a method for the simulation of any component that is rotated at some angle relative to the central axis of the modelled radiation unit. The performance of the new BEAMnrc source was validated against experimental measurements. The comparison with ion chamber data showed very good agreement between experiments and calculation for a number of oblique irradiation angles ranging from 0 degrees to 30 degrees . The routine was also cross-validated, in geometrically equivalent conditions, against a different radiation source available in the DOSXYZnrc code. The test showed excellent consistency between the two routines. The new radiation source can be particularly useful for the Monte Carlo simulation of radiation units in which the radiation beam is tilted with respect to the unit's central axis. To highlight this, a modern cone-beam CT unit is modelled using this new source and validated against measurement.

Putting it all together; dentistry and the Internet.

This last chapter in the series looks at how the Internet, 'warts and all', can be used in the practice setting. The web in particular has changed dramatically in the last three or four years, and the phrase 'Web 2.0' was coined to reflect this perceived change in the way that the web was being used. Web-based communities, social networking, the transition of websites from mere information pages to real software applications and the expansion in broadband access have all been important factors in this 'improved' WWW. Has dentistry been able to keep up with this pace of change and are dentists willing to embrace what the Internet has to offer?

Safe and efficient use of the Internet.

A minority of people abuse the freedom of the Internet to the detriment of the vast majority. Many people feel that the Internet requires more regulation to reduce the burden of hackers, viruses, hoaxes, adverts and spam that continue to proliferate unabated. Until this ever happens, it is down to the individual person or business to protect themselves against malicious attacks and to use the Internet in a safe and efficient manner.

Power searching.

The true power and value of the World Wide Web only becomes apparent once a user has learnt how to quickly and effectively find the information that they are seeking. Until then, searching the Internet can be an arduous and fruitless task. Knowing which website to use to start the hunt and how to select the most appropriate search words are only half the story. The other half is interpreting the results and then critically evaluating the information found.

Creating a practice website.

A website is a window to the outside world. For a dental practice, it may be the first point of contact for a prospective new patient and will therefore provide them with their 'first impression'; this may be days or weeks before actually visiting the practice. This section considers the different ways of creating a dental practice website and lists some of the main dental website design companies. It also describes what factors make a successful website and offers advice on how to ensure that it complies with current regulations and recommendations.

Introduction to the world wide web.

The World Wide Web used to be nicknamed the 'World Wide Wait'. Now, thanks to high speed broadband connections, browsing the web has become a much more enjoyable and productive activity. Computers need to know where web pages are stored on the Internet, in just the same way as we need to know where someone lives in order to post them a letter. This section explains how the World Wide Web works and how web pages can be viewed using a web browser.

Effective use of email.

Email is a crucial communication tool and everyone who uses it should have a good understanding of the email program that they use to send and receive email. In some cases this will be built into their dental system software and for others it may be a web-based email account using the Internet Explorer web browser. In this section we look at the workings of the most popular stand-alone program, Outlook Express, and discuss good email practice for home and work.

Introduction to email.

Email is a computer based method of sending messages from one computer to another. From its humble beginnings 40 years, it has matured to become a crucial tool in utilising the power of the Internet. More people have access to email than to any other Internet application, and despite the problems with spam email and viruses, email remains popular because of its low cost, universality and ease of use. This section looks at the advantages of email over other methods of communication, how email works and other ways of communicating using the Internet.

Connecting to the internet.

There are many and varied ways of connecting to the Internet. For the vast majority of the Internet's existence, most people connected using the maddeningly slow click-and-wait experience of a dial-up connection. By June 2005, the number of the newer and faster broadband connections in the UK exceeded dial-up connections for the first time (approximately 1/3 broadband cable and 2/3 broadband ADSL). By the middle of 2006, 40% of households in the UK had a broadband connection, compared to just 28% in 2005. In the last quarter of 2006, the total number of broadband subscriptions in the UK had topped the 13 million mark (one subscriber may equate to multiple users sharing one connection). Mobile Internet access via mobile phones and other devices will mark the biggest change in the way that we access the Internet and is likely to have a profound effect on our everyday lives. In this section, we look at the various ways of connecting to the Internet and compare the features, benefits and costs of each.

An introduction to the Internet.

The aim of this multipart series is to show members of the dental team why the Internet is becoming an essential tool and to encourage colleagues to 'get online'. The various ways of connecting to the Internet are discussed, comparing the advantages and disadvantages of each. How to use email and browse the World Wide Web is covered in some detail. There are plenty of practical tips on how to use the Internet safely and efficiently. The amount of information available on the Internet is vast and the series gives practical illustrations on how to be successful in searching for relevant information. There is an introduction on how to create a practice website and the final part looks at how to put all these skills together to make the most use of the Internet in the practice of dentistry.

The prevention of 'dry socket' with topical metronidazole in general dental practice.

OBJECTIVE: The purpose of the study was to determine if the intra-alveolar application of topical metronidazole gel could reduce the incidence of alveolar osteitis (dry socket) following routine tooth extraction in molar and premolar extraction sites. DESIGN: This was a multicentre, double blind, randomised, placebo-controlled clinical trial. A total of 302 patients took part, of which 23 returned with alveolar osteitis. Of these, eight had received the metronidazole gel and 15 the placebo. SETTING: The study was carried out in three general dental practices by general dental practitioners working in England over the period 2000-2003. MAIN OUTCOME MEASURES: Following extraction of either a molar or premolar tooth, either a 25% metronidazole gel or KY Jelly was syringed gently into the socket. A painful post operative complication was recorded if either a dry socket was present or the patient returned with pain. RESULTS AND CONCLUSIONS: The difference in the incidence of alveolar osteitis between the placebo and the active gel groups was not significant and it was concluded that 25% topical metronidazole gel was not effective in reducing the incidence of alveolar osteitis. It was found that the incidence of alveolar osteitis reduced with increasing age and was more likely to occur in a patient with a previous history of the condition.

Successful web searching.

This section of the series introduces the topic of WWW search engines and directory sites; showing you how to find information using a search engine and a directory. It also covers other ways of searching for information on the internet.

E-mail: what is e-mail?

This third part of the series explains what e-mail is and why it is the most widely used service on the internet. The principles behind sending and receiving e-mail messages are described. Also the various uses of e-mail are discussed.