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Shapiro BA, Warren J, Egol AB, Greenbaum DM, Jacobi J, Nasraway SA, Schein RM, Spevetz A, Stone JR. Practice parameters for intravenous analgesia and sedation for adult patients in the intensive care unit: an executive summary. Society of Critical Care Medicine. Crit Care Med 1995; 23:1596-600. [PMID: 7664563 DOI: 10.1097/00003246-199509000-00021] [Citation(s) in RCA: 299] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVE The development of practice parameters for intravenous analgesia and sedation for adult patients in the intensive care unit (ICU) setting for the purpose of guiding clinical practice. PARTICIPANTS A task force of more than 40 experts in disciplines related to the use of analgesic and sedative agents in the ICU was convened from the membership of the American College of Critical Care Medicine (ACCM) and the Society of Critical Care Medicine (SCCM). EVIDENCE The task force members provided the personal experience and determined the published literature (MEDLINE articles, textbooks, pharmacopeias, etc.) from which consensus would be sought. Published literature was reviewed and classified into one of four predetermined categories, according to study design and scientific value. CONSENSUS PROCESS The task force met several times as a whole, and numerous times in smaller groups by teleconference, over a 1-yr period to identify the pertinent literature and arrive at consensus recommendations for the whole task force to discuss. Consideration was given to the relationship between the weight of scientific information and the experts' viewpoints. Over the next year, draft documents were composed by a task force steering committee and debated by the task force members until consensus was reached by nominal group process. The task force draft was then reviewed, assessed, and edited by the Board of Regents of the ACCM. After steering committee approval, the draft document was reviewed and approved by the SCCM Council. DATA SYNTHESIS To facilitate rapid communication of the six recommendations contained within the complete and unabridged practice parameter document, an executive summary was prepared for publication by the ACCM Board of Regents, and this executive summary was approved by the task force steering committee and the SCCM Executive Council. CONCLUSIONS A consensus of experts provided six recommendations with supporting data for intravenous analgesia and sedation in the ICU setting: a) morphine sulfate is the preferred analgesic agent for critically ill patients; b) fentanyl is the preferred analgesic agent for critically ill patients with hemodynamic instability, for patients manifesting symptoms of histamine release with morphine, or morphine allergy; c) hydromorphone can serve as an acceptable alternative to morphine; d) midazolam or propofol are the preferred agents only for the short-term (< 24 hrs) treatment of anxiety in the critically ill adult; e) lorazepam is the preferred agent for the prolonged treatment of anxiety in the critically ill adult; f) haloperidol is the preferred agent for the treatment of delirium in the critically ill adult. This executive summary selectively presents supporting information and is not intended as a substitute for the complete document.
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Guideline |
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Shapiro BA, Zhang KZ. Comparing multiple RNA secondary structures using tree comparisons. COMPUTER APPLICATIONS IN THE BIOSCIENCES : CABIOS 1990; 6:309-18. [PMID: 1701685 DOI: 10.1093/bioinformatics/6.4.309] [Citation(s) in RCA: 122] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In a previous paper, an algorithm was presented for analyzing multiple RNA secondary structures utilizing a multiple string alignment algorithm. In this paper we present another approach to the problem of comparing many secondary structures by utilizing a very efficient tree-matching algorithm that will compare two trees in O([T1] X [T2] X L1 X L2) in the worst case and very close to O([T1] X [T2]) for average trees representing secondary structures. The result of the pairwise comparison algorithm is then used with a cluster algorithm to produce a multiple structure clustering which can be displayed in a taxonomy tree to show related structures.
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Stock MC, Woodward CG, Shapiro BA, Cane RD, Lewis V, Pecaro B. Perioperative complications of elective tracheostomy in critically ill patients. Crit Care Med 1986; 14:861-3. [PMID: 3757526 DOI: 10.1097/00003246-198610000-00005] [Citation(s) in RCA: 119] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This study was designed to examine prospectively the incidence of perioperative complications associated with elective tracheostomy in critically ill patients. An experienced surgeon and anesthesiologist participated in every tracheostomy procedure. In 81 procedures, there was no loss of airway control for greater than 20 sec, no airway obstruction, no blood loss exceeding 50 ml, and no aspiration. One patient (1.2%) had cardiovascular instability. During the next 48 h, two patients (2.4%) required wound packing to control hemorrhage but did not require blood transfusion and two patients (2.4%) had evidence of supraclavicular subcutaneous emphysema that was physiologically inconsequential. There was no perioperative mortality or major morbidity associated with the tracheostomy procedure. We conclude that, under controlled conditions, elective tracheostomy can be performed safely in critically ill patients.
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Sakaguchi K, Zambrano N, Baldwin ET, Shapiro BA, Erickson JW, Omichinski JG, Clore GM, Gronenborn AM, Appella E. Identification of a binding site for the human immunodeficiency virus type 1 nucleocapsid protein. Proc Natl Acad Sci U S A 1993; 90:5219-23. [PMID: 8506369 PMCID: PMC46687 DOI: 10.1073/pnas.90.11.5219] [Citation(s) in RCA: 115] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The nucleocapsid (NC) protein NCp7 of human immunodeficiency virus type 1 (HIV-1) is important for encapsidation of the virus genome, RNA dimerization, and primer tRNA annealing in vitro. Here we present evidence from gel mobility-shift experiments indicating that NCp7 binds specifically to an RNA sequence. Two complexes were identified in native gels. The more slowly migrating complex contained two RNA molecules and one peptide, while the more rapidly migrating one is composed of one RNA and one peptide. Further, mutational analysis of the RNA shows that the predicted stem and loop structure of stem-loop 1 plays a critical role. Our results show that NCp7 binds to a unique RNA structure within the psi region; in addition, this structure is necessary for RNA dimerization. We propose that NCp7 binds to the RNA via a direct interaction of one zinc-binding motif to stem-loop 1 followed by binding of the other zinc-binding motif to stem-loop 1, stem-loop 2, or the linker region of the second RNA molecule, forming a bridge between the two RNAs.
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Shapiro BA, Cane RD, Harrison RA. Positive end-expiratory pressure therapy in adults with special reference to acute lung injury: a review of the literature and suggested clinical correlations. Crit Care Med 1984; 12:127-41. [PMID: 6365452 DOI: 10.1097/00003246-198402000-00011] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Review |
41 |
95 |
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Shapiro BA. An algorithm for comparing multiple RNA secondary structures. COMPUTER APPLICATIONS IN THE BIOSCIENCES : CABIOS 1988; 4:387-93. [PMID: 2458170 DOI: 10.1093/bioinformatics/4.3.387] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A new distributed computational procedure is presented for rapidly determining the similarity of multiple conformations of RNA secondary structures. A data abstraction scheme is utilized to reduce the quantity of data that must be handled to determine the degree of similarity among multiple structures. The method has been used to compare 200 structures with easy visualization of both those structures and substructures that are similar and those that are vastly different. It has the capability of processing many more conformations as a function of research requirements. The algorithm is described as well as some suggestions for future uses and extensions.
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Shapiro BA, Warren J, Egol AB, Greenbaum DM, Jacobi J, Nasraway SA, Schein RM, Spevetz A, Stone JR. Practice parameters for sustained neuromuscular blockade in the adult critically ill patient: an executive summary. Society of Critical Care Medicine. Crit Care Med 1995; 23:1601-5. [PMID: 7664564 DOI: 10.1097/00003246-199509000-00022] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVE The development of practice parameters for achieving sustained neuromuscular blockade in the adult critically ill patient for the purpose of guiding clinical practice. PARTICIPANTS A task force of more than 40 experts in disciplines related to the use of neuromuscular blocking agents in the intensive care unit was convened from the membership of the American College of Critical Care Medicine (ACCM) and the Society of Critical Care Medicine (SCCM). EVIDENCE The task force members provided the personal experience and determined the published literature (MEDLINE articles, textbooks, pharmacopeias, etc.) from which consensus would be sought. Published literature was reviewed and classified into one of four predetermined categories, according to study design and scientific value. CONSENSUS PROCESS The task force met several times as a whole, and numerous times in smaller groups by teleconference, over a 1-yr period to identify the pertinent literature and arrive at consensus recommendations for the whole task force to discuss. Consideration was given to the relationship between the weight of scientific information and the experts' viewpoints. Over the next year, draft documents were composed by a task force steering committee and debated by the task force members until consensus was reached by nominal group process. The task force draft was then reviewed, assessed, and edited by the Board of Regents of the ACCM. After steering committee approval, the draft document was reviewed and approved by the SCCM Council. DATA SYNTHESIS To facilitate rapid communication of the three recommendations contained within the complete and unabridged practice parameter document, an executive summary was prepared for publication by the ACCM Board of Regents, and this executive summary was approved by the task force steering committee and the SCCM Executive Council. CONCLUSIONS A consensus of experts provided three recommendations with supporting data for achieving sustained neuromuscular blockade in critically ill patients: a) pancuronium is the preferred neuromuscular blocking agent for most critically ill patients; b) vecuronium is the preferred neuromuscular blocking agent for those patients with cardiac disease or hemodynamic instability in whom tachycardia may be deleterious; c) patients receiving neuromuscular blocking agents should be appropriately assessed for the degree of blockade that is being sustained. This executive summary selectively presents supporting information and is not intended as a substitute for the complete document.
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Shapiro BA, Mahutte CK, Cane RD, Gilmour IJ. Clinical performance of a blood gas monitor: a prospective, multicenter trial. Crit Care Med 1993; 21:487-94. [PMID: 8472565 DOI: 10.1097/00003246-199304000-00005] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
OBJECTIVE To prospectively assess the clinical performance of a fluorescent optode-based blood gas monitoring system that is designed to perform arterial pH, PCO2, and PO2 measurements as frequently as clinically required without violating the integrity of the arterial catheter tubing system or permanently removing blood from the patient. DESIGN A prospective, multicenter study to compare modern blood gas analyzer measurements with the coinciding measurements of the blood gas monitoring system. SETTING Four intensive care units (ICUs) in academic centers with varying patient populations, blood gas measurement routines, and blood gas laboratory facilities. PATIENTS Adult ICU patients (n = 117), with appropriately functioning radial arterial catheters in place, who were assessed as likely to require multiple arterial blood gas measurements for > or = 2 days. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS A total of 117 patients had 1,341 concurrent blood gas analyzer and monitor measurements of arterial pH, PCO2, and PO2 over a 1- to 4-day period. The range of values were 7.14 to 7.64 for arterial pH, 19 to 98 torr (2.5 to 13.0 kPa) for PaCO2, and 38 to 413 torr (5.1 to 54.9 kPa) for PaO2. Linear regression analysis of the optode-based monitor compared with the electrode-based blood gas analyzer demonstrated r2 values of .85 for pH, .92 for PCO2, and .94 for PO2. Comparative statistical analyses for bias (mean difference between analyzer and monitor) and precision (standard deviation of the mean difference [+/- SD] between analyzer and monitor) were respectively:-0.004 and +/- 0.027 for pH; -0.8 torr (-0.11 kPa) and +/- 2.4 torr (0.32 kPa) for PCO2; -2.2 torr (-0.31 kPa) and +/- 8.7 torr (1.2 kPa) for PO2. CONCLUSIONS Clinical performance of this fluorescent, optode-based blood gas monitoring system demonstrates stability, consistency, and accuracy comparable to modern blood gas analyzers. This system withstood the normal abuse and rigors of clinical conditions common to the ICU while reliably performing in critically ill patients for up to 80 hrs. Use of the device did not significantly alter the function or longevity normally expected from a 20-gauge radial artery catheter. We submit that this blood gas monitoring system can replace the use of blood gas analyzers for ICU patients with indwelling arterial catheters.
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Shapiro BA, Wu JC, Bengali D, Potts MJ. The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation. Bioinformatics 2001; 17:137-48. [PMID: 11238069 DOI: 10.1093/bioinformatics/17.2.137] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A massively parallel Genetic Algorithm (GA) has been applied to RNA sequence folding on three different computer architectures. The GA, an evolution-like algorithm that is applied to a large population of RNA structures based on a pool of helical stems derived from an RNA sequence, evolves this population in parallel. The algorithm was originally designed and developed for a 16384 processor SIMD (Single Instruction Multiple Data) MasPar MP-2. More recently it has been adapted to a 64 processor MIMD (Multiple Instruction Multiple Data) SGI ORIGIN 2000, and a 512 processor MIMD CRAY T3E. The MIMD version of the algorithm raises issues concerning RNA structure data-layout and processor communication. In addition, the effects of population variation on the predicted results are discussed. Also presented are the scaling properties of the algorithm from the perspective of the number of physical processors utilized and the number of virtual processors (RNA structures) operated upon.
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Cane RD, Peruzzi WT, Shapiro BA. Airway pressure release ventilation in severe acute respiratory failure. Chest 1991; 100:460-3. [PMID: 1864120 DOI: 10.1378/chest.100.2.460] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Airway pressure release ventilation (APRV), a new ventilatory support technique, was compared with conventional intermittent positive-pressure ventilation plus PEEP (CPPV) in 18 patients with severe acute respiratory failure. Patients were initially stabilized on CPPV and then switched to APRV. The APRV provided effective ventilatory support in 17 of 18 patients; APRV achieved similar levels of alveolar ventilation as CPPV (for APRV, mean PaCO2 = 45.0 +/- 6.2 mm Hg; vs for CPPV, mean PaCO2 = 43.3 +/- 5.7 mm Hg), with significantly lower mean maximum airway pressures (38.9 +/- 10.1 cm H2O vs 64.6 +/- 15.4 cm H2O; p = 0.0001) and mean VT (0.79 +/- 0.11 L vs 1.05 +/- 0.15 L; p = 0.0002). No significant differences in mean airway pressure, end-expiratory pressure, FIO2, ventilator rate, arterial blood gas levels, and hemodynamic function were noted between APRV and CPPV.
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Cheng SW, Lynch EC, Leason KR, Court DL, Shapiro BA, Friedman DI. Functional importance of sequence in the stem-loop of a transcription terminator. Science 1991; 254:1205-7. [PMID: 1835546 DOI: 10.1126/science.1835546] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Intrinsic transcription terminators of prokaryotes are distinguished by a common RNA motif: a stem-loop structure high in guanine and cytosine content, followed by multiple uridine residues. Models explaining intrinsic terminators postulate that the stem-loop sequence is necessary only to form structure. In the tR2 terminator of coliphage lambda, single-nucleotide changes reducing potential RNA stem stability eliminated tR2 activity, and a compensatory change that restored the stem structure restored terminator activity. However, multiple changes in the stem sequence that should have either maintained or increased stability reduced terminator activity. These results suggest that the ability of the stem-loop structure to signal transcription termination depends on sequence specificity and secondary structure.
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Shapiro BA, Bengali D, Kasprzak W, Wu JC. RNA folding pathway functional intermediates: their prediction and analysis. J Mol Biol 2001; 312:27-44. [PMID: 11545583 DOI: 10.1006/jmbi.2001.4931] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The massively parallel genetic algorithm (GA) for RNA structure prediction uses the concepts of mutation, recombination, and survival of the fittest to evolve a population of thousands of possible RNA structures toward a solution structure. As described below, the properties of the algorithm are ideally suited to use in the prediction of possible folding pathways and functional intermediates of RNA molecules given their sequences. Utilizing Stem Trace, an interactive visualization tool for RNA structure comparison, analysis of not only the solution ensembles developed by the algorithm, but also the stages of development of each of these solutions, can give strong insight into these folding pathways. The GA allows the incorporation of information from biological experiments, making it possible to test the influence of particular interactions between structural elements on the dynamics of the folding pathway. These methods are used to reveal the folding pathways of the potato spindle tuber viroid (PSTVd) and the host killing mechanism of Escherichia coli plasmid R1, both of which are successfully explored through the combination of the GA and Stem Trace. We also present novel intermediate folds of each molecule, which appear to be phylogenetically supported, as determined by use of the methods described below.
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Shapiro BA, Cane RD, Chomka CM, Bandala LE, Peruzzi WT. Preliminary evaluation of an intra-arterial blood gas system in dogs and humans. Crit Care Med 1989; 17:455-60. [PMID: 2707017 DOI: 10.1097/00003246-198905000-00016] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The reliability and accuracy of an intra-arterial fluorescent optode system to measure continuously pHa, PaCO2, and PaO2 were evaluated in a dog model and in a group of critically ill patients. Six hundred sixty-three arterial blood gas (ABG) samples were analyzed for pHa, PaCO2, and PaO2 in the dog studies. The intra-arterial blood gas system (IBGS) indicated a steady state in 420 instances for pH, 359 instances for PaCO2, and 256 instances for PaO2. Comparison of these ABG and IBGS values by linear regression analysis revealed r = .97 for pHa, .95 for PaCO2, and .96 for PaO2. The mean +/- SD of the difference between ABG and IBGS was -0.02 +/- 0.03 for pHa, 1.05 +/- 3.8 for PaCO2, and -17 +/- 13 for PaO2. Nonsteady states were correctly identified by the IBGS in every instance. Comparisons between 79 temporally matched ABG and IBGS values, exclusive of in vivo calibration samples, in 12 critically ill patients revealed r = .97 for pHa, .96 for PaCO2, and .99 for PaO2. The difference was 0.002 +/- 0.02 for pHa, 0.44 +/- 2.97 for PaCO2, and -1.22 +/- 9.34 for PaO2. We conclude that it is possible to measure continuously pHa, PaCO2, and PaO2 with the IBGS in critically ill patients for periods from 3 to 25.5 h while maintaining the ability to monitor BP and withdraw blood samples from the arterial cannula. Agreement between the two techniques is within clinically acceptable ranges for pHa and PaCO2, whereas PaO2 measurement by the IBGS requires further refinement.(ABSTRACT TRUNCATED AT 250 WORDS)
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Dayton ET, Konings DA, Powell DM, Shapiro BA, Butini L, Maizel JV, Dayton AI. Extensive sequence-specific information throughout the CAR/RRE, the target sequence of the human immunodeficiency virus type 1 Rev protein. J Virol 1992; 66:1139-51. [PMID: 1731093 PMCID: PMC240818 DOI: 10.1128/jvi.66.2.1139-1151.1992] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The significance and location of sequence-specific information in the CAR/RRE, the target sequence for the Rev protein of the human immunodeficiency virus type 1 (HIV-1), have been controversial. We present here a comprehensive experimental and computational approach combining mutational analysis, phylogenetic comparison, and thermodynamic structure calculations with a systematic strategy for distinguishing sequence-specific information from secondary structural information. A target sequence analog was designed to have a secondary structure identical to that of the wild type but a sequence that differs from that of the wild type at every position. This analog was inactive. By exchanging fragments between the wild-type sequence and the inactive analog, we were able to detect an unexpectedly extensive distribution of sequence specificity throughout the CAR/RRE. The analysis enabled us to identify a critically important sequence-specific region, region IIb in the Rev-binding domain, strongly supports a proposed base-pairing interaction in this location, and places forceful constraints on mechanisms of Rev action. The generalized approach presented can be applied to other systems.
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Cane RD, Shapiro BA, Templin R, Walther K. Unreliability of oxygen tension-based indices in reflecting intrapulmonary shunting in critically ill patients. Crit Care Med 1988; 16:1243-5. [PMID: 3191742 DOI: 10.1097/00003246-198812000-00014] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Measurement of intrapulmonary shunting (Qsp/Qt), a widely used method for monitoring disturbances of pulmonary oxygen transfer in critically ill patients, involves calculation of arterial and mixed venous oxygen contents. In circumstances where mixed venous blood samples are not readily available, oxygen tension-based indices such as the alveolar to arterial oxygen tension differences (P[A-a]O2), arterial oxygen tension to alveolar oxygen tension ratio (PaO2/PAO2), PaO2 to FIO2 ratio (PaO2/FIO2) and respiratory index (RI) are widely utilized to reflect Qsp/Qt. Oxygen content-based indices such as the estimated shunt are not as widely utilized as the oxygen tension indices. In 75 critically ill patients in whom a pulmonary artery catheter was being utilized to augment clinical care, comparisons were made between Qsp/Qt and P(A-a)O2, PaO2/PAO2, PaO2/FIO2, RI, and estimated shunt to determine which index best reflected Qsp/Qt. Correlations between Qsp/Qt and estimated shunt were good (r = .94) and poor for the P(A-a)O2 (r = .62), PaO2/PAO2 (r = .72), PaO2/FIO2 (r = .71), and RI (r = .74). We conclude that there are no real substitutes for venous oxygen contents in critically ill patients. When pulmonary artery blood is not available for analysis, oxygen tension-based indices are unreliable reflectors of Qsp/Qt while the estimated shunt, an oxygen content-based index, provides a more reliable reflection of Qsp/Qt.
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Benzon HT, Toleikis JR, Meagher LL, Shapiro BA, Ts'ao CH, Avram MJ. Changes in venous blood lactate, venous blood gases, and somatosensory evoked potentials after tourniquet application. Anesthesiology 1988; 69:677-82. [PMID: 3142309 DOI: 10.1097/00000542-198811000-00007] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The effects of inflation of a 7-cm tourniquet applied to the upper arm of eight volunteers on venous lactate, venous blood gases, and ulnar nerve somatosensory evoked potentials (SSEPs) were investigated. The inflation pressure was 100 mmHg over the systolic pressure. Venous blood samples for lactate and blood gas determinations were withdrawn before tourniquet inflation; immediately and at 2, 5, 10, 15 min after tourniquet deflation; and additionally at 30, 45, and 60 min after deflation in the last four volunteers. SSEP stimulating surface electrodes were placed over the ulnar nerve at the wrist. Recording electrodes were placed over the ipsilateral ulnar groove of the elbow, Erb's point, and on the contralateral cortex. Averaged responses were acquired before inflation of the tourniquet, every 5-10 min during tourniquet inflation, and every 5-10 min for 45-60 min after tourniquet deflation. The tourniquet was inflated for 36 +/- 11 min. After deflation of the tourniquet, postdeflation pain and paresthesias were felt by five volunteers; these occurred at 30-120 s after deflation and lasted for 75-120 s. The postdeflation pains were characterized as burning, cramping, paresthesias, buzzing, or severe expansion of the hand. The venous blood lactate levels were significantly elevated for 10 min, and the time course of its change did not correlate with reperfusion pain. The PO2 and O2Hb saturation in venous blood were significantly elevated for 10-15 min after deflation. The elevated lactate and PO2 levels in the presence of a restored blood flow probably result from continued anaerobic muscle metabolism secondary to capillary closure from the tourniquet-induced ischemia.(ABSTRACT TRUNCATED AT 250 WORDS)
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Shapiro BA, Cane RD, Harrison RA, Steiner MC. Changes in intrapulmonary shunting with administration of 100 percent oxygen. Chest 1980; 77:138-41. [PMID: 6986237 DOI: 10.1378/chest.77.2.138] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The effects of increasing the fractional concentration of oxygen in the inspired gas to 1.0 on intrapulmonary shunting (Qsp) was evaluated in 82 intubated cardiovascularly stable patients in intensive care, regardless of airway pressure therapy or preexistent pulmonary pathologic abnormalities. Intrapulmonary shunting following administration of 100 percent oxygen increased in 132 of 140 measurements, decreased in seven, and remained unchanged in one measurement. The direction of change of Qsp with 100 percent oxygen shows no correlation with either airway pressure therapy or preexisting pulmonary disease.
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Shapiro BA, Lichtenthal PR. Inhalation-based anesthetic techniques are the key to early extubation of the cardiac surgical patient. J Cardiothorac Vasc Anesth 1993; 7:135-6. [PMID: 8477014 DOI: 10.1016/1053-0770(93)90204-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Comment |
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Shapiro BA, Maizel J, Lipkin LE, Currey K, Whitney C. Generating non-overlapping displays of nucleic acid secondary structure. Nucleic Acids Res 1984; 12:75-88. [PMID: 6694904 PMCID: PMC320985 DOI: 10.1093/nar/12.1part1.75] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A new algorithm is presented which permits the display of nucleic acid secondary structure by computer. This algorithm circumvents the problem of overlapping portions of the molecule which is inherent in some other drawing programs. The results from this algorithm may also be used as input to the drawing algorithm previously reported in this journal [1] to untangle most of a drawing. The algorithm also represents the molecule in a form which makes visual comparisons for similarity quite easy since it guarantees that comparable features will reside in the same relative position in the drawings when the drawings are normalized.
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Abstract
OBJECTIVE To define the occurrence rate, time course, and potential etiologic factors of hyponatremia in patients with acute spinal cord injury. DESIGN Analysis of data obtained from a retrospective review of medical records and from a systematized, prospective database pertaining to patients with spinal cord injury. SETTING A university hospital with a federally funded regional spinal cord injury center and a dedicated spinal cord injury intensive care unit. PATIENTS Two hundred eighty-two patients admitted between January 1, 1988 and December 31, 1989 with acute (< 24-hr duration) spinal cord or vertebral column injury. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS The mean age of patients was 36.7 +/- 17.6 (SD) yrs; 225 (80%) of the patients were male and 57 (20%) were female. Hyponatremia, when it occurred, developed at a mean time of 6.4 +/- 6.7 days postadmission, reached its nadir at 8.7 +/- 8.8 days, and occurred in 28% of those patients with cervical injuries, 34% with thoracic injuries, and 27% with lumbar injuries (p = NS). Logistic regression analysis demonstrated that the type of spinal cord injury (Frankel class: range is A = complete neurologic lesion to E = no neurologic lesion) was the strongest predictor of hyponatremia. The occurrence rate of hyponatremia was as follows: Frankel class-A 62%; Frankel class-B 48%; Frankel class-C 41%; Frankel class-D 23%; Frankel class-E 16% (p < .0001). CONCLUSIONS The prevalence of hyponatremia in acute spinal cord injury is much higher than in the general medical or surgical patient population. This abnormality usually occurs within the first week postinjury. The most significant predictor of hyponatremia is the type rather than the level of spinal cord injury. The potential etiological factors are many and these factors are probably interrelated. The pathophysiological mechanisms that result in hyponatremia must be explored so that this occurrence and its consequences can be prevented.
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Shapiro BA, Wu JC. An annealing mutation operator in the genetic algorithms for RNA folding. COMPUTER APPLICATIONS IN THE BIOSCIENCES : CABIOS 1996; 12:171-80. [PMID: 8872384 DOI: 10.1093/bioinformatics/12.3.171] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
An annealing mutation operator in the genetic algorithms (GA) for RNA folding on a MasPar MP-2 has been designed. The mutation probability descends along a hyperbola with respect to the size of the secondary structure, hence the total number of mutations at each generation drops linearly. Especially for long sequences with thousands of nucleotides as opposed to hundreds of nucleotides, the new mutation operator can make the distribution of free energies over all processors on MasPar MP-2 converge only after hundreds of generations. Based upon this new mutation operator, a technique to terminate the GA is also developed. The new mutation operator runs very efficiently. Some variations of the annealing mutation operator are also discussed.
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Le SY, Shapiro BA, Chen JH, Nussinov R, Maizel JV. RNA pseudoknots downstream of the frameshift sites of retroviruses. GENETIC ANALYSIS, TECHNIQUES AND APPLICATIONS 1991; 8:191-205. [PMID: 1663382 PMCID: PMC7128882 DOI: 10.1016/1050-3862(91)90013-h] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/15/1991] [Revised: 07/30/1991] [Accepted: 07/30/1991] [Indexed: 12/28/2022]
Abstract
RNA pseudoknot structural motifs could have implications for a wide range of biological processes of RNAs. In this study, the potential RNA pseudoknots just downstream from the known and suspected retroviral frame-shift sites were predicted in the Rous sarcoma virus, primate immunodeficiency viruses (HIV-1, HIV-2, and SIV), equine infectious anemia virus, visna virus, bovine leukemia virus, human T-cell leukemia virus (types I and II), mouse mammary tumor virus, Mason-Pfizer monkey virus, and simian SRV-1 type-D retrovirus. Also, the putative RNA pseudoknots were detected in the gag-pol overlaps of two retrotransposons of Drosophila, 17.6 and gypsy, and the mouse intracisternal A particle. For each sequence, the thermodynamic stability and statistical significance of the secondary structure involved in the predicted tertiary structure were assessed and compared. Our results show that the stem-loop structures in the pseudoknots are both thermodynamically highly stable and statistically significant relative to other such configurations that potentially occur in the gag-pol or gag-pro and pro-pol junction domains of these viruses (300 nucleotides upstream and downstream from the possible frameshift sites are included). Moreover, the structural features of the predicted pseudoknots following the frameshift site of pro-pol overlaps of the HTLV-1 and HTLV-2 retroviruses are structurally well conserved. The occurrence of eight compensatory base changes in the tertiary interaction of the two related sequences allow the conservation of their tertiary structures in spite of the sequence divergence. The results support the possible control mechanism for frameshifting proposed by Brierley et al. and Jacks et al.
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Wang JT, Marr TG, Shasha D, Shapiro BA, Chirn GW. Discovering active motifs in sets of related protein sequences and using them for classification. Nucleic Acids Res 1994; 22:2769-75. [PMID: 8052532 PMCID: PMC308246 DOI: 10.1093/nar/22.14.2769] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We describe a method for discovering active motifs in a set of related protein sequences. The method is an automatic two step process: (1) find candidate motifs in a small sample of the sequences; (2) test whether these motifs are approximately present in all the sequences. To reduce the running time, we develop two optimization heuristics based on statistical estimation and pattern matching techniques. Experimental results obtained by running these algorithms on generated data and functionally related proteins demonstrate the good performance of the presented method compared with visual method of O'Farrell and Leopold. By combining the discovered motifs with an existing fingerprint technique, we develop a protein classifier. When we apply the classifier to the 698 groups of related proteins in the PROSITE catalog, it gives information that is complementary to the BLOCKS protein classifier of Henikoff and Henikoff. Thus, using our classifier in conjunction with theirs, one can obtain high confidence classifications (if BLOCKS and our classifier agree) or suggest a new hypothesis (if the two disagree).
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