Importance of feature selection stability in the classifier evaluation on high-dimensional genetic data
Classifiers trained on high-dimensional data, such as genetic datasets, often encounter situations where the number of features exceeds the number of objects. In these cases, classifiers typically rely on a small subset of features. For a robust algorithm, this subset should remain relatively stable with minor changes in the training data, such as the replacement of a few samples. While the stability of feature selection is a common focus in studies of feature selection algorithms, it is less emphasized in classifier evaluation, where only metrics such as accuracy are commonly used. We investigate the importance of feature selection stability through an empirical study of four classifiers (logistic regression, support vector machine, convex and piecewise Linear, and Random Forest) on seven high dimensional, publicly available, gene datasets. We measure the stability of feature selection using Lustgarten, Nogueira and Jaccard Index measures. We employed our own cross-validation procedure that guarantees a difference of exactly p objects between any two training sets which allows us to control the level of disturbance in the data. Our results show the existence of a drop in feature selection stability when we increase disturbance in the data in all 28 experiment configurations (seven datasets and four classifiers). The relationship is not linear, but resembles more of a hyperbolic pattern. In the evaluation of the tested classifiers, logistic regression demonstrated the highest stability. It was followed in order by support vector machine, convex and piecewise linear, with Random Forest exhibiting the lowest stability among them. This work provides evidence that all tested classifiers are very sensitive to even small changes in learning data in terms of features used by the model, while showing almost no sensitivity in terms of accuracy. The data and codes to reproduce the results in the article are available publicly on GitHub: https://github.com/tlukaszuk/feature-selection-stability-in-classifier-evaluation.
Łukaszuk et al. (2024) Importance of feature selection stability in the classifier evaluation on high-dimensional genetic data. PeerJ 12:e18405 https://doi.org/10.7717/peerj.18405
Comparison of iRoot BP Plus and mineral trioxide aggregate for pulpotomy in primary molars under general anesthesia: a 3-year retrospective study
Background Pulpotomy is a widely recommended treatment for deep caries and reversible pulpitis in primary teeth. However, there is a significant lack of large-scale clinical studies evaluating the long-term efficacy of pulpotomy in primary molars, especially in studies with follow-up periods extending beyond a two years. Aim This study aimed to evaluate the long-term efficacy of mineral trioxide aggregate (MTA) and iRoot BP Plus for pulpotomy in primary molars performed under general anesthesia and to investigate factors influencing the success rate. Methods In this retrospective study, a total of 942 primary molars from 422 children who met the inclusion criteria underwent pulpotomy. Propensity score matching method (PSM) was used to match the MTA and iRoot BP Plus groups in a 1:1 ratio based on covariates. Efficacy was assessed using the Zurn & Seale criteria. Kaplan-Meier survival analysis and Cox proportional hazards model were performed to analyze the outcomes. Results PSM resulted in 266 pairs of matched teeth from 532 teeth of 291 children (mean age: 4.64 ± 1.07 years, ranging from 2 to 8 years). Long-term clinical and radiographic evaluations revealed higher success rates for iRoot BP Plus (24-month: 99.54%/97.25%; 36-month: 97.22%/95.83%) compared to MTA (24-month: 94.76%/95.29%; 36-month: 92.50%/91.25%). Survival analysis indicated a statistically significant difference between two groups (P = 0.0042). Age, gender, tooth position, and decayed tooth surface showed no significant impact on pulpotomy success, whereas the choice of pulp capping materials significantly influenced the outcome (HR [95% CI]=0.3745[0.1857-0.7552], P = 0.006). Conclusion Clinical and radiographic evaluations support the use of iRoot BP Plus for pulpotomy in primary molars.
Zhao et al. (2024) Comparison of iRoot BP Plus and mineral trioxide aggregate for pulpotomy in primary molars under general anesthesia: a 3-year retrospective study. PeerJ 12:e18453 https://doi.org/10.7717/peerj.18453
Physical development of infants born to patients with COVID-19 during pregnancy: 2 years of age
Background SARS-CoV-2 infection during pregnancy and pandemic circumstances could negatively impact infant development. This study aimed to investigate the physical development, common pediatric illness incidence, and healthcare utilization over the first 2 years of life of infants born to COVID+ and COVID- patients. Comparisons were also made with infants born pre-pandemic. Methods This is a retrospective observational study at a major academic health system in New York City. Participants include all infants born to birthing persons with SARS-CoV-2 infection during pregnancy (N = 758) and without (N = 9,345) from 03/01/2020 to 08/17/2022, infants born pre-pandemic (N = 3,221) from 03/01/2017 to 08/17/2019, and birthing persons of all infants. Results There were no differences in weight, length, or head circumference curves between pandemic infants born to COVID+ and COVID- patients over the first 2 years of life (p > 0.05, repeated ANOVA). Annualized incidence of illness occurrence and healthcare utilization were similar between groups. Compared to pre-pandemic infants, the length of pandemic (COVID-) infants was lower from birth to 9 months (p < 0.0001). Pandemic infants additionally had more adverse perinatal outcomes including increased stillbirth (0.75% vs. 0.12%, p = 0.0001) and decreased gestational age (38.41 ± 2.71 vs. 38.68 ± 2.55 weeks, Cohen’s d = −0.10, p < 0.0001), birthweight (2,597 ± 335 vs. 3,142 ± 643 g, Cohen’s d = −1.06, p < 0.0001), and birth length (48.08 ± 4.61 vs. 49.09 ± 3.93 cm, Cohen’s d = −0.24, p < 0.0001). Conclusions Birthing persons’ SARS-CoV-2 infection status, birthing persons’ profiles, and pandemic circumstances negatively affected perinatal outcomes, newborn physical development, and healthcare utilization. These findings draw clinical attention to the need to follow infants closely and implement enrichment to ensure optimal developmental outcomes.
Eligulashvili et al. (2024) Physical development of infants born to patients with COVID-19 during pregnancy: 2 years of age. PeerJ 12:e18481 https://doi.org/10.7717/peerj.18481
Impact of accelerated aging on seed quality, seed coat physical structure and antioxidant enzyme activity of Maize (Zea mays L.)
Aging induces many deteriorative changes to seeds during storage like protein degradation, enzyme inactivation and loss of membrane integrity. In this study, we investigate the impact of accelerated aging on seed quality, seed coat physical structure and antioxidant enzyme activity of maize. Three genotypes African Tall, MAH 14-5 and a local landrace were selected and artificially aged for 96 and 120 h. The aging process led to a decrease in germination, vigour, and total dehydrogenase in seeds, while the electrical conductivity of seed leachates increased, indicating a decline in seed quality. Additionally, there was a variation in the microsculpture pattern of seed coats between genotypes. There was an accumulation of damage on the seed coat surface as the seeds aged and higher damage occurred in African Tall followed by MAH 14-5 and local landrace. Higher catalase, superoxide dismutase, peroxidase and polyphenol oxidase activity were reported in the seed coat of Local landrace and MAH 14-5 that resisted aging and deterioration while, lower catalase, superoxide dismutase, peroxidase and polyphenol oxidase activity was reported in African Tall seed coat that deteriorated during aging. Decrease antioxidant activity in aged seeds might be a possible cause of seed deterioration due to the accumulation of free radicals. Thus, these results clearly show the influence of seed coat structure and antioxidant activity on seed quality during aging.
Satya Srii et al. (2024) Impact of accelerated aging on seed quality, seed coat physical structure and antioxidant enzyme activity of Maize (Zea mays L.). PeerJ 12:e17988 https://doi.org/10.7717/peerj.17988
Examining the interplay between mental health indicators and quality of life measures among first-year law students: a cross-sectional study
Introduction This research explores the intricate relationships between mental health indicators (depression, stress, and anxiety) and various dimensions of quality of life among first-year law students. The study aims to understand how affective valence, mood states, physical activity, body image perception, and social relations influence mental health outcomes. Methods Data were collected from 75 first-year law students (46 females, 29 males), a group predominantly composed of young adults with limited financial means, living in various housing situations, primarily within urban environments, and generally reporting low levels of physical activity. Standardized questionnaires were used to assess mental health and quality of life, including the Depression, Anxiety, and Stress Scale-21 Items (DASS-21), Feeling Scale (FS), Exercise-Induced Feeling Inventory (EIFI), Modified Baecke Physical Activity Questionnaire (MBPAQ), World Health Organization Quality of Life-BREF (WHOQOL-BREF), and Contour Drawing Rating Scale (CDRS). Descriptive statistics, Pearson correlation, and regression analysis were employed to analyze the data. Results The analysis revealed significant correlations between depression (mean = 5.97, SD = 4.21), stress (mean = 7.81, SD = 4.80), and anxiety (mean = 6.17, SD = 4.58) with affective valence (p < 0.05), mood states (p < 0.05), physical activity (p < 0.05), body image perception (p < 0.05), and social relations quality (p < 0.05). Additionally, mood states (mean = 20.73, SD = 10.60), physical activity (mean = 8.43, SD = 1.35), body image perception (mean = 4.21, SD = 1.91), and social relations quality (mean = 12.46, SD = 2.33) were identified as significant predictors of mental health outcomes (p < 0.05). Conclusions These findings underscore the complex interplay between mental health indicators and various dimensions of quality of life, emphasizing the necessity for a comprehensive approach to mental health care. By identifying these predictors, we have gained a clearer understanding of the factors that impact mental health in this specific population. The insights gained highlight the value of interventions aimed at improving mood, increasing physical activity, enhancing body image, and strengthening social connections. These targeted strategies could effectively address mental health issues and promote well-being among law students. Future research should further investigate these relationships and develop tailored interventions to better support students’ mental health. This study contributes to understanding the complex interplay between mental health and quality of life, offering a foundation for both practical interventions and future research.
Muntean et al. (2024) Examining the interplay between mental health indicators and quality of life measures among first-year law students: a cross-sectional study. PeerJ 12:e18245 https://doi.org/10.7717/peerj.18245
Protein profile changes during priming explants to embryogenic response in Coffea canephora: identification of the RPN12 proteasome subunit involved in the protein degradation
Plant somatic embryogenesis encompasses somatic cells switch into embryogenic cells that can later produce somatic embryos with the ability to produce plantlets. Previously, we defined in vitro culture settings for the somatic embryogenesis process of Coffea canephora that comprise adequate plantlets with auxin plus cytokinin followed by cut-leaf explant cultivation with cytokinin, producing embryos with the ability to regenerate plantlets. Here, we confirmed that cultivating cut-leaf explants with cytokinin is sufficient to promote somatic embryos proliferation and the high yield of somatic embryos in the protocol requires adequate plantlets with auxin plus cytokinin. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels reveal auxin-plus cytokinin-dependent regulated proteins in plantlets with up and down abundance. Chitinase A class III, proteins involved in the metabolism and folding of proteins, photosynthesis, antioxidant activity, and chromatin organization were identified. The RPN12 protein, which is a subunit of the proteasome 26S, has an abundance that is not associated with transcript changes, suggesting post-translational regulation.
Carrillo-Bermejo et al. (2024) Protein profile changes during priming explants to embryogenic response in Coffea canephora: identification of the RPN12 proteasome subunit involved in the protein degradation. PeerJ 12:e18372 https://doi.org/10.7717/peerj.18372
Potential of epicatechin as antioxidant and antiaging in UV-induced BJ cells by regulating COL1A1, FGF-2, GPX-1, and MMP-1 gene, protein levels, and apoptosis
Background Oxidative stress caused by exposure to ultraviolet (UV) light on the skin can damage deoxyribonucleic acid (DNA) and cause keratinocytes to undergo apoptosis. Endogenous antioxidants which play a role in trapping free radicals are also unable to overcome excess reactive oxygen species (ROS) in the body due to UV exposure, so exogenous antioxidants are needed. Polyphenolic compounds extracted from natural ingredients such as flavonoids, quercetin, and epicatechin have quite strong antioxidant activity. This is influenced by the chemical structure of these compounds which are rich in hydroxyl groups and aromatic groups. This structure allows the compound to become an electron donor so that it can neutralize free radicals. In vitro research was used to see the potential effectiveness of epicatechin as an antiaging and antioxidant. The study aims to confirm the potential of epicatechin as an antiaging by in vitro assay. Methods The viability test of epicatechin on human skin fibroblast (BJ) cells was carried out using the water-soluble tetrazolium (WST) assay. BJ cells were UV-induced as a cell model of premature aging. Epicatechin 6.25, 12.5, and 25 µg/mL were administered to UV-induced BJ cells. The gene expression of Collagen I Alpha 1 (COL1A1), matrix metalloproteinase-1 (MMP-1), fibroblast growth factor-2 (FGF-2), and glutathione peroxidase-1 (GPX-1) were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Elastin (ELN), hyaluronidase (HAase), cyclooxigenase-2 (COX-2), 8-hydroxydeoxyguanosine (8-OhdG), and melatonin (MT) protein levels were analyzed by enzyme-linked immunosorbent assay (ELISA). The apoptosis of BJ cells was analyzed using flow cytometry. Results Treatment with epicatechin increased relative gene expression including COL1A1 (5.94), FGF-2 (8.34), and GPX-1 (8.09), and also decreased MMP-1 (2.90) relative gene expression compared to the UV-induced BJ cells. Epicatechin also increased levels of ELN (107.7 ng/mg protein) and MT (830 ng/mg protein) levels compared to the UV-induced BJ cells. Epicatechin treatment decreased levels of HAase (505.96 ng/mg protein), COX-2 (33.69 ng/mg protein), and 8-OHdG (97.87 ng/mg protein) compared to the UV-induced BJ cells. Epicatechin also succeeded in maintaining the percentage of live cells and reducing apoptosis, necrotic of UV-induced skin fibroblast cells. Conclusions Epicatechin has the potential to be an antiaging agent by in vitro assay.
Widowati et al. (2024) Potential of epicatechin as antioxidant and antiaging in UV-induced BJ cells by regulating COL1A1, FGF-2, GPX-1, and MMP-1 gene, protein levels, and apoptosis. PeerJ 12:e18382 https://doi.org/10.7717/peerj.18382
Seroprevalence and silent infection rate during SARS-CoV-2 pandemic among children and adolescents in Western Pomerania: a multicenter, cross-sectional study—the COVIDKID study
Background Limited data on SARS-CoV-2 seroprevalence in rural areas of northern Germany necessitate comprehensive cohort studies. We aimed to evaluate the seroprevalence, silent infection (SI) rates and risk factors for infections among children and adolescents in Western Pomerania from December 2020 to August 2022. Methods In this cross-sectional study, serum or plasma samples from children and adolescents (6 months to 17 years) were collected during routine blood draw. SARS-CoV-2 specific antibodies (S1 and nucleocapsid) and their neutralizing capacity were analyzed using commercially available enzyme-linked immunosorbent and neutralization assays. Socio-demographic data and information about SARS-CoV-2 infection or vaccination were obtained. Multivariable logistic regression was used to identify independent risk factors for SARS-CoV-2 infections and SI. Results A total of 1,131 blood samples were included into the study. Overall, SARS-CoV-2 seroprevalence was 25.1%, strongly influenced by the pandemic course, predominant virus variants, age and approval of vaccination. SI rate was 5.4% (95%-CI [3.7%–6.8%]) among unvaccinated and undiagnosed children over the entire study period with highest rates among adolescents. Main risk factor despite the time at risk for silent infections was an infected household member (Odds ratio = 9.88, 95%-CI [4.23–22.9], p < 0.001). Factors associated with overall infections (known and silent) also include the infection of a household member (Odds ratio = 17.8, 95%-CI [10.7–29.6], p < 0.001). Conclusions We believe that the introduction of governmental measures and systematic test strategies in schools strongly impacted on the SI rate, as we suspect that asymptomatic cases have already been identified, resulting in surprisingly low SI identified in our study.
Vollmer et al. (2024) Seroprevalence and silent infection rate during SARS-CoV-2 pandemic among children and adolescents in Western Pomerania: a multicenter, cross-sectional study—the COVIDKID study. PeerJ 12:e18384 https://doi.org/10.7717/peerj.18384
Examination of optical coherence tomography findings in patients with pregabalin use disorder
Background Pregabalin abuse is a rapidly growing health problem worldwide, and little is known about the effects of prolonged high-dose use in patients with pregabalin use disorder. Objective In this study, the effects of pregabalin abuse on retinal layers were investigated in patients with pregabalin use disorder (PGUD). Methods This study included 35 controls and 34 patients with PGUD, according to Diagnostic and Statistical Manual of Mental Disorders (DSM)-5 criteria. Optic coherence tomography (OCT) measurements including the retinal nerve fiber layer (RNFL), ganglion cell layer-inner plexiform layer (GCL-IPL) and ganglion cell complex (GCC) were performed. RNFL thickness was evaluated in four quadrants (inferior, superior, nasal, temporal). GCL-IPL and GCC thickness were evaluated in six sectors (superior, superonasal, inferonasal, inferior, inferotemporal, superotemporal). Results GCC inferonasal (p = 0.040, r = 0.354), GCC inferior (p = 0.018, r = 0.402) GCL-IPL inferior (p = 0.031, r = 0.370) and GCL-IPL inferotemporal (p = 0.029, r = 0.376) thickness were positively correlated with the duration of pregabalin use. There was no significant sector or quadrant-wise difference between groups (p > 0.05). Conclusion Our findings emphasized the drug’s potential neuroprotective effect. It should be taken into consideration that neurodegenerative changes due to substance use disorder occur with long-term. Longitudinal prospective studies investigating dose-duration relationship are needed.
Kılıç et al. (2024) Examination of optical coherence tomography findings in patients with pregabalin use disorder. PeerJ 12:e18395 https://doi.org/10.7717/peerj.18395
Transperineal prostate biopsy guided by which ultrasound transducer: transrectal or transperineal: a retrospective study
Background Prostate biopsies are primarily conducted using either the transrectal or transperineal approach, with the ultrasound probe positioned in the rectum to obtain a clear view of the prostate. Reports on the utilization of transperineal prostate biopsies with the ultrasound probe placed on the perineal skin are limited. Methods A retrospective investigation was conducted on 119 patients who underwent transperineal ultrasound guided transperineal prostate biopsy (TP-TPPB). Additionally, 85 patients who underwent transrectal ultrasound guided transperineal prostate biopsy (TR-TPPB) were included as controls. The prostate cancer detection rates (PCDRs) and postoperative complication rates were compared between the two groups, and their application values were also evaluated. Results The overall PCDRs were 35.3% (42/119) in the TP-TPPB and 32.9% (28/85) in the TR-TPPB group (χ2 = 0.122, p = 0.727). When categorized by PSA level, there was no significant difference between the two groups in PCDRs in any category (p > 0.05). However, the single-needle PCDRs in some regions (L4, L5, R2, and apex) showed significant differences (p < 0.05). There was no difference in postoperative complication rates between the groups. Conclusion The PCDRs and the postoperative complication rates of TP-TPPB and TR-TPPB are similar. However, TP-TPPB requires simpler equipment and does not require intestinal preparation, which is especially useful for patients with rectal contraindications, such as those with severe hemorrhoids and rectal/anal diseases.
Xiao et al. (2024) Transperineal prostate biopsy guided by which ultrasound transducer: transrectal or transperineal: a retrospective study. PeerJ 12:e18424 https://doi.org/10.7717/peerj.18424