30 Works

Data from: Genome-wide evidence for speciation with gene flow in Heliconius butterflies

Simon H. Martin, Kanchon K. Dasmahapatra, Nicola J. Nadeau, Camilo Salazar, James R. Walters, Fraser Simpson, Mark Blaxter, Andrea Manica, James Mallet & Chris D. Jiggins
Most speciation events probably occur gradually, without complete and immediate reproductive isolation, but the full extent of gene flow between diverging species has rarely been characterized on a genome-wide scale. Documenting the extent and timing of admixture between diverging species can clarify the role of geographic isolation in speciation. Here we use new methodology to quantify admixture at different stages of divergence in Heliconius butterflies, based on whole genome sequences of 31 individuals. Comparisons between...

Data from: Selective breeding and selection mapping using a novel wild-derived heterogeneous stock mice revealed two closely-linked loci for tameness

Yuki Matsumoto, Tatsuhiko Goto, Jo Nishino, Hirofumi Nakaoka, Akira Tanave, Toshiyuki Takano-Shimizu, Richard F. Mott & Tsuyoshi Koide
Tameness is a major behavioral factor for domestication, and can be divided into two potential components: motivation to approach humans (active tameness) and reluctance to avoid humans (passive tameness). We identified genetic loci for active tameness through selective breeding, selection mapping, and association analysis. In previous work using laboratory and wild mouse strains, we found that laboratory strains were predominantly selected for passive tameness but not active tameness during their domestication. To identify genetic regions...

sj-pdf-1-jrs-10.1177_01410768221131897 - Supplemental material for Using national electronic health records for pandemic preparedness: validation of a parsimonious model for predicting excess deaths among those with COVID-19–a data-driven retrospective cohort study

Mehrdad A Mizani, Ashkan Dashtban, Laura Pasea, Alvina G Lai, Johan Thygesen, Chris Tomlinson, Alex Handy, Jil B Mamza, Tamsin Morris, Sara Khalid, Francesco Zaccardi, Mary Joan Macleod, Fatemeh Torabi, Dexter Canoy, Ashley Akbari, Colin Berry, Thomas Bolton, John Nolan, Kamlesh Khunti, Spiros Denaxas, Harry Hemingway, Cathie Sudlow & Amitava Banerjee
Supplemental material, sj-pdf-1-jrs-10.1177_01410768221131897 for Using national electronic health records for pandemic preparedness: validation of a parsimonious model for predicting excess deaths among those with COVID-19–a data-driven retrospective cohort study by Mehrdad A Mizani, Ashkan Dashtban, Laura Pasea, Alvina G Lai, Johan Thygesen, Chris Tomlinson, Alex Handy, Jil B Mamza, Tamsin Morris, Sara Khalid, Francesco Zaccardi, Mary Joan Macleod, Fatemeh Torabi, Dexter Canoy, Ashley Akbari, Colin Berry, Thomas Bolton, John Nolan, Kamlesh Khunti, Spiros Denaxas, Harry...

Using national electronic health records for pandemic preparedness: validation of a parsimonious model for predicting excess deaths among those with COVID-19–a data-driven retrospective cohort study

Mehrdad A Mizani, Ashkan Dashtban, Laura Pasea, Alvina G Lai, Johan Thygesen, Chris Tomlinson, Alex Handy, Jil B Mamza, Tamsin Morris, Sara Khalid, Francesco Zaccardi, Mary Joan Macleod, Fatemeh Torabi, Dexter Canoy, Ashley Akbari, Colin Berry, Thomas Bolton, John Nolan, Kamlesh Khunti, Spiros Denaxas, Harry Hemingway, Cathie Sudlow & Amitava Banerjee
ObjectivesTo use national, pre- and post-pandemic electronic health records (EHR) to develop and validate a scenario-based model incorporating baseline mortality risk, infection rate (IR) and relative risk (RR) of death for prediction of excess deaths.DesignAn EHR-based, retrospective cohort study.SettingLinked EHR in Clinical Practice Research Datalink (CPRD); and linked EHR and COVID-19 data in England provided in NHS Digital Trusted Research Environment (TRE).ParticipantsIn the development (CPRD) and validation (TRE) cohorts, we included 3.8 million and 35.1...

STIMULATE-ICP-Delphi (symptoms, trajectory, inequalities and management: Understanding long-COVID to address and transform existing integrated care pathways Delphi): Study protocol.

Christina M van der Feltz-Cornelis, Jennifer Sweetman, Gail Allsopp, Emily Attree, Michael G Crooks, Daniel J Cuthbertson, Denise Forshaw, Mark Gabbay, Angela Green, Melissa Heightman, Toby Hillman, Lyth Hishmeh, Kamlesh Khunti, Gregory YH Lip, Paula Lorgelly, Hugh Montgomery, W David Strain, Emma Wall, Caroline Watkins, Nefyn Williams, Dan G Wootton, Amitava Banerjee & STIMULATE-ICP Consortium
INTRODUCTION: As mortality rates from COVID-19 disease fall, the high prevalence of long-term sequelae (Long COVID) is becoming increasingly widespread, challenging healthcare systems globally. Traditional pathways of care for Long Term Conditions (LTCs) have tended to be managed by disease-specific specialties, an approach that has been ineffective in delivering care for patients with multi-morbidity. The multi-system nature of Long COVID and its impact on physical and psychological health demands a more effective model of holistic,...

Data from: Sequence entropy of folding and the absolute rate of amino acid substitutions

Richard A. Goldstein & David D. Pollock
Adequate representations of protein evolution should consider how the acceptance of mutations depends on the sequence context in which they arise. However, epistatic interactions among sites in a protein result in hererogeneities in the substitution rate, both temporal and spatial, that are beyond the capabilities of current models. Here we use parallels between amino acid substitutions and chemical reaction kinetics to develop an improved theory of protein evolution. We constructed a mechanistic framework for modelling...

Data from: Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: a case study of male cheetahs in the Maasai Mara, Kenya

Femke Broekhuis, Emily Madsen, Kosiom Keiwua & David Macdonald
Intraspecific interactions between individuals or groups of individuals of the same species are an important component of population dynamics. Interactions can be static, such as spatial overlap, or dynamic based on the interactions of movements, and can be mediated through communication, such as the deployment of scent marks. Interactions and their behavioural outcomes can be difficult to determine, especially for species that live at low densities. With the use of GPS collars we quantify both...

Additional file 1 of Mapping between headache specific and generic preference-based health-related quality of life measures

Kamran Khan, Hema Mistry, Manjit Matharu, Chloe Norman, Stavros Petrou, Kimberley Stewart, Martin Underwood & Felix Achana
Additional file 1: Table S1. Model Performance for HIT-6 to EQ-5D-5L (Estimated using sub study data and validation using CHESS). Table S2. Model Performance for HIT-6 to SF-6D (Estimated using sub study data and validation using CHESS). Table S3. Model Performance for CH-QLQ to EQ-5D-5L (Estimated using sub study data and validation using CHESS). Table S4. Model Performance for CH-QLQ to SF-6D (Estimated using sub study data and validation using CHESS).

Mapping between headache specific and generic preference-based health-related quality of life measures

Kamran Khan, Hema Mistry, Manjit Matharu, Chloe Norman, Stavros Petrou, Kimberley Stewart, Martin Underwood & Felix Achana
Abstract Background The Headache Impact Test (HIT-6) and the Chronic Headache Questionnaire (CH-QLQ) measure headache-related quality of life but are not preference-based and therefore cannot be used to generate health utilities for cost-effectiveness analyses. There are currently no established algorithms for mapping between the HIT-6 or CH-QLQ and preference-based health-related quality-of-life measures for chronic headache population. Methods We developed algorithms for generating EQ-5D-5L and SF-6D utilities from the HIT-6 and the CHQLQ using both direct...

sj-pdf-1-jrs-10.1177_01410768221131897 - Supplemental material for Using national electronic health records for pandemic preparedness: validation of a parsimonious model for predicting excess deaths among those with COVID-19–a data-driven retrospective cohort study

Mehrdad A Mizani, Ashkan Dashtban, Laura Pasea, Alvina G Lai, Johan Thygesen, Chris Tomlinson, Alex Handy, Jil B Mamza, Tamsin Morris, Sara Khalid, Francesco Zaccardi, Mary Joan Macleod, Fatemeh Torabi, Dexter Canoy, Ashley Akbari, Colin Berry, Thomas Bolton, John Nolan, Kamlesh Khunti, Spiros Denaxas, Harry Hemingway, Cathie Sudlow & Amitava Banerjee
Supplemental material, sj-pdf-1-jrs-10.1177_01410768221131897 for Using national electronic health records for pandemic preparedness: validation of a parsimonious model for predicting excess deaths among those with COVID-19–a data-driven retrospective cohort study by Mehrdad A Mizani, Ashkan Dashtban, Laura Pasea, Alvina G Lai, Johan Thygesen, Chris Tomlinson, Alex Handy, Jil B Mamza, Tamsin Morris, Sara Khalid, Francesco Zaccardi, Mary Joan Macleod, Fatemeh Torabi, Dexter Canoy, Ashley Akbari, Colin Berry, Thomas Bolton, John Nolan, Kamlesh Khunti, Spiros Denaxas, Harry...

Interobserver Variability in the Assessment of Fluorescence Angiography in the Colon

Antonio S. Soares, Neil T. Clancy, Sophia Bano, Imran Raza, Michelle Diana, Laurence B. Lovat, Danail Stoyanov & Manish Chand
BackgroundFluorescence angiography in colorectal surgery is a technique that may lead to lower anastomotic leak rates. However, the interpretation of the fluorescent signal is not standardised and there is a paucity of data regarding interobserver agreement. The aim of this study is to assess interobserver variability in selection of the transection point during fluorescence angiography before anastomosis.MethodsAn online survey with still images of fluorescence angiography was distributed through colorectal surgery channels containing images from 13...

Data from: An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations.

Bernhard J Hofinger, Joanne R Russell, Christopher G Bass, Thomas Baldwin, Mario Dos Reis, Peter E Hedley, Yidan Li, Malcolm Macaulay, Robbie Waugh, Kim E Hammond-Kosack & Kostya Kanyuka
In barley, the eukaryotic translation initiation factor 4E (eIF4E) gene situated on chromosome 3H is recognised as an important source of resistance to the bymoviruses Barley yellow mosaic virus and Barley mild mosaic virus. In modern barley cultivars two recessive eIF4E alleles, rym4 and rym5, confer different isolate-specific resistances. In this study the sequence of eIF4E was analysed in 1090 barley landraces and non-current cultivars originating from 84 countries. An exceptionally high nucleotide diversity was...

Data from: Mental illness, poverty and stigma in India: a case control study

Jean-Francois Trani, Parul Bakhshi, Jill Kuhlberg, Sreelatha S. Venkataraman, Hemalatha Venkataraman, Nagendra N. Mishra, Nora E. Groce, Sushrut Jadhav & Smita Deshpande
Objective: To assess the effect of experienced stigma on depth of multidimensional poverty of persons with severe mental illness (PSMI) in Delhi, India, controlling for gender, age and caste. Design: Matching case (hospital)–control (population) study. Setting: University Hospital (cases) and National Capital Region (controls), India. Participants: A case–control study was conducted from November 2011 to June 2012. 647 cases diagnosed with schizophrenia or affective disorders were recruited and 647 individuals of same age, sex and...

Data from: A global genetic interaction network maps a wiring diagram of cellular function

Michael Costanzo, Benjamin VanderSluis, Elizabeth N. Koch, Anastasia Baryshnikova, Carles Pons, Guihong Tan, Wen Wang, Matej Usaj, Julia Hanchard, Susan D. Lee, Vicent Pelechano, Erin B. Styles, Maximilian Billmann, Jolanda Van Leeuwen, Nydia Van Dyk, Zhen-Yuan Lin, Elena Kuzmin, Justin Nelson, Jeff S. Piotrowski, Tharan Srikumar, Sondra Bahr, Yiqun Chen, Raamesh Deshpande, Christoph F. Kurat, Sheena C. Li … & Charles Boone
INTRODUCTION: Genetic interactions occur when mutations in two or more genes combine to generate an unexpected phenotype. An extreme negative or synthetic lethal genetic interaction occurs when two mutations, neither lethal individually, combine to cause cell death. Conversely, positive genetic interactions occur when two mutations produce a phenotype that is less severe than expected. Genetic interactions identify functional relationships between genes and can be harnessed for biological discovery and therapeutic target identification. They may also...

Mapping between headache specific and generic preference-based health-related quality of life measures

Kamran Khan, Hema Mistry, Manjit Matharu, Chloe Norman, Stavros Petrou, Kimberley Stewart, Martin Underwood & Felix Achana
Abstract Background The Headache Impact Test (HIT-6) and the Chronic Headache Questionnaire (CH-QLQ) measure headache-related quality of life but are not preference-based and therefore cannot be used to generate health utilities for cost-effectiveness analyses. There are currently no established algorithms for mapping between the HIT-6 or CH-QLQ and preference-based health-related quality-of-life measures for chronic headache population. Methods We developed algorithms for generating EQ-5D-5L and SF-6D utilities from the HIT-6 and the CHQLQ using both direct...

Interobserver Variability in the Assessment of Fluorescence Angiography in the Colon

Antonio S. Soares, Neil T. Clancy, Sophia Bano, Imran Raza, Michelle Diana, Laurence B. Lovat, Danail Stoyanov & Manish Chand
BackgroundFluorescence angiography in colorectal surgery is a technique that may lead to lower anastomotic leak rates. However, the interpretation of the fluorescent signal is not standardised and there is a paucity of data regarding interobserver agreement. The aim of this study is to assess interobserver variability in selection of the transection point during fluorescence angiography before anastomosis.MethodsAn online survey with still images of fluorescence angiography was distributed through colorectal surgery channels containing images from 13...

sj-pdf-1-jrs-10.1177_01410768221090672 - Supplemental material for Socioeconomic inequality, waiting time initiatives and austerity in Scotland: an interrupted time series analysis of elective hip and knee replacements and arthroscopies

Graham Kirkwood & Allyson M Pollock
Supplemental material, sj-pdf-1-jrs-10.1177_01410768221090672 for Socioeconomic inequality, waiting time initiatives and austerity in Scotland: an interrupted time series analysis of elective hip and knee replacements and arthroscopies by Graham Kirkwood and Allyson M Pollock in Journal of the Royal Society of Medicine

Data from: Competition and constraint drove Cope's rule in the evolution of giant flying reptiles

Roger B. J. Benson, Rachel A. Frigot, Anjali Goswami, Brian Andres & Richard J. Butler
The pterosaurs, Mesozoic flying reptiles, attained wingspans of more than 10 m that greatly exceed the largest birds and challenge our understanding of size limits in flying animals. Pterosaurs have been used to illustrate Cope’s rule, the influential generalization that evolutionary lineages trend to increasingly large body sizes. However, unambiguous examples of Cope’s rule operating on extended timescales in large clades remain elusive, and the phylogenetic pattern and possible drivers of pterosaur gigantism are uncertain....

Data from: Nest inheritance is the missing source of direct fitness in a primitively eusocial insect

Ellouise Leadbeater, Jonathan M. Carruthers, Jonathan P. Green, Neil S. Rosser & Jeremy P. Field
Animals that co-operate with non-relatives represent a challenge to inclusive fitness theory, unless co-operative behavior is shown to provide direct fitness benefits. Inheritance of breeding resources could provide such benefits, but this route to co-operation has been little investigated in the social insects. We show that nest inheritance can explain the presence of unrelated helpers in a classic social insect model, the primitively eusocial wasp Polistes dominulus. We found that subordinate helpers produced more direct...

Data from: Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies

Megan A. Supple, Heather M. Hines, Kanchon K. Dasmahapatra, James J. Lewis, Dahlia M. Nielsen, Christine Lavoie, David A. Ray, Camilo Salazar, W. Owen McMillan & Brian A. Counterman
Identifying the genetic changes driving adaptive variation in natural populations is key to understanding the origins of biodiversity. The mosaic of mimetic wing patterns in Heliconius butterflies makes an excellent system for exploring adaptive variation using next-generation sequencing. In this study, we use a combination of techniques to annotate the genomic interval modulating red color pattern variation, identify a narrow region responsible for adaptive divergence and convergence in Heliconius wing color patterns, and explore the...

Data from: Mouse screen reveals multiple new genes underlying mouse and human hearing loss

Neil J. Ingham, Selina A. Pearson, Valerie E. Vancollie, Victoria Rook, Morag A. Lewis, Jing Chen, Annalisa Buniello, Elisa Martelletti, Lorenzo Preite, Chi C. Lam, Felix D. Weiss, Zoe Powis, Pim Suwannarat, Christopher J. Lelliot, Sally J. Dawson, Jacqueline K. White & Karen P. Steel
Adult-onset hearing loss is very common but we know little about the underlying molecular pathogenesis, impeding development of therapies. We took a genetic approach to identify new molecules involved in hearing loss by screening a large cohort of newly-generated mouse mutants using a sensitive electrophysiological test, the auditory brainstem response. We review here the findings from this screen. Thirty-eight unexpected genes associated with raised thresholds were detected from our unbiased sample of 1,211 genes tested,...

Tuning cell behavior with nanoparticle shape

Loris Rizzello, Alessandro Poma, Eva Liatsi-Douvitsa, Giuseppe Battaglia, Valeria De Matteis, Cesare De Pace, Adrian Joseph, Claudia Contini, Edoardo Scarpa, Josep Martí, Loris Rizzello & Senio De Souza
We investigated how the shape of polymeric vesicles, made by the exact same material, impacts the replication activity and metabolic state of both cancer and non-cancer cell types. First, we isolated discrete geometrical structures (spheres and tubes) from a heterogeneous sample using density-gradient centrifugation. Then, we characterized the cellular internalization and the kinetics of uptake of both types of polymersomes in different cell types (either cancer or non-cancer cells). We also investigated the cellular metabolic...

Additional file 1 of Mapping between headache specific and generic preference-based health-related quality of life measures

Kamran Khan, Hema Mistry, Manjit Matharu, Chloe Norman, Stavros Petrou, Kimberley Stewart, Martin Underwood & Felix Achana
Additional file 1: Table S1. Model Performance for HIT-6 to EQ-5D-5L (Estimated using sub study data and validation using CHESS). Table S2. Model Performance for HIT-6 to SF-6D (Estimated using sub study data and validation using CHESS). Table S3. Model Performance for CH-QLQ to EQ-5D-5L (Estimated using sub study data and validation using CHESS). Table S4. Model Performance for CH-QLQ to SF-6D (Estimated using sub study data and validation using CHESS).

Supplemental Material - Interobserver Variability in the Assessment of Fluorescence Angiography in the Colon

Antonio S. Soares, Neil T. Clancy, Sophia Bano, Imran Raza, Michelle Diana, Laurence B. Lovat, Danail Stoyanov & Manish Chand
Supplemental Material for Interobserver Variability in the Assessment of Fluorescence Angiography in the Colon by Antonio S. Soares, Neil T. Clancy, Sophia Bano, Imran Raza, Michelle Diana, Laurence B. Lovat, Danail Stoyanov, and Manish Chand in Surgical Innovation

Socioeconomic inequality, waiting time initiatives and austerity in Scotland: an interrupted time series analysis of elective hip and knee replacements and arthroscopies

Graham Kirkwood & Allyson M Pollock
ObjectivesNational Health Service (NHS) waiting times have long been a political priority in Scotland. In 2002, the Scottish government launched a programme of investment and reform to reduce waiting times. The effect on waiting time inequality is unknown as is the impact of subsequent austerity measures.DesignAn interrupted time series analysis between the most and least socioeconomically deprived population quintiles since the introduction of waiting time initiative 1 July 2002 and austerity measures 1 April 2010.SettingAll...

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