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Book ; Online: Different relative scalings between transient forces and thermal fluctuations tune regimes of chromatin organization

Coletti, Anna / Walker, Benjamin / Bloom, Kerry / Newhall, Katherine

2024

Abstract: Within the nucleus, structural maintenance of chromosome protein complexes, namely condensin and cohesin, create an architecture to facilitate the organization and proper function of the genome. Condensin, in addition to performing loop extrusion, ... ...

Abstract	Within the nucleus, structural maintenance of chromosome protein complexes, namely condensin and cohesin, create an architecture to facilitate the organization and proper function of the genome. Condensin, in addition to performing loop extrusion, creates localized clusters of chromatin in the nucleolus through transient crosslinks. Large-scale simulations revealed three different dynamic behaviors as a function of timescale: slow crosslinking leads to no clusters, fast crosslinking produces rigid slowly changing clusters, while intermediate timescales are optimal for producing flexible clusters that mediate gene interaction. By mathematically analyzing different relative scalings of the two sources of stochasticity, thermal fluctuations and the force induced by the transient crosslinks, we predict these three distinct regimes of cluster behavior. Standard time-averaging that takes the fluctuations of the transient crosslink force to zero can predict the existence of clusters, but not their timescale-dependent lifetimes. Accounting for the interaction of both fluctuations from the crosslinks and thermal noise with an effective energy landscape does capture the timescale-dependent flexible cluster lifetimes. No clusters are predicted when the fluctuations of the transient crosslink force are taken to be large relative to thermal fluctuations. This mathematical perturbation analysis illuminates the importance of accounting for stochasticity in local incoherent transient forces to predict emergent complex biological behavior. Comment: 9 pages, 5 figures
Keywords	Physics - Biological Physics ; Mathematics - Probability ; 37H05 ; 92C37 ; 35Q92 ; 37N25
Subject code	612
Publishing date	2024-01-12
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: A Web-Based Therapist Training Tutorial on Prolonged Grief Disorder Therapy: Pre-Post Assessment Study.

Kobak, Kenneth / Shear, M Katherine / Skritskaya, Natalia A / Bloom, Colleen / Bottex, Gaelle

JMIR medical education

2023 Volume 9, Page(s) e44246

Abstract: Background: Prolonged grief disorder (PGD) is a newly recognized mental disorder characterized by pervasive intense grief that persists longer than cultural or social expectations and interferes with functioning. The COVID-19 epidemic has resulted in ... ...

Abstract	Background: Prolonged grief disorder (PGD) is a newly recognized mental disorder characterized by pervasive intense grief that persists longer than cultural or social expectations and interferes with functioning. The COVID-19 epidemic has resulted in increased rates of PGD, and few clinicians feel confident in treating this condition. PGD therapy (PGDT) is a simple, short-term, and evidence-based treatment developed in tandem with the validation of the PGD diagnosis. To facilitate the dissemination of PGDT training, we developed a web-based therapist tutorial that includes didactic training on PGDT concepts and principles as well as web-based multimedia patient scenarios and examples of clinical implementation of PGDT. Objective: We aimed to evaluate user satisfaction with the tutorial and whether the tutorial increased trainees' knowledge of PGDT principles and procedures. Moreover, we included a small number of pilot questions to evaluate the PGDT-related clinical skills. Methods: This study evaluated tutorial learning using a pre- and poststudy design. Participants were recruited from professional organization mailing lists, announcements to graduates of the Columbia School of Social Work, and through word of mouth. After signing consent, participants completed a brief demographic survey, a 55-item multiple-choice prestudy test on the concepts and principles of PGD and PGDT covered in the tutorial, and a 4-item pilot web-based prestudy test to gauge PGD clinical implementation skills. The link to the course content was then activated, and participants were given 8 weeks to complete the 11-module tutorial containing information, web-based exercises, simulated patient and video examples, and self-tests. Results: Overall, 406 clinicians signed consent, and 236 (58.1%) started the tutorial. Of these, 83.1% (196/236) completed all 11 modules. Trainee scores on our PDGT assessment improved substantially from pretraining to the postmodule assessment, with the total number of correct answers increasing from a mean of 29 (SD 5.5; 52.7% correct) to 36.7 (SD 5.2; 66.7% correct; t Conclusions: This pilot study provides support for the usefulness of this web-based training for teaching clinicians how to administer PGDT. The addition of patient scenarios for clinical implementation strategies holds promise for increasing the effectiveness of PGDT training and other evidence-based treatments. Trial registration: ClinicalTrials.gov NCT05121792; https://www.clinicaltrials.gov/ct2/show/NCT05121792.
Language	English
Publishing date	2023-03-27
Publishing country	Canada
Document type	Journal Article
ISSN	2369-3762
ISSN	2369-3762
DOI	10.2196/44246
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Symptoms, Surgical Events, and Length of Stay of Surgical Oncology Outpatients.

Bloom, Linda / Mazzella, AnnMarie / Flynn, Jessica / Panageas, Katherine

Journal of perianesthesia nursing : official journal of the American Society of PeriAnesthesia Nurses

2022 Volume 37, Issue 2, Page(s) 204–209

Abstract: Purpose: This study examined the incidence of postanesthesia symptoms, postoperative events, and length of stay (LOS) for surgical oncology outpatients in Phase II recovery during three time periods: before, one-month post, and one-year after the ... ...

Abstract	Purpose: This study examined the incidence of postanesthesia symptoms, postoperative events, and length of stay (LOS) for surgical oncology outpatients in Phase II recovery during three time periods: before, one-month post, and one-year after the implementation of revised PACU I to PACU II transfer procedures and discharge criteria. Design: Data for this retrospective analysis was obtained from the organizations' electronic medical records during the timeframe April 3, 2017 through August 5, 2018 after enhanced PACU I to PACU II transfer procedures were implemented on June 5, 2017. Records of surgical outpatients transferred from PACU I to PACU II who received regional pain control or preoperative anti-emetics were excluded from the analysis. Methods: Study approval was obtained through the Institutional Review Board [#19-308]. The records [n = 1091] were sorted and analyzed according to symptoms, events, and length of recovery. Incidence of symptoms, use of IV fluids, and medications administered in PACU II was tabulated for each time-period. Kruskal-Wallis tests were used to detect differences in length of stay variables across the three time periods. Findings: A significant decrease in PACU II LOS was observed following the implementation of revised PACU I to PACU II transfer criteria (P< .001). Although blood pressure changes decreased between each time period: 1.4% (T-1), 0.3% (T-2), and 0.2% (T-3), postanesthesia symptoms [dizziness, pain, and nausea] decreased from T-1 to T-2, with a small increase in T-3. The use of fentanyl and continuous IV fluids decreased between all time periods. Conclusions: Monitoring key variables related to patient outcomes involving LOS and symptom management ensures sustained practice changes, improves care, and optimizes surgical outpatient experience.
MeSH term(s)	Anesthesia Recovery Period ; Humans ; Length of Stay ; Outpatients ; Pain, Postoperative/drug therapy ; Retrospective Studies ; Surgical Oncology
Language	English
Publishing date	2022-01-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	1329844-6
ISSN	1532-8473 ; 0883-9433 ; 1089-9472
ISSN (online)	1532-8473
ISSN	0883-9433 ; 1089-9472
DOI	10.1016/j.jopan.2021.04.004
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Article ; Online: Pharmacologic Characterization of Substituted Nitazenes at

Kozell, Laura B / Eshleman, Amy J / Wolfrum, Katherine M / Swanson, Tracy L / Bloom, Shelley H / Benware, Sheila / Schmachtenberg, Jennifer L / Schutzer, Kamryn A / Schutzer, William E / Janowsky, Aaron / Abbas, Atheir I

The Journal of pharmacology and experimental therapeutics

2024 Volume 389, Issue 2, Page(s) 219–228

Abstract: The benzimidazole opioids (substituted nitazenes) are highly ... ...

Abstract	The benzimidazole opioids (substituted nitazenes) are highly potent
MeSH term(s)	Cricetinae ; Animals ; Humans ; Receptors, Opioid, delta/metabolism ; Receptors, Opioid, kappa/metabolism ; Cricetulus ; Receptors, Opioid, mu/metabolism ; Analgesics, Opioid/pharmacology ; Fentanyl/pharmacology ; Benzimidazoles
Chemical Substances	Receptors, Opioid, delta ; Receptors, Opioid, kappa ; Receptors, Opioid, mu ; Analgesics, Opioid ; Fentanyl (UF599785JZ) ; Benzimidazoles
Language	English
Publishing date	2024-04-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	3106-9
ISSN	1521-0103 ; 0022-3565
ISSN (online)	1521-0103
ISSN	0022-3565
DOI	10.1124/jpet.123.002052
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Article: Structural and genetic diversity in the secreted mucins,

Plender, Elizabeth G / Prodanov, Timofey / Hsieh, PingHsun / Nizamis, Evangelos / Harvey, William T / Sulovari, Arvis / Munson, Katherine M / Kaufman, Eli J / O'Neal, Wanda K / Valdmanis, Paul N / Marschall, Tobias / Bloom, Jesse D / Eichler, Evan E

bioRxiv : the preprint server for biology

2024

Abstract: The secreted mucins MUC5AC and MUC5B play critical defensive roles in airway pathogen entrapment and mucociliary clearance by encoding large glycoproteins with variable number tandem repeats (VNTRs). These polymorphic and degenerate protein coding VNTRs ... ...

Abstract	The secreted mucins MUC5AC and MUC5B play critical defensive roles in airway pathogen entrapment and mucociliary clearance by encoding large glycoproteins with variable number tandem repeats (VNTRs). These polymorphic and degenerate protein coding VNTRs make the loci difficult to investigate with short reads. We characterize the structural diversity of
Language	English
Publishing date	2024-03-20
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.18.585560
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Article: The power of weak, transient interactions across biology: A paradigm of emergent behavior.

Vasquez, Paula A / Walker, Ben / Bloom, Kerry / Kolbin, Daniel / Caughman, Neall / Freeman, Ronit / Lysy, Martin / Hult, Caitlin / Newhall, Katherine A / Papanikolas, Micah / Edelmaier, Christopher / Forest, M Gregory

Physica D. Nonlinear phenomena

2023 Volume 454

Abstract: A growing list of diverse biological systems and their equally diverse functionalities provides realizations of a paradigm of emergent behavior. In each of these biological systems, pervasive ensembles of weak, short-lived, spatially local interactions ... ...

Abstract	A growing list of diverse biological systems and their equally diverse functionalities provides realizations of a paradigm of emergent behavior. In each of these biological systems, pervasive ensembles of weak, short-lived, spatially local interactions act autonomously to convey functionalities at larger spatial and temporal scales. In this article, a range of diverse systems and functionalities are presented in a cursory manner with literature citations for further details. Then two systems and their properties are discussed in more detail: yeast chromosome biology and human respiratory mucus.
Language	English
Publishing date	2023-08-04
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1466587-6
ISSN	1872-8022 ; 0167-2789
ISSN (online)	1872-8022
ISSN	0167-2789
DOI	10.1016/j.physd.2023.133866
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Article ; Online: Pharmacologic Activity of Substituted Tryptamines at 5-Hydroxytryptamine (5-HT)

Kozell, Laura B / Eshleman, Amy J / Swanson, Tracy L / Bloom, Shelley H / Wolfrum, Katherine M / Schmachtenberg, Jennifer L / Olson, Randall J / Janowsky, Aaron / Abbas, Atheir I

The Journal of pharmacology and experimental therapeutics

2023 Volume 385, Issue 1, Page(s) 62–75

Abstract: Novel psychoactive substances, including synthetic substituted tryptamines, represent a potential public health threat. Additionally, some substituted tryptamines are being studied under medical guidance as potential treatments of psychiatric disorders. ... ...

Abstract	Novel psychoactive substances, including synthetic substituted tryptamines, represent a potential public health threat. Additionally, some substituted tryptamines are being studied under medical guidance as potential treatments of psychiatric disorders. Characterizing the basic pharmacology of substituted tryptamines will aid in understanding differences in potential for harm or therapeutic use. Using human embryonic kidney cells stably expressing 5-hydroxytryptamine (5-HT)
MeSH term(s)	Humans ; Tryptamines/pharmacology ; Serotonin/metabolism ; Serotonin Plasma Membrane Transport Proteins ; Hallucinogens ; Receptor, Serotonin, 5-HT2A/metabolism ; Receptor, Serotonin, 5-HT2C/metabolism
Chemical Substances	Tryptamines ; Serotonin (333DO1RDJY) ; Serotonin Plasma Membrane Transport Proteins ; Hallucinogens ; Receptor, Serotonin, 5-HT2A ; Receptor, Serotonin, 5-HT2C
Language	English
Publishing date	2023-01-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	3106-9
ISSN	1521-0103 ; 0022-3565
ISSN (online)	1521-0103
ISSN	0022-3565
DOI	10.1124/jpet.122.001454
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Article ; Online: Hypothalamic regulation of appetite.

Simpson, Katherine A / Martin, Niamh M / Bloom, Steve R

Expert review of endocrinology & metabolism

2018 Volume 3, Issue 5, Page(s) 577–592

Abstract: The prevalence of obesity is steadily rising and has huge health and financial implications for society. Weight gain is due to an imbalance between dietary intake and energy expenditure and research has focused on trying to understand the complex ... ...

Abstract	The prevalence of obesity is steadily rising and has huge health and financial implications for society. Weight gain is due to an imbalance between dietary intake and energy expenditure and research has focused on trying to understand the complex pathways involved in controlling these aspects. This review highlights the key areas of research in the hypothalamic control of appetite. The hypothalamus consists of several nuclei that integrate peripheral signals, such as adiposity and caloric intake, to regulate important pathways within the CNS controlling food intake. The best characterized pathways are the orexigenic neuropeptide Y/Agouti-related protein and the anorexigenic pro-opiomelanocortin/cocaine- and amphetamine-related transcript neurons in the arcuate nucleus of the hypothalamus. These project from the arcuate nucleus to other key hypothalamic nuclei, such as the paraventricular, dorsomedial, ventromedial and lateral hypothalamic nuclei. There are also projections to and from the brainstem, cortical areas and reward pathways, all of which influence food intake. The challenge at present is to understand the complexity of these pathways and try to find ways of modulating them in order to find potential therapeutic targets.
Language	English
Publishing date	2018-10-05
Publishing country	England
Document type	Journal Article
ISSN	1744-8417
ISSN (online)	1744-8417
DOI	10.1586/17446651.3.5.577
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Article ; Online: The learning and mentoring experiences of Paralympic coaches.

Fairhurst, Katherine E / Bloom, Gordon A / Harvey, William J

Disability and health journal

2017 Volume 10, Issue 2, Page(s) 240–246

Abstract: Background: Participation in the Paralympic Games has grown substantially, yet the same growth and development has not occurred with empirical literature for coaching in disability sport.: Objective: The purpose of the current study was to explore ... ...

Abstract	Background: Participation in the Paralympic Games has grown substantially, yet the same growth and development has not occurred with empirical literature for coaching in disability sport. Objective: The purpose of the current study was to explore Paralympic coaches' perceptions of their learning and educational experiences, including their formal and informal mentoring opportunities. Methods: Six highly successful and experienced Paralympic coaches were individually interviewed in this qualitative study. The interview data were analyzed following Braun and Clarke's guidelines for thematic analysis. Results: Results demonstrated that Paralympic coaches faced several challenges to acquire disability specific coaching knowledge and skills. These challenges led the participants to utilize an array of informal learning situations, such as actively seeking mentoring relationships when they first entered the field. After becoming expert coaches, they gave back to their sport by making mentoring opportunities available for aspiring coaches. Conclusion: The results of the current study address the value and importance of mentoring as a structured source of education and career development for aspiring Paralympic coaches.
MeSH term(s)	Attitude ; Disabled Persons ; Humans ; Learning ; Mentoring ; Physical Education and Training ; Qualitative Research ; Sports
Language	English
Publishing date	2017-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2414615-8
ISSN	1876-7583 ; 1936-6574
ISSN (online)	1876-7583
ISSN	1936-6574
DOI	10.1016/j.dhjo.2016.10.007
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Article: Linking influenza virus evolution within and between human hosts.

Xue, Katherine S / Bloom, Jesse D

Virus evolution

2020 Volume 6, Issue 1, Page(s) veaa010

Abstract: Influenza viruses rapidly diversify within individual human infections. Several recent studies have deep-sequenced clinical influenza infections to identify viral variation within hosts, but it remains unclear how within-host mutations fare at the ... ...

Abstract	Influenza viruses rapidly diversify within individual human infections. Several recent studies have deep-sequenced clinical influenza infections to identify viral variation within hosts, but it remains unclear how within-host mutations fare at the between-host scale. Here, we compare the genetic variation of H3N2 influenza within and between hosts to link viral evolutionary dynamics across scales. Synonymous sites evolve at similar rates at both scales, indicating that global evolution at these putatively neutral sites results from the accumulation of within-host variation. However, nonsynonymous mutations are depleted between hosts compared to within hosts, suggesting that selection purges many of the protein-altering changes that arise within hosts. The exception is at antigenic sites, where selection detectably favors nonsynonymous mutations at the global scale, but not within hosts. These results suggest that selection against deleterious mutations and selection for antigenic change are the main forces that act on within-host variants of influenza virus as they transmit and circulate between hosts.
Language	English
Publishing date	2020-02-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/veaa010
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