Miracle-dz/UniFAR-FTUs huggingface dataset:
Prenatal Particulate Matter Exposure Is Associated with Saliva DNA Methylation at Age 15: Applying Cumulative DNA Methylation Scores as an Exposure Biomarker

Exposure in utero to particulate matter (PM2.5 and PM10) is associated with maladaptive health outcomes. Although exposure to prenatal PM2.5 and PM10 has cord blood DNA methylation signatures at birth, signature persistence into childhood and saliva cross-tissue applicability has not been tested. In the Fragile Families and Child Wellbeing Study, a United States 20-city birth cohort, average residential PM2.5 and PM10 during the three months prior to birth was estimated using air quality monitors with inverse distance weighting. Saliva DNA methylation at ages 9 (n = 749) and 15 (n = 793) was measured using the Illumina HumanMethylation 450 k BeadArray. Cumulative DNA methylation scores for particulate matter were estimated by weighting participant DNA methylation at each site by independent meta-analysis effect estimates and standardizing the sums. Using a mixed-effects regression analysis, we tested the associations between cumulative DNA methylation scores at ages 9 and 15 and PM exposure during pregnancy, adjusted for child sex, age, race/ethnicity, maternal income-to-needs ratio, nonmartial birth status, and saliva cell-type proportions. Our study sample was 50.5% male, 56.3% non-Hispanic Black, and 19.8% Hispanic, with a median income-to-needs ratio of 1.4. Mean exposure levels for PM2.5 were 27.9 μg/m3/day (standard deviation: 7.0; 23.7% of observations exceeded safety standards) and for PM10 were 15.0 μg/m3/day (standard deviation: 3.1). An interquartile range increase in PM2.5 exposure (10.73 μg/m3/day) was associated with a −0.0287 standard deviation lower cumulative DNA methylation score for PM2.5 (95% CI: −0.0732, 0.0158, p = 0.20) across all participants. An interquartile range increase in PM10 exposure (3.20 μg/m3/day) was associated with a −0.1472 standard deviation lower cumulative DNA methylation score for PM10 (95% CI: −0.3038, 0.0095, p = 0.06) across all participants. The PM10 findings were driven by the age 15 subset where an interquartile range increase in PM10 exposure was associated with a −0.024 standard deviation lower cumulative DNA methylation score for PM10 (95% CI: −0.043, −0.005, p = 0.012). Findings were robust to adjustment for PM exposure at ages 1 and 3. In utero PM10-associated DNA methylation differences were identified at age 15 in saliva. Benchmarking the timing and cell-type generalizability is critical for epigenetic exposure biomarker assessment.
Full-Length SMRT Transcriptome Sequencing and SSR Analysis of Bactrocera dorsalis (Hendel)

Simple Summary In this study, a full-length transcriptome was analyzed with single-molecule real-time (SMRT) sequencing, which was first used to discover simple sequence repeat (SSR) genetic markers from B. dorsalis. Moreover, SSR markers from isoforms were screened for the identification of species diversity. These results could provide molecular biology methods for further population research. Abstract Bactrocera dorsalis (Hendel), as one of the most notorious and destructive invasive agricultural pests in the world, causes damage to over 250 different types of fruits and vegetables throughout tropical and subtropical areas. PacBio single-molecule real-time (SMRT) sequencing was used to generate the full-length transcriptome data of B. dorsalis. A total of 40,319,890 subreads (76.6 Gb, clean reads) were generated, including 535,241 circular consensus sequences (CCSs) and 386,916 full-length non-concatemer reads (FLNCs). Transcript cluster analysis of the FLNC reads revealed 22,780 high-quality reads (HQs). In total, 12,274 transcripts were functionally annotated based on four different databases. A total of 1978 SSR loci were distributed throughout 1714 HQ transcripts, of which 1926 were complete SSRs and 52 were complex SSRs. Among the total SSR loci, 2–3 nucleotide repeats were dominant, occupying 83.62%, of which di- and tri- nucleotide repeats were 39.38% and 44.24%, respectively. We detected 105 repeat motifs, of which AT/AT (50.19%), AC/GT (39.15%), CAA/TTG (32.46%), and ACA/TGT (10.86%) were the most common in di- and tri-nucleotide repeats. The repeat SSR motifs were 12–190 bp in length, and 1638 (88.02%) were shorter than 20 bp. According to the randomly selected microsatellite sequence, 80 pairs of primers were designed, and 174 individuals were randomly amplified by PCR using primers. The number of primers that had amplification products with clear bands and showed good polymorphism came to 41, indicating that this was a feasible way to explore SSR markers from the transcriptomic data of B. dorsalis. These results lay a foundation for developing highly polymorphic microsatellites for researching the functional genomics, population genetic structure, and genetic diversity of B. dorsalis.
The Paramount Role of Drosophila melanogaster in the Study of Epigenetics: From Simple Phenotypes to Molecular Dissection and Higher-Order Genome Organization

Simple Summary Since its adoption as a model organism more than a hundred years ago, the fruit fly Drosophila melanogaster has led to major discoveries in biology, notably in epigenetics. Epigenetics studies the changes in gene function inherited through mitosis or meiosis that are not due to modifications in the DNA sequence. The first discoveries in epigenetics emerged from analyses of the perturbations of simple phenotypes such as the bristle position or cuticle pigmentation. Identification of the mutated genes led to the discovery of major chromatin regulators, which were found to be conserved in other insects, and unexpectedly, in all metazoans. Many of them deposit post-translational modifications on histones, the proteins around which the DNA is wrapped. Others are chromatin remodeling complexes that move, eject, or exchange nucleosomes. We review here the role of D. melanogaster research in three important epigenetic fields: The formation of heterochromatin, the repression of mobile DNA elements by small RNAs, and the regulation of gene expression by the antagonistic Polycomb and Trithorax complexes. We then review how genetic tools available in D. melanogaster have allowed us to examine the role of histone marks and led to more global discoveries on chromatin organization. Lastly, we discuss the impact of varying environmental conditions on epigenetic regulation. Abstract Drosophila melanogaster has played a paramount role in epigenetics, the study of changes in gene function inherited through mitosis or meiosis that are not due to changes in the DNA sequence. By analyzing simple phenotypes, such as the bristle position or cuticle pigmentation, as read-outs of regulatory processes, the identification of mutated genes led to the discovery of major chromatin regulators. These are often conserved in distantly related organisms such as vertebrates or even plants. Many of them deposit, recognize, or erase post-translational modifications on histones (histone marks). Others are members of chromatin remodeling complexes that move, eject, or exchange nucleosomes. We review the role of D. melanogaster research in three epigenetic fields: Heterochromatin formation and maintenance, the repression of transposable elements by piRNAs, and the regulation of gene expression by the antagonistic Polycomb and Trithorax complexes. We then describe how genetic tools available in D. melanogaster allowed to examine the role of histone marks and show that some histone marks are dispensable for gene regulation, whereas others play essential roles. Next, we describe how D. melanogaster has been particularly important in defining chromatin types, higher-order chromatin structures, and their dynamic changes during development. Lastly, we discuss the role of epigenetics in a changing environment.
Foliar Fungal Endophytes in a Tree Diversity Experiment Are Driven by the Identity but Not the Diversity of Tree Species

Symbiotic foliar fungal endophytes can have beneficial effects on host trees and might alleviate climate-induced stressors. Whether and how the community of foliar endophytes is dependent on the tree neighborhood is still under debate with contradicting results from different tree diversity experiments. Here, we present our finding regarding the effect of the tree neighborhood from the temperate, densely planted and 12-years-old Kreinitz tree diversity experiment. We used linear models, redundancy analysis, Procrustes analysis and Holm-corrected multiple t-tests to quantify the effects of the plot-level tree neighborhood on the diversity and composition of foliar fungal endophytes in Fagus sylvatica, Quercus petraea and Picea abies. Against our expectations, we did not find an effect of tree diversity on endophyte diversity. Endophyte composition, however, was driven by the identity of the host species. Thirteen endophytes where overabundant in tree species mixtures, which might indicate frequent spillover or positive interactions between foliar endophytes. The independence of the diversity of endophytes from the diversity of tree species might be attributed to the small plot size and the high density of tree individuals. However, the mechanistic causes for these cryptic relationships still remain to be uncovered.
Oleanolic Acid-Enriched Olive Oil Alleviates the Interleukin-6 Overproduction Induced by Postprandial Triglyceride-Rich Lipoproteins in THP-1 Macrophages

Oleanolic acid (OA), a triterpene that is highly present in olive leaves, has been proposed as a component of functional foods for the prevention of metabolic syndrome, due to its anti-inflammatory activity. We analyzed the effects of OA on inflammatory parameters and signaling proteins in LPS-stimulated THP-1 macrophages. Thus, THP-1 macrophages were incubated with LPS for 48 h after pretreatment with OA at different concentrations. Pretreatment with OA was significantly effective in attenuating IL-6 and TNF-α overproduction induced by LPS in macrophages, and also improved the levels of AMPK-α. We also evaluated the effects of human triglyceride-rich lipoproteins (TRLs) derived from individuals consuming an OA-enriched functional olive oil. For this purpose, TRLs were isolated from healthy adolescents before, 2 and 5 h postprandially after the intake of a meal containing the functional olive oil or common olive oil, and were incubated with THP-1 macrophages. THP-1 macrophages incubated with TRLs isolated at 2 h after the consumption of the OA-enriched olive oil showed significant lower levels of IL-6 compared to the TRLs derived from olive oil. Our results suggest that OA might have potential to be used as a lipid-based formulation in functional olive oils to prevent inflammatory processes underlying metabolic syndrome in adolescents.
Numerical Investigation of a Designed-Inlet Optofluidic Beam Splitter for Split-Angle and Transmission Improvement

The beam splitter is one of the important elements in optical waveguide circuits. To improve the performance of an optofluidic beam splitter, a microchannel including a two-stage main channel with divergent side walls and two pairs of inlet channels is proposed. Besides, the height of the inlets injected with cladding fluid is set to be less than the height of other parts of the microchannel. When we inject calcium chloride solution (cladding fluid) and deionized water (core fluid) into the inlet channels, the gradient refractive index (GRIN) developed in fluids flowing through the microchannel splits the incident light beam into two beams with a larger split angle. Moreover, the designed inlets yield a GRIN distribution which increases the light collected around the middle horizontal line on the objective plane, and so enhances the transmission efficiency of the device. To demonstrate the performance of the proposed beam splitter, we use polydimethylsiloxane to fabricate the microchannel. The results obtained by simulation and experiment are compared to show the effectiveness of the device and the validity of numerical simulation. The influence of the microchannel geometry and the flow rate ratio on the performance of the proposed beam splitter is investigated.
Adherence to a Fish-Rich Dietary Pattern Is Associated with Chronic Hepatitis C Patients Showing Low Viral Load: Implications for Nutritional Management

Hepatitis C virus (HCV) infection is influenced by genetic (e.g., APOE polymorphisms) and environmental factors between the virus and the host. HCV modulates the host’s lipid metabolism but dietary components influence lipids and in vitro HCV RNA replication. Few data exist on the role of dietary features or patterns (DPs) in HCV infection. Herein, we aimed to evaluate the nutritional profiles of chronic HCV (CHC) and spontaneous clearance (SC) Mexican patients in the context of APOE alleles and their correlation with HCV-related variables. The fibrosis-related APOE ε3 allele prevailed in CHC and SC patients, who had four DPs (“meat and soft drinks”, DP1; “processed animal and fried foods”, DP2; “Mexican-healthy”, DP3; and “fish-rich”, DP4). In CHC subjects, polyunsaturated fatty acid intake (PUFA ≥ 4.9%) was negatively associated, and fiber intake (≥21.5 g/day) was positively associated with a high viral load (p < 0.036). High adherence to fish-rich DP4 was associated with a higher frequency of CHC individuals consuming PUFA ≥ 4.9% (p = 0.004) and low viral load (p = 0.036), but a lower frequency of CHC individuals consuming fiber ≥21.5 g/day (p = 0.038). In SC and CHC individuals, modifying unhealthy DPs and targeting HCV-interacting nutrients, respectively, could be part of a nutritional management strategy to prevent further liver damage.
Carbon Sequestration to Avoid Soil Degradation: A Review on the Role of Conservation Tillage

Human efforts to produce more food for increasing populations leave marks on the environment. The use of conventional agricultural practices, including intensive tillage based on the removal of crop residue, has magnified soil erosion and soil degradation. In recent years, the progressive increase in the concentration of greenhouse gases (GHGs) has created global interest in identifying different sustainable strategies in order to reduce their concentration in the atmosphere. Carbon stored in soil is 2–4 times higher than that stored in the atmosphere and four times more when compared to carbon stored in the vegetation. The process of carbon sequestration (CS) involves transferring CO2 from the atmosphere into the soil or storage of other forms of carbon to either defer or mitigate global warming and avoid dangerous climate change. The present review discusses the potential of soils in sequestering carbon and mitigating the accelerated greenhouse effects by adopting different agricultural management practices. A significant amount of soil organic carbon (SOC) could be sequestered by conversion of conventional tillage to conservation tillage. The most important aspect of conservation agriculture is thought to improve plant growth and soil health without damaging the environment. In the processes of climate change mitigation and adaptation, zero tillage has been found to be the most eco-friendly method among different tillage techniques. No-till practice is considered to enable sustainable cropping intensification to meet future agricultural demands. Although no-tillage suggests merely the absence of tillage, in reality, several components need to be applied to a conservation agriculture system to guarantee higher or equal yields and better environmental performance than conventional tillage systems.
Mechanism of Spontaneous Surface Modifications on Polycrystalline Cu Due to Electric Fields

We present a credible mechanism of spontaneous field emitter formation in high electric field applications, such as Compact Linear Collider in CERN (The European Organization for Nuclear Research). Discovery of such phenomena opens new pathway to tame the highly destructive and performance limiting vacuum breakdown phenomena. Vacuum breakdowns in particle accelerators and other devices operating at high electric fields is a common problem in the operation of these devices. It has been proposed that the onset of vacuum breakdowns is associated with appearance of surface protrusions while the device is in operation under high electric field. Moreover, the breakdown tolerance of an electrode material was correlated with the type of lattice structure of the material. Although biased diffusion under field has been shown to cause growth of significantly field-enhancing tips starting from initial nm-size protrusions, the mechanisms and the dynamics of the growth of the latter have not been studied yet. In the current paper we conduct molecular dynamics simulations of nanocrystalline copper surfaces and show the possibility of protrusion growth under the stress exerted on the surface by an applied electrostatic field. We show the importance of grain boundaries on the protrusion formation and establish a linear relationship between the necessary electrostatic stress for protrusion formation and the temperature of the system. Finally, we show that the time for protrusion formation decreases with the applied electrostatic stress, we give the Arrhenius extrapolation to the case of lower fields, and we present a general discussion of the protrusion formation mechanisms in the case of polycrystalline copper surfaces.
Enhancing Antibodies’ Binding Capacity through Oriented Functionalization of Plasmonic Surfaces

Protein A has long been used in different research fields due to its ability to specifically recognize immunoglobulins (Ig). The protein derived from Staphylococcus aureus binds Ig through the Fc region of the antibody, showing its strongest binding in immunoglobulin G (IgG), making it the most used protein in its purification and detection. The research presented here integrates, for the first time, protein A to a silicon surface patterned with gold nanoparticles for the oriented binding of IgG. The signal detection is conveyed through a metal enhanced fluorescence (MEF) system. Orienting immunoglobulins allows the exposition of the fragment antigen-binding (Fab) region for the binding to its antigen, substantially increasing the binding capacity per antibody immobilized. Antibodies orientation is of crucial importance in many diagnostics devices, particularly when either component is in limited quantities.
Nose to Brain Delivery of Phenytoin Sodium Loaded Nano Lipid Carriers: Formulation, Drug Release, Permeation and In Vivo Pharmacokinetic Studies

An acute epileptic seizure is a seizure emergency fatal condition that requires immediate medical attention. IV phenytoin sodium remains the second line therapeutic agent for the immediate treatment of status epilepticus. Phenytoin sodium formulated as nanolipid carriers (NLCs) seems to be promising as an intranasal delivery system for controlling acute seizures. Three different nanosized phenytoin sodium loaded NLCs (<50 nm, 50–100 nm and >100 nm) were prepared by melt emulsification and was further characterised. In vitro drug release studies showed immediate drug release from phenytoin sodium loaded NLCs of <50 nm size, which is highly essential for acute seizure control. The ex vivo permeation study indicated greater permeation from <50 nm sized NLC through the olfactory epithelium compared to thecontrol drug solution. Invivo pharmacokinetic studies revealed higher drug concentration in CSF/brain within 5 min upon intranasal administration of <50 nm sized phenytoin sodium NLCs than the control drug solution and marketed IV phenytoin sodium, indicating direct and rapid nose to brain drug transport through the olfactory epithelium. The study has shown that formulation strategies can enhance olfactory uptake, and phenytoin sodium NLCs of desired particle sizes (<50 nm) offer promising potential for nose to brain direct delivery of phenytoin sodium in treating acute epileptic seizures.
Investigation of Mechanical and Microstructural Properties of Welded Specimens of AA6061-T6 Alloy with Friction Stir Welding and Parallel-Friction Stir Welding Methods

The present study investigates the effect of two parameters of process type and tool offset on tensile, microhardness, and microstructure properties of AA6061-T6 aluminum alloy joints. Three methods of Friction Stir Welding (FSW), Advancing Parallel-Friction Stir Welding (AP-FSW), and Retreating Parallel-Friction Stir Welding (RP-FSW) were used. In addition, four modes of 0.5, 1, 1.5, and 2 mm of tool offset were used in two welding passes in AP-FSW and RP-FSW processes. Based on the results, it was found that the mechanical properties of welded specimens with AP-FSW and RP-FSW techniques experience significant increments compared to FSW specimens. The best mechanical and microstructural properties were observed in the samples welded by RP-FSW, AP-FSW, and FSW methods, respectively. Welded specimens with the RP-FSW technique had better mechanical properties than other specimens due to the concentration of material flow in the weld nugget and proper microstructure refinement. In both AP-FSW and RP-FSW processes, by increasing the tool offset to 1.5 mm, joint efficiency increased significantly. The highest weld strength was found for welded specimens by RP-FSW and AP-FSW processes with a 1.5 mm tool offset. The peak sample of the RP-FSW process (1.5 mm offset) had the closest mechanical properties to the base metal, in which the Yield Stress (YS), ultimate tensile strength (UTS), and elongation percentage (E%) were 76.4%, 86.5%, and 70% of base metal, respectively. In the welding area, RP-FSW specimens had smaller average grain size and higher hardness values than AP-FSW specimens.
Green Fabrication of Zinc Oxide Nanoparticles Using Phlomis Leaf Extract: Characterization and In Vitro Evaluation of Cytotoxicity and Antibacterial Properties

Green nanoparticle synthesis is an environmentally friendly approach that uses natural solvents. It is preferred over chemical and physical techniques due to the time and energy savings. This study aimed to synthesize zinc oxide nanoparticles (ZnO NPs) through a green method that used Phlomis leaf extract as an effective reducing agent. The synthesis and characterization of ZnO NPs were confirmed by UV-Vis spectrophotometry, Fourier Transform Infrared Spectroscopy (FTIR), X-ray Diffraction (XRD), Dynamic light scattering (DLS), Zeta potential, and Field Emission Scanning Electron Microscope (FESEM) techniques. In vitro cytotoxicity was determined in L929 normal fibroblast cells using MTT assay. The antibacterial activity of ZnO nanoparticles was investigated using a disk-diffusion method against S. aureus and E. coli, as well as minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) content concentrations. XRD results confirmed the nanoparticles’ crystalline structure. Nanoparticle sizes were found to be around 79 nm by FESEM, whereas the hydrodynamic radius of nanoparticles was estimated to be around 165 ± 3 nm by DLS. FTIR spectra revealed the formation of ZnO bonding and surfactant molecule adsorption on the surface of ZnO NPs. It is interesting to observe that aqueous extracts of Phlomis leave plant are efficient reducing agents for green synthesis of ZnO NPs in vitro, with no cytotoxic effect on L929 normal cells and a significant impact on the bacteria tested.