Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Information-Theory-Based Genetic Distance That Approximates Phenotypic Differences

Application of genetic distances to measure phenotypic relatedness is a challenging task, reflecting the complex relationship between genotype and phenotype. Accurate assessment of proximity among sequences with different phenotypic traits depends on how strongly the chosen distance is associated with structural and functional properties. In this study, we present a new distance measure Mutual Information and Entropy H (MIH) for categorical data such as nucleotide or amino acid sequences. MIH applies an information matrix (IM), which is calculated from the data and captures heterogeneity of individual positions as measured by Shannon entropy and coordinated substitutions among positions as measured by mutual information. In general, MIH assigns low weights to differences occurring at high entropy positions or at dependent positions. MIH distance was compared with other common distances on two experimental and two simulated data sets. MIH showed the best ability to distinguish cross-immunoreactive sequence pairs from non-cross-immunoreactive pairs of variants of the hepatitis C virus hypervariable region 1 (26,883 pairwise comparisons), and Major Histocompatibility Complex (MHC) binding peptides (n = 181) from non-binding peptides (n = 129). Analysis of 74 simulated RNA secondary structures also showed that the ratio between MIH distance of sequences from the same RNA structure and MIH of sequences from different structures is three orders of magnitude greater than for Hamming distances. These findings indicate that lower MIH between two sequences is associated with greater probability of the sequences to belong to the same phenotype. Examination of rule-based phenotypes generated in silico showed that (1) MIH is strongly associated with phenotypic differences, (2) IM of sequences under selection is very different from IM generated under random scenarios, and (3) IM is robust to sampling. In conclusion, MIH strongly approximates structural/functional distances and should have important applications to a wide range of biological problems, including evolution, artificial selection of biological functions and structures, and measuring phenotypic similarity.
Broad, variable absorption lines in the Seyfert Galaxy NGC 3516 - Probing the structure of the emission-line regions

Nineteen short-wavelength IUE archive images were analyzed in order to probe the structure of the active nucleus in NGC 3516, an SB0 Seyfert I galaxy. The measurements of these features are presented, and the strength, variability, and morphology of the emission and absorption lines and their relation to the continuum are analyzed. It is shown that the absorption must arise within 10 pc of the nonthermal continuum source and that its variability must stem from changes in the velocity space coverage of clouds optically thin to the Lyman continuum. Two possible sites of absorption are discussed: dense clouds in the narrow-line region and optically thin clouds in the broad-line region. A theoretical model that explains the anticorrelation of C IV absorption with continuum flux is described.
Fiber-optic seismic sensor

A vibration sensor is constructed by providing two preferably matched coils of fiber-optic material. When the sensor experiences vibration, a differential pressure is exerted on the two fiber coils. The differential pressure results in a variation in the relative optical path lengths between the two fibers so that light beams transmitted through the two fibers are differently delayed, the phase difference therebetween being a detectable indication of the vibration applied to the sensor.
(Not) far from home: No sex bias in dispersal, but limited genetic patch size, in an endangered species, the Spotted Turtle (Clemmys guttata)

Abstract Sex‐biased dispersal is common in many animals, with male‐biased dispersal often found in studies of mammals and reptiles, including interpretations of spatial genetic structure, ostensibly as a result of male–male competition and a lack of male parental care. Few studies of sex‐biased dispersal have been conducted in turtles, but a handful of studies, in saltwater turtles and in terrestrial turtles, have detected male‐biased dispersal as expected. We tested for sex‐biased dispersal in the endangered freshwater turtle, the spotted turtle (Clemmys guttata) by investigating fine‐scale genetic spatial structure of males and females. We found significant spatial genetic structure in both sexes, but the patterns mimicked each other. Both males and females typically had higher than expected relatedness at distances <25 km, and in many distance classes greater than 25 km, less than expected relatedness. Similar patterns were apparent whether we used only loci in Hardy–Weinberg equilibrium (n = 7) or also included loci with potential null alleles (n = 5). We conclude that, contrary to expectations, sex‐biased dispersal is not occurring in this species, possibly related to the reverse sexual dimorphism in this species, with females having brighter colors. We did, however, detect significant spatial genetic structure in males and females, separate and combined, showing philopatry within a genetic patch size of <25 km in C. guttata, which is concerning for an endangered species whose populations are often separated by distances greater than the genetic patch size.
Peristaltic transport of a third-order fluid in a circular cylindrical tube

The effect of a third-order fluid on the peristaltic transport is analysed in a circular cylindrical tube, such as some organs in the living body. The third-order flow of an incompressible fluid in a circular cylindrical tube, on which an axisymmetric travelling sinusoidal wave is imposed, is considered. The wavelength of the peristaltic waves is assumed to be large compared to the tube average radius, whereas the amplitude of the wave need not be small compared to the average radius. Both analytic (perturbation) and numerical solutions are given. For the perturbation solution, a systematic approach based on an asymptotic expansion of the solution in terms of a small Deborah number is used and solutions up to the first order are presented in closed forms. The numerical solution, valid for any Deborah number, represents a new approach to peristaltic flows, and its features illuminate the physical behaviour much more than the analytical research on this problem. Comparison is made between the analytic (perturbation) and numerical results. Furthermore, the obtained results could also have applications to a range of peristaltic flows for a variety of non-Newtonian fluids such as aqueous solutions of high-molecular weight polyethylene oxide and polyacrylamide.
Determination of the Heat-Transport Coefficient in Energy-Balance Climate Models by Extremization of Entropy Production

Abstract Entropy production has been calculated as a function of the coefficient of meridional heat transfer for two seasonal energy-balance climate models. Both models display extrema in entropy production at values of the coefficient appropriate to the present climate. Inclusion of time dependence in the models is found to be the essential feature for successful application of entropy extremization.
Terbinafine Induced Acute Generalized Exanthematous Pustulosis Treated with Adalimumab: Recalcitrant to Systemic Corticosteroid Therapy

Abstract Acute generalized exanthematous pustulosis (AGEP) is generally caused by drugs and is characterized by the rapid development of numerous non-follicular sterile pustules on an erythematous base, fever, and neutrophilia. We report an association between terbinafine, with AGEP, and adalimumab treatment. A 24-year-old teenage female patient with a history of onychomycosis was treated with terbinafine. On the second day of the first dose, multiple edematous and erythematous lesions appear with pinhead pustules. Neutrophilia was observed in the blood report. The clinical history, lesions, and laboratory evaluations were consistent with AGEP. We discontinued the terbinafine therapy, and the systemic corticosteroid was initiated; however, the patient’s condition worsened. Adalimumab subcutaneously was initiated, and the symptoms cleared up in weeks. The European Study of Severe Cutaneous Adverse Reactions (EuroSCAR) scoring system and Naranjo’s algorithm scale were used to check the possibility of a drug-induced adverse reaction. The Association of AGEP with the terbinafine drug is not rare. However, there are no reports or literature of drug-related rash or exanthematous eruptions unresponsive to corticosteroids and treated with adalimumab.
Numerical technique for integration of the Landau–Lifshitz equation

In the article, a finite difference scheme for the numerical integration of the Landau–Lifshitz equation is presented. The scheme is based on the application of the midpoint rule coupled with a suitable extrapolation formula. The important properties of the scheme are the conservation of magnetization magnitude, its linearity, its second order truncation error accuracy, and the absence of spatial coupling. The accuracy of the scheme has been extensively tested by comparing numerical solutions with exact analytical solutions and by applying the scheme to the analysis of magnetization dynamics in conducting thin films.
Estimation of Unknown Parameters in Optimum Allocation

The use of pooled standard deviation can reduce the efficiency loss in optimum allocation when strata standard deviations are estimated and several of them are equal. Also shown is that the pooled standard deviation is useful in optimum allocation under a multivariate setting. In addition to theoretical development, we provide the result of simulation study to support the theory.
Conduction and mechanical properties of atomic scale gold contacts

Using a dynamic atomic force microscopy (AFM) technique in ultrahigh vacuum, we have directly measured the stiffness and conduction characteristics of a gold tip and sample. The method involves the application of a small sinusoidal oscillating force to the tip at a frequency well below the primary resonance frequency of the cantilever. By measuring the change in amplitude during the approach and retraction of the sample we have a continuous and accurate measure of the contact stiffness. The high sensitivity of this technique has enabled us to measure the mechanical properties of the junction during its initial formation. The most interesting observations are made in the region of initial contact formation where it is not possible to obtain high mechanical sensitivity from the commonly used static force measurement technique. In this region, as the contact is compressed, the contact softens continuously while the conductance remains constant prior to discrete conductance jumps. These are accompanied by sim.
Topping and grafting affect the alkaloid content and gene expression patterns of tobacco ( Nicotiana tabacum L.)

Abstract In this study, we aimed to determine molecular mechanisms underlying the effects of topping and grafting in tobacco ( Nicotiana tabacum L.) by comparing the alkaloid contents and enrichment pathways of differentially expressed genes (DEGs) among plants subjected to different combinations of topping and grafting treatments. Plants of the tobacco variety “Zhongyan 100” and eggplant ( Solanum melongena L.) were grafted in four combinations as scions and rootstocks, respectively. The four treatment groups were tobacco with topping, tobacco without topping, topped tobacco grafted onto an eggplant rootstock, and non‐topped tobacco grafted onto an eggplant rootstock. Tobacco leaves were collected on the day of topping, at 7 days after topping, and after flue curing, the alkaloid contents of the collected leaves were determined. Leaves of plants subjected to the different treatments were collected for RNA sequencing and screened for DEGs, which were subsequently subjected to functional enrichment analyses. Analyses revealed reductions in the leaf alkaloid contents of tobacco subjected to combined topping and eggplant grafting. Gene annotation indicated that topping influences biological processes such as starch metabolism and stress response, whereas grafting affected the biosynthesis and metabolic pathways of secondary metabolites. Downregulated DEGs between non‐topped tobacco and eggplant‐grafted topped tobacco and between topped and non‐topped tobacco are mainly involved in inositol phosphate metabolic and biosynthetic processes. Downregulated DEGs between different grafting methods (eggplant‐grafted non‐topped tobacco vs. non‐topped tobacco and eggplant‐grafted topped tobacco vs. topped tobacco) are mainly involved in sesquiterpene synthase activity and photosynthesis. The findings of this study provide important insights into the molecular mechanisms underlying the effects of topping and grafting on tobacco plants.
Phylogenetic implications and characterization of the chloroplast genome of Atractylodes macrocephala (Compositae), an herb species to China

Abstract The rhizome of Atractylodes macrocephala is one of the most commonly used herbs in China. In this paper, we presented the complete chloroplast genome of A. macrocephala. The chloroplast genome of A. macrocephala is 153,256 bp in length as the circular, which harbors a large single-copy (LSC) region 84,291 bp, a small single-copy (SSC) region of 18,675 bp and separated by a pair of inverted-repeat (IR) regions of 25,145 bp for each one. The overall nucleotide content of the chloroplast genome is 37.7% GC content. This chloroplast genome contains 125 genes, which includes 88 protein-coding genes (PCGs), 29 transfer RNA (tRNAs) and 8 ribosome RNA (rRNAs). Phylogenetic implications based on chloroplast genomes of 16 the family Compositae plant species indicated that Atractylodes macrocephala was closely related to Atractylodes lancea in the family Compositae by the Maximum-Likelihood (ML) method.
The complete mitochondrial genome of Cheilinus trilobatus (Perciformes: Labridae)

Abstract Cheilinus trilobatus Lacépède, 1801 is a species of genus Cheilinus. In this study, we sequenced the complete mitochondrion genome of C. trilobatus. The mitochondrial genome was 17,292 bp, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one non-coding control region (D-loop). The nucleotide composition was 27.31% A, 25.1% T, 17.23% G, and 30.36% C. Phylogenetic analysis suggested that C. trilobatus was closely related to Cheilinus oxycephalus. The complete mitogenome of C. trilobatus provided basic data for the genetic diversity conservation of this species.
The complete chloroplast genome of Cynoglossum amabile Stapf & J. R. Drumm., 1906 (Boraginaceae), a traditional Chinese herbal medicine

Abstract Cynoglossum amabile Stapf & J. R. Drumm. , 1906 is a traditional Chinese herbal medicine from southwest China. To better determine its phylogenetic relatedness to other Boraginaceae species, the chloroplast (cp) genome of C. amabile was sequenced. The complete cp genome of C. amabile is 151,532 bp in length, containing a small single-copy (SSC) region with a length of 17,366 bp, a large single-copy (LSC) region with a length of 82,902 bp, and a pair of inverted repeats (IRs) regions each with a length of 25,632 bp. The overall GC content of the cp genome is 37.4%. The maximum-likelihood phylogenetic tree showed that Bothriospermum zeylanicum (J. Jacq.) Druce, 1917 was closely related to C. amabile.
Perveance of a planar diode with explosive emission finite-diameter cathodes

Perveance of a planar diode with explosive emission velvet cathodes of 20–100 mm diameters in a range of diode gaps of 0.5–5 cm is investigated experimentally. An empirical universal curve linking the diode perveance and the cathode radius-to-diode gap ratio is determined thus allowing application of a Child–Langmuir model to diodes of finite dimensions. Comparison of experimental results with two-dimensional (2D) computational models is made and a simple method to translate 2D simulation results to the three-dimensional diode configurations is suggested.
Dynamic Straggler Mitigation for Large-Scale Spatial Simulations

Spatial simulations have been widely used to study real-world environments, such as transportation systems. Applications like prediction and analysis of transportation require the simulation to handle millions of objects while running faster than real time. Running such large-scale simulation requires high computational power, which can be provided through parallel distributed computing. Implementations of parallel distributed spatial simulations usually follow a bulk synchronous parallel (BSP) model to ensure the correctness of simulation. The processing in BSP is divided into iterations of computation and communication, running on multiple workers, followed by a global barrier synchronisation to ensure that all communications are concluded. Unfortunately, the BSP model is plagued by the straggler problem, where a delay in any worker slows down the entire simulation. Stragglers may occur for many reasons, including imbalanced workload distribution or communication and synchronisation delays. The straggler problem can become more severe with increasing parallelism and continuous change of workload distribution among workers. This article proposes methods to dynamically mitigate stragglers and tackle communication delays. The proposed strategies can rebalance the workload distribution during simulation. These methods employ the spatial properties of the simulated environments to combine a flexible synchronisation model with decentralised dynamic load balancing and on-demand resource allocation. All proposed methods are implemented and evaluated using a microscopic traffic simulator as an example of large-scale spatial simulations. We run traffic simulations for Melbourne, Beijing and New York with different straggler scenarios. Our methods significantly improve simulation performance compared to advanced methods such as global dynamic load balancing.
Change of measures for Markov chains and the LlogL theorem for branching processes

Then P(., .) is also a transition function. Let Px and Px denote respectively the probability distribution of a Markov chain {Xj}o with Xo = x and transition functions P and P. Conditions for P, to be dominated by Px or to be singular with respect to Px are given in terms of the martingale sequence Wn V(Xn)/p" and its limit. This is applied to establish an LlogL theorem for supercritical branching processes with an arbitrary type space.
X‐ray microbeam speech production database

A broad review of literature describing lingual function during speech shows that speaker samples per study are typically small (N<3 in more than 80% of all cases), and that speech samples, and representational and analysis conventions are highly variable. Similar conclusions can be drawn for other articulators. Thus it is fair to argue that there is still not available any valid, statistically‐defensible sense of normal speech motor behavior, against which disordered articulatory behavior can be compared. Accordingly, a large‐sample, 50‐speaker x‐ray microbeam speech database will be developed at the University of Wisconsin, incorporating point‐parametrized representations of lingual, labial, mandibular, and velar movements in association with the resulting acoustic sound pressure wave, for a rich set of utterances and oral motor tasks, and lengthy recording interval (circa 18 min/speaker). The database is intended to be uniform across speakers in task inventory and descriptive kinematic framework; suffi.
A study of a homogeneous sample of optically selected Active Galactic nuclei. III: Optical observations

We present CCD observations in BVR optical bands of the homogeneous sample of 42 Seyfert 1 galaxies, that we also observed in near-IR JHK bands (Zitelli et al. 1993; Danese et al. 1992). We have applied to these data the same analysis procedure used for the infrared images, with the aim of separating the galaxian and nuclear fluxes, as well as investigating the main characteristics of the hosts. Nuclear fluxes have been estimated with typical global errors of 0.15 mag, while 0.3 mag errors are on average associated to host galaxy magnitudes. It is shown that in half of the host galaxies the bulge contribute more than 40% to the total observed fluxes even within small apertures. In the sample galaxies disks are dominating over the bulge in the large majority of the cases, suggesting that a significant fraction of Seyfert galaxies could be late-type spirals. Moreover the galactic morphological parameters are in the ranges of typical spiral galaxies
Procedure for Identifying Metaphorical Scenes (PIMS): The Case of Spatial and Abstract Relations

ABSTRACT This article tackles the tricky problem of identifying metaphors in language that includes prepositions. We demonstrate how the Procedure for Identifying Metaphorical Scenes (PIMS) reflected and evoked by linguistic expressions in discourse, Johansson Falck & Okonski, accepted) can be used to identify metaphorical relations reflected in language. The scenes evoked correspond to conceptualizations that are directly attested by the specific linguistic constructions in the sentences under analysis. We present two studies that test the reliability of the procedure and the sensitivity of the tool for prepositions. Results show that PIMS provides a simple procedure that increases both reliability and sensitivity for prepositional constructions. By focusing on the scenes evoked by linguistic constructions, the procedure highlights the contextual meanings of the constructions and the specific experiences that they code.
Metaphors and Related Expressions in Older Adults in the Field of Trauma and Stress-related Disorders: A Scoping Review

ABSTRACT A scoping review was conducted to explore the metaphors and related expressions older adults use to describe extremely stressful events that may lead to Post-Traumatic Stress Disorder (PTSD), Complex PTSD (CPTSD), Prolonged Grief Disorder (PGD), or Adjustment Disorder (AjD). Relevant databases from psychology, gerontology, and related fields were searched. In addition, relevant references found in included papers were considered. Inclusion criteria were: qualitative study, sample of older adults (age 65+), and focus on maladaptive rather than adaptive psychological aspects. Eleven studies focusing on PTSD, 5 on CPTSD, 13 on PGD, and 10 on AjD were included. Metaphors and other expressions related to extremely stressful events were then extracted and analyzed. Multiple linguistic expressions to describe extremely stressful events and stress-related symptoms were identified. Metaphors and related expressions often referred to the body and the theme of moving on with one’s life.