Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices.

SUMMARY: We introduce a novel unsupervised approach for the organization and visualization of multidimensional data. At the heart of the method is a presentation of the full pairwise distance matrix of the data points, viewed in pseudocolor. The ordering of points is iteratively permuted in search of a linear ordering, which can be used to study embedded shapes. Several examples indicate how the shapes of certain structures in the data (elongated, circular and compact) manifest themselves visually in our permuted distance matrix. It is important to identify the elongated objects since they are often associated with a set of hidden variables, underlying continuous variation in the data. The problem of determining an optimal linear ordering is shown to be NP-Complete, and therefore an iterative search algorithm with O(n3) step-complexity is suggested. By using sorting points into neighborhoods, i.e. SPIN to analyze colon cancer expression data we were able to address the serious problem of sample heterogeneity, which hinders identification of metastasis related genes in our data. Our methodology brings to light the continuous variation of heterogeneity--starting with homogeneous tumor samples and gradually increasing the amount of another tissue. Ordering the samples according to their degree of contamination by unrelated tissue allows the separation of genes associated with irrelevant contamination from those related to cancer progression. AVAILABILITY: Software package will be available for academic users upon request.

Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays.

Using an oligonucleotide array containing sequences complementary to approximately 3200 full-length human cDNAs and 3400 expressed sequence tags (GeneChip, Affymetrix), mRNA expression patterns were probed in 18 colon adenocarcinomas and 4 adenomas. Paired normal tissue was available and analyzed for each of the tumors. Relatively few changes in transcript expression are associated with colon cancer. Nineteen transcripts (0.48% of those detected) had at least 4-10.5-fold higher mRNA expression in carcinoma compared with paired normal samples, whereas 47 transcripts (1.3% of those detected) had at least 4-38-fold or lower expression in the tumor tissue compared with the normal samples. Some of these differences were confirmed by reverse transcription-PCR. Many of these transcripts were already known to be abnormally expressed in neoplastic tissue in general, or colon cancer in particular, and several of these differences were also observed in premalignant adenoma samples. A two-way hierarchical clustering algorithm successfully distinguished adenoma from adenocarcinoma and normal tissue, generating a phylogenetic tree that appropriately represented the clinical relationship between the three tissue types included in the analysis. This supports the concept that genome-wide expression profiling may permit a molecular classification of solid tumors.

Adverse sedation events in pediatrics: analysis of medications used for sedation.

OBJECTIVES: To perform a systematic investigation of medications associated with adverse sedation events in pediatric patients using critical incident analysis of case reports. METHODS: One hundred eighteen case reports from the adverse drug reporting system of the Food and Drug Administration, the US Pharmacopoeia, and the results of a survey of pediatric specialists were used. Outcome measures were death, permanent neurologic injury, prolonged hospitalization without injury, and no harm. The overall results of the critical incident analysis are reported elsewhere. The current investigation specifically examined the relationship between outcome and medications: individual and classes of drugs, routes of administration, drug combinations and interactions, medication errors and overdoses, patterns of drug use, practitioners, and venues of sedation. RESULTS: Ninety-five incidents fulfilled study criteria and all 4 reviewers agreed on causation; 60 resulted in death or permanent neurologic injury. Review of adverse sedation events indicated that there was no relationship between outcome and drug class (opioids; benzodiazepines; barbiturates; sedatives; antihistamines; and local, intravenous, or inhalation anesthetics) or route of administration (oral, rectal, nasal, intramuscular, intravenous, local infiltration, and inhalation). Negative outcomes (death and permanent neurologic injury) were often associated with drug overdose (n = 28). Some drug overdoses were attributable to prescription/transcription errors, although none of 39 overdoses in 34 patients seemed to be a decimal point error. Negative outcomes were also associated with drug combinations and interactions. The use of 3 or more sedating medications compared with 1 or 2 medications was strongly associated with adverse outcomes (18/20 vs 7/70). Nitrous oxide in combination with any other class of sedating medication was frequently associated with adverse outcomes (9/10). Dental specialists had the greatest frequency of negative outcomes associated with the use of 3 or more sedating medications. Adverse events occurred despite drugs being administered within acceptable dosing limits. Negative outcomes were also associated with drugs administered by nonmedically trained personnel and drugs administered at home. Some injuries occurred on the way to a facility after administration of sedatives at home; some took place in automobiles or at home after discharge from medical supervision. Deaths and injuries after discharge from medical supervision were associated with the use of medications with long half-lives (chloral hydrate, pentobarbital, promazine, promethazine, and chlorpromazine). CONCLUSIONS: Adverse sedation events were frequently associated with drug overdoses and drug interactions, particularly when 3 or more drugs were used. Adverse outcome was associated with all routes of drug administration and all classes of medication, even those (such as chloral hydrate) thought to have minimal effect on respiration. Patients receiving medications with long plasma half-lives may benefit from a prolonged period of postsedation observation. Adverse events occurred when sedative medications were administered outside the safety net of medical supervision. Uniform monitoring and training standards should be instituted regardless of the subspecialty or venue of practice. Standards of care, scope of practice, resource management, and reimbursement for sedation should be based on the depth of sedation achieved (ie, the degree of vigilance and resuscitation skills required) rather than on the drug class, route of drug administration, practitioner, or venue.

Capacitance cytometry: measuring biological cells one by one.

Measuring the DNA content of eukaryotic cells is a fundamental task in biology and medicine. We have observed a linear relationship between the DNA content of eukaryotic cells and the change in capacitance that is evoked by the passage of individual cells across a 1-kHz electric field. This relationship is species-independent; consequently, we have developed a microfluidic technique-"capacitance cytometry"-that can be used to quantify the DNA content of single eukaryotic cells and to analyze the cell-cycle kinetics of populations of cells. Comparisons with standard flow cytometry demonstrate the sensitivity of this new technique.

Adverse sedation events in pediatrics: a critical incident analysis of contributing factors.

OBJECTIVE: Factors that contribute to adverse sedation events in children undergoing procedures were examined using the technique of critical incident analysis. METHODOLOGY: We developed a database that consists of descriptions of adverse sedation events derived from the Food and Drug Administration's adverse drug event reporting system, from the US Pharmacopeia, and from a survey of pediatric specialists. One hundred eighteen reports were reviewed for factors that may have contributed to the adverse sedation event. The outcome, ranging in severity from death to no harm, was noted. Individual reports were first examined separately by 4 physicians trained in pediatric anesthesiology, pediatric critical care medicine, or pediatric emergency medicine. Only reports for which all 4 reviewers agreed on the contributing factors and outcome were included in the final analysis. RESULTS: Of the 95 incidents with consensus agreement on the contributing factors, 51 resulted in death, 9 in permanent neurologic injury, 21 in prolonged hospitalization without injury, and in 14 there was no harm. Patients receiving sedation in nonhospital-based settings compared with hospital-based settings were older and healthier. The venue of sedation was not associated with the incidence of presenting respiratory events (eg, desaturation, apnea, laryngospasm, approximately 80% in each venue) but more cardiac arrests occurred as the second (53.6% vs 14%) and third events (25% vs 7%) in nonhospital-based facilities. Inadequate resuscitation was rated as being a determinant of adverse outcome more frequently in nonhospital-based events (57.1% vs 2.3%). Death and permanent neurologic injury occurred more frequently in nonhospital-based facilities (92.8% vs 37.2%). Successful outcome (prolonged hospitalization without injury or no harm) was associated with the use of pulse oximetry compared with a lack of any documented monitoring that was associated with unsuccessful outcome (death or permanent neurologic injury). In addition, pulse oximetry monitoring of patients sedated in hospitals was uniformly associated with successful outcomes whereas in the nonhospital-based venue, 4 out of 5 suffered adverse outcomes. Adverse outcomes despite the benefit of an early warning regarding oxygenation likely reflect lack of skill in assessment and in the use of appropriate interventions, ie, a failure to rescue the patient. CONCLUSIONS: This study-a critical incident analysis-identifies several features associated with adverse sedation events and poor outcome. There were differences in outcomes for venue: adverse outcomes (permanent neurologic injury or death) occurred more frequently in a nonhospital-based facility, whereas successful outcomes (prolonged hospitalization or no harm) occurred more frequently in a hospital-based setting. Inadequate resuscitation was more often associated with a nonhospital-based setting. Inadequate and inconsistent physiologic monitoring (particularly failure to use or respond appropriately to pulse oximetry) was another major factor contributing to poor outcome in all venues. Other issues rated by the reviewers were: inadequate presedation medical evaluation, lack of an independent observer, medication errors, and inadequate recovery procedures. Uniform, specialty-independent guidelines for monitoring children during and after sedation are essential. Age and size-appropriate equipment and medications for resuscitation should be immediately available regardless of the location where the child is sedated. All health care providers who sedate children, regardless of practice venue, should have advanced airway assessment and management training and be skilled in the resuscitation of infants and children so that they can successfully rescue their patient should an adverse sedation event occur.

Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays.

Oligonucleotide arrays can provide a broad picture of the state of the cell, by monitoring the expression level of thousands of genes at the same time. It is of interest to develop techniques for extracting useful information from the resulting data sets. Here we report the application of a two-way clustering method for analyzing a data set consisting of the expression patterns of different cell types. Gene expression in 40 tumor and 22 normal colon tissue samples was analyzed with an Affymetrix oligonucleotide array complementary to more than 6,500 human genes. An efficient two-way clustering algorithm was applied to both the genes and the tissues, revealing broad coherent patterns that suggest a high degree of organization underlying gene expression in these tissues. Coregulated families of genes clustered together, as demonstrated for the ribosomal proteins. Clustering also separated cancerous from noncancerous tissue and cell lines from in vivo tissues on the basis of subtle distributed patterns of genes even when expression of individual genes varied only slightly between the tissues. Two-way clustering thus may be of use both in classifying genes into functional groups and in classifying tissues based on gene expression.

Expression of wild-type alpha-catenin protein in cells with a mutant alpha-catenin gene restores both growth regulation and tumor suppressor activities.

Recent studies indicate that disruption of the E-cadherin-mediated cell-cell adhesion system is frequently associated with human cancers of epithelial origin. Reduced levels of both E-cadherin and the associated protein, alpha-catenin, have been reported in human tumors. This report describes the characterization of a human ovarian carcinoma-derived cell line (Ov2008) which expresses a novel mutant form of the alpha-catenin protein lacking the extreme N terminus of the wild-type protein. The altered form of alpha-catenin expressed in Ov2008 cells fails to bind efficiently to beta-catenin and is localized in the cytoplasm. Deletion mapping has localized the beta-catenin binding site on alpha-catenin between amino acids 46 and 149, which encompasses the same region of the protein that is deleted in the Ov2008 variant. Restoration of inducible expression of the wild-type alpha-catenin protein in these cells caused them to assume the morphology typical of an epithelial sheet and retarded their growth in vitro. Additionally, the induction of alpha-catenin expression in Ov2008 cells injected into nude mice attenuated the ability of these cells to form tumors. These observations support the classification of alpha-catenin as a growth-regulatory and candidate tumor suppressor gene.

Sedation with intravenous midazolam in the pediatric intensive care unit.

Physical and emotional distress can have important effects on patients in the pediatric intensive care unit (ICU). Intravenous (IV) infusion of benzodiazepines is an important adjunct to assisted ventilation and other potentially distressing ICU procedures. Combined with intermittent or continuous infusion of opioids, the benzodiazepines provide smooth control of anxiety, pain, and agitation. Intravenous midazolam (Versed Roche Laboratories) is distinguished from diazepam (Valium, Roche Products) by its water solubility, short elimination half-life, and generally short duration of action. These pharmacological properties, which are also shared, in part, with the more slowly eliminated drug lorazepam (Ativan, Wyeth-Ayerst), facilitate titration of the rate of infusion against patient response and permit regulation of the depth of sedation. The major adverse effects of long-term benzodiazepine infusion are withdrawal symptoms and, occasionally, delayed awakening. The dosage needed to initiate and maintain sedation must be adjusted to body weight, degree of sedation desired, and concomitant medications, as well as to underlying health and cardiovascular status. Benzodiazepines, such as midazolam and lorazepam, represent important choices among drugs used for sedation in the pediatric ICU.

Pharmacology of pediatric resuscitation.

The resuscitation of children from cardiac arrest and shock remains a challenging goal. The pharmacologic principles underlying current recommendations for intervention in pediatric cardiac arrest have been reviewed. Current research efforts, points of controversy, and accepted practices that may not be most efficacious have been described. Epinephrine remains the most effective resuscitation adjunct. High-dose epinephrine is tolerated better in children than in adults, but its efficacy has not received full analysis. The preponderance of data continues to point toward the ineffectiveness and possible deleterious effects of overzealous sodium bicarbonate use. Calcium chloride is useful in the treatment of ionized hypocalcemia but may harm cells that have experienced asphyxial damage. Atropine is an effective agent for alleviating bradycardia induced by increased vagal tone, but because most bradycardia in children is caused by hypoxia, improved oxygenation is the intervention of choice. Adenosine is an effective and generally well-tolerated agent for the treatment of supraventricular tachycardia. Lidocaine is the drug of choice for ventricular dysrhythmias, and bretylium, still relatively unexplored, is in reserve. Many pediatricians use dopamine for shock in the postresuscitative period, but epinephrine is superior. Most animal research on cardiac arrest is based on models with ventricular fibrillation that probably are not reflective of cardiac arrest situations most often seen in pediatrics.

Hemodynamic effects of carcinine in the anesthetized, instrumented, open-chest rat.

OBJECTIVE: To determine the pharmacologic effect of carcinine (beta-alanyl histamine), a compound that has been shown to be a positive inotrope in the isolated perfused guinea pig heart, on hemodynamics in an intact, anesthetized rat model. DESIGN: Prospective dose-response study. SETTING: Animal research laboratory of a university medical center. SUBJECTS: Male Sprague-Dawley rats. INTERVENTIONS: Eight male Sprague-Dawley rats were anesthetized with ketamine and midazolam. A tracheostomy tube, and central venous and arterial catheters were inserted. An electromagnetic flow probe was placed around the ascending aorta through a right thoracotomy for measurement of cardiac output. Dosages of carcinine from 0 to 10 mg/kg were infused intravenously over 30 secs, and hemodynamic parameters were measured at baseline and at peak effect. MEASUREMENTS AND MAIN RESULTS: At dosages of 3 mg/kg and 10 mg/kg, carcinine significantly reduced mean arterial blood pressure, systemic vascular resistance index, and left ventricular stroke work index. There was no carcinine-induced effect on heart rate, central venous pressure, cardiac index, or stroke index. Lower doses of carcinine had no effect on the measured variables. CONCLUSIONS: In this open-chest rat model, the primary pharmacologic effect of carcinine is systemic arterial vasodilation. A negative inotropic effect is suggested. Hypotension is secondary to these carcinine-induced actions. These results differ from results previously published using an isolated guinea pig heart preparation. Our model suggests that efforts to develop a clinical role for carcinine should exploit vascular rather than cardiac effects. Species differences may also play a role.

Acute hypoxemic respiratory failure in children following bone marrow transplantation: an outcome and pathologic study.

OBJECTIVES: To describe the pulmonary pathology and clinical outcome in children with acute hypoxemic respiratory failure after bone marrow transplantation. DESIGN: Review of medical records and pathologic material of patients diagnosed with acute hypoxemic respiratory failure after bone marrow transplantation. SETTING: Pediatric intensive care unit (ICU) of a teaching hospital. PATIENTS AND METHODS: Retrospective review of a consecutive cohort of children, with a history of bone marrow transplantation admitted to the pediatric ICU during a 7-yr study period, and who met a published definition of acute hypoxemic respiratory failure. For each admission, the pediatric ICU course and outcome were reviewed. Pathologic material that was obtained from the patients was reexamined and assigned to one of the following categories: acute or organizing diffuse alveolar damage, pulmonary hemorrhage, nonspecific interstitial pneumonitis, or infectious pneumonia. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Forty-three patients satisfied criteria for inclusion in the study group. Indications for bone marrow transplantation were: solid tumor (30%), leukemia (44%), congenital immunodeficiency (19%), and aplastic anemia (7%). Patients were admitted to the pediatric ICU a median of 1 month (range 0 to 126) after bone marrow transplantation. Thirty-eight (88%) patients died in the pediatric ICU. Tissue histologic material was available from 21 (49%) patients. Six (29%) of 21 patients had acute diffuse alveolar damage; one (5%) had organizing diffuse alveolar damage; three (14%) had nonspecific interstitial pneumonitis; and two (10%) had pulmonary hemorrhage. Infectious pneumonia occurred in nine (43%) cases (five fungal; four viral). CONCLUSIONS: The acute mortality rate (88%) for children with acute hypoxemic respiratory failure after bone marrow transplantation is similar to that reported for adults with this combination of conditions. Diffuse alveolar damage, the histologic hallmark of adult respiratory distress syndrome, was present in a minority (33%) of patients. Infectious pneumonia was the most frequent cause of acute hypoxemic respiratory failure in patients who had pathologic tissue available, emphasizing the need for aggressive diagnostic studies and early institution of antifungal and antiviral therapy.

Critical care of children with acute brain injury.

Severe neurologic illness and injury in children may occur in a wide range of clinical and environmental settings. The majority of children who sustain traumatic brain injury will achieve a good outcome if intensive care is directed toward preventing secondary injury. The most important aspect of care is ensuring adequate oxygenation, ventilation, and perfusion. Together with standard supportive care, the aggressive use of intraventricular pressure monitoring and CSF drainage to treat intracranial hypertension can attenuate or prevent continuing brain injury. Sustained hyperventilation, aggressive diuresis, hypothermia, and induction of barbiturate coma are reserved for children for whom the first tier of therapy is not effective.

Pharmacokinetics of cardiovascular drugs in children. Inotropes and vasopressors.

Infants and children with congenital or acquired heart disease and children with systemic disease often require pharmacological support of their failing circulation. Catecholamines may serve as inotropic (enhance myocardial contractility) or vasopressor (elevate systemic vascular resistance) agents. Noncatecholamine inotropic agents, such as the cardiac glycosides or the bipyridines, may be used in place of, or in addition to, catecholamines. Developmental changes in neonates, infants and children will affect the response to inotropic or pressor therapy. Maturation of the gastrointestinal tract, liver and kidneys alters absorption, metabolism and elimination of drugs, although there are few clear examples of this among the vasoactive drugs considered in this review. Changes in body composition affect the volume of distribution (Vd) and clearance (CL) of drugs. Developmentally based pharmacodynamic differences also affect the responses to both therapeutic and toxic effects of inotropes. These pharmacodynamic differences are based in part upon developmental changes in myocardial structure, cardiac innervation and adrenergic receptor function. For example, the immature myocardium has fewer contractile elements and therefore a decreased ability to increase contractility; it also responds poorly to standard techniques of manipulating preload. Available data suggest that dopamine and dobutamine pharmacokinetics are similar to those in adults. Wide interindividual variability has been noted. A consistent relationship between CL and age has not been demonstrated, although one investigator demonstrated an almost 2-fold increase in the CL of dopamine in children under the age of 2 years. The CL of dopamine appears to be reduced in children with renal and hepatic failure. Fewer data are available regarding the pharmacokinetics of epinephrine (adrenaline), norepinephrine (noradrenaline) and isoprenaline (isoproterenol). Digoxin pharmacokinetics have been extensively evaluated in infants and children. The Vd for digoxin is increased in infants and children. Children beyond the neonatal period display increased CL of digoxin, approaching adult values during puberty. Although it was previously thought that children both needed and tolerated higher serum concentrations of digoxin than adults, more recent studies indicate that adequate clinical response can be achieved with serum concentrations similar to those aimed for in adults, with decreased toxicity. Evaluation of studies of digoxin pharmacokinetics is complicated by the presence of an endogenous substance with digoxin-like activity on radioimmunoassay. Limited studies of amrinone pharmacokinetics in infants and children indicate a dramatically larger Vd, and a decreased elimination half-life in older infants and children, compared with values observed in adults.