MSARI: multiple sequence alignments for statistical detection of RNA secondary structure

We present a highly accurate method for identifying genes with conserved RNA secondary structure by searching multiple sequence alignments of a large set of candidate orthologs for correlated arrangements of reverse-complementary regions. This approach is growing increasingly feasible as the genomes of ever more organisms are sequenced. A program called msari implements this method and is significantly more accurate than existing methods in the context of automatically generated alignments, making it particularly applicable to high-throughput scans. In our tests, it discerned clustalw-generated multiple sequence alignments of signal recognition particle or RNaseP orthologs from controls with 89.1% sensitivity at 97.5% specificity and with 74.4% sensitivity with no false positives in 494 controls. We used msari to conduct a comprehensive scan for secondary structure in mRNAs of coding genes, and we found many genes with known mRNA secondary structure and compelling evidence for secondary structure in other genes. msari uses a method for coping with sequence redundancy that is likely to have applications in a large set of other comparison-based search methods. The program is available for download from http://theory.csail.mit.edu/MSARi.     

Design and implementation of a high frequency electrical impedance tomography system

Electrical impedance tomography is an imaging modality being investigated for use in detection of breast cancer. Use of higher frequencies than have typically been employed may benefit the detection processes. In this current work we discuss the design and initial implementation of a system having a bandwidth of 10 MHz. Previous investigations into high frequency designs have proven more difficult than anticipated and shown that careful selection of systems architecture is critical to achieving broadband performance above 1 MHz. The design for this new system is based on a digital signal processor (DSP) which is used for control, signal generation and signal processing. Signal generation and detection, software design and preliminary system specifications are discussed.     

Preclinical readiness testing of the Arrow International CorAide left ventricular assist system

BACKGROUND: Left ventricular assist system technologies are currently being developed as effective alternatives to cardiac transplantation. In this study, in vivo testing of the Arrow International CorAide left ventricular assist system was conducted to determine its preclinical readiness based on demonstrated system performance and biocompatibility. METHODS: Arrow International CorAide blood pump assemblies were implanted in 7 calves for 1-month (n = 4) and 3-month (n = 3) durations without the use of chronic anticoagulation therapy. Hemodynamic performance, physiologic pump control, end-organ function, and device-related adverse events were evaluated during the studies and at autopsy. RESULTS: Hemodynamics were stable in all cases with a mean pump flow of 4.1 +/- 0.8 L/min and a mean arterial pressure of 101 +/- 4 mm Hg. In all calves, renal and hepatic function remained normal with no incidence of hemolysis, infection, bleeding, or embolism. The CorAide physiologic control algorithm demonstrated appropriate pump speed and flow adjustments in response to physiologically induced inputs, and the system's external electronic components demonstrated no hardware or software malfunction. All 7 cases were sacrificed electively. Autopsy revealed no sign of end-organ disease on gross and histologic examinations, and no device failure, malfunction, or mechanical wear of the pump blood-bearing surfaces was found. CONCLUSIONS: The Arrow CorAide left ventricular assist system demonstrated effective pump performance and good biocompatibility with no incidence of device-related adverse events. This system has completed its preclinical readiness testing and is approved for clinical trials in Europe in 2003.     

Sequence-specific DNA strand cleavage by <Superscript>111</Superscript>In-labeled peptide nucleic acids

Peptide nucleic acids (PNAs) bind tightly and sequence-specifically to single- and double-stranded nucleic acids, and are hence of interest in the design of gene-targeted radiotherapeutics that could deliver the radiodamage to designated DNA and/or RNA sites. As a first step towards this goal, we developed a procedure for incorporation of Auger electron-emitting radionuclide (indium-111) into PNA oligomers and studied the efficiency of PNA-directed cleavage of single-stranded DNA targets. Accordingly, diethylene triamine penta-acetic acid (DTPA) was conjugated to the lysine-appended mixed-base PNAs and sequence-homologous DNA oligomer with a proper linker for comparative studies. By chelation of PNA-DTPA and DNA-DTPA conjugates with ¹¹¹In³⁺ in acidic aqueous solutions, ¹¹¹In-labeled PNA and DNA oligomers were obtained. Targeting of single-stranded DNA with PNA-DTPA-[¹¹¹In] conjugates yielded highly localized DNA strand cleavage; the distribution of breaks along the target DNA strand has two maxima corresponding to both termini of PNA oligomer. After 10–14 days, the overall yield of breaks thus generated within the PNA-targeted DNA by ¹¹¹In decay was 5–7% versus 2% in the case of control oligonucleotide DNA-DTPA-[¹¹¹In]. The estimated yield of DNA strand breaks per nuclear decay is ~0.1 for the PNA-directed delivery of ¹¹¹In, which is three times more than for the DNA-directed delivery of this radionuclide. This in vitro study shows that ¹¹¹In-labeled PNAs are much more effective than radiolabeled DNA oligonucleotides for site-specific damaging of DNA targets. Accordingly, we believe that PNA oligomers are promising radionuclide delivery tools for future antisense/antigene radiotherapy trials.     

Sensorimotor anesthesia and hypotension after subarachnoid block: combined spinal-epidural versus single-shot spinal technique

The extent of the intrathecal compartment depends on the balance between cerebrospinal fluid and subatmospheric epidural pressure. Epidural insertion disrupts this relationship, and the full impact of loss-of-resistance on the qualities of subarachnoid block is unknown. In this study we sought to determine if subarachnoid block, induced by combined spinal-epidural (CSE) using loss-of-resistance to air could render higher sensory anesthesia than single-shot spinal (SSS) when an identical mass of intrathecal anesthetic was injected. Sixty patients, scheduled for minor gynecological procedures, were randomly allocated into three groups all receiving 10 mg of 0.5% hyperbaric bupivacaine. In the SSS group, intrathecal administration was through a 27-gauge Whitacre spinal needle inserted at the L3-4 level. For the CSE group, the epidural space was identified with an 18-gauge Tuohy needle using loss-of-resistance to 4 mL of air. After intrathecal administration, a 20-gauge catheter was left in the epidural space. No further drug or saline was administered through the catheter. The procedure was repeated in group CSE ((no-catheter)) except without insertion of a catheter. Sensorimotor anesthesia was assessed at regular 2.5-min intervals until T10 was reached. In all aspects, there was no difference between CSE and CSE ((no-catheter)). Peak sensory level in SSS was lower than CSE and CSE ((no-catheter)) (median T5 [max T3-min T6] versus (T3 [T1-4] and (T3 [T2-5]) (P < 0.01). During the first 10 min postblock, dermatomal thoracic block was the lowest in SSS (P < 0.05). Time for regression of sensory level to T10 was also shortest in SSS. Hypotension, ephedrine use and period of motor recovery were more pronounced in CSE and CSE ((no-catheter)). We conclude that subarachnoid block induced by CSE produces greater sensorimotor anesthesia and prolonged recovery compared with SSS. There is also a more frequent incidence of hypotension and vasoconstrictor use despite using identical doses and baricity of local anesthetic. IMPLICATIONS: This study confirms that induction of subarachnoid block by a combined-spinal epidural technique produces a greater sensorimotor anesthesia and results in prolonged recovery when compared with a single-shot spinal technique. There is a more frequent incidence of hypotension and vasoconstrictor administration despite identical doses of intrathecally administered local anesthetic.     

The safety and efficacy of a fentanyl patient-controlled transdermal system for acute postoperative analgesia: a multicenter, placebo-controlled trial

A noninvasive method of delivery of parenteral opioids for management of acute pain may offer logistic advantages for patients and nursing staff. A patient-controlled transdermal system (PCTS) under development consists of a preprogrammed, self-contained drug-delivery system that uses electrotransport technology (E-TRANS, ALZA Corp, Mountain View, CA) to deliver 40 micro g of fentanyl HCl over 10 min per on-demand dose for patient-controlled analgesia (PCA). In this randomized, double-blinded, placebo-controlled trial we compared the efficacy and safety of on-demand fentanyl HCl PCTS 40 microg against placebo for postoperative pain up to 24 h after major abdominal, orthopedic, or thoracic surgery in 205 patients. The primary efficacy measurement was the percentage of patients withdrawn from the study because of inadequate analgesia after completing at least 3 h of treatment. Secondary efficacy measures included mean pain intensity (using visual analog scales), patient global assessments, and investigator global assessments. Of 189 patients considered evaluable for efficacy, 25% of patients in the fentanyl HCl PCTS 40 microg group withdrew because of inadequate analgesia, compared with 40.4% of the placebo group (P < 0.05). Use of fentanyl HCl PCTS 40 micro g was associated with lower VAS scores and higher mean patient and investigator global assessment scores compared with placebo. No patient experienced clinically relevant respiratory depression. This study showed that a fentanyl HCl PCTS 40 microg for PCA was superior to placebo and well tolerated for the control of moderate to severe postoperative pain for up to 24 h after major surgery. IMPLICATIONS: This multicenter, randomized, double-blinded, placebo-controlled trial showed that an on-demand fentanyl HCl patient-controlled transdermal system (PCTS) was superior to placebo and well tolerated for the control of moderate to severe postoperative pain for up to 24 h after major surgery. This fentanyl HCl PCTS is a preprogrammed, needle free, self-contained drug-delivery system that uses electrotransport technology (iontophoresis) to deliver 40 microg of fentanyl per on-demand dose.