Different Types Of Comparisons Research Articles

Multigroup analysis of compositions of microbiomes with covariate adjustments and repeated measures

Microbiome differential abundance analysis methods for two groups are well-established in the literature. However, many microbiome studies involve more than two groups, sometimes even ordered groups such as stages of a disease, and require different types of comparison. Standard pairwise comparisons are inefficient in terms of power and false discovery rates. In this Article, we propose a general framework, ANCOM-BC2, for performing a wide range of multigroup analyses with covariate adjustments and repeated measures. We illustrate our methodology through two real datasets. The first example explores the effects of aridity on the soil microbiome, and the second example investigates the effects of surgical interventions on the microbiome of patients with inflammatory bowel disease.

How do I know how I am doing? Use of different types of comparison in judgment of well-being in patients seeking psychological treatment and healthy controls.

Judgment of well-being is formed on the spot, and we know little about its foundations. We aimed at examining the role of comparison standards in informing evaluations of well-being in a clinical and a nonclinical sample. In a semi-structured face-to-face interview, individuals seeking psychological treatment and healthy control individuals rated how they have been feeling in general and relative to specific comparison standards and were each time invited to substantiate their ratings. Independent coders assessed number, type, direction, and specificity of reported comparisons. When asked to explain why they chose a particular rating of their well-being, 93% of clinical participants and 61% of nonclinical participants spontaneously reported some type of comparison standard. Both groups reported highest well-being ratings relative to social and past temporal comparisons and lowest relative to prospective temporal comparison. Furthermore, clinical participants engaged in more upward than downward comparisons, whereas this was not the case for healthy control participants. Our findings suggest that evaluations of well-being are informed by different comparison types and that individuals with clinical complaints use more comparisons when evaluating their well-being. The results encourage further investigation of comparative thinking as an underlying mechanism of judgment of well-being and ill-being.

Defining comparative physiology: results from an online survey and systematic review

August Krogh's 1929 principle is referenced as the cornerstone of comparative physiology (CP). However, there are diverse views as to what type of research falls under the CP approach. This study had three aims: 1) determine how CP is defined through an online survey (OS) of physiologists and a systematic review (SR), 2) put forth an updated definition of CP by summarizing OS and SR results, and 3) outline the numerous CP research approaches. Professional physiology societies (n=54) were invited to share the OS with their members and a SR was conducted which yielded 197 and 70 definitions, respectively. The three most common words in descending order in the OS definitions were 'different', 'animals', and 'species' and in the SR definitions, 'animals', 'species', and 'organisms'. The three most prevalent themes from the OS and SR definitions were comparing/differences/diversity across species (78% and 51%, respectively), response to the environment/ecology (28% and 43%, respectively), and included evolution or adaptation (24% and 60%, respectively). Ten research approaches were identified, which include: broad comparison (i.e., many species generalization), specific comparison (e.g., two species; for traits that are different, exaggerated, extreme, missing, or not induced), or comparison while considering evolution (i.e., evolutionary physiology), ecology (i.e., ecophysiology), or human physiology/medicine. Only 5% and 33% of OS and SR definitions described or mentioned Krogh's principle. In conclusion, CP can best be defined as a compilation of research approaches that utilize different types of comparisons to elucidate physiological mechanisms, and not simply comparing physiologies as the name implies.

Validation of Monte carlo Geant4 multithreading code for a 6 MV photon beam of varian linac on the grid computing.

To evaluate the computation time efficiency of the multithreaded code (G4Linac-MT) in the dosimetry application, using the high performance of the HPC-Marwan grid to determine with high accuracy the initial parameters of the 6 MV photon beam of Varian CLINAC 2100C. The difficulty of Monte Carlo methods is the long computation time, this is one of the disadvantages of the Monte Carlo methods. Calculations are performed by the multithreaded code G4Linac-MT and Geant4.10.04.p02 using the HPC-Marwan computing grid to evaluate the computing speed for each code. The multithreaded version is tested in several CPUs to evaluate the computing speed according to the number of CPUs used. The results were compared to the measurements using different types of comparisons, TPR20.10, penumbra, mean dose error and gamma index. The results obtained for this work indicate a much higher computing time saving for the G4Linac-MT version compared to the Geant4.10.04 version, the computing time decreases with the number of CPUs used, can reach about 12 times if 64CPUs are used. After optimization of the initial electron beam parameters, the results of the dose simulations obtained for this work are in very good agreement with the experimental measurements with a mean dose error of up to 0.41% on the PDDs and 1.79% on the lateral dose. The gain in computation time leads us to perform Monte Carlo simulations with a large number of events which gives a high accuracy of the dosimetry results obtained in this work.

Molecular Pathway Analysis of Mutation Data for Biomarkers Discovery and Scoring of Target Cancer Drugs.

DNA mutations govern cancer development. Cancer mutation profiles vary dramatically among the individuals. In some cases, they may serve as the predictors of disease progression and response to therapies. However, the biomarker potential of cancer mutations can be dramatically (several orders of magnitude) enhanced by applying molecular pathway-based approach. We developed Oncobox system for calculation of pathway instability (PI) values for the molecular pathways that are aggregated mutation frequencies of the pathway members normalized on gene lengths and on number of genes in the pathway. PI scores can be effective biomarkers in different types of comparisons, for example, as the cancer type biomarkers and as the predictors of tumor response to target therapies. The latter option is implemented using mutation drug score (MDS) values, which algorithmically rank the drugs capacity of interfering with the mutated molecular pathways. Here, describe the mathematical basis and algorithms for PI and MDS values calculation, validation and implementation. The example analysis is provided encompassing 5956 human tumor mutation profiles of 15 cancer types from The Cancer Genome Atlas (TCGA) project, that totally make 2,316,670 mutations in 19,872 genes and 1748 molecular pathways, thus enabling ranking of 128 clinically approved target drugs. Our results evidence that the Oncobox PI and MDS approaches are highly useful for basic and applied aspects of molecular oncology and pharmacology research.

When You Don’t have to be Sequential: A Meta-Analysis

Comparison approach is a cognitive process that is often used in a variety of domains specially to support effective mathematics learning. Students with low mathematical proficiency often make mistakes when solving a mathematical problem using different types of solving strategies. These mistakes can be prevented by presenting different strategies using the comparison approach in mathematics learning. If students are encouraged to compare, the similarities and differences become highlighted. This study examines the benefits of different types of comparison approaches in mathematics learning through a systematic review of research literature published between 2009 -2018, resulting in a total of 20 interventions (20 studies) that met the criteria for this study. The findings showed that students’ conceptual knowledge, procedural knowledge, and procedural flexibility are related to the greater implementation of the intervention, which when used sufficiently, can improve long-term mathematics learning. This study suggests that teachers may need additional support in preparing mathematics instruction using the comparison approach and that knowing the benefits of different types of comparisons in mathematics learning may persuade and help them to decide what to compare and when to use comparisons.

Bootstrapping estimates of stability for clusters, observations and model selection

Clustering is a challenging problem in unsupervised learning. In lieu of a gold standard, stability has become a valuable surrogate to performance and robustness. In this work, we propose a non-parametric bootstrapping approach to estimating the stability of a clustering method, which also captures stability of the individual clusters and observations. This flexible framework enables different types of comparisons between clusterings and can be used in connection with two possible bootstrap approaches for stability. The first approach, scheme 1, can be used to assess confidence (stability) around clustering from the original dataset based on bootstrap replications. A second approach, scheme 2, searches over the bootstrap clusterings for an optimally stable partitioning of the data. The two schemes accommodate different model assumptions that can be motivated by an investigator’s trust (or lack thereof) in the original data and additional computational considerations. We propose a hierarchical visualization extrapolated from the stability profiles that give insights into the separation of groups, and projected visualizations for the inspection of the stability of individual operations. Our approaches show good performance in simulation and on real data. These approaches can be implemented using the R package bootcluster that is available on the Comprehensive R Archive Network (CRAN).

О КОГНИТИВНО-СЕМАНТИЧЕСКОМ ОПИСАНИИ КОМПАРАТИВНЫХ КЛАСТЕРОВ В АНГЛИЙСКОМ ЯЗЫКЕ

The article is devoted to the study of cognitive-semantic processes in comparative clusters with a range of one sentence based on the English-language examples. The main semes of properties of the compared entities that make up the cluster are identified. The author gives mereological substantiation for the main results of the process of comparison: identity, similarity, analogy and difference, and considers the interrelation of these mental phenomena with their objectification in the interpropositional comparative cluster as the most common. The complexity of the cluster is conditioned by the use of different types of comparison.

Documentation and analysis of traumatic injuries in clinical forensic medicine involving structured light three-dimensional surface scanning versus photography

Non-contact three-dimensional (3D) surface scanning has been applied in forensic medicine and has been shown to mitigate shortcoming of traditional documentation methods. The aim of this paper is to assess the efficiency of structured light 3D surface scanning in recording traumatic injuries of live cases in clinical forensic medicine. The work was conducted in Medico-Legal Centre in Benghazi, Libya. A structured light 3D surface scanner and ordinary digital camera with close-up lens were used to record the injuries and to have 3D and two-dimensional (2D) documents of the same traumas. Two different types of comparison were performed. Firstly, the 3D wound documents were compared to 2D documents based on subjective visual assessment. Additionally, 3D wound measurements were compared to conventional measurements and this was done to determine whether there was a statistical significant difference between them. For this, Friedman test was used. The study established that the 3D wound documents had extra features over the 2D documents. Moreover; the 3D scanning method was able to overcome the main deficiencies of the digital photography. No statistically significant difference was found between the 3D and conventional wound measurements. The Spearman's correlation established strong, positive correlation between the 3D and conventional measurement methods. Although, the 3D surface scanning of the injuries of the live subjects faced some difficulties, the 3D results were appreciated, the validity of 3D measurements based on the structured light 3D scanning was established. Further work will be achieved in forensic pathology to scan open injuries with depth information.

Eye gaze patterns reveal how we reason about fractions

ABSTRACTFractions are defined by numerical relationships, and comparing two fractions’ magnitudes requires within-fraction (holistic) and/or between-fraction (componential) relational comparisons. To better understand how individuals spontaneously reason about fractions, we collected eye-tracking data while they performed a fraction comparison task with conditions that promoted or obstructed different types of comparisons. We found evidence for both componential and holistic processing in this mixed-pairs task, consistent with the hybrid theory of fraction representation. Additionally, making within-fraction eye movements on trials that promoted a between-fraction comparison strategy was associated with slower responses. Finally, participants who performed better on a non-numerical test of reasoning took longer to respond to the most difficult fraction trials, which suggests that those who had greater facility with non-numerical reasoning attended more to numerical relationships. These findings extend prior research and support the continued investigation into the mechanistic links between numerical and non-numerical reasoning.

Multiple treatment comparisons in analysis of covariance with interaction

When multiple treatments are analyzed together with a covariate, a treatment-covariate interaction complicates the interpretation of the treatment effects. The construction of simultaneous confidence bands for differences of the treatment specific regression lines is one option to proceed. The application of these methods is difficult because they are described as a collection of special cases and the implementation requires additional programming or relies on non-standard or proprietary software. If inferential interest can be restricted to a pre-specified set of covariate values, a flexible alternative is to compute simultaneous confidence intervals for multiple contrasts of the treatment effects over this grid. This approach is available in the R software: next to treatment differences in the linear model, approximate simultaneous confidence intervals for ratios of expected values and asymptotic extensions to generalized linear models are straightforward. The paper summarizes the available methodology and presents three case studies to illustrate the application to different models, differences and ratios, as well as different types of between treatment comparisons. Simulation studies in the general linear model, for different parameters and different types of comparisons are provided. The R code to reproduce the case studies and a hint to a related R package is provided.

Supplement to CCM.D-K4 'Hydrometer' report: linkage of EURAMET.M.D-K4 comparison, SIM.M.D-K4 comparison and the supplementary SIM.M.D-S2 to CCM.D-K4 'Hydrometer'

Evaluation of different types of comparisons to a common set of reference values of a CIPM key comparison is essential to satisfy the concept of the CIPM Mutual Recognition Arrangement (CIPM MRA), where the DoEs of any participant who took part in comparisons should be within the Calibration and Measurement Capability (CMC) section of the CIPM MRA Key Comparison Data Base. The subject of this supplementary report is therefore to present the equivalence of each National Metrological Institute (NMI) participant in the CCM.D-K4 'Hydrometer' key comparison, which was performed in the density range 600 kg/m3 to 2000 kg/m3 at the temperature of 20 °C, and the linkage of the European and Inter-American NMI results performed in the RMO.M.D-K4 comparisons as well as those of the supplementary SIM.M.D-S2 to the common set of KCRVs of the CCM.D-K4 'Hydrometer'.The linking procedure has been obtained by numerical simulation, based on the Monte Carlo method, in which the differences in the results of the different comparison between the intended laboratory and one or more linking laboratory/ies, which took part in both comparisons, are correlated with a continuous function describing the DoEs of the linking laboratory/ies with respect to the common set of KCRVs of the CCM.D-K4.Main textTo reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Parallel Optimal Pairwise Biological Sequence Comparison

Many bioinformatics applications, such as the optimal pairwise biological sequence comparison, demand a great quantity of computing resource, thus are excellent candidates to run in high-performance computing (HPC) platforms. In the last two decades, a large number of HPC-based solutions were proposed for this problem that run in different platforms, targeting different types of comparisons with slightly different algorithms and making the comparative analysis of these approaches very difficult. This article proposes a classification of parallel optimal pairwise sequence comparison solutions, in order to highlight their main characteristics in a unified way. We then discuss several HPC-based solutions, including clusters of multicores and accelerators such as Cell Broadband Engines (CellBEs), Field-Programmable Gate Arrays (FPGAs), Graphics Processing Units (GPUs) and Intel Xeon Phi, as well as hybrid solutions, which combine two or more platforms, providing the actual landscape of the main proposals in this area. Finally, we present open questions and perspectives in this research field.

Parametric, asymmetric and stochastic-based 3D CAD model of Tonda Gentile Trilobata hazelnut variety

A family of parametric 3D CAD models based on stochastic distribution of not-engineering real life object has been studied. The subject considered was the Tonda Gentile Trilobata (TGT) hazelnut variety, which is the most important variety in the Langhe region in Piedmont, Italy. The aim was to obtain a master model which measured, or stochastically-obtained, values of parameters given as input, to generate a number of samples which have the same statistical distributions of the real world ones. These generated models could then be used in virtual simulations of machinery and equipment used by industries to process the hazelnut, making possible studies of modifications to improve the production process performance. A single parametric CAD model was considered with respect to several scanned models from real hazelnuts, with the possibility of generating families of solutions suitable for the simulation aims. The work was carried out in steps of increasing complexity checking accuracy using different types of comparisons to validate the different models.

Knee orthoses for treating patellofemoral pain syndrome.

Knee orthoses for treating patellofemoral pain syndrome.

PULMONARY TUBERCULOSIS TREATMENT OUTCOME AMONG FOREIGN NATIONALS RESIDING IN OSAKA CITY

Abstract In this study, we analyzed pulmonary tuberculosis treatment outcomes among foreign nationals of different backgrounds. The research was conducted between January 2006 and December 2011. One hundred fifty nine foreign nationals residing in Osaka city had pulmonary tuberculosis during this period. Patients were grouped according to treatment outcomes. We conducted three different types of comparisons. First, we compared backgrounds of patients with treatment success or default. Second, backgrounds of patients who continued treatment in Japan or who moved overseas (transfer out) were compared. Third, treatment outcomes of foreign nationals between 20 and 39 years of age were compared with those of age-matched Japanese patients registered between 2010 and 2011. (1) The treatment outcomes were as follows: cured, 53 cases (33.3%); treatment completed, 55 cases (34.6 %); treatment failure, 0 cases (0.0%); treatment default, 14 cases (8.8%); moved overseas, 17 cases (10.7%); moved to another location inside Japan, 13 cases (8.2%); died, 6 cases (3.8%); and under treatment, 1 case (0.6%). (2) Comparison of treatment success and default among foreign nationals with pulmonary tuberculosis revealed a default rate among smear-negative cases of 14.5%, significantly higher than in smear-positive cases (2.1%; P < 0.05). (3) We compared backgrounds between foreign nationals with pulmonary tuberculosis who continued taking treatment in Japan and those who moved abroad (transfer out). The rate of overseas transfer out (44.4%) was higher among patients not covered by health insurance. This was significantly higher than among patients covered by public insurance or assistance (9.0%; P < 0.01). (4) Comparison of foreign and Japanese nationals between 20 and 39 years of age revealed a default rate in foreign nationals with pulmonary tuberculosis of 13.6%. This was significantly higher than that of Japanese patients (4.0%; P < 0.01). The rate of transfer out among foreign nationals with pulmonary tuberculosis was 19.1%, also significantly higher than that of Japanese patients (5.3%; P < 0.001). The rates of treatment default and transfer out among patients between 20 to 39 years of age were significantly higher among foreign nationals than in Japanese patients. Lack of knowledge about treatment and language problems may contribute to this finding. This suggests that adequate support and definitive directly observed treatment short-course programs are needed for foreign nationals. Patients who moved abroad (overseas transfer out) may also be ultimately categorized as treatment default. However, it is difficult to determine final treatment outcomes of patients who moved abroad. Further measures are needed to ensure that foreign nationals continue to receive treatment when they transfer overseas.

Entropy Evaluation Based on Value Validity

Besides its importance in statistical physics and information theory, the Boltzmann-Shannon entropy S has become one of the most widely used and misused summary measures of various attributes (characteristics) in diverse fields of study. It has also been the subject of extensive and perhaps excessive generalizations. This paper introduces the concept and criteria for value validity as a means of determining if an entropy takes on values that reasonably reflect the attribute being measured and that permit different types of comparisons to be made for different probability distributions. While neither S nor its relative entropy equivalent S* meet the value-validity conditions, certain power functions of S and S* do to a considerable extent. No parametric generalization offers any advantage over S in this regard. A measure based on Euclidean distances between probability distributions is introduced as a potential entropy that does comply fully with the value-validity requirements and its statistical inference procedure is discussed.

Comparative judgments of symbolic and non-symbolic stimuli yield different patterns of reaction times

Are different magnitudes, such as Arabic numerals, length and area, processed by the same system? Answering this question can shed light on the building blocks of our mathematical abilities. A shared representation theory suggested that discriminability of all magnitudes complies with Weber's law. The current work examined this suggestion. We employed comparative judgment tasks to investigate different types of comparisons — conceptual comparison of numbers, physical comparison of numbers and physical comparison of different shapes. We used 8 different size ratios and plotted reaction time as a function of these ratios. Our findings suggest that the relationship between discriminability and size ratio is not always linear, as previously suggested; rather, it is modulated by the type of comparison and the type of stimuli. Hence, we suggest that the representation of magnitude is not as rigid as previously suggested; it changes as a function of task demands and familiarity with the compared stimuli.

The neural correlates of beauty comparison

Beauty is in the eye of the beholder. How attractive someone is perceived to be depends on the individual or cultural standards to which this person is compared. But although comparisons play a central role in the way people judge the appearance of others, the brain processes underlying attractiveness comparisons remain unknown. In the present experiment, we tested the hypothesis that attractiveness comparisons rely on the same cognitive and neural mechanisms as comparisons of simple nonsocial magnitudes such as size. We recorded brain activity with functional magnetic resonance imaging (fMRI) while participants compared the beauty or height of two women or two dogs. Our data support the hypothesis of a common process underlying these different types of comparisons. First, we demonstrate that the distance effect characteristic of nonsocial comparisons also holds for attractiveness comparisons. Behavioral results indicated, for all our comparisons, longer response times for near than far distances. Second, the neural correlates of these distance effects overlapped in a frontoparietal network known for its involvement in processing simple nonsocial quantities. These results provide evidence for overlapping processes in the comparison of physical attractiveness and nonsocial magnitudes.

Comparisons in Migration Studies

The paper presents and critically discusses the different types of comparison developed in migration studies with a special attention to European literature. It then identifies missing topics and issues to be covered by comparative research in the field by focussing on European and on North American research.