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Objective: Restenosis after transcarotid artery revascularization (TCAR) is a known complication. When identified in the early postoperative period, it may be related to technique. We evaluated our TCAR experience to identify potentially modifiable factors impacting restenosis., Methods: This is a single-institution, retrospective review of patients undergoing TCAR from November 2017 to July 2022. Restenosis was defined as >50% stenosis on duplex ultrasound (DUS) examination or computed tomographic angiography (CTA). Continuous variables were compared using Kruskal-Wallis's test. Categorical variables were compared using the Fisher's exact test., Results: Of 61 interventions, 11 (18%) developed restenosis within the median follow-up of 345 days (interquartile range, 103-623 days). Among these patients, 82% (9/11) had >50% stenosis, and 18% (2/11) had >80% stenosis. Both patients with high-grade restenosis were symptomatic and underwent revascularization. Diagnosis of post-TCAR restenosis was via DUS examination in 45% (5/11), CTA in 18% (2/11), or both CTA/DUS examination in 36% (4/11). Restenosis occurred within 1 month in 54% (6/11) and 6 months in 72% (8/11) of patients. However, three of the six patients with restenosis within 1 month had discordant findings on CTA vs DUS imaging. Patient comorbidities, degree of preoperative stenosis, medical management, balloon size, stent size, lesion characteristics, and predilatation angioplasty did not differ. Patients with restenosis were younger (P = .02), had prior ipsilateral endarterectomy (odds ratio [OR], 6.5; P = .02), had history of neck radiation (OR, 18.3; P = .01), and lower rate of postdilatation angioplasty (OR, 0.11; P = .04), without an increased risk of neurological events., Conclusions: Although post-TCAR restenosis occurred in 18% of patients, only 3% of patients had critical restenosis and required reintervention. Patient factors associated with restenosis were younger age, prior endarterectomy, and history of neck radiation. Although early restenosis may be mitigated by improved technique, the only technical factor associated with restenosis was less use of postdilatation angioplasty. Balancing neurological risk, this factor may have increased application in appropriate patients. Diagnosis of restenosis was inconsistent between imaging modalities; current surveillance paradigms and diagnostic thresholds may warrant reconsideration., Competing Interests: Disclosures J.Y. is a speaker bureau for W. L. Gore & Associates and a consultant for Silk Road. J.M. has grants for research and training from Abbott, Cook, Covidien, Endologix, and W. L. Gore & Associates., (Published by Elsevier Inc.)

Background: Anatomy is critical in risk stratification and therapeutic decision making in coronary disease. The relationship between anatomy and outcomes is not well described in PAD. We sought to develop an angiographic core lab within the VOYAGER-PAD trial. The current report describes the methods of creating this core lab, its study population, and baseline anatomic variables. Methods: Patients undergoing lower-extremity revascularization for symptomatic PAD were randomized in VOYAGER-PAD. The median follow up was 2.25 years. Events were adjudicated by a blinded Clinical Endpoint Committee. Angiograms were collected from study participants; those with available angiograms formed this core lab cohort. Angiograms were scored for anatomic and flow characteristics by trained reviewers blinded to treatment. Ten percent of angiograms were evaluated independently by two reviewers; inter-rater agreement was assessed. Clinical characteristics and the treatment effect of rivaroxaban were compared between the core lab cohort and noncore lab participants. Anatomic data by segment were analyzed. Results: Of 6564 participants randomized in VOYAGER-PAD, catheter-based angiograms from 1666 patients were obtained for this core lab. Anatomic and flow characteristics were collected across 16 anatomic segments by 15 reviewers. Concordance between reviewers for anatomic and flow variables across segments was 90.5% (24,417/26,968). Clinical characteristics were similar between patients in the core lab and those not included. The effect of rivaroxaban on the primary efficacy and safety outcomes was also similar. Conclusions: The VOYAGER-PAD angiographic core lab provides an opportunity to correlate PAD anatomy with independently adjudicated outcomes and provide insights into therapy for PAD. (ClinicalTrials.gov Identifier: NCT02504216) ., Competing Interests: Declaration of conflicting interestsThe authors declared the following potential conflicts of interest with respect to the research, authorship, and/or publication of this article: Drs Rogers, Hogan, Nehler, Capell, Berkowitz, Hess, Yčas, and Bonaca receive salary support from CPC, a nonprofit academic research organization affiliated with the University of Colorado that receives or has received research grant/consulting funding between February 2021 and June 2023 from the following organizations: Abbott Laboratories, Adamis Pharmaceuticals Corporation, Agios Pharmaceuticals, Inc., Alexion Pharma, Alnylam Pharmaceuticals, Inc., Amgen Inc., Angionetics, Inc., ARCA Biopharma, Inc., Array BioPharma, Inc., AstraZeneca and Affiliates, Atentiv LLC, Audentes Therapeutics, Inc., Bayer and Affiliates, Beth Israel Deaconess Medical Center, Better Therapeutics, Inc., BIDMC, Boston Clinical Research Institute, Bristol-Meyers Squibb Company, Cambrian Biopharma, Inc., Cardiol Therapeutics Inc., CellResearch Corp., Cook Medical Incorporated, Covance, CSL Behring LLC, Eidos Therapeutics, Inc., EP Trading Co. Ltd, EPG Communication Holdings Ltd, Epizon Pharma, Inc., Esperion Therapeutics, Inc., Everly Well, Inc., Exicon Consulting Pvt Ltd, Faraday Pharm-aceuticals, Inc., Foresee Pharmaceuticals Co. Ltd, Fortress Biotech, Inc., HDL Therapeutics Inc., HeartFlow Inc., Hummingbird Bioscience, Insmed Inc., Ionis Pharmaceuticals, IQVIA Inc., JanOne Biotech Holdings Inc., Janssen and Affiliates, Kaneka, Kowa Research Institute, Inc., Kyushu University, Lexicon Pharm-aceuticals, Inc., LSG Kyushu University, Medimmune Ltd, Medpace, Merck & Affiliates, Novartis Pharmaceuticals Corp., Novate Medical, Ltd, Novo Nordisk, Inc., Pan Industry Group, Pfizer Inc., PhaseBio Pharmaceuticals, Inc., PPD Development, LP, Prairie Education and Research Cooperative, Prothena Biosciences Limited, Regeneron Pharmaceuticals, Inc., Regio Biosciences, Inc., Rexgenero, Sanifit Therapeutics S.A., Sanofi-Aventis Groupe, Silence Therapeutics PLC, Smith & Nephew plc, Stealth Bio-Therapeutics Inc., State of Colorado CCPD Grant, The Brigham & Women’s Hospital, Inc., The Feinstein Institutes for Medical Research, Thrombosis Research Institute, University of Colorado, University of Pittsburgh, VarmX, Virta Health Corporation, WCT Atlas, Worldwide Clinical Trials Inc., WraSer, LLC, and Yale Cardiovascular Research Group. Dr Bonaca receives support from the AHA SFRN under award numbers 18SFRN3390085 (BWH-DH SFRN Center) and 18SFRN-33960262 (BWH-DH Clinical Project). Dr Bonaca also reports stock in Medtronic and Pfizer.

Motivation: Ab initio gene prediction in nonmodel organisms is a difficult task. While many ab initio methods have been developed, their average accuracy over long segments of a genome, and especially when assessed over a wide range of species, generally yields results with sensitivity and specificity levels in the low 60% range. A common weakness of most methods is the tendency to learn patterns that are species-specific to varying degrees. The need exists for methods to extract genetic features that can distinguish coding and noncoding regions that are not sensitive to specific organism characteristics., Results: A new method based on a neural network (NN) that uses a collection of sensors to create input features is presented. It is shown that accurate predictions are achieved even when trained on organisms that are significantly different phylogenetically than test organisms. A consensus prediction algorithm for a CoDing Sequence (CDS) is subsequently applied to the first nucleotide level of NN predictions that boosts accuracy through a data-driven procedure that optimizes a CDS/non-CDS threshold. An aggregate accuracy benchmark at the nucleotide level shows that this new approach performs better than existing ab initio methods, while requiring significantly less training data., Availability and Implementation: https://github.com/BioMolecularPhysicsGroup-UNCC/MachineLearning., Competing Interests: None declared., (© The Author(s) 2023. Published by Oxford University Press.)

Background: The use of thoracic endovascular aortic repair (TEVAR) for the management of acute uncomplicated type B aortic dissection (TBAD) has increased. Although the results from early studies were promising, larger randomized trials evaluating TEVAR are lacking. It is also unclear where sufficient equipoise exists for such trials. In the present study, we evaluated the number of readmissions and unplanned operations after TEVAR vs those after medical management as the initial treatment of acute uncomplicated TBAD and the frequency of each treatment in this population., Methods: We performed a multi-institutional retrospective review of patients with acute TBAD from 2015 to 2020 with the 1-year outcomes available, excluding patients with prior aortic intervention or chronic, iatrogenic or traumatic etiologies. The primary exposure was TEVAR vs medical management at the index admission. The patient demographics, clinical presentation, and imaging findings were analyzed using bivariate and multivariate logistic regression for the primary outcomes of unplanned readmission and/or operation after the initial admission. The secondary outcomes were mortality, myocardial infarction, stroke, renal failure requiring dialysis, retrograde type A dissection, and length of stay. We hypothesized that the readmissions would be higher with medical management., Results: A total of 216 patients with TBAD (47 with complicated and 169 with uncomplicated) from two large academic centers were identified. Of the 169 patients with uncomplicated TBAD, 83 (49%) had been treated medically and 86 (51%) had undergone TEVAR at the initial admission. No differences were found in the demographics or high-risk imaging features at presentation. The medically managed patients had had higher rates of unplanned readmission (34% vs 9%; P = .0001) and operation (28% vs 8%; P = .0007) but shorter lengths of stay (6.3 vs 13.1 days; P < .0001). No differences were found in mortality, although the rate of myocardial infarction was higher in the medically managed group (10.8% vs 2.3%; P = .02). Although 28% of the medically managed patients had later required operation, they had had morbidity and mortality similar to those of patients who had undergone initial TEVAR. Initial medical management was associated with unplanned readmission (odds ratio, 8.3; P = .02) and the need for operation (odds ratio, 4.56; P = .006). No differences were found in the outcomes according to the involved aortic zones., Conclusions: In the present study, medical management of acute uncomplicated TBAD was associated with higher rates of readmission and the need for unplanned operation compared with TEVAR. However, no differences were found in the 1-year mortality for the patients for whom medical management had failed. Because one half of the patients had undergone medical management and one half had undergone early TEVAR, this finding suggests clinical equipoise for the treatment of acute uncomplicated TBAD. Therefore, a larger randomized trial appears warranted to determine whether a clear benefit exists for early TEVAR., (Published by Elsevier Inc.)

Background: The aim of this study is to compare how instructions for use (IFU) affected perioperative and intermediate term outcomes for common iliac artery aneurysms (CIAA) treated with the Gore Excluder iliac branch endoprosthesis (IBE)., Methods: A retrospective analysis was performed of all patients treated at two affiliated academic centers from September 2016 to May 2020. Outcomes were compared between IFU and nonIFU IBE cases. Criteria for nonIFU included: (1) use with a nonGore aortic endoprosthesis (n = 10), (2) isolated IBE (n = 3), and (3) requiring nondedicated covered stents for additional extension into a more suitable landing zone in the ipsilateral internal iliac artery or one of its branches (n = 11). Perioperative and intermediate term data were collected for both groups. The primary end points were free from the major adverse event (MAE) at 30 days and primary effectiveness at 1 year., Results: A total of 51 CIAA (39 patients) were treated with an IBE. Overall, 15 patients were treated under IFU and 24 under nonIFU. The IFU group mean age was older (72 vs. 67 years, P = 0.03), and males (97%) were primarily treated. Comorbidities were similar except nonIFU had more patients with previous endovascular abdominal aortic aneurysm repair on presentation (0 vs. 4 cases, P = 0.04). Procedure (178 vs. 264 min, P = 0.02) and fluoroscopy (52 vs. 74 min, P = 0.04) times were longer in the nonIFU group. Technical success was 100% for both groups, and there was no difference in device related reintervention at 30 days (0 vs. 1, P = 0.44). There was no MAE in either group at 30 days. Intervention for any endoleak was similar between the groups (2 vs. 3, P = 0.94). Percent CIAA sac regression was similar between the groups (19% vs. 18%, P = 0.21). There was no difference for primary effectiveness at 1 year (93% vs. 92%, P = 0.85). There was one death per group at one year not related to an aortic or iliac cause., Conclusions: In properly selected patients with complex anatomy, IBE can be used with nondedicated aortic and internal iliac components with good early term outcomes., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Machine learning (ML) has been an important arsenal in computational biology used to elucidate protein function for decades. With the recent burgeoning of novel ML methods and applications, new ML approaches have been incorporated into many areas of computational biology dealing with protein function. We examine how ML has been integrated into a wide range of computational models to improve prediction accuracy and gain a better understanding of protein function. The applications discussed are protein structure prediction, protein engineering using sequence modifications to achieve stability and druggability characteristics, molecular docking in terms of protein-ligand binding, including allosteric effects, protein-protein interactions and protein-centric drug discovery. To quantify the mechanisms underlying protein function, a holistic approach that takes structure, flexibility, stability, and dynamics into account is required, as these aspects become inseparable through their interdependence. Another key component of protein function is conformational dynamics, which often manifest as protein kinetics. Computational methods that use ML to generate representative conformational ensembles and quantify differences in conformational ensembles important for function are included in this review. Future opportunities are highlighted for each of these topics.

The beta-lactamase enzyme provides effective resistance to beta-lactam antibiotics due to substrate recognition controlled by point mutations. Recently, extended-spectrum and inhibitor-resistant mutants have become a global health problem. Here, the functional dynamics that control substrate recognition in TEM beta-lactamase are investigated using all-atom molecular dynamics simulations. Comparisons are made between wild-type TEM-1 and TEM-2 and the extended-spectrum mutants TEM-10 and TEM-52, both in apo form and in complex with four different antibiotics (ampicillin, amoxicillin, cefotaxime and ceftazidime). Dynamic allostery is predicted based on a quasi-harmonic normal mode analysis using a perturbation scan. An allosteric mechanism known to inhibit enzymatic function in TEM beta-lactamase is identified, along with other allosteric binding targets. Mechanisms for substrate recognition are elucidated using multivariate comparative analysis of molecular dynamics trajectories to identify changes in dynamics resulting from point mutations and ligand binding, and the conserved dynamics, which are functionally important, are extracted as well. The results suggest that the H10-H11 loop (residues 214-221) is a secondary anchor for larger extended spectrum ligands, while the H9-H10 loop (residues 194-202) is distal from the active site and stabilizes the protein against structural changes. These secondary non-catalytically-active loops offer attractive targets for novel noncompetitive inhibitors of TEM beta-lactamase.

Background: Iliac artery anatomy can have a dramatic impact on the success of endovascular complex aortic aneurysm (CAA) procedures as endograft delivery systems need to be advanced and manipulated through these access vessels. The aim of this study was to evaluate the outcomes of iliac artery conduits with emphasizes on open vs endovascular conduits performed to facilitate CAA endovascular repair., Methods: All patients who had open or endovascular iliac conduits prior to endovascular CAA repair to treat thoracoabdominal, juxtarenal, or suprarenal aneurysms at the University of Colorado Hospital from January 2009 through January 2019 were included. Patients who presented with symptomatic or ruptured aortic aneurysms were excluded. Outcomes of interest included postoperative complications and mortality in patients undergoing iliac conduits., Results: Twenty-seven patients with a total of 42 conduits were included in the study. The majority of patients ( N = 15, 56%) were female and the average age was 72 ± 9 years. The calculated VQI cardiac index was .6% (range, .3%-.8%). Eighteen (43%) endovascular and 24 (57%) open iliac conduits were performed during the study period. Thirty (71%) conduits were performed in a staged fashion, while 12 (29%) were performed at the same time as endovascular CAA repair. The mean time between conduit and definitive aneurysm repair surgery was 130 ± 68 days in the endovascular and 107 ± 79 days in the open groups ( P = .87). No aneurysm rupture occurred during the staging period in either group. The median follow-up for the entire cohort was 18 ± 22 months. The median length of hospital stay for patients undergoing endovascular and open ICs was 6 (ranging, 1-28 days) and 7 days (ranging, 3-18 days), respectively. Patients undergoing open conduits had significantly more complications than those undergoing endovascular conduit (endoconduit) creation. A total of 4 (15%) patients died within 30 days after aneurysm repair. Out of 23 survivors, 18 (78%) patients were discharged home, 4 (18%) patients were discharged to a skilled nursing facility, and 1 (4%) patient was discharged to an acute rehabilitation facility. No mortality difference based on type of conduit was found., Conclusions: Overall complication rate associated with creation of open iliac artery conduits is not negligible. Endoconduits, which carry less morbidity than open conduits, are preferred as a first-line adjunctive access procedure to facilitate complex endovascular aortic aneurysm repair.

Objective: Atherectomy has become increasingly used as an endovascular treatment of lower extremity atherosclerotic disease in the United States. However, concerns and controversies about its indications and outcomes exist. The goal of the present systematic review and meta-analysis was to investigate the outcomes and complications related to atherectomy to treat femoropopliteal atherosclerotic disease., Methods: A systematic review in accordance with the recommendations from the PRISMA (preferred reporting items for systematic reviews and meta-analyses) statement was performed. Four major scientific repositories (MEDLINE, Embase, the Cochrane Library, and Thompson Web of Sciences) were queried from their inception to April 5, 2020. We reviewed and entered the data in a dedicated dataset. The outcomes included the patency rates, clinical and hemodynamic improvement, and morbidity and mortality associated with atherectomy interventions., Results: Twenty-four studies encompassing 1900 patients met the inclusion criteria for the present study. Of the 1900 patients, 74.3% had presented with Rutherford class 1 to 3 and 25.7% presented with Rutherford class 4 to 6; 1445 patients had undergone atherectomy, and 455 patients had been treated without atherectomy. The atherectomy group had undergone directional atherectomy (n = 851), rotational atherectomy (n = 851), laser atherectomy (n = 201), and orbital atherectomy (n = 78). Most of these patients had also received adjunct treatments, which varied across the studies and included a combination of stenting, balloon angioplasty, or drug-coated balloon angioplasty. Technical success was achieved in 92.3% of the cases. Distal embolization, vessel perforation, and dissection occurred in 3.4%, 1.9%, and 4% of the cases, respectively. The initial patency was 95.4%. At the 12-month median follow-up, the primary patency was 72.6%. The ankle brachial index had improved from a preoperative mean of 0.6 to a postoperative mean of 0.84. The incidence of major amputation and mortality during the follow-up period was 2.2% and 3.4%, respectively., Conclusions: The results from our review of the reported data suggest that femoropopliteal atherectomy can be completed safely, modestly improving the ankle brachial index and maintaining the 1-year patency in nearly three of four patients. However, these findings were based on heterogeneous studies that skewed the generalizable conclusions about atherectomy's efficacy. Atherectomy places a high cost burden on the healthcare system and is used in the United States at a higher rate than in other countries. Our review of the literature did not demonstrate clear atherectomy superiority to alternatives that would warrant the pervasive and increasing use of this costly technology. Future work should focus on developing high-quality randomized controlled trials to determine the specific patient and lesion characteristics for which atherectomy can add value., (Copyright © 2021 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.)

How can an income tax system be designed to exploit human nature and a free market to create a poverty free society, while balancing budgets without disproportional tax burdens? Such a tax system, with universal character, is deduced from the following guiding principles: (1) a single tax rate applies to all income types and levels; (2) the tax rate adjusts to satisfy budget projections; (3) government transfer only supplements the income of households with self-generated income below the poverty line; (4) deductions for basic living expenses, itemized investments and capital losses are allowed; (5) deductions cannot be applied to government transfer. A general framework emerges with three parameters that determine a minimum allowed tax deduction, a maximum allowed itemized deduction, and a maximum deduction defined by income percentage. An income distribution that mimics the United States, and a series of log-normal distributions are considered to quantitatively compare detailed characteristics of this tax system to progressive and flat tax systems. To minimize government dependency while maximizing after-tax income, the effective tax rate ( ETR ) as a function of income percentile takes the shape of the letter, V, inspiring the name victory tax, where the middle class has the lowest ETR .

Background: Cancer results in a hypercoagulable state that is associated with both venous and arterial thromboses. However, little is known about the effects of acute limb ischemia (ALI) in this cohort of patients. In the present systematic review and meta-analysis, we analyzed the available clinical data on cancer and its association with ALI and evaluated the outcomes in these patients after a diagnosis of ALI., Methods: Three databases, including PubMed, EMBASE, and the Cochrane Library, were queried. Studies that met the inclusion criteria were included regardless of the publication year, language, sample size, or follow-up length. All the steps of the meta-analysis were conducted in accordance with the PRISMA (preferred reporting items for systematic reviews and meta-analyses) and MOOSE (meta-analysis of observational studies in epidemiology) guidelines., Results: Seven studies from 6222 references with a total of 2899 patients were included. Of the 2899 patients, 1195 (41%) had had a diagnosis of ALI before their cancer diagnosis, and 1704 (59%) had presented with ALI after a cancer diagnosis. Nearly three quarters of ALI events were among patients with cancer of the skin and soft tissue (19%), genitourinary (18%), lung (17%), and gastrointestinal (16%) systems. ALI recurrence was similar between the two groups, and major amputation was more likely in patients with a diagnosis of ALI after a cancer diagnosis (7.4% vs 4.6%; P < .01). The incidence of mortality at 1 year was significantly greater for patients with established cancer who had presented with ALI compared with the patients who had presented with ALI before a cancer diagnosis (50.6% vs 29.9%; P < .01). After adjusting for study variability using the random effects model, the mortality at 1 year for all patients was 52.3% (95% confidence interval, 37.7%-66.5%). No significant heterogeneity (P = .73) was found between the two groups of patients, which varied by the timing of the ALI diagnosis in relation to the cancer diagnosis., Conclusions: The 1-year mortality after the development of ALI in patients with cancer was >50%. For patients presenting with ALI of unclear etiology, the presence of an underlying cancer should be considered., (Copyright © 2021 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.)

Purpose: The treatment of thoracoabdominal aortic aneurysm has largely shifted to endovascular techniques. However, severe iliofemoral arterial disease often presents a challenge during these interventions. As a result, iliac conduits have been introduced to facilitate aortic endovascular therapy. The goal of the current study was to gauge utilization and to analyze iliac artery conduit outcomes to facilitate endovascular therapy to treat aortic pathologies., Materials and Methods: A meta-analysis of 14 studies was conducted with the use of random effects modeling. The incidence of periprocedural adverse events was gauged based on iliac conduit vs nonconduit cases and planned vs unplanned iliac conduit placement. Outcomes of interest included length of hospital stay, morbidity and mortality associated to conduits, and all-cause mortality., Results: Iliac conduits, either open or endo-conduits, were utilized in 17% (95% CI: 9%-27%) of 16,855 cases, with technical successful rate of 94% (95% CI: 80%-100%). Periprocedural complications occurred in 32% (95% CI: 22%-42%) of the cases, with overall bleeding complication rate being 10% (95% CI: 5%-16%). Female patients, positive history for smoking, pulmonary disease, and peripheral artery disease at baseline were associated with more frequent utilization of iliac conduits. Conduit use was associated with longer hospitalization, higher periprocedural all-cause mortality (OR: 2.85; 95% CI: 1.75-4.64; p<0.001), and bleeding complication rate (OR: 2.38; 95% CI: 1.58-3.58; p<0.001). Sensitivity analysis among conduit cases showed that planned conduits were associated with fewer periprocedural complications compared to unplanned conduits (OR: 0.38; 95% CI: 0.20-0.73; p=0.004)., Conclusion: Iliac conduit placement is a feasible strategy, associated with high technical success to facilitate complex aortic endovascular repair. However, periprocedural adverse event rate, including bleeding complications is not negligible. All-cause mortality and morbidity rates among cases that require iliac conduits should be strongly considered during clinical decision making. High-quality comparative analyses between iliac conduit vs nonconduit cases and between several types of iliac conduit grafts aiming at facilitating endovascular aortic repair are still needed to determine the best strategy to address challenging iliac artery accesses.

Background: Principal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straightforward, specialized software to facilitate workflows and analysis of molecular dynamics simulation data to fully harness the power of PCA is lacking. The Java Essential Dynamics inspector (JEDi) software is a major upgrade from the previous JED software., Results: Employing multi-threading, JEDi features a user-friendly interface to control rapid workflows for interrogating conformational motions of biopolymers at various spatial resolutions and within subregions, including multiple chain proteins. JEDi has options for Cartesian-based coordinates (cPCA) and internal distance pair coordinates (dpPCA) to construct covariance (Q), correlation (R), and partial correlation (P) matrices. Shrinkage and outlier thresholding are implemented for the accurate estimation of covariance. The effect of rare events is quantified using outlier and inlier filters. Applying sparsity thresholds in statistical models identifies latent correlated motions. Within a hierarchical approach, small-scale atomic motion is first calculated with a separate local cPCA calculation per residue to obtain eigenresidues. Then PCA on the eigenresidues yields rapid and accurate description of large-scale motions. Local cPCA on all residue pairs creates a map of all residue-residue dynamical couplings. Additionally, kernel PCA is implemented. JEDi output gives high quality PNG images by default, with options for text files that include aligned coordinates, several metrics that quantify mobility, PCA modes with their eigenvalues, and displacement vector projections onto the top principal modes. JEDi provides PyMol scripts together with PDB files to visualize individual cPCA modes and the essential dynamics occurring within user-selected time scales. Subspace comparisons performed on the most relevant eigenvectors using several statistical metrics quantify similarity/overlap of high dimensional vector spaces. Free energy landscapes are available for both cPCA and dpPCA., Conclusion: JEDi is a convenient toolkit that applies best practices in multivariate statistics for comparative studies on the essential dynamics of similar biopolymers. JEDi helps identify functional mechanisms through many integrated tools and visual aids for inspecting and quantifying similarity/differences in mobility and dynamic correlations.

Exercise therapy and lower extremity revascularization both improve walking performance in symptomatic patients with peripheral artery disease. The combination of therapies provides greater benefit than either alone and may reduce the need for subsequent revascularization procedures, but further trials with longer follow-up are needed for the outcome of subsequent revascularization., Competing Interests: Dr. Capell has received grants to CPC Clinical Research from Bayer AG and Janssen Pharmaceuticals. Dr. McDermott has received research funding from Regeneron and other research support (consisting of study interventions or provision of outcome measurements) from Helixmith, ArtAssist, Chromadex, ReserveAge, Mars, and Hershey. Dr. Jacobs has received CPC payments from Phillips; consulting contracts through the University of Colorado with Abbott and Terumo; and clinical research support from Mercator and Terumo. Dr. Beckman has served as a consultant for Amgen, Bayer, GlaxoSmithKline, Janssen, Sanofi, and Novartis. Dr. Bonaca has received grants to CPC Clinical Research from Bayer AG, Janssen Pharmaceuticals, Amgen, AstraZeneca, Merck, Novo Nordisk, Pfizer, and Sanofi. Dr. Hiatt has received grants to CPC Clinical Research from Bayer AG, Janssen Pharmaceuticals, and Amgen. Dr. Biswas has reported that she has no relationships relevant to the contents of this paper to disclose., (© 2021 The Authors.)

Identifying mechanisms that control molecular function is a significant challenge in pharmaceutical science and molecular engineering. Here, we present a novel projection pursuit recurrent neural network to identify functional mechanisms in the context of iterative supervised machine learning for discovery-based design optimization. Molecular function recognition is achieved by pairing experiments that categorize systems with digital twin molecular dynamics simulations to generate working hypotheses. Feature extraction decomposes emergent properties of a system into a complete set of basis vectors. Feature selection requires signal-to-noise, statistical significance, and clustering quality to concurrently surpass acceptance levels. Formulated as a multivariate description of differences and similarities between systems, the data-driven working hypothesis is refined by analyzing new systems prioritized by a discovery-likelihood. Utility and generality are demonstrated on several benchmarks, including the elucidation of antibiotic resistance in TEM-52 beta-lactamase. The software is freely available, enabling turnkey analysis of massive data streams found in computational biology and material science.

Background: Acute limb ischemia (ALI) carries significant overall morbidity and mortality. Pregnant and postpartum women are physiologically hypercoagulable, but little is known about the impact of ALI in this cohort of patients. The goal of this systematic review was to gather available data on diagnosis and treatment of ALI during pregnancy and the postpartum period., Methods: A systematic review of studies on patients with ALI during pregnancy and the puerperium was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Three databases including PubMed MEDLINE, Embase, and Cochrane Library were queried. Manuscripts that provided data on diagnosis and treatment of ALI in pregnant and postpartum patients were included regardless of language or study design. Outcomes of interest included type of treatment for ALI (open and endovascular), morbidity, and mortality., Results: Fourteen manuscripts of 6222 references were included with a total of 14 patients. The median age of patients was 31.5 years. Embolism, present in eight (57%) patients, was slightly more common than thrombosis. All patients had a pregnancy complication or concomitant medical condition that might have predisposed to arterial occlusion either directly or indirectly by leading to iatrogenic arterial injury; peripartum cardiomyopathy, the most common, occurred in six (43%) patients. Open surgery was the preferred treatment option in 11 (79%) patients, followed by anticoagulation alone. No endovascular procedures were described. One patient underwent major amputation on presentation, and an additional patient required major amputation for recurrent ALI. No deaths occurred. Twelve (86%) patients had complete recovery with no other ALI-associated sequelae., Conclusions: ALI is rare in pregnant and postpartum women despite their transient physiologic hypercoagulability and is almost uniformly associated with pregnancy complications. Open surgical revascularization or anticoagulation alone appears to have acceptable outcomes as most patients present with embolism or thrombosis without underlying systemic arterial disease., (Copyright © 2020 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.)

Background: Pediatric traumatic vascular injuries are rare. Given the paucity of data to guide anti-coagulation (AC) management of these injuries in children, who have a lower overall risk for thrombosis compared to their adult counterparts, we sought to examine and summarize our recent experience., Method: We conducted a retrospective review of all patients (<18 years old) who sustained traumatic vascular injuries between 2010-2018 at a Level 1 and Level 2 Pediatric Trauma Center., Results: Ninety-nine patients had traumatic vascular injuries. Eighty-four patients sustained a major arterial injury, 26 had a major venous injury, and 11 had both arterial and venous injuries. The arterial injury cohort had a median age of 13.3 years. Most of the arterial injury patients (65/84, 77%) required vascular repair. In-hospital AC management for the arterial injury patients consisted of a post-operative heparin drip (18%, 15/84), aspirin (39%, 26/84), enoxaparin (23%, 19/84), or none (42%, 43/84). Approximately one-half of the patients with arterial injuries (54%, 45/84) were discharged home on AC therapy, most commonly aspirin. Fifty-six patients (66%) followed up post-injury, of which 25% (14/56) had experienced complications., Conclusion: Pediatric traumatic arterial injuries that require surgical intervention other than ligation should be considered for discharge AC - most commonly aspirin - in the absence of contraindications. Pediatric patients with vascular injuries to the aorta, carotid artery, inferior vena cava, portal vein, or lower extremities that are managed non-operatively should also be considered for AC. The preferred AC for pediatric venous injuries is enoxaparin, in the absence of contraindications., Study Type: Treatment Study LEVEL OF EVIDENCE: IV., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Background: Central venous occlusion may occur in hemodialysis patients, resulting in arm or facial swelling and failure of dialysis access. Endovascular management with balloon angioplasty or stenting has been described, but there are minimal data on the use of covered stents in this pathology. We sought to review a single institution's experience with the use of covered stents for central venous occlusive disease in hemodialysis patients., Methods: A retrospective review of all patients undergoing placement of covered stents between April 2014 and December 2016 for central venous occlusive disease to preserve a failing dialysis access was performed. Patients' records were reviewed to identify demographics, medical comorbidities, operative variables, primary patency rates, and secondary interventions., Results: A total of 29 patients were included in the analysis. Viabahn (W.L. Gore and Associates, Flagstaff, AZ) stent grafts were exclusively used in all patients. Technical success rate was 100%. The patients were predominantly female (65.5%), with a mean age of 67.9 ± 12.1 and medical comorbidities of hypertension (86%), diabetes (76%), and tobacco use (7%). The majority (86%) had prior angioplasty and 17 of 29 (59%) patients had previous central venous catheters. The right brachiocephalic vein was the most commonly stented vessel (28%). The median stent length and diameter used were 50 millimeters (range 25-100 millimeters) and 13 millimeters (range: 9-13 millimeters), respectively. The majority of patients (83%) received a single stent, with only 2 patients requiring more than one. Median follow-up was 24 months (range: 6-41 months). Four of 29 (13.8%) patients developed symptomatic stent restenosis requiring secondary intervention, all of which occurred in patients with primary stenosis between 50% and 75%. When compared to the patients without restenosis, longer stents were found to be significantly associated with restenosis (62.5 centimeters, interquartile range [IQR]: 0] vs. 50 centimeter, IQR: 0, P = 0.002). Primary patency rates were 92.9%, 91.7%, and 80.0% at 6, 12, and 24 months respectively. Secondary patency rates were 96.4%, 95.8%, and 93.3% at 6 months, 12 months, and 24 months, respectively. The overall primary patency rate was estimated at 86.2% using Kaplan-Meier analysis at 30.5 months (95% confidence interval: 26.5-34.5 months)., Conclusions: Covered stent grafts have reasonable primary patency and excellent secondary patency when used for central venous stenosis in dialysis patients. Stent-graft length is associated with poorer long-term patency rates., (Copyright © 2019 Elsevier Inc. All rights reserved.)

DD[E/D]-transposases catalyze the multistep reaction of cut-and-paste DNA transposition. Structurally, several DD[E/D]-transposases have been characterized, revealing a multi-domain structure with the catalytic domain possessing the RNase H-like structural motif that brings three catalytic residues (D, D, and E or D) into close proximity for the catalysis. However, the dynamic behavior of DD[E/D]-transposases during transposition remains poorly understood. Here, we analyze the rigidity and flexibility characteristics of two representative DD[E/D]-transposases Mos1 and Sleeping Beauty (SB) using the minimal distance constraint model (mDCM). We find that the catalytic domain of both transposases is globally rigid, with the notable exception of the clamp loop being flexible in the DNA-unbound form. Within this globally rigid structure, the central β-sheet of the RNase H-like motif is much less rigid in comparison to its surrounding α-helices, forming a cage-like structure. The comparison of the original SB transposase to its hyperactive version SB100X reveals the region where the change in flexibility/rigidity correlates with increased activity. This region is found to be within the RNase H-like structural motif and comprise the loop leading from beta-strand B3 to helix H1, helices H1 and H2, which are located on the same side of the central beta-sheet, and the loop between helix H3 and beta-strand B5. We further identify the RKEN214-217DAVQ mutations of the set of hyperactive mutations within the catalytic domain of SB transposase to be the driving factor that induces change in residue-pair rigidity correlations within SB transposase. Given that a signature RNase H-like structural motif is found in DD[E/D]-transposases and, more broadly, in a large superfamily of polynucleotidyl transferases, our results are relevant to these proteins as well., (© 2018 Wiley Periodicals, Inc.)

Spatial and temporal characteristics of molecular structure in ternary solutions of trehalose and choline dihydrogen phosphate (CDHP) are studied using molecular dynamics simulations at 300 K for a range of solute concentrations with a 2 : 1 stoichiometric ratio of trehalose to CDHP. For a given molecular configuration, water molecules are classified as interior (only neighboring other water molecules) or interfacial (at least one solute neighbor). As a tagged water molecule diffuses, it dynamically exchanges between interior and interfacial type as its local environment changes, with differences in hydrogen-bond strength between different molecular species creating a persistent preference for interfacial water. At high solute concentrations, interfacial and interior water have similar diffusivity, which allows for water to collectively act as a plasticizer. The percolation threshold for water, defined as the maximum solute concentration at which there still exists a water cluster that spans the simulation box, was found to be slightly under the liquid-glass transition, estimated to be near 84.5% solute concentration based on the onset of a volume hysteresis effect, which was not previously studied in the computational literature. The systems were observed to be highly inhomogeneous, with interlaced percolating networks of water and solute coexisting at intermediate concentrations. The density of interior water was found to decrease with increasing solute concentration, creating low-density regions within the matrix.

In high throughput applications, such as those found in bioinformatics and finance, it is important to determine accurate probability distribution functions despite only minimal information about data characteristics, and without using human subjectivity. Such an automated process for univariate data is implemented to achieve this goal by merging the maximum entropy method with single order statistics and maximum likelihood. The only required properties of the random variables are that they are continuous and that they are, or can be approximated as, independent and identically distributed. A quasi-log-likelihood function based on single order statistics for sampled uniform random data is used to empirically construct a sample size invariant universal scoring function. Then a probability density estimate is determined by iteratively improving trial cumulative distribution functions, where better estimates are quantified by the scoring function that identifies atypical fluctuations. This criterion resists under and over fitting data as an alternative to employing the Bayesian or Akaike information criterion. Multiple estimates for the probability density reflect uncertainties due to statistical fluctuations in random samples. Scaled quantile residual plots are also introduced as an effective diagnostic to visualize the quality of the estimated probability densities. Benchmark tests show that estimates for the probability density function (PDF) converge to the true PDF as sample size increases on particularly difficult test probability densities that include cases with discontinuities, multi-resolution scales, heavy tails, and singularities. These results indicate the method has general applicability for high throughput statistical inference.

Conformational fluctuations within scFv antibodies are characterized by a novel perturbation-response decomposition of molecular dynamics trajectories. Both perturbation and response profiles are stratified into stabilizing and destabilizing conditions. The linker between the VH and VL domains exhibits the dominant dynamical response by being coupled to nearly the entire protein, responding to both stabilizing and destabilizing perturbations. Perturbations within complementarity-determining regions (CDR) induce rich behavior in dynamic response. Among many effects, stabilizing any CDR loop in the VH domain triggers a destabilizing response in all CDR loops in the VL domain and vice versa. Destabilizing residues within the VL domain are likely to stabilize all CDR loops in the VH domain, and, when these residues are not buried, the CDR loops in the VL domain are also likely to be stabilized. These effects, described by shifts in normal mode characteristics, initiate a propensity for dynamic allostery with possible functional implications in bispecific antibodies.

Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD) trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF) about the average position of residues defined by C α -atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p -values from 1-sample Kolmogorov-Smirnov tests. These additional measures require knowing a probability density function, which we estimate by using a nonparametric maximum entropy method that quantifies rare events well. The same measures are applied to distance fluctuations between C α -atom pairs. Results from several implementations for quantitative comparison of a pair of MD trajectories are made based on fluctuations for on-residue and residue-residue local dynamics. We conclude that there is almost always a statistically significant difference between pairs of 100 ns all-atom simulations on moderate-sized proteins as evident from extraordinarily low p -values., Competing Interests: Conflicts of Interest: The authors declare no conflict of interest.

Background: Essential Dynamics (ED) is a common application of principal component analysis (PCA) to extract biologically relevant motions from atomic trajectories of proteins. Covariance and correlation based PCA are two common approaches to determine PCA modes (eigenvectors) and their eigenvalues. Protein dynamics can be characterized in terms of Cartesian coordinates or internal distance pairs. In understanding protein dynamics, a comparison of trajectories taken from a set of proteins for similarity assessment provides insight into conserved mechanisms. Comprehensive software is needed to facilitate comparative-analysis with user-friendly features that are rooted in best practices from multivariate statistics., Results: We developed a Java based Essential Dynamics toolkit called JED to compare the ED from multiple protein trajectories. Trajectories from different simulations and different proteins can be pooled for comparative studies. JED implements Cartesian-based coordinates (cPCA) and internal distance pair coordinates (dpPCA) as options to construct covariance (Q) or correlation (R) matrices. Statistical methods are implemented for treating outliers, benchmarking sampling adequacy, characterizing the precision of Q and R, and reporting partial correlations. JED output results as text files that include transformed coordinates for aligned structures, several metrics that quantify protein mobility, PCA modes with their eigenvalues, and displacement vector (DV) projections onto the top principal modes. Pymol scripts together with PDB files allow movies of individual Q- and R-cPCA modes to be visualized, and the essential dynamics occurring within user-selected time scales. Subspaces defined by the top eigenvectors are compared using several statistical metrics to quantify similarity/overlap of high dimensional vector spaces. Free energy landscapes can be generated for both cPCA and dpPCA., Conclusions: JED offers a convenient toolkit that encourages best practices in applying multivariate statistics methods to perform comparative studies of essential dynamics over multiple proteins. For each protein, Cartesian coordinates or internal distance pairs can be employed over the entire structure or user-selected parts to quantify similarity/differences in mobility and correlations in dynamics to develop insight into protein structure/function relationships.

We report a massive infected pseudoaneurysm of the right external iliac artery in the setting of Girdlestone pseudoarthroplasty (GSA) for chronic infection. Around the time of her GSA, the patient underwent cardiac catheterization with resultant pseudoaneurysm formation. Infection was likely due to spread from her previous chronic infection. Delay in presentation occurred due to attribution of her symptoms to her GSA. The patient underwent ligation of the right external iliac artery and hip disarticulation and was discharged on antibiotics. At follow-up, she had significantly reduced pain. Although vascular complications from orthopedic procedures are well described, this case seems to have been caused by secondary infection of her iatrogenic external iliac artery pseudoaneurysm., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Over 500,000 patients each year are diagnosed with critical limb ischemia (CLI), the most severe form of peripheral artery disease. CLI portends a grim prognosis; half the patients die from a cardiovascular cause within 5 years, a rate that is 5 times higher than a matched population without CLI. In 2014, the Centers for Medicare and Medicaid Services paid approximately $3.6 billion for claims submitted by hospitals for inpatient and outpatient care delivered to patients with CLI. Although significant advances in diagnosis, treatment, and follow-up of patients with CLI have been made, many challenges remain. In this article, we summarize selected presentations from the 2015 Vascular Interventional Advances Conference related to the modern demographics, diagnosis, and management of patients with CLI., (Copyright © 2016 Elsevier Inc. All rights reserved.)

A mechanical perturbation method that locally restricts conformational entropy along the protein backbone is used to identify putative allosteric sites in a series of antibody fragments. The method is based on a distance constraint model that integrates mechanical and thermodynamic viewpoints of protein structure wherein mechanical clamps that mimic substrate or cosolute binding are introduced. Across a set of six single chain-Fv fragments of the anti-lymphotoxin-β receptor antibody, statistically significant responses are obtained by averaging over 10 representative structures sampled from a molecular dynamics simulation. As expected, the introduced clamps locally rigidify the protein, but long-ranged increases in both rigidity and flexibility are also frequently observed. Expanding our analysis to every molecular dynamics frame demonstrates that the allosteric responses are modulated by fluctuations within the hydrogen-bond network where the native ensemble is comprised of conformations that both are, and are not, affected by the perturbation in question. Population shifts induced by the mutations alter the allosteric response by adjusting which hydrogen-bond networks are the most probable. These effects are compared using response maps that track changes across each single chain-Fv fragment, thus providing valuable insight into how sensitive allosteric mechanisms are to mutations., (Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

RiVax is a candidate ricin toxin subunit vaccine antigen that has proven to be safe in human phase I clinical trials. In this study, we introduced double and triple cavity-filling point mutations into the RiVax antigen with the expectation that stability-enhancing modifications would have a beneficial effect on overall immunogenicity of the recombinant proteins. We demonstrate that 2 RiVax triple mutant derivatives, RB (V81L/C171L/V204I) and RC (V81I/C171L/V204I), when adsorbed to aluminum salts adjuvant and tested in a mouse prime-boost-boost regimen were 5- to 10-fold more effective than RiVax at eliciting toxin-neutralizing serum IgG antibody titers. Increased toxin neutralizing antibody values and seroconversion rates were evident at different antigen dosages and within 7 days after the first booster. Quantitative stability/flexibility relationships analysis revealed that the RB and RC mutations affect rigidification of regions spanning residues 98-103, which constitutes a known immunodominant neutralizing B-cell epitope. A more detailed understanding of the immunogenic nature of RB and RC may provide insight into the fundamental relationship between local protein stability and antibody reactivity., (Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.)

Intravesical bacillus Calmette-Guérin (BCG) is first-line therapy for noninvasive bladder cancer. Although side effects are rare, systemic dissemination can result in mycotic aneurysms. We report the case of a rapidly developing thoracic aortic mycotic aneurysm presenting as massive hemoptysis from an aortobronchial fistula. This case was unusual in its location, rapidity of development, and failure of medical therapy. The diagnostic challenges and the need for a high index of suspicion are discussed., (Copyright © 2016 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.)

Chemokines form a family of signaling proteins mainly responsible for directing the traffic of leukocytes, where their biological activity can be modulated by their oligomerization state. We characterize the dynamics and thermodynamic stability of monomer and homodimer structures of CXCL7, one of the most abundant platelet chemokines, using experimental methods that include circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy, and computational methods that include the anisotropic network model (ANM), molecular dynamics (MD) simulations and the distance constraint model (DCM). A consistent picture emerges for the effects of dimerization and Cys5-Cys31 and Cys7-Cys47 disulfide bonds formation. The presence of disulfide bonds is not critical for maintaining structural stability in the monomer or dimer, but the monomer is destabilized more than the dimer upon removal of disulfide bonds. Disulfide bonds play a key role in shaping the characteristics of native state dynamics. The combined analysis shows that upon dimerization flexibly correlated motions are induced between the 30s and 50s loop within each monomer and across the dimer interface. Interestingly, the greatest gain in flexibility upon dimerization occurs when both disulfide bonds are present, and the homodimer is least stable relative to its two monomers. These results suggest that the highly conserved disulfide bonds in chemokines facilitate a structural mechanism that is tuned to optimally distinguish functional characteristics between monomer and dimer., (© 2015 Wiley Periodicals, Inc.)

The effects of somatic mutations that transform polyspecific germline (GL) antibodies to affinity mature (AM) antibodies with monospecificity are compared among three GL-AM Fab pairs. In particular, changes in conformational flexibility are assessed using a Distance Constraint Model (DCM). We have previously established that the DCM can be robustly applied across a series of antibody fragments (VL to Fab), and subsequently, the DCM was combined with molecular dynamics (MD) simulations to similarly characterize five thermostabilizing scFv mutants. The DCM is an ensemble based statistical mechanical approach that accounts for enthalpy/entropy compensation due to network rigidity, which has been quite successful in elucidating conformational flexibility and Quantitative Stability/Flexibility Relationships (QSFR) in proteins. Applied to three disparate antibody systems changes in QSFR quantities indicate that the VH domain is typically rigidified, whereas the VL domain and CDR L2 loop become more flexible during affinity maturation. The increase in CDR H3 loop rigidity is consistent with other studies in the literature. The redistribution of conformational flexibility is largely controlled by nonspecific changes in the H-bond network, although certain Arg to Asp salt bridges create highly localized rigidity increases. Taken together, these results reveal an intricate flexibility/rigidity response that accompanies affinity maturation.

Objective: The Supera stent (Abbott Laboratories, Abbott Park, Ill) has a unique biomimetic design allowing axial and longitudinal flexibility and fracture resistance. The aim of this retrospective study was to assess the midterm patency of Supera stents used to treat patients with superficial femoral and popliteal arterial disease by a single practice., Methods: From April 2010 to December 2011, 53 patients and 59 limbs with symptomatic femoropopliteal lesions underwent angioplasty and stenting with the Supera stent. Five patients had no follow-up and were excluded. Demographics of the patients, radiographic images, morphologic features of the lesions, procedural reports, reinterventions, and follow-up clinical visit notes were reviewed. Primary patency was defined as clinical resolution of symptoms with no secondary interventions. Primary and secondary patency rates at 12, 24, and 36 months were estimated by Kaplan-Meier analysis., Results: A total of 48 patients (42 men, six women; 54 limbs; mean age, 64.3 years [range, 51-87]) received Supera stents and had at least one follow-up visit as part of their treatment for femoropopliteal disease. Primary indications for intervention included claudication, rest pain, and tissue loss, at rates of 54% (29 of 54), 26% (14 of 54), and 20% (11 of 54), respectively; 22% of lesions were TransAtlantic Inter-Society Consensus type A or B and 78% were type C or D. Mean lesion length was 24.0 cm (range, 3-51). Mean follow-up was 27.5 months (range, 1-45). The ankle-brachial index increased from 0.58 ± 0.20 preoperatively to 0.77 ± 0.18 postoperatively (P = .00004). Primary, primary assisted, and secondary patency rates at latest follow-up were 79.6%, 88.9%, and 92.3%, respectively. Cumulative primary patency rates by Kaplan-Meier analysis at 12, 24, and 36 months were 85.6%, 83.1%, and 76.7%, respectively. Secondary patency rates by Kaplan-Meier estimates at 12, 24, and 36 months were 93.8%, 93.8%, and 89.3%, respectively. No stent fractures were found at the time of any reinterventions. Long lesions >30 cm (n = 18) showed equivalent patency to lesions of 1 to 15 cm (n = 18) and lesions 15 to 30 cm in length (n = 18)., Conclusions: Our midterm results show that Supera stents are durable in treating femoropopliteal lesions, with notably high patency rates in patients with long lesion lengths., (Copyright © 2015 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.)

Background: The body-bar Pebble Game (PG) algorithm is commonly used to calculate network rigidity properties in proteins and polymeric materials. To account for fluctuating interactions such as hydrogen bonds, an ensemble of constraint topologies are sampled, and average network properties are obtained by averaging PG characterizations. At a simpler level of sophistication, Maxwell constraint counting (MCC) provides a rigorous lower bound for the number of internal degrees of freedom (DOF) within a body-bar network, and it is commonly employed to test if a molecular structure is globally under-constrained or over-constrained. MCC is a mean field approximation (MFA) that ignores spatial fluctuations of distance constraints by replacing the actual molecular structure by an effective medium that has distance constraints globally distributed with perfect uniform density., Results: The Virtual Pebble Game (VPG) algorithm is a MFA that retains spatial inhomogeneity in the density of constraints on all length scales. Network fluctuations due to distance constraints that may be present or absent based on binary random dynamic variables are suppressed by replacing all possible constraint topology realizations with the probabilities that distance constraints are present. The VPG algorithm is isomorphic to the PG algorithm, where integers for counting "pebbles" placed on vertices or edges in the PG map to real numbers representing the probability to find a pebble. In the VPG, edges are assigned pebble capacities, and pebble movements become a continuous flow of probability within the network. Comparisons between the VPG and average PG results over a test set of proteins and disordered lattices demonstrate the VPG quantitatively estimates the ensemble average PG results well., Conclusions: The VPG performs about 20% faster than one PG, and it provides a pragmatic alternative to averaging PG rigidity characteristics over an ensemble of constraint topologies. The utility of the VPG falls in between the most accurate but slowest method of ensemble averaging over hundreds to thousands of independent PG runs, and the fastest but least accurate MCC.

Le Châtelier's principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Châtelier's principle states that an equilibrium shift will occur to offset the perturbation and a new equilibrium is established. We demonstrate that the effects of stabilizing mutations on the rigidity ⇔ flexibility equilibrium within the native state ensemble manifest themselves through enthalpy-entropy compensation as the protein structure adjusts to restore the global balance between the two. Specifically, we characterize the effects of mutation to single chain fragments of the anti-lymphotoxin-β receptor antibody using a computational Distance Constraint Model. Statistically significant changes in the distribution of both rigidity and flexibility within the molecular structure is typically observed, where the local perturbations often lead to distal shifts in flexibility and rigidity profiles. Nevertheless, the net gain or loss in flexibility of individual mutants can be skewed. Despite all mutants being exclusively stabilizing in this dataset, increased flexibility is slightly more common than increased rigidity. Mechanistically the redistribution of flexibility is largely controlled by changes in the H-bond network. For example, a stabilizing mutation can induce an increase in rigidity locally due to the formation of new H-bonds, and simultaneously break H-bonds elsewhere leading to increased flexibility distant from the mutation site via Le Châtelier. Increased flexibility within the VH β4/β5 loop is a noteworthy illustration of this long-range effect.

The Distance Constraint Model (DCM) is a computational modeling scheme that uniquely integrates thermodynamic and mechanical descriptions of protein structure. As such, quantitative stability-flexibility relationships (QSFR) that describe the interrelationships of thermodynamics and mechanics can be quickly computed. Using comparative QSFR analyses, we have previously investigated these relationships across a small number of protein orthologs, ranging from two to a dozen [1, 2]. However, our ultimate goal is provide a comprehensive analysis of whole protein families, which requires consideration of many more structures. To that end, we have developed homology modeling and assessment protocols so that we can robustly calculate QSFR properties for proteins without experimentally derived structures. The approach, which is presented here, starts from a large ensemble of potential homology models and uses a clustering algorithm to identify the best models, thus paving the way for a comprehensive QSFR analysis across hundreds of proteins in a protein family.

The Distance Constraint Model (DCM) is an ensemble-based biophysical model that integrates thermodynamic and mechanical viewpoints of protein structure. The DCM outputs a large number of structural characterizations that collectively allow for Quantified Stability-Flexibility Relationships (QSFR) to be identified and compared across protein families. Using five metallo-β-lactamases (MBLs) as a representative set, we demonstrate how QSFR properties are both conserved and varied across protein families. Similar to our characterizations on other protein families, the backbone flexibility of the five MBLs are overall visually conserved, yet there are interesting specific quantitative differences. For example, the plasmid-encoded NDM-1 enzyme, which leads to a fast spreading drug-resistant version of Klebsiella pneumoniae, has several regions of significantly increased rigidity relative to the other four. In addition, the set of intramolecular couplings within NDM-1 are also atypical. While long-range couplings frequently vary significantly across protein families, NDM-1 is distinct because it has limited correlated flexibility, which is isolated within the active site S3/S4 and S11/H6 loops. These loops are flexibly correlated in the other members, suggesting it is important to function, but the others also have significant amounts of correlated flexibility throughout the rest of their structures.

It has become commonplace to employ principal component analysis to reveal the most important motions in proteins. This method is more commonly known by its acronym, PCA. While most popular molecular dynamics packages inevitably provide PCA tools to analyze protein trajectories, researchers often make inferences of their results without having insight into how to make interpretations, and they are often unaware of limitations and generalizations of such analysis. Here we review best practices for applying standard PCA, describe useful variants, discuss why one may wish to make comparison studies, and describe a set of metrics that make comparisons possible. In practice, one will be forced to make inferences about the essential dynamics of a protein without having the desired amount of samples. Therefore, considerable time is spent on describing how to judge the significance of results, highlighting pitfalls. The topic of PCA is reviewed from the perspective of many practical considerations, and useful recipes are provided.

Free energy landscapes, backbone flexibility and residue-residue couplings for being co-rigid or co-flexible are calculated from the minimal Distance Constraint Model (mDCM) on an exploratory dataset consisting of VL, scFv and Fab antibody fragments. Experimental heat capacity curves are reproduced markedly well, and an analysis of quantitative stability/flexibility relationships (QSFR) is applied to a representative VL domain and several complexes in the scFv and Fab forms. Global flexibility in the denatured ensemble typically decreases in the larger complexes due to domain-domain interfaces. Slight decreases in global flexibility also occur in the native state of the larger fragments, but with a concurrent large increase in correlated flexibility. Typically, a VL fragment has more co-rigid residue pairs when isolated compared to the scFv and Fab forms, where correlated flexibility appears upon complex formation. This context dependence on residue- residue couplings in the VL domain across length scales of a complex is consistent with the evolutionary hypothesis of antibody maturation. In comparing two scFv mutants with similar thermodynamic stability, local and long-ranged changes in backbone flexibility are observed. In the case of anti-p24 HIV-1 Fab, a variety of QSFR metrics were found to be atypical, which includes comparatively greater co-flexibility in the VH domain and less co-flexibility in the VL domain. Interestingly, this fragment is the only example of a polyspecific antibody in our dataset. Finally, the mDCM method is extended to cases where thermodynamic data is incomplete, enabling high throughput QSFR studies on large numbers of antibody fragments and their complexes.