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Measuring diagnoses: ICD code accuracy.

OBJECTIVE: To examine potential sources of errors at each step of the described inpatient International Classification of Diseases (ICD) coding process. DATA SOURCES/STUDY SETTING: The use of disease codes from the ICD has expanded from classifying morbidity and mortality information for statistical purposes to diverse sets of applications in research, health care policy, and health care finance. By describing a brief history of ICD coding, detailing the process for assigning codes, identifying where errors can be introduced into the process, and reviewing methods for examining code accuracy, we help code users more systematically evaluate code accuracy for their particular applications. STUDY DESIGN/METHODS: We summarize the inpatient ICD diagnostic coding process from patient admission to diagnostic code assignment. We examine potential sources of errors at each step and offer code users a tool for systematically evaluating code accuracy. PRINCIPLE FINDINGS: Main error sources along the "patient trajectory" include amount and quality of information at admission, communication among patients and providers, the clinician's knowledge and experience with the illness, and the clinician's attention to detail. Main error sources along the "paper trail" include variance in the electronic and written records, coder training and experience, facility quality-control efforts, and unintentional and intentional coder errors, such as misspecification, unbundling, and upcoding. CONCLUSIONS: By clearly specifying the code assignment process and heightening their awareness of potential error sources, code users can better evaluate the applicability and limitations of codes for their particular situations. ICD codes can then be used in the most appropriate ways.

Data Collection↗

Comparison of paenibacillus azotofixans strains isolated from rhizoplane, rhizosphere, and non-root-associated soil from maize planted in two different brazilian soils

Paenibacillus azotofixans is a nitrogen-fixing bacterium often found in soil and in the rhizospheres of different grasses. In this study, two Brazilian clay soils were planted with cross-hybrid maize (BR-201) and four stages of plant growth were analyzed to characterize the P. azotofixans populations present in the rhizoplanes, rhizospheres, and non-root-associated soils (herein called nonrhizospheres). A total of 106 strains were isolated and identified as P. azotofixans with an API 50CH kit, by classical biochemical tests, and via the use of specific primers based on the 16S rRNA gene in PCRs. To compare the isolated strains, phenotypic characteristics were determined and three different probes were used in hybridization experiments: two nif probes and one probe comprising a 0.58-kb fragment cloned from the P. azotofixans C3L4 genome. These results were used to construct a dendrogram, in which two main clusters could be observed. One cluster contained exclusively strains from Varzea soil, and the other contained the majority of strains from Cerrado soil. The 60 strains from Varzea soil and the 46 strains from Cerrado soil were further analyzed with REP and BOX primers, respectively. Based on the patterns obtained, it was possible to identify 21 different groups among strains from Varzea soil and 4 different groups among strains from Cerrado soil. These different patterns were tested by multivariate analysis of variance, and differences in the populations of P. azotofixans during the four stages of plant growth were demonstrated. Moreover, strains isolated from the rhizoplanes, rhizospheres, and nonrhizospheres of maize planted in Cerrado and Varzea soils were shown to be statistically different; the diversity of P. azotofixans strains was affected by the soil type.

Journal Article↗

Contrasting patterns of phytoplankton community pigment composition in two salt marsh estuaries in southeastern United States.

Phytoplankton community pigment composition and water quality were measured seasonally along salinity gradients in two minimally urbanized salt marsh estuaries in South Carolina in order to examine their spatial and temporal distributions. The North Inlet estuary has a relatively small watershed with minimal fresh water input, while the Ashepoo, Combahee, and Edisto (ACE) Basin is characterized by a relatively greater influence of riverine drainage. Sampling stations were located in regions of the estuaries experiencing frequent diurnal tidal mixing and had similar salinity and temperature regimens. Phytoplankton community pigment composition was assessed by using high-performance liquid chromatography (HPLC) and multivariate statistical analyses. Shannon diversity index, principal-component, and cluster analyses revealed that phytoplankton community pigments in both estuaries were seasonally variable, with similar diversities but different compositions. The temporal pigment patterns indicated that there was a relatively weak correlation between the pigments in ACE Basin and the relative persistence of photopigment groups in North Inlet. The differences were presumably a consequence of the unpredictability and relatively greater influence of river discharge in the ACE Basin, in contrast to the greater environmental predictability of the more tidally influenced North Inlet. Furthermore, the timing, magnitude, and pigment composition of the annual phytoplankton bloom were different in the two estuaries. The bloom properties in North Inlet reflected the predominance of autochthonous ecological control (e.g., regenerated nutrients, grazing), and those in ACE Basin suggested that there was greater influence of allochthonous environmental factors (e.g., nutrient loading, changes in turbidity). These interestuarine differences in phytoplankton community structure and control provide insight into the organization of phytoplankton in estuaries.

Animals↗

Selecting tagging SNPs for association studies using power calculations from genotype data.

Recent studies have indicated that linkage disequilibrium (LD) between single nucleotide polymorphism (SNP) markers can be used to derive a reduced set of tagging SNPs (tSNPs) for genetic association studies. Previous strategies for identifying tSNPs have focused on LD measures or haplotype diversity, but the statistical power to detect disease-associated variants using tSNPs in genetic studies has not been fully characterized. We propose a new approach of selecting tSNPs based on determining the set of SNPs with the highest power to detect association. Two-locus genotype frequencies are used in the power calculations. To show utility, we applied this power method to a large number of SNPs that had been genotyped in Caucasian samples. We demonstrate that a significant reduction in genotyping efforts can be achieved although the reduction depends on genotypic relative risk, inheritance mode and the prevalence of disease in the human population. The tSNP sets identified by our method are remarkably robust to changes in the disease model when small relative risk and additive mode of inheritance are employed. We have also evaluated the ability of the method to detect unidentified SNPs. Our findings have important implications in applying tSNPs from different data sources in association studies.

Algorithms↗

Occurrence of protein structure elements in conserved sequence regions.

BACKGROUND: Conserved protein sequence regions are extremely useful for identifying and studying functionally and structurally important regions. By means of an integrated analysis of large-scale protein structure and sequence data, structural features of conserved protein sequence regions were identified. RESULTS: Helices and turns were found to be underrepresented in conserved regions, while strands were found to be overrepresented. Similar numbers of loops were found in conserved and random regions. CONCLUSION: These results can be understood in light of the structural constraints on different secondary structure elements, and their role in protein structural stabilization and topology. Strands can tolerate fewer sequence changes and nonetheless keep their specific shape and function. They thus tend to be more conserved than helices, which can keep their shape and function with more changes. Loop behavior can be explained by the presence of both constrained and freely changing loops in proteins. Our detailed statistical analysis of diverse proteins links protein evolution to the biophysics of protein thermodynamic stability and folding. The basic structural features of conserved sequence regions are also important determinants of protein structure motifs and their function.

Amino Acid Sequence↗

Performance indexes of a dot-enzyme-linked immunosorbent assay (dot-ELISA) and an enzyme-linked immunosorbent assay (IgG-ELISA) for field surveys of New World leishmaniasis.

Diagnostic performance indexes of sensitivity, specificity, positive predictive value and efficiency were determined for dot-ELISA and IgG-ELISA tests in 340 leishmaniasis sera. Sensitivity of the dot-ELISA was significantly lower than IgG-ELISA's; the two tests had indexes of specificity and positive predictive value of the same magnitude. Seventy-eight sera gave a negative dot-ELISA test result and a positive IgG-ELISA test result. When sera were classified according to different criteria as how to interpret this diversity, the kappa statistic did not corroborate the classification indicating that the two tests display a substantial strength of agreement. The results presented indicate that performance indexes accrued in a survey where variables are well known may be extrapolated to other population studies if the disease presents itself as highly prevalent (due to a selection bias or not) and may be expected to discriminate a disease status among test positives.

Enzyme-Linked Immunosorbent Assay↗

A new potential mosquito-borne virus: detection of Human-derived Jingmenvirus in several-species of mosquitoes from Yaoundé, Cameroon.

BACKGROUND: Tick-borne Jingmenviruses are becoming an increasing arbovirus concern due to the rising number of reported infections in humans and animals, as well as their wide geographic distribution. The involvement of other hematophagous arthropods as vectors of Jingmenviruses is still unknown. METHODS: Mosquitoes were sampled in two different biotopes in Cameroon (Yaoundé and Garoua) during the rainy and the dry seasons in 2022 and 2023. Metatranscriptomics Next Generation Sequencing was conducted using Illumina technology. Viral sequences detection revealed the presence of several contigs with high sequence identity to a human-derived Jingmenvirus (HdJV) previously discovered in plasma from an individual from Yaoundé, Cameroon. A draft viral genome was constituted for each Jingmenvirus-positive samples. Maximum likelihood phylogenetic reconstructions were used to position mosquito-associated viruses within the diversity of Jingmenviruses. Statistical analyses were conducted to estimate the prevalence of infected mosquitoes and the effect of different variables (region, season, year, mosquito species) on Jingmenvirus detection. RESULTS: HdJV was identified during the dry and the rainy seasons in 4 species of mosquitoes: Aedes albopictus, Culex quinquefasciatus and Culex wansoni from Yaoundé, and Anopheles gambiae s.l. from Garoua. The overall prevalence of HdJV-infected mosquitoes was estimated to 0.90% [0.41-1.69]; and the unique variable significantly associated with HdJV detection was the sampling area: Yaoundé showed the highest prevalence (2.29% [0.95-4.68]) compared to Garoua (0.18% [0.01-0.79]). Mosquito-associated Jingmenviruses shared a high nucleotide identity (between 98.64-100% according to the segment) and clustered in the same clade in the phylogenetic analysis, that they belong to the same viral species circulating in different mosquito species. The viral genome shared between 96.4% and 98.9% nucleotide identity with a HdJV detected in the plasma of a patient suffering from febrile illness originating from the same area, suggesting the possible involvement of mosquitoes as vectors of arboviral Jingmenviruses in human infections. CONCLUSIONS: This finding provides new insights into the ecology and transmission dynamics of Jingmenviruses, highlighting mosquitoes as potential vectors, alongside ticks, in the zoonotic transmission of this virus group.

Jingmenvirus↗

Prognostic factors for successful outcome following urethral rupture in dogs and cats.

Twenty dogs and 29 cats were identified with urethral rupture. Males predominated in both groups. The most common cause of urethral rupture in dogs was vehicular trauma, and in cats it was trauma associated with urethral obstruction and catheterization. Clinicopathological findings, type of surgical correction, time to surgery, type of urinary diversion, and duration of urinary diversion were not statistically associated with the outcome. In this study, the presence of multiple traumatic injuries was associated with a poor outcome.

Animals↗

The National Morbidity, Mortality, and Air Pollution Study. Part II: Morbidity and mortality from air pollution in the United States.

BACKGROUND: Epidemiologic time-series studies conducted in a number of cities have identified, in general, an association between daily changes in concentration of ambient particulate matter (PM) and daily number of deaths (mortality). Increased hospitalization (a measure of morbidity) among the elderly for specific causes has also been associated with PM. These studies have raised concerns about public health effects of particulate air pollution and have contributed to regulatory decisions in the United States. However, scientists have pointed out uncertainties that raise questions about the interpretation of these studies. One limitation to previous time-series studies of PM and adverse health effects is that the evidence for an association is derived from studies conducted in single locations using diverse analytic methods. Statistical procedures have been used to combine the results of these single location studies in order to produce a summary estimate of the health effects of PM. Difficulties with this approach include the process by which cities were selected to be studied, the different analytic methods applied to each single study, and the variety of methods used to measure or account for variables included in the analysis. These individual studies were also not able to account for the effects of gaseous air pollutants in a systematic manner.

Adolescent↗

Pelvic endometriosis.

The recent heightened interest in endometriosis has led to remarkable progress in the elucidation of the pathophysiology of this enigmatic disease. Presently, it is not clear why some individuals with endometriosis develop infertility and pelvic pain, whereas others with a similar degree of disease do not. Several tantalizing clues have been extracted from studies of the molecular pathogenesis, immunology, and biochemistry of endometriosis. Investigations are now under way to determine the specific relevance to infertility of macrophage aggregation; prostaglandin and related metabolite production by endometriotic lesions and macrophages; specific factors released by endometriosis that might directly impair ovum pick-up, fertilization, embryo transfer, or implantation; and ovulatory dysfunction including luteal phase deficiency and LUFS. There are probably a host of potential mechanisms of infertility in endometriosis; additional research should enable us to determine their regulatory features and to formulate effective clinical intervention. We now have a broader array of options for the treatment of endometriosis than ever before. However, most of the extant reported clinical experience consists of case reports and limited series of patients without the use of controls, follow-up intervals, and appropriate statistical analysis. The diverse course and presentation of the disease have limited our ability to develop a staging system that provides consistent scoring among different clinicians and appropriate relative emphasis on the various manifestations of the disease. Some additional resolution will be necessary to assess the relative contribution to infertility by fresh and recurrent lesions, endometriomas, and adhesions. These problems are now in sharp focus, and data should be available in the future giving us an accurate appraisal of the clinical effectiveness of danazol, gestrinone, GnRH analogues, conservative surgery, laparoscopic surgery including use of the laser, IVF-ET, and GIFT. Also, it is anticipated that potentially fertile patients with endometriosis might be identified so that they could avoid therapy altogether.

Endometriosis↗

Distinguishing between primary and secondary intergradation among morphologically differentiated populations of Anolis marmoratus.

Distinguishing between primary and secondary intergradation among differentiated populations, and the relative importance of drift and selection, are persistent problems in evolutionary biology. An historical perspective on population interactions can provide insight into the nature of contacts, and thus help resolve these questions. Continuously distributed populations of Anolis marmoratus from the island of Basse Terre in the Guadeloupean archipelago of the Lesser Antilles show a striking degree of geographic variation in morphology. Initial surveys of mtDNA variation from throughout the Guadeloupean Archipelago revealed one case where levels of sequence difference and phylogenetic relationships of alleles from morphologically differentiated populations from the east coast of Basse Terre were consistent with primary intergradation. In this paper, I examine the genetic population structure of a series of populations spanning this north-south cline in morphological variation to test the hypothesis of primary intergradation. Sequences of the mitochondrial cytochrome-b gene from 50 individuals representing five populations spanning the cline were obtained and fourteen unique haplotypes (differing by 2% or less) were detected. Patterns of nucleotide substitution among haplotypes do not deviate from neutral expectation indicating no effect of selection at the level of mtDNA sequences. Estimates of population structure and gene flow were made using both summary statistics for nucleotide diversity (Nst) and cladistic methods. The results are sensitive to the choice of gene flow model, and this is discussed in detail. Mitochondrial variation in the northern populations may not be at equilibrium, and the phylogeny of alleles is consistent with a recent increase in effective population size. Estimates of nucleotide diversity, gene flow, and the phylogenetic relationships of haplotypes indicate that the southern-most population (representing the extreme of morphological variation along this cline) has been relatively isolated from populations to the north and has experienced a reduced effective population size. The apparent clinal variation between the southern population and the others may therefore reflect secondary contact and introgression rather than primary intergradation.

Animals↗

The influence of linear elements on plant species diversity of Mediterranean rural landscapes: assessment of different indices and statistical approaches.

This paper mainly aims to study the linear element influence on the estimation of vascular plant species diversity in five Mediterranean landscapes modeled as land cover patch mosaics. These landscapes have several core habitats and a different set of linear elements--habitat edges or ecotones, roads or railways, rivers, streams and hedgerows on farm land--whose plant composition were examined. Secondly, it aims to check plant diversity estimation in Mediterranean landscapes using parametric and non-parametric procedures, with two indices: Species richness and Shannon index. Land cover types and landscape linear elements were identified from aerial photographs. Their spatial information was processed using GIS techniques. Field plots were selected using a stratified sampling design according to relieve and tree density of each habitat type. A 50x20 m2 multi-scale sampling plot was designed for the core habitats and across the main landscape linear elements. Richness and diversity of plant species were estimated by comparing the observed field data to ICE (Incidence-based Coverage Estimator) and ACE (Abundance-based Coverage Estimator) non-parametric estimators. The species density, percentage of unique species, and alpha diversity per plot were significantly higher (p < 0.05) in linear elements than in core habitats. ICE estimate of number of species was 32% higher than of ACE estimate, which did not differ significantly from the observed values. Accumulated species richness in core habitats together with linear elements, were significantly higher than those recorded only in the core habitats in all the landscapes. Conversely, Shannon diversity index did not show significant differences.

Biodiversity↗

The application of rarefaction techniques to molecular inventories of microbial diversity.

With the growing capacity to inventory microbial community diversity, the need for statistical methods to compare community inventories is also growing. Several approaches have been proposed for comparing the diversity of microbial communities: some adapted from traditional ecology and others designed specifically for molecular inventories of microbes. Rarefaction is one statistical method that is commonly applied in microbial studies, and this chapter discusses the procedure and its advantages and disadvantages. Rarefaction compares observed taxon richness at a standardized sampling effort using confidence intervals. Special emphasis is placed here on the need for precise, rather than unbiased, estimation methods in microbial ecology, but precision can be judged only with a very large sample or with multiple samples drawn from a single community. With low sample sizes, rarefaction curves also have the potential to lead to incorrect rankings of relative species richness, but this chapter discusses a new method with the potential to address this problem. Finally, this chapter shows how rarefaction can be applied to the comparison of the taxonomic similarity of microbial communities.

Bacteria↗

Cluster size diversity, percolation, and complex systems.

Diversity of cluster size has been used as a measurement of complexity in several systems that generate a statistical distribution of clusters. Using Monte Carlo simulations, we present a statistical analysis of the cluster size diversity and the number of clusters generated on randomly occupied lattices for the Euclidean dimensions 1 to 6. A tuning effect for diversity of cluster size and critical probabilities associated with the maximum diversity and the maximum number of clusters are reported. The probability of maximum diversity is related to the percolation threshold and several scaling relations between the variables measured are reported. The statistics of cluster size diversity has important consequences in the statistical description of the Universe as a complex system.

Journal Article↗

Locus-specific genetic diversity between human populations: an analysis of the literature.

The debate over classification of the human species according to racial or continental lines has involved reports on genetic differences in allele frequencies of a number of loci with important biomedical functions. Such differences are in contrast with the fact that, for human beings, intrapopulation genetic diversity is larger than that seen between populations. In an attempt to address the hypothesis that certain genes show high interpopulation diversity due to selective pressure, the literature was surveyed to quantify such diversity using Wrights Fst statistic. The gene-specific Fst values were then compared to pairwise population values of Fst taken over a large number of genes, which presumably reflect mostly neutral mechanisms of genetic diversity such as drift. The results showed that the majority of pairwise population values of Fst for over 30 genes of biomedical significance were either below or within the expected limits of Fst based on published values. These results do not support the idea that positive or diversifying natural selection plays an important role in increasing genetic diversity, even in genes that might be expected to be subject to selection pressure. Balancing selection, whereby the degree of genetic diversity is actually lower than that expected, appears to occur more frequently for these genes. The fact that allele frequency differences between populations might be "statistically significant" does not therefore necessarily imply a degree of genetic diversity greater than would be expected due to nonselective mechanisms.

Chromosome Mapping↗

[Diversity and frequency of scientific research design and statistical methods in the "Arquivos Brasileiros de Oftalmologia": a systematic review of the "Arquivos Brasileiros de Oftalmologia"--1993-2002].

PURPOSE: To verify the frequency of study design, applied statistical analysis and approval by institutional review offices (Ethics Committee) of articles published in the "Arquivos Brasileiros de Oftalmologia" during a 10-year interval, with later comparative and critical analysis by some of the main international journals in the field of Ophthalmology. METHODS: Systematic review without metanalysis was performed. Scientific papers published in the "Arquivos Brasileiros de Oftalmologia" between January 1993 and December 2002 were reviewed by two independent reviewers and classified according to the applied study design, statistical analysis and approval by the institutional review offices. To categorize those variables, a descriptive statistical analysis was used. RESULTS: After applying inclusion and exclusion criteria, 584 articles for evaluation of statistical analysis and, 725 articles for evaluation of study design were reviewed. Contingency table (23.10%) was the most frequently applied statistical method, followed by non-parametric tests (18.19%), Student's t test (12.65%), central tendency measures (10.60%) and analysis of variance (9.81%). Of 584 reviewed articles, 291 (49.82%) presented no statistical analysis. Observational case series (26.48%) was the most frequently used type of study design, followed by interventional case series (18.48%), observational case description (13.37%), non-random clinical study (8.96%) and experimental study (8.55%). CONCLUSION: We found a higher frequency of observational clinical studies, lack of statistical analysis in almost half of the published papers. Increase in studies with approval by institutional review Ethics Committee was noted since it became mandatory in 1996.

Bibliometrics↗

Diversity and genetic structure of the Mexican endemic epiphyte Tillandsia achyrostachys E. Morr. ex Baker var. achyrostachys (Bromeliaceae).

BACKGROUND AND AIMS: The monoecious, bird-pollinated epiphytic Tillandsia achyrostachys E. Morr. ex Baker var. achyrostachys is an endemic bromeliad of the tropical dry forests of Mexico with clonal growth. In the Sierra de Huautla Natural Reserve this species shows a host preference for Bursera copallifera (Sessé & Moc ex. DC) Bullock. As a result of deforestation in the study area, B. copallifera has become a rare tree species in the remaining forest patches. This human-induced disturbance has directly affected the population densities of T. achyrostachys. In this study the genetic consequences of habitat fragmentation were assessed by comparing the genetic diversity, gene flow and genetic differentiation in six populations of T. achyrostachys in the Sierra de Huautla Natural Reserve, Mexico. METHODS: Allozyme electrophoresis of sixteen loci (eleven polymorphic and five monomorphic) were used. The data were analysed with standard statistical approximations for obtaining diversity, genetic structure and gene flow. KEY RESULTS: Genetic diversity and allelic richness were: HE = 0.21 +/- 0.02, A = 1.86 +/- 0.08, respectively. F-statistics revealed a deficiency of heterozygous plants in all populations (Fit = 0.65 +/- 0.02 and Fis = 0.43 +/- 0.06). Significant genetic differentiation between populations was detected (Fst = 0.39 +/- 0.07). Average gene flow between pairs of populations was relatively low and had high variation (Nm = 0.46 +/- 0.21), which denotes a pattern of isolation by distance. The genetic structure of populations of T. achyrostachys suggests that habitat fragmentation has reduced allelic richness and genetic diversity, and increased significant genetic differentiation (by approx. 40 %) between populations. CONCLUSIONS: The F-statistic values (>0) and the level of gene flow found suggest that habitat fragmentation has broken up the former population structure. In this context, it is proposed that the host trees of T. achyrostachys should be considered as a conservation priority, since they represent the limiting factor to bromeliad population growth and connectivity.

Environment↗

Partitioning species diversity across landscapes and regions: a hierarchical analysis of alpha, beta, and gamma diversity.

Species diversity may be additively partitioned within and among samples (alpha and beta diversity) from hierarchically scaled studies to assess the proportion of the total diversity (gamma) found in different habitats, landscapes, or regions. We developed a statistical approach for testing null hypotheses that observed partitions of species richness or diversity indices differed from those expected by chance, and we illustrate these tests using data from a hierarchical study of forest-canopy beetles. Two null hypotheses were implemented using individual- and sample-based randomization tests to generate null distributions for alpha and beta components of diversity at multiple sampling scales. The two tests differed in their null distributions and power to detect statistically significant diversity components. Individual-based randomization was more powerful at all hierarchical levels and was sensitive to departures between observed and null partitions due to intraspecific aggregation of individuals. Sample-based randomization had less power but still may be useful for determining whether different habitats show a higher degree of differentiation in species diversity compared with random samples from the landscape. Null hypothesis tests provide a basis for inferences on partitions of species richness or diversity indices at multiple sampling levels, thereby increasing our understanding of how alpha and beta diversity change across spatial scales.

Animals↗