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1. FishNet: Deep Neural Networks for Low-Cost Fish Stock Estimation

Author

Mots'oehli, Moseli, Nikolaev, Anton, IGede, Wawan B., Lynham, John, Mous, Peter J., and Sadowski, Peter

Subjects
Computer Science - Computer Vision and Pattern Recognition, Economics - General Economics
Abstract

Fish stock assessment often involves manual fish counting by taxonomy specialists, which is both time-consuming and costly. We propose FishNet, an automated computer vision system for both taxonomic classification and fish size estimation from images captured with a low-cost digital camera. The system first performs object detection and segmentation using a Mask R-CNN to identify individual fish from images containing multiple fish, possibly consisting of different species. Then each fish species is classified and the length is predicted using separate machine learning models. To develop the model, we use a dataset of 300,000 hand-labeled images containing 1.2M fish of 163 different species and ranging in length from 10cm to 250cm, with additional annotations and quality control methods used to curate high-quality training data. On held-out test data sets, our system achieves a 92% intersection over union on the fish segmentation task, a 89% top-1 classification accuracy on single fish species classification, and a 2.3cm mean absolute error on the fish length estimation task., Comment: IEEE COINS 2024

Published
2024

3. Assessing the validity of a self-reported clinical diagnosis of schizophrenia

Author

Grace E. Woolway, Sophie E. Legge, Amy J. Lynham, Sophie E. Smart, Leon Hubbard, Ellie R. Daniel, Antonio F. Pardiñas, Valentina Escott-Price, Michael C. O’Donovan, Michael J. Owen, Ian R. Jones, and James T. R. Walters

Subjects
Psychiatry, RC435-571
Abstract

Abstract The increasing availability of biobanks is changing the way individuals are identified for genomic research. This study assesses the validity of a self-reported clinical diagnosis of schizophrenia. The study included 1744 clinically-ascertained participants with schizophrenia or schizoaffective disorder depressed-type (SA-D) diagnosed by self-report and/or research interview and 1453 UK Biobank participants with self-reported and/or medical record diagnosis of schizophrenia or SA-D. Unaffected controls included a total of 501,837 participants. We assessed the positive predictive values (PPV) of self-reported clinical diagnoses against research interview and medical record diagnoses. Polygenic risk scores (PRS) and phenotypes relating to demographics, education and employment were compared across diagnostic groups. The variance explained (r2) in schizophrenia PRS for each diagnostic group was compared to samples in the Psychiatric Genomics Consortium (PGC). In the clinically-ascertained participants, the PPV of self-reported schizophrenia for a research diagnosis of schizophrenia was 0.70, which increased to 0.81 after expanding the research diagnosis to schizophrenia or SA-D. In UK Biobank, the PPV of self-reported schizophrenia for a medical record diagnosis was 0.74. Compared to participants who self-reported, participants with a clinically-ascertained research diagnosis were younger and more likely to have a high school qualification. Participants with a medical record diagnosis in UK Biobank were less likely to be employed or have a high school qualification than those who self-reported. Schizophrenia PRS did not differ between participants that had a diagnosis from self-report, research diagnosis or medical records. Polygenic liability r2, for all diagnosis definitions, fell within the distribution of PGC schizophrenia cohorts. Self-reported measures of schizophrenia are justified in genomic research to maximise sample size and reduce the burden of in-depth interviews on participants, although within sample validation of diagnoses is recommended.

Published
2024
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5. Cosmic kidney disease: an integrated pan-omic, physiological and morphological study into spaceflight-induced renal dysfunction

Author

Siew, Keith, Nestler, Kevin A., Nelson, Charlotte, D’Ambrosio, Viola, Zhong, Chutong, Li, Zhongwang, Grillo, Alessandra, Wan, Elizabeth R., Patel, Vaksha, Overbey, Eliah, Kim, JangKeun, Yun, Sanghee, Vaughan, Michael B., Cheshire, Chris, Cubitt, Laura, Broni-Tabi, Jessica, Al-Jaber, Maneera Yousef, Boyko, Valery, Meydan, Cem, Barker, Peter, Arif, Shehbeel, Afsari, Fatemeh, Allen, Noah, Al-Maadheed, Mohammed, Altinok, Selin, Bah, Nourdine, Border, Samuel, Brown, Amanda L., Burling, Keith, Cheng-Campbell, Margareth, Colón, Lorianna M., Degoricija, Lovorka, Figg, Nichola, Finch, Rebecca, Foox, Jonathan, Faridi, Pouya, French, Alison, Gebre, Samrawit, Gordon, Peter, Houerbi, Nadia, Valipour Kahrood, Hossein, Kiffer, Frederico C., Klosinska, Aleksandra S., Kubik, Angela, Lee, Han-Chung, Li, Yinghui, Lucarelli, Nicholas, Marullo, Anthony L., Matei, Irina, McCann, Colleen M., Mimar, Sayat, Naglah, Ahmed, Nicod, Jérôme, O’Shaughnessy, Kevin M., Oliveira, Lorraine Christine De, Oswalt, Leah, Patras, Laura Ioana, Lai Polo, San-huei, Rodríguez-Lopez, María, Roufosse, Candice, Sadeghi-Alavijeh, Omid, Sanchez-Hodge, Rebekah, Paul, Anindya S., Schittenhelm, Ralf Bernd, Schweickart, Annalise, Scott, Ryan T., Choy Lim Kam Sian, Terry Chin, da Silveira, Willian A., Slawinski, Hubert, Snell, Daniel, Sosa, Julio, Saravia-Butler, Amanda M., Tabetah, Marshall, Tanuwidjaya, Erwin, Walker-Samuel, Simon, Yang, Xiaoping, Yasmin, Zhang, Haijian, Godovac-Zimmermann, Jasminka, Sarder, Pinaki, Sanders, Lauren M., Costes, Sylvain V., Campbell, Robert A. A., Karouia, Fathi, Mohamed-Alis, Vidya, Rodriques, Samuel, Lynham, Steven, Steele, Joel Ricky, Baranzini, Sergio, Fazelinia, Hossein, Dai, Zhongquan, Uruno, Akira, Shiba, Dai, Yamamoto, Masayuki, A.C.Almeida, Eduardo, Blaber, Elizabeth, Schisler, Jonathan C., Eisch, Amelia J., Muratani, Masafumi, Zwart, Sara R., Smith, Scott M., Galazka, Jonathan M., Mason, Christopher E., Beheshti, Afshin, and Walsh, Stephen B.

Published
2024
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7. Cosmic kidney disease: an integrated pan-omic, physiological and morphological study into spaceflight-induced renal dysfunction

Author

Keith Siew, Kevin A. Nestler, Charlotte Nelson, Viola D’Ambrosio, Chutong Zhong, Zhongwang Li, Alessandra Grillo, Elizabeth R. Wan, Vaksha Patel, Eliah Overbey, JangKeun Kim, Sanghee Yun, Michael B. Vaughan, Chris Cheshire, Laura Cubitt, Jessica Broni-Tabi, Maneera Yousef Al-Jaber, Valery Boyko, Cem Meydan, Peter Barker, Shehbeel Arif, Fatemeh Afsari, Noah Allen, Mohammed Al-Maadheed, Selin Altinok, Nourdine Bah, Samuel Border, Amanda L. Brown, Keith Burling, Margareth Cheng-Campbell, Lorianna M. Colón, Lovorka Degoricija, Nichola Figg, Rebecca Finch, Jonathan Foox, Pouya Faridi, Alison French, Samrawit Gebre, Peter Gordon, Nadia Houerbi, Hossein Valipour Kahrood, Frederico C. Kiffer, Aleksandra S. Klosinska, Angela Kubik, Han-Chung Lee, Yinghui Li, Nicholas Lucarelli, Anthony L. Marullo, Irina Matei, Colleen M. McCann, Sayat Mimar, Ahmed Naglah, Jérôme Nicod, Kevin M. O’Shaughnessy, Lorraine Christine De Oliveira, Leah Oswalt, Laura Ioana Patras, San-huei Lai Polo, María Rodríguez-Lopez, Candice Roufosse, Omid Sadeghi-Alavijeh, Rebekah Sanchez-Hodge, Anindya S. Paul, Ralf Bernd Schittenhelm, Annalise Schweickart, Ryan T. Scott, Terry Chin Choy Lim Kam Sian, Willian A. da Silveira, Hubert Slawinski, Daniel Snell, Julio Sosa, Amanda M. Saravia-Butler, Marshall Tabetah, Erwin Tanuwidjaya, Simon Walker-Samuel, Xiaoping Yang, Yasmin, Haijian Zhang, Jasminka Godovac-Zimmermann, Pinaki Sarder, Lauren M. Sanders, Sylvain V. Costes, Robert A. A. Campbell, Fathi Karouia, Vidya Mohamed-Alis, Samuel Rodriques, Steven Lynham, Joel Ricky Steele, Sergio Baranzini, Hossein Fazelinia, Zhongquan Dai, Akira Uruno, Dai Shiba, Masayuki Yamamoto, Eduardo A.C.Almeida, Elizabeth Blaber, Jonathan C. Schisler, Amelia J. Eisch, Masafumi Muratani, Sara R. Zwart, Scott M. Smith, Jonathan M. Galazka, Christopher E. Mason, Afshin Beheshti, and Stephen B. Walsh

Subjects
Science
Abstract

Abstract Missions into Deep Space are planned this decade. Yet the health consequences of exposure to microgravity and galactic cosmic radiation (GCR) over years-long missions on indispensable visceral organs such as the kidney are largely unexplored. We performed biomolecular (epigenomic, transcriptomic, proteomic, epiproteomic, metabolomic, metagenomic), clinical chemistry (electrolytes, endocrinology, biochemistry) and morphometry (histology, 3D imaging, miRNA-ISH, tissue weights) analyses using samples and datasets available from 11 spaceflight-exposed mouse and 5 human, 1 simulated microgravity rat and 4 simulated GCR-exposed mouse missions. We found that spaceflight induces: 1) renal transporter dephosphorylation which may indicate astronauts’ increased risk of nephrolithiasis is in part a primary renal phenomenon rather than solely a secondary consequence of bone loss; 2) remodelling of the nephron that results in expansion of distal convoluted tubule size but loss of overall tubule density; 3) renal damage and dysfunction when exposed to a Mars roundtrip dose-equivalent of simulated GCR.

Published
2024
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13. Avoiding critical thresholds through effective monitoring.

Author

Essington, Timothy, Samhouri, Jameal, Siple, Margaret, Halpern, Benjamin, White, Crow, Lynham, John, Salomon, Anne, Levin, Phillip, and Stier, Adrian

Subjects
Allee effect, adaptive management, depensation, management strategy evaluation, tipping point, value of information, Biomass, Conservation of Natural Resources, Ecosystem, Fisheries
Abstract

A major challenge in sustainability science is identifying targets that maximize ecosystem benefits to humanity while minimizing the risk of crossing critical system thresholds. One critical threshold is the biomass at which populations become so depleted that their population growth rates become negative-depensation. Here, we evaluate how the value of monitoring information increases as a natural resource spends more time near the critical threshold. This benefit emerges because higher monitoring precision promotes higher yield and a greater capacity to recover from overharvest. We show that precautionary buffers that trigger increased monitoring precision as resource levels decline may offer a way to minimize monitoring costs and maximize profits. In a world of finite resources, improving our understanding of the trade-off between precision in estimates of population status and the costs of mismanagement will benefit stakeholders that shoulder the burden of these economic and social costs.

Published
2022

14. Tiebout sorting in online communities

Author

Lynham, John and Neary, Philip R.

Subjects
Economics - General Economics
Abstract

This paper proposes a stylized, dynamic model to address the issue of sorting online. There are two large homogeneous groups of individuals. Everyone must choose between two online platforms, one of which has superior amenities (akin to having superior local public goods). Each individual enjoys interacting online with those from their own group but dislikes being on the same platform as those in the other group. Unlike a Tiebout model of residential sorting, both platforms have unlimited capacity so there are no constraints on cross-platform migration. It is clear how each group would like to sort themselves but, in the presence of the other type, only the two segregated outcomes are guaranteed to be equilibria. Integration on a platform can be supported in equilibrium as long as the platform is sufficiently desirable. If online integration of the two communities is a desired social outcome then the optimal policy is clear: make the preferred platform even more desirable. Revitalizing the inferior platform will never lead to integration and even increases the likelihood the segregation. Finally, integration is more elastic in response to an increase in platform amenities than to reductions in intolerance.

Published
2021

27. Cardiff Online Cognitive Assessment in a National Sample: Cross-Sectional Web-Based Study

Author

Amy Joanne Lynham, Ian R Jones, and James T R Walters

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Public aspects of medicine, RA1-1270
Abstract

BackgroundPsychiatric disorders are associated with cognitive impairment. We have developed a web-based, 9-task cognitive battery to measure the core domains affected in people with psychiatric disorders. To date, this assessment has been used to collect data on a clinical sample of participants with psychiatric disorders. ObjectiveThe aims of this study were (1) to establish a briefer version of the battery (called the Cardiff Online Cognitive Assessment [CONCA]) that can give a valid measure of cognitive ability (“g”) and (2) to collect normative data and demonstrate CONCA’s application in a health population sample. MethodsBased on 6 criteria and data from our previous study, we selected 5 out of the original 9 tasks to include in CONCA. These included 3 core tasks that were sufficient to derive a measure of “g” and 2 optional tasks. Participants from a web-based national cohort study (HealthWise Wales) were invited to complete CONCA. Completion rates, sample characteristics, performance distributions, and associations between cognitive performance and demographic characteristics and mental health measures were examined. ResultsA total of 3679 participants completed at least one CONCA task, of which 3135 completed all 3 core CONCA tasks. Performance on CONCA was associated with age (B=–0.05, SE 0.002; P

Published
2023
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28. GSK3 and lamellipodin balance lamellipodial protrusions and focal adhesion maturation in mouse neural crest migration

Author

Lisa Dobson, William B. Barrell, Zahra Seraj, Steven Lynham, Sheng-Yuan Wu, Matthias Krause, and Karen J. Liu

Subjects
CP: Cell biology, Biology (General), QH301-705.5
Abstract

Summary: Neural crest cells are multipotent cells that delaminate from the neuroepithelium, migrating throughout the embryo. Aberrant migration causes developmental defects. Animal models are improving our understanding of neural crest anomalies, but in vivo migration behaviors are poorly understood. Here, we demonstrate that murine neural crest cells display actin-based lamellipodia and filopodia in vivo. Using neural crest-specific knockouts or inhibitors, we show that the serine-threonine kinase glycogen synthase kinase-3 (GSK3) and the cytoskeletal regulator lamellipodin (Lpd) are required for lamellipodia formation while preventing focal adhesion maturation. Lpd is a substrate of GSK3, and phosphorylation of Lpd favors interactions with the Scar/WAVE complex (lamellipodia formation) at the expense of VASP and Mena interactions (adhesion maturation and filopodia formation). This improved understanding of cytoskeletal regulation in mammalian neural crest migration has general implications for neural crest anomalies and cancer.

Published
2023
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30. Opportunities for agent‐based modelling in human dimensions of fisheries

Author

Burgess, Matthew G, Carrella, Ernesto, Drexler, Michael, Axtell, Robert L, Bailey, Richard M, Watson, James R, Cabral, Reniel B, Clemence, Michaela, Costello, Christopher, Dorsett, Chris, Gaines, Steven D, Klein, Emily S, Koralus, Philipp, Leonard, George, Levin, Simon A, Little, Lorne Richard, Lynham, John, Madsen, Jens Koed, Merkl, Andreas, Owashi, Brandon, Saul, Steven E, Putten, Ingrid E, and Wilcox, Sharon

Subjects
complexity, ecosystem-based fishery management, governance, human behaviour, social-ecological systems, sustainability, Ecology, Fisheries Sciences, Fisheries
Published
2020

31. The Relationship Between Polygenic Risk Scores and Cognition in Schizophrenia

Author

Richards, Alexander L, Pardiñas, Antonio F, Frizzati, Aura, Tansey, Katherine E, Lynham, Amy J, Holmans, Peter, Legge, Sophie E, Savage, Jeanne E, Agartz, Ingrid, Andreassen, Ole A, Blokland, Gabriella AM, Corvin, Aiden, Cosgrove, Donna, Degenhardt, Franziska, Djurovic, Srdjan, Espeseth, Thomas, Ferraro, Laura, Gayer-Anderson, Charlotte, Giegling, Ina, van Haren, Neeltje E, Hartmann, Annette M, Hubert, John J, Jönsson, Erik G, Konte, Bettina, Lennertz, Leonhard, Olde Loohuis, Loes M, Melle, Ingrid, Morgan, Craig, Morris, Derek W, Murray, Robin M, Nyman, Håkan, Ophoff, Roel A, van Os, Jim, Petryshen, Tracey L, Quattrone, Diego, Rietschel, Marcella, Rujescu, Dan, Rutten, Bart PF, Streit, Fabian, Strohmaier, Jana, Sullivan, Patrick F, Sundet, Kjetil, Wagner, Michael, Escott-Price, Valentina, Owen, Michael J, Donohoe, Gary, O’Donovan, Michael C, and Walters, James TR

Subjects
Genetics, Prevention, Schizophrenia, Depression, Behavioral and Social Science, Mental Health, Brain Disorders, Serious Mental Illness, Human Genome, 2.1 Biological and endogenous factors, Aetiology, 2.3 Psychological, social and economic factors, Mental health, Bipolar Disorder, Datasets as Topic, Depressive Disorder, Major, Educational Status, Genome-Wide Association Study, Humans, Intelligence, Multifactorial Inheritance, Psychotic Disorders, psychiatry, genomics, intelligence, bioinformatics, GROUP Investigators, EUGEI WP2 Group, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Medical and Health Sciences, Psychology and Cognitive Sciences, Psychiatry
Abstract

BackgroundCognitive impairment is a clinically important feature of schizophrenia. Polygenic risk score (PRS) methods have demonstrated genetic overlap between schizophrenia, bipolar disorder (BD), major depressive disorder (MDD), educational attainment (EA), and IQ, but very few studies have examined associations between these PRS and cognitive phenotypes within schizophrenia cases.MethodsWe combined genetic and cognitive data in 3034 schizophrenia cases from 11 samples using the general intelligence factor g as the primary measure of cognition. We used linear regression to examine the association between cognition and PRS for EA, IQ, schizophrenia, BD, and MDD. The results were then meta-analyzed across all samples. A genome-wide association studies (GWAS) of cognition was conducted in schizophrenia cases.ResultsPRS for both population IQ (P = 4.39 × 10-28) and EA (P = 1.27 × 10-26) were positively correlated with cognition in those with schizophrenia. In contrast, there was no association between cognition in schizophrenia cases and PRS for schizophrenia (P = .39), BD (P = .51), or MDD (P = .49). No individual variant approached genome-wide significance in the GWAS.ConclusionsCognition in schizophrenia cases is more strongly associated with PRS that index cognitive traits in the general population than PRS for neuropsychiatric disorders. This suggests the mechanisms of cognitive variation within schizophrenia are at least partly independent from those that predispose to schizophrenia diagnosis itself. Our findings indicate that this cognitive variation arises at least in part due to genetic factors shared with cognitive performance in populations and is not solely due to illness or treatment-related factors, although our findings are consistent with important contributions from these factors.

Published
2020

32. InvitroSPI and a large database of proteasome-generated spliced and non-spliced peptides

Author

Hanna P. Roetschke, Guillermo Rodriguez-Hernandez, John A. Cormican, Xiaoping Yang, Steven Lynham, Michele Mishto, and Juliane Liepe

Subjects
Science
Abstract

Abstract Noncanonical epitopes presented by Human Leucocyte Antigen class I (HLA-I) complexes to CD8+ T cells attracted the spotlight in the research of novel immunotherapies against cancer, infection and autoimmunity. Proteasomes, which are the main producers of HLA-I-bound antigenic peptides, can catalyze both peptide hydrolysis and peptide splicing. The prediction of proteasome-generated spliced peptides is an objective that still requires a reliable (and large) database of non-spliced and spliced peptides produced by these proteases. Here, we present an extended database of proteasome-generated spliced and non-spliced peptides, which was obtained by analyzing in vitro digestions of 80 unique synthetic polypeptide substrates, measured by different mass spectrometers. Peptides were identified through invitroSPI method, which was validated through in silico and in vitro strategies. The peptide product database contains 16,631 unique peptide products (5,493 non-spliced, 6,453 cis-spliced and 4,685 trans-spliced peptide products), and a substrate sequence variety that is a valuable source for predictors of proteasome-catalyzed peptide hydrolysis and splicing. Potential artefacts and skewed results due to different identification and analysis strategies are discussed.

Published
2023
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34. Two Notes Opus review

Author

Lynham, Alex

Subjects
Music
Abstract

Byline: Alex Lynham Is this Two Notes' magnum opus? Two Notes Opus: What is it? Two Notes goes out of its way to identify a problem and solve it properly. [...]

Published
2024

38. SoundLad Liverpool Clean Machine

Author

Lynham, Alex

Subjects
Music
Abstract

Byline: Alex Lynham A slightly flawed masterpiece of a preamp pedal SoundLad Liverpool Clean Machine: What is it? What's exciting about the Clean Machine is that it's something a little [...]

Published
2023

39. Data on how abundance of resource inflows and punishment types affect resource extraction behavior

Author

Anna Lou Abatayo and John Lynham

Subjects
Resource curse, Common pool resources, Social ostracism, Financial Punishment, Computer applications to medicine. Medical informatics, R858-859.7, Science (General), Q1-390
Abstract

The data is collected through laboratory experiments on a dynamic common pool resource game, where, in an infinitely repeated number of rounds (i.e., game ended randomly), individuals made decisions about whether to exert a high or a low effort level to extract resources. Experiments were conducted using the student sample (consent provided and ethics approved) at the University of Hawaiʻi at Mānoa. A total of 8 sessions, 2 for each of the 4 treatments, were run with exactly 20 participants within a session. Individuals made decisions in groups of 10. Communication between any participant was not allowed. A session is randomly assigned (1) to vary whether the inflow of resources at the beginning of each round is high or low, and (2) to allow participants to either financially punish or socially punish defectors. A financial punishment resulted to a loss in profit for the punished while a social punishment displayed the words “You have extracted too much! You're being greedy!” on the computer screen of the punished. Individuals were assigned subject ID numbers and interacted using their subject IDs. The data is useful in understanding how resource inflow and type of punishment affects individual resource extraction behavior. The data could also be combined with other publicly available common pool resource datasets for a meta-analysis on individual behavior in the commons.

Published
2023
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40. Publisher Correction: Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection

Author

Pardiñas, Antonio F, Holmans, Peter, Pocklington, Andrew J, Escott-Price, Valentina, Ripke, Stephan, Carrera, Noa, Legge, Sophie E, Bishop, Sophie, Cameron, Darren, Hamshere, Marian L, Han, Jun, Hubbard, Leon, Lynham, Amy, Mantripragada, Kiran, Rees, Elliott, MacCabe, James H, McCarroll, Steven A, Baune, Bernhard T, Breen, Gerome, Byrne, Enda M, Dannlowski, Udo, Eley, Thalia C, Hayward, Caroline, Martin, Nicholas G, McIntosh, Andrew M, Plomin, Robert, Porteous, David J, Wray, Naomi R, Caballero, Armando, Geschwind, Daniel H, Huckins, Laura M, Ruderfer, Douglas M, Santiago, Enrique, Sklar, Pamela, Stahl, Eli A, Won, Hyejung, Agerbo, Esben, Als, Thomas D, Andreassen, Ole A, Bækvad-Hansen, Marie, Mortensen, Preben Bo, Pedersen, Carsten Bøcker, Børglum, Anders D, Bybjerg-Grauholm, Jonas, Djurovic, Srdjan, Durmishi, Naser, Pedersen, Marianne Giørtz, Golimbet, Vera, Grove, Jakob, Hougaard, David M, Mattheisen, Manuel, Molden, Espen, Mors, Ole, Nordentoft, Merete, Pejovic-Milovancevic, Milica, Sigurdsson, Engilbert, Silagadze, Teimuraz, Hansen, Christine Søholm, Stefansson, Kari, Stefansson, Hreinn, Steinberg, Stacy, Tosato, Sarah, Werge, Thomas, Collier, David A, Rujescu, Dan, Kirov, George, Owen, Michael J, O’Donovan, Michael C, and Walters, James TR

Subjects
GERAD1 Consortium, CRESTAR Consortium, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2019

41. DRAGON-Data: a platform and protocol for integrating genomic and phenotypic data across large psychiatric cohorts

Author

Amy J. Lynham, Sarah Knott, Jack F. G. Underwood, Leon Hubbard, Sharifah S. Agha, Jonathan I. Bisson, Marianne B. M. van den Bree, Samuel J. R. A. Chawner, Nicholas Craddock, Michael O'Donovan, Ian R. Jones, George Kirov, Kate Langley, Joanna Martin, Frances Rice, Neil P. Roberts, Anita Thapar, Richard Anney, Michael J. Owen, Jeremy Hall, Antonio F. Pardiñas, and James T. R. Walters

Subjects
Genetics, schizophrenia, developmental disorders, bipolar affective disorders, attention-deficit hyperactivity disorders, Psychiatry, RC435-571
Abstract

Background Current psychiatric diagnoses, although heritable, have not been clearly mapped onto distinct underlying pathogenic processes. The same symptoms often occur in multiple disorders, and a substantial proportion of both genetic and environmental risk factors are shared across disorders. However, the relationship between shared symptoms and shared genetic liability is still poorly understood. Aims Well-characterised, cross-disorder samples are needed to investigate this matter, but few currently exist. Our aim is to develop procedures to purposely curate and aggregate genotypic and phenotypic data in psychiatric research. Method As part of the Cardiff MRC Mental Health Data Pathfinder initiative, we have curated and harmonised phenotypic and genetic information from 15 studies to create a new data repository, DRAGON-Data. To date, DRAGON-Data includes over 45 000 individuals: adults and children with neurodevelopmental or psychiatric diagnoses, affected probands within collected families and individuals who carry a known neurodevelopmental risk copy number variant. Results We have processed the available phenotype information to derive core variables that can be reliably analysed across groups. In addition, all data-sets with genotype information have undergone rigorous quality control, imputation, copy number variant calling and polygenic score generation. Conclusions DRAGON-Data combines genetic and non-genetic information, and is available as a resource for research across traditional psychiatric diagnostic categories. Algorithms and pipelines used for data harmonisation are currently publicly available for the scientific community, and an appropriate data-sharing protocol will be developed as part of ongoing projects (DATAMIND) in partnership with Health Data Research UK.

Published
2023
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42. Mapping genomic loci implicates genes and synaptic biology in schizophrenia

Author

Trubetskoy, Vassily, Pardiñas, Antonio F., Qi, Ting, Panagiotaropoulou, Georgia, Awasthi, Swapnil, Bigdeli, Tim B., Bryois, Julien, Chen, Chia-Yen, Dennison, Charlotte A., Hall, Lynsey S., Lam, Max, Watanabe, Kyoko, Frei, Oleksandr, Ge, Tian, Harwood, Janet C., Koopmans, Frank, Magnusson, Sigurdur, Richards, Alexander L., Sidorenko, Julia, Wu, Yang, Zeng, Jian, Grove, Jakob, Kim, Minsoo, Li, Zhiqiang, Voloudakis, Georgios, Zhang, Wen, Adams, Mark, Agartz, Ingrid, Atkinson, Elizabeth G., Agerbo, Esben, Al Eissa, Mariam, Albus, Margot, Alexander, Madeline, Alizadeh, Behrooz Z., Alptekin, Köksal, Als, Thomas D., Amin, Farooq, Arolt, Volker, Arrojo, Manuel, Athanasiu, Lavinia, Azevedo, Maria Helena, Bacanu, Silviu A., Bass, Nicholas J., Begemann, Martin, Belliveau, Richard A., Bene, Judit, Benyamin, Beben, Bergen, Sarah E., Blasi, Giuseppe, Bobes, Julio, Bonassi, Stefano, Braun, Alice, Bressan, Rodrigo Affonseca, Bromet, Evelyn J., Bruggeman, Richard, Buckley, Peter F., Buckner, Randy L., Bybjerg-Grauholm, Jonas, Cahn, Wiepke, Cairns, Murray J., Calkins, Monica E., Carr, Vaughan J., Castle, David, Catts, Stanley V., Chambert, Kimberley D., Chan, Raymond C. K., Chaumette, Boris, Cheng, Wei, Cheung, Eric F. C., Chong, Siow Ann, Cohen, David, Consoli, Angèle, Cordeiro, Quirino, Costas, Javier, Curtis, Charles, Davidson, Michael, Davis, Kenneth L., de Haan, Lieuwe, Degenhardt, Franziska, DeLisi, Lynn E., Demontis, Ditte, Dickerson, Faith, Dikeos, Dimitris, Dinan, Timothy, Djurovic, Srdjan, Duan, Jubao, Ducci, Giuseppe, Dudbridge, Frank, Eriksson, Johan G., Fañanás, Lourdes, Faraone, Stephen V., Fiorentino, Alessia, Forstner, Andreas, Frank, Josef, Freimer, Nelson B., Fromer, Menachem, Frustaci, Alessandra, Gadelha, Ary, Genovese, Giulio, Gershon, Elliot S., Giannitelli, Marianna, Giegling, Ina, Giusti-Rodríguez, Paola, Godard, Stephanie, Goldstein, Jacqueline I., González Peñas, Javier, González-Pinto, Ana, Gopal, Srihari, Gratten, Jacob, Green, Michael F., Greenwood, Tiffany A., Guillin, Olivier, Gülöksüz, Sinan, Gur, Raquel E., Gur, Ruben C., Gutiérrez, Blanca, Hahn, Eric, Hakonarson, Hakon, Haroutunian, Vahram, Hartmann, Annette M., Harvey, Carol, Hayward, Caroline, Henskens, Frans A., Herms, Stefan, Hoffmann, Per, Howrigan, Daniel P., Ikeda, Masashi, Iyegbe, Conrad, Joa, Inge, Julià, Antonio, Kähler, Anna K., Kam-Thong, Tony, Kamatani, Yoichiro, Karachanak-Yankova, Sena, Kebir, Oussama, Keller, Matthew C., Kelly, Brian J., Khrunin, Andrey, Kim, Sung-Wan, Klovins, Janis, Kondratiev, Nikolay, Konte, Bettina, Kraft, Julia, Kubo, Michiaki, Kučinskas, Vaidutis, Kučinskiene, Zita Ausrele, Kusumawardhani, Agung, Kuzelova-Ptackova, Hana, Landi, Stefano, Lazzeroni, Laura C., Lee, Phil H., Legge, Sophie E., Lehrer, Douglas S., Lencer, Rebecca, Lerer, Bernard, Li, Miaoxin, Lieberman, Jeffrey, Light, Gregory A., Limborska, Svetlana, Liu, Chih-Min, Lönnqvist, Jouko, Loughland, Carmel M., Lubinski, Jan, Luykx, Jurjen J., Lynham, Amy, Macek, Jr, Milan, Mackinnon, Andrew, Magnusson, Patrik K. E., Maher, Brion S., Maier, Wolfgang, Malaspina, Dolores, Mallet, Jacques, Marder, Stephen R., Marsal, Sara, Martin, Alicia R., Martorell, Lourdes, Mattheisen, Manuel, McCarley, Robert W., McDonald, Colm, McGrath, John J., Medeiros, Helena, Meier, Sandra, Melegh, Bela, Melle, Ingrid, Mesholam-Gately, Raquelle I., Metspalu, Andres, Michie, Patricia T., Milani, Lili, Milanova, Vihra, Mitjans, Marina, Molden, Espen, Molina, Esther, Molto, María Dolores, Mondelli, Valeria, Moreno, Carmen, Morley, Christopher P., Muntané, Gerard, Murphy, Kieran C., Myin-Germeys, Inez, Nenadić, Igor, Nestadt, Gerald, Nikitina-Zake, Liene, Noto, Cristiano, Nuechterlein, Keith H., O’Brien, Niamh Louise, O’Neill, F. Anthony, Oh, Sang-Yun, Olincy, Ann, Ota, Vanessa Kiyomi, Pantelis, Christos, Papadimitriou, George N., Parellada, Mara, Paunio, Tiina, Pellegrino, Renata, Periyasamy, Sathish, Perkins, Diana O., Pfuhlmann, Bruno, Pietiläinen, Olli, Pimm, Jonathan, Porteous, David, Powell, John, Quattrone, Diego, Quested, Digby, Radant, Allen D., Rampino, Antonio, Rapaport, Mark H., Rautanen, Anna, Reichenberg, Abraham, Roe, Cheryl, Roffman, Joshua L., Roth, Julian, Rothermundt, Matthias, Rutten, Bart P. F., Saker-Delye, Safaa, Salomaa, Veikko, Sanjuan, Julio, Santoro, Marcos Leite, Savitz, Adam, Schall, Ulrich, Scott, Rodney J., Seidman, Larry J., Sharp, Sally Isabel, Shi, Jianxin, Siever, Larry J., Sigurdsson, Engilbert, Sim, Kang, Skarabis, Nora, Slominsky, Petr, So, Hon-Cheong, Sobell, Janet L., Söderman, Erik, Stain, Helen J., Steen, Nils Eiel, Steixner-Kumar, Agnes A., Stögmann, Elisabeth, Stone, William S., Straub, Richard E., Streit, Fabian, Strengman, Eric, Stroup, T. Scott, Subramaniam, Mythily, Sugar, Catherine A., Suvisaari, Jaana, Svrakic, Dragan M., Swerdlow, Neal R., Szatkiewicz, Jin P., Ta, Thi Minh Tam, Takahashi, Atsushi, Terao, Chikashi, Thibaut, Florence, Toncheva, Draga, Tooney, Paul A., Torretta, Silvia, Tosato, Sarah, Tura, Gian Battista, Turetsky, Bruce I., Üçok, Alp, Vaaler, Arne, van Amelsvoort, Therese, van Winkel, Ruud, Veijola, Juha, Waddington, John, Walter, Henrik, Waterreus, Anna, Webb, Bradley T., Weiser, Mark, Williams, Nigel M., Witt, Stephanie H., Wormley, Brandon K., Wu, Jing Qin, Xu, Zhida, Yolken, Robert, Zai, Clement C., Zhou, Wei, Zhu, Feng, Zimprich, Fritz, Atbaşoğlu, Eşref Cem, Ayub, Muhammad, Benner, Christian, Bertolino, Alessandro, Black, Donald W., Bray, Nicholas J., Breen, Gerome, Buccola, Nancy G., Byerley, William F., Chen, Wei J., Cloninger, C. Robert, Crespo-Facorro, Benedicto, Donohoe, Gary, Freedman, Robert, Galletly, Cherrie, Gandal, Michael J., Gennarelli, Massimo, Hougaard, David M., Hwu, Hai-Gwo, Jablensky, Assen V., McCarroll, Steven A., Moran, Jennifer L., Mors, Ole, Mortensen, Preben B., Müller-Myhsok, Bertram, Neil, Amanda L., Nordentoft, Merete, Pato, Michele T., Petryshen, Tracey L., Pirinen, Matti, Pulver, Ann E., Schulze, Thomas G., Silverman, Jeremy M., Smoller, Jordan W., Stahl, Eli A., Tsuang, Debby W., Vilella, Elisabet, Wang, Shi-Heng, Xu, Shuhua, Adolfsson, Rolf, Arango, Celso, Baune, Bernhard T., Belangero, Sintia Iole, Børglum, Anders D., Braff, David, Bramon, Elvira, Buxbaum, Joseph D., Campion, Dominique, Cervilla, Jorge A., Cichon, Sven, Collier, David A., Corvin, Aiden, Curtis, David, Forti, Marta Di, Domenici, Enrico, Ehrenreich, Hannelore, Escott-Price, Valentina, Esko, Tõnu, Fanous, Ayman H., Gareeva, Anna, Gawlik, Micha, Gejman, Pablo V., Gill, Michael, Glatt, Stephen J., Golimbet, Vera, Hong, Kyung Sue, Hultman, Christina M., Hyman, Steven E., Iwata, Nakao, Jönsson, Erik G., Kahn, René S., Kennedy, James L., Khusnutdinova, Elza, Kirov, George, Knowles, James A., Krebs, Marie-Odile, Laurent-Levinson, Claudine, Lee, Jimmy, Lencz, Todd, Levinson, Douglas F., Li, Qingqin S., Liu, Jianjun, Malhotra, Anil K., Malhotra, Dheeraj, McIntosh, Andrew, McQuillin, Andrew, Menezes, Paulo R., Morgan, Vera A., Morris, Derek W., Mowry, Bryan J., Murray, Robin M., Nimgaonkar, Vishwajit, Nöthen, Markus M., Ophoff, Roel A., Paciga, Sara A., Palotie, Aarno, Pato, Carlos N., Qin, Shengying, Rietschel, Marcella, Riley, Brien P., Rivera, Margarita, Rujescu, Dan, Saka, Meram C., Sanders, Alan R., Schwab, Sibylle G., Serretti, Alessandro, Sham, Pak C., Shi, Yongyong, St Clair, David, Stefánsson, Hreinn, Stefansson, Kari, Tsuang, Ming T., van Os, Jim, Vawter, Marquis P., Weinberger, Daniel R., Werge, Thomas, Wildenauer, Dieter B., Yu, Xin, Yue, Weihua, Holmans, Peter A., Pocklington, Andrew J., Roussos, Panos, Vassos, Evangelos, Verhage, Matthijs, Visscher, Peter M., Yang, Jian, Posthuma, Danielle, Andreassen, Ole A., Kendler, Kenneth S., Owen, Michael J., Wray, Naomi R., Daly, Mark J., Huang, Hailiang, Neale, Benjamin M., Sullivan, Patrick F., Ripke, Stephan, Walters, James T. R., and O’Donovan, Michael C.

Published
2022
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43. Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation

Author

Corsini, Paula M., Wang, Sunjun, Rehman, Saima, Fenn, Katherine, Sagar, Amin, Sirovica, Slobodan, Cleaver, Leanne, Edwards-Gayle, Charlotte J. C., Mastroianni, Giulia, Dorgan, Ben, Sewell, Lee M., Lynham, Steven, Iuga, Dinu, Franks, W. Trent, Jarvis, James, Carpenter, Guy H., Curtis, Michael. A., Bernadó, Pau, Darbari, Vidya C., and Garnett, James A.

Published
2022
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45. Measuring cognition across mood and psychotic disorders

Author

Lynham, Amy

Subjects
616.89
Abstract

Cognitive impairments are present in both schizophrenia and bipolar disorder and are strong predictors of functional outcomes for patients. One barrier in cognitive research of these disorders is the lack of large, well-characterised cross-disorder samples with cognitive data. The aims of this thesis were to examine cognition across the bipolar / schizophrenia diagnostic spectrum and to develop a new online cognitive battery for use in psychiatric research. Cognition was examined in participants with bipolar disorder, schizoaffective disorder and schizophrenia through a meta-analysis of existing studies and analysing data from a large well-characterised sample. The main finding was that there is a gradient of increasing cognitive impairment from bipolar disorder through schizoaffective disorder – bipolar type to schizoaffective disorder – depressive type and schizophrenia. Participants with the subtypes of schizoaffective disorder differed in their cognitive performance. Lifetime history of psychosis was associated with cognitive performance across disorders. An online cognitive battery was developed to assess the domains outlined by the Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) initiative. The battery was validated against the MATRICS Consensus Cognitive Battery and showed that the tasks provided valid measurements of the majority of the MATRICS domains. A large sample of participants with a range of psychiatric disorders was recruited online. An examination of cognition in participants with major depressive disorder, bipolar disorder and schizophrenia showed that cognitive profiles were similar across disorders but participants with schizophrenia have more severe impairments than participants with bipolar disorder. An important concluding observation was that poorer cognitive performance was associated with poorer functional outcome across disorders. The findings of this thesis add to a growing literature showing the importance of examining cognitive function across psychiatric disorders. To date, it is the first study to develop and utilise an online cognitive assessment for psychiatric research.

Published
2018

46. Fender Tone Master Pro & Tone Master FR-12 review

Author

Lynham, Alex

Subjects
Music
Abstract

Byline: Alex Lynham Fender releases its latest flagship amp modeller Fender Tone Master Pro & Tone Master FR-12: What is it? The modelling space is hotter than ever, and all [...]

Published
2023

47. Warm Audio Mutation Phasor ll review

Author

Lynham, Alex

Subjects
Music
Abstract

Byline: Alex Lynham Set phasers to stun Warm Audio Mutation Phasor ll: What is it? There are three main designs for phaser pedals. The EHX Small Stone is OTA-based, and [...]

Published
2023

48. BeSAD … 'It Was Truly an Awful Experience': An Exploration of Pre-Service Teachers' Experiences and Training Needs to Support Pupils Experiencing Issues of Bereavement, Separation and Divorce

Author

Lynham, Aoife, McConnell, Barbara, and McGuckin, Conor

Abstract

Research exploring the well-being and pastoral care of pupils attending primary and post-primary schools has become an issue of increased discourse and growing national and international concern in recent years. Society often expects that teachers can support or facilitate pupils experiencing such issues; however, there is little research that explores whether pre-service teachers encounter these issues on school placement and how they approach such concerns if they do. This paper reports on a study of pre-service teachers (N = 354) from the Republic of Ireland (RoI) and Northern Ireland (NI) and the frequency with which they encountered issues relating to bereavement, separation and divorce (BeSAD). To address the training needs, six semi-structured interviews with experts in the area of BeSAD and Initial Teacher Education (ITE) are also included. The quantitative component of the research indicated that nearly half of the pre-service teachers had encountered pupils who had experienced some form of BeSAD whilst on school placement. Respondents lacked confidence when supporting pupils experiencing BeSAD, particularly in relation to separation and divorce. The interviews conducted with experts from NI and the RoI (N = 6) identified the core role that teachers play as advocates for pupils who have experienced BeSAD.

Published
2020
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49. Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation

Author

Paula M. Corsini, Sunjun Wang, Saima Rehman, Katherine Fenn, Amin Sagar, Slobodan Sirovica, Leanne Cleaver, Charlotte J. C. Edwards-Gayle, Giulia Mastroianni, Ben Dorgan, Lee M. Sewell, Steven Lynham, Dinu Iuga, W. Trent Franks, James Jarvis, Guy H. Carpenter, Michael. A. Curtis, Pau Bernadó, Vidya C. Darbari, and James A. Garnett

Subjects
Microbial ecology, QR100-130
Abstract

Abstract Escherichia coli is a Gram-negative bacterium that colonises the human intestine and virulent strains can cause severe diarrhoeal and extraintestinal diseases. The protein SslE is secreted by a range of pathogenic and commensal E. coli strains. It can degrade mucins in the intestine, promotes biofilm maturation and it is a major determinant of infection in virulent strains, although how it carries out these functions is not well understood. Here, we examine SslE from the commensal E. coli Waksman and BL21 (DE3) strains and the enterotoxigenic H10407 and enteropathogenic E2348/69 strains. We reveal that SslE has a unique and dynamic structure in solution and in response to acidification within mature biofilms it can form a unique aggregate with amyloid-like properties. Furthermore, we show that both SslE monomers and aggregates bind DNA in vitro and co-localise with extracellular DNA (eDNA) in mature biofilms, and SslE aggregates may also associate with cellulose under certain conditions. Our results suggest that interactions between SslE and eDNA are important for biofilm maturation in many E. coli strains and SslE may also be a factor that drives biofilm formation in other SslE-secreting bacteria.

Published
2022
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50. Fishing activity before closure, during closure, and after reopening of the Northeast Canyons and Seamounts Marine National Monument

Author

John Lynham

Subjects
Medicine, Science
Abstract

Abstract Evaluation of the economic impacts of marine protected areas is hampered by the fact that it is impossible to observe what would have happened if the protected area had never been closed to fishing (the counterfactual). Catch reports and vessel tracks are used to perform an analysis of the potential negative economic impacts of establishing the Northeast Canyons and Seamounts Marine National Monument (located off the east coast of the United States of America) on three commercially important fisheries that were identified as having potential to be harmed. I conclude that there was little to no negative impact on any of the fisheries. I also test for, but find no evidence of, a Blue Paradox effect. Due to political factors largely unrelated to fisheries status, the protected area was reopened to commercial fishing on June 5th, 2020. I use this event, which was reversed sixteen months later, to test whether there were any economic benefits from reopening. I do not observe an increase in catch, a reduction in distance traveled, or an increase in relative fishing effort inside the protected area (compared to historical trends), consistent with the post-closure findings.

Published
2022
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