Miracle-dz/UniFAR-FTUs huggingface dataset:
A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats

Insights into the processes underpinning convergent evolution advance our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgression and thereby into the potential of these processes or (in their absence) the need to invoke novel mutations to underpin convergent evolution. Here, we were interested in understanding the processes involved in convergent evolution in open-habitat chats (wheatears of the genus Oenanthe and their relatives). To this end, based on whole-genome resequencing data from 50 taxa of 44 species, we established the species tree, characterized gene tree heterogeneity, and investigated the footprints of ILS and introgression within the latter. The species tree corroborates the pattern of abundant convergent evolution, especially in wheatears. The high levels of gene tree heterogeneity in wheatears are explained by ILS alone only for 30% of internal branches. For multiple branches with high gene tree heterogeneity, D-statistics and phylogenetic networks identified footprints of introgression. Finally, long branches without extensive ILS between clades sporting similar phenotypes provide suggestive evidence for a role of novel mutations in the evolution of these phenotypes. Together, our results suggest that convergent evolution in open-habitat chats involved diverse processes and highlight that phenotypic diversification is often complex and best depicted as a network of interacting lineages.
Structure parameters for temperature and humidity from simultaneous eddy-covariance and scintillometer measurements

Line-averaged values of the structure parameters of temperature and humidity, CT2 and Cq2, were estimated from simultaneous measurements with an optical and a microwave scintillometer over a path of 4.7 km length at the Meteorological Observatory Lindenberg during the LITFASS-2003 experiment. By cross-correlating the detected signals of the two scintillometers, the temperature-humidity structure parameter, CTq, and the temperature-humidity correlation, rTq, were also derived directly from the measurements. Comparison with corresponding values obtained from local measurements with an eddy-covariance system on a meteorological tower show a consistent behaviour in time (with some exceptions especially for Cq2 and rTq during nighttime). The deviations are of a magnitude between 20 % and 35 % of the typical daytime values of the structure parameters.
Systematic multi-trait AAV capsid engineering for efficient gene delivery

Broadening gene therapy applications requires manufacturable vectors that efficiently transduce target cells in humans and preclinical models. Conventional selections of adeno-associated virus (AAV) capsid libraries are inefficient at searching the vast sequence space for the small fraction of vectors possessing multiple traits essential for clinical translation. Here, we present Fit4Function, a generalizable machine learning (ML) approach for systematically engineering multi-trait AAV capsids. By leveraging a capsid library that evenly samples the manufacturable sequence space, reproducible screening data are generated to train accurate sequence-to-function models. Combining six models, we designed a multi-trait (liver-targeted, manufacturable) capsid library and validated 89% of library variants on all six predetermined criteria. Furthermore, the models, trained only on mouse in vivo and human in vitro Fit4Function data, accurately predicted AAV capsid variant biodistribution in macaque. Top candidates exhibited high production yields, efficient murine liver transduction, up to 1000-fold greater human hepatocyte transduction, and increased enrichment, relative to AAV9, in a screen for liver transduction in macaques. The Fit4Function strategy ultimately makes it possible to predict cross-species traits of peptide-modified AAV capsids and is a critical step toward assembling an ML atlas that predicts AAV capsid performance across dozens of traits.
Murine Vaginal Co-infection with Penicillinase-Producing Neisseria gonorrhoeae Fails to Alleviate Amoxicillin-Induced Chlamydial Persistence

Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) cause most bacterial sexually transmitted infections (STIs) worldwide. CT/NG co-infection is more common than expected due to chance, suggesting CT/NG interaction. However, CT/NG co-infection remains largely unstudied. Obligate intracellular CT has a characteristic biphasic developmental cycle consisting of two bacterial forms, infectious elementary bodies (EBs) and non-infectious, replicating reticulate bodies (RBs), which reside within host-derived, membrane-bound intracellular inclusions. Diverse stressors cause divergence from the normal chlamydial developmental cycle to an aberrant state called chlamydial persistence. Persistence can be induced by host-specific factors such as intracellular nutrient deprivation or cytokine exposure, and exogenous factors such as beta-lactam exposure, which disrupts RB to EB conversion. Persistent chlamydiae are atypical in appearance and, as such, are called aberrant bodies (ABs), but remain viable. The primary hallmark of persistence is reversibility of this temporary non-infectious state; upon removal of the stressor, persistent chlamydiae re-enter normal development, and production of infectious EBs resumes. The beta-lactam amoxicillin (AMX) has been shown to induce chlamydial persistence in a murine vaginal infection model, using the mouse pathogen C. muridarum (CM) to model human CT infection. This remains, to date, the sole experimentally tractable in vivo model of chlamydial persistence. Recently, we found that penicillinase-producing NG (PPNG) can alleviate AMX-induced CT and CM persistence in vitro. We hypothesized that PPNG vaginal co-infection would also alleviate AMX-induced CM persistence in mice. To evaluate this hypothesis, we modified the CM/AMX persistence mouse model, incorporating CM/PPNG co-infection. Contradicting our hypothesis, and recent in vitro findings, PPNG vaginal co-infection failed to alleviate AMX-induced CM persistence.
Mutation divergence over space in tumour expansion

Mutation accumulation in tumour evolution is one major cause of intra-tumour heterogeneity (ITH), which often leads to drug resistance during treatment. Previous studies with multi-region sequencing have shown that mutation divergence among samples within the patient is common, and the importance of spatial sampling to obtain a complete picture in tumour measurements. However, quantitative comparisons of the relationship between mutation heterogeneity and tumour expansion modes, sampling distances as well as the sampling methods are still few. Here, we investigate how mutations diverge over space by varying the sampling distance and tumour expansion modes using individual based simulations. We measure ITH by the Jaccard index between samples and quantify how ITH increases with sampling distance, the pattern of which holds in various sampling methods and sizes. We also compare the inferred mutation rates based on the distributions of Variant Allele Frequencies (VAF) under different tumour expansion modes and sampling sizes. In exponentially fast expanding tumours, a mutation rate can always be inferred in any sampling size. However, the accuracy compared to the true value decreases when the sampling size decreases, where small sampling sizes result in a high estimate of the mutation rate. In addition, such an inference becomes unreliable when the tumour expansion is slower such as in surface growth.
How Does Perceptual Discriminability Relate to Neuronal Receptive Fields?

Perception is an outcome of neuronal computations. Our perception changes only when the underlying neuronal responses change. Because visual neurons preferentially respond to adjustments in some pixel values of an image more than others, our perception has greater sensitivity in detecting change to some pixel combinations more than others. Here, we examined how perceptual discriminability varies to arbitrary image perturbations assuming different models of neuronal responses. In particular, we investigated that under the assumption of different neuronal computations, how perceptual discriminability relates to neuronal receptive fields – the change in pixel combinations that invokes the largest increase in neuronal responses. We assumed that perceptual discriminability reflects the magnitude of change (the L2 norm) in neuronal responses, and the L2 norm assumption gained empirical support. We examined how perceptual discriminability relates to deterministic and stochastic neuronal computations. In the case of deterministic neuronal computations, perceptual discriminability is completely determined by neuronal receptive fields. For multiple layers of canonical linear-nonlinear (LN) computations in particular (which is a feed-forward neural network), neuronal receptive fields are linear transforms of the first-layer neurons’ image filters. When one image is presented to the neural network, the first-layer neurons’ filters and the linear transform completely determine neuronal receptive fields across all layers, and perceptual discriminability to arbitrary distortions to the image. We expanded our analysis to examine stochastic neuronal computations, in which case perceptual discriminability can be summarized as the magnitude of change in stochastic neuronal responses, with the L2 norm being replaced by a Fisher-information computation. Using a practical lower bound on Fisher information, we showed that for stochastic neuronal computations, perceptual discriminability is completely determined by neuronal receptive fields, together with how responses co-variate across neurons.
Development and Tropical Transition of an Alpine Lee Cyclone. Part I: Case Analysis and Evaluation of Numerical Guidance

Abstract The development and tropical transition (TT) of a subsynoptic-scale cyclone in the Gulf of Genoa during the Mesoscale Alpine Project (MAP) demonstration of probabilistic hydrological and atmospheric simulation of flood events in the alpine region (D-PHASE) project is investigated using analyses and model simulations. Cyclogenesis occurs in association with the passage of a synoptic-scale trough and attendant surface cold front across the Alps on 15 November 2007. An embedded coherent tropopause disturbance (CTD) plays an important role in promoting the initial development of the lower-level vortex by simultaneously providing quasigeostrophic forcing for ascent and reducing the bulk column stability over warm Mediterranean waters. Persistent convection thereafter erodes the CTD as the storm transitions into a hurricane-like vortex. In addition to this upper-level forcing, a pair of diabatically generated lower-level cyclonic potential vorticity (PV) features associated with distinct flow regimes i.
p oWder N eutroN d iffractioN aNd m aterials c hemistrY /p hYsics r esearch iN c aNada (1949-2017)

The story of powder neutron diffraction at Chalk River is inextricably linked to the history of neutron science at Chalk River itself. Canada’s interest in nuclear research grew out of our involvement in World War II and the race to harness the power of the atom. In 1942, a joint Canadian-British laboratory was built in Montreal to assist in the war effort under the leadership of the National Research Council of Canada (NRC) [1]. There were many Europeans working in Canada at the time, including the UK’s John Cockcroft and France’s Lew Kowarski and Hans von Halban. Kowarski and von Halban were physicists that had recently escaped Nazi occupied Germany with 200 kg of heavy water (the largest supply in the world at the time) [2]. This formed the impetus for the design of a heavy water moderated reactor with the initial goal of producing plutonium for the Manhattan project. In 1944, the Montreal research group moved to a newly built laboratory at Chalk River, Ontario, where the first reactors in Canada were being built. In 1949, the National Research Universal reactor (NRU) project began, which was a Canadian design and would form the basis for the future for Canadian neutron beam research [3]. The 135 MW reactor is a significant Canadian success story, providing not only intense neutron beams for materials research, but also medical isotopes for over 20 million people in 80 countries, and a testing ground for innovative reactor and fuel rod design projects [4].
THE INFLUENCE OF PERSONAL AND ORGANIZATIONAL AREAS IN THE PRICE DECISION FROM THE PERSPECTIVE OF RISK TOLERANCE

The objective of the study was to identify the influence of the personal and organizational areas in the price decision under the perspective of risk tolerance in light of the Prospect Theory proposed by Kahneman and Tversky in 1979. The analysis in the organizational area is carried out in relation to the definition of the price and in the personal area in the perception of fairness in the formation of the price. Therefore, an experiment was carried out under laboratory conditions, applied virtually to 174 students of lato sensu specialization from the Administration and Accounting courses offered by the Federal University of Uberlândia. The participants were randomly assigned to two groups representing the personal and organizational areas, which make pricing decisions. Data were statistically analyzed using logistic regression and the results indicate that the area in which the decision was taken does not affect the individual's risk tolerance, differing from the results found in other studies in the area. Furthermore, it was possible to conclude that some demographic variables influence the manager in the decision regarding price definition and also the consumer (personal area) in the perception of fairness in price formation. The findings are consistent with the Prospect Theory, which defends that individuals take risks to avoid a loss and avoid risks in situations that can obtain a gain. The study results contribute to the presentation of empirical evidence on risk tolerance, complementing the literature in the scientific world and for organizations and society, demonstrating which demographic characteristics can affect the risk tolerance of the customer and the manager in price decisions.
Tweet with a Smile and a Unicorn: the use of emoji on Twitter in the Netherlands and England

With the immense growth of social media, emoji have also spread all over the world. Currently, there are more than a thousand of these colourful pictographs showing faces, creatures and objects. However, not all emoji see regular use, while others are extremely popular. This exploratory study attempts to answer the following question: how and why are emoji used on Twitter in the Netherlands and England? Through a quantitative analysis of two million tweets, current emoji usage in the two countries is described. A following qualitative study consisting of sixteen semi-structured interviews provides insight into why individuals use emoji and how they select emoji. Three important themes that influence the number of emoji used and the selection of emoji were found: the individual’s purpose on Twitter, the p erceived functionality of emoji and the individual’s selection criteria for emoji. Overall, emoji play an important role in online communication and seem more complex than their light-hearted appearance suggests.
A study on the feeding of shrimp larvae of Macrobrachium nipponense on algae in vitro

Experiments were carried out for the propagation and rearing of Macrobrachium nipponense and its feeding on algae, with the aim of determining the density, survival, and growth of larvae in vitro . Hatched larvae of zoae were reared at a density of 50 zoea/L with algae mixture: Chlorella vulgaris, Scenedesmus sp . , Pediastrium sp. , Microctinium sp. , Navicula sp. , Ulothrix sp. , Cyclotella sp. , Daitoma sp. at three concentrations of 0.5=A, 1.0=B, 1.5=C x 10⁵ cell/ml, and the survival % rates of zoea larvae were 45.00±5.00, 53.33±7.64, 50.00±5.00 respectively. Then, three densities: 25=A, 50=B, 75=C zoea/L were tested by feeding them with the best concentration of 1.0×10⁵ cell/ml for 10 days, with the result being survival % rates were 50.00±5.00, 51.67±7.64, 31.67±7.64, respectively. After that, stage post - larvae were reared at a density of (50=A,100=B, 150=C) Pl/pond and fed with a concentration of 1.0 x 10⁵ cell/ml of the algae mixture for 28 days, which resulted in survival % rates of 48.33±7.64, 40.00±5.00, 33.33±7.64, and this stage, weight was 50.67±2.08, 50.00±2.00, 40.33±2.52mg respectively. The results of the analysis of survival rates for different densities of zoea larvae found significant differences (P < 0.05) between density C and density of both A and B, of which there were no significant differences (P > 0.05) between them. There were no significant differences (p > 0.05) in the survival rates of zoea in different concentrations of the selected algae. Also, there were no significant differences (p > 0.05) in the survival rates and weight rate of post - larvae when fed on algae (B).
The domain derivative in rough-surface scattering and rigorous estimates for first-order perturbation theory

We investigate Fréchet differentiability of the scattered field with respect to variation in the boundary in the case of time–harmonic acoustic scattering by an unbounded, sound–soft, one–dimensional rough surface. We rigorously prove the differentiability of the scattered field and derive a characterization of the Fréchet derivative as the solution to a Dirichlet boundary value problem. As an application of these results we give rigorous error estimates for first–order perturbation theory, justifying small perturbation methods that have a long history in the engineering literature. As an application of our rigorous estimates we show that a plane acoustic wave incident on a sound–soft rough surface can produce an unbounded scattered field.
An Evaluation of Formula-Based Population Squared Cross-Validity Estimates and Factor Score Estimates in Prediction

Eight formula-based estimates of population squared cross-validity and nine estimates of factor scores were used in a prediction study involving 31 attitude type predictors and a criterion. These estimates were compared with the conventional cross-validation procedure and the use of data-level variables (raw scores or standardized raw scores) in two separate sample sizes of 150 and 250 cases. The major findings of this empirical study are: (1) Formula-based estimates of population squared cross-validity are as good as those obtained from the conventional cross-validation procedure, (2) factor score estimates are equally good in predicting population squared cross-validity, and (3) two formula-based estimates (Burket's and Rozeboom's) of population squared cross-validity in combination with one of the factor score methods appear to offer the most for practitioners concerned with prediction.
Robust Small Sample Inference for Generalised Estimating Equations: An Application of the Anova‐type Test

Asymptotically, the Wald‐type test for generalised estimating equations (GEE) models can control the type I error rate at the nominal level. However in small sample studies, it may lead to inflated type I error rates. Even with currently available small sample corrections for the GEE Wald‐type test, the type I error rate inflation is still serious when the tested contrast is multidimensional. This paper extends the ANOVA‐type test for heteroscedastic factorial designs to GEE and shows that the proposed ANOVA‐type test can also control the type I error rate at the nominal level in small sample studies while still maintaining robustness with respect to mis‐specification of the working correlation matrix. Differences of inference between the Wald‐type test and the proposed test are observed in a two‐way repeated measures ANOVA model for a diet‐induced obesity study and a two‐way repeated measures logistic regression for a collagen‐induced arthritis study. Simulation studies confirm that the proposed test has better control of the type I error rate than the Wald‐type test in small sample repeated measures models. Additional simulation studies further show that the proposed test can even achieve larger power than the Wald‐type test in some cases of the large sample repeated measures ANOVA models that were investigated.
Detection of infrared variability in Cygnus X-1

Near-infrared measurements of Cygnus X-1 in the J and K bands, carried out with the 1.5-m telescope a the Rothney Astrophysical Observatory, show significant variability with an amplitude of 0.3 mag in the J and K bands. The observations indicate the presence of two maxima at 5.6-d orbital phases 0.25 and 0.70. The variability in the infrared emission is suggested to be produced by the accretion disc which is responsible for the X-ray emission from the Cygnus X-1 system
K-CORRECTIONS FOR TYPE IA SUPERNOVAE

The usefulness of type Ia supernovae as distance indicators is a metter of current study and discussion. The avaialbel data suggest that the intrinsic dispersion in the absolute B magnitudes of SNe Ia at maximum light is less than 0.4 mag. Hence, SNe Ia offer considerable potential for cosmological studies out to redshifts of z~0.1 or greater. At these distances, however, the effects of the redshift on the observed magnitudes are not negligible and must be taken into account in order to compare the magnitudes and light curves of objects of different redshifts. In this paper we make use of the best spectra avaialbe for type Ia supernovae in order to calculate the effect of theredshift on the observed B and V magnitudes. We present K-temrs in the redshift range z=0.005-0.50 from a collection of spectra of SNe 1990N, 1991T, and 1992A covering from day -14 to day +76, counted from the time of maximum light in the blue band. The K-terms calculated for the V band from the different spectra show a well defined trend as a function of time. In the B band the K-terms show some scatter before maximum light due to the spectroscopic differences displayed by the trhee SNe selected. These spectral differences tend ti disappear for later epochs and, consequently the K-term curves in the B band after maximum light are much tighter. Our calculations enable us to interpolate K-terms for SNe Ia at maximum light, which should prove useful to study the Hubble diagram for these objects.
The observation and simulation of stochastically excited solar p modess

We use low-degree p-mode data, collected in integrated sunlight by the Birmingham Solar-Oscillations Network (BiSON), to derive the distribution of the observed strengths of the solar oscillations. We demonstrate that certain features of the observations cannot be explained by a model of the oscillations that is based upon a stochastically forced, damped harmonic oscillator. The solution of the equation of motion of the oscillator, as derived by the use of the Laplace transform, is presented, and its application to the simulation of real p-mode data, in the form of a coded algorithm, is discussed. A variety of tests are applied - both in the time and in the frequency domains - to artificially generated time series. These confirm that the model serves both as a useful diagnostic tool and for providing additional insight into the p-mode excitation and damping problem.
Radiation Force Exerted on Subwavelength Particles near a Nanoaperture

We report the first numerical analysis of the radiation force exerted on a subwavelength particle by an evanescent field localized near a subwavelength aperture. The radiation force is calculated by using the Maxwell stress tensor through the electric field distribution obtained with the finite-difference time-domain method. The result indicates that a particle moves towards the aperture. We found that if two particles exist the first particle is trapped and the second one is also attracted to the first one. The radiation force is found to be larger than the forces due to thermal fluctuations and to gravity.