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Development of an in vitro approach to point-of-contact inhalation toxicity testing of volatile compounds, using organotypic culture and air-liquid interface exposure.

Artik Mistry, Larry E Bowen, Michael W Dzierlenga, Jessica K Hartman, Scott D Slattery,

In vitro chemical risk assessment using human cells is emerging as an alternative to in vivo animal testing with reduced costs, fewer animal welfare concerns, and the possibility of greater human health relevance. In vitro inhalation toxicity testing of volatile compounds poses particular challenges. Here we report our efforts to ... Read more >>

Toxicol In Vitro (Toxicology in vitro : an international journal published in association with BIBRA)
[2020, 69:104968]

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Massively Parallel Quantum Chemistry: A high-performance research platform for electronic structure.

Chong Peng, Cannada A Lewis, Xiao Wang, Marjory C Clement, Karl Pierce, Varun Rishi, Fabijan Pavošević, Samuel Slattery, Jinmei Zhang, Nakul Teke, Ashutosh Kumar, Conner Masteran, Andrey Asadchev, Justus A Calvin, Edward F Valeev,

The Massively Parallel Quantum Chemistry (MPQC) program is a 30-year-old project that enables facile development of electronic structure methods for molecules for efficient deployment to massively parallel computing architectures. Here, we describe the historical evolution of MPQC's design into its latest (fourth) version, the capabilities and modular architecture of today's ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2020, 153(4):044120]

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The Impact of Covid-19 on Medical Student Education - Navigating Uncharted Territory.

T A Conlon, P Carthy, R Govern, S Slattery, J Yates, S Murphy,

Ir Med J (Irish medical journal)
[2020, 113(6):109]

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Cas9-generated auxotrophs of Phaeodactylum tricornutum are characterized by small and large deletions that can be complemented by plasmid-based genes

Samuel Slattery, Helen Wang, Daniel Giguere, Csanad Kocsis, Bradley Urquhart, Bogumil Karas, David Edgell,

ABSTRACT The model diatom Phaeodactylum tricornutum is an attractive candidate for synthetic biology applications. Development of auxotrophic strains of P. tricornutum would provide alternative selective markers to commonly used antibiotic resistance genes. Here, using CRISPR/Cas9, we show successful editing of genes in the uracil, histidine, and tryptophan biosynthetic pathways. Editing ... Read more >>

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A Novel Arsenate-Resistant Determinant Associated with ICEpMERPH, a Member of the SXT/R391 Group of Mobile Genetic Elements.

Michael P Ryan, Shannon Slattery, J Tony Pembroke,

ICEpMERPH, the first integrative conjugative element (ICE) of the SXT/R391 family isolated in the United Kingdom and Europe, was analyzed to determine the nature of its adaptive functions, its genetic structure, and its homology to related elements normally found in pathogenic Vibrio or Proteus species. Whole genome sequencing of Escherichia ... Read more >>

Genes (Basel) (Genes)
[2019, 10(12):]

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Machine learning mortality classification in clinical documentation with increased accuracy in visual-based analyses.

Susan M Slattery, Daniel C Knight, Debra E Weese-Mayer, William A Grobman, Doug C Downey, Karna Murthy,

AIM:The role of machine learning on clinical documentation for predictive outcomes remains undefined. We aimed to compare three neural networks on inpatient providers' notes to predict mortality in neonatal hypoxic-ischaemic encephalopathy (HIE). METHODS:Using Children's Hospitals Neonatal Database, non-anomalous neonates with HIE treated with therapeutic hypothermia were identified at a single-centre. ... Read more >>

Acta Paediatr (Acta paediatrica (Oslo, Norway : 1992))
[2020, 109(7):1346-1353]

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Analysis and Comparative Genomics of the SXT/R391 Family ICE, pMERPH

Michael Ryan, Shannon Slattery, Tony Pembroke,

The aim of this study was to analyse pMERPH, the first integrative and conjugative element (ICE) of the SXT/R391 family isolated in the United Kingdom and to determine its relationship to other members of the SXT/R391 family of ICEs. Whole Genome Sequencing of Escherichia coli isolate KH802 (which contains the ... Read more >>

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An Expanded Plasmid-Based Genetic Toolbox Enables Cas9 Genome Editing and Stable Maintenance of Synthetic Pathways in Phaeodactylum tricornutum.

Samuel S Slattery, Andrew Diamond, Helen Wang, Jasmine A Therrien, Jeremy T Lant, Teah Jazey, Kyle Lee, Zachary Klassen, Isabel Desgagné-Penix, Bogumil J Karas, David R Edgell,

With the completion of the genome sequence, and development of an efficient conjugation-based transformation system allowing the introduction of stable episomes, Phaeodactylum tricornutum has become an ideal platform for the study of diatom biology and synthetic biology applications. The development of plasmid-based genetic tools is the next step to improve ... Read more >>

ACS Synth Biol (ACS synthetic biology)
[2018, 7(2):328-338]

Cited: 17 times

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Evaluating opportunities for advancing the use of alternative methods in risk assessment through the development of fit-for-purpose in vitro assays.

Patrick D McMullen, Melvin E Andersen, Brian Cholewa, Harvey J Clewell, Katherine M Dunnick, Jessica K Hartman, Kamel Mansouri, Melyssa S Minto, Chantel I Nicolas, Martin B Phillips, Scott Slattery, Miyoung Yoon, Rebecca A Clewell,

An evolving regulatory, scientific, and legislative landscape is driving a fundamental change in how chemical safety decisions are made. As we move to implement changes, regulatory agencies and industry are beginning to adopt tiered approaches, which leverage high-throughput screening technologies for prioritization and read across, followed by interrogation of "hit ... Read more >>

Toxicol In Vitro (Toxicology in vitro : an international journal published in association with BIBRA)
[2018, 48:310-317]

Cited: 4 times

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Timing of administration of antenatal magnesium sulfate and umbilical cord blood magnesium levels in preterm babies.

Adam Reynolds, Suzanne Slattery, Susan Byrne, Elaine Neary, Sieglinde Müllers, Etaoin Kent, Fergal D Malone, Afif El-Khuffash, Cliona McGarvey, Breda C Hayes,

BACKGROUND:The optimum timing of administration of magnesium sulfate (MgSO4) in relation to delivery is not known. The general consensus is to achieve administration to the mother at least 4 hours prior to preterm delivery. OBJECTIVE:To investigate potential predictors of umbilical cord blood magnesium (Mg) concentrations, in particular, timing of antenatal MgSO4 ... Read more >>

J. Matern. Fetal. Neonatal. Med. (The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians)
[2019, 32(6):1014-1019]

Cited: 2 times

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2204: Evaluations of physiologic perturbations and their relationship with length of stay in neonatal hypoxic-ischemic encephalopathy.

Susan Slattery, Lei Liu, Haitao Chai, William Grobman, Jennie Duggan, Doug Downey, Karna Murthy,

OBJECTIVES/SPECIFIC AIMS: Neonatal hypoxic-ischemic encephalopathy (HIE) is frequently accompanied with physiologic perturbations and organ dysfunction. Markers of these perturbations and their associations with length of stay (LOS) are uncertain. To estimate the association between changes in selected physiologic and/or laboratory values with LOS in newborns with HIE. METHODS/STUDY POPULATION: Using ... Read more >>

(Journal of clinical and translational science)
[2017, 1(Suppl 1):12-13]

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Assessment, treatment goals and interventions for oedema/lymphoedema in palliative care.

Sinead Cobbe, Shirley Real, Sinead Slattery,

Little is known about the treatment of oedema in palliative care patients.To outline the assessment, goals, and interventions for patients with oedema.A 6-month chart review of a specialist physiotherapy-led oedema service was carried out.Of the sample group (n=63), 28.6% of patients had lymphoedema, 15.9% had non-lymphatic oedema, 46% had mixed ... Read more >>

Int J Palliat Nurs (International journal of palliative nursing)
[2017, 23(3):111-119]

Cited: 2 times

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Palliative Care Edema: Patient Population, Causal Factors, and Types of Edema Referred to a Specialist Palliative Care Edema Service.

Shirley Real, Sinead Cobbe, Sinead Slattery,

Edema in palliative care patients is a common symptom, however, the research base for all aspects of its care is extremely poor.To evaluate a specialist palliative care edema service in order to report on the patient population referred, the types of edema encountered, and the causes of edema.Prior to study, ... Read more >>

J Palliat Med (Journal of palliative medicine)
[2016, 19(7):771-777]

Cited: 2 times

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Letter: therapeutic trial is more informative than SeHCAT to diagnose bile acid malabsorption--authors' reply.

S A Slattery, O Niaz, Q Aziz, A C Ford, A D Farmer,

Aliment Pharmacol Ther (Alimentary pharmacology & therapeutics)
[2015, 42(6):781]

Cited: 0 times

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Clinical and genetic characterisation of infantile liver failure syndrome type 1, due to recessive mutations in LARS.

Jillian P Casey, Suzanne Slattery, Melanie Cotter, A A Monavari, Ina Knerr, Joanne Hughes, Eileen P Treacy, Deirdre Devaney, Michael McDermott, Eoghan Laffan, Derek Wong, Sally Ann Lynch, Billy Bourke, Ellen Crushell,

BACKGROUND:Recessive LARS mutations were recently reported to cause a novel syndrome, infantile liver failure syndrome type 1 (ILFS1), in six Irish Travellers. We have since identified four additional patients, including one of Ashkenazi origin, representing the largest ILFS1 cohort to date. Our study aims to define the ILFS1 clinical phenotype ... Read more >>

J. Inherit. Metab. Dis. (Journal of inherited metabolic disease)
[2015, 38(6):1085-1092]

Cited: 9 times

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Systematic review with meta-analysis: the prevalence of bile acid malabsorption in the irritable bowel syndrome with diarrhoea.

S A Slattery, O Niaz, Q Aziz, A C Ford, A D Farmer,

Irritable bowel syndrome is a widespread disorder with a marked socioeconomic burden. Previous studies support the proposal that a subset of patients with features compatible with diarrhoea-predominant IBS (IBS-D) have bile acid malabsorption (BAM).To perform a systematic review and meta-analysis to assess the prevalence of BAM in patients meeting the ... Read more >>

Aliment. Pharmacol. Ther. (Alimentary pharmacology & therapeutics)
[2015, 42(1):3-11]

Cited: 47 times

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A High-Content Assay for Biosensor Validation and for Examining Stimuli that Affect Biosensor Activity.

Scott D Slattery, Klaus M Hahn,

Biosensors are valuable tools used to monitor many different protein behaviors in vivo. Demand for new biosensors is high, but their development and characterization can be difficult. During biosensor design, it is necessary to evaluate the effects of different biosensor structures on specificity, brightness, and fluorescence responses. By co-expressing the ... Read more >>

Curr Protoc Cell Biol (Current protocols in cell biology)
[2014, 65:14.15.1-31]

Cited: 5 times

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APOL1 risk variants, race, and progression of chronic kidney disease.

Afshin Parsa, W H Linda Kao, Dawei Xie, Brad C Astor, Man Li, Chi-yuan Hsu, Harold I Feldman, Rulan S Parekh, John W Kusek, Tom H Greene, Jeffrey C Fink, Amanda H Anderson, Michael J Choi, Jackson T Wright, James P Lash, Barry I Freedman, Akinlolu Ojo, Cheryl A Winkler, Dominic S Raj, Jeffrey B Kopp, Jiang He, Nancy G Jensvold, Kaixiang Tao, Michael S Lipkowitz, Lawrence J Appel, , ,

BACKGROUND:Among patients in the United States with chronic kidney disease, black patients are at increased risk for end-stage renal disease, as compared with white patients. METHODS:In two studies, we examined the effects of variants in the gene encoding apolipoprotein L1 (APOL1) on the progression of chronic kidney disease. In the ... Read more >>

N Engl J Med (The New England journal of medicine)
[2013, 369(23):2183-2196]

Cited: 312 times

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Association of cardiac troponin T with left ventricular structure and function in CKD.

Rakesh K Mishra, Yongmei Li, Christopher DeFilippi, Michael J Fischer, Wei Yang, Martin Keane, Jing Chen, Jiang He, Radhakrishna Kallem, Edward J Horwitz, Mohammad Rafey, Dominic S Raj, Alan S Go, Michael G Shlipak, ,

Serum cardiac troponin T (cTnT) is associated with increased risk of heart failure and cardiovascular death in several population settings. We evaluated associations of cTnT levels with cardiac structural and functional abnormalities in a cohort of patients with chronic kidney disease (CKD) without heart failure.Cross-sectional.Chronic Renal Insufficiency Cohort (CRIC; N=3,243).The ... Read more >>

Am J Kidney Dis (American journal of kidney diseases : the official journal of the National Kidney Foundation)
[2013, 61(5):701-709]

Cited: 30 times

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A profile of hospice-at-home physiotherapy for community-dwelling palliative care patients.

Sinead Cobbe, Kathy Nugent, Shirley Real, Sinead Slattery, Margaret Lynch,

AIM: To profile a specialised palliative care physiotherapy service to community-dwelling patients. DESIGN: Retrospective audit. SETTING: Milford Care Centre, Limerick, Ireland. PARTICIPANTS: Patients referred to hospice-at-home physiotherapy during September 2010-February 2011. OUTCOME MEASURE: Edmonton Functional Assessment Tool (EFAT-2). RESULTS: 165 patients were referred, of whom 90% had cancer. Nurses referred ... Read more >>

Int J Palliat Nurs (International journal of palliative nursing)
[2013, 19(1):39-45]

Cited: 3 times

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Retinopathy and chronic kidney disease in the Chronic Renal Insufficiency Cohort (CRIC) study.

Juan E Grunwald, Judith Alexander, Gui-Shuang Ying, Maureen Maguire, Ebenezer Daniel, Revell Whittock-Martin, Candace Parker, Kathleen McWilliams, Joan C Lo, Alan Go, Raymond Townsend, Crystal A Gadegbeku, James P Lash, Jeffrey C Fink, Mahboob Rahman, Harold Feldman, John W Kusek, Dawei Xie, Bernard G Jaar, ,

OBJECTIVE:To investigate the association between retinopathy and chronic kidney disease. METHODS:In this observational, cross-sectional study, 2605 patients of the Chronic Renal Insufficiency Cohort (CRIC) study, a multicenter study of chronic kidney disease, were offered participation. Nonmydriatic fundus photographs of the disc and macula in both eyes were obtained in 1936 ... Read more >>

Arch. Ophthalmol. (Archives of ophthalmology (Chicago, Ill. : 1960))
[2012, 130(9):1136-1144]

Cited: 44 times

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Factors associated with depressive symptoms and use of antidepressant medications among participants in the Chronic Renal Insufficiency Cohort (CRIC) and Hispanic-CRIC Studies.

Michael J Fischer, Dawei Xie, Neil Jordan, Willem J Kop, Marie Krousel-Wood, Manjula Kurella Tamura, John W Kusek, Virginia Ford, Leigh K Rosen, Louise Strauss, Valerie L Teal, Kristine Yaffe, Neil R Powe, James P Lash, ,

Depressive symptoms are correlated with poor health outcomes in adults with chronic kidney disease (CKD). The prevalence, severity, and treatment of depressive symptoms and potential risk factors, including level of kidney function, in diverse populations with CKD have not been well studied.Cross-sectional analysis.Participants at enrollment into the Chronic Renal Insufficiency ... Read more >>

Am J Kidney Dis (American journal of kidney diseases : the official journal of the National Kidney Foundation)
[2012, 60(1):27-38]

Cited: 18 times

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CKD in Hispanics: Baseline characteristics from the CRIC (Chronic Renal Insufficiency Cohort) and Hispanic-CRIC Studies.

Michael J Fischer, Alan S Go, Claudia M Lora, Lynn Ackerson, Janet Cohan, John W Kusek, Alejandro Mercado, Akinlolu Ojo, Ana C Ricardo, Leigh K Rosen, Kaixiang Tao, Dawei Xie, Harold I Feldman, James P Lash, ,

Little is known regarding chronic kidney disease (CKD) in Hispanics. We compared baseline characteristics of Hispanic participants in the Chronic Renal Insufficiency Cohort (CRIC) and Hispanic-CRIC (H-CRIC) Studies with non-Hispanic CRIC participants.Cross-sectional analysis.Participants were aged 21-74 years with CKD using age-based estimated glomerular filtration rate (eGFR) at enrollment into the ... Read more >>

Am J Kidney Dis (American journal of kidney diseases : the official journal of the National Kidney Foundation)
[2011, 58(2):214-227]

Cited: 69 times

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A framework for image-based classification of mitotic cells in asynchronous populations.

Scott D Slattery, Justin Y Newberg, Adam T Szafran, Rebecca M Hall, Bill R Brinkley, Michael A Mancini,

High content screening (HCS) has emerged an important tool for drug discovery because it combines rich readouts of cellular responses in a single experiment. Inclusion of cell cycle analysis into HCS is essential to identify clinically suitable anticancer drugs that disrupt the aberrant mitotic activity of cells. One challenge for ... Read more >>

Assay Drug Dev Technol (Assay and drug development technologies)
[2012, 10(2):161-178]

Cited: 4 times

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The first five days: field and laboratory investigations during the early stages of the equine influenza outbreak in Australia, 2007.

P D Kirkland, R J Davis, D Wong, D Ryan, K Hart, B Corney, G Hewitson, K Cooper, A Biddle, S Eastwood, S Slattery, D Rayward, M Evers, T Wright, K Halpin, P Selleck, J Watson,

Until August 2007, Australia was one of only three countries internationally recognised to be free of equine influenza (EI). This report documents the diagnosis of the first cases of EI in Australian horses and summarises the investigations that took place over the next 5 days. During that time, a multifocal ... Read more >>

Aust Vet J (Australian veterinary journal)
[2011, 89 Suppl 1:6-10]

Cited: 17 times

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