Categorical Data Analysis for High-Dimensional Sparse Gene Expression Data.

Categorical data analysis becomes challenging when high-dimensional sparse covariates are involved, which is often the case for omics data. We introduce a statistical procedure based on multinomial logistic regression analysis for such scenarios, including variable screening, model selection, order selection for response categories, and variable selection. We perform our procedure on high-dimensional gene expression data with 801 patients, 2426 genes, and five types of cancerous tumors. As a result, we recommend three finalized models: one with 74 genes achieves extremely low cross-entropy loss and zero predictive error rate based on a five-fold cross-validation; and two other models with 31 and 4 genes, respectively, are recommended for prognostic multi-gene signatures.

Variable Selection for Sparse Data with Applications to Vaginal Microbiome and Gene Expression Data.

Sparse data with a high portion of zeros arise in various disciplines. Modeling sparse high-dimensional data is a challenging and growing research area. In this paper, we provide statistical methods and tools for analyzing sparse data in a fairly general and complex context. We utilize two real scientific applications as illustrations, including a longitudinal vaginal microbiome data and a high dimensional gene expression data. We recommend zero-inflated model selections and significance tests to identify the time intervals when the pregnant and non-pregnant groups of women are significantly different in terms of Lactobacillus species. We apply the same techniques to select the best 50 genes out of 2426 sparse gene expression data. The classification based on our selected genes achieves 100% prediction accuracy. Furthermore, the first four principal components based on the selected genes can explain as high as 83% of the model variability.

Combination effect of exercise training and eugenol supplementation on the hippocampus apoptosis induced by chlorpyrifos.

The aim of this study was to investigate the combination effect of exercise training and eugenol supplementation on the hippocampus apoptosis induced by CPF. 64 adult male albino rats were randomly selected and devided into eight groups of eight including: control, exercise (EXE), chlorpyrifos (CPF), Control + Oil (Co + Oil), Control + DMSO (Co + DMSO), chlorpyrifos + eugenol (CPF + Sup), chlorpyrifos + exercise (CPF + Exe) and, chlorpyrifos + exercise + eugenol (CPF + Exe + Eu). Four experimental groups received intraperitoneal injection (5 days a week) of 3.0 mg/kg body weight CPF in DMSO for 6 consecutive weeks. The exercise groups performed aerobic 5 days per week over 4 weeks. Eugenol were administered by gavage. Finally, the animals were sacrificed using CO2 gas (a half of the rats were anesthetized with ketamine and xylazine and then perfused) to evaluate hippocampus histology and parameters. The results of this study showed that CPF injection significantly decreased BDNF, AChE and ATP in CA1 area of the hippocampus (p ˂ 0.05). Also, CA1 apoptosis by tunnel assay, it was found that CPF receiving groups with different dosage, showed a significant increase compared to other groups, which was confirmed by increasing cytochrome C and procaspase-3 in CPF groups (p ˂ 0.05). The result of this study show that 4 weeks of exercise training and eugenol supplementation does not improve the destructive effects of CPF in CA1 area of the hippocampus. As a result, it is recommended that future studies longer periods for treatment with exercise and eugenol supplementation.

Synergic effects of aerobic exercise and eugenol supplement on germ cell development and testicular tissue structure in chlorpyrifos-treated animal model.

Insecticide chlorpyrifos (CPF) with increased oxidative stress, structural destruction, and hemostasis of testicular tissue leads to male infertility. The present study investigated the protective effect of exercise (Exe) and eugenol supplementation (Sup) on CPF-induced testicular spermatogenic disorders in male rats. In this experimental study, 21 adult male albino rats were divided into seven groups, control (Co: 6 weeks), CPF (6 weeks), Co + Oil (2 weeks healthy food and 4 weeks oil), Co + Dimethylsulfoxide (DMSO: 6 weeks), CPF + Sup (2 weeks CPF and 4 weeks CPF + Sup), CPF + Exe (2 weeks CPF and 4 weeks CPF + Exe), and CPF + Exe + Sup (2 weeks CPF and 4 weeks CPF + Exe + Sup) group. All treatments were done intraperitoneally (5 days a week). Exe groups were subjected to run at moderate exercise intensity for 5 days per week over 6 weeks. DMSO groups were administered to the equal volume of vehicle for 6 consecutive weeks. Finally, the animals were sacrificed with Co2 gas and then alterations in testicular histology and sperm parameters were evaluated. Protein expression of PLZF and IGFα in the CPF group showed a significant decrease compared with the control group (p Ë‚ 0.001 for both). It was shown that CPF + Exe + Sup (p Ë‚ 0.001) and CPF + Sup (p Ë‚ 0.01) groups had a significant increase in protein expression of PLZF, but the protein expression of IGFα showed a significant increase just in the CPF + Exe + Sup group (p Ë‚ 0.001). Also, CPF caused a significant decrease in Leydig counts, Sertoli cell count, spermatogonium counts, spermatocyte cell count, spermatid cell count, and tunica thickness as well as a significant increase in testicle diameter (p Ë‚ 0.01) and ducts diameter compared with the control group. It seems that aerobic exercise with eugenol supplementation suppresses the disruption effects of CPF on testicular tissue (cellular and structural) by increasing the antioxidant capacity and improving the secretion of sex hormones. Therefore, the aerobic exercise with supplement of the eugenol has potential therapeutic targets for male infertility that need further study.

Role or Synergistic Interaction of Adenosine and Vitamin D3 Alongside High-Intensity Interval Training and Isocaloric Moderate Intensity Training on Metabolic Parameters: Protocol for an Experimental Study.

BACKGROUND: Obesity is known as one of the major causes of epidemiologic diseases worldwide; therefore, the introduction of treatment strategies by medical professionals, such as the use of various medicines and exercise programs to reduce fat or prevent obesity, is on the rise. Recently, researchers have shown special interest in assessing the effect of lipolytic adenosine and vitamin D deficiency, as well as the effect of exercise, on decreasing body fat percentage. OBJECTIVE: This study has been designed to examine the effect of adenosine and vitamin D3 injections, in conjunction with high-intensity interval training and isocaloric moderate-intensity training, on the metabolic parameters of obesity induced by a high-fat diet. METHODS: This is an experimental study using 92 Wistar rats. At 6 weeks of age, the rats' weights will be recorded, after which they will have 1 week to adapt to their new environment before being divided into 12 groups. The rats will participate in a 2-stage experimental intervention, including a 13-week fattening diet phase followed by a 12-week exercise training phase consisting of an exercise program and the injection of adenosine and vitamin D3. Groups 1 and 2 will have a normal diet, and the other groups will have a diet of 40% fat, with free access to food and water up to the second half of the second stage of the study (end of the sixth week of training). After termination of the interventions, tissue collection and molecular assessments (blood for biochemical, tissues for gene expression analyses, and anthropometrical indexes) will be performed. RESULTS: The project was initiated in April 2017 and completed in December 2017. Data analysis is under way, and the first results are expected to be submitted for publication in November 2018. CONCLUSIONS: We hypothesize that weight loss-induced molecular changes and upregulation will be observed in line with an increase in lipolysis and beta oxidation in muscle and fat tissue as a result of performing isocaloric training in drug-receiving rats and groups on a high-fat diet. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR1-10.2196/10753.

Comparison of fit accuracy and torque maintenance of zirconia and titanium abutments for internal tri-channel and external-hex implant connections.

PURPOSE: This in vitro study aimed to evaluate the effect of implant connection design (external vs. internal) on the fit discrepancy and torque loss of zirconia and titanium abutments. MATERIALS AND METHODS: Two regular platform dental implants, one with external connection (Brånemark, Nobel Biocare AB) and the other with internal connection (Noble Replace, Nobel Biocare AB), were selected. Seven titanium and seven customized zirconia abutments were used for each connection design. Measurements of geometry, marginal discrepancy, and rotational freedom were done using video measuring machine. To measure the torque loss, each abutment was torqued to 35 Ncm and then opened by means of a digital torque wrench. Data were analyzed with two-way ANOVA and t-test at α=0.05 of significance. RESULTS: There were significant differences in the geometrical measurements and rotational freedom between abutments of two connection groups (P<.001). Also, the results showed significant differences between titanium abutments of internal and external connection implants in terms of rotational freedom (P<.001). Not only customized internal abutments but also customized external abutments did not have the exact geometry of prefabricated abutments (P<.001). However, neither connection type (P=.15) nor abutment material (P=.38) affected torque loss. CONCLUSION: Abutments with internal connection showed less rotational freedom. However, better marginal fit was observed in externally connected abutments. Also, customized abutments with either connection could not duplicate the exact geometry of their corresponding prefabricated abutment. However, neither abutment connection nor material affected torque loss values.

Comparative Evaluation of Fracture Resistance and Mode of Failure of Zirconia and Titanium Abutments with Different Diameters.

AIM: The purpose of the current study was to compare the fracture resistance and mode of failure of zirconia and titanium abutments with different diameters. MATERIALS AND METHODS: Fourteen groups of abutments including prefabricated zirconia, copy-milled zirconia and titanium abutments of an implant system (XiVE, Dentsply) were prepared in different diameters. An increasing vertical load was applied to each specimen until failure occurred. Fracture resistance was measured in each group using the universal testing machine. Moreover, the failure modes were studied and categorized as abutment screw fracture, connection area fracture, abutment body fracture, abutment body distortion, screw distortion and connection area distortion. Groups were statistically compared using univariate and post-hoc tests. The level of statistical significance was set at 5%. RESULTS: Fabrication method (p = 0.03) and diameter (p < 0.001) had significant effect on the fracture resistance of abutments. Fracture resistance of abutments with 5.5 mm diameter was higher than other diameters (p < 0.001). The observed modes of failure were dependent on the abutment material as well. All of the prefabricated titanium abutments fractured within the abutment screw. Abutment screw distortion, connection area fracture, and abutment body fracture were the common failure type in other groups. CONCLUSION: Diameter had a significant effect on fracture resistance of implant abutments, as abutments with greater diameters were more resistant to static loads. Copy-milled abutments showed lower fracture resistance as compared to other experimental groups. CLINICAL SIGNIFICANCE: Although zirconia abutments have received great popularity among clinicians and even patients selecting them for narrow implants should be with caution.