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PubMed2006

Further comparison of faecal egg count reduction test procedures: sensitivity and specificity.

In a recent communication (McKenna 2006), a comparison was made between four different methods for calculating results from faecal egg count reduction (FECR) tests (FECRTs). The first and most complex of these, referred to as FECRT1, involved the use of the formula: FECR = 100 x (1-[T2/T1][C1/C2]), where T1 and T2 represented the mean pre- and post-treatment faecal nematode egg counts (FECs) of a treated group, and C1 and C2 represented the mean pre- and post-treatment FECs of an untreated control group, respectively. The other three formulae consisted of more simplified versions of this procedure. In one of them (FECRT2), only post-treatment samples were considered, whereas the other two were based on comparisons between the FECs of groups of animals sampled at the time of anthelmintic treatment (pre-treatment) with those sampled several days later (post-treatment). Thus, FECRT2 was determined according to the formula: FECR = 100 x (1-[T2/C2]), while FECRT3 was calculated from FECR = 100 x (1-[T2/T1]). The fourth procedure (FECRT4) was based on a further simplification of FECRT3, where pre-treatment FECs from only one treatment group were used for comparison with all post-treatment results. This base-line pre-treatment group thus effectively functioned as an untreated control group and hence the formula for FECRT4 was FECR = 100 x (1-[T2/C1]). The study was based on an analysis of 210 previously published FECRTs performed in sheep or goats. In each case, FECRs were calculated using all four of these FECRT formulae, and their results compared. The results of these comparisons indicated that the use of any one of them was likely to result in similar estimates of anthelmintic efficacy and the detection of comparable numbers of cases of anthelmintic resistance continued.

Animals↗

PubMed2001

Similarities in body image in sisters: the role of sociocultural internalization and social comparison.

The sociocultural theory of body image disturbance states that Western women experience pressure from sources such as parents, peers, and the media to maintain thinness. Social comparison theory emphasises the role of comparing one's appearance to others. Body image disturbance; awareness and Internalization of sociocultural messages regarding thinness; and sibling social comparisons were examined in 41 closest-in-age sisters through self-report questionnaires. Sisters showed similar levels of body image disturbance and sociocultural awareness and internalization. Sibling comparisons were negative for younger sisters but neutral or positive for older sisters. Sociocultural internalization predicted body dissatisfaction in both sisters, and body size distortion in younger sisters. Negative sibling comparisons during teenage years predicted body size distortion and body dissatisfaction in younger sisters, and preference for thinness in older sisters.

Journal Article↗

PubMed2005

Standardized infection surveillance in long-term care: interfacility comparisons from a regional cohort of facilities.

OBJECTIVES: To measure infection rates in a regional cohort of long-term-care facilities (LTCFs) using standard surveillance methods and to analyze different methods for interfacility comparisons. SETTING: Seventeen LTCFs in Idaho. DESIGN: Prospective, active surveillance for LTCF-acquired infections using standard definitions and case-finding methods was conducted from July 2001 to June 2002. All surveillance data were combined and individual facility performance was compared with the aggregate employing a variety of statistical and graphic methods. RESULTS: The surveillance data set consisted of 472,019 resident-days of care with 1717 total infections for a pooled mean rate of 3.64 infections per 1000 resident-days. Specific infections included respiratory (828; rate, 1.75), skin and soft tissue (520; rate, 1.10), urinary tract (282; rate, 0.60), gastrointestinal (77; rate, 0.16), unexplained febrile illnesses (6; rate, 0.01), and bloodstream (4; rate, 0.01). Initially, methods adopted from the National Nosocomial Infections Surveillance System were used comparing individual rates with pooled means and percentiles of distribution. A more sensitive method appeared to be detecting statistically significant deviations (based on chi-square analysis) of the individual facility rates from the aggregate of all other facilities. One promising method employed statistical process control charts (U charts) adjusted to compare individual rates with aggregate monthly rates, providing simultaneous visual and statistical comparisons. Small multiples graphs were useful in providing images valid for rapid concurrent comparison of all facilities. CONCLUSION: Interfacility comparisons have been demonstrated to be valuable for hospital infection control programs, but have not been studied extensively in LTCFs.

Cohort Studies↗

PubMed2006

Directly administered antiretroviral therapy in methadone clinics is associated with improved HIV treatment outcomes, compared with outcomes among concurrent comparison groups.

BACKGROUND: Directly administered antiretroviral therapy (DAART) in methadone clinics has the potential to improve treatment outcomes for human immunodeficiency virus (HIV)-infected injection drug users (IDUs). METHODS: DAART was provided at 3 urban methadone clinics. Eighty-two participants who were initiating or reinitiating highly active antiretroviral therapy (HAART) received supervised doses of therapy at the clinic on the mornings on which they received methadone. Treatment outcomes in the DAART group were compared with outcomes in 3 groups of concurrent comparison patients, who were drawn from the Johns Hopkins HIV Cohort. The concurrent comparison patients were taking HAART on a self-administered basis. The 3 groups of concurrent comparison patients were as follows: patients with a history of IDU who were receiving methadone at the time HAART was used (the IDU-methadone group; 75 patients), patients with a history of IDU who were not receiving methadone at the time that HAART was used (the IDU-nonmethadone group; 244 patients), and patients with no history of IDU (the non-IDU group; 490 patients). RESULTS: At 12 months, 56% of DAART participants achieved an HIV type 1 RNA level <400 copies/mL, compared with 32% of participants in the IDU-methadone group (P=.009), 33% of those in the IDU-nonmethadone group (P=.001), and 44% of those in the non-IDU group (P=.077). The DAART group experienced a median increase in the CD4 cell count of 74 cells/mm3, compared with 21 cells/mm3 in the IDU-methadone group (P=.04), 33 cells/mm3 in the IDU-nonmethadone group (P=.09), and 84 cells/mm3 in the non-IDU group (P=.98). After adjustment for other covariates in a logistic regression model, DAART participants were significantly more likely to achieve viral suppression than were patients in each of the 3 comparison groups. CONCLUSIONS: These results suggest that methadone clinic-based DAART has the potential to provide substantial clinical benefit for HIV-infected IDUs.

Adult↗

PubMed2001

Comparison of dosimetric standards of Canada and France for photons at 60Co and higher energies.

We report the results of a comparison of the dosimetric standards of Canada and France for photon beams at 60Co and a few higher energies. The present primary standard of absorbed dose to water for NRC, Canada is based on measurements made with a sealed water calorimeter. The corresponding standard of the LNHB, France is based on measurements made with a graphite calorimeter at 60Co energy and transferred to absorbed dose to water for 60Co and higher-energy photon beams using both ion chambers and Fricke dosemeters as transfer instruments. To make this comparison, we used three graphite-walled NE2571 Farmer chambers. The absorbed dose to water determined by the LNHB was greater than that determined by NRC by 0.20% at 60Co energy. This difference is not significant given the uncertainties on the standards. In order to do the comparison for higher-energy photons, we interpolated the NRC data set at the beam qualities used at the LNHB. When %dd(10)x is used as the method of specifying beam quality, the determination of absorbed dose to water by the LNHB is about 0.2% greater than that determined by NRC and consistent with the results at 60Co. However, when using TPR20,10 as the beam quality specifier, the LNHB determination is greater than the NRC's determination by 0.8% and 1.2% at 12 and 20 MV respectively. This discrepancy, which systematically increases with increasing energy, eventually exceeds the uncertainties in the ratio of the standards, estimated to be 0.7%. This underscores the importance of selecting the method of specifying beam quality, either %dd(10)x or TPR20,10, at least for the 'soft' beams used by NRC in this comparison. In the case of the air kerma standards, which were also compared at 60Co energy, the LNHB determination was greater than NRC's by 0.14%, which is not significant given the uncertainties on the standards.

Calorimetry↗

PubMed2002

Genome comparison of Mycobacterium tuberculosis and other bacteria.

The availability of the complete genome sequence of Mycobacterium tuberculosis allows its phylogenetic analysis based on the whole genome rather than single genes. As a genome-based tree is more representative of whole organisms and less inconsistent than single-gene trees, it could provide a better index for interpretation and inference about the origin and nature of species. The standard bacterial phylogeny based on 16S ribosomal RNA sequence comparison shows that M. tuberculosis is more related to Gram-positive than to Gram-negative bacteria. Our results based on genome comparison in terms of shared orthologous genes challenge this implication. We demonstrate that M. tuberculosis is more related to Gram-negative than to Gram-positive bacteria by a quantitative analysis on the genome tree. The numerical distance data derived from genome comparison and those from 16S rRNA comparison show high significant correlation, implying that conserved gene content carries a strong phylogenetic signature in evolution.

Animals↗

PubMed1981

A comparison of in vivo and in vitro methods for determining availability of iron from meals.

A comparison is made between in vitro and human and rat in vivo methods for estimating food iron availability. Complex meals formulated to replicate meals used by Cook and Monsen (Am J Clin Nutr 1976;29:859) in human iron availability trials were used in the comparison. The meals were prepared by substituting pork, fish, cheese, egg, liver, or chicken for beef in two basic test meals and were evaluated for iron availability using in vitro and rat in vivo methods. When the criterion for comparison was the ability to show statistically significant differences between iron availability in the various meals, there was substantial agreement between the in vitro and human in vivo methods. There was less agreement between the human in vivo and the rat in vivo and between the in vivo and the rat in vivo and between the in vitro and the rat in vivo methods. Correlation analysis indicated significant agreement between in vitro and human in vivo methods. Correlation between the rat in vivo and human in vivo methods were also significant but correlations between the in vitro and rat in vivo methods were less significant and, in some cases, not significant. The comparison supports the contention that the in vitro method allows a rapid, inexpensive, and accurate estimation of nonheme iron availability in complex meals.

Animals↗

PubMed2005

Comparison of quartz standards for X-ray diffraction analysis: HSE A9950 (Sikron F600) and NIST SRM 1878.

A further comparison of the Health and Safety Executive (HSE) standard quartz, A9950 (Sikron F600), and the National Institute of Standards and Technology (NIST) Standard Reference Material (SRM) 1878, standard respirable alpha-quartz, has been carried out for the four principal diffraction peaks. In the earlier comparison by Jeyaratnam and Nagar (1993, Ann Occup Hyg; 37: 167-79), the standards were both treated in ways which might change the particle size distribution and therefore the proportion of crystalline quartz. The two standards have now been compared in the most direct way possible with the minimum of sample treatment. There are no significant differences in the diffraction peak positions for the two standards. Nor do the peak area intensities differ significantly. The peak height intensities are consistently and significantly higher for Sikron F600 than for NIST SRM 1878. The particle size broadening of the diffraction peaks is evidently greater for NIST 1878, whose mass median diameter is quoted as 1.6 microm against 2.6 microm for Sikron F600. Taking the certified reference value for SRM 1878 as 95.5 +/- 1.1% crystalline quartz, the HSE standard A9950 (Sikron F600) contains 96.3 +/- 1.4% crystalline quartz based on a comparison of peak area intensities. On the same basis but using peak height intensities, the nominal crystalline quartz content of A9950 (Sikron F600) is 101.2 +/- 1.8%. Results obtained by comparison of quartz standards may not be generally applicable because of the effect of sample treatment on particle size and crystalline quartz content.

Air Pollutants, Occupational↗

PubMed2005

A comparison of fibre counting across three European national proficiency testing schemes.

Proficiency testing (PT) schemes seek to improve and maintain consistency in asbestos fibre counting by circulating mounted samples to laboratories, which return counts for comparison with consensus reference values. This study compares the level of these consensus values in three (Spanish, Belgian and UK) national PT schemes. It also assesses the effect of the imminent change in the European standard rules for counting asbestos fibres, to the new rules from the World Health Organisation (WHO), which will include more fibres. Forty samples from the three schemes were circulated to six laboratories, two in each national scheme. The UK and Spanish laboratories counted using both the ERM and the WHO method. Belgian laboratories already use the WHO method, and they counted only by this method. Densities from counts in this sample exchange served as a common basis against which we compared the national reference values (R). This produced a geometric overall mean ratio of R to exchange mean density of 0.94 for the UK scheme, 1.01 for the Spanish and 0.97 for the Belgian scheme, and thus indicated remarkably similar levels. Nevertheless, non-trivial systematic inter-laboratory differences confirmed the need for regular PT and international inter-laboratory comparisons. Examination of previous data from the national PT schemes and from an international scheme (AFRICA) provided further comparisons for the same laboratories (either comparing the laboratory's data with R values or making direct comparisons between laboratories) that are consistent with those from this special exchange. The change in fibre counting rule (to include fibres apparently touching particles with diameter >3 microm) produced mean increases in reported densities that ranged among samples from 0 to 70% (highest individual estimate 170%); the effect was broadly similar for the three schemes. The laboratories gave mostly similar estimates of percentage increase; however, one laboratory occasionally produced high estimates indicating a possible need for training for using the new method.

Air Pollutants, Occupational↗

PubMed2003

Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments.

MOTIVATION: The development of powerful automatic methods for the comparison of protein sequences has become increasingly important. Profile-to-profile comparisons allow for the use of broader information about protein families, resulting in more sensitive and accurate comparisons of distantly related sequences. A key part in the comparison of two profiles is the method for the calculation of scores for the position matches. A number of methods based on various theoretical considerations have been proposed. We implemented several previously reported scoring functions as well as our own functions, and compared them on the basis of their ability to produce accurate short ungapped alignments of a given length. RESULTS: Our results suggest that the family of the probabilistic methods (log-odds based methods and prof_sim) may be the more appropriate choice for the generation of initial 'seeds' as the first step to produce local profile-profile alignments. The most effective scoring systems were the closely related modifications of functions previously implemented in the COMPASS and Picasso methods.

Algorithms↗

PubMed2005

Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons.

MOTIVATION: An increasing number of protein structures are being determined for which no biochemical characterization is available. The analysis of protein structure and function assignment is becoming an unexpected challenge and a major bottleneck towards the goal of well-annotated genomes. As shape plays a crucial role in biomolecular recognition and function, the examination and development of shape description and comparison techniques is likely to be of prime importance for understanding protein structure-function relationships. RESULTS: A novel technique is presented for the comparison of protein binding pockets. The method uses the coefficients of a real spherical harmonics expansion to describe the shape of a protein's binding pocket. Shape similarity is computed as the L2 distance in coefficient space. Such comparisons in several thousands per second can be carried out on a standard linux PC. Other properties such as the electrostatic potential fit seamlessly into the same framework. The method can also be used directly for describing the shape of proteins and other molecules. AVAILABILITY: A limited version of the software for the real spherical harmonics expansion of a set of points in PDB format is freely available upon request from the authors. Binding pocket comparisons and ligand prediction will be made available through the protein structure annotation pipeline Profunc (written by Roman Laskowski) which will be accessible from the EBI website shortly.

Algorithms↗

PubMed2000

Statistical methods for the comparison of measurements derived from orthodontic imaging.

Biometric comparison procedures for dental imaging methods with continuous outcome were reviewed, mainly concentrating on assessment and comparison of accuracy and precision according to the study design. Univariate graphical and numerical representations of corresponding deviations were summarized to derive a 'check list' of minimum information necessary to compare the measurement methods. The methods reviewed in this investigation are illustrated by the comparison of conventional (radiographic) cephalometry versus assessment using the DigiGraph in 50 female children. A paired t-test and the corresponding confidence interval approach were used to assess deviations in location of two imaging methods; the test procedures of Maloney/Rastogi, Hahn/Nelson, and Grubbs were surveyed as proposals for the comparison of precisions in paired data. The Krippendorff coefficient was used as an aggregate measure for method concordance. Since these methods can be performed by simple modification of standard options available in most statistical software packages, this review intends to enable dental researchers to choose the correct methods, and perform adequate data analysis and representation.

Algorithms↗

PubMed1995

A comparison of avoidable mortality in Lithuania and Sweden 1971-1990.

BACKGROUND: In reforming the Lithuanian health care system it is important to evaluate the health status of the population and the outcome of health care by comparison to Western European countries. The aim of this study is to examine the possibility of comparing data on avoidable mortality in Lithuania with Sweden and, when realistic, to compare avoidable mortality rates between Lithuania and Sweden. METHODS: Comparisons were made for the time period 1971-1990. During this period a basic tabulation list including 200 groups of causes of death modified from WHO's International Classification of Diseases was obligatory for all Soviet Republics. This limited the opportunity for comparisons with Western European countries. However, for most of the selected avoidable death indicators comparisons with Sweden were made possible by slightly modifying the indicators. RESULTS: In the age group 5-64 years in 1971-1975 the total mortality in Lithuania was 60% higher than that in Sweden. In 1986-1990 this gap had increased to 90%. For most avoidable death indicators the difference was even greater, i.e. the death rate in Lithuania was several times higher than that in Sweden. For instance, death rates for tuberculosis were 36 times higher and for appendicitis, cholelithiasis and cholecystitis six times higher in Lithuania. For several avoidable causes of death, such as tuberculosis, appendicitis and hypertensive and cerebrovascular disease the gap widened during the study period. CONCLUSIONS: The results indicate potential fields for improvement of the health care system in Lithuania. The importance of implementing international classification systems for epidemiological surveillance of the outcome of health care is stressed.

Adolescent↗

PubMed2002

GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing.

We present a prototype of a new database tool, GeneCensus, which focuses on comparing genomes globally, in terms of the collective properties of many genes, rather than in terms of the attributes of a single gene (e.g. sequence similarity for a particular ortholog). The comparisons are presented in a visual fashion over the web at GeneCensus.org. The system concentrates on two types of comparisons: (i) trees based on the sharing of generalized protein families between genomes, and (ii) whole pathway analysis in terms of activity levels. For the trees, we have developed a module (TreeViewer) that clusters genomes in terms of the folds, superfamilies or orthologs--all can be considered as generalized 'families' or 'protein parts'--they share, and compares the resulting trees side-by-side with those built from sequence similarity of individual genes (e.g. a traditional tree built on ribosomal similarity). We also include comparisons to trees built on whole-genome dinucleotide or codon composition. For pathway comparisons, we have implemented a module (PathwayPainter) that graphically depicts, in selected metabolic pathways, the fluxes or expression levels of the associated enzymes (i.e. generalized 'activities'). One can, consequently, compare organisms (and organism states) in terms of representations of these systemic quantities. Develop ment of this module involved compiling, calculating and standardizing flux and expression information from many different sources. We illustrate pathway analysis for enzymes involved in central metabolism. We are able to show that, to some degree, flux and expression fluctuations have characteristic values in different sections of the central metabolism and that control points in this system (e.g. hexokinase, pyruvate kinase, phosphofructokinase, isocitrate dehydrogenase and citric synthase) tend to be especially variable in flux and expression. Both the TreeViewer and PathwayPainter modules connect to other information sources related to individual-gene or organism properties (e.g. a single-gene structural annotation viewer).

Animals↗

PubMed2002

Comparison of whole genome assemblies of the human genome.

A fundamental problem in the human genome project is uncovering the correct assembly of the human genome. Many studies, including transcriptional analysis, SNP detection and characterization, gene finding and EST clustering, use genome assemblies as templates so it is important to determine the consistency among the various whole genome assemblies. A comparison of the order and orientation of the GenBank entries used to construct the NCBI and UCSC Goldenpath assemblies was made. In addition, a sequence level comparison was performed using MULTI, an efficient database search tool developed to make whole genome comparisons possible. The resulting comparisons show significant discrepancies in the sequence as well as in the order and orientation of GenBank entries used in constructing the NCBI and UCSC assemblies.

Chromosomes, Human↗

PubMed2001

Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: implications for understanding the mechanistic basis of the male mutation bias.

The sex chromosomes and autosomes spend different times in the germ line of the two sexes. If cell division is mutagenic and if the sexes differ in number of cell divisions, then we expect that sequences on the X and Y chromosomes and autosomes should mutate at different rates. Tests of this hypothesis for several mammalian species have led to conflicting results. At the same time, recent evidence suggests that the chromosomal location of genes on autosomes affects their rate of evolution at synonymous sites. This suggests a mutagenic source different from germ cell replication. To correctly interpret the previous estimates of male mutation bias, it is crucial to understand the degree and range of this local similarity. With a carefully chosen randomization protocol, local similarity in synonymous rates of evolution can be detected in human-rodent and mouse-rat comparisons. However, the synonymous-site similarity in the mouse-rat comparison remains weak. Simulations suggest that this difference between the mouse-human and the mouse-rat comparisons is not artifactual and that there is therefore a difference between humans and rodents in the local patterns of mutation or selection on synonymous sites (conversely, we show that the previously reported absence of a local similarity in nonsynonymous rates of evolution in the human-rodent comparison was a methodological artifact). We show that linkage effects have a long-range component: not one in a million random genomes shows such levels of autosomal heterogeneity. The heterogeneity is so great that more autosomes than expected by chance have rates of synonymous evolution comparable with that of the X chromosome. As autosomal heterogeneity cannot be owing to different times spent in the germ line, this demonstrates that the dominant determiner of synonymous rates of evolution is not, as has been conjectured, the time spent in the male germ line.

Animals↗

PubMed2003

Study of sexuality-related characteristics in young adults with schizophrenia treated with novel neuroleptics and in a comparison group of young adults.

This study compared characteristics related to sexual history, sexual activities, sexual functioning, and psychological tendencies associated with sexuality in 45 young adults with schizophrenia treated with novel neuroleptics and in 61 young adults from a comparison group. A smaller proportion of young adults with schizophrenia currently had a sexual partner or had ever engaged in sexual relations. They also had sexual relations and sexual desires less often. Whether affected by schizophrenia or not, a smaller proportion of women had ever masturbated, and a smaller proportion of men currently had a sexual partner. Women masturbated less often, felt less sexual desire, and desired sexual relations less often, compared with men. Proportionally more men with schizophrenia treated with risperidone or olanzapine than men in the comparison group had at least one sexual dysfunction, lacked sexual desire, and reported problems with sexual arousal and ejaculation. Women with schizophrenia were more likely to report problems with sexual arousal and galactorrhea, compared with women in the comparison group. Finally, young adults with schizophrenia were more likely to develop negative psychological tendencies associated with sexuality than were young adults in the comparison group. Sexual problems are highly prevalent among young adults with schizophrenia. Sexuality should occupy the space it deserves within psychosocial rehabilitation programs and the treatment of schizophrenia.

Adolescent↗

PubMed1995

Comparison of spatial arrangements of secondary structural elements in proteins.

We have developed a new method of protein structure comparison based on spatial arrangements of secondary structural elements (SSEs). Each SSE is represented by a single vector, and common spatial arrangements of vectors in a pair of proteins are detected. The method allows not only insertions and deletions of SSEs, but also topological permutations. It has a flexible target function that can be adjusted depending upon particular levels or definitions of structural similarity, and it is fast enough to allow structural comparisons for many pairs of proteins. The parameters for the target function are determined based on distributions of the geometrical variables for the spatial arrangements of the equivalent SSEs in well-known structural motifs. The obtained parameter set is tuned for detecting relatively strong structural similarity. We report several tests on examples including comparisons of known structural similarity and database searches for a target structure, and examine the results when this parameter set is used for the comparison of distantly related structures.

Alcohol Dehydrogenase↗