Analysis of gene expression dynamics and differential expression in viral infections using generalized linear models and quasi-likelihood methods.

Introduction: Our study undertakes a detailed exploration of gene expression dynamics within human lung organ tissue equivalents (OTEs) in response to Influenza A virus (IAV), Human metapneumovirus (MPV), and Parainfluenza virus type 3 (PIV3) infections. Through the analysis of RNA-Seq data from 19,671 genes, we aim to identify differentially expressed genes under various infection conditions, elucidating the complexities of virus-host interactions. Methods: We employ Generalized Linear Models (GLMs) with Quasi-Likelihood (QL) F-tests (GLMQL) and introduce the novel Magnitude-Altitude Score (MAS) and Relaxed Magnitude-Altitude Score (RMAS) algorithms to navigate the intricate landscape of RNA-Seq data. This approach facilitates the precise identification of potential biomarkers, highlighting the host's reliance on innate immune mechanisms. Our comprehensive methodological framework includes RNA extraction, library preparation, sequencing, and Gene Ontology (GO) enrichment analysis to interpret the biological significance of our findings. Results: The differential expression analysis unveils significant changes in gene expression triggered by IAV, MPV, and PIV3 infections. The MAS and RMAS algorithms enable focused identification of biomarkers, revealing a consistent activation of interferon-stimulated genes (e.g., IFIT1, IFIT2, IFIT3, OAS1) across all viruses. Our GO analysis provides deep insights into the host's defense mechanisms and viral strategies exploiting host cellular functions. Notably, changes in cellular structures, such as cilium assembly and mitochondrial ribosome assembly, indicate a strategic shift in cellular priorities. The precision of our methodology is validated by a 92% mean accuracy in classifying respiratory virus infections using multinomial logistic regression, demonstrating the superior efficacy of our approach over traditional methods. Discussion: This study highlights the intricate interplay between viral infections and host gene expression, underscoring the need for targeted therapeutic interventions. The stability and reliability of the MAS/RMAS ranking method, even under stringent statistical corrections, and the critical importance of adequate sample size for biomarker reliability are significant findings. Our comprehensive analysis not only advances our understanding of the host's response to viral infections but also sets a new benchmark for the identification of biomarkers, paving the way for the development of effective diagnostic and therapeutic strategies.

Fit of biokinetic data in molecular radiotherapy: a machine learning approach.

BACKGROUND: In literature are reported different analytical methods (AM) to choose the proper fit model and to fit data of the time-activity curve (TAC). On the other hand, Machine Learning algorithms (ML) are increasingly used for both classification and regression tasks. The aim of this work was to investigate the possibility of employing ML both to classify the most appropriate fit model and to predict the area under the curve (τ). METHODS: Two different ML systems have been developed for classifying the fit model and to predict the biokinetic parameters. The two systems were trained and tested with synthetic TACs simulating a whole-body Fraction Injected Activity for patients affected by metastatic Differentiated Thyroid Carcinoma, administered with [131I]I-NaI. Test performances, defined as classification accuracy (CA) and percentage difference between the actual and the estimated area under the curve (Δτ), were compared with those obtained using AM varying the number of points (N) of the TACs. A comparison between AM and ML were performed using data of 20 real patients. RESULTS: As N varies, CA remains constant for ML (about 98%), while it improves for F-test (from 62 to 92%) and AICc (from 50 to 92%), as N increases. With AM, [Formula: see text] can reach down to - 67%, while using ML [Formula: see text] ranges within ± 25%. Using real TACs, there is a good agreement between τ obtained with ML system and AM. CONCLUSIONS: The employing of ML systems may be feasible, having both a better classification and a better estimation of biokinetic parameters.

Exploration of surface tension measurement methods for pharmaceutical excipients.

Surface tension is a crucial functional indicator for various classes of pharmaceutical excipients, as highlighted in both the Pharmacopoeia of the People's Republic of China (ChP) < 9601 Guidelines for Functionality-related Characteristics of Pharmaceutical Excipients > and the United States Pharmacopoeia (USP) < 1059 Excipient Performance >. However, there are few systematic studies on surface tension measurement of pharmaceutical excipients, resulting in a lack of stable parameter support in practical applications. In this study, we aim to fill this gap by exploring three different methods for measuring surface tension. These methods were carefully developed taking into account the actual measurement process and statistical theory, thus ensuring their applicability and reliability. Through comparative analyses, we have identified the most suitable measurement methods for different classes of pharmaceutical excipients. In addition, this paper describes the surface adsorption behavior of various excipients. Therefore, this study provides valuable guidance for the determination of surface tension and the study of surface adsorption behavior, which lays the foundation for further comprehensive research in the field of surface tension of pharmaceutical excipients and the improvement of general pharmacopoeia specification.

On detecting the effect of exposure mixture.

To study the effect of exposure mixture on the continuous health outcomes, one can use the linear model with a weighted sum of multiple standardized exposure variables as an index predictor and its coefficient for the overall effect. The unknown weights typically range between zero and one, indicating contributions of individual exposures to the overall effect. Because the weight parameters present only when the parameter for overall effect is non-zero, testing hypotheses on the overall effect can be challenging, especially when the number of exposure variables is above two. This paper presents a working model based approach to estimate the parameter for overall effect and to test specific hypotheses, including two tests for detecting the overall effect and one test for detecting unequal weights when the overall effect is evident. The statistics are computationally easy and one can apply existing statistical software to perform the analysis. A simulation study shows that the proposed estimators for the parameters of interest may have better finite sample performance than some other estimators.

Homogeneity evaluation of liquid reference material developed for nuclear decommissioning.

Homogeneity assessment is explicitly required by ISO Guide 35. In connection with the INSIDER project, relevant reference material was chosen to be developed. For this purpose liquid material characterised for radionuclide content with accuracy better than 10% at the 95% confidence level and based on liquid effluent tank waste from JRC Ispra was produced by CMI and homogeneity of the selected radionuclides was evaluated.

Combining Gaussian Process with Hybrid Optimal Feature Decision in Cuffless Blood Pressure Estimation.

Noninvasive blood pressure estimation is crucial for cardiovascular and hypertension patients. Cuffless-based blood pressure estimation has received much attention recently for continuous blood pressure monitoring. This paper proposes a new methodology that combines the Gaussian process with hybrid optimal feature decision (HOFD) in cuffless blood pressure estimation. First, we can choose one of the feature selection methods: robust neighbor component analysis (RNCA), minimum redundancy, maximum relevance (MRMR), and F-test, based on the proposed hybrid optimal feature decision. After that, a filter-based RNCA algorithm uses the training dataset to obtain weighted functions by minimizing the loss function. Next, we combine the Gaussian process (GP) algorithm as the evaluation criteria, which is used to determine the best feature subset. Hence, combining GP with HOFD leads to an effective feature selection process. The proposed combining Gaussian process with the RNCA algorithm shows that the root mean square errors (RMSEs) for the SBP (10.75 mmHg) and DBP (8.02 mmHg) are lower than those of the conventional algorithms. The experimental results represent that the proposed algorithm is very effective.

Comparing the predictions by NIR spectroscopy based multivariate models for distillation fractions of crude oils by F-test.

The whole range of distillation fractions in industrially relevant crude oil samples is predicted by using two multivariate models based on near-infrared (NIR) spectra. The first versions of the models as well as the respective model updates are considered, with the updates largely aimed at expanding the models. The prediction results are compared across all the fractions and F-test is used to critically compare the performance of the models and the effectiveness of the limited updates. The results suggest that both multivariate methods perform very comparably, and the updates do not lead to statistically significant changes, which differs from what one could conclude from the nominal prediction errors. The near-equivalency of the prediction accuracy of the updated models is additionally illustrated by perusing predictions of a number of batches from one sour and one sweet crude arriving at the refinery during a four month period.

Preferring self-management behavior of patients with chronic kidney disease.

This study explores the preferred behavior of self-management among chronic kidney disease (CKD) patients and offers suggestions for different patients from personalized medicine. According to some related references, a questionnaire was designed in 2020 to collect data from 131 patients with CKD in a general hospital. The Sampling patients showed no difference in their disease progress. The questionnaire covered two aspects of demographic and behavior with 29 items on six dimensions. Statistical methods such as a descriptive analysis of the F test in behavior dimensions on demographic characteristics and Principal component analysis from items have been applied to classify some kinds of self-management behavior into different groups. In the demographic insight, employment status closely relates to self-management behavior, and income is insignificant. In the behavior aspects, according to some key items, we found four types of self-management behavior preferred in the sorting: cognitive-knowledge, Diet-exercise-medical, emotion management, and exercise-medical, which were defined by behavior dimensions. Although patients had the same disease progress, their self-management behavior mainly existed in four types based on critical factors. According to their favorite behavior and personality group, healthcare stakeholders can offer lean support for improving patients' self-management of CKD in China.

Spectral denoising based on Hilbert-Huang transform combined with F-test.

Due to the influence of uncontrollable factors such as the environment and instruments, noise is unavoidable in a spectral signal, which may affect the spectral resolution and analysis result. In the present work, a novel spectral denoising method is developed based on the Hilbert-Huang transform (HHT) and F-test. In this approach, the original spectral signal is first decomposed by empirical mode decomposition (EMD). A series of intrinsic mode functions (IMFs) and a residual (r) are obtained. Then, the Hilbert transform (HT) is performed on each IMF and r to calculate their instantaneous frequencies. The mean and standard deviation of instantaneous frequencies are calculated to further illustrate the IMF frequency information. Third, the F-test is used to determine the cut-off point between noise frequency components and non-noise ones. Finally, the denoising signal is reconstructed by adding the IMF components after the cut-off point. Artificially chemical noised signal, X-ray diffraction (XRD) spectrum, and X-ray photoelectron spectrum (XPS) are used to validate the performance of the method in terms of the signal-to-noise ratio (SNR). The results show that the method provides superior denoising capabilities compared with Savitzky-Golay (SG) smoothing.

Feature extraction from MRI ADC images for brain tumor classification using machine learning techniques.

BACKGROUND: Diffusion-weighted (DW) imaging is a well-recognized magnetic resonance imaging (MRI) technique that is being routinely used in brain examinations in modern clinical radiology practices. This study focuses on extracting demographic and texture features from MRI Apparent Diffusion Coefficient (ADC) images of human brain tumors, identifying the distribution patterns of each feature and applying Machine Learning (ML) techniques to differentiate malignant from benign brain tumors. METHODS: This prospective study was carried out using 1599 labeled MRI brain ADC image slices, 995 malignant, 604 benign from 195 patients who were radiologically diagnosed and histopathologically confirmed as brain tumor patients. The demographics, mean pixel values, skewness, kurtosis, features of Grey Level Co-occurrence Matrix (GLCM), mean, variance, energy, entropy, contrast, homogeneity, correlation, prominence and shade, were extracted from MRI ADC images of each patient. At the feature selection phase, the validity of the extracted features were measured using ANOVA f-test. Then, these features were used as input to several Machine Learning classification algorithms and the respective models were assessed. RESULTS: According to the results of ANOVA f-test feature selection process, two attributes: skewness (3.34) and GLCM homogeneity (3.45) scored the lowest ANOVA f-test scores. Therefore, both features were excluded in continuation of the experiment. From the different tested ML algorithms, the Random Forest classifier was chosen to build the final ML model, since it presented the highest accuracy. The final model was able to predict malignant and benign neoplasms with an 90.41% accuracy after the hyper parameter tuning process. CONCLUSIONS: This study concludes that the above mentioned features (except skewness and GLCM homogeneity) are informative to identify and differentiate malignant from benign brain tumors. Moreover, they enable the development of a high-performance ML model that has the ability to assist in the decision-making steps of brain tumor diagnosis process, prior to attempting invasive diagnostic procedures, such as brain biopsies.

Association of population migration with air quality: Role of city attributes in China during COVID-19 pandemic (2019-2021).

Atmospheric pollution studies have linked diminished human activity during the COVID-19 pandemic to improve air quality. This study was conducted during January to March (2019-2021) in 332 cities in China to examine the association between population migration and air quality, and examined the role of three city attributes (pollution level, city scale, and lockdown status) in this effect. This study assessed six air pollutants, namely CO, NO2, O3, PM10, PM2.5, and SO2, and measured meteorological data, with-in city migration (WCM) index, and inter-city migration (ICM) index. A linear mixed-effects model with an autoregressive distributed lag model was fitted to estimate the effect of the percent change in migration on air pollution, adjusting for potential confounding factors. In summary, lower migration was associated with decreased air pollution (other than O3). Pollution change in susceptibility is more likely to occur in NO2 decrease and O3 increase, but unsusceptibility is more likely to occur in CO and SO2, to city attributes from low migration. Cities that are less air polluted and population-dense may benefit more from decreasing PM10 and PM2.5. The associations between population migration and air pollution were stronger in cities with stringent traffic restrictions than in cities with no lockdowns. Based on city attributes, an insignificant difference was observed between the effects of ICM and WCM on air pollution. Findings from this study may gain knowledge about the potential interaction between migration and city attributes, which may help decision-makers adopt air-quality policies with city-specific targets and paths to pursue similar air quality improvements for public health but at a much lower economic cost than lockdowns.

Statistical tests for non-independent partitions of large autocorrelated datasets.

Large sets of autocorrelated data are common in fields such as remote sensing and genomics. For example, remote sensing can produce maps of information for millions of pixels, and the information from nearby pixels will likely be spatially autocorrelated. Although there are well-established statistical methods for testing hypotheses using autocorrelated data, these methods become computationally impractical for large datasets. • The method developed here makes it feasible to perform F-tests, likelihood ratio tests, and t-tests for large autocorrelated datasets. The method involves subsetting the dataset into partitions, analyzing each partition separately, and then combining the separate tests to give an overall test. • The separate statistical tests on partitions are non-independent, because the points in different partitions are not independent. Therefore, combining separate analyses of partitions requires accounting for the non-independence of the test statistics among partitions. • The methods can be applied to a wide range of data, including not only purely spatial data but also spatiotemporal data. For spatiotemporal data, it is possible to estimate coefficients from time-series models at different spatial locations and then analyze the spatial distribution of the estimates. The spatial analysis can be simplified by estimating spatial autocorrelation directly from the spatial autocorrelation among time series.

Objective Detection of the Speech Frequency Following Response (sFFR): A Comparison of Two Methods.

Speech frequency following responses (sFFRs) are increasingly used in translational auditory research. Statistically-based automated sFFR detection could aid response identification and provide a basis for stopping rules when recording responses in clinical and/or research applications. In this brief report, sFFRs were measured from 18 normal hearing adult listeners in quiet and speech-shaped noise. Two statistically-based automated response detection methods, the F-test and Hotelling's T2 (HT2) test, were compared based on detection accuracy and test time. Similar detection accuracy across statistical tests and conditions was observed, although the HT2 test time was less variable. These findings suggest that automated sFFR detection is robust for responses recorded in quiet and speech-shaped noise using either the F-test or HT2 test. Future studies evaluating test performance with different stimuli and maskers are warranted to determine if the interchangeability of test performance extends to these conditions.

Statistical Study on Additives Used to Improve Mechanical Properties of Polypropylene.

Polypropylene (PP) is a semi-crystalline polymer that is brittle under severe conditions. To meet industry needs, and to increase the applications of polypropylene, its mechanical properties should be improved. In this research, the mechanical properties of polypropylene, such as tensile strength at break, tensile strength at yield, % elongation, and Young's modulus, were improved using two types of additives. Additives used were calcium carbonate master batch filler composed of 80% calcium carbonate and 20% polyethylene, and a mixture of linear low-density polyethylene (LLDPE)/low density polyethylene (LDPE). Results showed that both tensile strength at break, and tensile strength at yield, decrease with increasing the amount of both additives. Percentage elongation of PP increased using both additives. The modulus of elasticity of PP increases by increasing the amount of both additives, until a value of 20 wt%. Analysis of variance (ANOVA test) or (F-test) shows significant differences between the effect of different weights of LLDPE/LDPE mixture and calcium carbonate filler on the four mechanical properties of polypropylene studied at a level of 0.05. T-tests are applied to compare between the effect of both calcium carbonate master batch filler and the mixture LLDPE/LDPE on the four mechanical properties of polypropylene studied. T-tests show no significant differences between the effect of both calcium carbonate master batch filler and the mixture LLDPE/LDPE on all mechanical properties of polypropylene studied at a level of 0.05.

How to use analysis of variance correctly——an analysis of variance for the univariate quantitative data collected from the Latin square design / 四川精神卫生

The purpose of this paper was to introduce the calculation formulas and the SAS implementation of the analysis of variance of the univariate quantitative data with the Latin square design. The Latin square design could be divided into two categories： the general Latin square design and the Greek Latin square design. The former could be used for the experimental situation with one experimental factor and two block factors， the latter could be used for the experimental situation with two experimental factors and two block factors. In fact， Latin square designs could be further subdivided by whether or not the repeated experiments were performed and whether the block factor was a single individual type. Generally speaking， in addition to satisfying the requirements of "independence， normality and homogeneity of variance"， the interaction between all factors was required to be non-existent or negligible when performing an analysis of variance on the quantitative data with Latin square design. When the quantitative data did not meet the preconditions mentioned above， it was recommended to use a mixed-effects model to build the model and solve it， or to solve the estimated values of the parameters in the ANOVA model based on the generalized estimating equation method.

How to use analysis of variance correctly——an analysis of variance for the univariate quantitative data collected from the crossover design / 四川精神卫生

The purpose of the paper was to introduce the calculation formulas and the SAS implementation of the analysis of variance for the quantitative data of the crossover design. In the calculation， three test statistics were involved， namely Ftreatment， Fstage and Findividual. They were three test statistics used to evaluate the statistical significance of the effect of the treatment factor， the stage factor， and the individual factor on the quantitative outcome variable， respectively. In general， it was assumed that there was no or negligible interaction among the three factors in a crossover design， so there was no need to evaluate whether the interaction term was statistically significant. With the help of SAS software， this paper conducted the univariate analysis of variance for the quantitative data of crossover designs for three examples of 2×2 crossover design， 3×3 crossover design and three-stage crossover design， and presented the calculation results and drew the statistical and professional conclusions.

How to use analysis of variance correctly——an analysis of variance for the univariate quantitative data collected from the balanced incomplete block design / 四川精神卫生

The purpose of this paper was to introduce the model， calculation formulas and the SAS implementation of the analysis of variance for the quantitative data with balanced incomplete block design. In the calculation， two test statistics were involved， namely FA and FB. Among them， the subscript "A" represented the experimental factor， and the subscript "B" represented the block factor B （i.e.， the important non-experimental factor）. In general， it was assumed that there was no or negligible interaction between the two factors in a balanced incomplete block design， so there was no need to evaluate whether the interaction term was statistically significant. Therefore， it was not necessary to do repeated experiments under each combination of two factors. With the help of SAS software， this paper conducted the analysis of variance for the quantitative data with balanced incomplete block design on two examples， and presented the calculation results and made the statistical and professional conclusions.

How to use analysis of variance correctly——an analysis of variance for the univariate quantitative data collected from the randomized complete block design / 四川精神卫生

The purpose of this paper was to introduce the model， calculation formulas and the SAS implementation of the univariate analysis of variance for the quantitative data with randomized complete block design. In the calculation， two test statistics were involved， namely FA and FB. Among them， the subscript "A" represented the experimental factor， and the subscript "B" represented the block factor （i.e.， the important non-experimental factor）. In general， it was assumed that there was no or negligible interaction between the two factors in a randomized block design， so there was no need to assess whether the interaction term was statistically significant. Therefore， it was not necessary to do repeated experiments under each combination of two factors. With the help of SAS software， this paper conducted the analysis of variance for the quantitative data with randomized complete block design for two instances without and with repeated experiments， gave the calculation results， and made the statistical and professional conclusions.

Determining optimum carvacrol treatment as a cardinal value of a secondary model.

Predictive microbiology methods were used to study the effect of carvacrol on the bacterial resistance to antimicrobials. Our objective was to estimate the optimum dose of carvacrol at concentrations below its MIC value (Minimum Inhibitory Concentration). As a fluorescent marker, ethidium bromide (EtBr) was applied to Escherichia coli to acquire raw data. The accumulation of EtBr was measured by its fluorescence signal (Fs), in the unit of RFU (Relative Fluorescence Unit). The temporal change of the fluorescence values, at a constant concentration of carvacrol, was described by a saturation curve (primary model). The difference, within the observation interval, between the fitted initial and maximum fluorescent values was chosen as the primary parameter to be fitted in the secondary model: a convex, asymmetric, bi-linear function of the carvacrol concentration changing between 0 and 0.5 MIC. Its breakpoint is the optimum value of the carvacrol, a cardinal parameter of the secondary model, where the chosen primary parameter assumes its highest value. This optimum was estimated with high uncertainty for individual experiments, but F-test showed that, with appropriate experimental and numerical procedure, its existence and value can be claimed with confidence. Our results demonstrate that the estimation of the optimum of the secondary model can be robust even if the full secondary model is uncertain.

Can we disregard the whole model? Omnibus non-inferiority testing for R2 in multi-variable linear regression and η̂2 in ANOVA.

Determining a lack of association between an outcome variable and a number of different explanatory variables is frequently necessary in order to disregard a proposed model (i.e., to confirm the lack of a meaningful association between an outcome and predictors). Despite this, the literature rarely offers information about, or technical recommendations concerning, the appropriate statistical methodology to be used to accomplish this task. This paper introduces non-inferiority tests for ANOVA and linear regression analyses, which correspond to the standard widely used F test for η̂2 and R2 , respectively. A simulation study is conducted to examine the Type I error rates and statistical power of the tests, and a comparison is made with an alternative Bayesian testing approach. The results indicate that the proposed non-inferiority test is a potentially useful tool for 'testing the null'.