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Catheter-directed thrombolysis (CDT) is increasingly performed for acute pulmonary embolism (PE) because it is presumed to provide similar therapeutic benefits to systemic thrombolysis, while decreasing the dose of thrombolytic required and the associated risks. Contemporary suction thrombectomy (ST) devices have entered the market as minimal or no-lytic alternatives, but there is no evidence on their comparative effectiveness. This study aims to compare clinical outcomes of these two interventional alternatives.Consecutive patients who underwent a ST catheter intervention for massive or submassive PE between 2011 and 2017 were identified. For each of these patients, a nearest-neighbor matching was implemented to identify at least three CDT patients who matched as closely as possible on the following six variables: PE type, age, gender, acute deep venous thrombosis, pulmonary disease, and year of procedure. The end point was clinical success defined as meeting all the following criteria: survival to hospital discharge without major bleeding (Global Utilization of Streptokinase and t-PA for Occluded Coronary Arteries moderate or severe), perioperative stroke or other major adverse procedure-related event, and decompensation for submassive or persistent shock for massive PE.Of 277 patients who received an intervention for acute PE, 54 CDT (63.5 ± 14.2 years of age; 18 massive PE) were matched with 18 ST (64.1 ± 14.1 years of age; 6 massive PE) patients. In the CDT group, 38 (70.4%) received ultrasound-assisted thrombolysis. The ST group had significantly more patients who had a major contraindication for lytics (1 [1.9%] for CDT vs 9 [50%] for ST; P .001). There was no difference in major bleeding (8 [14.8%] for CDT vs 3 [16.7%] for ST; P.999; Global Utilization of Streptokinase and t-PA for Occluded Coronary Arteries severe 1 [1.8%] for CDT vs 1 [5.6%] for ST; P.999), stroke (3.7% for CDT vs 0 for ST; P = .408), or death (3.7% for CDT vs 16.7% for ST; P = .096). One patient in the ST group suffered tricuspid valve rupture and two patients in CDT group required surgical thrombectomy. Clinical success was not statistically different between groups (75.9% for CDT vs 61.1% for ST; P = .224). The association was similar when assessing the right/left ventricular ratio improvement (0.30 ± 0.19 for CDT vs 0.17 ± 0.16 for ST; P = .097), or the subgroup of patients with submassive PE (86.1% for CDT vs 66.7% for ST; P = .135).CDT seems to have similar outcomes with ST in the management of acute PE, although larger, more homogenous data are needed. In our experience, ST should be viewed as a complementary alternative for patients with contraindication for thrombolytics or severely compromised hemodynamic profile and can yield good outcomes in an otherwise highly morbid population.

An alternative analgesic to morphine is methadone, which is used to control chronic pain and is used in opioid rehabilitation treatment programs due to methadone having a long half-life and being relatively inexpensive as compared to extended-release forms of morphine. Despite its benefits, methadone accumulates in adipose tissue due to being lipophilic, binds strongly to plasma proteins, and is metabolized in the liver by the cytochrome P450 system causing methadone levels to be variable and subject to influence according to the individual body compositions and concurrent use of cytochrome P450 inhibitors. In addition to methadone being able to cause both respiratory and central nervous system depression, methadone can also prolong the QT interval and cause potentially life-threatening arrhythmias including torsades de pointes. The susceptibility of unintentional overdosing of methadone due to its varied pharmacologic properties and potentially fatal induction of arrhythmias may cause the risks of methadone use to outweigh its benefits and therefore must be closely monitored.

Protein structure refinement is the challenging problem of operating on any protein structure prediction to improve its accuracy with respect to the native structure in a blind fashion. Although many approaches have been developed and tested during the last four CASP experiments, a majority of the methods continue to degrade models rather than improve them. Princeton_TIGRESS (Khoury et al., Proteins 2014;82:794-814) was developed previously and utilizes separate sampling and selection stages involving Monte Carlo and molecular dynamics simulations and classification using an SVM predictor. The initial implementation was shown to consistently refine protein structures 76% of the time in our own internal benchmarking on CASP 7-10 targets. In this work, we improved the sampling and selection stages and tested the method in blind predictions during CASP11. We added a decomposition of physics-based and hybrid energy functions, as well as a coordinate-free representation of the protein structure through distance-binning Cα-Cα distances to capture fine-grained movements. We performed parameter estimation to optimize the adjustable SVM parameters to maximize precision while balancing sensitivity and specificity across all cross-validated data sets, finding enrichment in our ability to select models from the populations of similar decoys generated for targets in CASPs 7-10. The MD stage was enhanced such that larger structures could be further refined. Among refinement methods that are currently implemented as web-servers, Princeton_TIGRESS 2.0 demonstrated the most consistent and most substantial net refinement in blind predictions during CASP11. The enhanced refinement protocol Princeton_TIGRESS 2.0 is freely available as a web server at http://atlas.engr.tamu.edu/refinement/. Proteins 2017; 85:1078-1098. © 2017 Wiley Periodicals, Inc.

Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research. Funding Agencies|Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS) under the Science Undergraduate Laboratory Internship (SULI) program; U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS) under the Visiting Faculty Program (VFP); United States-Israel Binational Science Foundation (BSF) [2009432]; Israel Science Foundation (ISF) [1122/14]; National Institute of General Medical Sciences [R01GM093123, GM083107, GM116960]; Purdue University start-up funds; Ralph W. and Grace M. Showalter Trust Award; Jim and Diann Robbers Cancer Research Grant for New Investigators Award; Brazilian agency: FAPESP; Brazilian agency: CAPES; Brazilian agency: CNPq; NIH [GM-14312]; NSF [MCB-10-19767]; National Institutes of Medicine [GM11574901]; Swedish Research Council [2012-5270, 2016-05369]; Swedish e-Science Research Center; Polish National Science Center [UMO-2013/10/M/ST4/00640]; IISc Mathematical Initiative Assistantship; National Academy of Sciences, India; National Institutes of Health [R01-GM100701, R01GM052032]; National Science Foundation; National Science Foundation Graduate Research Fellowship [DGE-1148900]; Princeton Institute for Computational Science and Engineering (PICSciE); Princeton University Office of Information Technology; UK Engineering and Physical Sciences Research Council [EP/M020576/1, EP/N031962/1]; National Research Foundation of Korea [2016R1A2A1A05005485]

Iliac vein stenting is recommended to treat venous outflow obstruction after catheter-directed thrombolysis for acute iliofemoral deep venous thrombosis (DVT). Data on the outcome of proximal and distal stent extension are limited. Proximal stent extension to the vena cava may obstruct the contralateral iliac vein, whereas distal extension below the inguinal ligament contradicts common practice for arterial stents. The aim of this retrospective study was to assess outcomes and predictors of failure of iliac vein stents and contralateral iliac vein thrombosis, taking into consideration stent positioning.Consecutive patients who underwent thrombolysis and stenting for DVT between May 2007 and September 2017 were identified from a prospectively maintained database. The intraoperative venograms were reviewed for proximal stent placement (covering50% contralateral iliac vein orifice) and distal placement across the inguinal ligament. End points were ipsilateral DVT recurrence, post-thrombotic syndrome (PTS; Villalta score ≥5), and contralateral DVT. Patients with chronic contralateral DVT or contralateral iliac vein stenting at baseline were excluded from the contralateral DVT outcome evaluation. Survival analysis and Cox regression models were used to determine outcomes.Of 142 patients lysed, 73 patients (12 bilateral DVTs; mean age, 45.8 ± 17.2 years; 46 female patients) were treated with various combinations of thrombolytic techniques and at least one self-expanding iliac stent (77 stented limbs). Thirty-day recurrence developed in nine (12.3%) patients. The 3-year primary patency and secondary patency rates were 75.2% and 82.2%, respectively. The single predictor for loss of primary patency was incomplete thrombolysis (≤50%; hazard ratio [HR], 7.41; P = .002). Overall, 3 of 12 (25%) stents extending below the inguinal ligament occluded at 1 month, 2 months, and 9 months, respectively. The overall rate of PTS (Villalta score ≥5) in the stented cohort was 14.4% at 5 years. This was predicted by incomplete lysis (50%; HR, 7.09; P = .040), stent extension below the inguinal ligament (HR, 6.68; P = .026), and male sex (HR, 6.02; P = .041). Of the 17 stents that extended into the contralateral common iliac vein and 58 stents that did not, there were 1 (5.9%) and 5 (8.6%) contralateral DVTs (P = .588) at an average follow-up of 27.4 ± 33.7 and 22.2 ± 22.3 months (P = .552), respectively.Iliac stenting after thrombolysis for acute DVT guarantees high patency and low PTS rates, provided adequate thrombus resolution has been achieved before stent placement. Stent placement below the inguinal ligament does not affect the patency but may be associated with a higher PTS rate. Stenting proximal to the iliocaval confluence, although a precipitating factor, may not independently increase the likelihood of contralateral DVT.

Objective Retrograde infrageniculate access is an alternative treatment strategy for patients who have failed to respond to antegrade endovascular intervention. This study compares the outcomes of infrageniculate retrograde arterial access with the conventional transfemoral access for the endovascular management of chronic lower extremity ischemia. Methods This was a retrospective single-center review of retrograde endovascular intervention (REI) from 2012 to 2016. Indications for intervention, comorbidities, complications, procedural success, limb outcomes, and mortality were analyzed. Technical failure was defined as the inability to complete the procedure because of failed access or unsuccessful recanalization. Infrageniculate access and transfemoral access were obtained with ultrasound or angiographic roadmap guidance. Patency rates were calculated for technically successful interventions. Results There were 47 patients (85% presenting with critical limb ischemia) who underwent sheathless REI after failed antegrade recanalization of TransAtlantic Inter-Society Consensus class D infrainguinal lesions, whereas 93 patients (83% with critical limb ischemia) underwent standard transfemoral access. There were 16 (34%) femoropopliteal, 14 (30%) tibial, and 17 (36%) multilevel interventions in the retrograde group compared with 41 (41%) femoropopliteal, 20 (20%) tibial, and 39 (39%) multilevel interventions in the transfemoral group. Access sites for the retrograde group included the dorsalis pedis (26%), midcalf peroneal (24%), anterior tibial (22%), posterior tibial (26%), and popliteal (2%) arteries. Overall technical success was achieved in 57% of the retrograde group compared with 78% of the transfemoral group. Mean follow-up was 20 months (range, 1-45 months). There were no significant differences in the primary patency rates between the two groups at 1 year and 2 years. The primary assisted patency rates were significantly better in the transfemoral group at 1 year (66% vs 46%; P = .031) and 2 years (56% vs 29%; P = .031). The secondary patency rates were higher in the transfemoral group at 1 year (93% vs 83%; P = .079) and 2 years (91% vs 76%; P = .079), although this did not reach statistical significance. The rate of reintervention was 41% for the retrograde group vs 40% for the transfemoral group. Most of the reinterventions (70% in the retrograde group and 61% in the transfemoral group) were endovascular interventions for a restenosis or occlusion. Conclusions Infrageniculate access for REI can result in primary patency rates similar to those of antegrade interventions and does not compromise the access site. Technical failure is high in this initial experience and is mostly due to failed recanalization. Limb salvage may be achieved after technical failure with either repeated antegrade intervention or surgical bypass.

In this work, we assess calculated hydration free energies of natural and unnatural amino acids compared to experimental hydration free energies of corresponding side-chain analogs using the ff03 charge model. Fine-grid, explicit water thermodynamic integration calculations using two widely used explicit water models (TIP3P and TIP4P-Ew) were performed on 19 natural amino acids and compared with experimental hydration free energies of corresponding side-chain analogs to establish expected accuracy levels for this charge model. Next, parameters previously derived for 17 unnatural amino acids and several new parameters optimized in this work were assessed using the same methodology. We found that the ff03 charge model is correlated with experimental hydration free energies but underestimates the solubilities of several polar natural and unnatural amino acids. Comparisons are presented with other forcefields and water models recently presented in the literature for both natural and modified amino acids.

The protein structure prediction problem continues to elude scientists. Despite the introduction of many methods, only modest gains were made over the last decade for certain classes of prediction targets. To address this challenge, a social-media based worldwide collaborative effort, named WeFold, was undertaken by 13 labs. During the collaboration, the laboratories were simultaneously competing with each other. Here, we present the first attempt at "coopetition" in scientific research applied to the protein structure prediction and refinement problems. The coopetition was possible by allowing the participating labs to contribute different components of their protein structure prediction pipelines and create new hybrid pipelines that they tested during CASP10. This manuscript describes both successes and areas needing improvement as identified throughout the first WeFold experiment and discusses the efforts that are underway to advance this initiative. A footprint of all contributions and structures are publicly accessible at http://www.wefold.org.

We describe the development and testing of ab initio derived, AMBER ff03 compatible charge parameters for a large library of 147 noncanonical amino acids including β- and N-methylated amino acids for use in applications such as protein structure prediction and de novo protein design. The charge parameter derivation was performed using the RESP fitting approach. Studies were performed assessing the suitability of the derived charge parameters in discriminating the activity/inactivity between 63 analogs of the complement inhibitor Compstatin on the basis of previously published experimental IC50 data and a screening procedure involving short simulations and binding free energy calculations. We found that both the approximate binding affinity (K*) and the binding free energy calculated through MM-GBSA are capable of discriminating between active and inactive Compstatin analogs, with MM-GBSA performing significantly better. Key interactions between the most potent Compstatin analog that contains a noncanonical amino acid are presented and compared to the most potent analog containing only natural amino acids and native Compstatin. We make the derived parameters and an associated web interface that is capable of performing modifications on proteins using Forcefield_NCAA and outputting AMBER-ready topology and parameter files freely available for academic use at http://selene.princeton.edu/FFNCAA . The forcefield allows one to incorporate these customized amino acids into design applications with control over size, van der Waals, and electrostatic interactions.

Protein structure refinement aims to perform a set of operations given a predicted structure to improve model quality and accuracy with respect to the native in a blind fashion. Despite the numerous computational approaches to the protein refinement problem reported in the previous three CASPs, an overwhelming majority of methods degrade models rather than improve them. We initially developed a method tested using blind predictions during CASP10 which was officially ranked in 5th place among all methods in the refinement category. Here, we present Princeton_TIGRESS, which when benchmarked on all CASP 7,8,9, and 10 refinement targets, simultaneously increased GDT_TS 76% of the time with an average improvement of 0.83 GDT_TS points per structure. The method was additionally benchmarked on models produced by top performing three-dimensional structure prediction servers during CASP10. The robustness of the Princeton_TIGRESS protocol was also tested for different random seeds. We make the Princeton_TIGRESS refinement protocol freely available as a web server at http://atlas.princeton.edu/refinement. Using this protocol, one can consistently refine a prediction to help bridge the gap between a predicted structure and the actual native structure. Proteins 2014; 82:794–814. © 2013 Wiley Periodicals, Inc.

Protein structure refinement is the challenging problem of operating on any protein structure prediction to improve its accuracy with respect to the native structure in a blind fashion. Although many approaches have been developed and tested during the last four CASP experiments, a majority of the methods continue to degrade models rather than improve them. Princeton_TIGRESS (Khoury et al., Proteins 2014;82:794-814) was developed previously and utilizes separate sampling and selection stages involving Monte Carlo and molecular dynamics simulations and classification using an SVM predictor. The initial implementation was shown to consistently refine protein structures 76% of the time in our own internal benchmarking on CASP 7-10 targets. In this work, we improved the sampling and selection stages and tested the method in blind predictions during CASP11. We added a decomposition of physics-based and hybrid energy functions, as well as a coordinate-free representation of the protein structure through distance-binning Cα-Cα distances to capture fine-grained movements. We performed parameter estimation to optimize the adjustable SVM parameters to maximize precision while balancing sensitivity and specificity across all cross-validated data sets, finding enrichment in our ability to select models from the populations of similar decoys generated for targets in CASPs 7-10. The MD stage was enhanced such that larger structures could be further refined. Among refinement methods that are currently implemented as web-servers, Princeton_TIGRESS 2.0 demonstrated the most consistent and most substantial net refinement in blind predictions during CASP11. The enhanced refinement protocol Princeton_TIGRESS 2.0 is freely available as a web server at http://atlas.engr.tamu.edu/refinement/. Proteins 2017; 85:1078-1098. © 2017 Wiley Periodicals, Inc.

Inferior vena cava (IVC) thrombosis may occur in patients with iliofemoral deep venous thrombosis (DVT), and its impact on thrombolysis outcomes is poorly defined. This study compared outcomes of patients undergoing thrombolysis for acute iliofemoral DVT with and without IVC involvement.Patients who underwent thrombolysis for iliofemoral DVT between May 2007 and March 2014 were identified from a prospectively maintained database and divided into two groups: those with IVC involvement and those without. End points were technical and clinical success (≥50% lysis or freedom from 30-day DVT recurrence), long-term DVT recurrence, and post-thrombotic syndrome (PTS; Villalta score ≥5). Multivariate regression models were used to determine predictors of anatomic and clinical failures.There were 102 patients (127 limbs) treated with various combinations of catheter-directed or pharmacomechanical thrombolysis. In 46 patients, thrombus extended into the IVC (54.3% extended up to the renal veins; 87% had ≥50% luminal reduction; 50% occurred in association with an indwelling thrombosed IVC filter). The caval group had fewer women and more previous DVTs but otherwise was similar to the noncaval group. Pharmacomechanical thrombolysis was used more frequently in the caval thrombus group (97.8% vs 82.1%; P = .011), and iliac vein stenting was used more often in the noncaval group (41.3% vs 62.5%; P = .033). Clinical success was similar between the two groups (88.7% for caval vs 89.3% for noncaval; P = .921). All failures in the caval group occurred in patients with an indwelling thrombosed IVC filter. Primary patency at 2 years for the caval and noncaval groups was 76.7% and 78.0%, respectively (P = .787). Valve reflux and PTS at 2 years were higher in the noncaval group (50.8% and 34.3% vs 23.3% and 11.5% in the caval group; P = .013 and P = .035). On multivariate analysis, incomplete lysis was predictive of recurrence (hazard ratio [HR], 22.7; P .001) and PTS (HR, 5.59; P = .010), whereas caval involvement (HR, 0.22; P = .005) was protective from PTS.IVC thrombosis does not have an impact on the technical success of thrombolysis in patients with iliofemoral DVT; the presence of a thrombosed IVC filter, though, may make failure more likely. Caval thrombosis may not affect primary patency but is associated with a lower incidence of PTS after successful lysis.

Accurate prediction of protein secondary structure remains a crucial step in most approaches to the protein-folding problem, yet the prediction of ordered secondary structure, specifically beta-strands, remains a challenge. We developed a consensus secondary structure prediction method, conSSert, which is based on support vector machines (SVM) and provides exceptional accuracy for the prediction of beta-strands with QE accuracy of over 0.82 and a Q2-EH of 0.86. conSSert uses as input probabilities for the three types of secondary structure (helix, strand, and coil) that are predicted by four top performing methods: PSSpred, PSIPRED, SPINE-X, and RAPTOR. conSSert was trained/tested using 4261 protein chains from PDBSelect25, and 8632 chains from PISCES. Further validation was performed using targets from CASP9, CASP10, and CASP11. Our data suggest that poor performance in strand prediction is likely a result of training bias and not solely due to the nonlocal nature of beta-sheet contacts. conSSert is freely available for noncommercial use as a webservice: http://ares.tamu.edu/conSSert/.

In this study we perform X-ray diffraction and XPS analysis to study the adsorption of the herbicide glyphosate on montmorillonite. Structures of the surface complexes are proposed based on the XPS and XRD patterns and explored using molecular modeling techniques. Adsorption isotherms showed multistep profiles at all pHs studied, indicating the adsorption on aluminol and/or silanol groups of the external surface and in the interlayer space. PMG intercalation was indicated by the XRD patterns. The increase of the basal spacing as a function of the number of water molecules in the calculations indicated the appropriateness of the theoretical model to simulate macroscopic behaviors of the water/clay mineral interactions. Final conformations of the system determined by molecular mechanics indicated that the charged amino moiety was attracted by the negative surfaces of the interlayer space in absence or presence of water molecules, with marked pH dependence. Negative values of the estimated adsorption energies at all pH values studied suggested that glyphosate molecules were adsorbed via the amino moiety or through monodentate or bidentate complexes formed between the phosphonate moiety and the internal surfaces of the clay mineral, explaining the basal spacing changes at high concentrations of PMG.

In this study we introduce a computationally-driven enzyme redesign workflow for altering cofactor specificity from NADPH to NADH. By compiling and comparing data from previous studies involving cofactor switching mutations, we show that their effect cannot be explained as straightforward changes in volume, hydrophobicity, charge, or BLOSUM62 scores of the residues populating the cofactor binding site. Instead, we find that the use of a detailed cofactor binding energy approximation is needed to adequately capture the relative affinity towards different cofactors. The implicit solvation models Generalized Born with molecular volume integration and Generalized Born with simple switching were integrated in the iterative protein redesign and optimization (IPRO) framework to drive the redesign of Candida boidinii xylose reductase (CbXR) to function using the non-native cofactor NADH. We identified 10 variants, out of the 8,000 possible combinations of mutations, that improve the computationally assessed binding affinity for NADH by introducing mutations in the CbXR binding pocket. Experimental testing revealed that seven out of ten possessed significant xylose reductase activity utilizing NADH, with the best experimental design (CbXR-GGD) being 27-fold more active on NADH. The NADPH-dependent activity for eight out of ten predicted designs was either completely abolished or significantly diminished by at least 90%, yielding a greater than 10(4)-fold change in specificity to NADH (CbXR-REG). The remaining two variants (CbXR-RTT and CBXR-EQR) had dual cofactor specificity for both nicotinamide cofactors.

SummaryF11R is the gene name for an adhesion protein, called the F11-receptor, aka JAM-A, which under normal physiological conditions is expressed constitutively on the surface of platelets and localized within tight junctions of endothelial cells (EC). Previous studies of the interactions between human platelets and EC suggested that F11R/JAM-A plays a crucial role in inflammatory thrombosis and atherosclerosis. The study reported here obtained in-vivo confirmation of this conclusion by investigating F11R/JAM-A protein and mRNA in patients with aortic and peripheral vascular disease and in an animal model of atherosclerosis. Molecular and immunofluorescence determinations revealed very high levels of F11R/JAM-A mRNA and F11R/JAM-A protein in atherosclerotic plaques of cardiovascular patients. Similar results were obtained with 12-week-old atherosclerosis-prone apoE-/- mice, an age in which atherosclerotic plaques are well established. Enhanced expression of the F11R/JAM-A message in cultured EC from human aortic and venous vessels was observed following exposure of the cells to cytokines. Determinations of platelet adhesion to cultured EC inflamed by combined cytokine treatment in the presence of F11R/JAM-A – antagonists provided data indicating that de novo expression of F11R/JAM-A on the luminal surface of inflamed EC has an important role in the conversion of EC to a thrombogenic surface. Further studies of these interactions under flow conditions and under in-vivo settings could provide a final proof of a causal role for F11R/JAM-A in the initiation of thrombosis. Based on our invitro and in-vivo studies to date, we propose that therapeutic drugs which antagonize the function of F11R/JAM-A should be tested as novel means for the prevention and treatment of atherosclerosis, heart attacks and stroke.

Neurovascular spinal cord injuries are very prevalent and in a busy trauma center radiology practice these injuries are commonly seen. Imaging neurovascular injuries has been greatly facilitated by magnetic resonance imaging (MRI) and magnetic resonance angiography (MRA). The histopathological changes that occur with spinal cord trauma have been found to correlate well with what is seen on MRI examinations. The MRI findings in spinal cord trauma have also been found to be useful in determining patient prognosis. Spinal cord infarcts due to arterial injury from trauma are relatively rare, but it has been shown by imaging that vertebral artery injuries are not an unusual occurrence. The specific findings associated with neurovascular injuries will be described with an emphasis on the findings on MRI and MRA examinations. MRI and MRA techniques have become the procedure of choice for evaluating neurovascular injuries because of their proven accuracy and because they are non-invasive. Conventional angiography, although, does remain quite useful for evaluating arterial injuries.

Cognitive task analysis of the complex skills involved in robotic arm maneuvering will help to ensure safer and more effective spaceflight operations.

In this work, we introduce Forcefield_PTM, a set of AMBER forcefield parameters consistent with ff03 for 32 common post-translational modifications. Partial charges were calculated through ab initio calculations and a two-stage RESP-fitting procedure in an ether-like implicit solvent environment. The charges were found to be generally consistent with others previously reported for phosphorylated amino acids, and trimethyllysine, using different parameterization methods. Pairs of modified and their corresponding unmodified structures were curated from the PDB for both single and multiple modifications. Background structural similarity was assessed in the context of secondary and tertiary structures from the global dataset. Next, the charges derived for Forcefield_PTM were tested on a macroscopic scale using unrestrained all-atom Langevin molecular dynamics simulations in AMBER for 34 (17 pairs of modified/unmodified) systems in implicit solvent. Assessment was performed in the context of secondary structure preservation, stability in energies, and correlations between the modified and unmodified structure trajectories on the aggregate. As an illustration of their utility, the parameters were used to compare the structural stability of the phosphorylated and dephosphorylated forms of OdhI. Microscopic comparisons between quantum and AMBER single point energies along key χ torsions on several PTMs were performed and corrections to improve their agreement in terms of mean squared errors and squared correlation coefficients were parameterized. This forcefield for post-translational modifications in condensed-phase simulations can be applied to a number of biologically relevant and timely applications including protein structure prediction, protein and peptide design, docking, and to study the effect of PTMs on folding and dynamics. We make the derived parameters and an associated interactive webtool capable of performing post-translational modifications on proteins using Forcefield_PTM available at http://selene.princeton.edu/FFPTM.

The protein structure prediction problem continues to elude scientists. Despite the introduction of many methods, only modest gains were made over the last decade for certain classes of prediction targets. To address this challenge, a social-media based worldwide collaborative effort, named WeFold, was undertaken by 13 labs. During the collaboration, the laboratories were simultaneously competing with each other. Here, we present the first attempt at "coopetition" in scientific research applied to the protein structure prediction and refinement problems. The coopetition was possible by allowing the participating labs to contribute different components of their protein structure prediction pipelines and create new hybrid pipelines that they tested during CASP10. This manuscript describes both successes and areas needing improvement as identified throughout the first WeFold experiment and discusses the efforts that are underway to advance this initiative. A footprint of all contributions and structures are publicly accessible at http://www.wefold.org.

The aim of de novo protein design is to find the amino acid sequences that will fold into a desired 3-dimensional structure with improvements in specific properties, such as binding affinity, agonist or antagonist behavior, or stability, relative to the native sequence. Protein design lies at the center of current advances drug design and discovery. Not only does protein design provide predictions for potentially useful drug targets, but it also enhances our understanding of the protein folding process and protein-protein interactions. Experimental methods such as directed evolution have shown success in protein design. However, such methods are restricted by the limited sequence space that can be searched tractably. In contrast, computational design strategies allow for the screening of a much larger set of sequences covering a wide variety of properties and functionality. We have developed a range of computational de novo protein design methods capable of tackling several important areas of protein design. These include the design of monomeric proteins for increased stability and complexes for increased binding affinity. To disseminate these methods for broader use we present Protein WISDOM (http://www.proteinwisdom.org), a tool that provides automated methods for a variety of protein design problems. Structural templates are submitted to initialize the design process. The first stage of design is an optimization sequence selection stage that aims at improving stability through minimization of potential energy in the sequence space. Selected sequences are then run through a fold specificity stage and a binding affinity stage. A rank-ordered list of the sequences for each step of the process, along with relevant designed structures, provides the user with a comprehensive quantitative assessment of the design. Here we provide the details of each design method, as well as several notable experimental successes attained through the use of the methods.

The aim of de novo protein design is to find the amino acid sequences that will fold into a desired 3-dimensional structure with improvements in specific properties, such as binding affinity, agonist or antagonist behavior, or stability, relative to the native sequence. Protein design lies at the center of current advances drug design and discovery. Not only does protein design provide predictions for potentially useful drug targets, but it also enhances our understanding of the protein folding process and protein-protein interactions. Experimental methods such as directed evolution have shown success in protein design. However, such methods are restricted by the limited sequence space that can be searched tractably. In contrast, computational design strategies allow for the screening of a much larger set of sequences covering a wide variety of properties and functionality. We have developed a range of computational de novo protein design methods capable of tackling several important areas of protein design. These include the design of monomeric proteins for increased stability and complexes for increased binding affinity. To disseminate these methods for broader use we present Protein WISDOM (http://www.proteinwisdom.org), a tool that provides automated methods for a variety of protein design problems. Structural templates are submitted to initialize the design process. The first stage of design is an optimization sequence selection stage that aims at improving stability through minimization of potential energy in the sequence space. Selected sequences are then run through a fold specificity stage and a binding affinity stage. A rank-ordered list of the sequences for each step of the process, along with relevant designed structures, provides the user with a comprehensive quantitative assessment of the design. Here we provide the details of each design method, as well as several notable experimental successes attained through the use of the methods.

Protein structure refinement aims to perform a set of operations given a predicted structure to improve model quality and accuracy with respect to the native in a blind fashion. Despite the numerous computational approaches to the protein refinement problem reported in the previous three CASPs, an overwhelming majority of methods degrade models rather than improve them. We initially developed a method tested using blind predictions during CASP10 which was officially ranked in 5th place among all methods in the refinement category. Here, we present Princeton_TIGRESS, which when benchmarked on all CASP 7,8,9, and 10 refinement targets, simultaneously increased GDT_TS 76% of the time with an average improvement of 0.83 GDT_TS points per structure. The method was additionally benchmarked on models produced by top performing three-dimensional structure prediction servers during CASP10. The robustness of the Princeton_TIGRESS protocol was also tested for different random seeds. We make the Princeton_TIGRESS refinement protocol freely available as a web server at http://atlas.princeton.edu/refinement. Using this protocol, one can consistently refine a prediction to help bridge the gap between a predicted structure and the actual native structure.

The incomplete measurement problem poses a significant obstacle for both model correlation and structural health monitoring (SHM). In practice, information about the health of a structure must be ascertained using measurement data from only a limited number of sensors. Several approaches to this problem have been proposed. One approach involves a reduced order model, such as that obtained using methods such as the Guyan reduction, the Improved Reduced System Model, or the System Equivalent Reduction Process. A second approach, which this work considers, involves an expansion of the test data to match a higher-fidelity model. This work presents a damage detection method utilizing Ritz vectors and the Method of Expanded Dynamic Residuals (MEDR). Ritz vectors have several advantages over eigenvectors for application to damage detection, including lower sensitivity to noise, and, as a result of their load-dependent nature, a greater sensitivity to localized damage. The MEDR restricts identified damage locations to those where there is physical connectivity, which eliminates the “smearing” that plagues direct expansion methods, and provides a physically meaningful estimate of the damage location. LA-UR-12-25460.

Objective Although the association of thoracic aortic aneurysm (TAA) with abdominal aortic aneurysm (AAA) is known, the exact magnitude of the association has not been described. Our goal was to quantify the incidence of TAA in patients with an AAA and assess predictive factors for its diagnosis. Methods This was a retrospective review of all patients diagnosed with AAA from 2000-2008. The subsequent development or diagnosis of a TAA was noted and the association between AAA and TAA described. Results A total of 2196 patients with an AAA were reviewed. 1082 (49.3%) had a chest computed tomography (CT) during follow-up. 117 patients (10.8%) had a synchronous and 136 (12.6%) a metachronous TAA. Mean time to diagnosis was 2.3 years. Mean diameter was 4.7 ± 1.4 cm for AAA, and 4.7 ± 1.0 for TAA. Indications for the chest CT were variable. Most common were AAA (15%), pulmonary embolus (14%), and lung cancer (11%). Only 38% of AAAs and 14% of TAAs were repaired during the study period. Of all patients with known AAA who were found to have a TAA, 61/253 (24%) underwent repair, had a rupture, or had a TAA >5.5 cm. At a mean follow-up of 43.6 months, there were 79 deaths (7%): 7 AAA-related and 13 from TAA ruptures. Predictors of TAA diagnosis by logistic regression include African American race (odds ratio [OR] = 1.8; P = .02), family history of TAA (OR = 7.6; P = .04), hypertension (OR = 1.7; P = .006), and obesity (OR = 1.7; P = .006). Diabetes, infrarenal AAA location, and smoking have a negative association. Conclusions TAAs are relatively common in patients with AAA. Routine or targeted screening with a chest CT at the time of AAA diagnosis may be indicated.

Post-translational modifications (PTMs) broadly contribute to the recent explosion of proteomic data and possess a complexity surpassing that of protein design. PTMs are the chemical modification of a protein after its translation, and have wide effects broadening its range of functionality. Based on previous estimates, it is widely believed that more than half of proteins are glycoproteins. Whereas mutations can only occur once per position, different forms of post-translational modifications may occur in tandem. With the number and abundances of modifications constantly being discovered, there is no method to readily assess their relative levels. Here we report the relative abundances of each PTM found experimentally and putatively, from high-quality, manually curated, proteome-wide data, and show that at best, less than one-fifth of proteins are glycosylated. We make available to the academic community a continuously updated resource (http://selene.princeton.edu/PTMCuration) containing the statistics so scientists can assess “how many” of each PTM exists.

Load dependent Ritz vectors have been found to be suitable alternatives to mode shape vectors for structural vibration analysis. While much research has focused on how to best set-up and perform modal property identification, there has been no investigation on such pretest planning for Ritz vectors. Pre-test planning is a vital part of successful vibration tests, especially when dealing with large complex structures. In such cases, it is common that a limited number of sensors and actuators must be placed in a configuration to obtain the most important dynamic information. In this study, previously developed modal sensor placement techniques were utilized to determine Ritz vector sensor sets for the NASA eight-bay truss structure. The techniques used were the eigenvector product, kinetic energy product, and effective independence. The Modal Assurance Criteria was employed to determine how well each technique performed. Since Ritz vectors are subject to change due to the excitation locations, the paper also investigated the effect of various loading configurations on the Ritz vector sensor placement results. Finally, Ritz vectors and mode shapes were combined in an effort to verify that a single sensor set could be used to identify both sets of basis vectors.

The tendon is a densely packed connective tissue structure consisting of type I collagen fibrils embedded in a matrix of proteoglycans. Tendons are relatively hypovascular but the predominant cell is the fibroblast, or tenocyte. Tenocytes are responsible for producing and maintaining a healthy matrix. Collagen fibrils are arranged in closely packed bundles to form fascicles. Tendons that move in a straight line, such as the Achilles tendon, are surrounded by loose areolar connective tissue called the “paratenon”. The paratenon is usually not visible on imaging studies unless it is surrounded by fluid on both sides. Tendons that bend sharply around corners, such as the long flexors of the foot, are subject to compressive forces and are enclosed by a tendon sheath. Tendons sheaths are lubricated by synovial fluid in order to reduce friction [1, 2].

F11R is the gene name for an adhesion protein, called the F11-receptor, aka JAM-A, which under normal physiological conditions is expressed constitutively on the surface of platelets and localized within tight junctions of endothelial cells (EC). Previous studies of the interactions between human platelets and EC suggested that F11R/JAM-A plays a crucial role in inflammatory thrombosis and atherosclerosis. The study reported here obtained in-vivo confirmation of this conclusion by investigating F11R/JAM-A protein and mRNA in patients with aortic and peripheral vascular disease and in an animal model of atherosclerosis. Molecular and immunofluorescence determinations revealed very high levels of F11R/JAM-A mRNA and F11R/JAM-A protein in atherosclerotic plaques of cardiovascular patients. Similar results were obtained with 12-week-old atherosclerosis-prone apoE-/- mice, an age in which atherosclerotic plaques are well established. Enhanced expression of the F11R/JAM-A message in cultured EC from human aortic and venous vessels was observed following exposure of the cells to cytokines. Determinations of platelet adhesion to cultured EC inflamed by combined cytokine treatment in the presence of F11R/JAM-A - antagonists provided data indicating that de novo expression of F11R/JAM-A on the luminal surface of inflamed EC has an important role in the conversion of EC to a thrombogenic surface. Further studies of these interactions under flow conditions and under in-vivo settings could provide a final proof of a causal role for F11R/JAM-A in the initiation of thrombosis. Based on our in-vitro and in-vivo studies to date, we propose that therapeutic drugs which antagonize the function of F11R/JAM-A should be tested as novel means for the prevention and treatment of atherosclerosis, heart attacks and stroke.

A 30-year-old male was admitted to our institution after a high-speed motor vehicle collision. The patient had remained hemodynamically stable and conscious throughout. He had a traffic pole perforating his left thigh (Figure 1 and Figure 2), but distal pulses were present and sensation was normal in all dermatomes. The patient also had multiple facial abrasions and a scalp laceration. Full-body computed tomography (CT) was performed. The scan showed a steel rod perforating the left thigh, revealing no other significant injury (Figure 3). Surprisingly, and despite the close proximity of the steel rod to the femoral vessels, no vascular lesions were observed on a contrast-enhanced CT scan. Emergency surgery was performed to remove the rod, and no major arterial or

EDITOR—Mean mortality of almost 10% and 30% (max 50%) is reported for elective and emergency gastro-oesophageal surgery in 29 units.1 Yet none had underperformed. A benchmark is set even though institutions were not randomised. A multifactorial model is created by using POSSUM to fit this dataset.2 POSSUM's overpredicting tendency …

Significant hypotension commonly occurs upon reperfusion of the donor liver. In this study we tried to determine if there is accumulation of prostacyclin in the portal system. Blood samples for prostacyclin in twelve patients undergoing orthotopic liver transplantation were studied. Samples were collected at the beginning and end of portal vein anastomosis. Hemodynamic measurements were determined 1 min before and 3 min after portal revascularization. The results show an increase of prostacyclin from 524 +/- 134 pg/ml (n less than 72 pg/ml) to 1132 +/- 264 pg/ml. Eight patients had a decrease in systolic blood pressure from 98 +/- 5 mmHg to 61 +/- mmHg with concomitant significant increase in cardiac output (6.0) from 6.9 +/- 0.7 to 9.9 +/- 1.05 L/mm and significant decrease in systemic vascular resistance (SVR) from 724 +/- 130 dynes/sec/cm to 309 +/- 98. In conclusion, 60% of patients undergoing OLT accumulate prostacyclin in the portal vein, which could be one of the causes of hypotension seen at reperfusion of the donor liver.

ObjectiveThis study assessed outcomes of revascularization strategies in young patients with premature arterial disease.MethodsLower extremity revascularization outcomes from 2000 to 2008 were retrospectively compared among consecutive patients with comparable indications and procedures: age 60 years (control group C). Patency, limb salvage, and survival by limb or patient level were assessed by Kaplan-Meier and Cox proportional hazards analyses.ResultsA total of 409 limbs in 298 patients were treated: 44% for claudication and 56% for critical limb ischemia (CLI). Group A patients were more likely to be smokers and have a hypercoagulable state but less likely to have diabetes and renal failure. Treatment indications were comparable among groups, and procedures were equally distributed between open surgical and endovascular interventions. Two perioperative deaths occurred in group C (2%). Mean follow-up was 29 months, and 16% of claudicant patients in group A progressed to CLI (B, 3%; C, 2%; P < .001). Overall, 2-year primary, primary assisted, and secondary patency were significantly lower in group A (50.5%, 65.2%, 68.2%; P = .045) vs B (65.7%, 81.4%, 86.8%; P = .01) and C (57.9%, 78.9%, 83.9%; P < .001). Claudicant patients in group A had an unexpectedly low 2-year freedom from major amputation after intervention of only 90%. Results were more comparable across groups for CLI. The 2-year freedom from reintervention was similar (A, 81.0%; B, 78.9%; C, 83.5%), irrespective of the indication for intervention (P = .60). Younger patients had a significantly higher 3-year survival (A, 89.5%; B, 85.3%) compared with patients aged >60 years (C, 71.4%; P = .005). The 2-year freedom from major amputation rate was significantly lower in claudicant patients in group A vs C undergoing endovascular revascularization (P = .002), but not in patients treated with open revascularization (P = .40). Predictors of loss of primary patency included age 60 years (P = .05).ConclusionsEndovascular options are commonly being used in young patients, especially those with claudication, but patency rates and outcomes remain very poor.

A systems performance-based strategy for modeling and conducting experiments relevant to the design and performance characterization of telerobotic systems is described. A developmental testbed consisting of a distributed telerobotics network and initial efforts to implement the strategy described is presented. Consideration is given to the general systems performance theory (GSPT) to tackle human performance problems as a basis for: measurement of overall telerobotic system (TRS) performance; task decomposition; development of a generic TRS model; and the characterization of performance of subsystems comprising the generic model. GSPT employs a resource construct to model performance and resource economic principles to govern the interface of systems to tasks. It provides a comprehensive modeling/measurement strategy applicable to complex systems including both human and artificial components. Application is presented within the framework of a distributed telerobotics network as a testbed. Insight into the design of test protocols which elicit application-independent data is described.

Evidence has accumulated that opioids can produce potent antinociceptive effects by interacting with opioid receptors in peripheral tissues. This study sought to compare the effects of morphine with those of bupivacaine administered intraarticularly upon pain following arthroscopic knee surgery. In a double-blind, randomized manner, 33 patients received either morphine (1 mg in 20 ml NaCl; n = 11), bupivacaine (20 ml, 0.25%; n = 11), or a combination of the two (n = 11) intraarticularly at the completion of surgery. After 1, 2, 3, and 4 h and at the end of the 1st and 2nd postoperative days, pain was assessed by a visual analogue scale, and supplemental analgesic requirements were recorded. Pain scores were significantly greater in the morphine group than in the other two groups at 1 h. There were no significant differences at 2 and 3 h. From 4 h until the end of the study period, pain scores were significantly greater in the bupivacaine group than in the other two groups. Analgesic requirements were significantly greater in the morphine group than in the other groups at 1 h but were significantly greater in the bupivacaine group than in the other groups throughout the remainder of the study period. We conclude that intraarticular morphine produces an analgesic effect of delayed onset but of remarkably long duration. The combination of these two drugs results in satisfactory analgesia throughout the entire observation period.

Although liver transplantation is now accepted as the ideal therapy for end-stage liver disease, relatively few centers have gained a large experience in children, and good results have been elusive. Technical difficulty and a high incidence of graft failure are among the obstacles to success. At the University of California at Los Angeles, 39% of our liver transplants are in the patients who are younger than 18 years. We have analyzed our experience with 103 patients to emphasize factors important to a favorable outcome with the procedure. One hundred twenty-three transplants were performed in 103 children (mean age, 5.2 years; 48% younger than 3 years). No reduced-size grafts were used. Scrupulous attention to technical details of the vascular reconstruction, including frequent use of the supraceliac aorta of the recipient and interrupted suture techniques, ensured construction of sound hepatic artery and portal vein anastomoses at the first operation. Preoperative exchange transfusions were used if the prothrombin time was prolonged beyond 7 seconds, resulting in an average blood loss of only 3.3 volumes. Cyclosporine dosage was maintained in the high therapeutic range for the first 4 weeks, and anti-T-cell antibody (OKT3) was used for rejection (38%). Amphotericin prophylaxis was used for biliary atresia patients with multiple previous operations. Eighty-two of one hundred three patients (80%) are alive. There were no intraoperative deaths. Actuarial survival rates at 6 months, 1 year, and 5 years are 80%, 79%, and 77%, respectively. Survival of patients who underwent transplantation at age less than 1 year is 65% versus 85% at age more than 1 year (p = 0.08). Retransplantation was performed in 19 patients (18%), with a survival rate of 58%. Hepatic artery thrombosis, the most frequent technical complication, occurred in only 16 patients (13%). Survival rates of ABO identical-match versus nonidentical-match grafts were 96% and 60%, respectively (p = 0.02). Graft survival was only 47% if more than one steroid cycle was needed, compared to 75% survival with OKT3 treatment. Despite impairment of renal function (glomerular filtration rate [GFR] less than 80 cc/kg/min) in 54% of patients and hypertension requiring therapy in 27%, 90% of the children demonstrated enhancement of growth, development, and functional status. The following conclusions were made. (1) Pediatric liver transplantation is the treatment of choice for all types of end-stage liver disease and should be considered early. (2) Factors that enhance survival include technical precision, aggressive retransplantation, antifungal chemoprophylaxis and therapy, and judicious immunosuppression with use of OKT3 for rejection.(ABSTRACT TRUNCATED AT 400 WORDS)