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Article ; Online: Germline Variants in Childhood Cutaneous Melanoma.

Johansson, Peter A / Palmer, Jane M / Hamilton, Hayley R / Whiteman, David C / Pritchard, Antonia L / Hayward, Nicholas K

The Journal of investigative dermatology

2023 Volume 143, Issue 8, Page(s) 1610–1613

MeSH term(s)	Humans ; Melanoma/genetics ; Skin Neoplasms/genetics ; Skin ; Germ-Line Mutation ; Genetic Predisposition to Disease ; Melanoma, Cutaneous Malignant
Language	English
Publishing date	2023-02-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80136-7
ISSN	1523-1747 ; 0022-202X
ISSN (online)	1523-1747
ISSN	0022-202X
DOI	10.1016/j.jid.2023.02.014
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Article ; Online: Comparison of induction agents for rapid sequence intubation in refractory status epilepticus: A single-center retrospective analysis.

Woodward, Matthew R / Kardon, Adam / Manners, Jody / Schleicher, Samantha / Pergakis, Melissa B / Ciryam, Prajwal / Podell, Jamie / Denney Zimmerman, William / Galvagno, Samuel M / Butt, Bilal / Pritchard, Jennifer / Parikh, Gunjan Y / Gilmore, Emily J / Badjatia, Neeraj / Morris, Nicholas A

Epilepsy & behavior reports

2024 Volume 25, Page(s) 100645

Abstract: Endotracheal intubation, frequently required during management of refractory status epilepticus (RSE), can be facilitated by anesthetic medications; however, their effectiveness for RSE control is unknown. We performed a single-center retrospective ... ...

Abstract	Endotracheal intubation, frequently required during management of refractory status epilepticus (RSE), can be facilitated by anesthetic medications; however, their effectiveness for RSE control is unknown. We performed a single-center retrospective review of patients admitted to a neurocritical care unit (NCCU) who underwent in-hospital intubation during RSE management. Patients intubated with propofol, ketamine, or benzodiazepines, termed anti-seizure induction (ASI), were compared to patients who received etomidate induction (EI). The primary endpoint was clinical or electrographic seizures within 12 h post-intubation. We estimated the association of ASI on post-intubation seizure using logistic regression. A sub-group of patients undergoing electroencephalography during intubation was identified to evaluate the immediate effect of ASI on RSE. We screened 697 patients admitted to the NCCU for RSE and identified 148 intubated in-hospital (n = 90 ASI, n = 58 EI). There was no difference in post-intubation seizure (26 % (n = 23) ASI, 29 % (n = 17) EI) in the cohort, however, there was increased RSE resolution with ASI in 24 patients with electrographic RSE during intubation (ASI: 61 % (n = 11/18) vs EI: 0 % (n = 0/6), p =.016). While anti-seizure induction did not appear to affect post-intubation seizure occurrence overall, a sub-group of patients undergoing electroencephalography during intubation had a higher incidence of seizure cessation, suggesting potential benefit in an enriched population.
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Journal Article
ISSN	2589-9864
ISSN (online)	2589-9864
DOI	10.1016/j.ebr.2024.100645
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Article ; Online: Easy phylotyping of

Waters, Nicholas R / Abram, Florence / Brennan, Fiona / Holmes, Ashleigh / Pritchard, Leighton

Access microbiology

2020 Volume 2, Issue 9, Page(s) acmi000143

Abstract: The Clermont PCR method for ... ...

Abstract	The Clermont PCR method for phylotyping
Language	English
Publishing date	2020-06-19
Publishing country	England
Document type	Journal Article
ISSN	2516-8290
ISSN (online)	2516-8290
DOI	10.1099/acmi.0.000143
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Article ; Online: Evaluating salvage electroconvulsive therapy for the treatment of prolonged super refractory status epilepticus: A case series.

Woodward, Matthew R / Doddi, Seshagiri / Marano, Christopher / Regenold, William / Pritchard, Jennifer / Chen, Stephanie / Margiotta, Megan / Chang, Wan-Tsu W / Alkhachroum, Ayham / Morris, Nicholas A

Epilepsy & behavior : E&B

2023 Volume 144, Page(s) 109286

Abstract: Background and objectives: Clinicians have treated super refractory status epilepticus (SRSE) with electroconvulsive therapy (ECT); however, data supporting the practice are scant and lack rigorous evaluation of continuous electroencephalogram (cEEG) ... ...

Abstract	Background and objectives: Clinicians have treated super refractory status epilepticus (SRSE) with electroconvulsive therapy (ECT); however, data supporting the practice are scant and lack rigorous evaluation of continuous electroencephalogram (cEEG) changes related to therapy. This study aims to describe a series of patients with SRSE treated at our institution with ECT and characterize cEEG changes using a blinded review process. Methods: We performed a single-center retrospective study of consecutive patients admitted for SRSE and treated with ECT from January 2014 to December 2022. Our primary outcome was the resolution of SRSE. Secondary outcomes included changes in ictal-interictal EEG patterns, anesthetic burden, treatment-associated adverse events, and changes in clinical examination. cEEG was reviewed pre- and post-ECT by blinded epileptologists. Results: Ten patients underwent treatment with ECT across 11 admissions (8 female, median age 57 years). At the time of ECT initiation, nine patients had ongoing SRSE while two had highly ictal patterns and persistent encephalopathy following anesthetic wean, consistent with late-stage SRSE. Super-refractory status epilepticus resolution occurred with a median time to cessation of 4 days (interquartile range [IQR]: 3-9 days) following ECT initiation. Background continuity improved in five patients and periodic discharge frequency decreased in six. There was a decrease in anesthetic use following the completion of ECT and an improvement in neurological exams. There were no associated adverse events. Discussion: In our cohort, ECT was associated with improvement of ictal-interictal patterns on EEG, and resolution of SRSE, and was not associated with serious adverse events. Further controlled studies are needed.
MeSH term(s)	Humans ; Female ; Middle Aged ; Electroconvulsive Therapy ; Retrospective Studies ; Status Epilepticus/therapy ; Drug Resistant Epilepsy ; Research Design
Language	English
Publishing date	2023-06-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2010587-3
ISSN	1525-5069 ; 1525-5050
ISSN (online)	1525-5069
ISSN	1525-5050
DOI	10.1016/j.yebeh.2023.109286
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Book ; Online: A Bibliometric Review of Neuromorphic Computing and Spiking Neural Networks

Pritchard, Nicholas J. / Wicenec, Andreas / Bennamoun, Mohammed / Dodson, Richard

2023

Abstract: Neuromorphic computing and spiking neural networks aim to leverage biological inspiration to achieve greater energy efficiency and computational power beyond traditional von Neumann architectured machines. In particular, spiking neural networks hold the ... ...

Abstract	Neuromorphic computing and spiking neural networks aim to leverage biological inspiration to achieve greater energy efficiency and computational power beyond traditional von Neumann architectured machines. In particular, spiking neural networks hold the potential to advance artificial intelligence as the basis of third-generation neural networks. Aided by developments in memristive and compute-in-memory technologies, neuromorphic computing hardware is transitioning from laboratory prototype devices to commercial chipsets; ushering in an era of low-power computing. As a nexus of biological, computing, and material sciences, the literature surrounding these concepts is vast, varied, and somewhat distinct from artificial neural network sources. This article uses bibliometric analysis to survey the last 22 years of literature, seeking to establish trends in publication and citation volumes (III-A); analyze impactful authors, journals and institutions (III-B); generate an introductory reading list (III-C); survey collaborations between countries, institutes and authors (III-D), and to analyze changes in research topics over the years (III-E). We analyze literature data from the Clarivate Web of Science using standard bibliometric methods. By briefly introducing the most impactful literature in this field from the last two decades, we encourage AI practitioners and researchers to look beyond contemporary technologies toward a potentially spiking future of computing. Comment: 8 pages, 4 figures
Keywords	Computer Science - Neural and Evolutionary Computing ; A.1
Subject code	001
Publishing date	2023-04-13
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: RFI Detection with Spiking Neural Networks

Pritchard, Nicholas J. / Wicenec, Andreas / Bennamoun, Mohammed / Dodson, Richard

2023

Abstract: Radio Frequency Interference (RFI) detection and mitigation is critical for enabling and maximising the scientific output of radio telescopes. The emergence of machine learning methods capable of handling large datasets has led to their application in ... ...

Abstract	Radio Frequency Interference (RFI) detection and mitigation is critical for enabling and maximising the scientific output of radio telescopes. The emergence of machine learning methods capable of handling large datasets has led to their application in radio astronomy, particularly in RFI detection. Spiking Neural Networks (SNNs), inspired by biological systems, are well-suited for processing spatio-temporal data. This study introduces the first application of SNNs to an astronomical data-processing task, specifically RFI detection. We adapt the nearest-latent-neighbours (NLN) algorithm and auto-encoder architecture proposed by previous authors to SNN execution by direct ANN2SNN conversion, enabling simplified downstream RFI detection by sampling the naturally varying latent space from the internal spiking neurons. We evaluate performance with the simulated HERA telescope and hand-labelled LOFAR dataset that the original authors provided. We additionally evaluate performance with a new MeerKAT-inspired simulation dataset. This dataset focuses on satellite-based RFI, an increasingly important class of RFI and is, therefore, an additional contribution. Our SNN approach remains competitive with the original NLN algorithm and AOFlagger in AUROC, AUPRC and F1 scores for the HERA dataset but exhibits difficulty in the LOFAR and MeerKAT datasets. However, our method maintains this performance while completely removing the compute and memory-intense latent sampling step found in NLN. This work demonstrates the viability of SNNs as a promising avenue for machine-learning-based RFI detection in radio telescopes by establishing a minimal performance baseline on traditional and nascent satellite-based RFI sources and is the first work to our knowledge to apply SNNs in astronomy. Comment: 10 pages, 5 figures, 4 tables
Keywords	Astrophysics - Instrumentation and Methods for Astrophysics ; Computer Science - Neural and Evolutionary Computing
Subject code	006
Publishing date	2023-11-24
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Functional genomic analysis of adult and pediatric brain tumor isolates.

Hoellerbauer, Pia / Biery, Matt C / Arora, Sonali / Rao, Yiyun / Girard, Emily J / Mitchell, Kelly / Dighe, Pratiksha / Kufeld, Megan / Kuppers, Daniel A / Herman, Jacob A / Holland, Eric C / Soroceanu, Liliana / Vitanza, Nicholas A / Olson, James M / Pritchard, Justin R / Paddison, Patrick J

bioRxiv : the preprint server for biology

2023

Abstract: Background: Adult and pediatric tumors display stark differences in their mutation spectra and chromosome alterations. Here, we attempted to identify common and unique gene dependencies and their associated biomarkers among adult and pediatric tumor ... ...

Abstract	Background: Adult and pediatric tumors display stark differences in their mutation spectra and chromosome alterations. Here, we attempted to identify common and unique gene dependencies and their associated biomarkers among adult and pediatric tumor isolates using functional genetic lethal screens and computational modeling. Methods: We performed CRISRP-Cas9 lethality screens in two adult glioblastoma (GBM) tumor isolates and five pediatric brain tumor isolates representing atypical teratoid rhabdoid tumors (ATRT), diffuse intrinsic pontine glioma, GBM, and medulloblastoma. We then integrated the screen results with machine learning-based gene-dependency models generated from data from >900 cancer cell lines. Results: We found that >50% of candidate dependencies of 280 identified were shared between adult GBM tumors and individual pediatric tumor isolates. 68% of screen hits were found as nodes in our network models, along with shared and tumor-specific predictors of gene dependencies. We investigated network predictors associated with ADAR, EFR3A, FGFR1 (pediatric-specific), and SMARCC2 (ATRT-specific) gene dependency among our tumor isolates. Conclusions: The results suggest that, despite harboring disparate genomic signatures, adult and pediatric tumor isolates share a preponderance of genetic dependences. Further, combining data from primary brain tumor lethality screens with large cancer cell line datasets produced valuable insights into biomarkers of gene dependency, even for rare cancers. Importance of the study: Our results demonstrate that large cancer cell lines data sets can be computationally mined to identify known and novel gene dependency relationships in adult and pediatric human brain tumor isolates. Gene dependency networks and lethality screen results represent a key resource for neuro-oncology and cancer research communities. We also highlight some of the challenges and limitations of this approach.
Language	English
Publishing date	2023-01-06
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.01.05.522885
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Article ; Online: A rare missense variant in protection of telomeres 1 (POT1) predisposes to a range of haematological malignancies.

Nathan, Vaishnavi / Johansson, Peter A / Palmer, Jane M / Hamilton, Hayley R / Howlie, Madeleine / Brooks, Kelly M / Hayward, Nicholas K / Pritchard, Antonia L

British journal of haematology

2020 Volume 192, Issue 2, Page(s) e57–e60

MeSH term(s)	Female ; Genetic Predisposition to Disease ; Germ-Line Mutation ; Hematologic Neoplasms/genetics ; Humans ; Male ; Mutation, Missense ; Pedigree ; Telomere-Binding Proteins/genetics
Chemical Substances	POT1 protein, human ; Telomere-Binding Proteins
Language	English
Publishing date	2020-11-20
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	80077-6
ISSN	1365-2141 ; 0007-1048
ISSN (online)	1365-2141
ISSN	0007-1048
DOI	10.1111/bjh.17218
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Article ; Online: riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions.

Waters, Nicholas R / Abram, Florence / Brennan, Fiona / Holmes, Ashleigh / Pritchard, Leighton

Nucleic acids research

2018 Volume 46, Issue 11, Page(s) e68

Abstract: The vast majority of bacterial genome sequencing has been performed using Illumina short reads. Because of the inherent difficulty of resolving repeated regions with short reads alone, only ∼10% of sequencing projects have resulted in a closed genome. ... ...

Abstract	The vast majority of bacterial genome sequencing has been performed using Illumina short reads. Because of the inherent difficulty of resolving repeated regions with short reads alone, only ∼10% of sequencing projects have resulted in a closed genome. The most common repeated regions are those coding for ribosomal operons (rDNAs), which occur in a bacterial genome between 1 and 15 times, and are typically used as sequence markers to classify and identify bacteria. Here, we exploit the genomic context in which rDNAs occur across taxa to improve assembly of these regions relative to de novo sequencing by using the conserved nature of rDNAs across taxa and the uniqueness of their flanking regions within a genome. We describe a method to construct targeted pseudocontigs generated by iteratively assembling reads that map to a reference genome's rDNAs. These pseudocontigs are then used to more accurately assemble the newly sequenced chromosome. We show that this method, implemented as riboSeed, correctly bridges across adjacent contigs in bacterial genome assembly and, when used in conjunction with other genome polishing tools, can assist in closure of a genome.
MeSH term(s)	Base Sequence ; Chromosome Mapping/methods ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Escherichia coli/genetics ; Genome, Bacterial/genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Klebsiella pneumoniae/genetics ; Sequence Analysis, DNA/methods ; Software
Chemical Substances	DNA, Bacterial ; DNA, Ribosomal
Language	English
Publishing date	2018-04-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gky212
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Article: Drought soil legacy overrides maternal effects on plant growth.

De Long, Jonathan R / Semchenko, Marina / Pritchard, William J / Cordero, Irene / Fry, Ellen L / Jackson, Benjamin G / Kurnosova, Ksenia / Ostle, Nicholas J / Johnson, David / Baggs, Elizabeth M / Bardgett, Richard D

Functional ecology

2019 Volume 33, Issue 8, Page(s) 1400–1410

Abstract: Maternal effects (i.e. trans-generational plasticity) and soil legacies generated by drought and plant diversity can affect plant performance and alter nutrient cycling and plant community dynamics. However, the relative importance and combined effects ... ...

Abstract	Maternal effects (i.e. trans-generational plasticity) and soil legacies generated by drought and plant diversity can affect plant performance and alter nutrient cycling and plant community dynamics. However, the relative importance and combined effects of these factors on plant growth dynamics remain poorly understood.We used soil and seeds from an existing plant diversity and drought manipulation field experiment in temperate grassland to test maternal, soil drought and diversity legacy effects, and their interactions, on offspring plant performance of two grassland species (
Language	English
Publishing date	2019-04-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2020307-X
ISSN	1365-2435 ; 0269-8463
ISSN (online)	1365-2435
ISSN	0269-8463
DOI	10.1111/1365-2435.13341
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