Publications by authors named "Arash Bahrami"

29 Publications

  • Page 1 of 1

High-resolution compositional mapping of surfaces in non-contact atomic force microscopy by a new multi-frequency excitation.

Ultramicroscopy 2021 Aug 21;227:113317. Epub 2021 May 21.

School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran. Electronic address:

In this paper, a new multi-frequency excitation method based on combination resonance is introduced to enhance the non-contact atomic force microscopy performance. In combination resonance, excitation frequencies are selected so that summation/subtraction of excitation frequencies is close to the natural frequencies of the microcantilever. Due to the nonlinear nature of this method, the probe response to excitation is very sensitive to change in tip-sample forces. This could be used to generate high-resolution compositional mapping and topographical images of the surface. The present study reveals that both amplitude and phase shift of the combination resonance are sensitive to change in parameters such as Hamaker constant, damping coefficient, Young's modulus and tip-sample initial distance. It is observed that because of high sensitivity to Hamaker constant a small change in the surface material leads to considerable variations in amplitude and phase shift. This sensitivity is employed to improve compositional mapping of the surface materials. It is also found out that the response amplitude in the combination resonance is very sensitive to change in the tip-sample initial distance. This sensitivity may be used to reduce the vertical noise and increase image resolution, especially in environments with low quality factors. Overall, using this technique the image contrast increases significantly and high resolution compositional mapping of surfaces is achieved.
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http://dx.doi.org/10.1016/j.ultramic.2021.113317DOI Listing
August 2021

Erratum: Surgical Techniques to Improve the Soft Tissue Triangle in Rhinoplasty: A Systematic Review.

Facial Plast Surg 2021 Jan 11. Epub 2021 Jan 11.

Otolaryngology and Facial Plastic Surgery Associates, Fort Worth, Texas.

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http://dx.doi.org/10.1055/s-0040-1718516DOI Listing
January 2021

Single-Point Fixation for Noncomminuted Zygomaticomaxillary Complex Fractures-A 20-Year Experience.

J Oral Maxillofac Surg 2020 May 7;78(5):778-781. Epub 2020 Jan 7.

Attending Physician, Department of Facial Plastic and Reconstructive Surgery, Otolaryngology and Facial Plastic Surgery Associates, Fort Worth, TX.

Purpose: Zygomaticomaxillary complex (ZMC) fractures occur often. However, no clinical consensus has been reached regarding the number of fixation points required when performing open reduction and internal fixation (ORIF). The objective of the present study was to explore the utility of single-point fixation in the management of noncomminuted ZMC fractures.

Patients And Methods: We analyzed the data from a retrospective case series of 211 patients treated during a 20-year period.

Results: The mean length of follow-up was 3.4 months. Of the 211 patients, 162 with noncomminuted ZMC fractures had been treated with single-point fixation of the zygomaticomaxillary buttress. During the follow-up period, 1 patient experienced tooth loss because of a root present in the fracture line, 7 experienced intraoral plate exposure, with 2 subsequently undergoing plate exchange, and 8 developed a wound infection. No patients required orthognathic surgery or cheek implants for malar asymmetry. No patient developed hypoglobus or enophthalmos, and none required revision ORIF of their ZMC fracture.

Conclusions: To the best of our knowledge, the present study represents the largest series in the literature reporting the surgical results and outcomes of patients with noncomminuted ZMC fractures treated with single-point fixation. In experienced hands, we believe this is a viable surgical option if appropriate surgical considerations are made.
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http://dx.doi.org/10.1016/j.joms.2019.12.030DOI Listing
May 2020

Progressive Scalp Thinning Over Mesh Cranioplasty and the Role of Lipotransfer.

Laryngoscope 2020 08 28;130(8):1926-1931. Epub 2019 Dec 28.

Otolaryngology and Facial Plastic Surgery Associates, Fort Worth, Texas, U.S.A.

Objectives: To evaluate the role of lipotransfer in progressive scalp thinning following titanium mesh cranioplasty.

Methods: Retrospective review of single surgeon, single tertiary referral experience of all patients who underwent mesh cranioplasty. Patient demographics, prior radiotherapy, frequency and timing of scalp thinning, and treatment course data were obtained.

Results: A total of 144 patients were included, 77 male and 67 female with mean ages 58.2 and 54.8, respectively. One hundred four patients (72%) developed mesh exposure or impending exposure requiring reconstruction. Fifty-six patients (54%) with scalp thinning were treated with lipotransfer, 40 of which were salvaged and the remainder of these patients definitively managed with cranioplasty and reconstruction. Prior radiotherapy was found to be associated with higher rates of mesh exposure (P = .0028), but not predictive of response to lipotransfer.

Conclusion: Lipotransfer is a useful technique in managing moderate scalp thinning following mesh cranioplasty. Mesh exposure or severe thinning require definitive cranioplasty and reconstruction.

Level Of Evidence: IV Laryngoscope, 130: 1926-1931, 2020.
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http://dx.doi.org/10.1002/lary.28463DOI Listing
August 2020

I-PINE web server: an integrative probabilistic NMR assignment system for proteins.

J Biomol NMR 2019 May 4;73(5):213-222. Epub 2019 Jun 4.

National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA.

Various methods for understanding the structural and dynamic properties of proteins rely on the analysis of their NMR chemical shifts. These methods require the initial assignment of NMR signals to particular atoms in the sequence of the protein, a step that can be very time-consuming. The probabilistic interaction network of evidence (PINE) algorithm for automated assignment of backbone and side chain chemical shifts utilizes a Bayesian probabilistic network model that analyzes sequence data and peak lists from multiple NMR experiments. PINE, which is one of the most popular and reliable automated chemical shift assignment algorithms, has been available to the protein NMR community for longer than a decade. We announce here a new web server version of PINE, called Integrative PINE (I-PINE), which supports more types of NMR experiments than PINE (including three-dimensional nuclear Overhauser enhancement and four-dimensional J-coupling experiments) along with more comprehensive visualization of chemical shift based analysis of protein structure and dynamics. The I-PINE server is freely accessible at http://i-pine.nmrfam.wisc.edu . Help pages and tutorial including browser capability are available at: http://i-pine.nmrfam.wisc.edu/instruction.html . Sample data that can be used for testing the web server are available at: http://i-pine.nmrfam.wisc.edu/examples.html .
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http://dx.doi.org/10.1007/s10858-019-00255-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6579641PMC
May 2019

Vesicle constriction by rings of Janus nanoparticles and aggregates of curved proteins.

Nanotechnology 2019 Aug 2;30(34):345101. Epub 2019 May 2.

School of Mechanical Engineering, College of Engineering, University of Tehran, North Kargar St., 14399-57131 Tehran, Iran.

Membrane constriction and associated scission by proteins and nano structures are crucial to many processes in cellular and synthetic biology. We report mechanical constriction of vesicles by rings of adsorbed Janus nanoparticles that represent synthetic nano structures and mimic contractile proteins, and by aggregates of curved crescents that mimic scaffold proteins. Membrane energetics from Monte Carlo simulations and simulated annealing of the elastic membrane model confirms spontaneous vesicle constriction by aggregates of sufficiently-curved crescents of various lengths and by rings of Janus nanoparticles with a variety of ring lengths, particle sizes, and particle area fractions. We show that shorter rings of smaller particles with higher area fractions reinforce the constriction by increasing the energetic drive towards the constricted vesicle with smaller constriction radius. We demonstrate that vesicle constriction by crescent aggregates strongly depends on the crescent curvature. In contrast to aggregates of sufficiently-curved crescents that are capable of inducing full vesicle constriction, those of near flat crescents with negligible curvature leave the vesicle unconstricted. Our results offer promising perspectives for designing membrane-constricting nano structures such as nanoparticle aggregates and clusters of synthetic curved proteins such as DNA origami scaffolds with applications in synthetic biology. Our findings reveal the significant contribution of highly-curved F-BAR domains to cell division and explain how contractile protein rings such as dynamin GTPase, actomyosin rings, and endosomal sorting complexes required for transport constrict the membrane.
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http://dx.doi.org/10.1088/1361-6528/ab1ed5DOI Listing
August 2019

Pharyngeal Reconstruction with Microvascular Free Tissue Transfer.

Semin Plast Surg 2019 Feb 8;33(1):78-80. Epub 2019 Mar 8.

Otolaryngology and Facial Plastic Surgery Associates, Fort Worth, Texas.

Reconstruction of pharyngoesophageal defects after total laryngectomies and extirpation of hypopharyngeal and upper esophageal carcinomas presents a challenging task. Goals of reconstruction include adequate voice rehabilitation and restoration of normal swallowing. The reconstructive armamentarium contains many options for reconstruction and creation of a new upper digestive tract. This review article focuses on the most commonly used free tissue transfer options for the reconstruction of these defects, with an assessment of their advantages and disadvantages.
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http://dx.doi.org/10.1055/s-0039-1677877DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6408241PMC
February 2019

Physico-mechanical and antimicrobial properties of tragacanth/hydroxypropyl methylcellulose/beeswax edible films reinforced with silver nanoparticles.

Int J Biol Macromol 2019 May 10;129:1103-1112. Epub 2018 Sep 10.

Drug Applied Research Center and Department of Medical Nanotechnology, School of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran.

The novel trinary bio-composite film based on Tragacanth/Hydroxypropyl methylcellulose/Beeswax reinforced silver nanoparticles (AgNPs) was developed. This study investigated the effect of AgNPs (2, 4 and 8%) on some physico-mechanical and antimicrobial properties of bio-composite film. It was discovered that AgNPs reduced the composite tensile strength from 33.64 to 16.12 MPa. However, water vapor permeability was improved by addition of the nanoparticles (4.57-2.16 × 10 g m/m s Pa). The use of AgNPs influenced the apparent color of bio-composite film. The microscopic surface structure and topography of the films were also examined by scanning electron microscopy and Fourier transform infrared, respectively. Dynamic mechanical thermal analysis results showed that the thermal stability of film was slightly decreased through incorporation with AgNPs. Finally, nano-composite films demonstrated strong antibacterial activity against tested pathogen bacteria in the contact surface zone. The antimicrobial results suggest that new nanocomposite film may be used as food active packaging.
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http://dx.doi.org/10.1016/j.ijbiomac.2018.09.045DOI Listing
May 2019

The radial forearm free flap for scalp and forehead reconstruction: A 20-year experience.

Clin Otolaryngol 2018 12 1;43(6):1611-1613. Epub 2018 Aug 1.

Department of Facial Plastic and Reconstructive Surgery, Otolaryngology and Facial Plastic Surgery Associates, Ottawa, Canada.

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http://dx.doi.org/10.1111/coa.13189DOI Listing
December 2018

Holmium Laser for Endoscopic Treatment of Benign Tracheal Stenosis.

Int Arch Otorhinolaryngol 2018 Jul 14;22(3):203-207. Epub 2017 Jul 14.

Department of Facial Plastics, Otolaryngology and Facial Plastic Surgery Associates, Fort Worth, Texas, United States.

 Laryngotracheal stenosis is a difficult problem with varied etiology and various treatment options. The holmium laser represents another tool for the treatment of benign tracheal stenosis.  To determine the utility of holmium laser treatment for benign tracheal stenosis with regards to safety and efficacy.  This was a retrospective case study examining patients with benign tracheal stenosis from 1998-2016 who underwent holmium laser treatment. Determining the safety of this procedure was the primary goal, and complications were monitored as a surrogate of safety.  A total of 123 patients who underwent holmium laser treatment for benign tracheal stenosis were identified. In total, 123 patients underwent 476 procedures, with follow-up ranging from 1 month to 14 years. No intraoperative or post-operative complications were identified as a direct result of the use of this particular laser.  The holmium laser is an effective and safe laser to use for tracheal stenosis treatment. It is a contact laser with a short acting distance, which reduces the risk of injury to distal airway structures. Given the favorable experience reported here, the holmium laser should be considered when tracheal surgery is attempted.
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http://dx.doi.org/10.1055/s-0037-1604201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6033607PMC
July 2018

Preoperative radiation and complication rates after double free flap reconstruction of head and neck cancer.

Am J Otolaryngol 2018 Sep - Oct;39(5):558-560. Epub 2018 Jun 18.

Otolaryngology and Facial Plastic Surgery Associates, Fort Worth, TX, USA. Electronic address:

Introduction: In this study, we explore whether preoperative external beam radiation affects complication rates in patients that have undergone double simultaneous free tissue transfer for head and neck defects.

Study Design, Setting, Subjects And Methods: Approval was obtained from the JPS Institutional Review Board. We performed a retrospective analysis of patients who underwent double free flap reconstruction of head and neck defects between August 1997 and April 2017. Minimum follow up was 6 months. Patients were grouped according to preoperative radiation status (XRT vs non-XRT). The chi-squared test was used for all comparisons. P-values and 95% confidence intervals (CI) were reported as (P, 95% CI).

Results: 90 flaps were performed on 45 patients. The most common flap combination utilized was fibula plus radial forearm free flap (RFF) in 17 out of 45 patients. There were no statistically significant differences in frequency of flap failure (0.35, -15.9-20.1), wound infection (0.75, -22.1-19.3), hematoma (0.16, -5.3-36.7), or fistula formation (0.69, -22.5-24.6). There were also no statistically significant differences in cardiac complications (0.57, -10.3-28.2) and DVT (0.22, -12.4-25.3).

Conclusion: Our findings suggest that double free flap patients who had preoperative radiation are not more likely to have complications compared to non- radiated patients. Simultaneous double free flaps should be reserved for the most complex cases. Extensive discussion should be had with the patient about possible morbidity and mortality.
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http://dx.doi.org/10.1016/j.amjoto.2018.06.015DOI Listing
January 2019

Cranioplasty Using a Mixture of Biologic and Nonbiologic Agents.

JAMA Facial Plast Surg 2018 Jan;20(1):9-13

Otolaryngology and Facial Plastic Surgery Associates, Fort Worth, Texas.

Importance: A surgeon faces challenges with cranioplasty techniques to achieve a successful result with relatively few complications.

Objective: To describe a unique technique for incorporating both biologic autologous bone and nonbiologic allograft materials for defect coverage in cranioplasty with favorable outcomes and low occurrence of complications.

Design, Setting, And Participants: A retrospective medical records review of all 26 patients who underwent primary cranioplasty procedure with a modified technique between January 2011 and December 2015 at a high-volume head and neck oncologic reconstructive practice was conducted; data analysis was also performed during that period. After several years of experience with traditional cranioplasty maneuvers, the modified technique has evolved to incorporate both autologous bone grafts and alloplastic materials in the formation of a shapeable on-lay material. Data were collected on demographics, need for cranioplasty, materials used, outcomes, and risk factors.

Main Outcomes And Measures: Rates of infection, hematoma, flap loss or resorption, cerebrospinal fluid leak, hardware exposure or malfunction, and repeated reconstruction.

Results: Of the 26 patients, 21 (81%) were men; mean (SD) age was 65.8 (14.3) years. Eight (31%) patients had a history of diabetes, 4 (15%) patients were receiving immunosuppressive drugs, and 5 (19%) patients were active smokers at the time of surgery. Neoplasia was the most common cause of the calvarial defect seen, responsible for 20 of 28 (71%) operative defects and necessitated procedures. All but 1 patient achieved successful mineralization following primary cranioplasty with the modified technique; this success was verified based on physical examination and follow-up imaging. Complications were rare and involved only 3 patients who developed postoperative infection; 1 (4%) of these patients lost the integrity of the cranioplasty. Thus, the rate of infection was 11% and loss rate was 4%. Preoperative and postoperative radiotherapy appeared to have no bearing on graft survival.

Conclusions And Relevance: The results using a unique technique for incorporating both biologic autologous bone and nonbiologic allograft materials for defect coverage in cranioplasty are favorable, with satisfactory aesthetic outcomes and limited postoperative complications.

Level Of Evidence: 4.
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http://dx.doi.org/10.1001/jamafacial.2017.0437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5833661PMC
January 2018

A Pediatric Patient With an Orbital Respiratory Epithelial Cyst.

J Craniofac Surg 2017 Nov;28(8):2098-2100

*Department of Otolaryngology-Facial Plastic Surgery, Philadelphia College of Osteopathic Medicine, Philadelphia, PA †New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY ‡Department of Pathology and Laboratory Medicine §Department of Plastic Surgery, St. Christopher's Hospital for Children, Philadelphia, PA.

Respiratory epithelial cysts are rare orbital cysts that can arise secondary to choristomatous rests of respiratory epithelium. Approximately 15 congenital cases have been described in the literature, making it a rare disease entity. We present a case of a 14-month-old Middle Eastern male with a right infraorbital respiratory epithelial cyst. Magnetic resonance imaging of the brain and orbits revealed a right infraorbital cyst hyperintense on T1-weighted images and followed fluid density on T2-weighted images. This cyst was noted to displace the globe superiorly and inferior rectus muscle laterally. This cyst was excised using a transconjunctival approach. Histologically, the cyst wall was lined by ciliated columnar cells with interspersed mucus-containing cells and ciliated transitional epithelium was present, establishing the diagnosis of respiratory epithelial cyst. To our knowledge, this is the youngest patient with a respiratory epithelial cyst of the orbit reported in the literature.
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http://dx.doi.org/10.1097/SCS.0000000000004169DOI Listing
November 2017

Levels of Some Heavy Metals in Raw Cow's Milk from Selected Milk Production Sites in Iran: Is There any Health Concern?

Health Promot Perspect 2015 25;5(3):176-82. Epub 2015 Oct 25.

Department of Nutrition, Faculty of Nutrition, Tabriz University of Medical Science, Tabriz, Iran.

Background: The aim of this study was to evaluate the content of mercury (Hg), arsenic (As), nickel (Ni) and tin (Sn) in raw cow's milk of traditional and industrial sites from 8 different sites in Arak City, Markazi Province, Iran.

Methods: In this cross sectional study, a total of 32 samples were collected from sub-cities of Arak, Iran via subjective sampling method. Both industrial and traditional dairy farms were selected for sampling. Twenty-five gram of each sample was turned to ash in ovens for metal analyses including Hg, As, Ni and Sn by anatomic absorption spectrometer.

Results: The residue amounts of Hg and As were lower than permissible limit suggested by Codex Alimentarius, but for Ni and Sn it was higher only in one of the collection sites. The average concentra-tion of Hg was significantly higher (P<0.05) in traditional farms as compared to industrial farms. Be-sides, amounts of Sn was significantly high in the traditional farms (P<0.05). Further, a high contents Ni was detected in industrial farms (P<0.05).

Conclusion: High Sn and Ni contents of some milk samples from this region might be potentially hazardous to consumers. Further, none of the other metals tested crossed permissible levels.
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http://dx.doi.org/10.15171/hpp.2015.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667257PMC
December 2015

Pseudosarcoma of the thigh: a rare case of massive localized lymphedema.

Int Surg 2015 Mar;100(3):461-5

1 Texas College of Osteopathic Medicine, Fort Worth, Texas, USA.

Massive localized lymphedema, also called pseudosarcoma, is a rare condition associated with morbid obesity. Accurate identification of this entity helps the physician make the distinction between this condition and other soft tissue tumors, especially with the increasing rate of obesity worldwide. Obesity and increased caloric intake lead to storage of the excess energy in the form of adipose tissue. The excess adipose tissue disturbs the lymphatic vessels, leading to massive edema localized mostly in the lower extremity, reaching a substantial size and weight that interferes with the quality of life of the individual in question. The mass can cause cosmetic but more importantly functional and structural defects, leading to altered biomechanics with increased risk of deep vein thromboembolism. Below is a presentation of a patient presenting with complaint of a massive medial thigh mass. After much investigation, consultation, and use of diagnostic radiologic modalities it was diagnosed as what is referred to in the literature as massive localized lymphedema, or pseudosarcoma. This mass was managed by surgical excision and the diagnosis was further confirmed by pathologic analysis. After the excision, our patient regained his ability to ambulate on his own, with the help of a rehabilitation program and physical therapy. Massive localized lymphedema needs to be on the differential diagnosis of any morbidly obese patient presenting with mass, especially in the lower extremities. Adequate knowledge about this condition enables the physician to make the distinction between pseudosarcoma and true soft tissue sarcomas.
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http://dx.doi.org/10.9738/INTSURG-D-14-00077.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4370536PMC
March 2015

Assignments of RNase A by ADAPT-NMR and enhancer.

Biomol NMR Assign 2015 Apr 12;9(1):81-8. Epub 2014 Mar 12.

National Magnetic Resonance Facility at Madison, University of Wisconsin - Madison, 433 Babcock Drive, Madison, WI, 53706, USA,

We report here backbone (1)H and (15)N assignments for ribonuclease A obtained by using ADAPT-NMR, a fully-automated approach for combined data collection, spectral analysis and resonance assignment. ADAPT-NMR was able to assign 98% of the resonances with 93% agreement with traditional data collection and assignment. Further refinement of the automated results with ADAPT-NMR enhancer led to complete (100%) assignments with 96% agreement with assignments by the traditional approach.
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http://dx.doi.org/10.1007/s12104-014-9549-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4162851PMC
April 2015

Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers.

J Magn Reson 2013 Nov 30;236:83-8. Epub 2013 Aug 30.

National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA; Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA. Electronic address:

ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for [U-(13)C, U-(15)N]-labeled proteins. Given the sequence of the protein and data for the orthogonal 2D (1)H-(15)N and (1)H-(13)C planes, the algorithm automatically directs the collection of tilted plane data from a variety of triple-resonance experiments so as to follow an efficient pathway toward the probabilistic assignment of (1)H, (13)C, and (15)N signals to specific atoms in the covalent structure of the protein. Data collection and assignment calculations continue until the addition of new data no longer improves the assignment score. ADAPT-NMR was first implemented on Varian (Agilent) spectrometers [A. Bahrami, M. Tonelli, S.C. Sahu, K.K. Singarapu, H.R. Eghbalnia, J.L. Markley, PLoS One 7 (2012) e33173]. Because of broader interest in the approach, we present here a version of ADAPT-NMR for Bruker spectrometers. We have developed two AU console programs (ADAPT_ORTHO_run and ADAPT_NMR_run) that run under TOPSPIN Versions 3.0 and higher. To illustrate the performance of the algorithm on a Bruker spectrometer, we tested one protein, chlorella ubiquitin (76 amino acid residues), that had been used with the Varian version: the Bruker and Varian versions achieved the same level of assignment completeness (98% in 20 h). As a more rigorous evaluation of the Bruker version, we tested a larger protein, BRPF1 bromodomain (114 amino acid residues), which yielded an automated assignment completeness of 86% in 55 h. Both experiments were carried out on a 500 MHz Bruker AVANCE III spectrometer equipped with a z-gradient 5 mm TCI probe. ADAPT-NMR is available at http://pine.nmrfam.wisc.edu/ADAPT-NMR in the form of pulse programs, the two AU programs, and instructions for installation and use.
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http://dx.doi.org/10.1016/j.jmr.2013.08.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858185PMC
November 2013

ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy.

Bioinformatics 2013 Feb 7;29(4):515-7. Epub 2012 Dec 7.

National Magnetics Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA.

Summary: ADAPT-nuclear magnetic resonance (ADAPT-NMR) offers an automated approach to the concurrent acquisition and processing of protein NMR data with the goal of complete backbone and side chain assignments. What the approach lacks is a useful graphical interface for reviewing results and for searching for missing peaks that may have prevented assignments or led to incorrect assignments. Because most of the data ADAPT-NMR collects are 2D tilted planes used to find peaks in 3D spectra, it would be helpful to have a tool that reconstructs the 3D spectra. The software package reported here, ADAPT-NMR Enhancer, supports the visualization of both 2D tilted planes and reconstructed 3D peaks on each tilted plane. ADAPT-NMR Enhancer can be used interactively with ADAPT-NMR to automatically assign selected peaks, or it can be used to produce PINE-SPARKY-like graphical dialogs that support atom-by-atom and peak-by-peak assignment strategies. Results can be exported in various formats, including XEASY proton file (.prot), PINE pre-assignment file (.str), PINE probabilistic output file, SPARKY peak list file (.list) and TALOS+ input file (.tab). As an example, we show how ADAPT-NMR Enhancer was used to extend the automated data collection and assignment results for the protein Aedes aegypti sterol carrier protein 2.

Availability: The program, in the form of binary code along with tutorials and reference manuals, is available at http://pine.nmrfam.wisc.edu/adapt-nmr-enhancer.
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http://dx.doi.org/10.1093/bioinformatics/bts692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570218PMC
February 2013

Robust, integrated computational control of NMR experiments to achieve optimal assignment by ADAPT-NMR.

PLoS One 2012 12;7(3):e33173. Epub 2012 Mar 12.

National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin - Madison, Madison, Wisconsin, United States of America.

ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) represents a groundbreaking prototype for automated protein structure determination by nuclear magnetic resonance (NMR) spectroscopy. With a [(13)C,(15)N]-labeled protein sample loaded into the NMR spectrometer, ADAPT-NMR delivers complete backbone resonance assignments and secondary structure in an optimal fashion without human intervention. ADAPT-NMR achieves this by implementing a strategy in which the goal of optimal assignment in each step determines the subsequent step by analyzing the current sum of available data. ADAPT-NMR is the first iterative and fully automated approach designed specifically for the optimal assignment of proteins with fast data collection as a byproduct of this goal. ADAPT-NMR evaluates the current spectral information, and uses a goal-directed objective function to select the optimal next data collection step(s) and then directs the NMR spectrometer to collect the selected data set. ADAPT-NMR extracts peak positions from the newly collected data and uses this information in updating the analysis resonance assignments and secondary structure. The goal-directed objective function then defines the next data collection step. The procedure continues until the collected data support comprehensive peak identification, resonance assignments at the desired level of completeness, and protein secondary structure. We present test cases in which ADAPT-NMR achieved results in two days or less that would have taken two months or more by manual approaches.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033173PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299752PMC
August 2012

RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts.

J Biomol NMR 2012 Apr 23;52(4):289-302. Epub 2012 Feb 23.

National Magnetic Resonance Facility at Madison, Madison, WI, USA.

The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ((1)H-(15)N 2D HMQC) and proton-proton nuclear Overhauser enhancement spectroscopy ((1)H-(1)H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino resonances for a majority of the NMR resonances, even when the initial predictions are only modestly accurate. RNA-PAIRS is available as a public web-server at http://pine.nmrfam.wisc.edu/RNA/.
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http://dx.doi.org/10.1007/s10858-012-9603-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3480180PMC
April 2012

PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy.

Bioinformatics 2009 Aug 3;25(16):2085-7. Epub 2009 Jun 3.

National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.

Summary: PINE-SPARKY supports the rapid, user-friendly and efficient visualization of probabilistic assignments of NMR chemical shifts to specific atoms in the covalent structure of a protein in the context of experimental NMR spectra. PINE-SPARKY is based on the very popular SPARKY package for visualizing multidimensional NMR spectra (T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco). PINE-SPARKY consists of a converter (PINE2SPARKY), which takes the output from an automated PINE-NMR analysis and transforms it into SPARKY input, plus a number of SPARKY extensions. Assignments and their probabilities obtained in the PINE-NMR step are visualized as labels in SPARKY's spectrum view. Three SPARKY extensions (PINE Assigner, PINE Graph Assigner, and Assign the Best by PINE) serve to manipulate the labels that signify the assignments and their probabilities. PINE Assigner lists all possible assignments for a peak selected in the dialog box and enables the user to choose among these. A window in PINE Graph Assigner shows all atoms in a selected residue along with all atoms in its adjacent residues; in addition, it displays a ranked list of PINE-derived connectivity assignments to any selected atom. Assign the Best-by-PINE allows the user to choose a probability threshold and to automatically accept as "fixed" all assignments above that threshold; following this operation, only the less certain assignments need to be examined visually. Once assignments are fixed, the output files generated by PINE-SPARKY can be used as input to PINE-NMR for further refinements.

Availability: The program, in the form of source code and binary code along with tutorials and reference manuals, is available at http://pine.nmrfam.wisc.edu/PINE-SPARKY.
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http://dx.doi.org/10.1093/bioinformatics/btp345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723000PMC
August 2009

Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy.

PLoS Comput Biol 2009 Mar 13;5(3):e1000307. Epub 2009 Mar 13.

Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin Madison, Madison, Wisconsin, United States of America.

The process of assigning a finite set of tags or labels to a collection of observations, subject to side conditions, is notable for its computational complexity. This labeling paradigm is of theoretical and practical relevance to a wide range of biological applications, including the analysis of data from DNA microarrays, metabolomics experiments, and biomolecular nuclear magnetic resonance (NMR) spectroscopy. We present a novel algorithm, called Probabilistic Interaction Network of Evidence (PINE), that achieves robust, unsupervised probabilistic labeling of data. The computational core of PINE uses estimates of evidence derived from empirical distributions of previously observed data, along with consistency measures, to drive a fictitious system M with Hamiltonian H to a quasi-stationary state that produces probabilistic label assignments for relevant subsets of the data. We demonstrate the successful application of PINE to a key task in protein NMR spectroscopy: that of converting peak lists extracted from various NMR experiments into assignments associated with probabilities for their correctness. This application, called PINE-NMR, is available from a freely accessible computer server (http://pine.nmrfam.wisc.edu). The PINE-NMR server accepts as input the sequence of the protein plus user-specified combinations of data corresponding to an extensive list of NMR experiments; it provides as output a probabilistic assignment of NMR signals (chemical shifts) to sequence-specific backbone and aliphatic side chain atoms plus a probabilistic determination of the protein secondary structure. PINE-NMR can accommodate prior information about assignments or stable isotope labeling schemes. As part of the analysis, PINE-NMR identifies, verifies, and rectifies problems related to chemical shift referencing or erroneous input data. PINE-NMR achieves robust and consistent results that have been shown to be effective in subsequent steps of NMR structure determination.
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http://dx.doi.org/10.1371/journal.pcbi.1000307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2645676PMC
March 2009

HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections.

J Biomol NMR 2007 Aug 4;38(4):341-51. Epub 2007 Jul 4.

National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA.

We describe a novel method for the robust, rapid, and reliable determination of J couplings in multi-dimensional NMR coupling data, including small couplings from larger proteins. The method, "High-resolution Iterative Frequency Identification of Couplings" (HIFI-C) is an extension of the adaptive and intelligent data collection approach introduced earlier in HIFI-NMR. HIFI-C collects one or more optimally tilted two-dimensional (2D) planes of a 3D experiment, identifies peaks, and determines couplings with high resolution and precision. The HIFI-C approach, demonstrated here for the 3D quantitative J method, offers vital features that advance the goal of rapid and robust collection of NMR coupling data. (1) Tilted plane residual dipolar couplings (RDC) data are collected adaptively in order to offer an intelligent trade off between data collection time and accuracy. (2) Data from independent planes can provide a statistical measure of reliability for each measured coupling. (3) Fast data collection enables measurements in cases where sample stability is a limiting factor (for example in the presence of an orienting medium required for residual dipolar coupling measurements). (4) For samples that are stable, or in experiments involving relatively stronger couplings, robust data collection enables more reliable determinations of couplings in shorter time, particularly for larger biomolecules. As a proof of principle, we have applied the HIFI-C approach to the 3D quantitative J experiment to determine N-C' RDC values for three proteins ranging from 56 to 159 residues (including a homodimer with 111 residues in each subunit). A number of factors influence the robustness and speed of data collection. These factors include the size of the protein, the experimental set up, and the coupling being measured, among others. To exhibit a lower bound on robustness and the potential for time saving, the measurement of dipolar couplings for the N-C' vector represents a realistic "worst case analysis". These couplings are among the smallest currently measured, and their determination in both isotropic and anisotropic media demands the highest measurement precision. The new approach yielded excellent quantitative agreement with values determined independently by the conventional 3D quantitative J NMR method (in cases where sample stability in oriented media permitted these measurements) but with a factor of 2-5 in time savings. The statistical measure of reliability, measuring the quality of each RDC value, offers valuable adjunct information even in cases where modest time savings may be realized.
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http://dx.doi.org/10.1007/s10858-007-9173-7DOI Listing
August 2007

High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection.

J Am Chem Soc 2005 Sep;127(36):12528-36

National Magnetic Resonance Facility at Madison, Center for Eukaryotic Structural Genomics, Graduate Program in Biophysics, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

We describe a novel approach to the rapid collection and processing of multidimensional NMR data: "high-resolution iterative frequency identification for NMR" (HIFI-NMR). As with other reduced dimensionality approaches, HIFI-NMR collects n-dimensional data as a set of two-dimensional (2D) planes. The HIFI-NMR algorithm incorporates several innovative features. (1) Following the initial collection of two orthogonal 2D planes, tilted planes are selected adaptively, one-by-one. (2) Spectral space is analyzed in a rigorous statistical manner. (3) An online algorithm maintains a model that provides a probabilistic representation of the three-dimensional (3D) peak positions, derives the optimal angle for the next plane to be collected, and stops data collection when the addition of another plane would not improve the data model. (4) A robust statistical algorithm extracts information from the plane projections and is used to drive data collection. (5) Peak lists with associated probabilities are generated directly, without total reconstruction of the 3D spectrum; these are ready for use in subsequent assignment or structure determination steps. As a proof of principle, we have tested the approach with 3D triple-resonance experiments of the kind used to assign protein backbone and side-chain resonances. Peaks extracted automatically by HIFI-NMR, for both small and larger proteins, included approximately 98% of real peaks obtained from control experiments in which data were collected by conventional 3D methods. HIFI-NMR required about one-tenth the time for data collection and avoided subsequent data processing and peak-picking. The approach can be implemented on commercial NMR spectrometers and is extensible to higher-dimensional NMR.
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http://dx.doi.org/10.1021/ja052120iDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4311751PMC
September 2005

Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO).

J Biomol NMR 2005 Jul;32(3):219-33

Biochemistry Department, National Magnetic Resonance Facility at Madison, 433, Babcock Drive, Madison, WI 53706, USA.

We present a novel automated strategy (PISTACHIO) for the probabilistic assignment of backbone and sidechain chemical shifts in proteins. The algorithm uses peak lists derived from various NMR experiments as input and provides as output ranked lists of assignments for all signals recognized in the input data as constituting spin systems. PISTACHIO was evaluated by comparing its performance with raw peak-picked data from 15 proteins ranging from 54 to 300 residues; the results were compared with those achieved by experts analyzing the same datasets by hand. As scored against the best available independent assignments for these proteins, the first-ranked PISTACHIO assignments were 80-100% correct for backbone signals and 75-95% correct for sidechain signals. The independent assignments benefited, in a number of cases, from structural data (e.g. from NOESY spectra) that were unavailable to PISTACHIO. Any number of datasets in any combination can serve as input. Thus PISTACHIO can be used as datasets are collected to ascertain the current extent of secure assignments, to identify residues with low assignment probability, and to suggest the types of additional data needed to remove ambiguities. The current implementation of PISTACHIO, which is available from a server on the Internet, supports input data from 15 standard double- and triple-resonance experiments. The software can readily accommodate additional types of experiments, including data from selectively labeled samples. The assignment probabilities can be carried forward and refined in subsequent steps leading to a structure. The performance of PISTACHIO showed no direct dependence on protein size, but correlated instead with data quality (completeness and signal-to-noise). PISTACHIO represents one component of a comprehensive probabilistic approach we are developing for the collection and analysis of protein NMR data.
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http://dx.doi.org/10.1007/s10858-005-7944-6DOI Listing
July 2005

Three-dimensional structure of the AAH26994.1 protein from Mus musculus, a putative eukaryotic Urm1.

Protein Sci 2005 Aug;14(8):2095-102

Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA.

We have used NMR spectroscopy to determine the solution structure of protein AAH26994.1 from Mus musculus and propose that it represents the first three-dimensional structure of a ubiquitin-related modifier 1 (Urm1) protein. Amino acid sequence comparisons indicate that AAH26994.1 belongs to the Urm1 family of ubiquitin-like modifier proteins. The best characterized member of this family has been shown to be involved in nutrient sensing, invasive growth, and budding in yeast. Proteins in this family have only a weak sequence similarity to ubiquitin, and the structure of AAH26994.1 showed a much closer resemblance to MoaD subunits of molybdopterin synthases (known structures are of three bacterial MoaD proteins with 14%-26% sequence identity to AAH26994.1). The structures of AAH26994.1 and the MoaD proteins each contain the signature ubiquitin secondary structure fold, but all differ from ubiquitin largely in regions outside of this fold. This structural similarity bolsters the hypothesis that ubiquitin and ubiquitin-related proteins evolved from a protein-based sulfide donor system of the molybdopterin synthase type.
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http://dx.doi.org/10.1110/ps.051577605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279321PMC
August 2005

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements.

J Biomol NMR 2005 May;32(1):71-81

Biochemistry Department, National Magnetic Resonance Facility at Madison, 433 Babcock Drive, Madison, WI 53706, USA.

We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ("PECAN", Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states.
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http://dx.doi.org/10.1007/s10858-005-5705-1DOI Listing
May 2005

Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications.

J Biomol NMR 2005 May;32(1):13-22

National Magnetic Resonance Facility at Madison, Biochemistry Department, 433 Babcock Drive, Madison, WI 53706, USA.

Statistical analysis reveals that the set of differences between the secondary shifts of the alpha- and beta-carbons for residues i of a protein (Deltadelta13C(alpha)i - Deltadelta13C(beta)i) provides the means to detect and correct referencing errors for 1H and 13C nuclei within a given dataset. In a correctly referenced protein dataset, linear regression plots of Deltadelta13C(alpha)i, Deltadelta13C(beta)i, or Deltadelta1H(alpha)i vs. (Deltadelta13C(alpha)i - Deltadelta13C(beta)i) pass through the origin from two directions, the helix-to-coil and strand-to-coil directions. Thus, linear analysis of chemical shifts (LACS) can be used to detect referencing errors and to recalibrate the 1H and 13C chemical shift scales if needed. The analysis requires only that the signals be identified with distinct residue types (intra-residue spin systems). LACS allows errors in calibration to be detected and corrected in advance of sequence-specific assignments and secondary structure determinations. Signals that do not fit the linear model (outliers) deserve scrutiny since they could represent errors in identifying signals with a particular residue, or interesting features such as a cis-peptide bond. LACS provides the basis for the automated detection of such features and for testing reassignment hypotheses. Early detection and correction of errors in referencing and spin system identifications can improve the speed and accuracy of chemical shift assignments and secondary structure determinations. We have used LACS to create a database of offset-corrected chemical shifts corresponding to nearly 1800 BMRB entries: 300 with and 1500 without corresponding three-dimensional (3D) structures. This database can serve as a resource for future analysis of the effects of amino acid sequence and protein secondary and tertiary structure on NMR chemical shifts.
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http://dx.doi.org/10.1007/s10858-005-1717-0DOI Listing
May 2005
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