Miracle-dz/UniFAR-FTUs huggingface dataset:
Timing of Chromosome DNA Integration throughout the Yeast Cell Cycle

The dynamic mechanism of cell uptake and genomic integration of exogenous linear DNA still has to be completely clarified, especially within each phase of the cell cycle. We present a study of integration events of double-stranded linear DNA molecules harboring at their ends sequence homologies to the host’s genome, all throughout the cell cycle of the model organism Saccharomyces cerevisiae, comparing the efficiency of chromosomal integration of two types of DNA cassettes tailored for site-specific integration and bridge-induced translocation. Transformability increases in S phase regardless of the sequence homologies, while the efficiency of chromosomal integration during a specific cycle phase depends upon the genomic targets. Moreover, the frequency of a specific translocation between chromosomes XV and VIII strongly increased during DNA synthesis under the control of Pol32 polymerase. Finally, in the null POL32 double mutant, different pathways drove the integration in the various phases of the cell cycle and bridge-induced translocation was possible outside the S phase even without Pol32. The discovery of this cell-cycle dependent regulation of specific pathways of DNA integration, associated with an increase of ROS levels following translocation events, is a further demonstration of a sensing ability of the yeast cell in determining a cell-cycle-related choice of DNA repair pathways under stress.
Inferring Gene Regulatory Networks from RNA-seq Data Using Kernel Classification

Simple Summary Understanding the relationships between genes is crucial to identify the genetic program of organisms. This research could potentially have implications for this understanding. This study aims to build a genetic network for the yeast genome by recognizing interacting genes. This is performed by incorporating different mathematical methodologies and classification techniques to predict relations between two genes. High accuracy is achieved across several tests to identify network interactions. Our findings provide new insights and potential interactions between genes in the yeast genome network. Our results are highly relevant to the field, as they emphasize the power of classification and its role in improving the current understanding of the yeast genome network. Abstract Gene expression profiling is one of the most recognized techniques for inferring gene regulators and their potential targets in gene regulatory networks (GRN). The purpose of this study is to build a regulatory network for the budding yeast Saccharomyces cerevisiae genome by incorporating the use of RNA-seq and microarray data represented by a wide range of experimental conditions. We introduce a pipeline for data analysis, data preparation, and training models. Several kernel classification models; including one-class, two-class, and rare event classification methods, are used to categorize genes. We test the impact of the normalization techniques on the overall performance of RNA-seq. Our findings provide new insights into the interactions between genes in the yeast regulatory network. The conclusions of our study have significant importance since they highlight the effectiveness of classification and its contribution towards enhancing the present comprehension of the yeast regulatory network. When assessed, our pipeline demonstrates strong performance across different statistical metrics, such as a 99% recall rate and a 98% AUC score.
Thrombophilia and Immune-Related Genetic Markers in Long COVID

Aiming to evaluate the role of ten functional polymorphisms in long COVID, involved in major inflammatory, immune response and thrombophilia pathways, a cross-sectional sample composed of 199 long COVID (LC) patients and a cohort composed of 79 COVID-19 patients whose follow-up by over six months did not reveal any evidence of long COVID (NLC) were investigated to detect genetic susceptibility to long COVID. Ten functional polymorphisms located in thrombophilia-related and immune response genes were genotyped by real time PCR. In terms of clinical outcomes, LC patients presented higher prevalence of heart disease as preexistent comorbidity. In general, the proportions of symptoms in acute phase of the disease were higher among LC patients. The genotype AA of the interferon gamma (IFNG) gene was observed in higher frequency among LC patients (60%; p = 0.033). Moreover, the genotype CC of the methylenetetrahydrofolate reductase (MTHFR) gene was also more frequent among LC patients (49%; p = 0.045). Additionally, the frequencies of LC symptoms were higher among carriers of IFNG genotypes AA than among non-AA genotypes (Z = 5.08; p < 0.0001). Two polymorphisms were associated with LC in both inflammatory and thrombophilia pathways, thus reinforcing their role in LC. The higher frequencies of acute phase symptoms among LC and higher frequency of underlying comorbidities might suggest that acute disease severity and the triggering of preexisting condition may play a role in LC development.
Meta-Analysis of the Effect of Nitric Oxide Application on Heavy Metal Stress Tolerance in Plants

Substantial single-species studies have reported the facility of nitric oxide (NO) in alleviating heavy metal-induced stress in plants. Understanding the mechanisms of NO-involved stress alleviation is progressing; however, a quantitative description of the alleviative capacity of NO against heavy metal stress is still lacking. We combined the results of 86 studies using meta-analysis to statistically assess the responses of heavy metal-stressed plants to NO supply across several metal stresses and plant families. The results showed that plant biomass was consistently improved following NO supply to metal-stressed plants. NO played an important role in mitigating oxidative damage caused by heavy metal stress by significantly stimulating the activities of antioxidant enzymes. Moreover, NO supply consistently increased the Ca, Fe, and Mg contents in both leaves and roots. Plant tissues accumulated less heavy metals when exposed to heavy metal stress after NO addition. Additionally, the best concentration of SNP (an NO donor) for hydroponic culture is in the range of 75–150 μM. We further confirmed that NO application can generally alleviate plant heavy metal stress and its action pathway. The results presented here can help guide future applications of NO as a plant growth regulator in agriculture and breeding plants for heavy metal stress tolerance.
Economic and financial education for investment and financing decision-making in a graduate degree: Experimental evaluation of the effectiveness of two delivery methods

Abstract The author of this study offers new evidence on the effectiveness of chatbots as an instructional mode via a randomized controlled experiment in which college seniors were given online training on the convenience of pursuing a master’s degree and the suitability of taking out a graduate student loan. Two educational formats, a YouTube video and a Facebook chatbot, were used for delivering that training to the experimental subjects. Economic education improved the economic knowledge needed to calculate a master’s degree’s viability. The effectiveness of financial education in improving student loan debt literacy was also verified. The effectiveness of the chatbot-based learning was greater than that of the video format for providing economic education. Only the chatbot delivery method was effective in providing financial education.
Public key suppression and recovery using a PANDA ring resonator for high security communication

An interesting security technique that uses the dark-bright soliton conversion control within the microring resonator is proposed. The obtained outputs for a dark-bright soliton dynamic state can be controlled and used to form the public key suppression for communication security application. However, a good design should be possible to be fabricated; therefore, by using the parameters based on the practical device parameters, the simulation results obtained have shown that the proposed system can indeed be achieved. The public key suppression and public key recovery can be used in a highly secure communication system and has potential applications in optical cryptography.
The validity of the extended energy principle

A recent analysis of plasma stability based on modifications of the extended energy principle for magnetohydrodynamic stability led to conclusions that are too optimistic. The original interpretation of this principle is indeed applicable. The present analysis demonstrates explicitly the fallacy of using the wrong functional for {delta}W in the extended energy principle. It then shows that the original energy principle functional {delta}W{sub B} is also obtained for a model in which a surface mass is incorporated to provide pressure balance. This work therefore indicates, but does not prove, that the eigenfunctions that are obtained from a minimization of the extended energy principle with the proper kinetic energy norm provide a good representation of what would be achieved with an exact treatment.
A latent-observed dissimilarity measure

Quantitatively assessing relationships between latent variables and observed variables is important for understanding and developing generative models and representation learning. In this paper, we propose latent-observed dissimilarity (LOD) to evaluate the dissimilarity between the probabilistic characteristics of latent and observed variables. We also define four essential types of generative models with different independence/conditional independence configurations. Experiments using tractable real-world data show that LOD can effectively capture the differences between models and reflect the capability for higher layer learning. They also show that the conditional independence of latent variables given observed variables contributes to improving the transmission of information and characteristics from lower layers to higher layers.
Subspace iteration search method for generalized eigenvalue problems with sparse complex unsymmetric matrices in finite-element analysis of waveguides

In this paper, a numerical method for the robust computation of the number of eigenvalues within a closed contour of a generalized complex eigenvalue problem is presented. As a result of this computation, it is possible to perform a systematic search for the eigenvalues, ensuring that no eigenvalues are forgotten, and to optimize their calculation. Application is made to the finite-element modal analysis of inhomogeneous waveguides.
Anti-cancer potentials of aervine validated through in silico molecular docking, dynamics simulations, pharmacokinetic prediction and in vitro assessment of caspase – 3 in SW480 cell line

ABSTRACT Colon cancer is the third most lethal type of cancer in the world. Resistance to chemotherapy remains a serious barrier in the treatment of several forms of cancer, particularly colon cancer. Therefore, it is essential to develop alternative treatment methods. The docking score study of the aervine produced a low dock score for the 2BDF target compared to the 1IKN and 4OAR targets. Comparing the aervine to the reference compounds Capecitabine for 2BDF, Topotecan Hydrochloride for 1IKN and Tamoxifen for 4OAR, the binding affinity of the aervine was found to be higher. Further molecular dynamic simulation results for aervine and reference standard drugs for each cancer types reveals that aervine possess good binding affinity simulation trajectories towards all three cancer targets. The MTT assay revealed that aervine has a highest cytotoxic impact against a colorectal cancer cell line, with an IC50 value of 122.12 ± 1. 26µg/ ml. Aervine produces reactive oxygen species, induces caspase-3 pathway in SW480 cells, and promotes apoptosis. This research shows that aervine can be developed as a new 2BDF target inhibitor against colorectal cancer.
International geomagnetic reference field revision 1987

The International Geomagnetic Reference Field (IGRF) is a series of mathematical models of the main geomagnetic field and its secular variation, the models consisting of sets of spherical harmonic (or Gauss) coefficients. The IGRF has become a widely used means of deriving values of geomagnetic field components in, for example, studies of magnetic anomalies and investigations of charged particle motions in the ionosphere and the magnetosphere.
The generalized linear complementarity problem applied to the complete analysis of resistive piecewise-linear circuits

The link between the linear complementary problem (LCP) and piecewise-linear (PWL) resistive circuits is extended by allowing a generalized form of the LCP. Using this generalized LCP (GLCP) a very broad class of circuits can be described and analyzed. The authors give an algorithm to find all solutions of this GLCP and hence of a PWL circuit. The same technique can be applied to driving-point and transfer characteristics. <<ETX>>
Chemical beam epitaxy of GaN on Si (111) using AlAs buffer layers

The chemical beam epitaxy of GaN on Si (111) using an AlAs buffer layer has been investigated. Transmission electron microscopy of cross-section samples reveals a nanoscale columnar structure consisting of the hexagonal GaN polytype. Selected area diffraction indicates an epitaxial relationship between the GaN and Si substrate which is described by GaN [0001] ∥ Si [111] and GaN (100) ∥ Si (11). Raman spectroscopy of the samples shows that the AlAs longitudinal optical (LO) and transverse optical (TO) modes are observed at 360 and 400 cm-1, respectively, and that the GaN E2 TO and A1 LO modes occur at 562 and 733 cm-1, respectively. Raman peaks between 616 and 673 cm-1 are attributed to an interlayer of AlN formed by the nitridation of the AlAs buffer layer.
Development and Optimization of 3D-Printed Flexible Electronic Coatings: A New Generation of Smart Heating Fabrics for Automobile Applications

Textile-based Joule heaters in combination with multifunctional materials, fabrication tactics, and optimized designs have changed the paradigm of futuristic intelligent clothing systems, particularly in the automobile field. In the design of heating systems integrated into a car seat, conductive coatings via 3D printing are expected to have further benefits over conventional rigid electrical elements such as a tailored shape and increased comfort, feasibility, stretchability, and compactness. In this regard, we report on a novel heating technique for car seat fabrics based on the use of smart conductive coatings. For easier processes and integration, an extrusion 3D printer is employed to achieve multilayered thin films coated on the surface of the fabric substrate. The developed heater device consists of two principal copper electrodes (so-called power buses) and three identical heating resistors made of carbon composites. Connections between the copper power bus and the carbon resistors are made by means of sub-divide the electrodes, which is critical for electrical–thermal coupling. Finite element models (FEM) are developed to predict the heating behavior of the tested substrates under different designs. It is pointed out that the most optimized design solves important drawbacks of the initial design in terms of temperature regularity and overheating. Full characterizations of the electrical and thermal properties, together with morphological analyses via SEM images, are conducted on different coated samples, making it possible to identify the relevant physical parameters of the materials as well as confirm the printing quality. It is discovered through a combination of FEM and experimental evaluations that the printed coating patterns have a crucial impact on the energy conversion and heating performance. Our first prototype, thanks to many design optimizations, entirely meets the specifications required by the automobile industry. Accordingly, multifunctional materials together with printing technology could offer an efficient heating method for the smart textile industry with significantly improved comfort for both the designer and user.
Whole Blood Expression Levels of Long Noncoding RNAs: HOTAIRM1, GAS5, MZF1-AS1, and OIP5-AS1 as Biomarkers in Adolescents with Obesity-Related Asthma

Asthma is a heterogeneous entity encompassing distinct endotypes and varying phenotypes, characterized by common clinical manifestations, such as shortness of breath, wheezing, and variable airflow obstruction. Two major asthma endotypes based on molecular patterns are described: type 2 endotype (allergic-asthma) and T2 low endotype (obesity-related asthma). Long noncoding RNAs (lncRNAs) are transcripts of more than 200 nucleotides in length, currently involved in many diverse biological functions, such as chromatin remodeling, gene transcription, protein transport, and microRNA processing. Despite the efforts to accurately classify and discriminate all the asthma endotypes and phenotypes, if long noncoding RNAs could play a role as biomarkers in allergic asthmatic and adolescent obesity-related asthma, adolescents remain unknown. To compare expression levels of lncRNAs: HOTAIRM1, OIP5-AS1, MZF1-AS1, and GAS5 from whole blood of Healthy Adolescents (HA), Obese adolescents (O), allergic asthmatic adolescents (AA) and Obesity-related asthma adolescents (OA). We measured and compared expression levels from the whole blood of the groups mentioned above through RT-q-PCR. We found differentially expressed levels of these lncRNAs between the groups of interest. In addition, we found a discriminative value of previously mentioned lncRNAs between studied groups. Finally, we generated an interaction network through bioinformatics. Expression levels of OIP5-AS1, MZF1-AS1, HOTAIRM1, and GAS5 in whole blood from the healthy adolescent population, obese adolescents, allergic asthma adolescents, and obesity-related asthma adolescents are differently expressed. Moreover, these lncRNAs could act as molecular biomarkers that help to discriminate between all studied groups, probably through molecular mechanisms with several genes and miRNAs implicated.
New termination for ultrawide-band slot spirals

Slot-spiral antennas utilizing very shallow reflecting cavities have previously been demonstrated by the authors for extremely broadband-conformal applications. We have previously demonstrated the importance of an integrated planar balun and feed for realizing the slot spiral's bandwidth potential. Of equal importance, is the development of a termination that is applicable to the slot radiator. In this paper, we demonstrate a new slot spiral arm termination which, in conjunction with the reflecting cavity and planar infinite balun, allows for very thin yet extremely broadband spirals. The included measurements show that a slot spiral with a diameter of 5.75" and a thickness of merely 0.5" delivers a typical gain of 5 dB/sub ic/ from 750 MHz to 4 GHz with good axial ratio performance. Additional loading (both inductive and dielectric) applied to the same spiral can extend its operational bandwidth down to 200 MHz for the same size aperture.
Effect of the Size and Shape of Dendronized Iron Oxide Nanoparticles Bearing a Targeting Ligand on MRI, Magnetic Hyperthermia, and Photothermia Properties—From Suspension to In Vitro Studies

Functionalized iron oxide nanoparticles (IONPs) are increasingly being designed as a theranostic nanoplatform combining specific targeting, diagnosis by magnetic resonance imaging (MRI), and multimodal therapy by hyperthermia. The effect of the size and the shape of IONPs is of tremendous importance to develop theranostic nanoobjects displaying efficient MRI contrast agents and hyperthermia agent via the combination of magnetic hyperthermia (MH) and/or photothermia (PTT). Another key parameter is that the amount of accumulation of IONPs in cancerous cells is sufficiently high, which often requires the grafting of specific targeting ligands (TLs). Herein, IONPs with nanoplate and nanocube shapes, which are promising to combine magnetic hyperthermia (MH) and photothermia (PTT), were synthesized by the thermal decomposition method and coated with a designed dendron molecule to ensure their biocompatibility and colloidal stability in suspension. Then, the efficiency of these dendronized IONPs as contrast agents (CAs) for MRI and their ability to heat via MH or PTT were investigated. The 22 nm nanospheres and the 19 nm nanocubes presented the most promising theranostic properties (respectively, r2 = 416 s−1·mM−1, SARMH = 580 W·g−1, SARPTT = 800 W·g−1; and r2 = 407 s−1·mM−1, SARMH = 899 W·g−1, SARPTT = 300 W·g−1). MH experiments have proven that the heating power mainly originates from Brownian relaxation and that SAR values can remain high if IONPs are prealigned with a magnet. This raises hope that heating will maintain efficient even in a confined environment, such as in cells or in tumors. Preliminary in vitro MH and PTT experiments have shown the promising effect of the cubic shaped IONPs, even though the experiments should be repeated with an improved set-up. Finally, the grafting of a specific peptide (P22) as a TL for head and neck cancers (HNCs) has shown the positive impact of the TL to enhance IONP accumulation in cells.
An analytical model of rainfall interception by forests

The description of the evaporation of rainfall intercepted by forests in terms of a regression of evaporation loss on incident rainfall is discussed and some of the assumptions implicit in that method are re-examined. The two major factors which control the evaporation of intercepted rainfall are identified. These are: (i) the amount of time that the canopy spends saturated during rainfall and the evaporation rate applicable under these conditions; and (ii) the canopy saturation capacity and the number of times this store is emptied, by drying out after the cessation of rainfall. A model is then constructed which is conceptually similar to the Rutter model, but which replaces that model's numerical approach with an analysis by storm events. The evaporation from a saturated canopy during rainfall is estimated from the Penman-Monteith equation; the evaporation after rain has ceased, the effect of small storms insufficient to saturate the canopy, wetting-up the canopy and evaporation from the trunks are added as separate terms. The model has been tested against data from Thetford Forest in East Anglia, with satisfactory agreement between observation and estimation. It is suggested that the model may be capable of making useful estimates of the evaporation of intercepted rainfall, solely from rainfall measurements.
First Experimental Evidence of Anti-Stokes Laser-Induced Fluorescence Emission in Microdroplets and Microfluidic Systems Driven by Low Thermal Conductivity of Fluorocarbon Carrier Oil

With the advent of many optofluidic and droplet microfluidic applications using laser-induced fluorescence (LIF), the need for a better understanding of the heating effect induced by pump laser excitation sources and good monitoring of temperature inside such confined microsystems started to emerge. We developed a broadband highly sensitive optofluidic detection system, which enabled us to show for the first time that Rhodamine-B dye molecules can exhibit standard photoluminescence as well as blue-shifted photoluminescence. We demonstrate that this phenomenon originates from the interaction between the pump laser beam and dye molecules when surrounded by the low thermal conductive fluorocarbon oil, generally used as a carrier medium in droplet microfluidics. We also show that when the temperature is increased, both Stokes and anti-Stokes fluorescence intensities remain practically constant until a temperature transition is reached, above which the fluorescence intensity starts to decrease linearly with a thermal sensitivity of about −0.4%/°C for Stokes emission or −0.2%/°C for anti-Stokes emission. For an excitation power of 3.5 mW, the temperature transition was found to be about 25 °C, whereas for a smaller excitation power (0.5 mW), the transition temperature was found to be about 36 °C.