Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of submergence ratio on flow and drag forces generated by a long rectangular array of rigid cylinders at the sidewall of an open channel

Abstract This paper discusses how the submergence ratio, defined as the ratio between the flow depth, D, and the height, h, of the solid rigid cylinders forming the array affects flow and turbulence structure inside and around a rectangular array of cylinders placed adjacent to one of the channel sidewalls. As the array becomes submerged, a vertical shear layer develops in between the top face of the array and the free surface, which strongly increases flow three-dimensionality and modifies how the momentum exchange between the array and the surrounding open water regions occurs with respect to the case of an emerged array where only a horizontal shear layer forms as part of the incoming flow approaching the array is deflected laterally. Eddy-resolving simulations are conducted for several values of the solid volume fraction, ϕ, and of the submergence ratio, 1.0 ≤ D/h ≤ 4.0. Similar to the limiting case of an emerged array (D/h = 1.0), the width- and depth-averaged streamwise velocity inside the array reaches a constant value after an initial adjustment region in the submerged-array cases. For D/h ≥ 1.33, the mean normal velocities through the top and side faces of the array do not become equal to zero downstream of the initial adjustment region. The flow inside the array reaches an equilibrium regime where the local flux of fluid leaving the array through its side face is balanced by the local flux of fluid entering the array through its top face. This regime is observed until close to the end of the array. For D/h ≥ 2.0, the horizontal shear layer vortices do not generate successive regions of high and low streamwise velocity and bed friction velocity inside the array, as is observed in the emerged cases. With respect to the emerged case, the size of the shear layer vortices and the shear layer width increase for low submergence ratios before decreasing rapidly for D/h ≥ 1.33. Significant three-dimensional effects are present inside the array and the horizontal shear layer for cases with both emerged and submerged arrays. In the ϕ = 0.08 cases, strong upwelling and downwelling motions are observed inside the array for D/h ≥ 1.33, while the circulation of the streamwise-oriented cell of secondary flow forming close to the lateral face of the array peaks when the submergence ratio is close to 1.33. For constant ϕ, the total streamwise drag force normalized with the height and width of the array increases with increasing submergence ratio. As the array submergence increases, the cylinders near the front of the array contribute less to the total force acting on the cylinders forming the array. For constant D/h, the total streamwise drag force acting on the array increases with ϕ for the submerged and emerged cases.
Can one generalize the concept of energy-momentum tensor?

The answer to the question is yes! Considering here the very simple case of a real Klein-Gordon field in Minkowski space-time, we find a class of rank 4 superenergy tensors generalizing the usual energy-momentum tensor. Then, we construct explicitely an infinite tower of rank 2(n +1) tensors that we call weak n-superenergy tensors and we determine the corresponding quantum operators.
Fine tuning of the repetition rate and stabilization of harmonically mode-locked fiber laser with CW component in the spectrum

Harmonically mode-locked (HML) fiber lasers delivering pulses with pulse repetition rate (PRR) in the GHz range have become a valuable alternative to semiconductor and solid-state lasers ensuring high beam quality, reliability, userfriendly light output, inherent to laser configurations in all-fiber format. The main drawback of HML laser technology is the noise-induced irregularities of the time interval between pulses known as the HML timing jitter. Ensuring low-level supermode noise and precise pulse repetition rate tuneability in all-fiber-integrated harmonically mode-locked laser sources establishes a new level of their versatility and extends areas of their applications. We report on new techniques enabling both the mitigation of supermode laser noise and highly precise setting of the PRR in a soliton fiber laser harmonically mode-locked by nonlinear polarization evolution. The principle of operation relies on resonant interaction between the soliton pulses and a narrow-band continuous wave (CW) component cooperatively generated within the same laser cavity.
Numerical optimization of tunable Dy-doped ZBLAN fiber lasers for yellow emission

The interest in fiber lasers operating in the yellow range of the visible spectrum has greatly increased alongside the improvement of blue pump laser diodes, as well as the recent fabrication of high-quality Dysprosium-doped fluoride fibers, to be used as the active medium. In this work, a matrix-based simulation model which exploits the rate equations was applied to examine the influence of excited state absorption on the performances of a tunable yellow source. Simulation results provide useful guidelines to improve the tunability range of the yellow fiber laser, by properly selecting the reflectivity of the output mirror and the active fiber length.
On the Use of Hydrodynamic Instability Test as an Efficient Tool for Evaluating Viscoelastic Fluid Models

The so-called ''second-order'' rheological model has been of widespread use in studies related to viscoelastic fluids. The model, however, has been shown by Fosdick and Rajagopal (1979) to violate certain Thermodynamics constraints. The so-called ''secondgrade'' model has been proposed as a remedy to comply with thermodynamics. But no experimental data has ever been presented to verify the appropriateness of the parameters used in this particular model. In the present work, it will be shown that instead of relying on hard-to-measure elastic properties of a fluid to see which model is the right one, it is much easier to resort to their instability response in plane Poiseuile flow for this purpose. To that end, it will be shown that in plane Poiseuille flow, the instability picture of second-grade fluids are dramatically different from second-order fluids. That is, while for second-order model, fluid’s elasticity has a destabilizing effect, for second-grade model, in contrast, it is predicted to have a stabilizing effect.
Early Cenozoic increases in mammal diversity cannot be explained solely by expansion into larger body sizes

A prominent hypothesis in the diversification of placental mammals after the Cretaceous–Palaeogene (K/Pg) boundary suggests that the extinction of non‐avian dinosaurs resulted in the ecological release of mammals, which were previously constrained to small body sizes and limited species richness. This ‘dinosaur incumbency hypothesis’ may therefore explain increases in mammalian diversity via expansion into larger body size niches, that were previously occupied by dinosaurs, but does not directly predict increases in other body size classes. To evaluate this, we estimate sampling‐standardized diversity patterns of terrestrial North American fossil mammals within body size classes, during the Cretaceous and Palaeogene. We find strong evidence for post‐extinction diversity increases in all size classes. Increases in the diversity of small‐bodied species (less than 100 g, the common body size class of Cretaceous mammals, and much smaller than the smallest non‐avialan dinosaurs (c. 400 g)) were similar to those of larger species. We propose that small‐bodied mammals had access to greater energetic resources or were able to partition resources more finely after the K/Pg mass extinction. This is likely to be the result of a combination of widespread niche clearing due to the K/Pg mass extinctions, alongside a suite of biotic and abiotic changes that occurred during the Late Cretaceous and across the K/Pg boundary, such as shifting floral composition, and novel key innovations among eutherian mammals.
A possibly deep branching artiopodan arthropod from the lower Cambrian Sirius Passet Lagerstätte (North Greenland)

Artiopoda was a diverse group of Palaeozoic euarthropods that proliferated in the early Palaeozoic, epitomized by the ubiquitous trilobites. Their possible phylogenetic position outside mandibulates and chelicerates offers the potential for understanding the evolution of euarthropods in more detail. However, this opportunity remains unexploited given that identification of deep‐splitting artiopodans remains to be fully explored. Here, we describe a new non‐trilobite artiopodan from the lower Cambrian Sirius Passet Lagerstätte, North Greenland. Thulaspis tholops gen. et sp. nov. is a large species with a broad, domed head shield, followed by a trunk consisting of 15 thoracic tergites and a small pygidium, giving the body an ovoid appearance when viewed dorsally. Thulaspis is distinctive with its rounded genae and anterior thoracic pleural tips, as well as short pleural spines posteriorly. A heart‐shaped hypostome with an anterior lobe is present. Appendages, partly obscured by the tergal skeleton, have many moderate length gnathobasic spines, and large flap‐like exopods with a fringe of small setae. Cladistic analyses recover Thulaspis as the sister taxon to Squamacula, a genus found in the Chengjiang and Emu Bay Shale biotas, in either a polytomy with a number of artiopodan taxa or as a sister group to all other artiopodans, indicating an important role in understanding the roots of artiopodan anatomy and evolution.
Three‐dimensional reconstruction of the in situ mode of life of the Cambrian coral Cambroctoconus: asexual reproduction and colony growth in immediate response to cryptic habitats

The Cambrian cnidarian Cambroctoconus orientalis occurs in clusters exhibiting pendent growth in crypts within thrombolite frameworks. Here we successfully reconstruct its three‐dimensional (3D) in situ mode of life. The 3D reconstruction shows the initial individuals of colonies and attachment structures, budding sites and growth modes of coralla in response to the extent of sheltered spaces. The earliest individuals were attached to the framework by a suction‐cup‐like structure and were basically orthogonal to the walls, growing downward. Their calicular bases were pierced by a hole. Individuals were initially cylindrical and gradually formed an octagonal column during growth. Budding occurred everywhere, and toroidal budding traces are abundant upon the corallite surfaces. The attachment structures were secondarily reinforced by continuous secretion from the coenenchymal tissue. Offsets continued to grow only when sufficient growth space was available, while producing as many individuals as possible. Growth of individuals was commonly halted by the surrounding framework. Growth directions were in part modified by corallite curvature to avoid collisions between corallites and to make full use of the intricate void spaces. In deteriorating conditions, offset corallites appeared through regeneration rather than budding from the remaining soft tissues. Active exploitation of the sheltered spaces within thrombolites, which remained dominant during the Cambrian, was thus conducted by C. orientalis. Notably, the cryptobionts treated herein adopted subtle growth strategies that have not previously been fully understood and are not easily interpreted with reference to organisms living in open spaces.
Between rhetorical questions and information requests: A versatile interrogative clause in Estonian

Abstract This article investigates the pragmatic and functional aspects of an interrogative question pattern in Estonian: questions introduced by the adjective huvitav (‘interesting’). Despite appearances, this question is usually not used to elicit an answer in an information request. Instead, its uses vary from self-addressed to rhetorical questions, also allowing the addition of a biased (critical, ironical) positioning to the interrogation. It can be related to subjective as well as intersubjective dimensions of language use. Examples primarily from two corpora are discussed: fiction texts and their translations (Estonian–French) from the Estonian–French bilingual corpus; excerpts from the debates of the Estonian Parliament; and to a lesser extent, examples from conversations are also included in the analysis. Like similar devices described in other languages (vajon in Hungarian, oare in Romanian), this pattern is impossible to use in situations where a clearly competent addressee is in a position to answer the question directly and the speaker is aware of it; instead, it is especially for cases where, for different reasons, the competence of the addressee is not questioned or challenged directly: asking tentative questions, using rhetorically designed questions to convey critics, or other biased meanings.
Some cross-country evidence on information rigidity in inflation forecasts

Abstract The study investigates the existence and extent of information rigidity in inflation forecasts among 25 developed and 18 developing economies during 2002–2017 period utilizing a survey data set never explored before on this issue. In general, the study finds some evidence of information rigidity. Rigidity is present during the recession period of global financial crisis of 2007 for both the developed and the developing countries alike, and we find weak evidence of information gathering picking up during the recession period. We also find that forecast revisions depend on both own country and cross-country lagged revisions. Therefore, one source of information rigidity is not to incorporate overseas events in forecast revisions quickly and completely.
Focused small field of view magnetic particle imaging for the detection and quantification of tumour associated macrophages

Tumour Associated Macrophages (TAMs) play a crucial role in breast cancer progression and have the potential to be used as a biomarker for patient prognosis. Magnetic particle imaging (MPI) is an emerging modality which can detect cells labelled with superparamagnetic iron oxide (SPIO) nanoparticles and can be used for non-invasive TAM assessment. However, MPI TAM detection is limited by its effective dynamic range. This limitation occurs when SPIO nanoparticles injected intravenously accumulate in the liver resulting in a large MPI signal which shadows regions of interest with lower signals (i.e the tumour) preventing their isolation and quantification. In this study we test an advanced reconstruction algorithm which allows us to prescribe a small focused field of view (FOV) on lower signals of interest. We then demonstrate the success of this method with an in vivo tumour model and show enhanced image quality and successful quantification of TAMs in mouse mammary tumours with different metastatic potentials (4T1 and E0771). Utilizing in vivo MPI, we did not see significant differences in the MPI signal for 4T1 tumours compared to E0771. These findings highlight the potential of MPI for in vivo TAM quantification offering a promising avenue for broader applications in cancer research and potentially overcoming constraints of MPI in other in vivo imaging contexts.
TRAILS: Tree reconstruction of ancestry using incomplete lineage sorting

Genome-wide genealogies of multiple species carry detailed information about demographic and selection processes on individual branches of the phylogeny. Here, we introduce TRAILS, a hidden Markov model that accurately infers time-resolved population genetics parameters, such as ancestral effective population sizes and speciation times, for ancestral branches using a multi-species alignment of three species and an outgroup. TRAILS leverages the information contained in incomplete lineage sorting fragments by modelling genealogies along the genome as rooted three-leaved trees, each with a topology and two coalescent events happening in discretized time intervals within the phylogeny. Posterior decoding of the hidden Markov model can be used to infer the ancestral recombination graph for the alignment and details on demographic changes within a branch. Since TRAILS performs posterior decoding at the base-pair level, genome-wide scans based on the posterior probabilities can be devised to detect deviations from neutrality. Using TRAILS on a human-chimp-gorilla-orangutan alignment, we recover speciation parameters and extract information about the topology and coalescent times at high resolution. Author summary DNA sequences can be compared to reconstruct the evolutionary history of different species. While the ancestral history is usually represented by a single phylogenetic tree, speciation is a more complex process, and, due to the effect of recombination, different parts of the genome might follow different genealogies. For example, even though humans are more closely related to chimps than to gorillas, around 15% of our genome is more similar to the gorilla genome than to the chimp one. Even for those parts of the genome that do follow the same human-chimp topology, we might encounter a last common ancestor at different time points in the past for different genomic fragments. Here, we present TRAILS, a new framework that utilizes the information contained in all these genealogies to reconstruct the speciation process. TRAILS infers unbiased estimates of the speciation times and the ancestral effective population sizes, improving the accuracy when compared to previous methods. TRAILS also reconstructs the genealogy at the highest resolution, inferring, for example, when common ancestry was found for different parts of the genome. This information can also be used to detect deviations from neutrality, effectively inferring natural selection that happened millions of years ago. We validate the method using extensive simulations, and we apply TRAILS to a human-chimp-gorilla multiple genome alignment, from where we recover speciation parameters that are in good agreement with previous estimates.
Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant

Sex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigated in animals and brown algae, less is known about evolutionary forces in dioecious angiosperms. In this study, we separately compared the expression of sex-biased genes between female and male floral buds and between female and male flowers at anthesis in dioecious Trichosanthes pilosa (Cucurbitaceae). In floral buds, sex-biased gene expression was pervasive, and had significantly different roles in sexual dimorphism such as physiology. We observed higher rates of sequence evolution for male-biased genes in floral buds compared to female-biased and unbiased genes. Male-biased genes under positive selection were mainly associated with functions to abiotic stress and immune responses, suggesting that high evolutionary rates are driven by adaptive evolution. Additionally, relaxed purifying selection may contribute to accelerated evolution in male-biased genes generated by gene duplication. Our findings, for the first time in angiosperms, suggest evident rapid evolution of male-biased genes, advance our understanding of the patterns and forces driving the evolution of sexual dimorphism in dioecious plants.
GeNNius: an ultrafast drug–target interaction inference method based on graph neural networks

Drug-target interaction (DTI) prediction is a relevant but challenging task in the drug repurposing field. In-silico approaches have drawn particular attention as they can reduce associated costs and time commitment of traditional methodologies. Yet, current state-of-the-art methods present several limitations: existing DTI prediction approaches are computationally expensive, thereby hindering the ability to use large networks and exploit available datasets and, the generalization to unseen datasets of DTI prediction methods remains unexplored, which could potentially improve the development processes of DTI inferring approaches in terms of accuracy and robustness. In this work, we introduce Gennius (Graph Embedding Neural Network Interaction Uncovering System), a Graph Neural Network (GNN)-based method that outperforms state-of-the-art models in terms of both accuracy and time efficiency across a variety of datasets. We also demonstrated its prediction power to uncover new interactions by evaluating not previously known DTIs for each dataset. We further assessed the generalization capability of Gennius by training and testing it on different datasets, showing that this framework can potentially improve the DTI prediction task by training on large datasets and testing on smaller ones. Finally, we investigated qualitatively the embeddings generated by Gennius, revealing that the GNN encoder maintains biological information after the graph convolutions while diffusing this information through nodes, eventually distinguishing protein families in the node embedding space. Code Availability https://github.com/ubioinformat/GeNNius
Influence of individual differences in executive functions of WM on the continued influence effect of misinformation

ABSTRACT Misinformation often affects people’s cognition and judgment even when they are aware of a retraction; this is known as the continued influence effect of misinformation (CIE). The aim of the present study was to verify if there were differences in the continued influence effect with respect to the individual’s EF availability of WM (i.e. inhibition, shifting and updating). The Stroop task, number shifting task and the n-back task were adopted to investigate the three executive functions of inhibition, shifting and updating, respectively. The results showed that differences in inhibition, but not in shifting and updating, had a significant negative effect on the CIE. The continued effect of misinformation was lower for individuals with high function of inhibition. The current study showed that high-inhibition individuals were less affected by the misinformation. The study extends our understanding of the relationship between executive functions and the CIE.