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Perspectives on Psychological Science :... May 2021Because of the strong overreliance on values in the scientific literature, some researchers have argued that we need to move beyond values and embrace practical...
Because of the strong overreliance on values in the scientific literature, some researchers have argued that we need to move beyond values and embrace practical alternatives. When proposing alternatives to values statisticians often commit the "statistician's fallacy," whereby they declare which statistic researchers really "want to know." Instead of telling researchers what they want to know, statisticians should teach researchers which questions they can ask. In some situations, the answer to the question they are most interested in will be the value. As long as null-hypothesis tests have been criticized, researchers have suggested including minimum-effect tests and equivalence tests in our statistical toolbox, and these tests have the potential to greatly improve the questions researchers ask. If anyone believes values affect the quality of scientific research, preventing the misinterpretation of values by developing better evidence-based education and user-centered statistical software should be a top priority. Polarized discussions about which statistic scientists should use has distracted us from examining more important questions, such as asking researchers what they want to know when they conduct scientific research. Before we can improve our statistical inferences, we need to improve our statistical questions.
Topics: Humans; Knowledge; Probability; Research; Research Personnel; Software
PubMed: 33560174
DOI: 10.1177/1745691620958012 -
BMC Medical Research Methodology Sep 2020Researchers often misinterpret and misrepresent statistical outputs. This abuse has led to a large literature on modification or replacement of testing thresholds and... (Review)
Review
BACKGROUND
Researchers often misinterpret and misrepresent statistical outputs. This abuse has led to a large literature on modification or replacement of testing thresholds and P-values with confidence intervals, Bayes factors, and other devices. Because the core problems appear cognitive rather than statistical, we review some simple methods to aid researchers in interpreting statistical outputs. These methods emphasize logical and information concepts over probability, and thus may be more robust to common misinterpretations than are traditional descriptions.
METHODS
We use the Shannon transform of the P-value p, also known as the binary surprisal or S-value s = -log(p), to provide a measure of the information supplied by the testing procedure, and to help calibrate intuitions against simple physical experiments like coin tossing. We also use tables or graphs of test statistics for alternative hypotheses, and interval estimates for different percentile levels, to thwart fallacies arising from arbitrary dichotomies. Finally, we reinterpret P-values and interval estimates in unconditional terms, which describe compatibility of data with the entire set of analysis assumptions. We illustrate these methods with a reanalysis of data from an existing record-based cohort study.
CONCLUSIONS
In line with other recent recommendations, we advise that teaching materials and research reports discuss P-values as measures of compatibility rather than significance, compute P-values for alternative hypotheses whenever they are computed for null hypotheses, and interpret interval estimates as showing values of high compatibility with data, rather than regions of confidence. Our recommendations emphasize cognitive devices for displaying the compatibility of the observed data with various hypotheses of interest, rather than focusing on single hypothesis tests or interval estimates. We believe these simple reforms are well worth the minor effort they require.
Topics: Bayes Theorem; Cognition; Cohort Studies; Confidence Intervals; Humans; Probability; Semantics
PubMed: 32998683
DOI: 10.1186/s12874-020-01105-9 -
Frontiers in Bioinformatics 2022The human mind shows extraordinary capability at recognizing patterns, while at the same time tending to underestimate the natural scope of random processes. Taken... (Review)
Review
The human mind shows extraordinary capability at recognizing patterns, while at the same time tending to underestimate the natural scope of random processes. Taken together, this easily misleads researchers in judging whether the observed characteristics of their data are of significance or just the outcome of random effects. One of the best tools to assess whether observed features fall into the scope of pure randomness is statistical significance testing, which quantifies the probability to falsely reject a chosen null hypothesis. The central parameter in this context is the -value, which can be calculated from the recorded data sets. In case of -values smaller than the level of significance, the null hypothesis is rejected, otherwise not. While significance testing has found widespread application in many sciences including the life sciences, it is hardly used in (bio-)physics. We propose here that significance testing provides an important and valid addendum to the toolbox of quantitative (single molecule) biology. It allows to support a quantitative judgement (the hypothesis) about the data set with a probabilistic assessment. In this manuscript we describe ways for obtaining valid -values in two selected applications of single molecule microscopy: (i) Nanoclustering in single molecule localization microscopy. Previously, we developed a method termed 2-CLASTA, which allows to calculate a valid -value for the null hypothesis of an underlying random distribution of molecules of interest while circumventing overcounting issues. Here, we present an extension to this approach, yielding a single overall -value for data pooled from multiple cells or experiments. (ii) Single molecule trajectories. Data from a single molecule trajectory are inherently correlated, thus prohibiting a direct analysis via conventional statistical tools. Here, we introduce a block permutation test, which yields a valid -value for the analysis and comparison of single molecule trajectory data. We exemplify the approach based on FRET trajectories.
PubMed: 36304307
DOI: 10.3389/fbinf.2022.811053 -
Frontiers in Psychology 2020A widely cited roadblock to bridging ecological psychology and enactivism is that the former identifies with realism and the latter identifies with constructivism, which...
A widely cited roadblock to bridging ecological psychology and enactivism is that the former identifies with realism and the latter identifies with constructivism, which critics charge is subjectivist. A pragmatic reading, however, suggests non-mental forms of constructivism that simultaneously fit core tenets of enactivism and ecological realism. After advancing a pragmatic version of enactive constructivism that does not obviate realism, I reinforce the position with an empirical illustration: , a communal unicellular organism that leaves slime trails that form chemical barriers that it avoids in foraging explorations. Here, environmental building and sensorimotor engagement are part of the same process with coordinating around self-created, affordance-bearing geographies, which nonetheless exist independently in ways described by ecological realists. For ecological psychologists, affordances are values, meaning values are external to the perceiver. I argue that agent-enacted values have the same status and thus do not obviate ecological realism or generate subjectivism. The constructivist-realist debate organizes around the emphasis that enactivists and ecological theorists respectively place on the inner constitution of organisms vs. the structure of environments. Building on alimentary themes introduced in the example and also in Gibson's work, I go on to consider how environment, brain, visceral systems, and even bacteria within them enter perceptual loops. This highlights almost unfathomable degrees of mutually modulating internal and external synchronization. It also shows instances in which internal conditions alter worldly configurations and invert values, in Gibson's sense of the term, albeit without implying subjectivism. My aim is to cut across the somatic focus of enactive constructivism and the external environment-oriented emphasis of ecological realism and show that enactivism can enrich ecological accounts of value.
PubMed: 33192781
DOI: 10.3389/fpsyg.2020.538644 -
Revista Brasileira de Terapia Intensiva 2021To determine the prevalence of and risk factors for insufficient knowledge related to p-values among critical care physicians and respiratory therapists in Argentina.
OBJECTIVE
To determine the prevalence of and risk factors for insufficient knowledge related to p-values among critical care physicians and respiratory therapists in Argentina.
METHODS
This cross-sectional online survey contained 25 questions about respondents' characteristics, self-perception and p-value knowledge (theory and practice). Descriptive and multivariable logistic regression analyses were conducted.
RESULTS
Three hundred seventy-six respondents were analyzed. Two hundred thirty-seven respondents (63.1%) did not know about p-values. According to the multivariable logistic regression analysis, a lack of training on scientific research methodology (adjusted OR 2.50; 95%CI 1.37 - 4.53; p = 0.003) and the amount of reading (< 6 scientific articles per year; adjusted OR 3.27; 95%CI 1.67 - 6.40; p = 0.001) were found to be independently associated with the respondents' lack of p-value knowledge.
CONCLUSION
The prevalence of insufficient knowledge regarding p-values among critical care physicians and respiratory therapists in Argentina was 63%. A lack of training on scientific research methodology and the amount of reading (< 6 scientific articles per year) were found to be independently associated with the respondents' lack of p-value knowledge.
Topics: Critical Care; Cross-Sectional Studies; Health Knowledge, Attitudes, Practice; Humans; Risk Factors; Surveys and Questionnaires
PubMed: 33886857
DOI: 10.5935/0103-507X.20210009 -
Iranian Journal of Otorhinolaryngology Sep 2023Considering the inconsistent results regarding the association between the severity and duration of olfactory dysfunction (OD), and the viral load in coronavirus disease...
INTRODUCTION
Considering the inconsistent results regarding the association between the severity and duration of olfactory dysfunction (OD), and the viral load in coronavirus disease 2019 (COVID-19) patients, we aimed to conduct this study.
MATERIALS AND METHODS
This is a prospective cohort study in which COVID-19 patients were evaluated for the initial cycle threshold value (Ct values) measured by the nasopharyngeal samples along with olfactory function measured by the University of Pennsylvania Smell Identification Test (UPSIT) within 2 months of COVID-19 onset.
RESULTS
Among 309 COVID-19 patients who were included in this study, 108 (34.9%), 112 (36.2%) and 89 (28.8%) were normosmic, hyposmic, and anosmic, respectively based on the UPSIT. The severity of COVID-19 and the rate of hospitalization were higher in anosmic patients (p<0.0001, and p<0.0001, respectively). Moreover, significant associations between the initial Ct value and the severity of OD at admission and follow-ups were detected (p<0.0001 and p<0.0001, respectively). Anosmic patients had higher Ct values in comparison with hyposmic (approx. 3-fold) and normosmic (approx. 12-fold) patients. The recovery rate after one- and two-month follow-ups was 47% and 84%, respectively. At the follow-ups, OD-recovered patients significantly had lower Ct values (mean Ct value: 27.79 ± 2 and 28.21 ± 2.08) in comparison with those who have not recovered yet (mean Ct value: 30.19 ± 3.36, and 33.6 ± 3.37) (p<0.0001, and p<0.0001, respectively).
CONCLUSIONS
Ct value seems to be a significant factor not only in predicting OD severity in COVID-19 patients but also in the OD recovery duration. This finding may be helpful to investigate the underlying mechanisms of OD in COVID-19 patients.
PubMed: 38090619
DOI: 10.22038/IJORL.2023.71462.3429 -
Contrast Media & Molecular Imaging 2022The purpose of this study was to investigate the absolute value of peripheral blood lymphocytes in patients with primary immune thrombocytopenia and the diagnostic...
The purpose of this study was to investigate the absolute value of peripheral blood lymphocytes in patients with primary immune thrombocytopenia and the diagnostic effect on patients with primary immune thrombocytopenia. From January 2020 to June 2021, 76 patients with primary immune thrombocytopenia and 80 healthy check-ups admitted to our hospital were selected as study subjects and divided into a control group (80 patients, healthy check-ups) and an observation group (76 patients, primary immune thrombocytopenia), according to the health status of the organism. Early morning fasting venous blood was collected from both groups, and the absolute value of peripheral blood lymphocytes was measured and compared using a fully automated hematology analyzer to investigate the diagnostic value of absolute peripheral blood lymphocytes in primary immune thrombocytopenia. The CD3+, CD3+CD4+, CD4+/CD8+, and CD16+CD56+ assay values in the observation group were lower than those in the control group, and the CD3+CD8+, CD19+, and ALC assay values were higher than those in the control group ( < 0.05). The CD3+CD8+ detection values of newly diagnosed patients were similar to those of relapsed refractory patients ( > 0.05); CD3+, CD3+CD4+, CD4+/CD8+, and CD16+CD56+ detection values of newly diagnosed patients were lower than those of relapsed refractory patients, and CD19+ and ALC detection values were higher than those of relapsed refractory patients; CD3+, CD3+CD4+, CD4+, CD4+/CD8+, and CD16+CD56+ detection values of mild patients were lower than those of relapsed refractory patients; CD3+, CD3+CD4+, CD4+/CD8+, and CD16+CD56+ detection values were higher in mild patients than in severe patients, and CD3+CD8+, CD19+, and ALC detection values were lower than in severe patients ( < 0.05). The absolute lymphocyte values were of high diagnostic value in primary immune thrombocytopenia, with a sensitivity and specificity of 93.42% and 90.00%. The application of absolute peripheral blood lymphocyte value in the clinical diagnosis of primary immune thrombocytopenia can achieve a better detection and diagnosis effect, which has a positive impact on the early diagnosis rate and can help patients to obtain more timely, effective and targeted treatment, and is worthy of promotion.
Topics: Humans; Lymphocytes; Purpura, Thrombocytopenic, Idiopathic
PubMed: 36072617
DOI: 10.1155/2022/9833941 -
PloS One 2022Severe acute respiratory syndrome coronavirus (SARS-CoV2) has imposed catastrophic impressions on the world. After all the focused researches conducted in the COVID-19...
INTRODUCTION
Severe acute respiratory syndrome coronavirus (SARS-CoV2) has imposed catastrophic impressions on the world. After all the focused researches conducted in the COVID-19 area, many features remain obscure. We have surveyed 1,363 outpatients with suspected COVID-19 in Tehran, Iran. The analysis emphasized on characteristics of patients with positive PCR or serology of SARS-CoV-2.
METHODS
The nasopharyngeal swabs were tested for SARS-CoV2 PCR. Serum specimens were tested for SARS-CoV2 IgG and IgM. Clinical presentations of the patients, history of chronic diseases or drug use, contact with a possible COVID-19 patient and previous infection with SARS-COV2 were investigated.
RESULTS
Of the total 1,363 investigated patients, 22% had positive SARS-CoV-2 PCRs, 82% had positive IgG, 38% had positive IgM, and 31% had both positive IgM and IgG values. Positive serologic tests were significantly associated with a positive PCR test obtained previously in the course of the current disease (P value<0.001). IgG and IgM antibody values were significantly associated with underlying disease, cough, fever, chills, fatigue, and myalgia (all P values <0.001). Dyspnea was significantly associated with IgG levels (P value = 0.01), yet it was not associated with IgM serology (P value = 0.2). Positive serology tests were not associated with symptoms of coryza. GI symptoms were not associated with positive IgG test (P value = 0.1), yet it did show an association with positive IgM test (P value = 0.02). Cough, fever, chills, myalgia fatigue, dyspnea, and GI symptoms were all significantly associated with positive PCR (all P values <0.001), and symptoms of coryza did not show a significant relationship (P value = 0.8).
CONCLUSION
Assessing antibody titers in outpatients is invaluable due to the epidemiological importance of investigations in mild or even asymptomatic cases. Since the number of such studies in non-hospitalized patients is not high, the current study can be used as a comparison model.
Topics: Antibodies, Viral; COVID-19; Chills; Cough; Cross-Sectional Studies; Dyspnea; Fatigue; Humans; Immunoglobulin G; Immunoglobulin M; Iran; Myalgia; RNA, Viral; SARS-CoV-2; Serologic Tests
PubMed: 35421183
DOI: 10.1371/journal.pone.0266923 -
Royal Society Open Science Dec 2017We wish to answer this question: If you observe a 'significant' -value after doing a single unbiased experiment, what is the probability that your result is a false...
We wish to answer this question: If you observe a 'significant' -value after doing a single unbiased experiment, what is the probability that your result is a false positive? The weak evidence provided by values between 0.01 and 0.05 is explored by exact calculations of false positive risks. When you observe = 0.05, the odds in favour of there being a real effect (given by the likelihood ratio) are about 3 : 1. This is far weaker evidence than the odds of 19 to 1 that might, wrongly, be inferred from the value. And if you want to limit the false positive risk to 5%, you would have to assume that you were 87% sure that there was a real effect before the experiment was done. If you observe 0.001 in a well-powered experiment, it gives a likelihood ratio of almost 100 : 1 odds on there being a real effect. That would usually be regarded as conclusive. But the false positive risk would still be 8% if the prior probability of a real effect were only 0.1. And, in this case, if you wanted to achieve a false positive risk of 5% you would need to observe = 0.00045. It is recommended that the terms 'significant' and 'non-significant' should never be used. Rather, values should be supplemented by specifying the prior probability that would be needed to produce a specified (e.g. 5%) false positive risk. It may also be helpful to specify the minimum false positive risk associated with the observed value. Despite decades of warnings, many areas of science still insist on labelling a result of < 0.05 as 'statistically significant'. This practice must contribute to the lack of reproducibility in some areas of science. This is before you get to the many other well-known problems, like multiple comparisons, lack of randomization and hacking. Precise inductive inference is impossible and replication is the only way to be sure. Science is endangered by statistical misunderstanding, and by senior people who impose perverse incentives on scientists.
PubMed: 29308247
DOI: 10.1098/rsos.171085 -
American Journal of Translational... 2021To investigate the value of the neutrophil-to-lymphocyte ratio (NLR) and Interleukin 18 (IL-18) level in patients with deep vein thrombosis after receiving surgery for...
OBJECTIVE
To investigate the value of the neutrophil-to-lymphocyte ratio (NLR) and Interleukin 18 (IL-18) level in patients with deep vein thrombosis after receiving surgery for spinal degeneration; and we explore their significance in clinical practice.
METHODS
This study was conducted in 296 patients who were treated in our hospital for spinal degeneration. After surgery, these patients were followed up for 1 month. After performing the color Doppler ultrasound examination, patients were divided into the thrombus group (n = 72) and the non-thrombus group (n = 224) based on the occurrence of deep vein thrombosis. Baseline data, NLR values and IL-18 levels before surgery, and at 1, 3, 5, and 7 days after surgery were compared between the two groups. Logistic regression analysis was implemented to analyze the risk factors for postoperative deep vein thrombosis. Patients in the thrombosis group were allocated to the mild, moderate, and severe group on the basis of the degree of thrombosis. NLR values and IL-18 levels at 3 days after surgery were compared among the three groups. The correlations between both NLR value and IL-18 level and the severity of deep vein thrombosis were analyzed with Pearson correlation. Receiver operating characteristic curve was used to assess the clinical value of NLR value and IL-18 level at 3 days after surgery in predicting postoperative deep vein thrombosis.
RESULTS
There were significant differences concerning age, the history of diabetes, and obesity between the two groups (all P<0.05). NLR values and IL-18 levels in both groups after surgery were increased when compared with before surgery (all P<0.01). In addition, NLR values and IL-18 levels reached a peak at 3 days after surgery. Compared with the non-thrombus group, NLR values and IL-18 levels in the thrombus group at 1, 3, 5, and 7 days after surgery were increased (all P<0.01). NLR value and IL-18 level in the thrombosis group at 3 days after surgery were increased with a worsened degree of thrombosis. In other words, both NLR value and IL-18 level were positively correlated with the degree of deep vein thrombosis. The results of logistic regression analysis displayed that age ≥60 years old, body mass index ≥23 kg/m, NLR value >4.34%, and IL-18 level >115.71 ng/mL were independent risk factors for postoperative deep vein thrombosis. The results of the ROC curve showed that the area under curves, which represent the formation of postoperative deep vein thrombosis, were above 0.7 when using NLR value and IL-18 level at 3 days after surgery (both P<0.001).
CONCLUSION
Compared with the non-thrombus group, NLR value and IL-18 level in the thrombosis group after receiving surgery for spinal degeneration are significantly increased. In addition, the more severe the thrombosis is, the higher the NLR value and IL-18 level at 3 days after surgery. Therefore, NLR value and IL-18 level at 3 days after surgery have certain clinical value in predicting postoperative deep vein thrombosis and prognosis.
PubMed: 34306476
DOI: No ID Found