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Article ; Online: Transcription factor expression levels and environmental signals constrain transcription factor innovation.

Shepherd, Matthew J / Reynolds, Mitchell / Pierce, Aidan P / Rice, Alan M / Taylor, Tiffany B

2023 Volume 169, Issue 8

MeSH term(s)	Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcription, Genetic ; Gene Expression Regulation ; Pseudomonas fluorescens/genetics ; Gene Expression Regulation, Bacterial ; Bacterial Proteins/genetics
Chemical Substances	Transcription Factors ; Bacterial Proteins
Language	English
Publishing date	2023-08-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1180712-x
ISSN	1465-2080 ; 1350-0872
ISSN (online)	1465-2080
ISSN	1350-0872
DOI	10.1099/mic.0.001378
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Usage of Mobile Applications or Mobile Health Technology to Improve Diet Quality in Adults.

Scarry, Alan / Rice, Jennifer / O'Connor, Eibhlís M / Tierney, Audrey C

Nutrients

2022 Volume 14, Issue 12

Abstract: ... to male participants in the studies was 4:1. The majority of the mobile applications or M-health ...

Abstract	The use of mobile applications for dietary purposes has dramatically increased along with the consistent development of mobile technology. Assessing diet quality as a dietary pattern or an indicator across key food groups in comparison to those recommended by dietary guidelines is useful for identifying optimal nutrient intake. This systematic review aims to explore mobile applications and their impact on the diet quality of the user. The electronic databases of The Cumulative Index to Nursing and Allied Health Literature (Cinahl), The American Psychological Association's (APA Psycinfo), and PubMed were systematically searched for randomised and non-randomised controlled trials to retrieve papers from inception to November 2021. Ten studies with 1638 participants were included. A total of 5342 studies were retrieved from the database searches, with 10 articles eligible for final inclusion in the review. The sample sizes ranged from 27 to 732 participants across the included studies, with 1638 total participants. The ratio of female to male participants in the studies was 4:1. The majority of the mobile applications or M-health interventions were used to highlight dietary health changes (six studies), with the remainder used to reduce weight or blood sugar levels (four studies). Each study used a different measure to quantify diet quality. Studies were either assessed by diet quality scoring or individual dietary assessment, of the ten studies, six studies reported an improvement in diet quality following diet-related mobile application use. Mobile applications may be an effective way to improve diet quality in adults; however, there is a need for more targeted and longer-term studies that are expressly designed to investigate the impact using mobile applications has on diet quality.
MeSH term(s)	Adult ; Biomedical Technology ; Diet ; Female ; Humans ; Male ; Mobile Applications ; Technology ; Telemedicine
Language	English
Publishing date	2022-06-12
Publishing country	Switzerland
Document type	Journal Article ; Review ; Systematic Review
ZDB-ID	2518386-2
ISSN	2072-6643 ; 2072-6643
ISSN (online)	2072-6643
ISSN	2072-6643
DOI	10.3390/nu14122437
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Usage of Mobile Applications or Mobile Health Technology to Improve Diet Quality in Adults

Scarry, Alan / Rice, Jennifer / O’Connor, Eibhlís M. / Tierney, Audrey C.

Nutrients. 2022 June 12, v. 14, no. 12

2022

Abstract: ... to male participants in the studies was 4:1. The majority of the mobile applications or M-health ...

Abstract	The use of mobile applications for dietary purposes has dramatically increased along with the consistent development of mobile technology. Assessing diet quality as a dietary pattern or an indicator across key food groups in comparison to those recommended by dietary guidelines is useful for identifying optimal nutrient intake. This systematic review aims to explore mobile applications and their impact on the diet quality of the user. The electronic databases of The Cumulative Index to Nursing and Allied Health Literature (Cinahl), The American Psychological Association’s (APA Psycinfo), and PubMed were systematically searched for randomised and non-randomised controlled trials to retrieve papers from inception to November 2021. Ten studies with 1638 participants were included. A total of 5342 studies were retrieved from the database searches, with 10 articles eligible for final inclusion in the review. The sample sizes ranged from 27 to 732 participants across the included studies, with 1638 total participants. The ratio of female to male participants in the studies was 4:1. The majority of the mobile applications or M-health interventions were used to highlight dietary health changes (six studies), with the remainder used to reduce weight or blood sugar levels (four studies). Each study used a different measure to quantify diet quality. Studies were either assessed by diet quality scoring or individual dietary assessment, of the ten studies, six studies reported an improvement in diet quality following diet-related mobile application use. Mobile applications may be an effective way to improve diet quality in adults; however, there is a need for more targeted and longer-term studies that are expressly designed to investigate the impact using mobile applications has on diet quality.
Keywords	blood glucose ; databases ; eating habits ; females ; food quality ; males ; nutrition assessment ; optimal nutrition ; systematic review ; telemedicine
Language	English
Dates of publication	2022-0612
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2518386-2
ISSN	2072-6643
ISSN	2072-6643
DOI	10.3390/nu14122437
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Community as therapy: The theory of social practice.

Pernice, Francesca M / Hinchey, Liza M / Rice, Kevin / Drews, Jessica / Michon, Amber / Jenuwine, Mackenzie / Christian, Janay / Doyle, Alan / Madison, Elliott / Kessler, Lisa / Bayer, Craig / Napolitano, Cyrus / Jedrzejczak, Kinga

Psychiatric rehabilitation journal

2023

Abstract: Objective: Though the efficacy of the Clubhouse model's interventions and practices in supporting recovery from serious mental illness (SMI) have been demonstrated by prior research, the causal mechanisms and theory driving these outcomes have yet to be ...

Abstract	Objective: Though the efficacy of the Clubhouse model's interventions and practices in supporting recovery from serious mental illness (SMI) have been demonstrated by prior research, the causal mechanisms and theory driving these outcomes have yet to be comprehensively defined. This theory article aims to synthesize existing knowledge of these methods to define a unified theory of social practice, outline its role in SMI recovery, and discuss future implications. Method: Historical, theoretical, and practical foundations of social practice were synthesized to define a current theory of social practice and expand the term to apply to the methods and interventions that define the Clubhouse model. Results: Based on prior theory and findings, we define social practice as "the informed application of a specialized form of environmental therapy that utilizes an intentional community to assist people in their recovery." Key facets of social practice in the Clubhouse model of SMI recovery are discussed, including the efficacy of the practice in addressing SMI outcomes such as isolation and low self-efficacy, as well as its impact on both internal and external motivational forces. Conclusions and implications for practice: The theory of social practice describes a process of engaging people to become collaborators and contributors to a social environment. This article describes the philosophy and practices of Clubhouses and introduces the theory of social practice as an empirical means of unifying and communicating the methods, practices, and outcomes of both the Clubhouse model and the broader implications of intentional community as therapy. (PsycInfo Database Record (c) 2023 APA, all rights reserved).
Language	English
Publishing date	2023-12-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2070454-9
ISSN	1559-3126 ; 1095-158X
ISSN (online)	1559-3126
ISSN	1095-158X
DOI	10.1037/prj0000588
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Prediction of vaginal birth after cesarean using information at admission for delivery: a calculator without race or ethnicity.

Grobman, William A / Sandoval, Grecio J / Rice, Madeline Murguia / Chauhan, Suneet P / Clifton, Rebecca G / Costantine, Maged M / Gibson, Kelly S / Metz, Torri D / Parry, Samuel / Reddy, Uma M / Rouse, Dwight J / Saade, George R / Simhan, Hyagriv N / Thorp, John M / Tita, Alan T N / Yee, Lynn / Longo, Monica / Landon, Mark B

American journal of obstetrics and gynecology

2023 Volume 230, Issue 3S, Page(s) S804–S806

MeSH term(s)	Pregnancy ; Female ; Humans ; Vaginal Birth after Cesarean ; Ethnicity ; Trial of Labor ; Hospitalization
Language	English
Publishing date	2023-07-14
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	80016-8
ISSN	1097-6868 ; 0002-9378
ISSN (online)	1097-6868
ISSN	0002-9378
DOI	10.1016/j.ajog.2023.02.008
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Dosage-sensitive genes in evolution and disease.

Rice, Alan M / McLysaght, Aoife

BMC biology

2017 Volume 15, Issue 1, Page(s) 78

Abstract: For a subset of genes in our genome a change in gene dosage, by duplication or deletion, causes a phenotypic effect. These dosage-sensitive genes may confer an advantage upon copy number change, but more typically they are associated with disease, ... ...

Abstract	For a subset of genes in our genome a change in gene dosage, by duplication or deletion, causes a phenotypic effect. These dosage-sensitive genes may confer an advantage upon copy number change, but more typically they are associated with disease, including heart disease, cancers and neuropsychiatric disorders. This gene copy number sensitivity creates characteristic evolutionary constraints that can serve as a diagnostic to identify dosage-sensitive genes. Though the link between copy number change and disease is well-established, the mechanism of pathogenicity is usually opaque. We propose that gene expression level may provide a common basis for the pathogenic effects of many copy number variants.
MeSH term(s)	Biological Evolution ; DNA Copy Number Variations ; Evolution, Molecular ; Gene Dosage ; Genetic Diseases, Inborn/genetics ; Genome, Human ; Humans
Language	English
Publishing date	2017-09-01
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2133020-7
ISSN	1741-7007 ; 1741-7007
ISSN (online)	1741-7007
ISSN	1741-7007
DOI	10.1186/s12915-017-0418-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Dosage sensitivity is a major determinant of human copy number variant pathogenicity.

Rice, Alan M / McLysaght, Aoife

Nature communications

2017 Volume 8, Page(s) 14366

Abstract: Human copy number variants (CNVs) account for genome variation an order of magnitude larger than single-nucleotide polymorphisms. Although much of this variation has no phenotypic consequences, some variants have been associated with disease, in ... ...

Abstract	Human copy number variants (CNVs) account for genome variation an order of magnitude larger than single-nucleotide polymorphisms. Although much of this variation has no phenotypic consequences, some variants have been associated with disease, in particular neurodevelopmental disorders. Pathogenic CNVs are typically very large and contain multiple genes, and understanding the cause of the pathogenicity remains a major challenge. Here we show that pathogenic CNVs are significantly enriched for genes involved in development and genes that have greater evolutionary copy number conservation across mammals, indicative of functional constraints. Conversely, genes found in benign CNV regions have more variable copy number. These evolutionary constraints are characteristic of genes in pathogenic CNVs and can only be explained by dosage sensitivity of those genes. These results implicate dosage sensitivity of individual genes as a common cause of CNV pathogenicity. These evolutionary metrics suggest a path to identifying disease genes in pathogenic CNVs.
MeSH term(s)	Computational Biology/methods ; DNA Copy Number Variations/physiology ; Datasets as Topic ; Evolution, Molecular ; Gene Dosage/physiology ; Genome, Human/physiology ; Genomics/methods ; Humans ; Neurodevelopmental Disorders/genetics ; Phenotype
Language	English
Publishing date	2017-02-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/ncomms14366
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Dosage sensitivity is a major determinant of human copy number variant pathogenicity

Alan M. Rice / Aoife McLysaght

Nature Communications, Vol 8, Iss 1, Pp 1-

2017 Volume 11

Abstract: Copy number variants (CNVs) cause significant genomic variation in humans and may be benign or may cause disease. Here, the authors show that pathogenic CNVs are evolutionarily constrained compared with benign, pointing to dosage sensitivity as a ... ...

Abstract	Copy number variants (CNVs) cause significant genomic variation in humans and may be benign or may cause disease. Here, the authors show that pathogenic CNVs are evolutionarily constrained compared with benign, pointing to dosage sensitivity as a potential cause of disease.
Keywords	Science ; Q
Language	English
Publishing date	2017-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Transcription, mRNA Export, and Immune Evasion Shape the Codon Usage of Viruses.

Mordstein, Christine / Cano, Laura / Morales, Atahualpa Castillo / Young, Bethan / Ho, Alexander T / Rice, Alan M / Liss, Michael / Hurst, Laurence D / Kudla, Grzegorz

Genome biology and evolution

2021 Volume 13, Issue 9

Abstract: The nucleotide composition, dinucleotide composition, and codon usage of many viruses differ from their hosts. These differences arise because viruses are subject to unique mutation and selection pressures that do not apply to host genomes; however, the ... ...

Abstract	The nucleotide composition, dinucleotide composition, and codon usage of many viruses differ from their hosts. These differences arise because viruses are subject to unique mutation and selection pressures that do not apply to host genomes; however, the molecular mechanisms that underlie these evolutionary forces are unclear. Here, we analyzed the patterns of codon usage in 1,520 vertebrate-infecting viruses, focusing on parameters known to be under selection and associated with gene regulation. We find that GC content, dinucleotide content, and splicing and m6A modification-related sequence motifs are associated with the type of genetic material (DNA or RNA), strandedness, and replication compartment of viruses. In an experimental follow-up, we find that the effects of GC content on gene expression depend on whether the genetic material is delivered to the cell as DNA or mRNA, whether it is transcribed by endogenous or exogenous RNA polymerase, and whether transcription takes place in the nucleus or cytoplasm. Our results suggest that viral codon usage cannot be explained by a simple adaptation to the codon usage of the host-instead, it reflects the combination of multiple selective and mutational pressures, including the need for efficient transcription, export, and immune evasion.
MeSH term(s)	Codon/genetics ; Codon Usage ; Evolution, Molecular ; Genome, Viral ; Immune Evasion ; RNA, Messenger/genetics ; Viruses/genetics
Chemical Substances	Codon ; RNA, Messenger
Language	English
Publishing date	2021-05-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evab106
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Plasma glycoproteomic biomarkers identify metastatic melanoma patients with reduced clinical benefit from immune checkpoint inhibitor therapy.

Pickering, Chad / Aiyetan, Paul / Xu, Gege / Mitchell, Alan / Rice, Rachel / Najjar, Yana G / Markowitz, Joseph / Ebert, Lisa M / Brown, Michael P / Tapia-Rico, Gonzalo / Frederick, Dennie / Cong, Xin / Serie, Daniel / Lindpaintner, Klaus / Schwarz, Flavio / Boland, Genevieve M

Frontiers in immunology

2023 Volume 14, Page(s) 1187332

Abstract: The clinical success of immune-checkpoint inhibitors (ICI) in both resected and metastatic melanoma has confirmed the validity of therapeutic strategies that boost the immune system to counteract cancer. However, half of patients with metastatic disease ... ...

Abstract	The clinical success of immune-checkpoint inhibitors (ICI) in both resected and metastatic melanoma has confirmed the validity of therapeutic strategies that boost the immune system to counteract cancer. However, half of patients with metastatic disease treated with even the most aggressive regimen do not derive durable clinical benefit. Thus, there is a critical need for predictive biomarkers that can identify individuals who are unlikely to benefit with high accuracy so that these patients may be spared the toxicity of treatment without the likely benefit of response. Ideally, such an assay would have a fast turnaround time and minimal invasiveness. Here, we utilize a novel platform that combines mass spectrometry with an artificial intelligence-based data processing engine to interrogate the blood glycoproteome in melanoma patients before receiving ICI therapy. We identify 143 biomarkers that demonstrate a difference in expression between the patients who died within six months of starting ICI treatment and those who remained progression-free for three years. We then develop a glycoproteomic classifier that predicts benefit of immunotherapy (HR=2.7; p=0.026) and achieves a significant separation of patients in an independent cohort (HR=5.6; p=0.027). To understand how circulating glycoproteins may affect efficacy of treatment, we analyze the differences in glycosylation structure and discover a fucosylation signature in patients with shorter overall survival (OS). We then develop a fucosylation-based model that effectively stratifies patients (HR=3.5; p=0.0066). Together, our data demonstrate the utility of plasma glycoproteomics for biomarker discovery and prediction of ICI benefit in patients with metastatic melanoma and suggest that protein fucosylation may be a determinant of anti-tumor immunity.
MeSH term(s)	Humans ; Immune Checkpoint Inhibitors/therapeutic use ; Artificial Intelligence ; Melanoma/drug therapy ; Neoplasms, Second Primary ; Biomarkers
Chemical Substances	Immune Checkpoint Inhibitors ; Biomarkers
Language	English
Publishing date	2023-06-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1187332
Database	MEDical Literature Analysis and Retrieval System OnLINE

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