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Article ; Online: Addendum to British Society for Haematology Guideline for the management of mantle cell lymphoma, 2018 (Br. J. Haematol. 2018; 182: 46-62): Risk assessment of potential CAR T candidates receiving a covalent Bruton tyrosine kinase inhibitor for relapsed/refractory disease.

O'Reilly, Maeve A / Sanderson, Robin / Wilson, William / Iyengar, Sunil / Lambert, Jonathan / McCulloch, Rory / Eyre, Toby A

British journal of haematology

2022 Volume 199, Issue 1, Page(s) 40–44

MeSH term(s)	Adult ; Hematology ; Humans ; Lymphoma, Mantle-Cell/drug therapy ; Neoplasm Recurrence, Local ; Protein Kinase Inhibitors/adverse effects ; Receptors, Chimeric Antigen ; Risk Assessment
Chemical Substances	Protein Kinase Inhibitors ; Receptors, Chimeric Antigen
Language	English
Publishing date	2022-07-27
Publishing country	England
Document type	Journal Article
ZDB-ID	80077-6
ISSN	1365-2141 ; 0007-1048
ISSN (online)	1365-2141
ISSN	0007-1048
DOI	10.1111/bjh.18378
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Article ; Online: USE OF A STATEWIDE SOLID ORGAN INJURY PROCOTCOL TO OPTIMIZE TRIAGE, TREATMENT, AND TRANSFER FOR PEDIATRIC ABDOMINAL TRAUMA.

Swendiman, Robert A / Russell, Katie W / Larsen, Kezlyn / Eyre, Matthew / Fenton, Stephen J

The journal of trauma and acute care surgery

2024

Abstract: Background: The Utah Pediatric Trauma Network (UPTN) is a non-competitive collaboration of all 51 hospitals in the state of Utah with the purpose of improving pediatric trauma care. Created in 2019, UPTN has implemented evidence-based guidelines based ... ...

Abstract	Background: The Utah Pediatric Trauma Network (UPTN) is a non-competitive collaboration of all 51 hospitals in the state of Utah with the purpose of improving pediatric trauma care. Created in 2019, UPTN has implemented evidence-based guidelines based on hospital resources and capabilities with quarterly review of data collected in a network-specific database. A blunt solid organ injury (SOI) protocol was developed to optimize treatment of these injuries statewide. The purpose of this study was to review the effectiveness of the SOI guideline. Methods: The UPTN REDCap® database was retrospectively reviewed from 2021 through 2022. We compared admissions from the Level 1 pediatric trauma center (PED1) to non-pediatric hospitals (non-PED1) of children with low grade (I-II) and high grade (III-V) SOIs. Results: In 2 years, 172 patients were treated for blunt SOI, with or without concomitant injuries. There were 48 (28%) low grade and 124 (72%) high grade SOIs. 33 (69%) patients were triaged with low grade SOI injuries at a non-PED1 center, and 17 (35%) were transferred to the PED1 hospital. Most had multiple injuries, but 7 (44%) were isolated, and none required a transfusion or any procedure/operation at either hospital. Of the 124 patients with high grade injuries, 41 (33%) primarily presented to the PED1 center, and 44 (35%) were transferred there. Of these, 2 required a splenectomy and none required angiography. 39 children were treated at non-PED1 centers without transfer, and 4 required splenectomy and 6 underwent angiography/embolization procedures. No patient with an isolated SOI died. Conclusions: Implementation of SOI guidelines across UPTN successfully allowed non-pediatric hospitals to safely admit children with low grade isolated SOI, keeping families closer to home, while standardizing pediatric triage for blunt abdominal trauma in the state. Level of evidence: III - Retrospective study.
Language	English
Publishing date	2024-01-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2651070-4
ISSN	2163-0763 ; 2163-0755
ISSN (online)	2163-0763
ISSN	2163-0755
DOI	10.1097/TA.0000000000004261
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Zs.A 127: Show issues

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Article ; Online: Algorithmic fairness and bias mitigation for clinical machine learning with deep reinforcement learning.

Yang, Jenny / Soltan, Andrew A S / Eyre, David W / Clifton, David A

Nature machine intelligence

2023 Volume 5, Issue 8, Page(s) 884–894

Abstract: As models based on machine learning continue to be developed for healthcare applications, greater effort is needed to ensure that these technologies do not reflect or exacerbate any unwanted or discriminatory biases that may be present in the data. Here ... ...

Abstract	As models based on machine learning continue to be developed for healthcare applications, greater effort is needed to ensure that these technologies do not reflect or exacerbate any unwanted or discriminatory biases that may be present in the data. Here we introduce a reinforcement learning framework capable of mitigating biases that may have been acquired during data collection. In particular, we evaluated our model for the task of rapidly predicting COVID-19 for patients presenting to hospital emergency departments and aimed to mitigate any site (hospital)-specific and ethnicity-based biases present in the data. Using a specialized reward function and training procedure, we show that our method achieves clinically effective screening performances, while significantly improving outcome fairness compared with current benchmarks and state-of-the-art machine learning methods. We performed external validation across three independent hospitals, and additionally tested our method on a patient intensive care unit discharge status task, demonstrating model generalizability.
Language	English
Publishing date	2023-07-31
Publishing country	England
Document type	Journal Article
ISSN	2522-5839
ISSN (online)	2522-5839
DOI	10.1038/s42256-023-00697-3
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Article ; Online: Interpretable machine learning-based decision support for prediction of antibiotic resistance for complicated urinary tract infections.

Yang, Jenny / Eyre, David W / Lu, Lei / Clifton, David A

npj antimicrobials and resistance

2023 Volume 1, Issue 1, Page(s) 14

Abstract: Urinary tract infections are one of the most common bacterial infections worldwide; however, increasing antimicrobial resistance in bacterial pathogens is making it challenging for clinicians to correctly prescribe patients appropriate antibiotics. In ... ...

Abstract	Urinary tract infections are one of the most common bacterial infections worldwide; however, increasing antimicrobial resistance in bacterial pathogens is making it challenging for clinicians to correctly prescribe patients appropriate antibiotics. In this study, we present four interpretable machine learning-based decision support algorithms for predicting antimicrobial resistance. Using electronic health record data from a large cohort of patients diagnosed with potentially complicated UTIs, we demonstrate high predictability of antibiotic resistance across four antibiotics - nitrofurantoin, co-trimoxazole, ciprofloxacin, and levofloxacin. We additionally demonstrate the generalizability of our methods on a separate cohort of patients with uncomplicated UTIs, demonstrating that machine learning-driven approaches can help alleviate the potential of administering non-susceptible treatments, facilitate rapid effective clinical interventions, and enable personalized treatment suggestions. Additionally, these techniques present the benefit of providing model interpretability, explaining the basis for generated predictions.
Language	English
Publishing date	2023-11-02
Publishing country	England
Document type	Journal Article
ISSN	2731-8745
ISSN (online)	2731-8745
DOI	10.1038/s44259-023-00015-2
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Article ; Online: Patterns of selection in the evolution of a transposable element.

Dazenière, Julie / Bousios, Alexandros / Eyre-Walker, Adam

G3 (Bethesda, Md.)

2022 Volume 12, Issue 5

Abstract: Transposable elements are a major component of most eukaryotic genomes. Here, we present a new approach which allows us to study patterns of natural selection in the evolution of transposable elements over short time scales. The method uses the alignment ...

Abstract	Transposable elements are a major component of most eukaryotic genomes. Here, we present a new approach which allows us to study patterns of natural selection in the evolution of transposable elements over short time scales. The method uses the alignment of all elements with intact gag/pol genes of a transposable element family from a single genome. We predict that the ratio of nonsynonymous to synonymous variants in the alignment should decrease as a function of the frequency of the variants, because elements with nonsynonymous variants that reduce transposition will have fewer progeny. We apply our method to Sirevirus long-terminal repeat retrotransposons that are abundant in maize and other plant species and show that nonsynonymous to synonymous variants declines as variant frequency increases, indicating that negative selection is acting strongly on the Sirevirus genome. The asymptotic value of nonsynonymous to synonymous variants suggests that at least 85% of all nonsynonymous mutations in the transposable element reduce transposition. Crucially, these patterns in nonsynonymous to synonymous variants are only predicted to occur if the gene products from a particular transposable element insertion preferentially promote the transposition of the same insertion. Overall, by using large numbers of intact elements, this study sheds new light on the selective processes that act on transposable elements.
MeSH term(s)	DNA Transposable Elements/genetics ; Evolution, Molecular ; Retroelements/genetics ; Selection, Genetic ; Terminal Repeat Sequences/genetics ; Zea mays/genetics
Chemical Substances	DNA Transposable Elements ; Retroelements
Language	English
Publishing date	2022-03-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkac056
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Article ; Online: A Comparison of Markov and Mechanistic Models for Soil-Transmitted Helminth Prevalence Projections in the Context of Survey Design.

Eyre, Max T / Bulstra, Caroline A / Johnson, Olatunji / de Vlas, Sake J / Diggle, Peter J / Fronterrè, Claudio / Coffeng, Luc E

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2024 Volume 78, Issue Supplement_2, Page(s) S146–S152

Abstract: Globally, there are over 1 billion people infected with soil-transmitted helminths (STHs), mostly living in marginalized settings with inadequate sanitation in sub-Saharan Africa and Southeast Asia. The World Health Organization recommends an integrated ... ...

Abstract	Globally, there are over 1 billion people infected with soil-transmitted helminths (STHs), mostly living in marginalized settings with inadequate sanitation in sub-Saharan Africa and Southeast Asia. The World Health Organization recommends an integrated approach to STH morbidity control through improved access to sanitation and hygiene education and the delivery of preventive chemotherapy (PC) to school-age children delivered through schools. Progress of STH control programs is currently estimated using a baseline (pre-PC) school-based prevalence survey and then monitored using periodical school-based prevalence surveys, known as Impact Assessment Surveys (IAS). We investigated whether integrating geostatistical methods with a Markov model or a mechanistic transmission model for projecting prevalence forward in time from baseline can improve IAS design strategies. To do this, we applied these 2 methods to prevalence data collected in Kenya, before evaluating and comparing their performance in accurately informing optimal survey design for a range of IAS sampling designs. We found that, although both approaches performed well, the mechanistic method more accurately projected prevalence over time and provided more accurate information for guiding survey design. Both methods performed less well in areas with persistent STH hotspots where prevalence did not decrease despite multiple rounds of PC. Our findings show that these methods can be useful tools for more efficient and accurate targeting of PC. The general framework built in this paper can also be used for projecting prevalence and informing survey design for other neglected tropical diseases.
MeSH term(s)	Humans ; Helminthiasis/epidemiology ; Helminthiasis/transmission ; Prevalence ; Kenya/epidemiology ; Soil/parasitology ; Markov Chains ; Child ; Helminths/isolation & purification ; Animals ; Models, Statistical ; Adolescent ; Schools
Chemical Substances	Soil
Language	English
Publishing date	2024-04-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Comparative Study
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciae022
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Zs.A 1505: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 480: Show issues

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Article ; Online: Playing it safe: The relationship between parent attitudes to risk and injury, and children's adventurous play and physical activity.

Jerebine, Alethea / Mohebbi, Mohammadreza / Lander, Natalie / Eyre, Emma L J / Duncan, Michael J / Barnett, Lisa M

Psychology of sport and exercise

2023 Volume 70, Page(s) 102536

Abstract: Background: Children naturally seek risk in play and adventurous play outdoors confers many benefits, including the potential to increase moderate-to-vigorous physical activity (MVPA). This study aimed to investigate the relationship between parent ... ...

Abstract	Background: Children naturally seek risk in play and adventurous play outdoors confers many benefits, including the potential to increase moderate-to-vigorous physical activity (MVPA). This study aimed to investigate the relationship between parent attitudes to risk and injury, and their elementary school-aged child's daily adventurous play and MVPA. Methods: A panel sample of 645 Australian parents/guardians completed an online survey consisting of several validated measures of risk and injury attitudes, and physical activity and play behaviour. Data were analysed via descriptive statistics, univariate and multivariable regressions using Stata 17. A series of exploratory univariate logistic regressions were conducted, followed by a series of multivariable logistic regressions fitted to test the association between parent risk and injury attitudes and (i) children's MVPA, (ii) active play and (iii) adventurous play, while adjusting for socio-demographic factors. Results: Most adult participants (81%) were female. The mean age of the child participants (53% male) was 8.6 years (SD = 2.4). On average, parents were positive about children's engagement with risk, however, 78% of parents had low tolerance of risk when presented with specific play scenarios, and attitudes towards injuries varied, with mothers more concerned than fathers. After adjusting for confounders, children with parents who were tolerant of risk in play were more likely to meet the MVPA guideline of ≥60 min daily (OR 2.86, CI: 1.41, 5.82, p < 0.004) and spend more time playing adventurously (OR 3.03, CI: 1.82, 5.06, p < 0.001). Positive associations for MVPA and adventurous play were observed across all models examining parent attitudes to risk and injury. Younger children engaged in more play and physical activity, however, more positive parent attitudes appeared to moderate the age-related influences. Conclusions: We found a divergence between the outcomes parents desire for their children through engagement with risk and the play activities they are comfortable with in practice. Parent attitudes to risk and injury are potentially modifiable factors that may increase children's affordances for adventurous play and physical activity. Interventions that provide parents with practical approaches to address injury concerns and support children's risk-taking in play outdoors are recommended.
MeSH term(s)	Child ; Adult ; Humans ; Male ; Female ; Australia/epidemiology ; Exercise ; Parents ; Mothers ; Recreation
Language	English
Publishing date	2023-09-09
Publishing country	Netherlands
Document type	Journal Article
ISSN	1878-5476
ISSN (online)	1878-5476
DOI	10.1016/j.psychsport.2023.102536
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Article ; Online: A new approach to postvasectomy semen analyses eliminates the need to evaluate a fresh specimen.

Kiessling, Ryan J / Hauser, Alexander / Eyre, Robert C / Kiessling, Ann A

Andrology

2022 Volume 11, Issue 3, Page(s) 464–470

Abstract: Background: According to current guidelines, confirmation that vasectomy results in sterility depends on microscopic examination of postvasectomy semen for the presence of spermatozoa. Guidelines established in 2012 require examination of a fresh ... ...

Abstract	Background: According to current guidelines, confirmation that vasectomy results in sterility depends on microscopic examination of postvasectomy semen for the presence of spermatozoa. Guidelines established in 2012 require examination of a fresh specimen within 2 h of collection, which necessitates the patient making an appointment with either the surgeon's office or a licensed clinical laboratory. Twenty-five to 42% of patients fail to comply with postvasectomy semen analysis (PVSA). Objectives: To determine if an at-home semen collection kit can substitute for the evaluation of a fresh specimen and improve patient compliance with postvasectomy spermatozoa assessment. Materials and methods: The kit contains a patented aldehyde-fixative that maintains spermatozoa and semen cells in suspension for quantitation. Patients order a PVSA kit to be delivered to their home and can collect a semen specimen and return it to the laboratory through regular US mail. Results: From January 2011 through December 2018, 6096 men undergoing vasectomy by 184 urologists in 33 states in the US ordered PVSA kits, of which 5408 (89%) returned at least one for analysis. Of those, 398 men (7.4%) returned the first kit with greater than 10,000 spermatozoa/ml within a year of vasectomy, of which only 4.4% contained greater than 100,000 spermatozoa/ml 12 weeks postsurgery. This suggests that fewer than 5% of postvasectomy patients might need follow-up fresh semen analyses, greatly easing the logistical burden of PVSA. Ninety percent of surgeons returning a patient satisfaction questionnaire said their patients "never" complained about using PVSA kits. Discussion and conclusion: These data support the adoption of a new standard for PVSA that does not involve an initial evaluation of a fresh semen specimen.
MeSH term(s)	Male ; Humans ; Semen Analysis/methods ; Semen ; Spermatozoa ; Surveys and Questionnaires ; Body Fluids ; Vasectomy
Language	English
Publishing date	2022-11-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2696108-8
ISSN	2047-2927 ; 2047-2919
ISSN (online)	2047-2927
ISSN	2047-2919
DOI	10.1111/andr.13331
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Zs.A 6983: Show issues

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Article ; Online: Mitochondrial DNA Sequence Diversity in Mammals: A Correlation between the Effective and Census Population Sizes.

James, Jennifer / Eyre-Walker, Adam

Genome biology and evolution

2020 Volume 12, Issue 12, Page(s) 2441–2449

Abstract: What determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Because neutral diversity depends upon the product of the effective population size and mutation rate, there is an expectation that ... ...

Abstract	What determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Because neutral diversity depends upon the product of the effective population size and mutation rate, there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here, we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest data set to date, using 639 mammalian species. In a multiple regression, we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of nonsynonymous to synonymous diversity, is also significantly negatively correlated to both range size and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12-20%, providing one of the first quantifications of the relationship between diversity and the census population size.
MeSH term(s)	Animals ; DNA, Mitochondrial/genetics ; Gene Pool ; Genetic Variation ; Mammals/genetics ; Mutation Rate ; Population Density ; Selection, Genetic
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2020-10-22
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evaa222
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Article ; Online: The Utah Pediatric Trauma Network, a statewide pediatric trauma collaborative can safely help nonpediatric hospitals admit children with mild traumatic brain injury.

Fenton, Stephen J / Swendiman, Robert A / Eyre, Matthew / Larsen, Kezlyn / Russell, Katie W

The journal of trauma and acute care surgery

2023 Volume 95, Issue 3, Page(s) 376–382

Abstract: Background: Created in 2019, the Utah Pediatric Trauma Network (UPTN) is a transparent noncompetitive collaboration of all hospitals in Utah with the purpose of improving pediatric trauma care. The UPTN implements evidence-based guidelines based on ... ...

Abstract	Background: Created in 2019, the Utah Pediatric Trauma Network (UPTN) is a transparent noncompetitive collaboration of all hospitals in Utah with the purpose of improving pediatric trauma care. The UPTN implements evidence-based guidelines based on hospital resources and capabilities with quarterly review of data collected in a network-specific database. The first initiative was to help triage the care of traumatic brain injury (TBI) to prevent unnecessary transfers while ensuring appropriate care. The purpose of this study was to review the effectiveness of this network wide guideline. Methods: The UPTN REDCap database was retrospectively reviewed between January 2019 and December 2021. Comparisons were made between the pediatric trauma center (PED1) and nonpediatric hospitals (non-PED1) in admissions of children with very mild, mild, or complicated mild TBI. Results: Of the total 3,315 cases reviewed, 294 were admitted to a non-PED1 hospital and 1,061 to the PED1 hospital with very mild/mild/complicated mild TBI. Overall, kids treated at non-PED1 were older (mean, 14.9 vs. 7.7 years; p = 0.00001) and more likely to be 14 years or older (37% vs. 24%, p < 0.00001) compared with those at PED1. Increased admissions occurred post-UPTN at non-PED1 hospitals compared with pre-UPTN (43% vs. 14%, p < 0.00001). Children admitted to non-PED1 hospitals post-UPTN were younger (9.1 vs. 15.7 years, p = 0.002) with more kids younger than 14 years (67% vs. 38%, p = 0.014) compared with pre-UPTN. Two kids required next-day transfer to a higher-level center (1 to PED1), and none required surgery or neurosurgical evaluation. The mean length of stay was 21.8 hours (interquartile range, 11.9-25.4). Concomitantly, less children with very mild TBI were admitted to PED1 post-UPTN (6% vs. 27%, p < 0.00001) and more with complicated mild TBI (63% vs. 50%, p = 0.00003) than 2019. Conclusion: Implementation of TBI guidelines across the UPTN successfully allowed nonpediatric hospitals to safely admit children with very mild, mild, or complicated mild TBI. In addition, admitted kids were more like those treated at the PED1 hospital. Level of evidence: Prognostic/Epidemiological; Level IV.
MeSH term(s)	Child ; Humans ; Brain Concussion ; Utah/epidemiology ; Retrospective Studies ; Hospitalization ; Brain Injuries, Traumatic/diagnosis ; Brain Injuries, Traumatic/therapy ; Hospitals ; Trauma Centers
Language	English
Publishing date	2023-01-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2651070-4
ISSN	2163-0763 ; 2163-0755
ISSN (online)	2163-0763
ISSN	2163-0755
DOI	10.1097/TA.0000000000003871
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