Multi-Way Multi-Group Segregation and Diversity Indices

Background: How can we compute a segregation or diversity index from a three-way or multi-way contingency table, where each variable can take on an arbitrary finite number of values and where the index takes values between zero and one? Previous methods only exist for two-way contingency tables or dichotomous variables. A prototypical three-way case is the segregation index of a set of industries or departments given multiple explanatory variables of both sex and race. This can be further extended to other variables, such as disability, number of years of education, and former military service. Methodology/Principal Findings: We extend existing segregation indices based on Euclidean distance (square of coefficient of variation) and Boltzmann/Shannon/Theil index from two-way to multi-way contingency tables by including multiple summations. We provide several biological applications, such as indices for age polyethism and linkage disequilibrium. We also provide a new heuristic conceptualization of entropy-based indices. Higher order association measures are often independent of lower order ones, hence an overall segregation or diversity index should be the arithmetic mean of the normalized association measures at all orders. These methods are applicable when individuals selfidentify as multiple races or even multiple sexes and when individuals work part-time in multiple industries. Conclusions/Significance: The policy implications of this work are enormous, allowing people to rigorously test whethe

Lack of Agreement in Pediatric Emergency Department Discharge Diagnoses from Clinical and Administrative Data Sources

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75409/1/j.1553-2712.2007.tb01852.x.pd

High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

Replication and pathogenesis of the human immunodeficiency virus (HIV) is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We invent high-throughput SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) technology, which uses many of the same tools as DNA sequencing, to quantify RNA backbone flexibility at single-nucleotide resolution and from which robust structural information can be immediately derived. We analyze the structure of HIV-1 genomic RNA in four biologically instructive states, including the authentic viral genome inside native particles. Remarkably, given the large number of plausible local structures, the first 10% of the HIV-1 genome exists in a single, predominant conformation in all four states. We also discover that noncoding regions functioning in a regulatory role have significantly lower (p-value < 0.0001) SHAPE reactivities, and hence more structure, than do viral coding regions that function as the template for protein synthesis. By directly monitoring protein binding inside virions, we identify the RNA recognition motif for the viral nucleocapsid protein. Seven structurally homologous binding sites occur in a well-defined domain in the genome, consistent with a role in directing specific packaging of genomic RNA into nascent virions. In addition, we identify two distinct motifs that are targets for the duplex destabilizing activity of this same protein. The nucleocapsid protein destabilizes local HIV-1 RNA structure in ways likely to facilitate initial movement both of the retroviral reverse transcriptase from its tRNA primer and of the ribosome in coding regions. Each of the three nucleocapsid interaction motifs falls in a specific genome domain, indicating that local protein interactions can be organized by the long-range architecture of an RNA. High-throughput SHAPE reveals a comprehensive view of HIV-1 RNA genome structure, and further application of this technology will make possible newly informative analysis of any RNA in a cellular transcriptome

Radiation Performance of 1 Gbit DDR SDRAMs Fabricated in the 90 nm CMOS Technology Node

We present Single Event Effect (SEE) and Total Ionizing Dose (TID) data for 1 Gbit DDR SDRAMs (90 nm CMOS technology) as well as comparing this data with earlier technology nodes from the same manufacturer

Recurrent and High‐frequency Use of the Emergency Department by Pediatric Patients

Objectives The authors sought to describe the epidemiology of and risk factors for recurrent and high‐frequency use of the emergency department (ED) by children. Methods This was a retrospective cohort study using a database of children aged 0 to 17 years, inclusive, presenting to 22 EDs of the Pediatric Emergency Care Applied Research Network (PECARN) during 2007, with 12‐month follow‐up after each index visit. ED diagnoses for each visit were categorized as trauma, acute medical, or chronic medical conditions. Recurrent visits were defined as any repeat visit; high‐frequency use was defined as four or more recurrent visits. Generalized estimating equations (GEEs) were used to measure the strength of associations between patient and visit characteristics and recurrent ED use. Results A total of 695,188 unique children had at least one ED visit each in 2007, with 455,588 recurrent ED visits in the 12 months following the index visits. Sixty‐four percent of patients had no recurrent visits, 20% had one, 8% had two, 4% had three, and 4% had four or more recurrent visits. Acute medical diagnoses accounted for most visits regardless of the number of recurrent visits. As the number of recurrent visits per patient rose, chronic diseases were increasingly represented, with asthma being the most common ED diagnosis. Trauma‐related diagnoses were more common among patients without recurrent visits than among those with high‐frequency recurrent visits (28% vs. 9%; p < 0.001). High‐frequency recurrent visits were more often within the highest severity score classifications. In multivariable analysis, recurrent visits were associated with younger age, black or Hispanic race or ethnicity, and public health insurance. Conclusions Risk factors for recurrent ED use by children include age, race and ethnicity, and insurance status. Although asthma plays an important role in recurrent ED use, acute illnesses account for the majority of recurrent ED visits. Resumen Objetivos Describir la epidemiología y los factores de riesgo de revista e hiperfrecuentación del servicio de urgencias (SU) por parte de los pacientes pediátricos. Metodología Estudio de cohorte retrospectivo mediante una base de datos de niños entre 0 y 17 años inclusive, que acudieron a 22 SU de la Pediatric Emergency Care Applied Research Network durante 2007, con un seguimiento de 12 meses tras cada visita índice. Los diagnósticos del SU de cada visita se clasificaron como traumatológico, médico agudo o enfermedades médicas crónicas. Las revisitas se definieron como cualquier visita repetida; la hiperfrecuentación se definió como cuatro o más revisitas. Se utilizaron ecuaciones de estimación generalizada para medir la fuerza de las asociaciones entre las características al paciente y la visita y la revisita del SU. Resultados Un total de 695.188 niños tuvieron al menos una visita al SU en 2007, con 455.588 revisitas al SU en los 12 meses tras las visitas índice. Un 64% de los pacientes no tuvieron revisitas, un 20% tuvo una, un 8% tuvo dos, un 4% tuvo tres y un 4% tuvo cuatro o más revisitas. Los diagnósticos médicos agudos representan la mayoría de las visitas, con independencia del número de revisitas. A medida que el número de revisitas por paciente aumentaba, las enfermedades crónicas estaban más representadas, y el asma fue el diagnóstico más común en el SU. Los diagnósticos relacionados con lo traumatológico fueron más frecuentes entre los pacientes sin revisitas que entre aquéllos con hiperfrecuentación (28% vs. 9%; p < 0,001). La alta frecuencia de revisitas fue más frecuente en las clasificaciones de gravedad más altas. En el análisis multivariable, las revisitas se asociaron con una edad más joven, raza o etnia negra o hispana, y la tenencia de un seguro de salud público. Conclusiones Los factores de riesgo para la revisita al SU por los niños incluyen la edad, la raza o etnia, y el tipo de seguro médico. Aunque el asma juega un papel importante en la revisita al SU, las enfermedades agudas representan la mayoría de la revistas al SU.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106853/1/acem12347.pd

Urinary ATP as an indicator of infection and inflammation of the urinary tract in patients with lower urinary tract symptoms

BACKGROUND: Adenosine-5'-triphosphate (ATP) is a neurotransmitter and inflammatory cytokine implicated in the pathophysiology of lower urinary tract disease. ATP additionally reflects microbial biomass thus has potential as a surrogate marker of urinary tract infection (UTI). The optimum clinical sampling method for ATP urinalysis has not been established. We tested the potential of urinary ATP in the assessment of lower urinary tract symptoms, infection and inflammation, and validated sampling methods for clinical practice. METHODS: A prospective, blinded, cross-sectional observational study of adult patients presenting with lower urinary tract symptoms (LUTS) and asymptomatic controls, was conducted between October 2009 and October 2012. Urinary ATP was assayed by a luciferin-luciferase method, pyuria counted by microscopy of fresh unspun urine and symptoms assessed using validated questionnaires. The sample collection, storage and processing methods were also validated. RESULTS: 75 controls and 340 patients with LUTS were grouped as without pyuria (n = 100), pyuria 1-9 wbc ?l(-1) (n = 120) and pyuria ?10 wbc ?l(-1) (n = 120). Urinary ATP was higher in association with female gender, voiding symptoms, pyuria greater than 10 wbc ?l(-1) and negative MSU culture. ROC curve analysis showed no evidence of diagnostic test potential. The urinary ATP signal decayed with storage at 23°C but was prevented by immediate freezing at ??-20°C, without boric acid preservative and without the need to centrifuge urine prior to freezing. CONCLUSIONS: Urinary ATP may have a role as a research tool but is unconvincing as a surrogate, clinical diagnostic marker

An automated quasi-continuous capillary refill timing device

Capillary refill time (CRT) is a simple means of cardiovascular assessment which is widely used in clinical care. Currently, CRT is measured through manual assessment of the time taken for skin tone to return to normal colour following blanching of the skin surface. There is evidence to suggest that manually assessed CRT is subject to bias from ambient light conditions, a lack of standardisation of both blanching time and manually applied pressure, subjectiveness of return to normal colour, and variability in the manual assessment of time. We present a novel automated system for CRT measurement, incorporating three components: a non-invasive adhesive sensor incorporating a pneumatic actuator, a diffuse multi-wavelength reflectance measurement device, and a temperature sensor; a battery operated datalogger unit containing a self contained pneumatic supply; and PC based data analysis software for the extraction of refill time, patient skin surface temperature, and sensor signal quality. Through standardisation of the test, it is hoped that some of the shortcomings of manual CRT can be overcome. In addition, an automated system will facilitate easier integration of CRT into electronic record keeping and clinical monitoring or scoring systems, as well as reducing demands on clinicians. Summary analysis of volunteer (n = 30) automated CRT datasets are presented, from 15 healthy adults and 15 healthy children (aged from 5 to 15 years), as their arms were cooled from ambient temperature to 5°C. A more detailed analysis of two typical datasets is also presented, demonstrating that the response of automated CRT to cooling matches that of previously published studies

A tree-based decision model to support prediction of the severity of asthma exacerbations in children

This paper describes the development of a tree-based decision model to predict the severity of pediatric asthma exacerbations in the emergency department (ED) at 2 h following triage. The model was constructed from retrospective patient data abstracted from the ED charts. The original data was preprocessed to eliminate questionable patient records and to normalize values of age-dependent clinical attributes. The model uses attributes routinely collected in the ED and provides predictions even for incomplete observations. Its performance was verified on independent validating data (split-sample validation) where it demonstrated AUC (area under ROC curve) of 0.83, sensitivity of 84%, specificity of 71% and the Brier score of 0.18. The model is intended to supplement an asthma clinical practice guideline, however, it can be also used as a stand-alone decision tool

Rapid tests and urine sampling techniques for the diagnosis of urinary tract infection (UTI) in children under five years: a systematic review

Background: Urinary tract infection (UTI) is one of the most common sources of infection in children under five. Prompt diagnosis and treatment is important to reduce the risk of renal scarring. Rapid, cost-effective, methods of UTI diagnosis are required as an alternative to culture. Methods: We conducted a systematic review to determine the diagnostic accuracy of rapid tests for detecting UTI in children under five years of age. Results: The evidence supports the use of dipstick positive for both leukocyte esterase and nitrite (pooled LR+ = 28.2, 95% CI: 17.3, 46.0) or microscopy positive for both pyuria and bacteriuria (pooled LR+ = 37.0, 95% CI: 11.0, 125.9) to rule in UTI. Similarly dipstick negative for both LE and nitrite (Pooled LR- = 0.20, 95% CI: 0.16, 0.26) or microscopy negative for both pyuria and bacteriuria (Pooled LR- = 0.11, 95% CI: 0.05, 0.23) can be used to rule out UTI. A test for glucose showed promise in potty-trained children. However, all studies were over 30 years old. Further evaluation of this test may be useful. Conclusion: Dipstick negative for both LE and nitrite or microscopic analysis negative for both pyuria and bacteriuria of a clean voided urine, bag, or nappy/pad specimen may reasonably be used to rule out UTI. These patients can then reasonably be excluded from further investigation, without the need for confirmatory culture. Similarly, combinations of positive tests could be used to rule in UTI, and trigger further investigation