Publications by authors named "Mark D Walsh"

17 Publications

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3 -5 crosstalk contributes to transcriptional bursting.

Genome Biol 2021 Feb 4;22(1):56. Epub 2021 Feb 4.

School of Life Sciences, University of Warwick, Coventry, UK.

Background: Transcription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates. It occurs in bursts, which results in vastly different numbers of an mRNA species in isogenic cell populations. Several factors contributing to transcriptional bursting have been identified, usually classified as intrinsic, in other words local to single genes, or extrinsic, relating to the macroscopic state of the cell. However, some possible contributors have not been explored yet. Here, we focus on processes at the 3 and 5 ends of a gene that enable reinitiation of transcription upon termination.

Results: Using Bayesian methodology, we measure the transcriptional bursting in inducible transgenes, showing that perturbation of polymerase shuttling typically reduces burst size, increases burst frequency, and thus limits transcriptional noise. Analysis based on paired-end tag sequencing (PolII ChIA-PET) suggests that this effect is genome wide. The observed noise patterns are also reproduced by a generative model that captures major characteristics of the polymerase flux between the ends of a gene and a phase-separated compartment.

Conclusions: Interactions between the 3 and 5 ends of a gene, which facilitate polymerase recycling, are major contributors to transcriptional noise.
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http://dx.doi.org/10.1186/s13059-020-02227-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7860045PMC
February 2021

Commentary on: Deferiprone Stimulates Aged Dermal Fibroblasts via HIF-1α Modulation.

Authors:
Mark D Walsh

Aesthet Surg J 2020 Aug 14. Epub 2020 Aug 14.

Dr Walsh is an Assistant Professor of Surgery and Associate Program Director, Division of Plastic and Reconstructive Surgery, Department of Surgery, Emory University School of Medicine, Atlanta, GA.

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http://dx.doi.org/10.1093/asj/sjaa205DOI Listing
August 2020

Nicotinamide Nucleotide Transhydrogenase as a Novel Treatment Target in Adrenocortical Carcinoma.

Endocrinology 2018 08;159(8):2836-2849

Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom.

Adrenocortical carcinoma (ACC) is an aggressive malignancy with poor response to chemotherapy. In this study, we evaluated a potential new treatment target for ACC, focusing on the mitochondrial reduced form of NAD phosphate (NADPH) generator nicotinamide nucleotide transhydrogenase (NNT). NNT has a central role within mitochondrial antioxidant pathways, protecting cells from oxidative stress. Inactivating human NNT mutations result in congenital adrenal insufficiency. We hypothesized that NNT silencing in ACC cells will induce toxic levels of oxidative stress. To explore this, we transiently knocked down NNT in NCI-H295R ACC cells. As predicted, this manipulation increased intracellular levels of oxidative stress; this resulted in a pronounced suppression of cell proliferation and higher apoptotic rates, as well as sensitization of cells to chemically induced oxidative stress. Steroidogenesis was paradoxically stimulated by NNT loss, as demonstrated by mass spectrometry-based steroid profiling. Next, we generated a stable NNT knockdown model in the same cell line to investigate the longer lasting effects of NNT silencing. After long-term culture, cells adapted metabolically to chronic NNT knockdown, restoring their redox balance and resilience to oxidative stress, although their proliferation remained suppressed. This was associated with higher rates of oxygen consumption. The molecular pathways underpinning these responses were explored in detail by RNA sequencing and nontargeted metabolome analysis, revealing major alterations in nucleotide synthesis, protein folding, and polyamine metabolism. This study provides preclinical evidence of the therapeutic merit of antioxidant targeting in ACC as well as illuminating the long-term adaptive response of cells to oxidative stress.
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http://dx.doi.org/10.1210/en.2018-00014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6093335PMC
August 2018

Promoting Limb Salvage through Multi-Disciplinary Care of the Diabetic Patient.

Curr Treat Options Cardiovasc Med 2017 Jul;19(7):55

Division of Vascular Surgery, Atlanta VA Medical Center, Surgery and Research Services, Emory University, 101 Woodruff Circle Suite 5105, Atlanta, GA, 30322, USA.

Opinion Statement: Despite an explosion in the number of options available for helping diabetic patients heal wounds, major amputation remains a critical issue for these persons. Since diabetes prematurely ages tissues and no organ system is immune to its presence, it makes inherent sense that multi-disciplinary team approaches to these patients is necessary to make significant strides forward. Here, we present literature from the fields of podiatric surgery/medicine, vascular and plastic surgery and introduce the successes that a multi-disciplinary limb salvage center can have on the lives and limbs of patients with diabetes.
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http://dx.doi.org/10.1007/s11936-017-0547-1DOI Listing
July 2017

Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways.

Cell Syst 2016 11 10;3(5):467-479.e12. Epub 2016 Nov 10.

School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK. Electronic address:

Experimental procedures for preparing RNA-seq and single-cell (sc) RNA-seq libraries are based on assumptions regarding their underlying enzymatic reactions. Here, we show that the fairness of these assumptions varies within libraries: coverage by sequencing reads along and between transcripts exhibits characteristic, protocol-dependent biases. To understand the mechanistic basis of this bias, we present an integrated modeling framework that infers the relationship between enzyme reactions during library preparation and the characteristic coverage patterns observed for different protocols. Analysis of new and existing (sc)RNA-seq data from six different library preparation protocols reveals that polymerase processivity is the mechanistic origin of coverage biases. We apply our framework to demonstrate that lowering incubation temperature increases processivity, yield, and (sc)RNA-seq sensitivity in all protocols. We also provide correction factors based on our model for increasing accuracy of transcript quantification in existing samples prepared at standard temperatures. In total, our findings improve our ability to accurately reflect in vivo transcript abundances in (sc)RNA-seq libraries.
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http://dx.doi.org/10.1016/j.cels.2016.10.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167349PMC
November 2016

Scrotal abscess as initial presentation of squamous cell carcinoma.

Case Rep Urol 2013 11;2013:807346. Epub 2013 Sep 11.

Department of Urology, Atlanta VA Medical Center and Emory University School of Medicine, 1365 Clifton Road, Atlanta, GA 30322, USA.

We report a case of scrotal squamous cell carcinoma in a 67-year-old man that presented as a recurrent nonhealing scrotal abscess. Radical scrotectomy and bilateral simple orchiectomy were performed. A pudendal thigh flap was used for wound closure. To our knowledge, this is the first report of its use after radical surgery for scrotal cancer. The clinical features, staging, and treatment of scrotal squamous cell carcinoma are reviewed. In this report, we highlight the importance of including scrotal cancer in the differential diagnosis when evaluating a scrotal abscess.
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http://dx.doi.org/10.1155/2013/807346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3786534PMC
October 2013

Meta-analysis of inter-patient pharmacokinetic variability of liposomal and non-liposomal anticancer agents.

Nanomedicine 2014 Jan 24;10(1):109-17. Epub 2013 Jul 24.

Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina (UNC) Eshelman School of Pharmacy, Chapel Hill, NC, USA; Translational Oncology and Nanoparticle Drug Development Initiative (TOND(2)I) Lab, UNC, Chapel Hill, NC, USA; Molecular Therapeutics, UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA; UNC GLP Bioanalytical Facility, Chapel Hill, NC, USA; Institute for Pharmacogenomics and Individualized Therapy (IPIT), Chapel Hill, NC, USA; Carolina Center of Cancer Nanotechnology Excellence (C-CCNE), Chapel Hill, NC, USA; North Carolina Biomedical Innovation Network (NC BIN), Chapel Hill, NC, USA. Electronic address:

Unlabelled: A meta-analysis was conducted to evaluate the inter-patient pharmacokinetic (PK) variability of liposomal and small molecule (SM) anticancer agents. Inter-patient PK variability of 9 liposomal and SM formulations of the same drug was evaluated. PK variability was measured as coefficient of variance (CV%) of area under the plasma concentration versus time curve (AUC) and the fold-difference between AUCmax and AUCmin (AUC range). CV% of AUC and AUC ranges were 2.7-fold (P<0.001) and 16.7-fold (P=0.13) greater, respectively, for liposomal compared with SM drugs. There was an inverse linear relationship between the clearance (CL) of liposomal agents and PK variability with a lower CL associated with greater PK variability (R(2)=0.39). PK variability of liposomal agents was greater when evaluated from 0-336 h compared with 0-24h. PK variability of liposomes is significantly greater than SM. The factors associated with the PK variability of liposomal agents need to be evaluated.

From The Clinical Editor: In this meta-analysis, the inter-patient pharmacokinetic variability of 9 liposomal and small molecule anti-cancer agents was studied. The authors determined that several parameters are in favor of the liposomal formulation; however, the PK variability of the formulation was higher compared with small molecule agents, the reason for which remains to be determined in future studies.
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http://dx.doi.org/10.1016/j.nano.2013.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3877184PMC
January 2014

Plasma, tumor and tissue pharmacokinetics of Docetaxel delivered via nanoparticles of different sizes and shapes in mice bearing SKOV-3 human ovarian carcinoma xenograft.

Nanomedicine 2013 Jul 6;9(5):686-93. Epub 2012 Dec 6.

Department of Pharmaceutical Sciences, University of North Carolina, Chapel Hill, NC 27599, USA.

Unlabelled: The particle fabrication technique PRINT® was used to fabricate monodisperse size and shape specific poly(lactide-co-glycolide) particles loaded with the chemotherapeutic Docetaxel. The pharmacokinetics of two cylindrical shaped particles with diameter=80nm; height=320nm (PRINT-Doc-80×320) and d=200nm; h=200nm (PRINT-Doc-200×200) were compared to Docetaxel in mice bearing human ovarian carcinoma SKOV-3 flank xenografts. The Docetaxel plasma exposure was ~20-fold higher for both particles compared to docetaxel. Additionally, the volume of distribution (Vd) of Docetaxel in PRINT formulations was ~18-fold (PRINT-Doc-80×320) and ~33-fold (PRINT-Doc-200×200) lower than Docetaxel. The prolonged duration of Docetaxel in plasma when dosed with PRINT formulations subsequently led to increased tumor exposure of Docetaxel from 0 to 168h (~53% higher for PRINT-Doc-80×320 and ~76% higher for PRINT-Doc-200×200 particles). PRINT-Doc-80×320 had lower exposures in the liver, spleen and lung compared with PRINT-Doc-200×200. Thus, the use of particles with smaller feature size may be preferred to decrease clearance by organs of the mononuclear phagocyte system.

From The Clinical Editor: In this study, the plasma, tumor, and tissue pharmacokinetics of different Docetaxel nanoparticles of precise shape and size were characterized in mice with human ovarian carcinoma xenograft. It is concluded that the use of particles with smaller feature size may be preferred to decrease clearance by organs of the mononuclear phagocyte system.
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http://dx.doi.org/10.1016/j.nano.2012.11.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706026PMC
July 2013

Pharmacokinetics and antitumor efficacy of XMT-1001, a novel, polymeric topoisomerase I inhibitor, in mice bearing HT-29 human colon carcinoma xenografts.

Clin Cancer Res 2012 May 5;18(9):2591-602. Epub 2012 Mar 5.

Division of Pharmacotherapy & Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA.

Purpose: To evaluate the pharmacokinetics and tissue disposition of macromolecular camptothecin (CPT) drug conjugate, XMT-1001, and irinotecan (CPT-11) in mice bearing HT-29 xenograft tumors.

Experimental Design: The antitumor efficacy of XMT-1001 was evaluated in the mouse HT-29 human colon carcinoma xenograft model. XMT-1001 was administered intravenously to female athymic nude (nu/nu) mice bearing established HT-29 xenograft tumors (n = 10) at 15, 30, and 60 mg CPT equivalents/kg on weekly or biweekly schedules. The tumor growth inhibition and tumor growth delay endpoints were used for efficacy evaluation. In the pharmacokinetic study, XMT-1001 was administered intravenously at a pharmacologically relevant dose of 60 mg CPT equivalents/kg × 1 via tail vein or an equimolar dose of CPT-11 at 100 mg/kg i.p. × 1. Mice (n = 3 per time point) were euthanized from 0.083 to 336 hours after XMT-1001 administration and from 0.083 to 24 hours after CPT-11. Plasma, tumor, and tissues were collected from all animals. A liquid chromatography-tandem mass spectrometry assay was used to measure XMT-1001, conjugate release products, CPT-20-O-(N-succinimido-glycinate; CPT-SI) and CPT-20-O-(N-succinamidoyl-glycinate; CPT-SA), and CPT.

Results: After XMT-1001 administration, the majority of the plasma exposure is accounted for by conjugated CPT. XMT-1001 exhibited a prolonged exposure of conjugated drug, active conjugate primary release products, CPT-SI and CPT-SA, and active CPT, which was associated with greater antitumor response compared with CPT-11.

Conclusions: XMT-1001 provides an extended systemic and tumor exposure of conjugated drug and shows improved antitumor effect compared with CPT-11.
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http://dx.doi.org/10.1158/1078-0432.CCR-11-1554DOI Listing
May 2012

Complex abdominal wall hernias: a new classification system and approach to management based on review of 133 consecutive patients.

Ann Plast Surg 2011 May;66(5):497-503

Division of Plastic, Reconstructive, Maxillofacial and Oral Surgery, Duke University Medical Center, Durham, NC, USA.

Background: Plastic surgeons are increasingly involved in the repair of complex ventral hernias. Although this typically involves recurrent incisional hernias, operative strategies can be applied to most abdominal wall defects, including chronic wounds with or without exposed mesh, enterocutaneous fistulas, or hernias associated with significant pannus formation.

Methods: This is a retrospective review of a single institution/single surgeon experience of complex ventral hernia repair performed over a 5-year period. Patients were classified into different hernia types based on their characteristics and underwent hernia repair according to the presented algorithm.

Results: A total of 133 patients underwent a complex ventral hernia repair between January 2005 and September 2009. The separation of components technique was used in the majority of cases. Permanent or biologic mesh was added in select patients. Adjunctive procedures were performed as indicated. The majority of short-term (less than 1 year) recurrences occurred in patients expected to have impaired wound healing due to comorbid conditions. In these patients, the recurrence rate was reduced when autologous repair was reinforced with mesh.

Conclusion: Autologous tissue is the preferred method for reconstruction of complex ventral hernias. In certain instances, such as contamination, use of an acellular dermal matrix mesh is added as a temporizing measure. A subset of patients who will be prone to recurrence remains. Long-term follow-up is needed to confirm reliable and reproducible results.
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http://dx.doi.org/10.1097/SAP.0b013e3182145387DOI Listing
May 2011

The role of intrathoracic free flaps for chronic empyema.

Ann Thorac Surg 2011 Mar;91(3):865-8

Division of Plastic and Reconstructive Surgery, Emory University, Atlanta, Georgia 30308, USA.

Background: The management of chronic empyema associated with a bronchopleural fistula can be a particularly challenging problem. Successful eradication may not occur without interposition of healthy vascularized tissue. Pedicled muscle flaps for coverage on the thorax have been well described. However, secondary to trauma or previous surgical procedures, a pedicle flap may not be sufficiently sized or available. Free tissue transfer is an attractive option to provide the appropriate vascularized tissue.

Methods: Six patients with chronic empyema-bronchopleural fistulae were reconstructed with 4 rectus abdominis myocutaneous and 2 gracilis muscle flaps. The choice of recipient vessels was dictated by existing local anatomy but included intercostal, thoracodorsal, thoracoacromial, azygous, and circumflex humeral vessels. One flap required interposition saphenous vein grafts for both artery and vein.

Results: Patient follow-up ranged from 2 to 14 years. There were no episodes of flap loss or postoperative mortality. Empyema resolution without recurrent bronchopleural fistula was achieved in all patients.

Conclusions: Free tissue transfer is an excellent option for vascularized tissue interposition in patients who are not candidates for pedicled muscle transfer. Multiple potential recipient vessels provide tremendous versatility, arguing for early consideration of free tissue transfer.
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http://dx.doi.org/10.1016/j.athoracsur.2010.10.019DOI Listing
March 2011

Exportin 1 inhibition attenuates nuclear factor-kappaB-dependent gene expression.

Shock 2008 Feb;29(2):160-6

Department of Surgery, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA.

Activation of nuclear factor (NF)-kappaB is mediated by signal-induced phosphorylation of IkappaBalpha, subsequent IkappaBalpha degradation, and then translocation of unbound NF-kappaB to the nucleus. Termination of gene expression occurs when IkappaBalpha binds NF-kappaB subunits (Rel A) in the nucleus. Leptomycin B specifically inhibits export of IkappaBalpha and the inactive IkappaBalpha/Rel A complex via the nuclear export protein exportin 1. We hypothesized that inhibition of IkappaBalpha nuclear export would increase nuclear IkappaBalpha and attenuate NF-kappaB inflammatory gene expression in pulmonary microvascular endothelial cells. We found that inhibition of exportin 1 causes nuclear accumulation of both endogenous NF-kappaB (Rel A) and IkappaBalpha. IL-1beta causes nuclear accumulation of NF-kappaB (Rel A) but does not increase nuclear IkappaBalpha. Inhibition of exportin 1 before IL-1beta prevented an increase in the nuclear ratio of NF-kappaB (Rel A) to IkappaBalpha and decreases NF-kappaB DNA binding. Furthermore, inhibition of exportin 1 attenuates IL-1beta-induced phosphorylation of IkappaBalpha without affecting IkappaB kinase phosphorylation. Lastly, inhibition of exportin 1 attenuates monocyte chemoattractant protein, IL-8, and intercellular adhesion molecule expression in response to IL-1beta stimulation. We suggest that the decrease in cell activation due to exportin 1 inhibition is a result of termination of NF-kappaB DNA binding due to increased concentration of IkappaBalpha in the nucleus.
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http://dx.doi.org/10.1097/shk.0b013e3180ca9deeDOI Listing
February 2008

Dendritic cells as therapeutic adjuncts in surgical disease.

Surgery 2005 Nov;138(5):844-50

Department of Surgery, University of Colorado Health Sciences Center, Denver, CO 80262, USA.

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http://dx.doi.org/10.1016/j.surg.2005.02.003DOI Listing
November 2005

Polymerized hemoglobin induces heme oxygenase-1 protein expression and inhibits intercellular adhesion molecule-1 protein expression in human lung microvascular endothelial cells.

J Am Coll Surg 2005 Oct;201(4):579-84

Department of Surgery, University of Colorado Health Sciences Center/Denver Health Medical Center, 80204, USA.

Background: Our clinical trials using a polymerized hemoglobin solution (PolyHb) as a red cell substitute in severely injured patients suggested that this hemoglobin-based oxygen carrier has a systemic antiinflammatory effect. Heme oxygenase-1 (HO-1) has recently been shown to be cytoprotective, and is known to be induced by heme moieties. We investigated the effects of this hemoglobin-based oxygen carrier on HO-1 induction and proinflammatory activation of pulmonary endothelium.

Study Design: Human lung microvascular endothelial cells were grown to confluence and preincubated with either cell media (control) or with an equal volume mixture of polymerized hemoglobin/cell media (experimental). The cell cultures were subsequently stimulated with lipopolysaccharide. HO-1 expression was detected by protein immunoblot and further quantified by ELISA; intercellular adhesion molecule-1 protein expression was measured by flow cytometry.

Results: Polymerized hemoglobin induced synthesis of HO-1 protein in human lung microvascular endothelial cells and, concurrently, inhibited lipopolysaccharide-induced intercellular adhesion molecule-1 protein cell surface expression.

Conclusions: Polymerized hemoglobin attenuates lipopolysaccharide-stimulated expression of intercellular adhesion molecule-1 protein, which is associated with upregulation of the cytoprotective protein HO-1 in human pulmonary endothelial cells. This antiinflammatory effect offers a novel mechanism by which hemoglobin-based oxygen carrier solutions may be exploited therapeutically as resuscitative fluids.
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http://dx.doi.org/10.1016/j.jamcollsurg.2005.05.011DOI Listing
October 2005

Melanoma inhibits macrophage activation by suppressing toll-like receptor 4 signaling.

J Am Coll Surg 2005 Sep;201(3):418-25

Department of Surgery, University of Colorado Health Sciences Center, Denver, CO, USA.

Background: Activated macrophages defend against tumors by secreting cytokines to recruit secondary immune cells, presenting antigen to T cells, and by direct tumor cytotoxicity. Peritoneal macrophages harvested from melanoma-bearing mice are less cytotoxic to melanoma cells, and produce less superoxide, nitric oxide, and tumor necrosis factor-alpha (TNF-alpha) than those from nontumor-bearing mice. Similar impairment of macrophage activation occurs in vitro using media harvested from cultured melanoma cells. Stimulation of Toll-like receptor 4 (TLR-4) activates macrophages and results in the release of TNF-alpha. We hypothesized that melanoma inhibits macrophage activation by suppressing TLR-4 signaling.

Study Design: Melanoma conditioned media (MCM) was generated from B16 melanoma cells. Peritoneal macrophages from TLR-4 competent or TLR-4 incompetent mice were exposed to control or MCM for 24 hours; then stimulated with lipopolysaccharide. TNF-alpha secretion, TNF-alpha mRNA production, nuclear factor-kappaB (NF-kappaB) activation, and TLR-4 surface expression were measured.

Results: Peritoneal macrophages exposed to MCM produced considerably less TNF-alpha in response to stimulus than controls (691 pg/mL versus 2,066 pg/mL, p < 0.001). TNF-alpha production by TLR-4 incompetent macrophages was not affected by MCM (454 pg/mL versus 480 pg/mL). Stimulated TNF-alpha mRNA and activated NF-kappaB were decreased in MCM treated C57BL/6 macrophages (by 38% and 33%, respectively). TLR-4 surface expression, however, was not decreased by exposure to MCM.

Conclusions: Melanoma inhibits macrophage activation by suppressing TLR-4 signaling downstream of the TLR-4 receptor.
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http://dx.doi.org/10.1016/j.jamcollsurg.2005.04.035DOI Listing
September 2005

Destructive maxillomandibular brown tumor in severe hyperparathyroidism.

J Am Coll Surg 2005 Aug;201(2):315

University of Colorado Health Sciences Center, Denver, CO, USA.

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http://dx.doi.org/10.1016/j.jamcollsurg.2005.01.027DOI Listing
August 2005