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Article ; Online: Implementing Individualized quality control plans and managing risk at the point-of-care for molecular diagnostics.

Laryea, Erving T / Nichols, James H

2023 , Page(s) 1–7

Abstract: Introduction: Faster turnaround times can lead to rapid patient treatment. Implementing a point-of-care (POC) molecular COVID-19 test requires careful planning. In the POC setting, there are numerous operators and regular monitoring of their activities ... ...

Abstract	Introduction: Faster turnaround times can lead to rapid patient treatment. Implementing a point-of-care (POC) molecular COVID-19 test requires careful planning. In the POC setting, there are numerous operators and regular monitoring of their activities is key to the successful implementation of a POC molecular test. Test errors can arise from samples, operators, reagents, the testing system, and even from the environment. These sources of error should be considered when implementing a new test. Areas covered: We outline the importance of establishing well-defined policies for staff to follow at the preanalytic, analytic and postanalytic phases of SARS-CoV-2 testing. As these factors are crucial for the accuracy and reliability of the test results. The key discussion points are from the CLSI EP23-Ed2 document on developing individualized quality control plans and medical literature search engines such as EMBASE, MEDLINE and MedlinePlus. Expert opinion: The risk management principles applied when implementing nucleic acid POC tests can identify specific control processes to help mitigate common sources of error when conducting molecular testing at the POC.
Language	English
Publishing date	2023-10-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2112530-2
ISSN	1744-8352 ; 1473-7159
ISSN (online)	1744-8352
ISSN	1473-7159
DOI	10.1080/14737159.2023.2277374
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Article ; Online: A retrospective cohort study of socioeconomic deprivation and post-liver transplant survival in adults.

Hendele, James B / Nichols, Jordan T / Vutien, Philip / Perkins, James D / Reyes, Jorge / Dick, André A S

Liver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society

2024

Abstract: The Area Deprivation Index is a granular measure of neighborhood socioeconomic deprivation. The relationship between neighborhood socioeconomic deprivation and recipient survival following liver transplantation (LT) is unclear. To investigate this, the ... ...

Abstract	The Area Deprivation Index is a granular measure of neighborhood socioeconomic deprivation. The relationship between neighborhood socioeconomic deprivation and recipient survival following liver transplantation (LT) is unclear. To investigate this, the authors performed a retrospective cohort study of adults who underwent LT at the University of Washington Medical Center from January 1, 2004, to December 31, 2020. The primary exposure was a degree of neighborhood socioeconomic deprivation as determined by the Area Deprivation Index score. The primary outcome was posttransplant recipient mortality. In a multivariable Cox proportional analysis, LT recipients from high-deprivation areas had a higher risk of mortality than those from low-deprivation areas (HR: 1.81; 95% CI: 1.03-3.18, p =0.04). Notably, the difference in mortality between area deprivation groups did not become statistically significant until 6 years after transplantation. In summary, LT recipients experiencing high socioeconomic deprivation tended to have worse posttransplant survival. Further research is needed to elucidate the extent to which neighborhood socioeconomic deprivation contributes to mortality risk and identify effective measures to improve survival in more socioeconomically disadvantaged LT recipients.
Language	English
Publishing date	2024-01-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	2006866-9
ISSN	1527-6473 ; 1527-6465
ISSN (online)	1527-6473
ISSN	1527-6465
DOI	10.1097/LVT.0000000000000337
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Zs.A 4702: Show issues

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Article: Weight management recommendations for youth with Down syndrome: Expert recommendations.

Ptomey, Lauren T / Oreskovic, Nicolas M / Hendrix, James A / Nichols, Dominica / Agiovlasitis, Stamatis

Frontiers in pediatrics

2023 Volume 10, Page(s) 1064108

Abstract: Youth with Down syndrome (DS) have a higher prevalence of overweight and obesity compared to the general youth population. Due to physiological and cognitive differences observed in youth with DS, weight management recommendations developed for the ... ...

Abstract	Youth with Down syndrome (DS) have a higher prevalence of overweight and obesity compared to the general youth population. Due to physiological and cognitive differences observed in youth with DS, weight management recommendations developed for the general population, may not be suitable for youth with DS. However, there are no recent recommendations for weight management in youth with DS. A workgroup of clinicians and researchers with extensive experience working with youth with DS came together to give clinicians and families guidance for weight management in youth with DS. Recommendations were developed by the workgroup
Language	English
Publishing date	2023-02-03
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2711999-3
ISSN	2296-2360
ISSN	2296-2360
DOI	10.3389/fped.2022.1064108
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Article: TFAP2 paralogs regulate midfacial development in part through a conserved

Nguyen, Timothy T / Mitchell, Jennyfer M / Kiel, Michaela D / Jones, Kenneth L / Williams, Trevor J / Nichols, James T / Van Otterloo, Eric

bioRxiv : the preprint server for biology

2023

Abstract: Cranial neural crest development is governed by positional gene regulatory networks (GRNs). Fine-tuning of the GRN components underly facial shape variation, yet how those in the midface are connected and activated remain poorly understood. Here, we show ...

Abstract	Cranial neural crest development is governed by positional gene regulatory networks (GRNs). Fine-tuning of the GRN components underly facial shape variation, yet how those in the midface are connected and activated remain poorly understood. Here, we show that concerted inactivation of
Language	English
Publishing date	2023-06-16
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.06.16.545376
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Article ; Online: TFAP2 paralogs regulate midfacial development in part through a conserved ALX genetic pathway.

Nguyen, Timothy T / Mitchell, Jennyfer M / Kiel, Michaela D / Kenny, Colin P / Li, Hong / Jones, Kenneth L / Cornell, Robert A / Williams, Trevor J / Nichols, James T / Van Otterloo, Eric

Development (Cambridge, England)

2024 Volume 151, Issue 1

Abstract: Cranial neural crest development is governed by positional gene regulatory networks (GRNs). Fine-tuning of the GRN components underlies facial shape variation, yet how those networks in the midface are connected and activated remain poorly understood. ... ...

Abstract	Cranial neural crest development is governed by positional gene regulatory networks (GRNs). Fine-tuning of the GRN components underlies facial shape variation, yet how those networks in the midface are connected and activated remain poorly understood. Here, we show that concerted inactivation of Tfap2a and Tfap2b in the murine neural crest, even during the late migratory phase, results in a midfacial cleft and skeletal abnormalities. Bulk and single-cell RNA-seq profiling reveal that loss of both TFAP2 family members dysregulates numerous midface GRN components involved in midface morphogenesis, patterning and differentiation. Notably, Alx1, Alx3 and Alx4 (ALX) transcript levels are reduced, whereas ChIP-seq analyses suggest TFAP2 family members directly and positively regulate ALX gene expression. Tfap2a, Tfap2b and ALX co-expression in midfacial neural crest cells of both mouse and zebrafish implies conservation of this regulatory axis across vertebrates. Consistent with this notion, tfap2a zebrafish mutants present with abnormal alx3 expression patterns, Tfap2a binds ALX loci and tfap2a-alx3 genetic interactions are observed. Together, these data demonstrate TFAP2 paralogs regulate vertebrate midfacial development in part by activating expression of ALX transcription factor genes.
MeSH term(s)	Animals ; Mice ; Zebrafish/genetics ; Zebrafish/metabolism ; Zebrafish Proteins/genetics ; Cell Differentiation/genetics ; Transcription Factor AP-2/genetics ; Transcription Factor AP-2/metabolism ; Genes, Homeobox ; Neural Crest ; Gene Expression Regulation, Developmental
Chemical Substances	Zebrafish Proteins ; Transcription Factor AP-2
Language	English
Publishing date	2024-01-02
Publishing country	England
Document type	Journal Article
ZDB-ID	90607-4
ISSN	1477-9129 ; 0950-1991
ISSN (online)	1477-9129
ISSN	0950-1991
DOI	10.1242/dev.202095
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Article ; Online: Periodontal Disease Treatment After Stroke or Transient Ischemic Attack: The PREMIERS Study, a Randomized Clinical Trial.

Sen, Souvik / Curtis, James / Hicklin, David / Nichols, Cynthia / Glover, Saundra / Merchant, Anwar T / Hardin, James W / Logue, Makenzie / Meyer, Jaclyn / Mason, Emma / Huang, David Y / Susin, Cristiano / Moss, Kevin / Beck, James

Stroke

2023 Volume 54, Issue 9, Page(s) 2214–2222

Abstract: Background: Patients with stroke/transient ischemic attack and periodontal disease (PD) are at increased risk for cardiovascular events. PD treatments that can improve stroke risk factors were tested if they might assist patients with cerebrovascular ... ...

Abstract	Background: Patients with stroke/transient ischemic attack and periodontal disease (PD) are at increased risk for cardiovascular events. PD treatments that can improve stroke risk factors were tested if they might assist patients with cerebrovascular disease. Methods: In this multicenter phase II trial, patients with stroke/transient ischemic attack and moderately severe PD were randomly assigned to intensive or standard PD treatment arms. The primary outcome measure was a composite of death, myocardial infarction, and recurrent stroke, as well as adverse events. Secondary outcome included changes in stroke risk factors. Results: A total of 1209 patients with stroke/transient ischemic attack were screened, of whom 481 met the PD eligibility criteria; 280 patients were randomized to intensive arm (n=140) and standard arm (n=140). In 12-month period, primary outcome occurred in 11 (8%) in the intensive arm and 17 (12%) in the standard arm. The intensive arm was nonsuperior to the standard arm (hazard ratio, 0.65 [95% CI, 0.30-1.38]) with similar rates of adverse events (sepsis 2.1% versus 0.7%; dental bleeding 1.4% versus 0%; and infective endocarditis 0.7% versus 0%). Secondary-outcome improvements were noted in both arms with diastolic blood pressure and high-density lipoprotein cholesterol ( Conclusions: In patients with recent stroke/transient ischemic attack and PD, intensive PD treatment was not superior to standard PD treatment in prevention of stroke/myocardial infarction/death. Fewer events were noted in the intensive arm and the 2 arms were comparable in the safety outcomes. Secondary-outcome measures showed a trend toward improvement, with significant changes noted in diastolic blood pressure and high-density lipoprotein in both the treatment arms.
MeSH term(s)	Humans ; Ischemic Attack, Transient/drug therapy ; Neoplasm Recurrence, Local/complications ; Stroke/etiology ; Myocardial Infarction/complications ; Periodontal Diseases/therapy
Language	English
Publishing date	2023-08-07
Publishing country	United States
Document type	Randomized Controlled Trial ; Multicenter Study ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80381-9
ISSN	1524-4628 ; 0039-2499 ; 0749-7954
ISSN (online)	1524-4628
ISSN	0039-2499 ; 0749-7954
DOI	10.1161/STROKEAHA.122.042047
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Article ; Online: Shifting Zebrafish Lethal Skeletal Mutant Penetrance by Progeny Testing.

Brooks, Elliott P / Nichols, James T

Journal of visualized experiments : JoVE

2017 , Issue 127

Abstract: Zebrafish mutant phenotypes are often incompletely penetrant, only manifesting in some mutants. Interesting phenotypes that inconsistently appear can be difficult to study, and can lead to confounding results. The protocol described here is a ... ...

Abstract	Zebrafish mutant phenotypes are often incompletely penetrant, only manifesting in some mutants. Interesting phenotypes that inconsistently appear can be difficult to study, and can lead to confounding results. The protocol described here is a straightforward breeding paradigm to increase and decrease penetrance in lethal zebrafish skeletal mutants. Because lethal mutants cannot be selectively bred directly, the classic selective breeding strategy of progeny testing is employed. This method also includes protocols for Kompetitive Allele Specific PCR (KASP) genotyping zebrafish and staining larval zebrafish cartilage and bone. Applying the husbandry strategy described here can increase the penetrance of an interesting skeletal phenotype enabling more reproducible results in downstream applications. In addition, decreasing the mutant penetrance through this selective breeding strategy can reveal the developmental processes that most crucially require the function of the mutated gene. While the skeleton is specifically considered here, we propose that this methodology will be useful for all zebrafish mutant lines.
MeSH term(s)	Animals ; Mutation ; Penetrance ; Zebrafish/genetics ; Zebrafish Proteins/genetics
Chemical Substances	Zebrafish Proteins
Language	English
Publishing date	2017-09-01
Publishing country	United States
Document type	Journal Article ; Video-Audio Media ; Research Support, N.I.H., Extramural
ISSN	1940-087X
ISSN (online)	1940-087X
DOI	10.3791/56200
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Article: Distinct and redundant roles for zebrafish

Stenzel, Amanda / Mumme-Monheit, Abigail / Sucharov, Juliana / Walker, Macie / Mitchell, Jennyfer M / Appel, Bruce / Nichols, James T

Frontiers in endocrinology

2022 Volume 13, Page(s) 1033843

Abstract: The Notch pathway is a cell-cell communication system which is critical for many developmental processes, including craniofacial development. Notch receptor activation induces expression of several well-known canonical targets including those encoded by ... ...

Abstract	The Notch pathway is a cell-cell communication system which is critical for many developmental processes, including craniofacial development. Notch receptor activation induces expression of several well-known canonical targets including those encoded by the
MeSH term(s)	Animals ; Zebrafish/genetics ; Zebrafish/metabolism ; Zebrafish Proteins/genetics ; Zebrafish Proteins/metabolism ; Receptors, Notch/genetics ; Bone and Bones/metabolism ; Mammals/metabolism
Chemical Substances	Zebrafish Proteins ; Receptors, Notch
Language	English
Publishing date	2022-12-12
Publishing country	Switzerland
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2592084-4
ISSN	1664-2392
ISSN	1664-2392
DOI	10.3389/fendo.2022.1033843
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Article ; Online: Biotransformation Potential of Cationic Surfactants in Fish Assessed with Rainbow Trout Liver S9 Fractions.

Droge, Steven T J / Armitage, James M / Arnot, Jon A / Fitzsimmons, Patrick N / Nichols, John W

Environmental toxicology and chemistry

2021 Volume 40, Issue 11, Page(s) 3123–3136

Abstract: Biotransformation may substantially reduce the extent to which organic environmental contaminants accumulate in fish. Presently, however, relatively little is known regarding the biotransformation of ionized chemicals, including cationic surfactants, in ... ...

Abstract	Biotransformation may substantially reduce the extent to which organic environmental contaminants accumulate in fish. Presently, however, relatively little is known regarding the biotransformation of ionized chemicals, including cationic surfactants, in aquatic organisms. To address this deficiency, a rainbow trout liver S9 substrate depletion assay (RT-S9) was used to measure in vitro intrinsic clearance rates (CL
MeSH term(s)	Animals ; Biotransformation ; Liver/metabolism ; Metabolic Clearance Rate ; Oncorhynchus mykiss/metabolism ; Surface-Active Agents/metabolism
Chemical Substances	Surface-Active Agents
Language	English
Publishing date	2021-09-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	46234-2
ISSN	1552-8618 ; 0730-7268
ISSN (online)	1552-8618
ISSN	0730-7268
DOI	10.1002/etc.5189
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Article ; Online: Provision of dietary education in UK-based cardiac rehabilitation: a cross-sectional survey conducted in conjunction with the British Association for Cardiovascular Prevention and Rehabilitation.

James, Emily / Butler, Tom / Nichols, Simon / Goodall, Stuart / O'Doherty, Alasdair F

The British journal of nutrition

2023 Volume 131, Issue 5, Page(s) 880–893

Abstract: Dietary education is a core component of cardiac rehabilitation (CR). It is unknown how or what dietary education is delivered across the UK. We aimed to characterise practitioners who deliver dietary education in UK CR and determine the format and ... ...

Abstract	Dietary education is a core component of cardiac rehabilitation (CR). It is unknown how or what dietary education is delivered across the UK. We aimed to characterise practitioners who deliver dietary education in UK CR and determine the format and content of the education sessions. A fifty-four-item survey was approved by the British Association for Cardiovascular Prevention and Rehabilitation (BACPR) committee and circulated between July and October 2021 via two emails to the BACPR mailing list and on social media. Practitioners providing dietary education within CR programmes were eligible to respond. Survey questions encompassed: practitioner job title and qualifications, resources, and the format, content and individual tailoring of diet education. Forty-nine different centres responded. Nurses (65·1 %) and dietitians (55·3 %) frequently provided dietary education. Practitioners had no nutrition-related qualifications in 46·9 % of services. Most services used credible resources to support their education, and 24·5 % used BACPR core competencies. CR programmes were mostly community based (40·8 %), lasting 8 weeks (range: 2-25) and included two (range: 1-7) diet sessions. Dietary history was assessed at the start (79·6 %) and followed up (83·7 %) by most centres; barriers to completing assessment were insufficient time, staffing or other priorities. Services mainly focused on the Mediterranean diet while topics such as malnutrition and protein intake were lower priority topics. Service improvement should focus on increasing qualifications of practitioners, standardisation of dietary assessment and improvement in protein and malnutrition screening and assessment.
MeSH term(s)	Humans ; Cardiac Rehabilitation ; Cross-Sectional Studies ; Cardiovascular Diseases/prevention & control ; Diet ; Malnutrition ; United Kingdom
Language	English
Publishing date	2023-10-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	280396-3
ISSN	1475-2662 ; 0007-1145
ISSN (online)	1475-2662
ISSN	0007-1145
DOI	10.1017/S0007114523002374
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