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Article: Lineage dynamics in growing biofilms: Spatial patterns of standing vs.

Young, Ellen / Allen, Rosalind J

2022 Volume 13, Page(s) 915095

Abstract: Microbial biofilms show high phenotypic and genetic diversity, yet the mechanisms underlying diversity generation and maintenance remain unclear. Here, we investigate how spatial patterns of growth activity within a biofilm lead to spatial patterns of ... ...

Abstract	Microbial biofilms show high phenotypic and genetic diversity, yet the mechanisms underlying diversity generation and maintenance remain unclear. Here, we investigate how spatial patterns of growth activity within a biofilm lead to spatial patterns of genetic diversity. Using individual-based computer simulations, we show that the active layer of growing cells at the biofilm interface controls the distribution of lineages within the biofilm, and therefore the patterns of standing and
Language	English
Publishing date	2022-07-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.915095
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Article ; Online: Active layer dynamics drives a transition to biofilm fingering.

Young, Ellen / Melaugh, Gavin / Allen, Rosalind J

NPJ biofilms and microbiomes

2023 Volume 9, Issue 1, Page(s) 17

Abstract: The emergence of spatial organisation in biofilm growth is one of the most fundamental topics in biofilm biophysics and microbiology. It has long been known that growing biofilms can adopt smooth or rough interface morphologies, depending on the balance ... ...

Abstract	The emergence of spatial organisation in biofilm growth is one of the most fundamental topics in biofilm biophysics and microbiology. It has long been known that growing biofilms can adopt smooth or rough interface morphologies, depending on the balance between nutrient supply and microbial growth; this 'fingering' transition has been linked with the average width of the 'active layer' of growing cells at the biofilm interface. Here we use long-time individual-based simulations of growing biofilms to investigate in detail the driving factors behind the biofilm-fingering transition. We show that the transition is associated with dynamical changes in the active layer. Fingering happens when gaps form in the active layer, which can cause local parts of the biofilm interface to pin, or become stationary relative to the moving front. Pinning can be transient or permanent, leading to different biofilm morphologies. By constructing a phase diagram for the transition, we show that the controlling factor is the magnitude of the relative fluctuations in the active layer thickness, rather than the active layer thickness per se. Taken together, our work suggests a central role for active layer dynamics in controlling the pinning of the biofilm interface and hence biofilm morphology.
MeSH term(s)	Biofilms/growth & development
Language	English
Publishing date	2023-04-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2817021-0
ISSN	2055-5008 ; 2055-5008
ISSN (online)	2055-5008
ISSN	2055-5008
DOI	10.1038/s41522-023-00380-w
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Article ; Online: Introducing W. Ray Kim, MD, our 2024 AASLD president.

Lim, Young-Suk / Kwong, Allison J / Allen, Alina M

Hepatology (Baltimore, Md.)

2023 Volume 79, Issue 1, Page(s) 21–24

MeSH term(s)	Societies, Medical ; Gastroenterology
Language	English
Publishing date	2023-10-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	604603-4
ISSN	1527-3350 ; 0270-9139
ISSN (online)	1527-3350
ISSN	0270-9139
DOI	10.1097/HEP.0000000000000650
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Article ; Online: Arterial Stiffness as a Prognostic Marker for Peripheral Artery Disease Risk: Clinical Relevance and Considerations.

Allen, Michael F / Pekas, Elizabeth J / Park, Song-Young

JACC. Asia

2023 Volume 3, Issue 2, Page(s) 298–300

Language	English
Publishing date	2023-04-18
Publishing country	United States
Document type	Editorial ; Comment
ISSN	2772-3747
ISSN (online)	2772-3747
DOI	10.1016/j.jacasi.2023.03.001
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Article ; Online: Prolonged sitting and peripheral vascular function: potential mechanisms and methodological considerations.

Pekas, Elizabeth J / Allen, Michael F / Park, Song-Young

Journal of applied physiology (Bethesda, Md. : 1985)

2023 Volume 134, Issue 4, Page(s) 810–822

Abstract: Sitting time is associated with increased risks for subclinical atherosclerosis and cardiovascular disease development, and this is thought to be partially due to sitting-induced disturbances in macro- and microvascular function as well as molecular ... ...

Abstract	Sitting time is associated with increased risks for subclinical atherosclerosis and cardiovascular disease development, and this is thought to be partially due to sitting-induced disturbances in macro- and microvascular function as well as molecular imbalances. Despite surmounting evidence supporting these claims, contributing mechanisms to these phenomena remain largely unknown. In this review, we discuss evidence for potential mechanisms of sitting-induced perturbations in peripheral hemodynamics and vascular function and how these potential mechanisms may be targeted using active and passive muscular contraction methods. Furthermore, we also highlight concerns regarding the experimental environment and population considerations for future studies. Optimizing prolonged sitting investigations may allow us to not only better understand the hypothesized sitting-induced transient proatherogenic environment but to also enhance methods and devise mechanistic targets to salvage sitting-induced attenuations in vascular function, which may ultimately play a role in averting atherosclerosis and cardiovascular disease development.
MeSH term(s)	Humans ; Vasodilation ; Cardiovascular Diseases/etiology ; Hemodynamics ; Brachial Artery ; Atherosclerosis
Language	English
Publishing date	2023-02-16
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	219139-8
ISSN	1522-1601 ; 0021-8987 ; 0161-7567 ; 8750-7587
ISSN (online)	1522-1601
ISSN	0021-8987 ; 0161-7567 ; 8750-7587
DOI	10.1152/japplphysiol.00730.2022
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Article ; Online: Rearrangement of GUV-confined actin networks in response to micropipette aspiration.

Wubshet, Nadab H / Young, Cole J / Liu, Allen P

Cytoskeleton (Hoboken, N.J.)

2024

Abstract: Although diverse actin network architectures found inside the cell have been individually reconstituted outside of the cell, how different types of actin architectures reorganize under applied forces is not entirely understood. Recently, bottom-up ... ...

Abstract	Although diverse actin network architectures found inside the cell have been individually reconstituted outside of the cell, how different types of actin architectures reorganize under applied forces is not entirely understood. Recently, bottom-up reconstitution has enabled studies where dynamic and phenotypic characteristics of various actin networks can be recreated in an isolated cell-like environment. Here, by creating a giant unilamellar vesicle (GUV)-based cell model encapsulating actin networks, we investigate how actin networks rearrange in response to localized stresses applied by micropipette aspiration. We reconstitute actin bundles and branched bundles in GUVs separately and mechanically perturb them. Interestingly, we find that, when aspirated, protrusive actin bundles that are otherwise randomly oriented in the GUV lumen collapse and align along the axis of the micropipette. However, when branched bundles are aspirated, the network remains intact and outside of the pipette while the GUV membrane is aspirated into the micropipette. These results reveal distinct responses in the rearrangement of actin networks in a network architecture-dependent manner when subjected to physical forces.
Language	English
Publishing date	2024-02-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2534372-5
ISSN	1949-3592 ; 1949-3584
ISSN (online)	1949-3592
ISSN	1949-3584
DOI	10.1002/cm.21836
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Article ; Online: Oval and round window reinforcement surgery leads to improvements in sound tolerance and quality of life for hyperacusis patients.

Young, Allen / Holmes, Sean / Nayak, Neil / Silverstein, Herbert

American journal of otolaryngology

2024 Volume 45, Issue 3, Page(s) 104231

Abstract: Purpose: Hyperacusis is an audiological disorder in which patients become persistently sensitive and intolerant to everyday environmental sounds. For those patients that fail conservative options, a minimally invasive surgical procedure has been ... ...

Abstract	Purpose: Hyperacusis is an audiological disorder in which patients become persistently sensitive and intolerant to everyday environmental sounds. For those patients that fail conservative options, a minimally invasive surgical procedure has been developed. Materials & methods: Retrospective case series of 73 adult patients with hyperacusis who underwent oval and round window reinforcement surgery between 1/2017-6/2023. Small pieces of temporalis fascia were used to reinforce the round and oval windows. Patients were separated into two groups based on their preoperative speech Loudness Discomfort Level (LDL). Patients with a preoperative speech LDL ≤ 70 dB were placed in the "low LDL group" whereas patients with a preoperative speech LDL >70 dB were placed in the "high LDL group." Preoperative and one-week postoperative audiogram and speech LDLs were compared. Quality of life was assessed using the Glasgow Benefit Inventory (GBI) survey. Results: 73 patients met inclusion criteria - 21 patients in the low LDL group and 52 in the high LDL group. Patients in the high LDL group significantly improved their LDLs by an average of 3.5 dB (P < 0.0001). 42 patients (80.8 %) in the high LDL group had improvement and would recommend the surgery for hyperacusis. Patients in the low LDL group significantly improved their LDL by an average of 12.9 dB (P = 0.032). Ten patients (47.6 %) from the low LDL group experienced improvement and would recommend hyperacusis surgery. Conclusion: Many patients with hyperacusis who undergo oval and round window reinforcement can receive significant improvement in sound tolerance and quality of life. Patients with a pre-op speech LDL > 70 dB have the greatest potential for improvement with surgery (80.8 %), probably because their hyperacusis was less severe.
Language	English
Publishing date	2024-03-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	604541-8
ISSN	1532-818X ; 0196-0709
ISSN (online)	1532-818X
ISSN	0196-0709
DOI	10.1016/j.amjoto.2024.104231
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Article ; Online: Primary left ventricular leiomyosarcoma: a case report.

Balachandran, Vipin / Young, Vanessa / Baillie, Tina / James, Allen

Journal of cardiothoracic surgery

2024 Volume 19, Issue 1, Page(s) 168

Abstract: Cardiac leiomyosarcomas are a rare subset of the already infrequent, primary malignant cardiac neoplasia spectrum. The most common site for a primary leiomyosarcoma of the ventricle is on the right with fewer than five globally reported cases in the left ...

Abstract	Cardiac leiomyosarcomas are a rare subset of the already infrequent, primary malignant cardiac neoplasia spectrum. The most common site for a primary leiomyosarcoma of the ventricle is on the right with fewer than five globally reported cases in the left ventricle. Most present with non-specific symptoms but attention is usually sought after the appearance of compressive symptoms or arrhythmias. We present a case of a left ventricular leiomyosarcoma in a 50-year old female patient that had a delayed diagnosis and its subsequent surgical resection and oncological management with docetaxel and gemcitabine. This case highlights the need for a high index of suspicion for cardiac masses especially if there are competing chronic diseases with similar symptomatology. Given the rare presentation of left ventricular leiomyosarcomas, case reports may provide valuable information that is otherwise unavailable.
MeSH term(s)	Female ; Humans ; Middle Aged ; Heart Ventricles/pathology ; Leiomyosarcoma/diagnosis ; Leiomyosarcoma/surgery ; Leiomyosarcoma/pathology ; Heart Neoplasms/diagnosis ; Heart Neoplasms/surgery ; Heart Neoplasms/pathology
Language	English
Publishing date	2024-04-02
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	2227224-0
ISSN	1749-8090 ; 1749-8090
ISSN (online)	1749-8090
ISSN	1749-8090
DOI	10.1186/s13019-024-02680-4
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Article ; Online: Flexible and Rigid Bronchoscopy for Critically Ill Children on Extracorporeal Membrane Oxygenation.

Young, Ashley / Patel, Krupa / Allen, Kiona / Ghadersohi, Saied / Rowland, Matthew / Hazkani, Inbal

The Laryngoscope

2024

Abstract: Background: We aim to describe our experience with bronchoscopy to diagnose and relieve tracheobronchial obstruction in anticipation of decannulation in children on extracorporeal membrane oxygenation (ECMO) support.: Methods: A retrospective cohort ... ...

Abstract	Background: We aim to describe our experience with bronchoscopy to diagnose and relieve tracheobronchial obstruction in anticipation of decannulation in children on extracorporeal membrane oxygenation (ECMO) support. Methods: A retrospective cohort study of children on ECMO between 1/2018 and 12/2022. Results: A total of 107 children required ECMO support during the study period for cardiac (n = 48, 45%), pulmonary (n = 38, 36%), or cardiopulmonary dysfunction (n = 21, 20%). Thirty-seven (35%) patients underwent 99 bronchoscopies while on ECMO. Most (76%, n = 75) experienced no improvement or worsening of chest radiography 24 hours following bronchoscopy. Clinical improvement in tidal volumes 48 hours after the first bronchoscopy was noted in 13/25 patients with available data (p = 0.05). Adverse events were seen in 18 (49%) patients who underwent bronchoscopy, including pneumothorax (n = 8, 22%), pneumonia (n = 7, 19%), pulmonary hemorrhage (n = 6, 16%), and sepsis (n = 5, 14%). ECMO courses were longer (25.4 ± 37.2 vs 6.1 ± 8.8 days, p < 0.0001) and more likely to be complicated by pneumonia (p = 0.0004) and sepsis (p = 0.047) in patients who underwent bronchoscopy compared with those who did not. Adverse events following bronchoscopy were associated with the number of bronchoscopies (p = 0.0003) and the presence of obstructive materials but not with the type of bronchoscopy or indication for ECMO. Mortality rates were similar between patients who underwent bronchoscopy and those who did not. Conclusion: Children requiring bronchoscopy represent a subset of the sickest children on ECMO. Bronchoscopy may provide benefit in children with persistent cardiopulmonary failure who could not otherwise be decannulated. Adverse events are associated with the number of bronchoscopies and the presence of obstructive material. Level of evidence: 4 Laryngoscope, 2024.
Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	80180-x
ISSN	1531-4995 ; 0023-852X
ISSN (online)	1531-4995
ISSN	0023-852X
DOI	10.1002/lary.31460
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Article ; Online: SIMPEL: using stable isotopes to elucidate dynamics of context specific metabolism.

Kambhampati, Shrikaar / Hubbard, Allen H / Koley, Somnath / Gomez, Javier D / Marsolais, Frédéric / Evans, Bradley S / Young, Jamey D / Allen, Doug K

Communications biology

2024 Volume 7, Issue 1, Page(s) 172

Abstract: The capacity to leverage high resolution mass spectrometry (HRMS) with transient isotope labeling experiments is an untapped opportunity to derive insights on context-specific metabolism, that is difficult to assess quantitatively. Tools are needed to ... ...

Abstract	The capacity to leverage high resolution mass spectrometry (HRMS) with transient isotope labeling experiments is an untapped opportunity to derive insights on context-specific metabolism, that is difficult to assess quantitatively. Tools are needed to comprehensively mine isotopologue information in an automated, high-throughput way without errors. We describe a tool, Stable Isotope-assisted Metabolomics for Pathway Elucidation (SIMPEL), to simplify analysis and interpretation of isotope-enriched HRMS datasets. The efficacy of SIMPEL is demonstrated through examples of central carbon and lipid metabolism. In the first description, a dual-isotope labeling experiment is paired with SIMPEL and isotopically nonstationary metabolic flux analysis (INST-MFA) to resolve fluxes in central metabolism that would be otherwise challenging to quantify. In the second example, SIMPEL was paired with HRMS-based lipidomics data to describe lipid metabolism based on a single labeling experiment. Available as an R package, SIMPEL extends metabolomics analyses to include isotopologue signatures necessary to quantify metabolic flux.
MeSH term(s)	Carbon Isotopes/chemistry ; Mass Spectrometry/methods ; Metabolomics/methods ; Carbon
Chemical Substances	Carbon Isotopes ; Carbon (7440-44-0)
Language	English
Publishing date	2024-02-12
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-024-05844-z
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