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Thompson D. Carrier, Neil & TabeaScharrer (eds). Mobile urbanity: Somali presence in urban East Africa. xii, 252 pp., maps, illus., bibliogrs. Oxford, New York: Berghahn Books, 2019. £99.00 (cloth). JOURNAL OF THE ROYAL ANTHROPOLOGICAL INSTITUTE 2022. [DOI: 10.1111/1467-9655.13683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Phen HM, Godfrey WS, Edwards K, Thompson D, Bradbury TL. Use of a threaded-coupled femoral extraction device allows for higher extraction force when compared to loop or vice grip devices; A potted stem analysis. J Clin Orthop Trauma 2022; 26:101789. [PMID: 35211376 PMCID: PMC8844747 DOI: 10.1016/j.jcot.2022.101789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 01/24/2022] [Accepted: 01/30/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Extraction of a well-fixed femoral stem during revision total hip arthroplasty presents a technical challenge to the operating surgeon. The option of several stem designs during implantation necessitates the availability of extraction tools to be utilised intra-operatively. This study aims to compare the amount of axial force generated from using a threaded-coupled extraction device, loop extraction device, and vice-grip universal extraction set on a potted total hip arthroplasty stem construct. METHODS A size 7 Stryker Accolade® II femoral stem (Stryker, Mahwah, NJ) was potted within a 5.20 cm inner diameter polyvinyl chloride pipe using a potting medium with tensile strength and lap shear of 1000psi. This construct was coupled to a material testing system whose force transducer was calibrated to a recording speed of 1000 frames per second. The extractors were coupled to the potted stem, and a force of 1.32 J was applied ten times sequentially to each construct. Force was recorded in Newtons. RESULTS The maximum average force for the threaded, loop, and Shukla extractors was 111.46 ± 1.77 N, 90.22 ± 0.87 N, and 64.70 ± 9.03 N (p < 0.01). Loss of coupling was not experienced with any extractor. CONCLUSION Within our study, the forces observed per constant load when utilising a threaded-coupled extraction device that attaches to the shoulder of the implant were significantly higher than those seen when using an extraction device that couples to the neck of the femoral stem.
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Thompson D, Zammit A, Yuen J, Hand C, Likeman M, Singleton W, Nelson R, Fellows G. Paediatric Cavernous Malformation of the Trigeminal Nerve: Case Report and Review of the Literature. Pediatr Neurosurg 2022; 57:207-212. [PMID: 35398849 DOI: 10.1159/000524522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 04/06/2022] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Intradural, extra-axial cerebral cavernous malformations (CCMs) are rare entities and are mostly reported in relation to the optic apparatus or the facial/vestibulocochlear complex. Cranial nerve CCMs tend to follow a clinically aggressive course, with a tendency to progressive neurological dysfunction following intra-lesional haemorrhage or less commonly due to the effects of subarachnoid haemorrhage. CASE PRESENTATION We report the first case of a trigeminal CCM presenting in a child with otalgia and left-sided headaches. The patient was initially managed with radiological surveillance but required surgical management following deterioration. We describe the successful treatment of the lesion with microsurgical resection. CONCLUSION A CCM should be considered in the differential diagnosis of mass lesions arising in the region of the trigeminal nerve. Surgical resection is recommended to prevent neurological deterioration and may result in significant symptomatic improvement.
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Graby J, Khavandi A, Thompson D, Downie P, Antoniades C, Rodrigues JCL. CT coronary angiography-guided cardiovascular risk screening in asymptomatic patients: is it time? Clin Radiol 2021; 76:801-811. [PMID: 34404515 DOI: 10.1016/j.crad.2021.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/13/2021] [Indexed: 12/14/2022]
Abstract
Cardiovascular disease (CVD) is the leading cause of death in the UK, whilst millions live with various forms of the disease. Coronary artery disease constitutes a significant portion of this morbidity and mortality, and is the leading cause of premature death. Increasing focus is thus being placed on the optimisation of CVD prevention, where risk screening plays a key role. Indeed, the decline in age-adjusted cardiovascular mortality achieved up to now has been largely attributed to primary preventative therapies (e.g., statins) introduced earlier in the disease process. National initiatives exist to improve cardiovascular health at a population level, but in its current form, CVD screening at the individual level is predominantly undertaken using multivariate risk scores based on population-based data. These have multiple innate flaws, highlighted in this review. Non-invasive imaging plays a key role in the screening of other disease processes, helping to personalise the screening process. Although the coronary artery calcium score as a screening tool has a role in national and international guidance, whether a shift to screening with computed tomography coronary angiography (CTCA) is now appropriate is open for discussion. Image acquisition techniques continue to improve with reducing radiation exposure and an ever-expanding evidence-base for additional prognostic data offered by CTCA. This enables the potential identification of sub-clinical atherosclerosis, including with novel artificial intelligence techniques. This review aims to report current guidelines regarding cardiac CT imaging in the asymptomatic primary prevention setting, advances in various CT technologies and future opportunities for progress in this field.
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Cann AA, Weber RR, Harden LA, Thompson D, Nadolski J, Mattes J, Karwowska A, Shahjahan S, Milanovich JR. Physiological Health and Survival of Captive-Reared and Released Juvenile Blanding's Turtles. Physiol Biochem Zool 2021; 94:411-428. [PMID: 34569914 DOI: 10.1086/716832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractConservation translocations are important in maintaining viable wildlife populations of vulnerable species within their indigenous ranges. To be effective, population restoration efforts (e.g., head start programs) must consider the species' life history, regional ecology, and physiology and the health status of wild and translocated populations. The decline of Blanding's turtles (Emydoidea blandingii) has prompted the initiation of head start programs, but the health and short-term survival of head-started juveniles released to the wild is largely unknown. From May to October 2016 and 2017, we radio tracked captive-reared, recently released juvenile Blanding's turtles and monitored their survivorship and monthly physiological health. We aimed to (1) compare physiological metrics of juveniles before and after release from captivity and between head-started cohorts, (2) identify seasonal trends in physiological metrics of recently released juveniles, (3) compare physiological metrics of recently released and formerly released juveniles, and (4) identify predictors of juvenile survivorship after release from captivity. Juvenile short-term survival was low compared with other studies. Most physiological metrics did not change after release from captivity, negating significant juvenile stress before or after release. Physiological metrics for recently released cohorts varied seasonally, suggesting that these juveniles were likely in good health. Some physiological metrics differed between recently released and formerly released juveniles, demonstrating a potential postrelease acclimatization period. Finally, no physiological metrics significantly predicted survival, but surviving juveniles had a higher percentage of fat. In all, juvenile deaths were not due to poor turtle health but rather to predation from human-subsidized mesocarnivores. Therefore, head-started juvenile Blanding's turtles released in suburban areas may benefit from antipredator training and mesocarnivore control at release sites.
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Palant A, Zippel-Schultz B, Ski CF, Brandts J, Eurlings C, Furtado Da Luz Brzychcyk E, Hill L, Dixon L, Fitzsimons D, Thompson D, Mueller-Wieland D, Schuett KA, Hoedemakers T, Brunner La-Rocca HP, Helms TM. Understanding needs and expectations of heart failure patients and their caregivers regarding digital health - the PASSION-HF project. Eur J Cardiovasc Nurs 2021. [DOI: 10.1093/eurjcn/zvab060.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Funding Acknowledgements
Type of funding sources: Public grant(s) – EU funding. Main funding source(s): INTERREG-NWE
Background/Introduction
Current heart failure (HF) healthcare provision is not sufficient. Due to demographic changes and subsequent increases in comorbidities, along with unequal distribution of medical care in rural areas, alternative approaches need be sought. The use of eHealth applications has potential to enable patients to become more self-sufficient. The "PASSION-HF" project aims to develop an interactive decision-making system – a virtual doctor – that provides solutions based on current guidelines and artificial intelligence. Patient independence is maximized through 24/7 access to personalized HF-management. Furthermore, the application defines decision points, where medical professionals need to be included.
Purpose
To understand needs and expectations of HF patients and their informal caregivers in regard to a virtual doctor.
Methods
We conducted an exploratory mixed-methods study within the Netherlands, UK, Ireland and Germany. Semi-structured qualitative interviews were supplemented by a standardized questionnaire. The interviews focused on i) acceptance and motivation to use a virtual doctor and ii) experience and perception of current health care provision. The interviews were analysed using the content analysis according to Mayring (2010) with the help of "ATLAS.TI" software. Additional information about the role of informal caregivers, technology acceptance and decision-making processes was collected via questionnaires.
Results
A total of 49 patients and 33 informal caregivers were interviewed. Most patients were male (76%), aged between 60 and 69 years (43%). Three key themes were identified in regard to an interactive decision-making system: 1) Reassurance, because patients felt uncertain about their condition and their symptoms, they had a strong desire for an application that could monitor their health 24/7, was able to spot deteriorations, before they occured and gave them instant feedback about their current health status; 2) Personalized advice, e.g. patients wanted the virtual doctor to adapt medication, sport activities and food recommendations to their current health status; and 3) Transparency, e.g. patients wanted to know, where the recommendations are coming from and justifications for management modifications. Interview findings also identified that the HF-nurses play a significant role in the care and management of the condition. Across all countries with HF-nurses, they were the primary point of contact, when patients had any HF related concerns.
Conclusion
The findings provide valuable information for the development and implementation of eHealth solutions. Patients want reassurance, independently of the availability of healthcare services, combined with personalized advice regarding day-to-day management of their HF. For the next step, we are planning a multicentre clinical trial to test the prototype of the application. Here all decisions are examined by a clinical committee and benefits are evaluated.
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Jagun O, Banerjee P, Thompson D, Taylor M. The Skin of Colour Training Day UK: training the medical workforce in ethnic dermatology. Clin Exp Dermatol 2021; 47:245-246. [PMID: 34115898 DOI: 10.1111/ced.14800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/01/2022]
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Gravas S, Palacios J, Thompson D, Concas F, Kamola P, Roehrborn C, Oelke M, Kattan M, Averbeck M, Manyak M, Lulic Z. A new risk calculator to predict changes in IPSS score and risk of AUR / BPH-related surgery in BPH patients with moderate-severe symptoms at risk of disease progression receiving placebo, dutasteride, tamsulosin, or combination therapy. Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)00430-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Nelson K, Thompson D, Hopkinson C, Petrone R, Chasmer L. Peatland-fire interactions: A review of wildland fire feedbacks and interactions in Canadian boreal peatlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:145212. [PMID: 33486170 DOI: 10.1016/j.scitotenv.2021.145212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Boreal peatlands store a disproportionately large quantity of soil carbon (C) and play a critical role within the global C-climate system; however, with climatic warming, these C stores are at risk. Increased wildfire frequency and severity are expected to increase C loss from boreal peatlands, contributing to a shift from C sink to source. Here, we provide a comprehensive review of pre- and post-fire hydrological and ecological interactions that affect the likelihood of peatland burning, address the connections between peatland fires and the C-climate cycle, and provide a conceptual model of peatland processes as they relate to wildland fire, hydro-climate, and ecosystem change. Despite negative ecohydrological feedback mechanisms that may compensate for increased C loss initially, the cumulative effects of climatic warming, anthropogenic peatland fragmentation, and subsequent peatland drying will increase C loss to the atmosphere, driving a positive C feedback cycle. However, the extent to which negative and positive feedbacks will compensate for one another and the timelines for each remains unclear. We suggest that a multi-disciplinary approach of combining process knowledge with remotely sensed data and ecohydrological and wildland fire models is essential for better understanding the role of boreal peatlands and wildland fire in the global climate system.
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Thompson D. Utilization of the iOS Shortcuts App to Generate a Surgical Logbook Tool: Feasibility Study. JMIR Perioper Med 2021; 4:e24644. [PMID: 33983132 PMCID: PMC8160782 DOI: 10.2196/24644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/04/2021] [Accepted: 04/17/2021] [Indexed: 11/24/2022] Open
Abstract
Background Surgical audit is an essential aspect of modern reflective surgical practice and is key to improving surgical outcomes. The surgical logbook is an important method of data collection for both personal and unit audits; however, current electronic data collection tools, especially mobile apps, lack the minimum recommended data fields. Objective This feasibility study details the creation of a free, effective surgical logbook tool with the iOS Shortcuts app and investigates the time investment required to maintain a surgical logbook with this tool. In addition, we investigate the potential utility of the Shortcuts app in creating medical data collection tools. Methods Using the iOS Shortcuts app, we created a shortcut “Operation Note,” which collects surgical logbook data by using the minimum and extended audit data sets recommended by the Royal Australasian College of Surgeons. We practically assessed the feasibility of the tool, assessing the time requirement for entry, accuracy, and completeness of the entered data. Results The shortcut collected accurate and useful data for a surgical audit. Data entry took on average 65 seconds per case for the minimum data set, and 135 seconds per case for the extended data set, with a mean difference of 68 seconds (P<.001; 95% CI 61.6-77.7). Conclusions This feasibility study demonstrates the utility of the iOS Shortcuts app in the creation of a surgical logbook and the time-consuming nature of data collection for surgical audit. Our iOS Operation Note shortcut is a free, rapid, and customizable alternative to currently available logbook apps and offers surgical trainees and consultants a method for recording surgical operations, complications, and demographic data.
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Jacobs J, Li Q, Cheng Z, O'Brien K, Thompson D, Uitto J, Sabbagh Y. 167 INZ-701 prevents ectopic mineralization in an Abcc6 mouse model of pseudoxanthoma elasticum. J Invest Dermatol 2021. [DOI: 10.1016/j.jid.2021.02.187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Moore DC, Thompson D. A Review of the Bruton Tyrosine Kinase Inhibitors in B-Cell Malignancies. J Adv Pract Oncol 2021; 12:439-447. [PMID: 34123480 PMCID: PMC8163255 DOI: 10.6004/jadpro.2021.12.4.8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The B-cell receptor signaling pathway plays an integral role in the proliferation and survival of malignant B cells. Targeting the B-cell receptor pathway via the inhibition of Bruton tyrosine kinase (BTK) has evolved the treatment of a variety of B-cell malignancies, including chronic lymphocytic leukemia, mantle cell lymphoma, marginal zone lymphoma, and Waldenström macroglobulinemia. Currently, there are three BTK inhibitors approved by the U.S. Food and Drug Administration: ibrutinib, acalabrutinib, and zanubrutinib. This article reviews the pharmacology, clinical efficacy, safety, dosing, drug-drug interactions, and implications for advanced practitioners of BTK inhibitors in the treatment of B-cell malignancies.
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Hope TA, Graves CE, Calais J, Ehman E, Johnson GB, Thompson D, Aslam M, Duh QY, Gosnell J, Shen W, Roman S, Sosa JA, Kluijfhout W, Seib CS, Villanueva-Meyer J, Pampaloni MH, Suh I. Accuracy of 18F-fluorocholine PET for the detection of parathyroid adenomas: prospective single center study. J Nucl Med 2021; 62:1511-1516. [PMID: 33674400 DOI: 10.2967/jnumed.120.256735] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/03/2021] [Indexed: 11/16/2022] Open
Abstract
Purpose: The purpose of this prospective study was to determine the correct localization rate (CLR) of 18F-fluorocholine (FCH) positron emission tomography (PET) for the detection of parathyroid adenomas in comparison to sestamibi imaging. Materials and Methods: This was a single-arm prospective trial. Ninety-eight patients with biochemical evidence of primary hyperparathyroidism were imaged prior to parathyroidectomy using FCH PET/MRI. Sestamibi imaging performed separately from the study was evaluated for comparison. The primary endpoint of the study was the CLR on a patient level. Each imaging study was interpreted by 3 blinded readers on a per-region basis. Lesions were validated by histopathologic analysis of surgical specimens. Results: Of the 98 patients who underwent FCH imaging, 77 subsequently underwent parathyroidectomy and 60 of those had sestamibi imaging. The CLR for FCH in patients who underwent parathyroidectomy based on the blinded reader consensus was 75% [0.63, 0.82]. In patients who underwent surgery and had an available sestamibi study, the CLR increased from 17% [0.10, 0.27] for sestamibi to 70% [0.59, 0.79] for FCH PET. Conclusion: In this prospective study using blinded readers, the CLR for FCH was 75%. In patients with paired sestamibi, the use of FCH PET increased the CLR from 17% to 70%. FCH PET is a superior imaging modality for the localization of parathyroid adenomas.
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Kunpalin Y, Richter J, Mufti N, Bosteels J, Ourselin S, De Coppi P, Thompson D, David AL, Deprest J. Cranial findings detected by second-trimester ultrasound in fetuses with myelomeningocele: a systematic review. BJOG 2021; 128:366-374. [PMID: 32926566 PMCID: PMC8436766 DOI: 10.1111/1471-0528.16496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2020] [Indexed: 12/14/2022]
Abstract
Background Abnormal intracranial findings are often detected at mid‐trimester ultrasound (US) in fetuses with myelomeningocele (MMC). It is unclear whether these findings constitute a spectrum of the disease or are an independent finding, which should contraindicate fetal surgery. Objective To ascertain the spectrum and frequency of US‐detected cranial findings in fetuses with MMC. Search strategy MEDLINE, Embase, Web of Science and CENTRAL were searched from January 2000 to June 2020. Selection criteria Study reporting incidence of cranial US findings in consecutive cases of second‐trimester fetuses with MMC. Data collection and analysis Publication quality was assessed by Newcastle–Ottawa Scale (NOS) and modified NOS. Meta‐analysis could not be performed as a result of high clinical diversity and study heterogeneity. Main results Fourteen cranial US findings were reported in 15 studies. Findings in classic Chiari II malformation (CIIM) spectrum included posterior fossa funnelling (96%), small transcerebellar diameter (82–96%), ‘banana’ sign (50–100%), beaked tectum (65%) and ‘lemon’ sign (53–100%). Additional cranial findings were small biparietal diameter (BPD) and head circumference (HC) (<5th centile; 53 and 71%, respectively), ventriculomegaly (45–89%), abnormal pointed shape of the occipital horn (77–78%), thinning of the posterior cerebrum, perinodular heterotopia (11%), abnormal gyration (3%), corpus callosum disorders (60%) and midline interhemispheric cyst (42%). Conclusions We identified 14 cranial findings by second‐trimester US in fetuses with MMC. The relatively high incidence of these findings and their unclear prognostic significance might not contraindicate fetal surgery in the case of normal fetal genetic testing. Some cranial findings may independently affect postnatal outcome, however. Long‐term detailed follow‐up is required to investigate this. Tweetable abstract A high rate of cranial abnormalities found on second‐trimester ultrasound in fetuses with myelomeningocele. A high rate of cranial abnormalities found on second‐trimester ultrasound in fetuses with myelomeningocele.
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Thompson D, Perry LA, Renouf J, Vodanovich D, Hong Lee AH, Dimiri J, Wright G. Prognostic utility of inflammation-based biomarkers, neutrophil-lymphocyte ratio and change in neutrophil-lymphocyte ratio, in surgically resected lung cancers. Ann Thorac Med 2021; 16:148-155. [PMID: 34012481 PMCID: PMC8109682 DOI: 10.4103/atm.atm_382_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND/OBJECTIVE: Given the poor overall survival (OR) and progression-free survival (PFS) rates for lung cancers managed with surgical resection, there is a need to identify the prognostic markers that would improve the risk stratification of patients with operable lung cancer to inform treatment decisions. We investigate the prognostic utility of two established inflammation-based scores, the neutrophil–lymphocyte ratio (NLR) and the change in neutrophil–lymphocyte ratio (ΔNLR), throughout the operative period in a prospective cohort of patients with lung cancer who underwent surgical resection. METHODS: Demographic, clinical, and treatment details for 345 patients with lung cancer who underwent surgical resection between 2000 and 2019 at multiple centers across Melbourne, Victoria (Australia), were prospectively collected. Preoperative NLR and ΔNLR were calculated after which Cox univariate and multivariate analyses were conducted for OS and PFS against the known prognostic factors. RESULTS: Both univariate and multivariate analyses showed that preoperative NLR >4.54, as well as day 1 and day 2 postoperative NLR (P < 0.01), was associated with increased risk for postoperative mortality (hazard ratio 1.8; P < 0.01) and PFS (P < 0.05), whereas ΔNLR was not a significant predictor of OS or PFS. CONCLUSION: Elevated NLR among patients with lung cancer who underwent surgical resection was prognostic for poor OS and PFS, whereas ΔNLR was not found to be prognostic for either OS or PFS. Further research may yet reveal a prognostic value for ΔNLR when compared across a greater time period.
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Haubold B, Klötzl F, Hellberg L, Thompson D, Cavalar M. Fur: Find Unique Genomic Regions for Diagnostic PCR. Bioinformatics 2021; 37:2081-2087. [PMID: 33515232 PMCID: PMC8352509 DOI: 10.1093/bioinformatics/btab059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/04/2020] [Accepted: 01/26/2021] [Indexed: 11/12/2022] Open
Abstract
Motivation Unique marker sequences are highly sought after in molecular diagnostics. Nevertheless, there are only few programs available to search for marker sequences, compared to the many programs for similarity search. We therefore wrote the program Fur for Finding Unique genomic Regions. Results Fur takes as input a sample of target sequences and a sample of closely related neighbors. It returns the regions present in all targets and absent from all neighbors. The recently published program genmap can also be used for this purpose and we compared it to fur. When analyzing a sample of 33 genomes representing the major phylogroups of E.coli, fur was 40 times faster than genmap but used three times more memory. On the other hand, genmap yielded three times more markers, but they were less accurate when tested in silico on a sample of 237 E.coli genomes. We also designed phylogroup-specific PCR primers based on the markers proposed by genmap and fur, and tested them by analyzing their virtual amplicons in GenBank. Finally, we used fur to design primers specific to a Lactobacillus species, and found excellent sensitivity and specificity in vitro. Availability and implementation Fur sources and documentation are available from https://github.com/evolbioinf/fur. The compiled software is posted as a docker container at https://hub.docker.com/r/haubold/fox. Supplementary information Supplementary data are available at Bioinformatics online.
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Rodgers SE, Rowney F, Thompson D, Mizen A, White M, Lovell R, Fry R, Watkins A, Wheeler B, Akbari A, Stratton G, Lyons R, White R, Nieuwenhuijsen M, Geary R, Rodgers S. Is Wellbeing Associated with Time Spent in Nature? Int J Popul Data Sci 2020. [DOI: 10.23889/ijpds.v5i5.1619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
IntroductionGreen and blue spaces (GBS), such as parks, woodlands, rivers, and beaches, are thought to be important for mental health and wellbeing. Our longitudinal cohort contains objective household-level environment data linked at the invidual level to routinely recorded mental health data, augmented with cross sectional self-reported health behaviours, including leisure visits to the outdoors.
Objectives and ApproachOur overall approach will evaluate if residential proximity to GBS is associated with mental health and wellbeing, and if any associations aremodified by visits to outdoors spaces following individual-level data linkage. Here, we examined cross-sectional survey data on time spent visiting nature outdoors. Wellbeing outcomes were assessed using self-reported scores. Data were analysed using generalised additive models in the SAIL Databank.
ResultsUsing a sample of National Survey for Wales respondents (2016/17, n=3,481), over 40% of adults in Wales reported spending less than 30 minutes outdoors each week. Weekly time outdoors was positively associated with wellbeing (p=0.007) and life satisfaction (p=0.03) having adjusted for potential confounders including, age, rurality, loneliness, employment status. Confidence intervals varied along the fitted GAM model. Models using a second wave of survey data (n≈7,000), anonymously record-linked to residential environment and health data will explore these associations further.
ConclusionA previous study based in England (White et al. 2019) found an upper wellbeing benefit threshold of 2 hours per week for time spent in nature. This was not apparent in our preliminary models, but may be revealed in further analyses. We will next incorporate longitudinal mental health and environmental data for 2 million adults living in Wales, UK. Linking to ambient and accessible residential GBS, while taking into account changes due to migration and actual visits, will allow us to provide valuable guidance to local government, who are often responsible for provisioning and maintaining outdoor facilities.
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Thompson D, John A, Fry R, Watkins A. Self-Reported Well-Being Indicators and Case Identification of Common Mental Health Disorders in Routinely Collected Health Data. Int J Popul Data Sci 2020. [DOI: 10.23889/ijpds.v5i5.1618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
IntroductionCommon mental health disorders (CMD) are significant contributors to impaired health and well-being, and drive greater health resource utilisation. Electronic health records (EHR) are increasingly used for case identification of CMD when ascertaining social determinants of mental health. We seek to compare self-reported well-being indicators in groups identified using EHR-based CMD methods.
Objectives and ApproachThe National Survey for Wales (NSW) contains self-reported well-being indicators (Warwick Edinburgh Mental Well-being Scale, WEMWBS) recorded annually on ~7,000 individuals. We combined data from two NSWs and linked well-being indicators with Welsh Longitudinal General Practice (WLGP) data within the Secure Anonymised Information Linkage (SAIL) Databank, using individual response dates. We then used WGLP data to algorithmically derive identifiers of CMD cases within survey respondents. This individual-level linkage enables a comparison of NSW responses in CMD and non-CMD cases, and to assess sensitivity and specificity of the current CMD algorithm.
ResultsSurvey participants comprised 18,450 adults aged 16+ and living in Wales during 16/17 or 18/19. WEMWBS responses indicate 2,338 (12.6%) participants could be considered possibly depressed, and 2,268 (12.3%) probably depressed with low mental well-being (LMW). For participants with LMW, a 42/58 percentage split is observed between male/female respondents, compared to a 45/55 respective split of those not identified with LMW. Participants with LMW recorded low measures for overall satisfaction with life, 998 (44%) reported a value of 5 or less (/10) compared to 1123 (7%) participants not identified with LMW. Similarly, 828 (37%) participants identified with LMW reported 5 or less (/10) on the life worthwhile index, compared to 800 (5%) of non-LMW participants.
Conclusion / ImplicationsLinkage to the NSW provides a rich data source to compare objective well-being to algorithmically derived CMD cases from routinely collected primary care data. The individual-level linkage involved will allow for the wider determinants of mental health disorders to be examined.
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Lyons J, Akbari A, Torabi F, Davies GI, North L, Griffiths R, Bailey R, Hollinghurst J, Fry R, Turner SL, Thompson D, Rafferty J, Mizen A, Orton C, Thompson S, Au-Yeung L, Cross L, Gravenor MB, Brophy S, Lucini B, John A, Szakmany T, Davies J, Davies C, Thomas DR, Williams C, Emmerson C, Cottrell S, Connor TR, Taylor C, Pugh RJ, Diggle P, John G, Scourfield S, Hunt J, Cunningham AM, Helliwell K, Lyons R. Understanding and responding to COVID-19 in Wales: protocol for a privacy-protecting data platform for enhanced epidemiology and evaluation of interventions. BMJ Open 2020; 10:e043010. [PMID: 33087383 PMCID: PMC7580065 DOI: 10.1136/bmjopen-2020-043010] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
INTRODUCTION The emergence of the novel respiratory SARS-CoV-2 and subsequent COVID-19 pandemic have required rapid assimilation of population-level data to understand and control the spread of infection in the general and vulnerable populations. Rapid analyses are needed to inform policy development and target interventions to at-risk groups to prevent serious health outcomes. We aim to provide an accessible research platform to determine demographic, socioeconomic and clinical risk factors for infection, morbidity and mortality of COVID-19, to measure the impact of COVID-19 on healthcare utilisation and long-term health, and to enable the evaluation of natural experiments of policy interventions. METHODS AND ANALYSIS Two privacy-protecting population-level cohorts have been created and derived from multisourced demographic and healthcare data. The C20 cohort consists of 3.2 million people in Wales on the 1 January 2020 with follow-up until 31 May 2020. The complete cohort dataset will be updated monthly with some individual datasets available daily. The C16 cohort consists of 3 million people in Wales on the 1 January 2016 with follow-up to 31 December 2019. C16 is designed as a counterfactual cohort to provide contextual comparative population data on disease, health service utilisation and mortality. Study outcomes will: (a) characterise the epidemiology of COVID-19, (b) assess socioeconomic and demographic influences on infection and outcomes, (c) measure the impact of COVID-19 on short -term and longer-term population outcomes and (d) undertake studies on the transmission and spatial spread of infection. ETHICS AND DISSEMINATION The Secure Anonymised Information Linkage-independent Information Governance Review Panel has approved this study. The study findings will be presented to policy groups, public meetings, national and international conferences, and published in peer-reviewed journals.
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Callender C, Velazquez D, Dave J, Olvera N, Chen T, Goldsworthy N, Thompson D. Comprehensive Nutrition and Cooking Education Programming Recommendations from Families in Underserved Communities. J Acad Nutr Diet 2020. [DOI: 10.1016/j.jand.2020.06.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ledoux T, Cepni A, Taylor A, Crumbley C, Thompson D, Moran N, Olvera N, O'Connor D. Exploring Parent Feeding Practices, the Home Environment, and Toddler Diet. J Acad Nutr Diet 2020. [DOI: 10.1016/j.jand.2020.06.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Thompson D, Glowacki G, Ludwig D, Reklau R, Kuhns AR, Golba CK, King R. Benefits of Head‐starting for Blanding's Turtle Size Distributions and Recruitment. WILDLIFE SOC B 2020. [DOI: 10.1002/wsb.1054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Madan A, Thompson D, Fowler JC, Ajami NJ, Salas R, Frueh BC, Bradshaw MR, Weinstein BL, Oldham JM, Petrosino JF. The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness. J Affect Disord 2020; 264:98-106. [PMID: 32056780 DOI: 10.1016/j.jad.2019.12.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/09/2019] [Accepted: 12/13/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Emerging evidence implicates the gut microbiota in central nervous system functioning via its effects on inflammation, the hypothalamic-pituitary axis, and/or neurotransmission. Our understanding of the cellular underpinnings of the brain-gut relationship is based almost exclusively on animal models with some small-scale human studies. This study examined the relationship between the gut microbiota and psychiatric symptom severity and treatment response among inpatients with serious mental illness. METHOD We collected data from adult inpatients (N = 111). Measures of diagnoses, suicide severity, trauma, depression, and anxiety were collected shortly after admission, while self-collected fecal swabs were collected early in the course of hospitalization and processed using 16S rRNA gene sequencing and whole genome shotgun sequencing methods. RESULTS Results indicate that depression and anxiety severity shortly after admission were negatively associated with bacterial richness and alpha diversity. Additional analyses revealed a number of bacterial taxa associated with depression and anxiety severity. Gut microbiota richness and alpha diversity early in the course of hospitalization was a significant predictor of depression remission at discharge. CONCLUSIONS This study is among the first to demonstrate a gut microbiota relationship with symptom severity among psychiatric inpatients as well as a relationship to remission of depression post-treatment. These findings are consistent with animal models and limited human studies as well as with the broader literature implicating inflammation in the pathophysiology of depression. These findings offer the foundation for further studies of novel therapeutic approaches to the treatment, prevention of, or recurrence of serious mental illness.
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Khanna R, Fenton S, Cattran D, Thompson D, Deitel M, Oreopoulos D. Tuberculous Peritonitis in Patients Undergoing Continuous Ambulatory Peritoneal Dialysis (CAPD). Perit Dial Int 2020. [DOI: 10.1177/089686088000100302] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Thompson D, Albarki H, Lodhia C, Fitzpatrick N. A 3D printed smartphone adaptor for nasolaryngoscopy. Laryngoscope Investig Otolaryngol 2020; 5:31-36. [PMID: 32128428 PMCID: PMC7042649 DOI: 10.1002/lio2.355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/11/2020] [Accepted: 01/20/2020] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVE The objective of this project is to create a three-dimensional (3D) printed smartphone adaptor for flexible nasolaryngoscopy (FNL) to provide an affordable alternative to commercial options and a better fit than generic telescope phone adaptors. METHOD We designed an adaptor using computer aided software to connect an iPhone XS to an Olympus Rhino-Laryngo Fibre Scope. We experimented with various 3D printing materials and iterative designs to create a case that allowed for quality recording of a nasolaryngoscope exam using the iPhone's built in ×2 telescopic zoom lens. RESULTS Our 3D printed adaptor provides a cost-effective alternative to commercially available FNL smartphone adaptors and is capable of capturing high-quality images and videos of the nasopharynx and larynx. These images are useful for senior clinician review, decrease the need for repeat examination, can be utilized for education, avail telehealth review, and provides a way to digitally record examinations to electronic medical records for future comparison without the need for an endoscopy tower. CONCLUSION Smartphone adaptors for FNL have been established to be of clinical value. Despite being simple devices, they continue to be expensive. This potentially limits access to junior clinicians, who stand to gain most from the ability to review images of examinations with senior colleagues. Our 3D printed smartphone case provides a cost-effective alternative, with a better fit than generic adaptors, at a print cost of $29 AUD. This is $131 AUD less than the next cheapest commercial alternative. The files are freely available for use and modification. LEVEL OF EVIDENCE 4.
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