Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantum Interference Between Decay Channels of a Three-Level Atom Placed Between Two Parallel Plates

We investigate the generation of quantum interference induced by spontaneous emission from two transitions of a V-type three-level atom embedded between two parallel plates (one or both the plates have infinite permeability, i.e. μ→∞). The result shows that, due to the anisotropy of vacuum, quantum interference still exists although the two dipole matrix elements of the atom are orthogonal to each other. When the atom is located very close to one of the plates, the quantum interference effect is particularly prominent. The strength of quantum interference displays oscillating behaviour with the position of the atom. With the increase of the distance between the plates, the oscillation becomes dense.
Optimization of silver-dielectric-silver nanoshell for sensing applications

In this paper, resonance light scattering (RLS) properties of a silver-dielectric-silver nanoshell, based on quasi-static approach and plasmon hybridization theory, are investigated. Scattering spectrum of silver-dielectric-silver nanoshell has two intense and clearly separated RLS peaks and provides a potential for biosensing based on surface plasmon resonance and surface-enhanced Raman scattering. The two RLS peaks in silver-dielectric-silver nanoshell are optimized by tuning the geometrical dimensions. In addition, the optimal geometry is discussed to obtain the high sensitivity of silver-dielectric-silver nanoshell. As the silver core radius increases, the sensitivity of silver-dielectric-silver nanoshell decreases whereas increasing the middle dielectric thickness increases the sensitivity of silver-dielectric-silver nanoshell.
Kinetic theory study of steady condensation of a polyatomic gas

The steady one-dimensional flow of a monatomic vapor condensing onto a planar surface kept at constant and uniform temperature has been the subject of a number of investigations based on the kinetic theory of gases. It has been shown that, depending on the upstream value of the Mach number normal to the surface, a steady solution exists only when the problem parameters lie on a surface in the parameters spaces (upstream subsonic flow), or when the problem parameters lie in a proper subregion of the whole parameters space (upstream supersonic flow). Similar detailed studies do not exist for a polyatomic vapor, in spite of their potential relevance for many applications. The present paper aims at describing the effects of internal degrees of freedom on the relationships which determine the existence of steady one-dimensional condensation flows. The study is based on the numerical solution of the Boltzmann equation for a gas with rotational degrees of freedom. Inelastic collision are described by the Borgnak.
A ROSAT PSPC observation of Abell 478: the distribution of X-ray absorbing matter in a massive cooling flow

We present the analysis of an observation of the X-ray luminous cluster of galaxies Abell 478 made with the Position Sensitive Proportional Counter (PSPC) on ROSAT. The X-ray emission from the central regions of the cluster is shown to be absorbed by a column density in excess of the Galactic value obtained from 21-cm H I observations, confirming the results of previous observations with the Solid State Spectrometer on the Einstein Observatory. We have measured the radial variation of column density and temperature within the cluster, in annuli concentric with the peak of the X-ray emission. The PSPC spectra show that the excess absorption is concentrated within the inner ∼300 kpc, and so must be intrinsic to the cluster
Therapeutic collaboration in a comfort zone: a non-improved borderline patient psychotherapy case study (Colaboración terapéutica en una zona de confort: estudio de un caso de psicoterapia de un paciente borderline que no experimentó mejoría)

ABSTRACT The quality of dyad interaction seems crucial to the client’s decision to drop out of psychotherapy. To characterize the client’s lack of change and the patterns of therapeutic collaboration in a dropout of psychodynamic therapy for Borderline Personality Disorder (BPD), we used the Therapeutic Collaboration Coding System (TCCS) to assess collaborative work and the Assimilation of Problematic Experiences Scale (APES) to rate client change. The software GridWare was used to characterize patterns of therapeutic collaboration and the R software to describe the client’s change. The dyad worked in a comfort zone for the client, with the therapist supporting the client’s problematic perspective and the client responding with Safety. The APES results showed that the client did not change, remaining in control through avoidance of thinking and discussing his problematic experience. Our results challenge the potential impact of therapists’ interventions on BPD clients’ comfort zones, suggesting that too much focus on their Therapeutic Zone of Proximal Development’s actual level might not be productive.
Understanding the role of men in women's use of the vaginal ring and oral PrEP during pregnancy and breastfeeding: multi-stakeholder perspectives

We examined men’s influence on women’s interest in biomedical HIV prevention during pregnancy and breastfeeding through structured questionnaires and focus group discussions with currently or recently pregnant and breastfeeding (P/BF) women (n = 65), men with P/BF partners (n = 63) and mothers/mothers-in-law of P/BF women (n = 68) in eastern and southern Africa. Data were transcribed, coded and summarised into analytical memos. Men were depicted by most participants as joint decision-makers and influencers of women’s use of HIV prevention. Cultural and religious norms depicting men as heads, breadwinners and protectors of the family were cited to legitimise their involvement in decision-making. Male partner education and engagement were recommended to garner their support in women’s HIV prevention. This study elucidates how P/BF women’s ability to prevent HIV is shaped by traditional and contemporary gender norms in social settings and locations where the study was conducted. Findings may aid intervention design to engage men for P/BF women’s effective use of microbicide and oral PrEP.
Health impact assessment of volatile organic compounds (VOCs) emission from the combustion of agricultural wastes

Abstract Emissions of components of VOCs from combustion of agro-waste materials were quantified. Agro-waste materials comprising corn cobs, corn husks, bean chaff and rice husks were burnt at a temperature of 400°C in a muffle furnace, and the emissions were quantified according to standard procedures. Health risk associated with exposure to the emissions, based on carcinogenicity and non-carcinogenicity, was evaluated using excess lifetime carcinogenic risk (ECLR) and hazard quotient (HQ), respectively. The results showed identification of 11 compounds comprising undecane, benzene, bromoform, ethylbenzene, styrene, toluene, p-xylene, 1,3-dimethylbenzene, o-xylene and phenol. The concentrations of the identified compounds ranged from 0.01 to 7.35 µg/m3, with chlorobenzene (emission from corn cobs) having the highest concentration and 1,3-dimethylbenzene having the lowest concentration (across all samples). The results also showed that ELCR and HQ values were below the recommended levels. The result concluded that although short-term exposures to the emission from combustion are not likely to cause health issues, prolonged exposure should be avoided as this could complicate issues for individuals with existing health challenges.
Effect of social skills training on interpersonal interactions of children with autism: an interventional research

Autism is a neuro-developmental disorder typically appears prior to the age of three years, and seriously limits the normal development of children. However, there is a wide variety of effective intervention programs and strategies designed to help children with autism. Hence, this research aimed to see the effect of social skills training on interpersonal interaction of children with autism. Using pre-post equivalent experimental and control group design, data were collected from a sample of eight children using Autism Social Skills Profile Rating Scale before and after the implementation of social skills training. Data were analyzed through frequency, percentage, mean, standard deviation, and independent samples t-test. The pre-intervention assessment revealed that participants of the experimental and the control groups did not significantly differ but both groups scored below half on the total scale point and almost one-third of the maximum score on social reciprocity and social participation sub-scales. The result of the intervention also indicated that children in both groups demonstrated positive changes in their overall social skills including the sub-scales. However, it was found out that the experimental group has greater mean scores as compared to the control group on total scale, social participation and social reciprocity subscales. But the increment on detrimental social behaviors subscale in the experimental group was with a decreasing rate. Based on this finding, it can be concluded that social skills training intervention improves social skills of children with autism. Therefore, it is recommended that further intensive and comprehensive intervention is very critical to more improve the social skills of children with autism.
Biochemical activity is the default DNA state in eukaryotes

Genomes encode for genes and the regulatory signals that enable those genes to be transcribed, and are continually shaped by evolution. Genomes, including those of human and yeast, encode for numerous regulatory elements and transcripts that have limited evidence of conservation or function. Here, we sought to create a genomic null hypothesis by quantifying the gene regulatory activity of evolutionarily naïve DNA, using RNA-seq of evolutionarily distant DNA expressed in yeast and computational predictions of random DNA activity in human cells and tissues. In yeast, we found that >99% of bases in naïve DNA expressed as part of one or more transcripts. Naïve transcripts are sometimes spliced, and are similar to evolved transcripts in length and expression distribution, indicating that stable expression and/or splicing are insufficient to indicate adaptation. However, naïve transcripts do not achieve the extreme high expression levels as achieved by evolved genes, and frequently overlap with antisense transcription, suggesting that selection has shaped the yeast transcriptome to achieve high expression and coherent gene structures. In humans, we found that, while random DNA is predicted to have minimal activity, dinucleotide content-matched randomized DNA is predicted to have much of the regulatory activity of evolved sequences, including active chromatin marks at between half (DNase I and H3K4me3) and 1/16th (H3K27ac and H3K4me1) the rate of evolved DNA, and the repression-associated H3K27me3 at about twice the rate of evolved DNA. Naïve human DNA is predicted to be more cell type-specific than evolved DNA and is predicted to generate co-occurring chromatin marks, indicating that these are not reliable indicators of selection. However, extreme high activity is rarely achieved by naïve DNA, consistent with these arising via selection. Our results indicate that evolving regulatory activity from naïve DNA is comparatively easy in both yeast and humans, and we expect to see many biochemically active and cell type-specific DNA sequences in the absence of selection. Such naïve biochemically active sequences have the potential to evolve a function or, if sufficiently detrimental, selection may act to repress them.
Derivation of Steady-State First-order Rate Constant Equations for Enzyme-Substrate Complex Dissociation, as well as Zero-order Rate Constant Equations in Relation to Background Assumptions

The maximum velocity (Vmax) of catalysis and the substrate concentration ([ST]) at half the Vmax, the KM, are regarded as steady-state (SS) parameters even though they are the outcomes of zero-order kinetics (ZOK). The research was aimed at disputing such a claim with the following objectives: To: 1) carry out an overview of issues pertaining to the validity of assumptions; 2) derive the needed steady-state (SS) equations distinct from Michaelian equations that can be fitted to both experimental variables and kinetic parameters; 3) calculate the SS first-order rate constant for the dissociation of enzyme-substrate complex (ES) to free substrate, S and enzyme, E; 4) derive the equation of rate constant as a function of the reciprocal of the duration of each catalytic event in the reaction pathway. The experimental values of the data were generated by Bernfeld and Lineweaver-Burk methods. The calculated SS 1st order-order rate constant was « the zero-order Michaelian value, and the difference is ≈ 97.59 % of the zero-order value; the SS catalytic rate differed from the zero-order catalytic rate by ≈ 76.41 % of the latter value; and it was ≈ 93.87 % with respect to the 2nd order rate constant for the formation of enzyme-substrate complex. The equations of time-dependent rate constants, KM, and dissociation constants were derived. The concentration [ST] of the S must be > the concentration ([E0]) of the E for the quasi-steady-state assumption (or approximation) to hold. The SS kinetic parameters are not equivalent to zero-order parameters.
Census of exposed aggregation-prone regions in proteomes

Loss of solubility usually leads to the detrimental elimination of protein function. In some cases, the protein aggregation is also required for beneficial functions. Given the duality of this phenomenon, it remains a fundamental question how natural selection controls the aggregation. The exponential growth of genomic sequence data and recent progress with in silico predictors of the aggregation allows approaching this problem by a large-scale bioinformatics analysis. Most of the aggregation-prone regions are hidden within the 3D structures and, therefore, they cannot realize their potential to aggregate. Thus, the most realistic census of the aggregation prone regions requires crossing aggregation prediction with information about the location of the natively unfolded regions. This allows us to detect so-called “Exposed Aggregation-prone Regions” (EARs). Here, we analyzed the occurrence and distribution of the EARs in 76 full reference proteomes from the three kingdoms of life. For this purpose, we used a bioinformatics pipeline, which provides a consensual result based on several predictors of aggregation. Our analysis revealed a number of new statistically significant correlations about the presence of EARs in different organisms, their dependence on protein length, cellular localizations, co-occurrence with short linear motifs, and the level of protein expression. We also obtained a list of proteins with the conserved aggregation-prone sequences for further experimental tests. Insights gained from this work led to a deeper understanding of the functional and evolutionary relations of the protein aggregation.
Fatecode: Cell fate regulator prediction using classification autoencoder perturbation

Cell reprogramming, which guides the conversion between cell states, is a promising technology for tissue repair and regeneration. Typically, a group of key genes, or master regulators, are manipulated to control cell fate, with the ultimate goal of accelerating recovery from diseases or injuries. Of importance is the ability to correctly identify the master regulators from single-cell transcriptomics datasets. To accomplish that goal, we propose Fatecode, a computational method that combines in silico perturbation experiments with cell trajectory modeling using deep learning to predict master regulators and key pathways controlling cell fate. Fatecode uses only scRNA-seq data from wild-type samples to learn and predict how cell type distribution changes following a perturbation. We assessed Fatecode’s performance using simulations from a mechanistic gene regulatory network model and diverse gene expression profiles covering blood and brain development. Our results suggest that Fatecode can detect known master regulators of cell fate from single-cell transcriptomics datasets. That capability points to Fatecode’s potential in accelerating the discovery of cell fate regulators that can be used to engineer and grow cells for therapeutic use in regenerative medicine applications.
Rewarding Capacity of Optogenetically Activating a Giant GABAergic Central-Brain Interneuron in Larval Drosophila

Larvae of the fruit fly Drosophila melanogaster are a powerful study case for understanding the neural circuits underlying behavior. Indeed, the numerical simplicity of the larval brain has permitted the reconstruction of its synaptic connectome, and genetic tools for manipulating single, identified neurons allow neural circuit function to be investigated with relative ease and precision. We focus on one of the most complex neurons in the brain of the larva (of either sex), the GABAergic anterior paired lateral neuron (APL). Using behavioral and connectomic analyses, optogenetics, Ca2+ imaging, and pharmacology, we study how APL affects associative olfactory memory. We first provide a detailed account of the structure, regional polarity, connectivity, and metamorphic development of APL, and further confirm that optogenetic activation of APL has an inhibiting effect on its main targets, the mushroom body Kenyon cells. All these findings are consistent with the previously identified function of APL in the sparsening of sensory representations. To our surprise, however, we found that optogenetically activating APL can also have a strong rewarding effect. Specifically, APL activation together with odor presentation establishes an odor-specific, appetitive, associative short-term memory, whereas naive olfactory behavior remains unaffected. An acute, systemic inhibition of dopamine synthesis as well as an ablation of the dopaminergic pPAM neurons impair reward learning through APL activation. Our findings provide a study case of complex circuit function in a numerically simple brain, and suggest a previously unrecognized capacity of central-brain GABAergic neurons to engage in dopaminergic reinforcement. SIGNIFICANCE STATEMENT The single, identified giant anterior paired lateral (APL) neuron is one of the most complex neurons in the insect brain. It is GABAergic and contributes to the sparsening of neuronal activity in the mushroom body, the memory center of insects. We provide the most detailed account yet of the structure of APL in larval Drosophila as a neurogenetically accessible study case. We further reveal that, contrary to expectations, the experimental activation of APL can exert a rewarding effect, likely via dopaminergic reward pathways. The present study both provides an example of unexpected circuit complexity in a numerically simple brain, and reports an unexpected effect of activity in central-brain GABAergic circuits.
Unraveling MLL1-fusion Leukemia: Epigenetic Revelations from an iPS Cell Point Mutation

Our understanding of acute leukemia pathology is heavily dependent on 11q23 chromosomal translocations involving the mixed lineage leukemia-1 (MLL1) gene, a key player in histone H3 lysine 4 (H3K4) methylation. These translocations result in distinct MLL1-fusion (MLL1F) proteins that are thought to drive leukemogenesis. However, the mechanism behind increased H3K4 trimethylation in MLL1F-leukemic stem cells (MLL1F-LSCs), following loss of catalytic SET domain of MLL1 (known for H3K4 mono- and dimethylation), remains unclear. In our investigation, we introduced a homozygous loss-of-function point mutation in MLL1 within human induced pluripotent stem cells. Remarkably, this mutation mimics the histone methylation, gene expression, and EMT phenotypes of MLL1F-LSCs- without the need for a translocation or functional wild-type MLL1. This observation underscores the essential role of MLL1’s enzymatic activity in restraining the cascade of epigenetic changes associated with the gene activating H3K4 trimethylation mark, which we show is catalyzed by mislocalized SETd1a H3K4 trimethyltransferase in the absence of MLL1’s enzymatic activity. Challenging existing models, our findings imply that MLL1F-induced leukemias arise from a dominant-negative impact on MLL1’s histone methyltransferase activity. We advocate for a therapeutic paradigm shift, targeting SETd1a for precision medicine. This work opens new avenues for addressing the complexities of MLL1-associated leukemias and improving targeted therapies. Summary Epigenomic and gene expression changes in iPS cells with a mutated MLL1 histone methyltransferase suggest an oncogenic mechanism for MLL1-fusion leukemias.
How sexual dimorphism in phenotypic plasticity may evolve

Phenotypes are partly shaped by the environment, which can impact both short-term adaptation and long-term evolution. In dioecious species, the two sexes may exhibit diﬀerent degrees of phenotypic plasticity and theoretical models indicate that such diﬀerences may confer an adaptive advantage when the population is subject to directional selection, either because of a systematically varying environment or of a load of deleterious mutations. The eﬀect stems from the fundamental asymmetry between the two sexes: female fertility is more limited than male fertility. Whether this asymmetry is suﬃcient for sexual dimorphism in phenotypic plasticity to evolve is, however, not obvious. Here, we show that even in conditions where it provides an adaptive advantage, dimorphic phenotypic plasticity may be evolutionarily unstable due to sexual selection. This is the case, in particular, for panmictic populations where mating partners are formed at random. However, we show that the eﬀects of sexual selection can be counteracted when mating occurs within groups of related individuals. Under this condition, sexual dimorphism in phenotypic plasticity can not only evolve but oﬀset the twofold cost of males. We demonstrate these points with a simple mathematical model through a combination of analytical and numerical results.
Genomic description of critical upstream cannabinoid biosynthesis genes

Cannabinoid production is one of the key attributes of the plant Cannabis sativa and the characterization of the genes involved is an essential first step to develop tools for their optimization. We used bioinformatic approaches to annotate and explore variation in the coding genes for critical enzymes comprising the cannabinoid pathway: Olivetol Synthase (OLS), Olivetolic Acid Cyclase (OAC), and Cannabigerolic Acid Synthase (CBGAS), in multiple C. sativa genomes. These upstream genes of the Cannabinoid Oxidocyclase Genes THCAS, CBDAS, and CBCAS generate the necessary precursor molecules to produce the cannabinoids THC and CBD. We found that these genes vary in copy number and confirm that OLS, OAC, CBGAS, and the Cannabinoid Oxidocyclases are on separate chromosomes, while homologs are found in proximity. CBGAS, located on Chromosome X, suggests potential dosage effects in female plants. Except for the Cannabinoid Oxidocyclase genes, the other genes have multiple exons, up to 10 in CBGAS. Through differential exon usage explorations in CBGAS we found evidence for potential regulatory differences. This study provides valuable insight on the genomic identity and variation of cannabinoid biosynthesis genes that will benefit future research on the origin and evolution of this pathway, driver of economic, social, and medicinal value.