Using colocation to support human memory

The progress of health care in the western world has been marked by an increase in life expectancy. Advances in life expectancy have meant that more people are living with acute health problems, many of which are related to impairment of memory. This paper describes a pair of scenarios that use RFID to assist people who may suffer frommemory defects to extend their capability for independent living. We present our implementation of an RFID glove, describe its operation, and show how it enables the application scenarios

TRECVID 2004 experiments in Dublin City University

In this paper, we describe our experiments for TRECVID 2004 for the Search task. In the interactive search task, we developed two versions of a video search/browse system based on the Físchlár Digital Video System: one with text- and image-based searching (System A); the other with only image (System B). These two systems produced eight interactive runs. In addition we submitted ten fully automatic supplemental runs and two manual runs. A.1, Submitted Runs: • DCUTREC13a_{1,3,5,7} for System A, four interactive runs based on text and image evidence. • DCUTREC13b_{2,4,6,8} for System B, also four interactive runs based on image evidence alone. • DCUTV2004_9, a manual run based on filtering faces from an underlying text search engine for certain queries. • DCUTV2004_10, a manual run based on manually generated queries processed automatically. • DCU_AUTOLM{1,2,3,4,5,6,7}, seven fully automatic runs based on language models operating over ASR text transcripts and visual features. • DCUauto_{01,02,03}, three fully automatic runs based on exploring the benefits of multiple sources of text evidence and automatic query expansion. A.2, In the interactive experiment it was confirmed that text and image based retrieval outperforms an image-only system. In the fully automatic runs, DCUauto_{01,02,03}, it was found that integrating ASR, CC and OCR text into the text ranking outperforms using ASR text alone. Furthermore, applying automatic query expansion to the initial results of ASR, CC, OCR text further increases performance (MAP), though not at high rank positions. For the language model-based fully automatic runs, DCU_AUTOLM{1,2,3,4,5,6,7}, we found that interpolated language models perform marginally better than other tested language models and that combining image and textual (ASR) evidence was found to marginally increase performance (MAP) over textual models alone. For our two manual runs we found that employing a face filter disimproved MAP when compared to employing textual evidence alone and that manually generated textual queries improved MAP over fully automatic runs, though the improvement was marginal. A.3, Our conclusions from our fully automatic text based runs suggest that integrating ASR, CC and OCR text into the retrieval mechanism boost retrieval performance over ASR alone. In addition, a text-only Language Modelling approach such as DCU_AUTOLM1 will outperform our best conventional text search system. From our interactive runs we conclude that textual evidence is an important lever for locating relevant content quickly, but that image evidence, if used by experienced users can aid retrieval performance. A.4, We learned that incorporating multiple text sources improves over ASR alone and that an LM approach which integrates shot text, neighbouring shots and entire video contents provides even better retrieval performance. These findings will influence how we integrate textual evidence into future Video IR systems. It was also found that a system based on image evidence alone can perform reasonably and given good query images can aid retrieval performance

Evaluating the harmonisation potential of diverse cohort datasets

Data discovery, the ability to find datasets relevant to an analysis, increases scientific opportunity, improves rigour and accelerates activity. Rapid growth in the depth, breadth, quantity and availability of data provides unprecedented opportunities and challenges for data discovery. A potential tool for increasing the efficiency of data discovery, particularly across multiple datasets is data harmonisation.A set of 124 variables, identified as being of broad interest to neurodegeneration, were harmonised using the C-Surv data model. Harmonisation strategies used were simple calibration, algorithmic transformation and standardisation to the Z-distribution. Widely used data conventions, optimised for inclusiveness rather than aetiological precision, were used as harmonisation rules. The harmonisation scheme was applied to data from four diverse population cohorts.Of the 120 variables that were found in the datasets, correspondence between the harmonised data schema and cohort-specific data models was complete or close for 111 (93%). For the remainder, harmonisation was possible with a marginal a loss of granularity.Although harmonisation is not an exact science, sufficient comparability across datasets was achieved to enable data discovery with relatively little loss of informativeness. This provides a basis for further work extending harmonisation to a larger variable list, applying the harmonisation to further datasets, and incentivising the development of data discovery tools

Rapid identification of a Mycobacterium tuberculosis full genetic drug resistance profile through whole genome sequencing directly from sputum.

INTRODUCTION: Resistance to second-line tuberculosis drugs is common, but slow to diagnose with phenotypic drug sensitivity testing. Rapid molecular tests speed up diagnosis, but can only detect limited mutations. Whole genome sequencing (WGS) of culture isolates can generate a complete genetic drug resistance profile, but is delayed by the initial culture step. In the case presented here, successful WGS directly from sputum was achieved using targeted enrichment. CASE REPORT: A 29-year-old Nigerian woman was diagnosed with tuberculosis. Xpert MTB/RIF and Hain line probe assays identified rpoB and inhA mutations consistent with rifampicin and intermediate isoniazid resistance, and a further possible mutation conferring fluoroquinolone resistance. WGS directly from sputum identified a further inhA mutation consistent with high-level isoniazid resistance and confirmed the absence of fluoroquinolone resistance. Isoniazid was stopped, and the patient has completed 18 months of a fluoroquinolone-based regimen without relapse. DISCUSSION: Compared to rapid molecular tests (which can only examine a limited number of mutations) and WGS of culture isolates (which requires a culture step), WGS directly from sputum can quickly generate a complete genetic drug resistance profile. In this case, WGS altered the clinical management of drug-resistant tuberculosis and demonstrated potential for guiding individualized drug treatment where second-line drug resistance is common

CREATE Research Symposium 2022 Book of Abstracts

This is the book of Abstracts for a recent symposium held by the CREATE research Group in TU Dublin

Raman analysis of a shocked planetary surface analogue: Implications for habitability on Mars

The scientific aims of the ExoMars Raman laser spectrometer (RLS) include identifying biological signatures and evidence of mineralogical processes associated with life. The RLS instrument was optimised to identify carbonaceous material, including reduced carbon. Previous studies suggest that reduced carbon on the Martian surface (perhaps originating from past meteoric bombardment) could provide a feedstock for microbial life. Therefore, its origin, form, and thermal history could greatly inform our understanding of Mars' past habitability. Here, we report on the Raman analysis of a Nakhla meteorite analogue (containing carbonaceous material) that was subjected to shock through projectile impact to simulate the effect of meteorite impact. The characterisation was performed using the RLS Simulator, in an equivalent manner to that planned for ExoMars operations. The spectra obtained verify that the flight-representative system can detect reduced carbon in the basaltic sample, discerning between materials that have experienced different levels of thermal processing due to impact shock levels. Furthermore, carbon signatures acquired from the cratered material show an increase in molecular disorder (and we note that this effect will be more evident at higher levels of thermal maturity). This is likely to result from intense shearing forces, suggesting that shock forces within basaltic material may produce more reactive carbon. This result has implications for potential (past) Martian habitability because impacted, reduced carbon may become more biologically accessible. The data presented suggest the RLS instrument will be able to characterise the contribution of impact shock within the landing site region, enhancing our ability to assess habitability

Application of the hollow fibre infection model (HFIM) in antimicrobial development: a systematic review and recommendations of reporting

Item does not contain fulltextOBJECTIVES: This systematic review focuses on the use of the in vitro hollow fibre infection model (HFIM) for microbial culture. We summarize the direction of the field to date and propose best-practice principles for reporting of the applications. METHODS: Searches in six databases (MEDLINE®, EMBASE®, PubMed®, BIOSIS®, SCOPUS® and Cochrane®) up to January 2020 identified 129 studies meeting our inclusion criteria. Two reviewers independently assessed and extracted data from each publication. The quality of reporting of microbiological and technical parameters was analysed. RESULTS: Forty-seven out of 129 (36.4%) studies did not report the minimum pharmacokinetic parameters required in order to replicate the pharmacokinetic profile of HFIM experiments. Fifty-three out of 129 (41.1%) publications did not report the medium used in the HFIM. The overwhelming majority of publications did not perform any technical repeats [107/129 (82.9%)] or biological repeats [97/129 (75.2%)]. CONCLUSIONS: This review demonstrates that most publications provide insufficient data to allow for results to be evaluated, thus impairing the reproducibility of HFIM experiments. Therefore, there is a clear need for the development of laboratory standardization and improved reporting of HFIM experiments

A genome-wide association study identifies risk alleles in plasminogen and P4HA2 associated with giant cell arteritis

Giant cell arteritis (GCA) is the most common form of vasculitis in individuals older than 50 years in Western countries. To shed light onto the genetic background influencing susceptibility for GCA, we performed a genome-wide association screening in a well-powered study cohort. After imputation, 1,844,133 genetic variants were analysed in 2,134 cases and 9,125 unaffected controls from ten independent populations of European ancestry. Our data confirmed HLA class II as the strongest associated region (independent signals: rs9268905, P = 1.94E-54, per-allele OR = 1.79; and rs9275592, P = 1.14E-40, OR = 2.08). Additionally, PLG and P4HA2 were identified as GCA risk genes at the genome-wide level of significance (rs4252134, P = 1.23E-10, OR = 1.28; and rs128738, P = 4.60E-09, OR = 1.32, respectively). Interestingly, we observed that the association peaks overlapped with different regulatory elements related to cell types and tissues involved in the pathophysiology of GCA. PLG and P4HA2 are involved in vascular remodelling and angiogenesis, suggesting a high relevance of these processes for the pathogenic mechanisms underlying this type of vasculitis

BHPR research: qualitative1. Complex reasoning determines patients' perception of outcome following foot surgery in rheumatoid arhtritis

Background: Foot surgery is common in patients with RA but research into surgical outcomes is limited and conceptually flawed as current outcome measures lack face validity: to date no one has asked patients what is important to them. This study aimed to determine which factors are important to patients when evaluating the success of foot surgery in RA Methods: Semi structured interviews of RA patients who had undergone foot surgery were conducted and transcribed verbatim. Thematic analysis of interviews was conducted to explore issues that were important to patients. Results: 11 RA patients (9 ♂, mean age 59, dis dur = 22yrs, mean of 3 yrs post op) with mixed experiences of foot surgery were interviewed. Patients interpreted outcome in respect to a multitude of factors, frequently positive change in one aspect contrasted with negative opinions about another. Overall, four major themes emerged. Function: Functional ability & participation in valued activities were very important to patients. Walking ability was a key concern but patients interpreted levels of activity in light of other aspects of their disease, reflecting on change in functional ability more than overall level. Positive feelings of improved mobility were often moderated by negative self perception ("I mean, I still walk like a waddling duck”). Appearance: Appearance was important to almost all patients but perhaps the most complex theme of all. Physical appearance, foot shape, and footwear were closely interlinked, yet patients saw these as distinct separate concepts. Patients need to legitimize these feelings was clear and they frequently entered into a defensive repertoire ("it's not cosmetic surgery; it's something that's more important than that, you know?”). Clinician opinion: Surgeons' post operative evaluation of the procedure was very influential. The impact of this appraisal continued to affect patients' lasting impression irrespective of how the outcome compared to their initial goals ("when he'd done it ... he said that hasn't worked as good as he'd wanted to ... but the pain has gone”). Pain: Whilst pain was important to almost all patients, it appeared to be less important than the other themes. Pain was predominately raised when it influenced other themes, such as function; many still felt the need to legitimize their foot pain in order for health professionals to take it seriously ("in the end I went to my GP because it had happened a few times and I went to an orthopaedic surgeon who was quite dismissive of it, it was like what are you complaining about”). Conclusions: Patients interpret the outcome of foot surgery using a multitude of interrelated factors, particularly functional ability, appearance and surgeons' appraisal of the procedure. While pain was often noted, this appeared less important than other factors in the overall outcome of the surgery. Future research into foot surgery should incorporate the complexity of how patients determine their outcome Disclosure statement: All authors have declared no conflicts of interes