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Article ; Online: Network Hamiltonian Models for Unstructured Protein Aggregates, with Application to γD-Crystallin.

Diessner, Elizabeth M / Freites, J Alfredo / Tobias, Douglas J / Butts, Carter T

The journal of physical chemistry. B

2023 Volume 127, Issue 3, Page(s) 685–697

Abstract: ... variant W42R in solution, performed by Wong, E. K.; Prytkova, V.; Freites, J. A.; Butts, C. T.; Tobias, D ...

Abstract	Network Hamiltonian models (NHMs) are a framework for topological coarse-graining of protein-protein interactions, in which each node corresponds to a protein, and edges are drawn between nodes representing proteins that are noncovalently bound. Here, this framework is applied to aggregates of γD-crystallin, a structural protein of the eye lens implicated in cataract disease. The NHMs in this study are generated from atomistic simulations of equilibrium distributions of wild-type and the cataract-causing variant W42R in solution, performed by Wong, E. K.; Prytkova, V.; Freites, J. A.; Butts, C. T.; Tobias, D. J. Molecular Mechanism of Aggregation of the Cataract-Related γD-Crystallin W42R Variant from Multiscale Atomistic Simulations.
MeSH term(s)	Humans ; Intrinsically Disordered Proteins/metabolism ; Protein Aggregates ; gamma-Crystallins/chemistry ; Cataract/metabolism ; Lens, Crystalline/metabolism
Chemical Substances	Intrinsically Disordered Proteins ; Protein Aggregates ; gamma-Crystallins
Language	English
Publishing date	2023-01-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.2c07672
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Article ; Online: Percutaneous Retrieval of Retained Gallstones.

McCarley, Saudia / Yu, Bernice / Guay, Robert / Ong, Adrian / Sacks, David / Butts, Christopher A

The American surgeon

2022 Volume 89, Issue 6, Page(s) 2918–2919

Abstract: Laparoscopic cholecystectomy has become the gold standard for patients with gallbladder disease. However, spilled gallstones occur in up to 18% of laparoscopic cholecystectomies, which may result in retained gallstones. Though most do not cause issues, ... ...

Abstract	Laparoscopic cholecystectomy has become the gold standard for patients with gallbladder disease. However, spilled gallstones occur in up to 18% of laparoscopic cholecystectomies, which may result in retained gallstones. Though most do not cause issues, there may be abscess formation from 4 months to 10 years postoperatively. We present a 78-year-old patient who formed a subhepatic abscess 3 months postoperatively from his laparoscopic cholecystectomy secondary to a 1 cm retained gallstone. The abscess was percutaneously drained by interventional radiology (IR), and the stone was subsequently removed by IR using a percutaneous approach. Open and laparoscopic approaches have been previously described for abscess drainage and removal of gallstones. In this case, both the abscess and stone were drained and removed percutaneously by IR. Though this is an uncommon entity, percutaneous decompression can aid in preventing such patients from undergoing additional surgery.
MeSH term(s)	Humans ; Aged ; Gallstones/complications ; Gallstones/diagnostic imaging ; Gallstones/surgery ; Abscess/etiology ; Abdominal Abscess/surgery ; Cholecystectomy, Laparoscopic/adverse effects ; Drainage/adverse effects
Language	English
Publishing date	2022-03-25
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	202465-2
ISSN	1555-9823 ; 0003-1348
ISSN (online)	1555-9823
ISSN	0003-1348
DOI	10.1177/00031348221084944
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Article: The use of live and continuous training 'ultrarounds' to enhance use of point-of-care ultrasound on a busy ambulatory assessment unit.

Onen, Barbara / Ghaffari, Ehsan / Gaied, Joseph / De Butts, Richard / Bowen, Jordan / Lasserson, Daniel

Future healthcare journal

2022 Volume 9, Issue Suppl 2, Page(s) 36–37

Language	English
Publishing date	2022-10-05
Publishing country	England
Document type	Journal Article
ZDB-ID	3016427-8
ISSN	2514-6653 ; 2514-6645
ISSN (online)	2514-6653
ISSN	2514-6645
DOI	10.7861/fhj.9-2-s36
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Article ; Online: Designing a Road Map for Action to Address Bias and Racism Within a Large Academic Medical Center.

Butts, Gary C / Abner, Pamela / Hess, Leona / Palermo, Ann-Gel S / Cotilletta, Ben / Gianelli, Arthur / Richardson, Lynne D

Academic medicine : journal of the Association of American Medical Colleges

2023 Volume 98, Issue 12, Page(s) 1381–1389

Abstract: Abstract: The convergence of the COVID-19 pandemic, the Black Lives Matter Movement, and the public anguish and outrage resulting from the murder of George Floyd in 2020 intensified the commitment of many health care institutions to pursue racial and ... ...

Abstract	Abstract: The convergence of the COVID-19 pandemic, the Black Lives Matter Movement, and the public anguish and outrage resulting from the murder of George Floyd in 2020 intensified the commitment of many health care institutions to pursue racial and social justice and achieve health equity. The authors describe the Road Map for Action to Address Racism, which was developed to unify and systematize antiracism efforts across the Mount Sinai Health System. A 51-member Task Force to Address Racism, comprising faculty, staff, students, alumni, health system leaders, and trustees, developed recommendations to achieve the goal of becoming an antiracist and equitable health care and learning institution by intentionally addressing all forms of racism and promoting greater diversity, inclusion, and equity for its workforce and community. Grounded in the principles of Collective Impact, the Task Force developed a set of 11 key strategies to effect systemwide change. The strategies affected all aspects of the organization: business systems and financial operations, delivery of care, workforce development and training, leadership development, medical education, and community engagement. The authors describe Road Map implementation, currently in process, including the appointment of strategy leaders, evolution of a governance structure integrating stakeholders from across the health system, development of an evaluation framework, communication and engagement efforts, and process measures and progress to date. Lessons learned include the importance of recognizing the work of dismantling racism as integral to, not apart from, the institution's day-to-day work, and the need for specialized expertise and a significant investment of time to coordinate Road Map implementation. Going forward, rigorous assessment of quantitative and qualitative outcomes and a commitment to sharing successes and challenges will be critical to eradicating systems that have perpetuated inequities in the biomedical sciences and medicine and in the delivery of health care.
MeSH term(s)	Humans ; Racism/prevention & control ; Pandemics ; Academic Medical Centers ; Health Facilities ; Bias
Language	English
Publishing date	2023-06-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	96192-9
ISSN	1938-808X ; 1040-2446
ISSN (online)	1938-808X
ISSN	1040-2446
DOI	10.1097/ACM.0000000000005289
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Article: The "teach-back" method improves surgical informed consent and shared decision-making: a proof of concept study.

Seely, Kevin D / Higgs, Jordan A / Butts, Lindsey / Roe, Jason M / Merrill, Colton B / Zapata, Isain / Nigh, Andrew

Patient safety in surgery

2022 Volume 16, Issue 1, Page(s) 33

Abstract: Introduction: The teach-back method is a communication tool that can improve patient safety and shared decision-making. Its utility in patient care has been studied extensively in many areas of clinical medicine. However, the literature on teach-back in ...

Abstract	Introduction: The teach-back method is a communication tool that can improve patient safety and shared decision-making. Its utility in patient care has been studied extensively in many areas of clinical medicine. However, the literature on teach-back in surgical patient education and informed consent is limited, and few studies have been conducted to test its impact on perioperative patient interactions. The objective of this study was to evaluate if the teach-back method can improve informed consent and surgeon trust. An assessment of the time required to be implemented was also evaluated. Methods: A standardized interaction role-playing a pre-operative informed consent discussion was designed. Laparoscopic cholecystectomy was selected as the proposed procedure. Standardized patients were split into two groups: teach-back and a control group. The control group was delivered a script that discloses the risks and benefits of laparoscopic cholecystectomy followed by a concluding prompt for any questions. The teach-back group was presented the same script followed by the teach-back method. Interactions were timed and patients completed a quiz assessing their knowledge of the risks and benefits and a survey assessing subjective perceptions about the interaction. Statistical analysis through Generalized Linear Models (GLMs) was used to compare visit length, performance on the comprehension quiz, and subjective surgeon trust perceptions. Results: 34 participants completed the scenario, the comprehension quiz, and the survey (n = 34). Analysis of the subjective evaluation of the physician and encounter was significant for increased physician trust (p = 0.0457). The intervention group performed higher on the knowledge check by an average of one point when compared to the control group (p = 0.0479). The visits with intervention took an average of 2.45 min longer than the control group visits (p = 0.0014). People who had the actual procedure in the past (evaluated as a confounder) were not significantly more likely to display the same effect as the teach-back method, suggesting that the knowledge and trust gained were not based on previous experiences with the procedure. Conclusion: When employed correctly by surgeons in the perioperative setting, the teach-back method enhances shared decision-making, comprehension, and surgeon trust. Incorporating the teach-back method into risk and benefit disclosures effectively informs and more fully engages patients in the informed consent process. Notably, the added benefits from using teach-back can be obtained without a burdensome increase in the length of visit.
Language	English
Publishing date	2022-10-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2409244-7
ISSN	1754-9493
ISSN	1754-9493
DOI	10.1186/s13037-022-00342-9
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Article: Spatially resolved detection of small molecules from press-dried plant tissue using MALDI imaging.

Long, Zane G / Le, Jonathan V / Katz, Benjamin B / Lopez, Belen G / Tenenbaum, Emily D / Semmling, Bonnie / Schmidt, Ryan J / Grün, Felix / Butts, Carter T / Martin, Rachel W

Applications in plant sciences

2023 Volume 11, Issue 5, Page(s) e11539

Abstract: Premise: Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a chemical imaging method that can visualize spatial distributions of particular molecules. Plant tissue imaging has so far mostly used cryosectioning, which ... ...

Abstract	Premise: Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a chemical imaging method that can visualize spatial distributions of particular molecules. Plant tissue imaging has so far mostly used cryosectioning, which can be impractical for the preparation of large-area imaging samples, such as full flower petals. Imaging unsectioned plant tissue presents its own difficulties in extracting metabolites to the surface due to the waxy cuticle. Methods: We address this by using established delipidation techniques combined with a solvent vapor extraction prior to applying the matrix with many low-concentration sprays. Results: Using this procedure, we imaged tissue from three different plant species (two flowers and one carnivorous plant leaf). Material factorization analysis of the resulting data reveals a wide range of plant-specific small molecules with varying degrees of localization to specific portions of the tissue samples, while facilitating detection and removal of signal from background sources. Conclusions: This work demonstrates applicability of MALDI-MSI to press-dried plant samples without freezing or cryosectioning, setting the stage for spatially resolved molecule identification. Increased mass resolution and inclusion of tandem mass spectrometry are necessary next steps to allow more specific and reliable compound identification.
Language	English
Publishing date	2023-09-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2699923-7
ISSN	2168-0450
ISSN	2168-0450
DOI	10.1002/aps3.11539
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Article ; Online: Ramucirumab plus erlotinib versus placebo plus erlotinib in previously untreated EGFR-mutated metastatic non-small-cell lung cancer (RELAY): exploratory analysis of next-generation sequencing results.

Garon, E B / Reck, M / Nishio, K / Heymach, J V / Nishio, M / Novello, S / Paz-Ares, L / Popat, S / Aix, S Ponce / Graham, H / Butts, B D / Visseren-Grul, C / Nakagawa, K

ESMO open

2023 Volume 8, Issue 4, Page(s) 101580

Abstract: Background: Ramucirumab plus erlotinib (RAM + ERL) demonstrated superior progression-free survival (PFS) over placebo + ERL (PBO + ERL) in the phase III RELAY study of patients with epidermal growth factor receptor (EGFR)-mutated metastatic non-small- ... ...

Abstract	Background: Ramucirumab plus erlotinib (RAM + ERL) demonstrated superior progression-free survival (PFS) over placebo + ERL (PBO + ERL) in the phase III RELAY study of patients with epidermal growth factor receptor (EGFR)-mutated metastatic non-small-cell lung cancer (EGFR+ mNSCLC; NCT02411448). Next-generation sequencing (NGS) was used to identify clinically relevant alterations in circulating tumor DNA (ctDNA) and explore their impact on treatment outcomes. Patients and methods: Eligible patients with EGFR+ mNSCLC were randomized 1 : 1 to ERL (150 mg/day) plus RAM (10 mg/kg)/PBO every 2 weeks. Liquid biopsies were to be prospectively collected at baseline, cycle 4 (C4), and postdiscontinuation follow-up. EGFR and co-occurring/treatment-emergent (TE) genomic alterations in ctDNA were analyzed using Guardant360 NGS platform. Results: In those with valid baseline samples, detectable activating EGFR alterations in ctDNA (aEGFR+) were associated with shorter PFS [aEGFR+: 12.7 months (n = 255) versus aEGFR-: 22.0 months (n = 131); hazard ratio (HR) = 1.87, 95% confidence interval (CI) 1.42-2.51]. Irrespective of detectable/undetectable baseline aEGFR, RAM + ERL was associated with longer PFS versus PBO + ERL [aEGFR+: median PFS (mPFS) = 15.2 versus 11.1 months, HR = 0.63, 95% CI 0.46-0.85; aEGFR-: mPFS = 22.1 versus 19.2 months, HR = 0.80, 95% CI 0.49-1.30]. Baseline alterations co-occurring with aEGFR were identified in 69 genes, most commonly TP53 (43%), EGFR (other than aEGFR; 25%), and PIK3CA (10%). PFS was longer in RAM + ERL, irrespective of baseline co-occurring alterations. Clearance of baseline aEGFR by C4 was associated with longer PFS (mPFS = 14.1 versus 7.0 months, HR = 0.481, 95% CI 0.33-0.71). RAM + ERL improved PFS outcomes, irrespective of aEGFR mutation clearance. TE gene alterations were most commonly in EGFR [T790M (29%), other (19%)] and TP53 (16%). Conclusions: Baseline aEGFR alterations in ctDNA were associated with shorter mPFS. RAM + ERL was associated with improved PFS outcomes, irrespective of detectable/undetectable aEGFR, co-occurring baseline alterations, or aEGFR+ clearance by C4. aEGFR+ clearance by C4 was associated with improved PFS outcomes. Monitoring co-occurring alterations and aEGFR+ clearance may provide insights into mechanisms of EGFR tyrosine kinase inhibitor resistance and the patients who may benefit from intensified treatment schedules.
MeSH term(s)	Humans ; Carcinoma, Non-Small-Cell Lung/drug therapy ; Carcinoma, Non-Small-Cell Lung/genetics ; Carcinoma, Non-Small-Cell Lung/pathology ; Erlotinib Hydrochloride/pharmacology ; Erlotinib Hydrochloride/therapeutic use ; ErbB Receptors/genetics ; Lung Neoplasms/drug therapy ; Lung Neoplasms/genetics ; Lung Neoplasms/pathology ; Protein Kinase Inhibitors/pharmacology ; Protein Kinase Inhibitors/therapeutic use ; Mutation ; High-Throughput Nucleotide Sequencing ; Ramucirumab
Chemical Substances	Erlotinib Hydrochloride (DA87705X9K) ; ErbB Receptors (EC 2.7.10.1) ; Protein Kinase Inhibitors ; EGFR protein, human (EC 2.7.10.1)
Language	English
Publishing date	2023-06-28
Publishing country	England
Document type	Randomized Controlled Trial ; Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2059-7029
ISSN (online)	2059-7029
DOI	10.1016/j.esmoop.2023.101580
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Article ; Online: sPDGFRβ and neuroinflammation are associated with AD biomarkers and differ by race: The ASCEND Study.

Butts, Brittany / Huang, Hanfeng / Hu, William T / Kehoe, Patrick Gavin / Miners, James Scott / Verble, Danielle D / Zetterberg, Henrik / Zhao, Liping / Trotti, Lynn Marie / Benameur, Karima / Scorr, Laura M / Wharton, Whitney

Alzheimer's & dementia : the journal of the Alzheimer's Association

2023 Volume 20, Issue 2, Page(s) 1175–1189

Abstract: ... African American (B/AA) and non-Hispanic White (NHW) participants.: Methods: Adults (45-65 years ... of vascular injury, and cytokines at baseline and year 2. CSF sPDGFRβ and tau were significantly lower in B/AA ...

Abstract	Introduction: There remains an urgent need to identify preclinical pathophysiological mechanisms of Alzheimer's disease (AD) development in high-risk, racially diverse populations. We explored the relationship between cerebrospinal fluid (CSF) markers of vascular injury and neuroinflammation with AD biomarkers in middle-aged Black/African American (B/AA) and non-Hispanic White (NHW) participants. Methods: Adults (45-65 years) with a parental history of AD were enrolled (n = 82). CSF and blood biomarkers were collected at baseline and year 2. Results: CSF total tau (t-tau), phosphorylated tau (p-tau), and amyloid beta (Aβ)40 were elevated at year 2 compared to baseline. CSF soluble platelet-derived growth factor receptor β (sPDGFRβ) levels, a marker of pericyte injury, correlated positively with t-tau, p-tau, Aβ40 markers of vascular injury, and cytokines at baseline and year 2. CSF sPDGFRβ and tau were significantly lower in B/AA than NHW. Discussion: Vascular dysfunction and neuroinflammation may precede cognitive decline and disease pathology in the very early preclinical stages of AD, and there are race-related differences in these relationships. Highlights: Cerebrospinal fluid (CSF) Alzheimer's disease (AD) biomarkers changed over 2 years in high-risk middle-aged adults. Markers of vascular dysfunction were associated with the CSF biomarkers amyloid beta and tau. AD biomarkers were lower in Black compared to non-Hispanic White individuals. Markers of vascular dysfunction were lower among Black individuals.
MeSH term(s)	Middle Aged ; Humans ; Alzheimer Disease/pathology ; Amyloid beta-Peptides/cerebrospinal fluid ; Neuroinflammatory Diseases ; Vascular System Injuries ; tau Proteins/cerebrospinal fluid ; Cognitive Dysfunction/cerebrospinal fluid ; Biomarkers/cerebrospinal fluid ; Peptide Fragments/cerebrospinal fluid
Chemical Substances	Amyloid beta-Peptides ; tau Proteins ; Biomarkers ; Peptide Fragments
Language	English
Publishing date	2023-11-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2211627-8
ISSN	1552-5279 ; 1552-5260
ISSN (online)	1552-5279
ISSN	1552-5260
DOI	10.1002/alz.13457
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Article ; Online: Chromosome-level assembly and annotation of the blue catfish Ictalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies.

Wang, Haolong / Su, Baofeng / Butts, Ian A E / Dunham, Rex A / Wang, Xu

GigaScience

2022 Volume 11

Abstract: ... single-nucleotide polymorphism (SNP) density is 0.32% between the most aquaculturally important blue catfish strains (D&B and Rio ...

Abstract	Background: The blue catfish is of great value in aquaculture and recreational fisheries. The F1 hybrids of female channel catfish (Ictalurus punctatus) × male blue catfish (Ictalurusfurcatus) have been the primary driver of US catfish production in recent years because of superior growth, survival, and carcass yield. The channel-blue hybrid also provides an excellent model to investigate molecular mechanisms of environment-dependent heterosis. However, transcriptome and methylome studies suffered from low alignment rates to the channel catfish genome due to divergence, and the genome resources for blue catfish are not publicly available. Results: The blue catfish genome assembly is 841.86 Mbp in length with excellent continuity (8.6 Mbp contig N50, 28.2 Mbp scaffold N50) and completeness (98.6% Eukaryota and 97.0% Actinopterygii BUSCO). A total of 30,971 protein-coding genes were predicted, of which 21,781 were supported by RNA sequencing evidence. Phylogenomic analyses revealed that it diverged from channel catfish approximately 9 million years ago with 15.7 million fixed nucleotide differences. The within-species single-nucleotide polymorphism (SNP) density is 0.32% between the most aquaculturally important blue catfish strains (D&B and Rio Grande). Gene family analysis discovered significant expansion of immune-related families in the blue catfish lineage, which may contribute to disease resistance in blue catfish. Conclusions: We reported the first high-quality, chromosome-level assembly of the blue catfish genome, which provides the necessary genomic tool kit for transcriptome and methylome analysis, SNP discovery and marker-assisted selection, gene editing and genome engineering, and reproductive enhancement of the blue catfish and hybrid catfish.
MeSH term(s)	Animals ; Female ; Male ; Aquaculture ; Catfishes/genetics ; Chromosomes ; Epigenesis, Genetic ; Hybrid Vigor ; Ictaluridae/genetics ; Reproduction ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2022-07-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2708999-X
ISSN	2047-217X ; 2047-217X
ISSN (online)	2047-217X
ISSN	2047-217X
DOI	10.1093/gigascience/giac070
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Article ; Online: Heart Failure After Cavopulmonary Connection: Conversion to Biventricular Circulatory Support.

Davies, Ryan R / Lantz Apn, Jodie L / Mullowney, Sara K / Butts, Ryan J / Pirolli, Timothy / Jaquiss, Robert D B / Sutcliffe, David L

The Annals of thoracic surgery

2021 Volume 112, Issue 3, Page(s) e185–e188

Abstract: Mechanical support of patients with superior cavopulmonary connection is challenging; multiple factors contribute to failure: elevated pulmonary vascular resistance, aortopulmonary collateral flow, venovenous collaterals, ventricular dysfunction, and ... ...

Abstract	Mechanical support of patients with superior cavopulmonary connection is challenging; multiple factors contribute to failure: elevated pulmonary vascular resistance, aortopulmonary collateral flow, venovenous collaterals, ventricular dysfunction, and atrioventricular valve regurgitation. We report 2 cases of conversion from a single ventricle circulation to biventricular mechanical support by reestablishing caval continuity. Both patients have demonstrated recovery of end-organ function and participation in rehabilitation. This method of support results in improved systemic venous pressures and pulmonary blood flow compared with systemic mechanical circulatory support with a cavopulmonary connection and transfers some of the complexity of the transplant to the ventricular assist device implant.
MeSH term(s)	Child, Preschool ; Female ; Fontan Procedure ; Heart Failure/therapy ; Heart-Assist Devices ; Humans ; Infant ; Male ; Postoperative Complications/therapy
Language	English
Publishing date	2021-01-19
Publishing country	Netherlands
Document type	Case Reports ; Journal Article
ZDB-ID	211007-6
ISSN	1552-6259 ; 0003-4975
ISSN (online)	1552-6259
ISSN	0003-4975
DOI	10.1016/j.athoracsur.2020.12.042
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