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PubMed1986

Frequency and diversity of use of statistical techniques in oncology journals.

We describe the frequency with which various statistical techniques are reported in almost 5,000 articles published in five major American oncology journals during 1983 and 1984. A reader familiar with about a dozen techniques can expect to understand approximately 90% of the quantitative concepts cited in these journals. With the exception of survival analysis, these were typically the techniques encountered in many introductory statistical texts. Oncology training program preceptors concerned about making their graduates more effective consumers of the literature can use these findings in structuring exposure to quantitative skills. In four of the five journals reviewed, failure to identify the statistical methodology was among the ten most commonly encountered "techniques." This made it impossible to identify the analytical procedures used in many articles, and hence to judge their scientific validity. We encourage more editorial boards to adopt guidelines requiring a standardized format for presenting results based on a statistical analysis.

Actuarial Analysis↗
PubMedDate not supplied

A statistical view of FMRFamide neuropeptide diversity.

FMRFamide-like peptide (FLP) amino acid sequences have been collected and statistically analyzed. FLP amino acid composition as a function of position in the peptide is graphically presented for several major phyla. Results of total amino acid composition and frequencies of pairs of FLP amino acids have been computed and compared with corresponding values from the entire GenBank protein sequence database. The data for pairwise distributions of amino acids should help in future structure-function studies of FLPs. To aid in future peptide discovery, a computer program and search protocol was developed to identify FLPs from the GenBank protein database without the use of keywords.

Amino Acid Sequence↗
PubMed2004

A survey of statistics in three UK general practice journal.

BACKGROUND: Many medical specialities have reviewed the statistical content of their journals. To our knowledge this has not been done in general practice. Given the main role of a general practitioner as a diagnostician we thought it would be of interest to see whether the statistical methods reported reflect the diagnostic process. METHODS: Hand search of three UK journals of general practice namely the British Medical Journal (general practice section), British Journal of General Practice and Family Practice over a one-year period (1 January to 31 December 2000). RESULTS: A wide variety of statistical techniques were used. The most common methods included t-tests and Chi-squared tests. There were few articles reporting likelihood ratios and other useful diagnostic methods. There was evidence that the journals with the more thorough statistical review process reported a more complex and wider variety of statistical techniques. CONCLUSIONS: The BMJ had a wider range and greater diversity of statistical methods than the other two journals. However, in all three journals there was a dearth of papers reflecting the diagnostic process. Across all three journals there were relatively few papers describing randomised controlled trials thus recognising the difficulty of implementing this design in general practice.

Bibliometrics↗
PubMed2006

Branch and bound computation of exact p-values.

UNLABELLED: P-value computation is often used in bioinformatics to quantify the surprise, or significance, associated with a given observation. An implementation is provided that computes the exact p-value associated with any observed sample, against a null multinomial distribution, using the likelihood-ratio statistic. The efficient branch and bound code, far exceeding the full enumeration implemented by commercial packages, is especially useful with small sample, sparse data and rare events, common scenarios in bioinformatics, where approximations are often inaccurate and inappropriate. This code base can also be adapted to compute exact p-values of other statistics in diverse sampling scenarios. AVAILABILITY: Freely available at http://www.soe.ucsc.edu/~jill/src/.

Algorithms↗
PubMed2004

Investigation of bacterial diversity in Brazilian tropical estuarine sediments reveals high actinobacterial diversity.

Phylogenetic and statistical analyses of 16S rRNA gene libraries were used for the investigation of actinobacterial communities present in two tropical estuarine sediments (Santos-São Vicente estuary, Brazil). The libraries were constructed from samples collected at the brackish end of the estuary, highly hydrocarbon-contaminated, and at the marine end, uncontaminated. Clones from the marine end of the estuary were all related to sequences from non-cultured Actinobacteria and unidentified bacteria recovered from a wide range of environmental samples, whereas clones from the brackish end were mainly related to sequences from cultured Actinobacteria. Statistical analyses showed that the community recovered from the hydrocarbon-contaminated sediment sample, at the brackish end, was less diverse than the uncontaminated one, at the marine end, and that the communities from the two libraries were differently structured, suggesting that these may have not originated from the same community. The recognition of the spatial pattern of actinobacterial distribution in a natural environment is a first step towards understanding the way these communities are organized, providing valuable data for further investigations of their taxonomic and functional diversity.

Actinobacteria↗
PubMed2005

Assessing the limits of genomic data integration for predicting protein networks.

Genomic data integration--the process of statistically combining diverse sources of information from functional genomics experiments to make large-scale predictions--is becoming increasingly prevalent. One might expect that this process should become progressively more powerful with the integration of more evidence. Here, we explore the limits of genomic data integration, assessing the degree to which predictive power increases with the addition of more features. We focus on a predictive context that has been extensively investigated and benchmarked in the past-the prediction of protein-protein interactions in yeast. We start by using a simple Naive Bayes classifier for integrating diverse sources of genomic evidence, ranging from coexpression relationships to similar phylogenetic profiles. We expand the number of features considered for prediction to 16, significantly more than previous studies. Overall, we observe a small, but measurable improvement in prediction performance over previous benchmarks, based on four strong features. This allows us to identify new yeast interactions with high confidence. It also allows us to quantitatively assess the inter-relations amongst different genomic features. It is known that subtle correlations and dependencies between features can confound the strength of interaction predictions. We investigate this issue in detail through calculating mutual information. To our surprise, we find no appreciable statistical dependence between the many possible pairs of features. We further explore feature dependencies by comparing the performance of our simple Naive Bayes classifier with a boosted version of the same classifier, which is fairly resistant to feature dependence. We find that boosting does not improve performance, indicating that, at least for prediction purposes, our genomic features are essentially independent. In summary, by integrating a few (i.e., four) good features, we approach the maximal predictive power of current genomic data integration; moreover, this limitation does not reflect (potentially removable) inter-relationships between the features.

Algorithms↗
PubMed2026

Metabolomic and structural signatures of pigmented and non-pigmented Himalayan rice landraces.

BACKGROUND: This study investigated the anti-oxidant properties, starch composition, pasting behavior, structural properties, textural properties and non-targeted metabolomic profiles of pigmented and non-pigmented rice landraces as potential next-generation functional food ingredients. RESULTS: Pigmented rice demonstrated 1.34 times more anti-oxidant activity as compared to non-pigmented rice. Pigmented landraces showcased superior nutritional and functional attributes, including higher total dietary fiber and starch content. Fourier-transform infrared (FTIR) analysis revealed distinct molecular signatures with enhanced peak transmittance, while X-ray diffraction (XRD) indicated greater crystallinity ranging from 36-44.3% in pigmented rice compared with 30-40% in non-pigmented rice, suggesting improved digestibility and processing versatility. Pigmented rice recorded less amylose content hence tended to possess increased adhesiveness values whereas non-pigmented rice revealed greater amylose content hence was coupled with greater hardness values. Field-emission scanning electron microscopy (FE-SEM) images revealed that pigmented rice had densely packed and polygonal starch granules whereas non-pigmented rice had loosely packed starch granules with intergranular voids. Untargeted gas chromatography-mass spectrometry (GC-MS) profiling identified 84 metabolites, including unique compounds such as 3,3-dimethylbutanol and ethanoic acid, along with shared metabolites such as sucrose and linoleic acid, highlighting notable biochemical diversity. Multivariate statistical analyses using principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway mapping further differentiated the metabolomic landscapes, with variable importance in the projection (VIP) scores identifying key bioactive contributors. CONCLUSION: Pigmented rice landraces exhibited significant functional and nutritional advantages, making them promising candidates for functional food development and nutritional improvement programs. These findings support their potential role in advancing sustainable and health-oriented food systems. © 2026 Society of Chemical Industry.

Oryza↗
PubMed2005

The influence of climate and soil properties on calcium nutrition and vitality of silver fir (Abies alba Mill.).

As a part of a broader research into the nutrition of silver fir (Abies alba Mill.), the variation of calcium concentrations was investigated in needles and soil in two subsequent, climatologically diverse years. Statistically significant differences between plots were determined in Ca concentrations in soils. Concentrations of Ca in needles were statistically different regarding plot, defoliation class, sampling date within the same year and also between years. Fir trees on acid-rock based soils had lower, often inadequate concentrations of Ca in needles; the opposite was true for trees growing on Ca-rich soils. Trees of lower vitality generally exhibited poor Ca nutrition. Drought in the second year of research caused poor absorption of Ca on all plots and in all defoliation classes, but the combined influence of climate and soil properties affected especially trees of low vitality on acid-rock based soils.

Abies↗
PubMed1999

Combinatorial discovery process yields antimicrobial peptoids.

N-alkylated glycine trimers are generically referred to as peptoids. The identification of antimicrobial peptoids from a statistically unbiased diverse combinatorial chemistry library led to the design of the optimization peptoid library that we describe in this manuscript. This optimization library was designed using structural information from the most active peptoids in the unbiased library. Screening of the optimization library for antimicrobial activity identified a single pool of peptoids with activity against both Staphylococcus aureus and Escherichia coli. The active peptoids from this pool were active against drug sensitive and drug resistant organisms and represent novel antibacterial compounds.

Anti-Bacterial Agents↗
PubMed1993

A critical review of the 10 pivotal caries clinical studies used in a recent meta-analysis comparing the anticaries efficacy of sodium fluoride and sodium monofluorophosphate dentifrices.

The 10 pivotal caries clinical studies employed in a recent meta-analysis to compare the anticaries efficacy of sodium fluoride (NaF) and sodium monofluorophosphate (MFP) dentifrices were subjected to a critical review. When reporting the meta-analysis, the author (Johnson) considered these 10 pivotal caries clinical studies as "head-to-head" comparisons of NaF and MFP dentifrices. For the most part, it is difficult to find any common denominator among these 10 caries clinical studies since there were so many diverse factors associated with them. The 10 pivotal studies were conducted over a 20-year period of time in many different geographic areas of the world, using different protocols and study designs, different clinical examiners and caries assessment criteria, as well as evaluating commercially outdated or specially formulated dentifrices. Any attempt to integrate the results from these 10 studies is further complicated by the diversity of statistical methodology used to evaluate the results obtained from the studies. Also, in two of the 10 studies, the comparison of the fluoride dentifrices was obscured by the fact that the participating children used a fluoride mouthrinse during the course of the study. In any case, when all relevant dentifrice comparisons are made, the results of a critical review of the 10 pivotal ("head-to-head") caries clinical studies indicate the following: (1) In three of the studies (Gerdin/Zacherl/Forsman), depending upon how the data is viewed, it can either be shown that NaF dentifrices are favored over MFP dentifrices or that MFP dentifrices are favored over NaF dentifrices. (2) In one of the studies (Edward & Torell), the results are published only in abstract form and a full report of the study is not available. (3) In one of the studies (Koch, Petersson, Kling & Kling) it is reported that MFP dentifrices are favored over NaF dentifrices. (4) In two of the studies (Edlund & Koch, Koch et al) it is reported that NaF dentifrices are favored over MFP dentifrices. However, in both of these studies, there were serious imbalances in baseline caries status favoring the NaF dentifrice groups over the MFP dentifrice groups. In other words, the children using the MFP dentifrices were more prone to caries formation during the course of these studies than the children using the NaF dentifrices. Further, in these two studies there is a serious question regarding the soluble fluoride level of the commercially available MFP dentifrice that was used.(ABSTRACT TRUNCATED AT 400 WORDS)

Adolescent↗
PubMed1997

[The structure of a population of smooth myocytes (aspects of the intraorganic organization of smooth muscle tissue)].

Comparative analysis of smooth muscular tissue of bronchi and of rectal pelvic region was performed using electron microscopic and cytophotometric methods. Smooth myocyte population of organs studied were demonstrated to include three cell types: small, medium and large ones. The population structure of smooth muscular tissue has similar pattern in bronchi and intestine, despite the established statistically significant diversity in their smooth myocyte volumetric parameters. Small smooth myocyte subpopulation was found to contain the cells considered to be smooth muscular tissue cambial elements by their ultrastructural and cytophotometrical characteristics.

Bronchi↗
PubMed1998

Theoretical calculation and prediction of brain-blood partitioning of organic solutes using MolSurf parametrization and PLS statistics.

Sixty-three structurally diverse compounds were investigated to statistically model the brain-blood partitioning of organic solutes using theoretically computed molecular descriptors and multivariate statistics. The program MolSurf was used to compute theoretical molecular descriptors related to physicochemical properties such as lipophilicity, polarity, polarizability, and hydrogen bonding. The multivariate Partial Least Squares Projections to Latent Structures (PLS) method was used to delineate the relationship between the brain-blood partitioning of organic solutes and the theoretically computed molecular descriptors. Good statistical models were derived. Properties associated with polarity and Lewis base strength had the largest impact on the blood-brain partitioning and should be kept to a minimum to promote high partitioning. The absence of atoms capable of hydrogen bonding interactions as well as high lipophilicity and the presence of polarizable surface electrons, i.e., valence electrons, were also found to promote high brain-blood partitioning. The results indicate that theoretically computed molecular MolSurf descriptors in conjunction with multivariate statistics of PLS type can be used to successfully model the brain-blood partitioning of organic solutes and hence differentiate drugs with poor partitioning from those with acceptable partitioning at an early stage of the preclinical drug-discovery process.

Blood-Brain Barrier↗
PubMed2006

The evolution of worker caste diversity in social insects.

Morphological diversification of workers is predicted to improve the division of labor within social insect colonies, yet many species have monomorphic workers. Individual-level selection on the reproductive capacities of workers may counter colony-level selection for diversification, and life-history differences between species (timing of caste determination, colony size, genetic variation available) may mediate the strength of this selection. We tested this through phylogenetically independent contrast analyses on a new data set for 35 ant species. Evidence was found that early divergence of queen-worker developmental pathways may facilitate the evolution of worker diversity because queen-worker dimorphism was strongly positively associated with diversity. By contrast, risks for colonies that invest in specialized workers and colony size effects on costs of worker reproduction seem unlikely to strongly affect the evolution of worker diversity because there was no significant association between colony size and diversity when controlling statistically for queen-worker dimorphism. Finally, worker diversity was greater in species with multiple lineages per colony, and it was negatively associated with relatedness in monogynous species. This could be due to high intracolonial genetic variance favoring the expression and evolution of great worker diversity or to diversity evolving more easily when there is selection for repression of worker reproduction (worker policing).

Animals↗
PubMed2002

Influence of the structural diversity of data sets on the statistical quality of three-dimensional quantitative structure-activity relationship (3D-QSAR) models: predicting the estrogenic activity of xenoestrogens.

Federal legislation has resulted in the two-tiered in vitro and in vivo screening of some 80 000 structurally diverse chemicals for possible endocrine disrupting effects. To maximize efficiency and minimize expense, prioritization of these chemicals with respect to their estrogenic disrupting potential prior to this time-consuming and labor-intensive screening process is essential. Computer-based quantitative structure-activity relationship (QSAR) models, such as those obtained using comparative molecular field analysis (CoMFA), have been demonstrated as useful for risk assessment in this application. In general, however, CoMFA models to predict estrogenicity have been developed from data sets with limited structural diversity. In this study, we constructed CoMFA models based on biological data for a structurally diverse set of compounds spanning eight chemical families. We also compared two standard alignment schemes employed in CoMFA, namely, atom-fit and flexible field-fit, with respect to the predictive capabilities of their respective models for structurally diverse data sets. The present analysis indicates that flexible field-fit alignment fares better than atom-fit alignment as the structural diversity of the data set increases. Values of log(RP), where RP = relative potency, predicted by the final flexible field-fit CoMFA models are in good agreement with the corresponding experimental values. These models should be effective for predicting the endocrine disrupting potential of existing chemicals as well as prospective and newly prepared chemicals before they enter the environment.

Animals↗
PubMed2006

Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.).

BACKGROUND: The goal of our study was a systematic survey of the molecular diversity in barley genetic resources. To this end 953 cultivated barley accessions originating from all inhabited continents except Australia were genotyped with 48 SSR markers. Molecular diversity was evaluated with routine statistics (allelic richness, gene diversity, allele frequency, heterozygosity and unique alleles), Principal Coordinate Analysis (PCoA), and analysis of genome-wide linkage disequilibrium. RESULTS: A genotyping database for 953 cultivated barley accessions profiled with 48 SSR markers was established. The PCoA revealed structuring of the barley population with regard to (i) geographical regions and (ii) agronomic traits. Geographic origin contributed most to the observed molecular diversity. Genome-wide linkage disequilibrium (LD) was estimated as squared correlation of allele frequencies (r2). The values of LD for barley were comparable to other plant species (conifers, poplar, maize). The pattern of intrachromosomal LD with distances between the genomic loci ranging from 1 to 150 cM revealed that in barley LD extended up to distances as long as 50 cM with r2 > 0.05, or up to 10 cM with r2 > 0.2. Few loci mapping to different chromosomes showed significant LD with r2 > 0.05. The number of loci in significant LD as well as the pattern of LD were clearly dependent on the population structure. The LD in the homogenous group of 207 European 2-rowed spring barleys compared to the highly structured worldwide barley population was increased in the number of loci pairs with r2 > 0.05 and had higher values of r2, although the percentage of intrachromosomal loci pairs in significant LD based on P < 0.001 was 100% in the whole set of varieties, but only 45% in the subgroup of European 2-rowed spring barleys. The value of LD also varied depending on the polymorphism of the loci selected for genotyping. The 17 most polymorphic loci (PIC > 0.80) provided higher LD values as compared to 19 low polymorphic loci (PIC < 0.73) in both structured (all accessions) and non-structured (European 2-rowed spring varieties) barley populations. CONCLUSION: A global population of cultivated barley accessions was highly structured. Clustering highlighted the accessions with the same geographic origin, as well as accessions possessing similar agronomic characters. LD in barley extended up to 50 cM, and was strongly dependent on the population structure. The data on LD were summarized as a genome-wide LD map for barley.

Chromosome Mapping↗
PubMed2006

Evolutionary dynamics of Ralstonia solanacearum.

We investigated the genetic diversity, extent of recombination, natural selection, and population divergence of Ralstonia solanacearum samples obtained from sources worldwide. This plant pathogen causes bacterial wilt in many crops and constitutes a serious threat to agricultural production due to its very wide host range and aggressiveness. Five housekeeping genes, dispersed around the chromosome, and three virulence-related genes, located on the megaplasmid, were sequenced from 58 strains belonging to the four major phylogenetic clusters (phylotypes). Whereas genetic variation is high and consistent for all housekeeping loci studied, virulence-related gene sequences are more diverse. Phylogenetic and statistical analyses suggest that this organism is a highly diverse bacterial species containing four major, deeply separated evolutionary lineages (phylotypes I to IV) and a weaker subdivision of phylotype II into two subgroups. Analysis of molecular variations showed that the geographic isolation and spatial distance have been the significant determinants of genetic variation between phylotypes. R. solanacearum displays high clonality for housekeeping genes in all phylotypes (except phylotype III) and significant levels of recombination for the virulence-related egl and hrpB genes, which are limited mainly to phylotype strains III and IV. Finally, genes essential for species survival are under purifying selection, and those directly involved in pathogenesis might be under diversifying selection.

Evolution, Molecular↗