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Article: Accurate Prediction of Inhibitor Binding to HIV-1 Protease Using CANDOCK.

Falls, Zackary / Fine, Jonathan / Chopra, Gaurav / Samudrala, Ram

2022 Volume 9, Page(s) 775513

Abstract: The human immunodeficiency virus 1 (HIV-1) protease is an important target for treating HIV infection. Our goal was to benchmark a novel molecular docking protocol and determine its effectiveness as a therapeutic repurposing tool by predicting inhibitor ... ...

Abstract	The human immunodeficiency virus 1 (HIV-1) protease is an important target for treating HIV infection. Our goal was to benchmark a novel molecular docking protocol and determine its effectiveness as a therapeutic repurposing tool by predicting inhibitor potency to this target. To accomplish this, we predicted the relative binding scores of various inhibitors of the protease using CANDOCK, a hierarchical fragment-based docking protocol with a knowledge-based scoring function. We first used a set of 30 HIV-1 protease complexes as an initial benchmark to optimize the parameters for CANDOCK. We then compared the results from CANDOCK to two other popular molecular docking protocols Autodock Vina and Smina. Our results showed that CANDOCK is superior to both of these protocols in terms of correlating predicted binding scores to experimental binding affinities with a Pearson coefficient of 0.62 compared to 0.48 and 0.49 for Vina and Smina, respectively. We further leveraged the Database of Useful Decoys: Enhanced (DUD-E) HIV protease set to ascertain the effectiveness of each protocol in discriminating active versus decoy ligands for proteases. CANDOCK again displayed better efficacy over the other commonly used molecular docking protocols with area under the receiver operating characteristic curve (AUROC) of 0.94 compared to 0.71 and 0.74 for Vina and Smina. These findings support the utility of CANDOCK to help discover novel therapeutics that effectively inhibit HIV-1 and possibly other retroviral proteases.
Language	English
Publishing date	2022-01-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711776-5
ISSN	2296-2646
ISSN	2296-2646
DOI	10.3389/fchem.2021.775513
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Article ; Online: Minimally Invasive Hepatopancreatobiliary Surgery at a Large Regional Health System: Assessing the Safety of Program Expansion.

Falls, Samantha J / Maxwell, Conor M / Kaye, Dylan J / Dighe, Shruti G / Schiffman, Suzanne C / Bartlett, David L / Wagner, Patrick L / Allen, Casey J

The American surgeon

2023 Volume 90, Issue 1, Page(s) 85–91

Abstract: Background: Complex, minimally invasive hepatopancreatobiliary surgery (MIS HPB) is safe at high-volume centers, yet outcomes during early implementation are unknown. We describe our experience during period of rapid growth in an MIS HPB program at a ... ...

Abstract	Background: Complex, minimally invasive hepatopancreatobiliary surgery (MIS HPB) is safe at high-volume centers, yet outcomes during early implementation are unknown. We describe our experience during period of rapid growth in an MIS HPB program at a large regional health system. Methods: During an increase in MIS HPB (60% greater from preceding year), hospital records of patients who underwent HPB surgery between 1/1/2019 and 12/31/2020 were reviewed. Operative time, estimated blood loss (EBL), conversion rates, length of stay (LOS), and perioperative outcomes were assessed. Results: 267 patients' cases were reviewed. The population was 62 ± 13 years, 50% female, 90% white. MIS was more frequently performed for hepatic than pancreatic resections (59% vs 21%, Discussion: During a surgical expansion phase within our regional health system, MIS HPB offered improved perioperative outcomes when compared to open surgery. These data support the safety of implementation even during intervals of rapid programmatic growth.
MeSH term(s)	Humans ; Female ; Male ; Liver/surgery ; Hepatectomy ; Pancreatectomy ; Length of Stay ; Pancreas/surgery ; Minimally Invasive Surgical Procedures ; Retrospective Studies
Language	English
Publishing date	2023-08-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	202465-2
ISSN	1555-9823 ; 0003-1348
ISSN (online)	1555-9823
ISSN	0003-1348
DOI	10.1177/00031348231192073
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Article ; Online: Variation in space and time: a long-term examination of density-dependent dispersal in a woodland rodent.

Denomme-Brown, Simon T / Cottenie, Karl / Falls, J Bruce / Falls, E Ann / Brooks, Ronald J / McAdam, Andrew G

Oecologia

2020 Volume 193, Issue 4, Page(s) 903–912

Abstract: Dispersal is a fundamental ecological process that can be affected by population density, yet studies report contrasting effects of density on propensity to disperse. In addition, the relationship between dispersal and density is seldom examined using ... ...

Abstract	Dispersal is a fundamental ecological process that can be affected by population density, yet studies report contrasting effects of density on propensity to disperse. In addition, the relationship between dispersal and density is seldom examined using densities measured at different spatial scales or over extensive time series. We used 51 years of trapping data to examine how dispersal by wild deer mice (Peromyscus maniculatus) was affected by changes in both local and regional population densities. We examined these patterns over both the entire time series and also in 10-year shifting windows to determine whether the nature and strength of the relationship changed through time. Probability of dispersal decreased with increased local and regional population density, and the negative effect of local density on dispersal was more pronounced in years with low regional densities. In addition, the strength of negative density-dependent dispersal changed through time, ranging from very strong in some decades to absent in other periods of the study. Finally, while females were less likely to disperse, female dispersal was more density-dependent than male dispersal. Our study shows that the relationship between density and dispersal is not temporally static and that investigations of density-dependent dispersal should consider both local and regional population densities.
MeSH term(s)	Animals ; Female ; Forests ; Male ; Mice ; Population Density ; Population Dynamics ; Rodentia
Language	English
Publishing date	2020-08-18
Publishing country	Germany
Document type	Journal Article
ZDB-ID	123369-5
ISSN	1432-1939 ; 0029-8549
ISSN (online)	1432-1939
ISSN	0029-8549
DOI	10.1007/s00442-020-04728-3
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Article ; Online: Comprehensive framework of factors accounting for worse aortic aneurysm outcomes in females: A scoping review.

De Freitas, Simon / Falls, Garietta / Weis, Tahlia / Bakhshi, Kirran / Korepta, Lindsey M / Bechara, Carlos F / Erben, Young / Arya, Shipra / Fatima, Javairiah

Seminars in vascular surgery

2023 Volume 36, Issue 4, Page(s) 508–516

Abstract: Sex-based outcome studies have consistently documented worse results for females undergoing care for abdominal aortic aneurysms. This review explores the underlying factors that account for worse outcomes in the females sex. A scoping review of studies ... ...

Abstract	Sex-based outcome studies have consistently documented worse results for females undergoing care for abdominal aortic aneurysms. This review explores the underlying factors that account for worse outcomes in the females sex. A scoping review of studies reporting sex-based disparities on abdominal aortic aneurysms was performed. The review was conducted in accordance with the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for scoping reviews. Factors that account for worse outcomes in the females sex were identified, grouped into themes, and analyzed. Key findings of each study are reported and a comprehensive framework of these factors is presented. A total of 35 studies were identified as critical in highlighting sex-based disparities in care of patients with aortic aneurysms. We identified the following 10 interrelated themes in the chain of aneurysm care that account for differential outcomes in females: natural history, risk factors, pathobiology, biomechanics, screening, morphology, device design and adherence to instructions for use, technique, trial enrollment, and social determinants. Factors accounting for worse outcomes in the care of females with aortic aneurysms were identified and described. Some factors are immediately actionable, such as screening criteria, whereas device design improvement will require further research and development. This comprehensive framework of factors affecting care of aneurysms in females should serve as a blueprint to develop education, outreach, and future research efforts to improve outcomes in females.
MeSH term(s)	Humans ; Female ; Aortic Aneurysm, Abdominal/diagnostic imaging ; Aortic Aneurysm, Abdominal/epidemiology ; Aortic Aneurysm, Abdominal/surgery ; Risk Factors ; Outcome Assessment, Health Care ; Treatment Outcome
Language	English
Publishing date	2023-10-29
Publishing country	United States
Document type	Systematic Review ; Journal Article ; Review
ZDB-ID	645131-7
ISSN	1558-4518 ; 0895-7967
ISSN (online)	1558-4518
ISSN	0895-7967
DOI	10.1053/j.semvascsurg.2023.10.007
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Article ; Online: Caspase 1 Enhances Transport and Golgi Organization Protein 1 Expression to Promote Procollagen Export From the Endoplasmic Reticulum in Systemic Sclerosis Contributing to Fibrosis.

Connolly, Lianne M / McFalls, Caya M / McMahon, Isabelle G / Bhat, Akash M / Artlett, Carol M

Arthritis & rheumatology (Hoboken, N.J.)

2023 Volume 75, Issue 10, Page(s) 1831–1841

Abstract: Objective: Transport and Golgi Organization protein 1 (TANGO1) is a protein that regulates the export of procollagen from the endoplasmic reticulum and has a role in the organization of exit sites for general protein export. What regulates the ... ...

Abstract	Objective: Transport and Golgi Organization protein 1 (TANGO1) is a protein that regulates the export of procollagen from the endoplasmic reticulum and has a role in the organization of exit sites for general protein export. What regulates the expression of TANGO1 and the role of TANGO1 in fibrosis is poorly understood and has never been studied in the setting of systemic sclerosis (SSc). We undertook this study to determine the role of TANGO1 in SSc fibrosis. Methods: SSc (n = 15) and healthy (n = 12) primary fibroblast lung cell lines were investigated for the expression of TANGO1. Histologic analyses for TANGO1 were performed on lung biopsy samples (n = 12 SSc patient samples and n = 8 healthy control samples). Results: SSc fibroblasts showed increased expression of TANGO1 protein in cultured fibroblasts. TANGO1 colocalizes with α-smooth muscle actin (α-SMA)-positive cells in SSc lung tissue and is highly up-regulated in the neointima of SSc vessels. TANGO1 expression was dependent on the inflammasome activation of caspase 1. It was also dependent on signaling from the interleukin-1 (IL-1) and transforming growth factor β (TGFβ) receptors. The decrease in TANGO1 down-regulated export of larger cargos including collagen and laminin. Reduced TANGO1 protein had no effect on smaller molecular weight cargoes; however, the secretion of elastin was significantly reduced. Conclusion: TANGO1 is markedly increased in SSc fibroblasts and was found to be elevated in lung tissue in association with α-SMA-positive cells. TANGO1 expression is driven by inflammasome-dependent caspase 1 activation and is mediated by IL-1 and TGFβ downstream signaling. These observations suggest that during fibrosis, caspase 1 promotes the up-regulation of TANGO1 and the organization of endoplasmic reticulum exits sites, ultimately contributing to procollagen export and fibrosis.
MeSH term(s)	Humans ; Caspase 1/metabolism ; Endoplasmic Reticulum/metabolism ; Fibroblasts/metabolism ; Fibrosis ; Inflammasomes/metabolism ; Interleukin-1/metabolism ; Procollagen/metabolism ; Scleroderma, Systemic/pathology ; Transforming Growth Factor beta/metabolism
Chemical Substances	Caspase 1 (EC 3.4.22.36) ; Inflammasomes ; Interleukin-1 ; Procollagen ; Transforming Growth Factor beta ; ARNT protein, human
Language	English
Publishing date	2023-08-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2756371-6
ISSN	2326-5205 ; 2326-5191
ISSN (online)	2326-5205
ISSN	2326-5191
DOI	10.1002/art.42535
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Article: Examining the Effects of Heterospecific Abundance on Dispersal in Forest Small Mammals

Denomme-Brown, Simon T. / Cottenie, Karl / Falls, J. Bruce / Falls, E. Ann / Brooks, Ronald J. / McAdam, Andrew G.

Journal of mammalogy. 2022 Jan. 6, v. 102, no. 6

2022

Abstract: The effects of conspecific densities on dispersal have been well documented. However, while positive and negative density-dependent dispersal based on conspecific densities often are shown to be the result of intraspecific competition or facilitation, ... ...

Abstract	The effects of conspecific densities on dispersal have been well documented. However, while positive and negative density-dependent dispersal based on conspecific densities often are shown to be the result of intraspecific competition or facilitation, respectively, the effects of heterospecific densities on dispersal have been examined far less frequently. This gap in knowledge warrants investigation given the potential for the analogous processes of interspecific competition and heterospecific attraction to influence dispersal patterns and behavior. Here we use a long-term live-trapping study of deer mouse (Peromyscus maniculatus), eastern chipmunk (Tamias striatus), red-backed vole (Myodes gapperi), and jumping mice (Napaeozapus insignis and Zapus hudsonius) to examine the effects of variation in conspecific and heterospecific abundances on dispersal frequency. In terms of conspecific abundance, jumping mice were more likely to disperse from areas with fewer conspecifics, while red-backed voles and chipmunks did not respond to variation in conspecific abundances in their dispersal frequencies. While there were no statistically significant effects of variation in heterospecific abundances on dispersal frequency, some effect sizes for heterospecific abundance effects on dispersal met or exceeded those of conspecific abundances. Conspecific abundances clearly can affect dispersal by some species in this system, but the effects of heterospecific abundances on dispersal frequency are less clear. Based on effect sizes, it appears that there may be potential for heterospecific effects on dispersal by some species in the community, although the strength and causes of these relationships remain unclear.
Keywords	Myodes gapperi ; Napaeozapus insignis ; Peromyscus maniculatus ; Tamias striatus ; Zapus hudsonius ; conspecificity ; forests ; interspecific competition ; intraspecific competition ; mammalogy ; voles
Language	English
Dates of publication	2022-0106
Size	p. 1484-1496.
Publishing place	American Society of Mammalogists
Document type	Article
ZDB-ID	218314-6
ISSN	0022-2372
ISSN	0022-2372
DOI	10.1093/jmammal/gyab096
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Article ; Online: An RNA-seq study of the mPFC of rats with different addiction phenotypes.

McFalls, Ashley J / Imperio, Ceasar G / Woodward, Emma / Krikorian, Claire / Stoltsfus, Brooke / Wronowski, Benjamin / Grigson, Patricia S / Freeman, Willard M / Vrana, Kent E

Brain research bulletin

2022 Volume 191, Page(s) 107–120

Abstract: Addiction is a disease of brain-reward circuitry whereby attention, motivation, memory and emotional systems become enslaved to the goal of seeking and acquiring drug, instead of responding to the natural rewards for which these systems evolved. At the ... ...

Abstract	Addiction is a disease of brain-reward circuitry whereby attention, motivation, memory and emotional systems become enslaved to the goal of seeking and acquiring drug, instead of responding to the natural rewards for which these systems evolved. At the intersection of reward/limbic structures, the medial prefrontal cortex (mPFC) receives and consolidates signals regarding environment and orchestrates the most appropriate response (i.e., decision-making and attention). As such, mPFC function plays a critical role in the vulnerability or resilience to drug addiction. In our model of drug-induced reward devaluation, an outbred group of Sprague-Dawley rats parsed into two distinct drug-taking phenotypes: those, referred to as small suppressors (SS) that readily ingest a heroin-paired sweet cue and then take little drug, and those, referred to large suppressors (LS), that avoid the heroin-paired cue, but then respond greatly for the drug of abuse. In the present study, we analyzed the mPFC transcriptome of rats from these divergent groups to discover differences in gene expression that underlie these distinct phenotypes. Genes found to be differentially expressed were those associated with schizophrenia and dopamine signaling, signal transduction, development and synaptic plasticity. These genes may underlie the circumstance whereby some individuals succumb to addiction, while others do not, and may reveal new pharmacological targets for the treatment of drug addiction.
MeSH term(s)	Animals ; Rats ; Heroin/metabolism ; RNA-Seq ; Rats, Sprague-Dawley ; Prefrontal Cortex/metabolism ; Phenotype ; Self Administration
Chemical Substances	Heroin (70D95007SX)
Language	English
Publishing date	2022-10-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	197620-5
ISSN	1873-2747 ; 0361-9230
ISSN (online)	1873-2747
ISSN	0361-9230
DOI	10.1016/j.brainresbull.2022.09.023
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Article: Variation in space and time: a long-term examination of density-dependent dispersal in a woodland rodent

Denomme-Brown, Simon T / Cottenie, Karl / Falls, J. Bruce / Falls, E. Ann / Brooks, Ronald J / McAdam, Andrew G

Oecologia. 2020 Aug., v. 193, no. 4

2020

Abstract	Dispersal is a fundamental ecological process that can be affected by population density, yet studies report contrasting effects of density on propensity to disperse. In addition, the relationship between dispersal and density is seldom examined using densities measured at different spatial scales or over extensive time series. We used 51 years of trapping data to examine how dispersal by wild deer mice (Peromyscus maniculatus) was affected by changes in both local and regional population densities. We examined these patterns over both the entire time series and also in 10-year shifting windows to determine whether the nature and strength of the relationship changed through time. Probability of dispersal decreased with increased local and regional population density, and the negative effect of local density on dispersal was more pronounced in years with low regional densities. In addition, the strength of negative density-dependent dispersal changed through time, ranging from very strong in some decades to absent in other periods of the study. Finally, while females were less likely to disperse, female dispersal was more density-dependent than male dispersal. Our study shows that the relationship between density and dispersal is not temporally static and that investigations of density-dependent dispersal should consider both local and regional population densities.
Keywords	Peromyscus maniculatus ; deer ; females ; males ; population density ; probability ; rodents ; space and time ; time series analysis ; woodlands
Language	English
Dates of publication	2020-08
Size	p. 903-912.
Publishing place	Springer Berlin Heidelberg
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	123369-5
ISSN	1432-1939 ; 0029-8549
ISSN (online)	1432-1939
ISSN	0029-8549
DOI	10.1007/s00442-020-04728-3
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Article ; Online: Cultivating Relationships as a Community-Based Recruitment Strategy in Transdisciplinary Aging Research: Lessons From an Academic-Community Partnership.

Diallo, Ana F / Mackiewicz, Marissa / Sargent, Lana / Roman, Youssef M / Slattum, Patricia W / Waters, Leland / Bennett, Johnathan / Battle, Kimberly / Zanjani, Faika / Gendron, Tracey / Winship, Jodi / Ford, Gregory / Falls, Katherine / Price, Elvin T / Parsons, Pamela / Chung, Jane

Family & community health

2023 Volume 47, Issue 1, Page(s) 32–40

Abstract: Participation of Black American older adults in community-engaged research remains challenging in health sciences. The objectives of this study were to describe the specific efforts, successes, and challenges in recruiting Black American older adults in ... ...

Abstract	Participation of Black American older adults in community-engaged research remains challenging in health sciences. The objectives of this study were to describe the specific efforts, successes, and challenges in recruiting Black American older adults in research led by the Health and Wellness in Aging Across the Lifespan core, part of the Virginia Commonwealth University Institute for Inclusion, Inquiry, and Innovation (iCubed). We conducted a cross-case analysis of 6 community-engaged research projects using the community-engaged research continuum model. Successful recruitment strategies comprised a multifaceted approach to community-based collaboration, including a wellness program with a long standing relationship with the community, engaging key stakeholders and a community advisory board, and building a community-based coalition of stakeholders. Posting flyers and modest monetary compensation remain standard recruitment strategies. The cross-case analysis offered critical lessons on the community's nature and level of engagement in research. Relationship building based on trust and respect is essential to solving complex aging issues in the community.
MeSH term(s)	Humans ; Aged ; Geroscience ; Community-Based Participatory Research/methods ; Health Promotion/methods ; Trust ; Aging
Language	English
Publishing date	2023-10-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	449879-3
ISSN	1550-5057 ; 0160-6379
ISSN (online)	1550-5057
ISSN	0160-6379
DOI	10.1097/FCH.0000000000000383
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Article: Socioeconomic Effects on Psychosocial Factors Among Low-Income Older Adults.

Sargent, Lana / Zanjani, Faika / Winship, Jodi / Gendron, Tracey / Mackiewicz, Marissa / Diallo, Ana / Waters, Leland / Battle, Kimberly / Ford, Gregory / Falls, Katherine / Chung, Jane / Price, Elvin T / Cisewski, Melissa / Parsons, Pamela / Health, Vcu iCubed

Gerontology & geriatric medicine

2022 Volume 8, Page(s) 23337214221084866

Abstract: Objectives: Older adults have been disproportionately affected by COVID-19. The primary goal of this study is to determine the socioeconomic effects on psychosocial factors among low-income independent-living older adults, in an urban setting, during ... ...

Abstract	Objectives: Older adults have been disproportionately affected by COVID-19. The primary goal of this study is to determine the socioeconomic effects on psychosocial factors among low-income independent-living older adults, in an urban setting, during the COVID-pandemic. Methods: Participants were recruited through Virginia Commonwealth University's Richmond Health and Wellness Program. Telephone surveys ( Results: The sample population was between 51 and 87 years of age, 88% were Black, 57% reported incomes of $10,000/year or less, and 60% reported a high-school education or less. There were income effects for social activities/isolation (f = 3.69, Discussion: Overall results highlight the social patterns for a diverse sample of low-income urban older adults; education and income are identified as risk factors for social losses, COVID-infection experiences, racial/ethnic discrimination during the COVID-pandemic, and positive change behaviors.
Language	English
Publishing date	2022-03-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844974-5
ISSN	2333-7214 ; 2333-7214
ISSN (online)	2333-7214
ISSN	2333-7214
DOI	10.1177/23337214221084866
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