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Contributions of Surgical Critical Care Program Directors Society to the training of surgeons. J Trauma Acute Care Surg 2023; 94:e29-e32. [PMID: 36577131 DOI: 10.1097/ta.0000000000003863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND In 1986, Surgical Critical Care (SCC) was formally recognized as a specialty by the American Board of Surgery (ABS), however it took another two decades to develop a formal national training structure in SCC. In 2003, the program directors of SCC fellowships began to meet and the Surgical Critical Care Program Directors Society (SCCPDS) was officially formed in 2004, with recognition of the SCCPDS as a non-profit organization in 2008. Over the next several years, and in conjunction with other interested groups, such as the American Association for the Surgery of Trauma (AAST) and the Society of Critical Care Medicine (SCCM), SCCPDS created a formal curriculum, developed a unified system for the fellowship application process, and increased recruitment and match such that now approximately 1 in 6 general surgery graduates are pursuing training in SCC. In discussion with past and present leadership of SCCPDS, there are several ongoing initiatives to further improve the educational opportunities of the fellows and increase inclusion of other organizations and other specialties interested in SCC. The purpose of this article is to discuss the role of SCCPDS in the development and evolution of SCC and Acute Care Surgery (ACS) training. LEVEL OF EVIDENCE Expert Opinion; Level V.
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Gestalt clinical severity score (GCSS) as a predictor of patient severity of illness or injury. Am J Emerg Med 2023; 66:11-15. [PMID: 36640694 DOI: 10.1016/j.ajem.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/26/2022] [Accepted: 01/02/2023] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVE To determine if clinical judgement is accurate to predict the severity of injury or illness, and can be used at patient arrival when other formal scoring systems are not yet available. DESIGN A multicenter pilot study using a prospective observational convenience sample of patients arriving by EMS to the emergency department (ED) or Trauma Center. SETTING Two urban, Level 1 trauma centers at academic tertiary care hospitals. PATIENTS Medical and trauma patients age 18 and older transported by EMS (N = 216). Exclusion criteria (prior to arrival): intubation, assisted ventilation (BVM or NPPV), CPR in progress, prisoners, or previously present motor or speech deficits. MEASUREMENTS Completion of a novel 15-point scale of Verbal, Motor, and Facial Expression within 1-2 min of arrival by a clinician outside of the treatment team. Primary endpoint was the immediate disposition from the ED or Trauma Center: Home, Brief Observation (<24 h), Admission to Floor, ICU (OR and IR as surrogates since these patients ultimately go to the ICU), or Morgue. RESULTS Univariate analysis revealed a strong, positive monotonic correlation between GCSS and disposition (Rho = 0.693, p < .0001). Multivariable logistic regression revealed the "best" model included GCSS and age (group 18-44 years old versus all the other age groups) (p < .0001). There was a 156% increase in the odds of being discharged home (versus being admitted) for a one-unit increase in GCSS (OR = 2.56, 95% CI 1.94, 3.37). CONCLUSIONS Physicians can make accurate predictions of severity of injury and illness using a gestalt method and the scoring system we have developed as patient disposition correlates well with GCSS score. GCSS is most accurate with the 18-44 age group.
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Endothelial cell-leukemia interactions remodel drug responses, uncovering T-ALL vulnerabilities. Blood 2023; 141:503-518. [PMID: 35981563 PMCID: PMC10082359 DOI: 10.1182/blood.2022015414] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/07/2022] [Accepted: 07/24/2022] [Indexed: 02/07/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive and often incurable disease. To uncover therapeutic vulnerabilities, we first developed T-ALL patient-derived tumor xenografts (PDXs) and exposed PDX cells to a library of 433 clinical-stage compounds in vitro. We identified 39 broadly active drugs with antileukemia activity. Because endothelial cells (ECs) can alter drug responses in T-ALL, we developed an EC/T-ALL coculture system. We found that ECs provide protumorigenic signals and mitigate drug responses in T-ALL PDXs. Whereas ECs broadly rescued several compounds in most models, for some drugs the rescue was restricted to individual PDXs, suggesting unique crosstalk interactions and/or intrinsic tumor features. Mechanistically, cocultured T-ALL cells and ECs underwent bidirectional transcriptomic changes at the single-cell level, highlighting distinct "education signatures." These changes were linked to bidirectional regulation of multiple pathways in T-ALL cells as well as in ECs. Remarkably, in vitro EC-educated T-ALL cells transcriptionally mirrored ex vivo splenic T-ALL at single-cell resolution. Last, 5 effective drugs from the 2 drug screenings were tested in vivo and shown to effectively delay tumor growth and dissemination thus prolonging overall survival. In sum, we developed a T-ALL/EC platform that elucidated leukemia-microenvironment interactions and identified effective compounds and therapeutic vulnerabilities.
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Vaccination after spleen embolization: A practice management guideline from the Eastern Association for the Surgery of Trauma. Injury 2022; 53:3569-3574. [PMID: 36038390 DOI: 10.1016/j.injury.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 02/02/2023]
Abstract
BACKGROUND Angioembolization is an important adjunct in the non-operative management of adult trauma patients with splenic injury. Multiple studies have shown that angioembolization may increase the non-operative splenic salvage rate for patients with high-grade splenic injuries. We performed a systematic review and developed evidence-based recommendations regarding the need for post-splenectomy vaccinations after splenic embolization in trauma patients. METHODS A systematic review and meta-analysis of currently available evidence were performed utilizing the Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology. RESULTS Nine studies were identified and analyzed. A total of 240 embolization patients were compared to 443 control patients who neither underwent splenectomy nor were embolized. There was no statistical difference between the splenic immune function of embolized and control patients. In addition, a total of 3974 splenectomy patients was compared with 686 embolization patients. Embolization patients had fewer infectious complications and a greater degree of preserved splenic immune function. CONCLUSION In adult trauma patients who have undergone splenic angioembolization, we conditionally recommend against routine post-splenectomy vaccinations. STUDY TYPE systematic review/meta-analysis Level of evidence: level III.
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CEC05-02 Rodent models for studies of genetic diversity and case studies of their use in toxicology. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Survey of surgical critical care applicant and program director views on virtual interviews for fellowship training: a Surgical Critical Care Program Directors Society sponsored study. Trauma Surg Acute Care Open 2022; 7:e000898. [PMID: 35415269 PMCID: PMC8961168 DOI: 10.1136/tsaco-2022-000898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/10/2022] [Indexed: 11/28/2022] Open
Abstract
Background The COVID-19 pandemic forced postgraduate interview processes to move to a virtual platform. There are no studies on the opinions of faculty and applicants regarding this format. The aim of this study was to assess the opinions of surgical critical care (SCC) applicants and program directors regarding the virtual versus in-person interview process. Methods An anonymous survey of the SCC Program Director’s Society members and applicants to the 2019 (in-person) and 2020 (virtual) interview cycles was done. Demographic data and Likert scale based responses were collected using Research Electronic Data Capture. Results Fellowship and program director responses rates were 25% (137/550) and 58% (83/143), respectively. Applicants in the 2020 application cycle attended more interviews. The majority of applicants (57%) and program faculty (67%) strongly liked/liked the virtual interview format but felt an in-person format allows better assessment of the curriculum and culture of the program. Both groups felt that an in-person format allows applicants and faculty to establish rapport better. Only 9% and 16% of SCC program directors wanted a purely virtual or purely in-person interview process, respectively. Applicants were nearly evenly split between preferring a purely in-person versus virtual interviews in the future. Discussion The virtual interview format allows applicants and program directors to screen a larger number of programs and applications. However, the virtual format is less useful than an in-person interview format for describing unique aspects of a training program and for allowing faculty and applicants to establish rapport. Future strategies using both formats may be optimal, but such an approach requires further study. Level of evidence Epidemiologic level IV
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Baseline data for distribution of contaminants by natural disasters: results from a residential Houston neighborhood during Hurricane Harvey flooding. Heliyon 2019; 5:e02860. [PMID: 31763489 PMCID: PMC6861583 DOI: 10.1016/j.heliyon.2019.e02860] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/05/2019] [Accepted: 11/13/2019] [Indexed: 11/24/2022] Open
Abstract
Hurricane Harvey made landfall in Texas August 25, 2017, bringing massive rains and flooding that impacted soils in a residential neighborhood in East Houston. Trace elements, organochlorine pesticides, polycyclic aromatic hydrocarbons (PAHs), polybrominated diphenyl ether fire retardants (PBDEs) and polychlorinated biphenyls (PCBs) were determined in 24 soil samples. The highest concentrations found in soils were total PAHs, which ranged from 1,310 μg/kg to 85,700 μg/kg with a mean of 12,600 μg/kg. Analysis of specific PAH ratios indicate the source of the PAHs were dominated by pyrogenic rather than petrogenic sources. Chlordanes were detectable in the area where the likely local source is for ant control. The trace metal concentrations were below any environmental health concern concentrations but As, Cd, Hg, Pb, Se, Ag, Zn were enriched over the crustal abundance. While Hurricane Harvey was responsible for the redistribution of many contaminants, the large volume of rain and floodwater likely transported contaminants from the land areas and into the Houston Ship Channel and Galveston Bay. The findings from this study will serve as baseline data for determining the mobilization of contaminants caused by natural disasters.
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A comparison of segmented abdominopelvic fluid volumes with conventional CT signs of abdominal compartment syndrome in a trauma population. Abdom Radiol (NY) 2019; 44:2648-2655. [PMID: 30953097 DOI: 10.1007/s00261-019-02000-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE To compare the utility of abdominopelvic fluid volume measurements with established computed tomography signs for refractory post-traumatic abdominal compartment syndrome. METHODS This retrospective observational cohort study included 64 consecutive adult trauma patients with preoperative CT and diagnosis of refractory abdominal compartment syndrome requiring decompressive laparotomy at a level I trauma referral center between 2004 and 2014. We hypothesized that abdominal fluid volume measurements would be more predictive of the need for early laparotomy than previously described conventional CT signs of refractory ACS. Abdominopelvic fluid volumes were determined quantitatively using semi-automated segmentation software. The following conventional imaging parameters were recorded: abdominal anteroposterior:transverse ratio (round belly sign); infrahepatic vena cava diameter; distal abdominal aortic diameter; largest single small bowel wall diameter; hydronephrosis, inguinal herniation; and mesenteric and body wall edema. For outcome analysis, patients were stratified into two groups: those who underwent early (< 24 h) and late (≥ 24 h) decompressive laparotomy following CT. Correlation analysis, comparison of means, and multivariate logistic regression were performed. RESULTS Abdominal fluid volumes (p = 0.001) and anteroposterior:transverse ratio (p = 0.009) were increased and inferior vena cava diameter (p = 0.009) was decreased in the early decompressive laparotomy group. Multivariate analysis including conventional CT variables, fluid volumes, and laboratory values revealed abdominal fluid volumes (p = 0.012; Δ in log odds of 1.002/mL) as the only independent predictor of early decompressive laparotomy. CONCLUSIONS Segmented abdominopelvic free fluid volumes had greater predictive utility for decision to perform early decompressive laparotomy than previously described ACS-related CT signs in trauma patients who developed refractory abdominal compartment syndrome.
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Abstract
Present literature seems to support the nonoperative management of penetrating renal trauma although data remain limited. We conducted a nine-year retrospective review of nonoperative versus operative management and mechanism of injury [stab wound (SW) versus gunshot wound (GSW)] among patients admitted with penetrating renal trauma. Of 203 patients, the median age was 24 years, with the majority being male and having GSW injuries. More than half (52.2%) were treated nonoperatively (69.9% of SW and 40% of GSW injured patients). When compared with all operative patients combined, nonoperative patients had a lower median Injury Severity Score (17 vs 26, P < 0.001), lower transfusion requirement (27.4% vs 77.3%, P < 0.001), shorter median hospital stay (4.7 vs 12.6 days, P < 0.001), and lower mortality (1.9% vs 13.4%, P = 0.002). Gunshot wound patients had a higher median Injury Severity Score (26 vs 14, P < 0.001), higher median American Association for the Surgery of Trauma-Organ Injury Score (3 vs 2, P = 0.001), greater need for transfusion (69.2% vs 29.3%, P < 0.001), longer median hospital length of stay (12.1 vs 3.9 days, P < 0.001), and greater mortality (12.5% vs 0%, P < 0.001) than SW patients. Nonoperative management of penetrating renal injury is safe in selected patients. In addition, renal GSW injuries are associated with a greater morbidity and mortality.
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Penetrating Renal Trauma: Nonoperative Management Is Safe in Selected Patients. Am Surg 2019; 85:266-272. [PMID: 30947772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Present literature seems to support the nonoperative management of penetrating renal trauma although data remain limited. We conducted a nine-year retrospective review of nonoperative versus operative management and mechanism of injury [stab wound (SW) versus gunshot wound (GSW)] among patients admitted with penetrating renal trauma. Of 203 patients, the median age was 24 years, with the majority being male and having GSW injuries. More than half (52.2%) were treated nonoperatively (69.9% of SW and 40% of GSW injured patients). When compared with all operative patients combined, nonoperative patients had a lower median Injury Severity Score (17 vs 26, P < 0.001), lower transfusion requirement (27.4% vs 77.3%, P < 0.001), shorter median hospital stay (4.7 vs 12.6 days, P < 0.001), and lower mortality (1.9% vs 13.4%, P = 0.002). Gunshot wound patients had a higher median Injury Severity Score (26 vs 14, P < 0.001), higher median American Association for the Surgery of Trauma-Organ Injury Score (3 vs 2, P = 0.001), greater need for transfusion (69.2% vs 29.3%, P < 0.001), longer median hospital length of stay (12.1 vs 3.9 days, P < 0.001), and greater mortality (12.5% vs 0%, P < 0.001) than SW patients. Nonoperative management of penetrating renal injury is safe in selected patients. In addition, renal GSW injuries are associated with a greater morbidity and mortality.
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Using Adherence Agreements in Heart Transplant Candidates: What's Important? J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Therapeutic drug monitoring of isoniazid and rifampicin during anti-tuberculosis treatment in Auckland, New Zealand. Int J Tuberc Lung Dis 2018; 20:955-60. [PMID: 27287650 DOI: 10.5588/ijtld.15.0792] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SETTING There is uncertainty as to the optimal therapeutic concentrations of anti-tuberculosis drugs to achieve cure. OBJECTIVE To characterise the use of therapeutic drug monitoring (TDM), and identify risk factors and outcomes for those with concentrations below the drug interval. DESIGN Patients treated for tuberculosis (TB) who had rifampicin (RMP) or isoniazid (INH) concentrations measured between 1 January 2005 and 31 December 2012 were studied retrospectively. Matched concentrations and drug dosing time were assessed according to contemporary regional drug intervals (RMP > 6 μmol/l, INH > 7.5 μmol/l) and current international recommendations (RMP > 10 μmol/l, INH > 22 μmol/l). Outcomes were assessed using World Health Organization criteria. RESULTS Of 865 patients, 121 had concentrations of either or both medications. RMP concentrations were within the regional drug intervals in 106/114 (93%) and INH in 91/100 (91%). Concentrations were within international drug intervals for RMP in 76/114 (67%) and INH in 53/100 (53%). Low weight-based dose was the only statistically significant risk factor for concentrations below the drug interval. Of the 35 patients with low concentrations, 21 were cured, 9 completed treatment and 5 transferred out. There were no relapses during follow-up (mean 66.5 months). CONCLUSION There were no clinically useful characteristics to guide use of TDM. Many patients had concentrations below international therapeutic intervals, but were successfully treated.
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Definitive Wound Closure Techniques in Fournier's Gangrene. Am Surg 2018; 84:86-92. [PMID: 29428033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Necrotizing soft tissue infection of the perineum, or Fournier's gangrene (FG), is a morbid and mortal diagnosis. Despite the severity of FG, the optimal definitive wound closure strategy is unknown, as are long-term wound outcomes. A retrospective review was performed over a 3-year period at a single trauma center. Patients were managed according to our institutional approach focusing on primary wound closure and secondary intention healing in residual wounds. Overall 168 patients were included. Complete primary wound closure was accomplished in 39.9 per cent of patients. Patients undergoing primary wound closure were primarily male (89.6 vs 64.4%, P < 0.001), had lower mean sequential organ failure assessment (SOFA) scores (1.70 ± 2.30 vs 2.98 ± 3.36, P = 0.004), more often had perineum-limited FG (67.2 vs 42.6%, P = 0.003), and required fewer debridements (2.40 vs 2.79, P = 0.02). On logistic regression, predictors of primary closure included gender (odds ratio 4.643, 95% confidence interval 1.885-11.437, P = 0.001) and SOFA score (odds ratio 0.834, 95% confidence interval 0.727-0.957, P = 0.01). Wound healing rates increased over time, to an 82.1 per cent wound healing rate without further intervention at greater than six months of follow-up. Wounds healed with secondary intention ranged from 70 to 9520 cm3 and primary closure ranged from 126 to 6912 cm3, whereas wounds requiring skin grafts ranged from 405 to 16,170 cm3. Complete primary wound closure is often achievable in FG patients. Using this standardized approach to FG wound management, even large wounds and wounds undergoing secondary intention healing will often close with long-term wound care and do not require flap creation or early skin grafting.
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LET'S AGREE TO AGREE: EVALUATION OF ADHERENCE AGREEMENTS IN PATIENTS BEING CONSIDERED FOR HEART TRANSPLANTATION. Can J Cardiol 2017. [DOI: 10.1016/j.cjca.2017.07.456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Abstract 2744: Inter-site comparison of performance of an ultra-sensitive sequencing technology for circulating tumor DNA. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The combination of liquid biopsies and ultra-sensitive next-generation sequencing (NGS) holds tremendous promise in oncology for the detection and surveillance of somatic mutations that correlate with diagnosis, prognosis, response prediction, resistance monitoring and tumor burden. We have developed a capture-based NGS workflow that provides ultra-sensitive detection of 4 mutation classes - single nucleotide variants (SNVs), insertions/deletions, copy number amplifications (CNAs) and fusions - from low input cell-free DNA isolated from plasma. Sensitivity and specificity of 2 different AVENIO ctDNA Analysis Kits (for Research Use Only) across 3 sites for 48 samples that included contrived DNA blends with known mutations validated by digital PCR and normal reference plasma samples were assessed. The AVENIO ctDNA Targeted Kit (Targeted) was designed to detect mutations in 17 genes, across 80kb, included in NCCN Guidelines for solid tumors plus additional variants relevant for therapy selection. The AVENIO ctDNA Expanded Kit (Expanded) was designed to detect mutations in 77 genes, across 200kb, associated with solid tumor including variants relevant for clinical trial research. Testing sites achieved 100% sensitivity for SNVs and fusions at 0.5% and 1% allelic frequency, respectively, from 30 ng of input DNA for both kits. Median coverage of 4,200-6,400X was greater with the Targeted kit relative to that of 2,700-3,800X with the Expanded kit. Specificity was 100% for the Targeted kit either by sample or variant. The Expanded kit had a specificity of 91.7-100% by sample and 99.7-100% by variant. At an expected 5X or 8X copy number amplification for multiple genes, both the Targeted and Expanded kits were 100% sensitive and 93.1-98.4% specific per gene. The specificity for fusion detection was 100% for both kits down to 1% mutant allele frequency. The AVENIO ctDNA Analysis Kits for plasma and NGS applications provide exquisite sensitivity and specificity for the simultaneous detection of 4 different mutation classes.
Citation Format: Stephanie Yaung, Alex Lovejoy, Dan Klass, Fergal Casey, Aruna Arcot, Melissa Loyzer, William Chiu, Nabil Azhar, Sophie Beckert, Maria Lange, Sandra Siemann, Sebastian Froehler, Shelly Gunn, John F. Palma. Inter-site comparison of performance of an ultra-sensitive sequencing technology for circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2744. doi:10.1158/1538-7445.AM2017-2744
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In reply 2. Int J Tuberc Lung Dis 2016; 20:1696-1697. [PMID: 27931349 DOI: 10.5588/ijtld.16.0550-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Empirical estimation of the incubation period for hand-foot-and-mouth disease from school outbreaks. Int J Infect Dis 2016. [DOI: 10.1016/j.ijid.2016.11.330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Abstract
Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data.
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Non-Adherence to Medical Advice Does Not Impact Survival in a Bridge to Transplant (BTT) Left Ventricular Assist Device (LVAD) Program. J Heart Lung Transplant 2016. [DOI: 10.1016/j.healun.2016.01.994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Deriving generic distributions from historical data for interspecies, intraspecies, and subchronic–chronic extrapolation, and how to deal with other uncertainties. Toxicol Lett 2015. [DOI: 10.1016/j.toxlet.2015.08.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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INTRA-PROVINCIAL COLLABORATION FOR VAD PATIENT CARE TRANSITIONS. Can J Cardiol 2014. [DOI: 10.1016/j.cjca.2014.07.703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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TRANSITION FROM BRIDGE TO TRANSPLANT TO DESTINATION THERAPY FOR VENTRICULAR ASSIST DEVICE PATIENTS. Can J Cardiol 2014. [DOI: 10.1016/j.cjca.2014.07.720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Plasma SPARC Following Stereotactic Body Radiation Therapy (SBRT) Predicts for Progression-Free Survival in Locally-Advanced Pancreatic Cancer. Int J Radiat Oncol Biol Phys 2013. [DOI: 10.1016/j.ijrobp.2013.06.1771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Who's on the Line: Describing the Utilization of the 24 hour VAD Hotline at St. Paul's Hospital. Can J Cardiol 2013. [DOI: 10.1016/j.cjca.2013.07.766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Quetiapine may reduce hospital admission rates in patients with mental health problems and alcohol addiction. CASE REPORTS 2013; 2013:bcr-2013-009817. [DOI: 10.1136/bcr-2013-009817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Erratum to: MDCT diagnosis of post-traumatic hepatic arterio-portal fistulas. Emerg Radiol 2013. [DOI: 10.1007/s10140-013-1105-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Extracellular Domain Mutations in EGFR Occur Uniquely in Glioblastoma and Favor Ligand-independent Formation of the Active State. Int J Radiat Oncol Biol Phys 2012. [DOI: 10.1016/j.ijrobp.2012.07.459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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NP014 The Many Faces of Cardiac Sarcoidosis. Can J Cardiol 2012. [DOI: 10.1016/j.cjca.2012.07.829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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131 N-linked Glycosylation Regulates the Function and Membrane Localization of KCC4. Eur J Cancer 2012. [DOI: 10.1016/s0959-8049(12)70831-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Sitosterolaemia: role of different pathology disciplines in its diagnosis and management. Pathology 2012. [DOI: 10.1016/s0031-3025(16)32820-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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1.16 Cryo-Electron Microscopy and Tomography of Virus Particles. COMPREHENSIVE BIOPHYSICS 2012. [PMCID: PMC7151817 DOI: 10.1016/b978-0-12-374920-8.00120-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Human infectious disease is classified into five etiologies: bacterial, viral, parasitic, fungal, and prion. Viral infections are unique in that they recruit human cellular machinery to replicate themselves and spread infection. The number of viruses causing human disease is vast, and viruses can be broadly categorized by their structures. Many viruses, such as influenza, appear to be amorphous particles, whereas others, such as herpes simplex virus, rhinovirus, dengue virus, and adenovirus, have roughly symmetric structural components. Icosahedral viruses have been a target of electron microscopists for years, and they were some of the first objects to be reconstructed three-dimensionally from electron micrographs. The ease with which highly purified and conformationally uniform virus samples can be produced makes them an ideal target structural studies. Apart from their biological significance, these virus samples have played a pivotal role in the development of new methodologies in the field of molecular biology as well as in cryo-electron microscopy and cryo-electron tomography.
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FoxH1 function in target gene selection and in transcriptional noise control. Dev Biol 2011. [DOI: 10.1016/j.ydbio.2011.05.519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Semi-isometric registration of line features for flexible fitting of protein structures. COMPUTER GRAPHICS FORUM : JOURNAL OF THE EUROPEAN ASSOCIATION FOR COMPUTER GRAPHICS 2010; 29:2243-2252. [PMID: 21124809 PMCID: PMC2993115 DOI: 10.1111/j.1467-8659.2010.01813.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this paper, we study a registration problem that is motivated by a practical biology problem - fitting protein structures to low-resolution density maps. We consider registration between two sets of lines features (e.g., helices in the proteins) that have undergone not a single, but multiple isometric transformations (e.g., hinge-motions). The problem is further complicated by the presence of symmetry in each set. We formulate the problem as a clique-finding problem in a product graph, and propose a heuristic solution that includes a fast clique-finding algorithm unique to the structure of this graph. When tested on a suite of real protein structures, the algorithm achieved high accuracy even for very large inputs containing hundreds of helices.
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Abstract
Abstract
Background: Pharmacogenomics is an emerging area for breast cancer research. Little is known about how well patients understand pharmacogenomics or the rationale for research in this area. The objective of this study was to analyze patient understanding of a clinical trial involving CYP2D6 genotyping to guide tamoxifen (T) therapy for breast cancer.Methods: We conducted a survey of understanding of pharmacogenomics and the purposes of a clinical trial among patients (pts) eligible for LCCC0801, a prospective Phase 2 study of CYP2D6 genotype-guided therapy for pts on tamoxifen for breast cancer. In this trial, we evaluated baseline endoxifen (E) levels and the impact of increased T dose to 40 mg/day among pts with any dysfunctional CYP2D6 alleles. The primary endpoint of change in E levels is not yet reported. All trial participants and those who declined participation were eligible for this survey. The research nurse administered 11 written questions at time of consent related to the purpose of this study and the nature of pharmacogenomic research. Pts had unlimited time to complete the survey written in a 5 point scale (strongly agree, agree, not sure, disagree, strongly disagree). For pts declining to enroll in the parent study, we offered an identical companion survey to which they could separately give consent.Results: Of 118 pts in the parent study, 117 completed the survey. Following informed consent, all respondents expressed confidence that they understood the purpose of the trial, 75% strongly agreed that they understood the purpose of the study. 98% of participants understood that this was a study of how different people respond to T, but 42% also incorrectly felt that this was a study of how different types of breast cancer respond to T, and 30% incorrectly felt that this study evaluated genetic risk for developing breast cancer. Though the consent form clearly stated that there may be no direct benefit to participants and that the purpose of the study was to help future pts, 68% reported that they would benefit directly, and only 22% felt the study was designed only to help future pts. When asked if the study involved genetics, 14% of pts disagreed, or were unsure. 45% of participants were uncomfortable or unsure with “having your doctor determine your T dose from the results of a genetic test.” Among a small sample of pts who declined trial participation but consented to the survey (13/30 decliners, 43%), compared to trial participants, fewer reported strong confidence in understanding the purpose of the trial (38% vs. 75%, p=0.0034), and a greater percentage identified an inaccurate purpose of the trial (69% vs. 42%, p = 0.043).Conclusions: After informed consent, a high percentage of participants in a pharmacogenomic clinical trial are able to correctly identify the primary purpose of the research, but a substantial minority hold false views about what the trial is designed to investigate. The majority of participants believe that they will directly benefit from trial participation, and few may understand that the primary purpose of the study is to improve care for future patients. Opportunities exist for improved understanding and communication of pharmacogenomic research and further evaluation of this area is needed.
Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6082.
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Estimating contrast transfer function and associated parameters by constrained non-linear optimization. J Microsc 2009; 233:391-403. [PMID: 19250460 DOI: 10.1111/j.1365-2818.2009.03137.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The three-dimensional reconstruction of macromolecules from two-dimensional single-particle electron images requires determination and correction of the contrast transfer function (CTF) and envelope function. A computational algorithm based on constrained non-linear optimization is developed to estimate the essential parameters in the CTF and envelope function model simultaneously and automatically. The application of this estimation method is demonstrated with focal series images of amorphous carbon film as well as images of ice-embedded icosahedral virus particles suspended across holes.
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Backbone structure of the infectious Epsilon15 virus capsid revealed by electron cryomicroscopy. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308098528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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A phenomenological study of the metal-oxide interface: the role of catalysis in hydrogen production from renewable resources. CHEMSUSCHEM 2008; 1:905-910. [PMID: 18988246 DOI: 10.1002/cssc.200800196] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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Automated characterization of gene expression patterns with an atlas of the mouse brain. CONFERENCE PROCEEDINGS : ... ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL CONFERENCE 2007; 2004:2917-20. [PMID: 17270888 DOI: 10.1109/iembs.2004.1403829] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A spatio-temporal map of gene activity in the brain would be an important contribution to the understanding of brain development, disease, and function. Such a resource is now possible using high-throughput in situ hybridization, a method for transcriptome-wide acquisition of cellular resolution gene expression patterns in serial tissue sections. However, querying an enormous quantity of image data requires computational methods for describing and organizing gene expression patterns in a consistent manner. In addressing this, we have developed procedures for automated annotation of gene expression patterns in the postnatal mouse brain.
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Structural biology of old world and new world alphaviruses. ARCHIVES OF VIROLOGY. SUPPLEMENTUM 2006:179-85. [PMID: 16358426 DOI: 10.1007/3-211-29981-5_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Structure of the acrosomal bundle, a biological machine, at 9.5 Å resolution. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305097138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Electron cryomicroscopy of epsilon 15 phage. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305080931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Structure of protein assemblies by comparative modeling and electron microscopy. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305099897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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A method for automated detection of gene expression required for the establishment of a digital transcriptome-wide gene expression atlas. J Microsc 2005; 217:275-81. [PMID: 15725131 DOI: 10.1111/j.1365-2818.2005.01450.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Acquiring information about the expression of a gene in different cell populations and tissues can provide key insight into the function of the gene. A high-throughput in situ hybridization (ISH) method was recently developed for rapid and reproducible acquisition of gene expression patterns in serial tissue sections at cellular resolution. Characterizing and analysing expression patterns on thousands of sections requires efficient methods for locating cells and estimating the level of expression in each cell. Such cellular quantification is an essential step in both annotating and quantitatively comparing high-throughput ISH results. Here we describe a novel automated and efficient methodology for performing this quantification on postnatal mouse brain.
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Abstract
We report the nanoscale loading and confinement of aquated Gd3+n-ion clusters within ultra-short single-walled carbon nanotubes (US-tubes); these Gd3+n@US-tube species are linear superparamagnetic molecular magnets with Magnetic Resonance Imaging (MRI) efficacies 40 to 90 times larger than any Gd3+-based contrast agent (CA) in current clinical use.
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Effect of ketoconazole (KET) on the pharmacokinetics (PK) of atrasentan (ABT-627, ATN). J Clin Oncol 2004. [DOI: 10.1200/jco.2004.22.90140.4727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Disseminated Ochroconis gallopavum infection in a renal transplant recipient: the first reported case and a review of the literature. Clin Nephrol 2003; 60:415-23. [PMID: 14690259 DOI: 10.5414/cnp60415] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ochroconis gallopavum is a potentially fatal dematiaceous fungus causing opportunistic infections in immunocompromised hosts. We report the first case of disseminated O. gallopavum infection in a 13-year-old renal transplant recipient, which involved the brain, lung and spleen. He was treated with amphotericin B, itraconazole and voriconazole, a new antifungal agent first used to treat such an infection. Besides antifungal treatment, all immunosuppressive agents were stopped and automated peritoneal dialysis was resumed. The initial infection was under control with both clinical and radiological improvements after treatment. However, the patient later acquired Acremonium spp. peritonitis; he failed to respond to high-dose amphotericin B, and finally succumbed. A total of 13 reported O. gallopavum human infections, including the one described here, are reviewed. The most common site of involvement is the brain and the crude mortality rate is up to 46%. As the disease is potentially lethal in immunocompromised hosts, empirical antifungal coverage should be considered in post-renal transplant recipients with suspected brain abscess. Early biopsy of lesion for histopathological and microbiological diagnosis would be essential in managing such cases.
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Operative management and outcome of iliac vessel injury: a ten-year experience. Am Surg 2003; 69:581-6. [PMID: 12889621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The purpose of this study is to review demographics and examine and stratify risk factors related to the outcome of operatively treated iliac vascular injuries. We conducted a retrospective review of 78 cases of iliac vessel injury. Patients with blunt and penetrating injury had statistically similar length of hospital stay and intensive care unit stay, incidence of shock, and mortality. Shock on admission and bleeding hematoma are linked, and shock increased mortality with an odds ratio of 5.2 (P = 0.002). A review of operative technique and outcome demonstrated a low mortality of 25 per cent in arterial bypass of an isolated arterial injury versus a mortality of 83 per cent in the combined injury group. Patients treated with primary repair of venous injuries had a lower incidence of shock and mortality compared with patients treated with venous ligation. We conclude that, if matched for severity of injury and physiologic instability, the mechanism of injury does not affect mortality. Shock is the most significant prognostic factor for mortality. Operative management must be based on presence of shock.
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Operative Management and Outcome of Iliac Vessel Injury: A Ten-Year Experience. Am Surg 2003. [DOI: 10.1177/000313480306900708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The purpose of this study is to review demographics and examine and stratify risk factors related to the outcome of operatively treated iliac vascular injuries. We conducted a retrospective review of 78 cases of iliac vessel injury. Patients with blunt and penetrating injury had statistically similar length of hospital stay and intensive care unit stay, incidence of shock, and mortality. Shock on admission and bleeding hematoma are linked, and shock increased mortality with an odds ratio of 5.2 ( P = 0.002). A review of operative technique and outcome demonstrated a low mortality of 25 per cent in arterial bypass of an isolated arterial injury versus a mortality of 83 per cent in the combined injury group. Patients treated with primary repair of venous injuries had a lower incidence of shock and mortality compared with patients treated with venous ligation. We conclude that, if matched for severity of injury and physiologic instability, the mechanism of injury does not affect mortality. Shock is the most significant prognostic factor for mortality. Operative management must be based on presence of shock.
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