Miracle-dz/UniFAR-FTUs huggingface dataset:
Overview of Gene Regulatory Network Inference Based on Differential Equation Models.

Reconstruction of gene regulatory networks (GRN) plays an important role in understanding the complexity, functionality and pathways of biological systems, which could support the design of new drugs for diseases. Because differential equation models are flexible and strong, these models have been utilized to identify biochemical reactions and gene regulatory networks. This paper investigates the differential equation models for reverse engineering gene regulatory networks. We introduce three kinds of differential equation models, including ordinary differential equation (ODE), time-delayed differential equation (TDDE) and stochastic differential equation (SDE). ODE models include linear ODE, nonlinear ODE and S-system model. We also discuss the evolutionary algorithms, which are utilized to search the optimal structures and parameters of differential equation models. This investigation could provide a comprehensive understanding of differential equation models, and lead to the discovery of novel differential equation models.
The Impact of the Circadian Genes CLOCK and ARNTL on Myocardial Infarction

The circadian rhythm regulates various physiological mechanisms, and its disruption can promote many disorders. Disturbance of endogenous circadian rhythms enhances the chance of myocardial infarction (MI), showing that circadian clock genes could have a crucial function in the onset of the disease. This case-control study was performed on 1057 participants. It was hypothesized that the polymorphisms of one nucleotide (SNP) in three circadian clock genes (CLOCK, ARNTL, and PER2) could be associated with MI. Statistically significant differences, estimated by the Chi-square test, were found in the distribution of alleles and genotypes between MI and no-MI groups of the CLOCK (rs6811520 and rs13124436) and ARNTL (rs3789327 and rs12363415) genes. According to the results of the present study, the polymorphisms in the CLOCK and ARNTL genes could be related to MI.
Association between human health and indoor air pollution in the Gulf Cooperation Council (GCC) countries: a review

Abstract Studies on the assessment of indoor air pollutants in terms of concentration and characterization in the Gulf Cooperation Council (GCC) countries have been recently carried out. This review assesses the health effects associated with indoor air pollution exposures in GCC, including other air pollutants (siloxanes, flame retardants, synthetic phenolic antioxidants) which were not explored in a previous study. In addition, the influence of ventilation conditions due to different indoor environments was also investigated. It was revealed that there is a lack of human health assessment studies on most indoor air pollutants in almost all GCC countries, except the United Arab Emirates, Kingdom of Saudi Arabia and Kuwait, where few attempts were made for some specific pollutants. Commonly reported plausible health effects potentially associated with indoor air pollution were related to respiratory symptoms and sick building syndrome (SBS). Many of the current health assessment studies in GCC countries were based on predictions and/or estimates of exposures rather than clinically based observational studies. Measured ventilation levels and indoor air velocities in most buildings failed to meet the American Society of Heating, Refrigerating and Air-conditioning Engineers (ASHRAE) threshold limits of 8 L/s/p and 0.18–0.25 m/s, respectively. Additionally, limited studies have investigated respiratory symptoms and SBS potentially attributable to poor ventilation in the region. It is highly recommended that future indoor air quality (IAQ) studies in GCC should focus more on epidemiologic and intervention studies.
No preferential carbon-allocation to storage over growth in clipped birch and oak saplings

Abstract Herbivory is one of the most globally distributed disturbances affecting carbon (C)-cycling in trees, yet our understanding of how it alters tree C-allocation to different functions such as storage, growth or rhizodeposition is still limited. Prioritized C-allocation to storage replenishment vs growth could explain the fast recovery of C-storage pools frequently observed in growth-reduced defoliated trees. We performed continuous 13C-labeling coupled to clipping to quantify the effects of simulated browsing on the growth, leaf morphology and relative allocation of stored vs recently assimilated C to the growth (bulk biomass) and non-structural carbohydrate (NSC) stores (soluble sugars and starch) of the different organs of two tree species: diffuse-porous (Betula pubescens Ehrh.) and ring-porous (Quercus petraea [Matt.] Liebl.). Carbon-transfers from plants to bulk and rhizosphere soil were also evaluated. Clipped birch and oak trees shifted their C-allocation patterns above-ground as a means to recover from defoliation. However, such increased allocation to current-year stems and leaves did not entail reductions in the allocation to the rhizosphere, which remained unchanged between clipped and control trees of both species. Betula pubescens and Q. petraea showed differences in their vulnerability and recovery strategies to clipping, the ring-porous species being less affected in terms of growth and architecture by clipping than the diffuse-porous. These contrasting patterns could be partly explained by differences in their C cycling after clipping. Defoliated oaks showed a faster recovery of their canopy biomass, which was supported by increased allocation of new C, but associated with large decreases in their fine root biomass. Following clipping, both species recovered NSC pools to a larger extent than growth, but the allocation of 13C-labeled photo-assimilates into storage compounds was not increased as compared with controls. Despite their different response to clipping, our results indicate no preventative allocation into storage occurred during the first year after clipping in either of the species.
Physical Exercise, Fitness, Cognitive Functioning, and Psychosocial Variables in an Adolescent Sample

The objective of this paper was to evaluate the relationship between physical exercise and physical fitness with cognitive and psychosocial functioning in a group of adolescents. 167 teenagers between 14 and 15 years old (M = 14.53; SD = 0.50) from the city of Malaga (Spain) participated in the study. This research used a comparative and predictive type of design. The Tanita® Body Composition Monitor BC-601, some Eurofit battery tests, the D2 Attention Test, the WISC-IV Scale Symbols and Keys tests, the Form 5 Self-Concept Questionnaire (AF5), the General Self-Efficacy Scale (GSE) and the General Health Questionnaire (GHQ-28) were used to evaluate the study variables. The results found in this research pointed to a positive relationship between physical exercise and physical fitness with cognitive and psychosocial functioning in the adolescents analyzed. For example, adolescents who practiced more physical exercise had better scores on variables such as selective attention (p < 0.001; η2 = 0.10), processing speed (p < 0.001; η2 = 0.09) or general self-efficacy (p < 0.001; η2 = 0.15). In addition, cardiorespiratory fitness was the best predictor of test scores to assess cognitive ability and psychosocial variables. These findings suggest the need to promote physical exercise among young people because of its implications for various facets of their health and development
A Retrospective Mixed Longitudinal Study of Tooth Formation in Children With Clefts

Objective: To test for systematic age changes in cleft children based on dental age. Design: Retrospective case–control longitudinal study. Setting: One orthodontic solo practice. Patients: Nonsyndromic, complete cleft lip and palateCLP cases, either unilateral or bilateral (102 children; 370 radiographs), between 4 and 16 years of age. Interventions: Children were treated with a team approach, but only orthodontic radiographs were studied. Main Outcome Measure: The principal outcome measure was dental age of the cleft cases compared to a sex-specific sample of phenotypically normal children (1107 children), from the same geographical region. Multiple panoramic radiographs taken during the course of orthodontic treatment were examined to track patterns of dental age as children matured. Analysis used linear mixed models primarily testing for sex, cleft type (unilateral, bilateral), and hypodontia differences. Initial expectation was that cleft children would exhibit delayed dental ages from postnatal stressors and would become more deviant with maturity. Results: In childhood (4-6 years), both sexes were significantly delayed (P < .001), but dental age normalized around 8 to 10 years. Boys experienced faster maturation thereafter than girls (P < .001). Only trivial differences occurred between unilateral CLP and bilateral CLP samples.Hypodontia further depressed maturation rates (P < .001). Dental age improved in a decidedly curvilinear fashion (P < .001), with greater change at earlier ages. Conclusions: This report agrees with other contemporary studies, showing childhood catch-up. Older studies observed that clefting caused significant delays that worsened with growth. This potential “seachange” suggests better recovery and quicker normalization of children with clefts, perhaps due to improved management.
Analysis of Yeast Killer Toxin K1 Precursor Processing via Site-Directed Mutagenesis: Implications for Toxicity and Immunity

The killer phenotype in the baker’s yeast Saccharomyces cerevisiae relies on two double-stranded RNA viruses that are persistently present in the cytoplasm. As they carry the same receptor populations as sensitive cells, killer yeast cells need—in contrast to various bacterial toxin producers—a specialized immunity mechanism. The ionophoric killer toxin K1 leads to the formation of cation-specific pores in the plasma membrane of sensitive yeast cells. Based on the data generated in this study, we were able to update the current model of toxin processing, validating the temporary inactivation of the toxic α subunit during maturation in the secretory pathway of the killer yeast. ABSTRACT K1 represents a heterodimeric A/B toxin secreted by virus-infected Saccharomyces cerevisiae strains. In a two-staged receptor-mediated process, the ionophoric activity of K1 leads to an uncontrolled influx of protons, culminating in the breakdown of the cellular transmembrane potential of sensitive cells. K1 killer yeast necessitate not only an immunity mechanism saving the toxin-producing cell from its own toxin but, additionally, a molecular system inactivating the toxic α subunit within the secretory pathway. In this study, different derivatives of the K1 precursor were constructed to analyze the biological function of particular structural components and their influence on toxin activity as well as the formation of protective immunity. Our data implicate an inactivation of the α subunit during toxin maturation and provide the basis for an updated model of K1 maturation within the host cell’s secretory pathway. IMPORTANCE The killer phenotype in the baker’s yeast Saccharomyces cerevisiae relies on two double-stranded RNA viruses that are persistently present in the cytoplasm. As they carry the same receptor populations as sensitive cells, killer yeast cells need—in contrast to various bacterial toxin producers—a specialized immunity mechanism. The ionophoric killer toxin K1 leads to the formation of cation-specific pores in the plasma membrane of sensitive yeast cells. Based on the data generated in this study, we were able to update the current model of toxin processing, validating the temporary inactivation of the toxic α subunit during maturation in the secretory pathway of the killer yeast.
Self-Reported Health and Patterns of Romantic Love in Adolescents from Eight European Countries and Regions

Purpose: Sexual minority youth (SMY) are at increased risk of poor health, but it remains unclear whether this phenomenon is universal. In this study, nationally representative samples of 15-year olds from eight European countries and regions were investigated to test if adolescents who have been in love with same- or both-gender partners report poorer health than those exclusively in love with opposite-gender partners or who have never been in love. Methods: A subsample of 13,674 adolescents participating in the 2014 Health Behaviour in School-aged Children (HBSC) study was used. We conducted binary logistic regression, adjusted for gender, region, and relative family affluence, to analyze associations between self-reported romantic love, multiple psychosomatic symptoms, and poor self-rated health. Results: Adolescents reporting same-gender love (adjusted odds ratio [aOR] = 1.50, 95% confidence interval [CI]: 1.11–2.02) and both-gender love (aOR = 3.57, 95% CI: 2.65–4.83) had significantly higher odds for multiple psychosomatic symptoms than those who reported opposite-gender love. Similarly, both SMY groups had higher odds of poor self-rated health (aOR = 2.95, 95% CI: 1.64–5.31 and aOR = 3.08, 95% CI: 1.79–5.31, respectively). Those who reported that they have never been in love had significantly lower odds for multiple symptoms. Adjustment for sociodemographic variables and stratifying by gender did not substantially change the odds ratios. Conclusion: Adolescents in love with same- and both-gender partners reported poorer subjective health outcomes than those in love with opposite-gender partners or who reported never being in love, suggesting that SMY health inequalities are found across various European countries and regions.
A stochastic model for simulating ribosome kinetics in vivo

Computational modelling of in vivo protein synthesis is highly complicated, as it requires the simulation of ribosomal movement over the entire transcriptome, as well as consideration of the concentration effects from 40+ different types of tRNAs and numerous other protein factors. Here I report on the development of a stochastic model for protein translation that is capable of simulating the dynamical process of in vivo protein synthesis in a prokaryotic cell containing several thousand unique mRNA sequences, with explicit nucleotide information for each, and report on a number of biological predictions which are beyond the scope of existing models. In particular, I show that, when the complex network of concentration dependent interactions between elongation factors, tRNAs, ribosomes, and other factors required for protein synthesis are included in full detail, several biological phenomena, such as the increasing peptide elongation rate with bacterial growth rate, are predicted as emergent properties of the model. The stochastic model presented here demonstrates the importance of considering the translational process at this level of detail, and provides a platform to interrogate various aspects of translation that are difficult to study in more coarse-grained models.
Volatile Organic Compounds from Orchids: From Synthesis and Function to Gene Regulation

Orchids are one of the most significant plants that have ecologically adapted to every habitat on earth. Orchids show a high level of variation in their floral morphologies, which makes them popular as ornamental plants in the global market. Floral scent and color are key traits for many floricultural crops. Volatile organic compounds (VOCs) play vital roles in pollinator attraction, defense, and interaction with the environment. Recent progress in omics technology has led to the isolation of genes encoding candidate enzymes responsible for the biosynthesis and regulatory circuits of plant VOCs. Uncovering the biosynthetic pathways and regulatory mechanisms underlying the production of floral scents is necessary not only for a better understanding of the function of relevant genes but also for the generation of new cultivars with desirable traits through molecular breeding approaches. However, little is known about the pathways responsible for floral scents in orchids because of their long life cycle as well as the complex and large genome; only partial terpenoid pathways have been reported in orchids. Here, we review the biosynthesis and regulation of floral volatile compounds in orchids. In particular, we focused on the genes responsible for volatile compounds in various tissues and developmental stages in Cymbidium orchids. We also described the emission of orchid floral volatiles and their function in pollination ecology. Taken together, this review will provide a broad scope for the study of orchid floral scents.
Mendelian Randomization of Circulating Polyunsaturated Fatty Acids and Colorectal Cancer Risk

Background: Results from epidemiologic studies examining polyunsaturated fatty acids (PUFA) and colorectal cancer risk are inconsistent. Mendelian randomization may strengthen causal inference from observational studies. Given their shared metabolic pathway, examining the combined effects of aspirin/NSAID use with PUFAs could help elucidate an association between PUFAs and colorectal cancer risk. Methods: Information was leveraged from genome-wide association studies (GWAS) regarding PUFA-associated SNPs to create weighted genetic scores (wGS) representing genetically predicted circulating blood PUFAs for 11,016 non-Hispanic white colorectal cancer cases and 13,732 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). Associations per SD increase in the wGS were estimated using unconditional logistic regression. Interactions between PUFA wGSs and aspirin/NSAID use on colorectal cancer risk were also examined. Results: Modest colorectal cancer risk reductions were observed per SD increase in circulating linoleic acid [ORLA = 0.96; 95% confidence interval (CI) = 0.93–0.98; P = 5.2 × 10−4] and α-linolenic acid (ORALA = 0.95; 95% CI = 0.92–0.97; P = 5.4 × 10−5), whereas modest increased risks were observed for arachidonic (ORAA = 1.06; 95% CI = 1.03–1.08; P = 3.3 × 10−5), eicosapentaenoic (OREPA = 1.04; 95% CI = 1.01–1.07; P = 2.5 × 10−3), and docosapentaenoic acids (ORDPA = 1.03; 95% CI = 1.01–1.06; P = 1.2 × 10−2). Each of these effects was stronger among aspirin/NSAID nonusers in the stratified analyses. Conclusions: Our study suggests that higher circulating shorter-chain PUFAs (i.e., LA and ALA) were associated with reduced colorectal cancer risk, whereas longer-chain PUFAs (i.e., AA, EPA, and DPA) were associated with an increased colorectal cancer risk. Impact: The interaction of PUFAs with aspirin/NSAID use indicates a shared colorectal cancer inflammatory pathway. Future research should continue to improve PUFA genetic instruments to elucidate the independent effects of PUFAs on colorectal cancer.
RP11‐81H3.2 promotes gastric cancer progression through miR‐339‐HNRNPA1 interaction network

Recent studies have demonstrated that various long non‐coding RNAs (lncRNAs) participate in the gastric cancer (GC) development and metastasis. Some lncRNAs exert their regulatory function by interacting with microRNAs. Here we identified a novel lncRNA RP11‐81H3.2 that was highly expressed in the GC tissue and cell lines. RP11‐81H3.2 knockdown significantly inhibited the proliferation, migration, and invasion of GC cells. Mechanistically, we demonstrated that RP11‐81H3.2 directly interacted with miR‐339 while miR‐339 regulated the HNRNPA1 expression by targeting HRRNPA1 3’‐UTR. RP11‐81H3.2‐miR‐339‐HNRNPA1 interaction network regulated the GC cell proliferation, migration, and invasion. Moreover, our results confirmed that RP11‐81H3.2 knockdown suppressed the tumor growth of GC in a xenograft model in vivo. In summary, the results suggest that RP11‐81H3.2 functions as an oncogene in GC and could be utilized as a promising diagnosis and therapeutic marker for GC treatment.
Testosterone Promotes the Proliferation of Chicken Embryonic Myoblasts Via Androgen Receptor Mediated PI3K/Akt Signaling Pathway

Testosterone (T) is essential for muscle fiber formation and growth. However, the specific mechanism by which T regulates skeletal muscle development in chicken embryos remains unclear. In this study, the role of T in myoblast proliferation both in vivo and in vitro was investigated. Results showed that the T administration significantly increased the ratio of breast muscle and leg muscle. T induced a significant increase in the cross-sectional area (CSA) and density of myofiber and the ratio of PAX7-positive cells in the skeletal muscle. Exogenous T also induced the upregulation of myogenic regulatory factors (MRFs) and cyclin-dependent kinases (CDK2)/Cyclin D1 (CCND1) and protein levels of androgen receptor (AR), p-Akt and PAX7. Furthermore, T treatment significantly promoted myoblasts cultured in vitro entering a new cell cycle and increased PAX7-positive cells. The mRNA and protein expression of AR and PAX7 were upregulated when treated with T compared to that of the control. The addition of T induced proliferation accompanied by increasing AR level as well as PI3K (Phosphoinositide 3-kinase)/Akt activation. However, T-induced proliferation was attenuated by AR, PI3K, and Akt-specific inhibitors. These data indicated that the pro-proliferative effect of T was regulated though AR in response to the activation of PI3K/Akt signalling pathway.
Color Stability and Micro-Hardness of Bulk-Fill Composite Materials after Exposure to Common Beverages

Objectives: To assess the color stability and surface microhardness of Bulk-Fill composite materials available in the Saudi Arabia market. Methods: Five composite materials (Filtek Z350, Filtek Bulk-Fill, Tetric N-Ceram Bulk-Fill, Sonic Fill 2, and SDR) were investigated. Samples (n = 20; 10 mm in diameter and 2 mm in thickness) were fabricated using a stainless-steel mold and were immersed in tea, coffee, berry juice, and distilled water (control). Baseline (T0) shades of specimens were recorded using a spectrophotometer and after 10 (T1), 30 (T2), 60 (T3), and 90 days (T4) of immersion. Measurements were obtained against a black background and CIE L*a*b* data was used to calculate ΔE for each group. Vickers microhardness values were obtained at T0 and T4. Data was analyzed using mixed model repeated measure ANOVA at 0.05 significance level. Results: Time, material, and solution effects have statistically significant effect on ΔE. Tea was the most staining solution. Z350 was associated with the highest ΔE values while SDR showed the lowest values. No other materials showed significant difference between each other. Solutions were statistically different from each other. All materials were different from each other regarding microhardness. Conclusion: Bulk-Fill materials showed more color stability but lower microhardness values compared to universal resin control.