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Improving integrative 3D modeling into low- to medium- resolution EM structures with evolutionary couplings

Caitlyn McCafferty, David Taylor, Edward Marcotte,

Electron microscopy (EM) continues to provide near-atomic resolution structures for well-behaved proteins and protein complexes. Unfortunately, structures of some complexes are limited to low- to medium-resolution due to biochemical or conformational heterogeneity. Thus, the application of unbiased systematic methods for fitting individual structures into EM maps is important. A method ... Read more >>

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Simplified geometric representations of protein structures identify complementary interaction interfaces.

Caitlyn L McCafferty, Edward M Marcotte, David W Taylor,

Protein-protein interactions are critical to protein function, but three-dimensional (3D) arrangements of interacting proteins have proven hard to predict, even given the identities and 3D structures of the interacting partners. Specifically, identifying the relevant pairwise interaction surfaces remains difficult, often relying on shape complementarity with molecular docking while accounting for ... Read more >>

Proteins (Proteins)
[2020, :]

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Adsorption of Blood Components to Extracorporeal Membrane Oxygenation (ECMO) Surfaces in Humans: A Systematic Review.

Sam Callaghan, Tengyi Cai, Conor McCafferty, Suelyn Van Den Helm, Steve Horton, Graeme MacLaren, Paul Monagle, Vera Ignjatovic,

The accumulation of blood proteins and cells on extracorporeal membrane oxygenation (ECMO) circuits has been proposed as a contributing factor to the coagulopathic state of many patients. This systematic review aims to summarize and discuss the existing knowledge of blood components binding to the ECMO circuits in human patients. A ... Read more >>

J Clin Med (Journal of clinical medicine)
[2020, 9(10):]

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Epithelial-to-mesenchymal transition and its association with PD-L1 and CD8 in thyroid cancer.

Marra Jai Aghajani, Tao Yang, Ulf Schmitz, Alexander James, Charles Eugenio McCafferty, Paul de Souza, Navin Niles, Tara L Roberts,

Programmed cell death-ligand 1 (PD-L1) has recently been shown to play a role in the regulation of epithelial-to-mesenchymal transition (EMT); however, the relationship between PD-L1 expression, EMT and the inflammatory tumour microenvironment has yet to be investigated in thyroid cancer. To address this issue, we examined the expression of CD8, ... Read more >>

Endocr Connect (Endocrine connections)
[2020, 9(10):1028-1041]

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Clinical and experimental insight into pathophysiology, comorbidity and therapy of absence seizures.

Vincenzo Crunelli, Magor L Lőrincz, Cian McCafferty, Régis C Lambert, Nathalie Leresche, Giuseppe Di Giovanni, François David,

Absence seizures in children and teenagers are generally considered relatively benign because of their non-convulsive nature and the large incidence of remittance in early adulthood. Recent studies, however, show that 30% of children with absence seizures are pharmaco-resistant and 60% are affected by severe neuropsychiatric comorbid conditions, including impairments in ... Read more >>

Brain (Brain : a journal of neurology)
[2020, 143(8):2341-2368]

Cited: 1 time

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Thalamic Stimulation Improves Postictal Cortical Arousal and Behavior.

Jingwen Xu, Maria Milagros Galardi, Brian Pok, Kishan K Patel, Charlie W Zhao, John P Andrews, Shobhit Singla, Cian P McCafferty, Li Feng, Eric T Musonza, Adam J Kundishora, Abhijeet Gummadavelli, Jason L Gerrard, Mark Laubach, Nicholas D Schiff, Hal Blumenfeld,

The postictal state following seizures is characterized by impaired consciousness and has a major negative impact on individuals with epilepsy. Previous work in disorders of consciousness including the postictal state suggests that bilateral deep brain stimulation (DBS) of the thalamic intralaminar central lateral nucleus (CL) may improve level of arousal. ... Read more >>

J Neurosci (The Journal of neuroscience : the official journal of the Society for Neuroscience)
[2020, 40(38):7343-7354]

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Plasma Proteomic Analysis Reveals Age-Specific Changes in Platelet- and Endothelial Cell-Derived Proteins and Regulators of Plasma Coagulation and Fibrinolysis.

Conor McCafferty, Xavier Busuttil-Crellin, Tengyi Cai, Paul Monagle, Neil A Goldenberg, Vera Ignjatovic,

This post hoc study of a plasma proteomic database investigated hemostatic proteins in the context of developmental hemostasis. Twenty-seven hemostatic proteins changed expression with age, and the hemostatic profile of neonates was unique. Appreciating developmental hemostasis through proteomics may lead to more personalized medicine for hospitalized children. ... Read more >>

J Pediatr (The Journal of pediatrics)
[2020, 221S:S29-S36]

Cited: 1 time

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Epithelial-to-Mesenchymal Transition and its Association with PD-L1 and CD8 T cells in Thyroid Cancer

Marra Aghajani, Tao Yang, Ulf Schmitz, Alexander James, Charles Eugenio McCafferty, Paul de Souza, Navin Niles, Tara Roberts,

<h4>Background: </h4> Programmed cell death-ligand 1 (PD-L1) has recently been shown to play a role in the regulation of epithelial-to-mesenchymal transition (EMT) in some cancers. However, the relationship between PD-L1 expression, EMT and the inflammatory tumour microenvironment has yet to be investigated in thyroid cancer. <h4>Methods:</h4> To address this issue, ... Read more >>

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What problems do you face that digital health could solve?

Conor McCafferty, Slavica Praporski, Vera Ignjatovic,

Lancet Haematol (The Lancet. Haematology)
[2020, 7(4):e281]

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Guidelines for panel design, optimization, and performance of whole blood multi-color flow cytometry of platelet surface markers.

Xavier Busuttil-Crellin, Conor McCafferty, Suelyn Van Den Helm, Hui Ping Yaw, Paul Monagle, Matthew Linden, Vera Ignjatovic,

Flow cytometry is a valuable tool in determining the phenotype and function of platelets accurately. The emergence of platelet flow cytometry in recent years provides an attractive alternative to other platelet analytical techniques, with advantages such as requiring small volumes and being highly sensitive to minimal changes in receptor function ... Read more >>

Platelets (Platelets)
[2020, 31(7):845-852]

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Outcomes of a church-based lifestyle intervention among Australian Samoans in Sydney - Le Taeao Afua diabetes prevention program.

Dorothy W Ndwiga, Freya MacMillan, Kate A McBride, Ronda Thompson, Jennifer Reath, Olataga Alofivae-Doorbinia, Penelope Abbott, Charles McCafferty, Marra Aghajani, Elaine Rush, David Simmons,

AIMS:To evaluate the effectiveness of a culturally adapted, church-based lifestyle intervention among Australian Samoans living in Sydney. METHODS:This was a prospective, pre-post study of a church-wide education and support programme delivered by Community Coach Facilitators and Peer Support Facilitators to prevent, and promote self-management of, Type 2 diabetes. Participants completed ... Read more >>

Diabetes Res Clin Pract (Diabetes research and clinical practice)
[2020, 160:108000]

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A phenomenological exploration of change towards healthier food purchasing behaviour in women from a lower socioeconomic background using a health app.

Sarah Jane Flaherty, Mary B McCarthy, Alan M Collins, Claire McCafferty, Fionnuala M McAuliffe,

Food purchasing is dominated by routines and habits that may hamper the use of reflective decision-making and impede change. Disrupting existing behavioural patterns may address this challenge. Individuals from a lower socioeconomic background are more likely to report unhealthier purchasing and targeted initiatives are required. Health apps offer a potential ... Read more >>

Appetite (Appetite)
[2020, 147:104566]

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Simplified geometric representations of protein structures identify complementary interaction interfaces

Caitlyn McCafferty, Edward Marcotte, David Taylor,

<h4>ABSTRACT</h4> Protein-protein interactions are critical to protein function, but three-dimensional (3D) arrangements of interacting proteins have proven hard to predict, even given the identities and 3D structures of the interacting partners. Specifically, identifying the relevant pairwise interaction surfaces remains difficult, often relying on shape complementarity with molecular docking while accounting ... Read more >>

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Investigation of the in vitro effect of aspirin and tirofiban in children compared to adults.

Conor McCafferty, Xavier Busuttil-Crellin, Jessica Cowley, Matthew Linden, Paul Monagle, Vera Ignjatovic,

Thromb Res (Thrombosis research)
[2019, 181:67-70]

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Plasma proteomics and the paediatric patient.

Conor McCafferty, Jessica Chaaban, Vera Ignjatovic,

<h4>Introduction</h4>Plasma proteomics has been extensively utilized for studies that investigate various disease settings (e.g. cardiovascular disease), as well as to monitor the effect of pharmaceuticals on the plasma proteome (e.g. chemotherapy). However, plasma proteomic studies focusing on children represent a very small proportion of the plasma proteomic studies completed to ... Read more >>

Expert Rev Proteomics (Expert review of proteomics)
[2019, 16(5):401-411]

Cited: 1 time

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Online Video Instruction on Hand Expression of Colostrum in Pregnancy is an Effective Educational Tool.

Therese A O'Sullivan, Joy Cooke, Chris McCafferty, Roslyn Giglia,

The use of antenatal colostrum expression in the weeks prior to birth may help improve long-term breastfeeding, but few large-scale studies exist. Typically, antenatal colostrum expression instruction relies on face-to-face education, making large interventions costly. We aimed to determine whether an expert online instructional video can improve knowledge and confidence ... Read more >>

Nutrients (Nutrients)
[2019, 11(4):]

Cited: 1 time

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The past and future roles of competition and habitat in the range-wide occupancy dynamics of Northern Spotted Owls.

Charles B Yackulic, Larissa L Bailey, Katie M Dugger, Raymond J Davis, Alan B Franklin, Eric D Forsman, Steven H Ackers, Lawrence S Andrews, Lowell V Diller, Scott A Gremel, Keith A Hamm, Dale R Herter, J Mark Higley, Rob B Horn, Christopher McCafferty, Janice A Reid, Jeremy T Rockweit, Stan G Sovern,

Slow ecological processes challenge conservation. Short-term variability can obscure the importance of slower processes that may ultimately determine the state of a system. Furthermore, management actions with slow responses can be hard to justify. One response to slow processes is to explicitly concentrate analysis on state dynamics. Here, we focus ... Read more >>

Ecol Appl (Ecological applications : a publication of the Ecological Society of America)
[2019, 29(3):e01861]

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An update on gastrointestinal endoscopy-associated infections and their contributing factors.

Charles Eugenio McCafferty, Marra Jai Aghajani, David Abi-Hanna, Iain Bruce Gosbell, Slade Owen Jensen,

<h4>Introduction</h4>During clinical use, gastrointestinal endoscopes are grossly contaminated with patient's native flora. These endoscopes undergo reprocessing to prevent infectious transmission upon future use. Endoscopy-associated infections and outbreaks have been reported, with a recent focus on the transmission of multi-drug resistant organisms. This review aims to provide an update on endoscopy-associated ... Read more >>

Ann Clin Microbiol Antimicrob (Annals of clinical microbiology and antimicrobials)
[2018, 17(1):36]

Cited: 3 times

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How do adults define the treats they give to children? A thematic analysis.

Claire McCafferty, Liran Christine Shan, Robert Mooney, Clare O'Rourke, Kirsty Pourshahidi, Barbara Livingstone, John Kearney, Clare Corish, Mimi Tatlow-Golden, Celine Murrin,

One in four children on the Island of Ireland are overweight or obese. The consumption of energy-dense, nutrient-poor foods such as snacks, contribute to one fifth of children's calorie intake. However the snack food literature has failed to draw firm conclusions between snack food intake and obesity. Within this literature, ... Read more >>

Appetite (Appetite)
[2019, 133:115-122]

Cited: 1 time

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Increased amygdalar metabotropic glutamate receptor 7 mRNA in a genetic mouse model of impaired fear extinction.

Richard M O'Connor, Cian P McCafferty, Javier A Bravo, Nicolas Singewald, Andrew Holmes, John F Cryan,

<h4>Rationale</h4>Post-traumatic stress disorder (PTSD) is a devastating anxiety-related disorder which develops subsequent to a severe psychologically traumatic event. Only ~ 9% of people who experience such a trauma develop PTSD. It is clear that a number of factors, including genetics, influence whether an individual will develop PTSD subsequent to a trauma. ... Read more >>

Psychopharmacology (Berl) (Psychopharmacology)
[2019, 236(1):265-272]

Cited: 1 time

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Is it still a real treat? Adults' treat provision to children.

Liran Christine Shan, Claire McCafferty, Mimi Tatlow-Golden, Claire O'Rourke, Robert Mooney, M Barbara E Livingstone, L Kirsty Pourshahidi, Clare Corish, John M Kearney, Patrick Wall, Celine Murrin,

Consumption of high-energy foods in the absence of hunger has been identified as a key target to address in the area of obesity. For children, such foods are often provided by adults as treats. There is limited understating of adults' treat giving. The present study aimed to understand adults' provision ... Read more >>

Appetite (Appetite)
[2018, 130:228-235]

Cited: 2 times

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The validity of adenosine triphosphate measurement in detecting endoscope contamination.

C E McCafferty, D Abi-Hanna, M J Aghajani, G T Micali, I Lockart, K Vickery, I B Gosbell, S O Jensen,

<h4>Background</h4>Endoscopic procedures are vital to gastrointestinal disease diagnosis and management, but risk infection transmission. In Australia, endoscopes undergo monthly-to-quarterly microbiological testing, to prevent patient infection. Endoscopes are used more frequently, meaning contamination may not be detected by this surveillance before infection transmission occurs.<h4>Aim</h4>To evaluate the use of adenosine triphosphate (ATP) ... Read more >>

J Hosp Infect (The Journal of hospital infection)
[2018, 100(3):e142-e145]

Cited: 1 time

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Cortical drive and thalamic feed-forward inhibition control thalamic output synchrony during absence seizures.

Cian McCafferty, François David, Marcello Venzi, Magor L Lőrincz, Francis Delicata, Zoe Atherton, Gregorio Recchia, Gergely Orban, Régis C Lambert, Giuseppe Di Giovanni, Nathalie Leresche, Vincenzo Crunelli,

Behaviorally and pathologically relevant cortico-thalamo-cortical oscillations are driven by diverse interacting cell-intrinsic and synaptic processes. However, the mechanism that gives rise to the paroxysmal oscillations of absence seizures (ASs) remains unknown. Here we report that, during ASs in behaving animals, cortico-thalamic excitation drives thalamic firing by preferentially eliciting tonic rather ... Read more >>

Nat Neurosci (Nature neuroscience)
[2018, 21(5):744-756]

Cited: 13 times

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Genetic rescue of absence seizures.

Cian McCafferty, William M Connelly, Roberta Celli, Richard T Ngomba, Ferdinando Nicoletti, Vincenzo Crunelli,

CNS Neurosci Ther (CNS neuroscience & therapeutics)
[2018, 24(8):745-758]

Cited: 1 time

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Clinicopathologic and Prognostic Significance of Programmed Cell Death Ligand 1 Expression in Patients with Non-Medullary Thyroid Cancer: A Systematic Review and Meta-Analysis.

Marra Aghajani, Susannah Graham, Charles McCafferty, Christina Abdel Shaheed, Tara Roberts, Paul DeSouza, Tao Yang, Navin Niles,

BACKGROUND:Evidence has shown that programmed cell death ligand 1 (PD-L1) overexpression is associated with poor prognosis and resistance to immune therapies in several human cancers. However, data on the prognostic significance of PD-L1 expression in thyroid cancer are limited and remain controversial. This systematic review and meta-analysis aimed to evaluate ... Read more >>

Thyroid (Thyroid : official journal of the American Thyroid Association)
[2018, 28(3):349-361]

Cited: 7 times

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