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Article ; Online: A Pocket Guide to CCR5-Neurotropic Flavivirus Edition.

Garg, Amit / Lim, Jean K

2023 Volume 16, Issue 1

Abstract: CCR5 is among the most studied chemokine receptors due to its profound significance in human health and disease. The notion that CCR5 is a functionally redundant receptor was challenged through the demonstration of its unique protective role in the ... ...

Abstract	CCR5 is among the most studied chemokine receptors due to its profound significance in human health and disease. The notion that CCR5 is a functionally redundant receptor was challenged through the demonstration of its unique protective role in the context of West Nile virus in both mice and humans. In the nearly two decades since this initial discovery, numerous studies have investigated the role of CCR5 in the context of other medically important neurotropic flaviviruses, most of which appear to support a broad neuroprotective role for this receptor, although how CCR5 exerts its protective effect has been remarkably varied. In this review, we summarize the mechanisms by which CCR5 controls neurotropic flaviviruses, as well as results from human studies evaluating a genetic link to CCR5, and propose unexplored areas of research that are needed to unveil even more exciting roles for this important receptor.
MeSH term(s)	Humans ; Animals ; Mice ; Flavivirus ; West Nile virus/genetics ; Receptors, Chemokine ; Receptors, CCR5/genetics
Chemical Substances	Receptors, Chemokine ; CCR5 protein, human ; Receptors, CCR5
Language	English
Publishing date	2023-12-23
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v16010028
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Dengue and Zika: The Complexities of Being Related.

Krammer, Florian / Lim, Jean K

Trends in immunology

2019 Volume 40, Issue 6, Page(s) 467–469

Abstract: Following the recent Zika virus (ZIKV) outbreak in the Americas, a major question that has arisen is how dengue virus (DENV) immunity impacts Zika virus infection and disease. A recent study (Rodriguez-Barraquer, I. et al. Science 2019;363:607-610) shows ...

Abstract	Following the recent Zika virus (ZIKV) outbreak in the Americas, a major question that has arisen is how dengue virus (DENV) immunity impacts Zika virus infection and disease. A recent study (Rodriguez-Barraquer, I. et al. Science 2019;363:607-610) shows that DENV immunity is, for the most part, protective against ZIKV, but exceptions may exist.
MeSH term(s)	Dengue ; Dengue Virus ; Humans ; Zika Virus ; Zika Virus Infection
Language	English
Publishing date	2019-05-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Comment
ZDB-ID	2036831-8
ISSN	1471-4981 ; 1471-4906
ISSN (online)	1471-4981
ISSN	1471-4906
DOI	10.1016/j.it.2019.04.008
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Article ; Online: Interventions to Promote Safety Culture in Cancer Care: A Systematic Review.

Le, Dan / Lim, Charles H / Fazelzad, Rouhi / Morley, Lyndon / Bissonnette, Jean-Pierre / Powis, Melanie / Krzyzanowska, Monika K

Journal of patient safety

2023 Volume 20, Issue 1, Page(s) 48–56

Abstract: Objectives: There is limited guidance on how to effectively promote safety culture in health care settings. We performed a systematic review to identify interventions to promote safety culture, specifically in oncology settings.: Methods: Medical ... ...

Abstract	Objectives: There is limited guidance on how to effectively promote safety culture in health care settings. We performed a systematic review to identify interventions to promote safety culture, specifically in oncology settings. Methods: Medical Subject Headings and text words for "safety culture" and "cancer care" were combined to conduct structured searches of MEDLINE, EMBASE, CDSR, CINAHL, Cochrane CENTRAL, PsycINFO, Scopus, and Web of Science for peer-reviewed articles published from 1999 to 2021. To be included, articles had to evaluate a safety culture intervention in an oncology setting using a randomized or nonrandomized, pre-post (controlled or uncontrolled), interrupted time series, or repeated-measures study design. The review followed PRISMA guidelines; quality of included citations was assessed using the ROBINS-I risk of bias tool. Results: Eighteen articles meeting the inclusion criteria were retained, reporting on interventions in radiation (14 of 18), medical (3 of 18), or general oncology (1 of 18) settings. Articles most commonly addressed incident learning systems (7 of 18), lean initiatives (4 of 18), or quality improvement programs (3 of 18). Although 72% of studies reported improvement in safety culture, there was substantial heterogeneity in the evaluation approach; rates of reporting of adverse events (9 of 18) or Agency for Healthcare Research and Quality Safety Culture survey results (9 of 18) were the most commonly used metrics. Most of the studies had moderate (28%) or severe (67%) risk of bias. Conclusions: Despite a growing evidence base describing interventions to promote safety culture in cancer care, definitive recommendations were difficult to make because of heterogeneity in study designs and outcomes. Implementation of incident learning systems seems to hold most promise.
MeSH term(s)	Humans ; Learning ; Neoplasms/therapy ; Safety Management ; United States ; Clinical Trials as Topic
Language	English
Publishing date	2023-12-01
Publishing country	United States
Document type	Journal Article ; Systematic Review
ZDB-ID	2394324-5
ISSN	1549-8425 ; 1549-8417
ISSN (online)	1549-8425
ISSN	1549-8417
DOI	10.1097/PTS.0000000000001181
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Article ; Online: Re: Electronic medical records - a disappointing mirage for clinicians and research.

Leow, Jeffrey J / Lim, Ee Jean / Chen, Kenneth

BJU international

2023 Volume 133 Suppl 3, Page(s) 76

Language	English
Publishing date	2023-10-16
Publishing country	England
Document type	Letter
ZDB-ID	1462191-5
ISSN	1464-410X ; 1464-4096 ; 1358-8672
ISSN (online)	1464-410X
ISSN	1464-4096 ; 1358-8672
DOI	10.1111/bju.16193
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Article ; Online: Concurrent and longitudinal associations of developmental language disorder with peer victimization in adolescence: evidence from a co-twin study.

Oncioiu, Sînziana Ioana / Nation, Kate / Lim, Kai Xiang / Pingault, Jean-Baptiste / Bowes, Lucy

Journal of child psychology and psychiatry, and allied disciplines

2024

Abstract: Background: Children with developmental language disorder (DLD) experience higher levels of peer victimization than their peers. However, it is not known if such associations reflect genetic and environmental confounding. We used a co-twin control ... ...

Abstract	Background: Children with developmental language disorder (DLD) experience higher levels of peer victimization than their peers. However, it is not known if such associations reflect genetic and environmental confounding. We used a co-twin control design to investigate the association of language difficulties (DLD and separately poor pragmatic language) with peer victimization and compare the developmental trajectories of peer victimization across adolescence for those with and without language difficulties. Methods: Participants were 3,400 pairs of twins in the Twins Early Development Study (TEDS), a UK-based population birth cohort. Language abilities were assessed via online tests at age 11 and peer victimization was self-reported at ages 11, 14 and 16. Language difficulties were defined as language abilities at least -1.25 SD below the mean of the TEDS sample. We performed linear regressions and latent growth curve modeling at a population level and within monozygotic and same-sex dizygotic twin pairs. Results: At population level, youth with DLD experienced higher levels of peer victimization at ages 11 (β = 0.27, 95% Confidence Interval (CI) 0.20-0.35), 14 (β = 0.15, 95% CI 0.03-0.27) and 16 (β = 0.17, 95% CI 0.03-0.32) and a sharper decline in peer victimization between ages 11 and 16 compared to their peers without DLD. The associations between DLD and peer victimization were reduced in strength and not statistically significant in within-twin models. Moreover, there was no difference in the rate of change in peer victimization between twin pairs discordant for DLD. Results were similar for the association of poor pragmatic language with peer victimization. Conclusions: Associations between language difficulties (DLD and separately, poor pragmatic language) and peer victimization were confounded by genetic and shared environmental factors. Identifying specific factors underlying these associations is important for guiding future work to reduce peer victimization among adolescents with language difficulties.
Language	English
Publishing date	2024-02-29
Publishing country	England
Document type	Journal Article
ZDB-ID	218136-8
ISSN	1469-7610 ; 0021-9630 ; 0373-8086
ISSN (online)	1469-7610
ISSN	0021-9630 ; 0373-8086
DOI	10.1111/jcpp.13969
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Article ; Online: Performance of Three Large Language Models on Dermatology Board Examinations.

Mirza, Fatima N / Lim, Rachel K / Yumeen, Sara / Wahood, Samer / Zaidat, Bashar / Shah, Asghar / Tang, Oliver Y / Kawaoka, John / Seo, Su-Jean / DiMarco, Christopher / Muglia, Jennie / Goldbach, Hayley S / Wisco, Oliver / Qureshi, Abrar A / Libby, Tiffany J

The Journal of investigative dermatology

2023 Volume 144, Issue 2, Page(s) 398–400

MeSH term(s)	Dermatology ; Physical Examination ; Language
Language	English
Publishing date	2023-08-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	80136-7
ISSN	1523-1747 ; 0022-202X
ISSN (online)	1523-1747
ISSN	0022-202X
DOI	10.1016/j.jid.2023.06.208
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Article ; Online: GPER1 is required to protect fetal health from maternal inflammation.

Harding, Alfred T / Goff, Marisa A / Froggatt, Heather M / Lim, Jean K / Heaton, Nicholas S

Science (New York, N.Y.)

2021 Volume 371, Issue 6526, Page(s) 271–276

Abstract: Type I interferon (IFN) signaling in fetal tissues causes developmental abnormalities and fetal demise. Although pathogens that infect fetal tissues can induce birth defects through the local production of type I IFN, it remains unknown why systemic IFN ... ...

Abstract	Type I interferon (IFN) signaling in fetal tissues causes developmental abnormalities and fetal demise. Although pathogens that infect fetal tissues can induce birth defects through the local production of type I IFN, it remains unknown why systemic IFN generated during maternal infections only rarely causes fetal developmental defects. Here, we report that activation of the guanine nucleotide-binding protein-coupled estrogen receptor 1 (GPER1) during pregnancy is both necessary and sufficient to suppress IFN signaling and does so disproportionately in reproductive and fetal tissues. Inactivation of GPER1 in mice halted fetal development and promoted fetal demise, but only in the context of maternal inflammation. Thus, GPER1 is a central regulator of IFN signaling during pregnancy that allows dynamic antiviral responses in maternal tissues while also preserving fetal health.
MeSH term(s)	Animals ; Benzodioxoles/pharmacology ; CRISPR-Cas Systems ; Female ; Fetal Diseases/immunology ; Fetal Diseases/virology ; Fetus/immunology ; Fetus/virology ; Humans ; Inflammation/immunology ; Influenza A virus/immunology ; Influenza, Human/immunology ; Interferon Type I/immunology ; Maternal-Fetal Exchange/immunology ; Mice ; Mice, Inbred C57BL ; Placenta/immunology ; Placenta/virology ; Pregnancy ; Pregnancy Complications, Infectious/immunology ; Quinolines/pharmacology ; Receptors, Estrogen/antagonists & inhibitors ; Receptors, Estrogen/metabolism ; Receptors, G-Protein-Coupled/antagonists & inhibitors ; Receptors, G-Protein-Coupled/metabolism
Chemical Substances	4-(6-bromo-1,3-benzodioxol-5-yl)-3a,4,5,9b-3H-cyclopenta(c)quinoline ; Benzodioxoles ; GPER1 protein, human ; GPER1 protein, mouse ; Interferon Type I ; Quinolines ; Receptors, Estrogen ; Receptors, G-Protein-Coupled
Language	English
Publishing date	2021-01-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aba9001
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Article ; Online: Investigation of machine learning algorithms for taxonomic classification of marine metagenomes.

Park, Helen / Lim, Shen Jean / Cosme, Jonathan / O'Connell, Kyle / Sandeep, Jilla / Gayanilo, Felimon / Cutter, George R / Montes, Enrique / Nitikitpaiboon, Chotinan / Fisher, Sam / Moustahfid, Hassan / Thompson, Luke R

Microbiology spectrum

2023 , Page(s) e0523722

Abstract: ... neural network architectures to map input sequence data (k-mers) to output labels (taxonomic groups ...

Abstract	Microbial communities play key roles in ocean ecosystems through regulation of biogeochemical processes such as carbon and nutrient cycling, food web dynamics, and gut microbiomes of invertebrates, fish, reptiles, and mammals. Assessments of marine microbial diversity are therefore critical to understanding spatiotemporal variations in microbial community structure and function in ocean ecosystems. With recent advances in DNA shotgun sequencing for metagenome samples and computational analysis, it is now possible to access the taxonomic and genomic content of ocean microbial communities to study their structural patterns, diversity, and functional potential. However, existing taxonomic classification tools depend upon manually curated phylogenetic trees, which can create inaccuracies in metagenomes from less well-characterized communities, such as from ocean water. Herein, we explore the utility of deep learning tools-DeepMicrobes and a novel Residual Network architecture-that leverage natural language processing and convolutional neural network architectures to map input sequence data (k-mers) to output labels (taxonomic groups) without reliance on a curated taxonomic tree. We trained both models using metagenomic reads simulated from marine microbial genomes in the MarRef database. The performance of both models (accuracy, precision, and percent microbe predicted) was compared with the standard taxonomic classification tool Kraken2 using 10 complex metagenomic data sets simulated from MarRef. Our results demonstrate that time, compute power, and microbial genomic diversity still pose challenges for machine learning (ML). Moreover, our results suggest that high genome coverage and rectification of class imbalance are prerequisites for a well-trained model, and therefore should be a major consideration in future ML work. IMPORTANCE Taxonomic profiling of microbial communities is essential to model microbial interactions and inform habitat conservation. This work develops approaches in constructing training/testing data sets from publicly available marine metagenomes and evaluates the performance of machine learning (ML) approaches in read-based taxonomic classification of marine metagenomes. Predictions from two models are used to test accuracy in metagenomic classification and to guide improvements in ML approaches. Our study provides insights on the methods, results, and challenges of deep learning on marine microbial metagenomic data sets. Future machine learning approaches can be improved by rectifying genome coverage and class imbalance in the training data sets, developing alternative models, and increasing the accessibility of computational resources for model training and refinement.
Language	English
Publishing date	2023-09-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.05237-22
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Article ; Online: Open-Spaced Ridged Hydrogel Scaffolds Containing TiO

Siddiqui, Ahad M / Thiele, Frederic / Stewart, Rachel N / Rangnick, Simone / Weiss, Georgina J / Chen, Bingkun K / Silvernail, Jodi L / Strickland, Tammy / Nesbitt, Jarred J / Lim, Kelly / Schwarzbauer, Jean E / Schwartz, Jeffrey / Yaszemski, Michael J / Windebank, Anthony J / Madigan, Nicolas N

International journal of molecular sciences

2023 Volume 24, Issue 12

Abstract: The spinal cord has a poor ability to regenerate after an injury, which may be due to cell loss, cyst formation, inflammation, and scarring. A promising approach to treating a spinal cord injury (SCI) is the use of biomaterials. We have developed a novel ...

Abstract	The spinal cord has a poor ability to regenerate after an injury, which may be due to cell loss, cyst formation, inflammation, and scarring. A promising approach to treating a spinal cord injury (SCI) is the use of biomaterials. We have developed a novel hydrogel scaffold fabricated from oligo(poly(ethylene glycol) fumarate) (OPF) as a 0.08 mm thick sheet containing polymer ridges and a cell-attractive surface on the other side. When the cells are cultured on OPF via chemical patterning, the cells attach, align, and deposit ECM along the direction of the pattern. Animals implanted with the rolled scaffold sheets had greater hindlimb recovery compared to that of the multichannel scaffold control, which is likely due to the greater number of axons growing across it. The immune cell number (microglia or hemopoietic cells: 50-120 cells/mm
MeSH term(s)	Rats ; Animals ; Hydrogels/chemistry ; Organophosphonates/metabolism ; Cicatrix/pathology ; Rats, Sprague-Dawley ; Nerve Regeneration ; Spinal Cord Injuries/drug therapy ; Spinal Cord Injuries/metabolism ; Spinal Cord/metabolism ; Axons/pathology ; Tissue Scaffolds/chemistry
Chemical Substances	Hydrogels ; Organophosphonates ; titanium dioxide (15FIX9V2JP) ; poly(ethylene glycol fumarate)
Language	English
Publishing date	2023-06-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms241210250
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Article: Chemokine receptors as important regulators of pathogenesis during arboviral encephalitis.

Michlmayr, Daniela / Lim, Jean K

Frontiers in cellular neuroscience

2014 Volume 8, Page(s) 264

Abstract: The central nervous system (CNS) is a highly complex network comprising long-lived neurons and glial cells. Accordingly, numerous mechanisms have evolved to tightly regulate the initiation of inflammatory responses within the brain. Under ... ...

Abstract	The central nervous system (CNS) is a highly complex network comprising long-lived neurons and glial cells. Accordingly, numerous mechanisms have evolved to tightly regulate the initiation of inflammatory responses within the brain. Under neuroinflammatory conditions, as in the case of viral encephalitides, the infiltration of leukocytes is often required for efficient viral clearance and recovery. The orchestration of leukocyte migration into the inflamed CNS is largely coordinated by a large family of chemotactic cytokines and their receptors. In this review, we will summarize our current understanding of how chemokines promote protection or pathogenesis during arbovirus induced encephalitis, focusing on neurotropic flaviviruses and alphaviruses. Furthermore, we will highlight the latest developments in chemokine and chemokine receptor based drugs that could have potential as therapeutics and have been shown to play a pivotal role in shaping the outcome of disease.
Language	English
Publishing date	2014-09-30
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2452963-1
ISSN	1662-5102
ISSN	1662-5102
DOI	10.3389/fncel.2014.00264
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