Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete de novo assembly of Tricholoma bakamatsutake chromosomes revealed the structural divergence and differentiation of Tricholoma genomes

Tricholoma bakamatsutake, which is an edible ectomycorrhizal fungus associated with Fagaceae trees, may have diverged before the other species in Tricholoma section Caligata. We generated a highly contiguous whole-genome sequence for T. bakamatsutake SF-Tf05 isolated in an oak (Quercus salicina) forest in Japan. The assembly of high-fidelity long reads, with a median read length of 12.3 kb, resulted in 13 chromosome-sized contigs comprising 142,068,211 bases with an average GC content of 43.94%. The 13 chromosomes were predicted to encode 11,060 genes. A contig (122,566 bases) presumably containing the whole circular mitochondrial genome was also recovered. The chromosome-wide comparison of T. bakamatsutake and T. matsutake (TMA_r1.0) indicated that the basic number of chromosomes (13) was conserved, but the structures of the corresponding chromosomes diverged, with multiple inversions and translocations. Gene conservation and cluster analyses revealed at least three groups in Tricholoma. Specifically, all T. bakamatsutake strains belonged to the “bakamatsutake” clade, which is most proximal to the “caligatum” clade consisting of T. caligatum and T. fulvocastaneum. The constructed highly contiguous telomere-to-telomere genome sequence of a T. bakamatsutake isolate will serve as a fundamental resource for future research on the evolution and differentiation of Tricholoma species.
Light sensitive short hypocotyl (LSH) confer symbiotic nodule identity in the legume Medicago truncatula

Legumes grow specialized root nodules that are distinct from lateral roots in morphology and function, with nodules intracellularly hosting beneficial nitrogen-fixing bacteria that provide the plant with a nitrogen source. We have previously shown that a lateral root-like program underpins nodule initiation, but there must be additional developmental programs that confer nodule identity. Here, we show that two members of the LIGHT SENSITIVE SHORT HYPOCOTYL (LSH) transcription factor family, predominantly known to define organ boundaries and meristem complexity in the shoot, function as regulators of nodule organ identity. LSH1/LSH2 function upstream of and together with the known nodule regulators Nuclear Factor Y-A1 and NODULE ROOT1/2. The principal outcome of LSH1/LSH2 function is the production of cells able to accommodate nitrogen-fixing bacteria, the unique nodule feature. We conclude that the coordinate recruitment of a pre-existing primordium identity program, in parallel to a root initiation program, underpins the divergence between lateral roots and nodules.
LINE1-Mediated Reverse Transcription and Genomic Integration of SARS-CoV-2 mRNA Detected in Virus-Infected but Not in Viral mRNA-Transfected Cells

SARS-CoV-2 sequences can be reverse-transcribed and integrated into the genomes of virus-infected cells by a LINE1-mediated retrotransposition mechanism. Whole genome sequencing (WGS) methods detected retrotransposed SARS-CoV-2 subgenomic sequences in virus-infected cells overexpressing LINE1, while an enrichment method (TagMap) identified retrotranspositions in cells that did not overexpress LINE1. LINE1 overexpression increased retrotranspositions about 1,000-fold as compared to non-overexpressing cells. Nanopore WGS can directly recover retrotransposed viral and flanking host sequences but its sensitivity depends on the depth of sequencing (a typical 20-fold sequencing depth would only examine 10 diploid cell equivalents). In contrast, TagMap enriches for the host-virus junctions and can interrogate up to 20,000 cells and is able to detect rare viral retrotranspositions in LINE1 non-overexpressing cells. Although Nanopore WGS is 10 – 20-fold more sensitive per tested cell, TagMap can interrogate 1,000 – 2,000-fold more cells and therefore can identify infrequent retrotranspositions. When comparing SARS-CoV-2 infection and viral nucleocapsid mRNA transfection by TagMap, retrotransposed SARS-CoV-2 sequences were only detected in infected but not in transfected cells. Retrotransposition in virus-infected in contrast to transfected cells may be facilitated because virus infection in contrast to viral RNA transfection results in significantly higher viral RNA levels and stimulates LINE1-expression which causes cellular stress.
An allele-resolved nanopore-guided tour of the human placental methylome

The placenta is a temporary organ present during pregnancy that is responsible for coordinating all aspects of pregnancy between the mother and fetus. It has a distinct epigenetic, transcriptomic, and mutational landscape with low levels of methylation, high numbers of transcribed loci, and a high mutational burden relative to somatic tissues. We present this landscape through the application of nanopore sequencing technology to provide a more comprehensive picture of female placental genomics and methylomics along with integrated haplotype-resolved transcriptomic analyses across eight trios. Whole genome sequencing of trios allows robust phasing, permitting comprehensive genome-wide investigation of parent-of-origin methylation and transcription. This enhanced view facilitates identifications of many new differentially methylated regions (DMRs), both conserved and differing between individuals, as well as novel imprinted genes including ILDR2 and RASA1 which are potentially important for healthy placental and fetal development.
Multi‐omic network analysis identified betacellulin as a novel target of omega‐3 fatty acid attenuation of western diet‐induced nonalcoholic steatohepatitis

Clinical and preclinical studies have established that supplementing diets with ω3 polyunsaturated fatty acids (PUFA) can reduce hepatic dysfunction in nonalcoholic steatohepatitis (NASH). Herein, we used multi-omic network analysis to unveil novel mechanistic targets of ω3 PUFA effects in a preclinical mouse model of western diet induced NASH. After identifying critical molecular processes responsible for the effects of ω3 PUFA, we next performed meta-analysis of human liver cancer transcriptomes and uncovered betacellulin as a key EGFR-binding protein that was induced in liver cancer and downregulated by ω3 PUFAs in animals with NASH. We then confirmed that betacellulin acts by promoting proliferation of quiescent hepatic stellate cells, stimulating transforming growth factor–β2 and increasing collagen production. When used in combination with TLR2/4 agonists, betacellulin upregulated integrins in macrophages thereby potentiating inflammation and fibrosis. Taken together, our results suggest that suppression of betacellulin is one of the key mechanisms associated with anti-inflammatory and antifibrotic effects of ω3 PUFA during NASH. Synopsis Multi-omic network analysis points to mitochondrial cardiolipin precursors as candidate key lipids whereby ω3 fatty acids restore mitochondrial functioning. Multi-omic network analysis suggests betacellulin (BTC) as one of the key mediators of NASH suppressed by ω3 polyunsaturated fatty acids. Reduction of liver fibrosis by omega-3 fatty acids (especially by docosahexaenoic acid, DHA) is accomplished by simultaneous inhibition of betacellulin and TLR agonists. BTC promotes collagen production and induces TGFB2 in hepatic stellate cells. BTC together with TLR2/4 agonists stimulate expression of integrins in macrophages. DHA suppresses BTC-EGFR pathway in NASH animal model potentially preventing progression to hepatocellular carcinoma.
BHLHE40/41 regulate macrophage/microglia responses associated with Alzheimer’s disease and other disorders of lipid-rich tissues

Background Genetic and experimental evidence strongly implicates myeloid cells in the etiology of AD and suggests that AD-associated alleles and genes may modulate disease risk by altering the transcriptional and cellular responses of macrophages (like microglia) to damage of lipid-rich tissues (like the brain). Specifically, recent single-cell/nucleus RNA sequencing (sc/nRNA-seq) studies identified a transcriptionally distinct state of subsets of macrophages in aging or degenerating brains (usually referred to as disease- associated microglia or DAM) and in other diseased lipid-rich tissues (e.g., obese adipose tissue, fatty liver, and atherosclerotic plaques). We collectively refer to these subpopulations as lipid-associated macrophages or LAMs. Importantly, this particular activation state is characterized by increased expression of genes involved in the phagocytic clearance of lipid-rich cellular debris (efferocytosis), including several AD risk genes. Methods We used sc/nRNA-seq data from human and mouse microglia from healthy and diseased brains and macrophages from other lipid-rich tissues to reconstruct gene regulatory networks and identify transcriptional regulators whose regulons are enriched for LAM response genes (LAM TFs) across species. We then used gene knock- down/knock-out strategies to validate some of these LAM TFs in human THP-1 macrophages and iPSC-derived microglia in vitro, as well as mouse microglia in vivo. Results We nominate 11 strong candidate LAM TFs shared across human and mouse networks (BHLHE41, HIF1A, ID2, JUNB, MAF, MAFB, MEF2A, MEF2C, NACA, POU2F2 and SPI1). We also demonstrate a strong enrichment of AD risk alleles in the cistrome of BHLHE41 (and its close homolog BHLHE40), thus implicating its regulon in the modulation of disease susceptibility. Loss or reduction of BHLHE40/41 expression in human THP-1 macrophages and iPSC-derived microglia, as well as loss of Bhlhe40/41 in mouse microglia led to increased expression of LAM response genes, specifically those involved in cholesterol clearance and lysosomal processing, with a concomitant increase in cholesterol efflux and storage, as well as lysosomal mass and degradative capacity. Conclusions Taken together, this study nominates transcriptional regulators of the LAM response, experimentally validates BHLHE40/41 in human and mouse macrophages/microglia, and provides novel targets for therapeutic modulation of macrophage/microglia function in AD and other disorders of lipid-rich tissues. Graphical abstract
Reynolds Number Dependence in Supersonic Jet Noise

An experimental study of the noise production by high speed jets over a wide range of Reynolds numbers has been performed. Two jets of nominal Mach numbers 1.5 and 2.3 were run over a Reynolds number range from 5300 to 107,000. Microphone measurements of the radiated noise and hot-wire measurements of the flow fluctuations demonstrate that at low Reynolds numbers coherent flow instabilities produce a dominant portion of the noise. In the nominal Mach number 2.3 jet these instability waves convect downstream supersonically with respect to the ambient air. In the nominal Mach number 1.5 jet the instabilities convect downstream subsonically. In both cases however, sound pressure level amplitude contours show that the low Reynolds number jets radiate noise comparable to intermediate and high Reynolds number jets. These measurements constitute substantial evidence that a flow instability model of the dominant noise generators may be appropriate for conventional high Reynolds number supersonic jets. a0 C D d M m n r Re St u U Nomenclature speed of sound outside jet wavespeed in the downstream direction diameter of the jet effective diameter of the jet Mach number of the jet at the exit normalized mass velocity fluctuations = azimuthal mode number = radial distance from jet centerline = Reynolds number = p Ud/n. = Strouhal number =fd/ (/(/is frequency) = local velocity =mean centerline velocity of the jet at the nozzle exit
Approximate controllability of the semilinear heat equation

This article is concerned with the study of approximate controllability for the semilinear heat equation in a bounded domain Ω when the control acts on any open and nonempty subset of Ω or on a part of the boundary. In the case of both an internal and a boundary control, the approximate controllability in LP(Ω) for 1 ≦ p < + ∞ is proved when the nonlinearity is globally Lipschitz with a control in L∞. In the case of the interior control, we also prove approximate controllability in C0(Ω). The proof combines a variational approach to the controllability problem for linear equations and a fixed point method. We also prove that the control can be taken to be of “quasi bang-bang” form.
How Adults Understand and Reason about Fractions

We investigated what strategies adults use to compare magnitudes of fractions, and how the strategies vary with overall mathematical knowledge. Because little is known about how people think about fractions, prior research has attempted to assess the extent to which people think of fractions compared to how they think about whole numbers (Bonato, Fabbri, Umilta & Zorzi, 2007; Schneider & Siegler, 2010; Meert, Gregoire, Noel, 2009). In particular, Bonato et al. (2007) has examined the degree to which fractional magnitude comparisons can yield an understanding of the mental representation of fractions. Schneider & Siegler (2010) argue that these assessments cannot be made independently from understanding the strategies for comparison that a particular pair of fractions elicits. The current study extends prior research by comparing fraction magnitude comparison strategies of students at a selective university, with high math proficiency, with those of students at a community college, with lower math proficiency. The goals of this thesis were to identify, explain and define the strategies that are used in fraction magnitude comparisons by adults, investigate how these strategies vary with the math proficiency of the adults, and evaluate whether adults who do not consistently use desirable strategies recognize desirability of good alternative strategies. Our findings indicate that strategy use and consistency of using good and poor strategies vary with overall math knowledge and performance on our magnitude comparison task; that lower performing participants more frequently used strategies that would yield incorrect results and less often recognize when to switch to good alternative strategies compared to the high performing participants.
A scaling relation for warm‐phase orographic precipitation: a Lagrangian analysis for 2D mountains

The precipitation produced by orographic clouds is the result of the interaction between nonlinear dynamical and microphysical processes. Focusing on warm‐phase stable clouds, we propose that the precipitation efficiency is essentially controlled by the bulk Damköhler number of the system, i.e. the ratio of the characteristic advective to the microphysical time‐scale of the cloud. These time‐scales are investigated thoroughly for single air parcels along temporally highly resolved trajectories from quasi‐two‐dimensional numerical simulations with vertical Froude numbers between 0.38 and 2.31. Based on these results, analytical formulations for the Damköhler number of single parcels and for a bulk Damköhler number for the entire cloud are developed, which depend only on the far upstream flow properties and the cloud droplet number density.
Multi-Agent Case-Based Reasoning: a Network Intrusion Detection System

We propose a multi-agent case-based reasoning system to detect malicious traffic in a network. We introduce ten topic agents, including nine different attack categories and one agent covering normal, benign traffic. Using the four knowledge containers, we fill our case base with the labeled training data of the commonly used UNSW_NB15 data set, in sum 82332 cases with (mostly numeric) 47 attribute features. We calculate average values for each attribute and search for outliers to identify characteristic attributes for each attack category, increasing weights in the amalgamation function for those attributes. For local similarities, we define polynomial similarity functions with heavily decreasing similarity for differing attribute-values pairs between case and query, depending on the range of the attribute values. Purpose. The proposed system is aimed to detect malicious traffic, such as denial of service attacks, to alert the security engineer of a company or even an individual person. The system can either be included into already existing intrusion detection systems, support regular log analysis, or used for forensic analysis. Findings . We were able to successfully detect Generic and Fuzzer attacks with a high true-positive rate. With additional adjustments, we are confident to successfully detect more attack categories. Implications and value. Despite only detecting two out of nine attacks, we are confident for this approach to provide an important step into the right direction with possible improvements and opportunities for fruitful synergies and discussions inside the security domain and case-based reasoning community.
Intrinsic Analysis of Learned Representations in Encoder-Decoder Architectures

Encoder-decoder architectures have widespread use, both in research and the industry. Recently, similarity analysis applied to the representations of neural networks has contributed to a better understanding of the architectures. Previous work has found that for two instances (under different initialization) of the same layer of a given model, the learned representation becomes more and more dissimilar the farther away that layer is from the input layer. Since the encoder-decoder is often mirrored (causing a representational bottleneck), we investigate how the representation changes and if the objective of reconstructing the input influences this. Using representation similarity analysis, we find out that corresponding layers from the encoder and decoder are not very similar to each other and are more similar to their neighbor layers. In addition, our experiments show that except for classification tasks, the representations of the same decoder with different initialization become more and more similar the closer a layer is to the output layer. Some of our analysis includes comparing the average distances between the layers to the average distance of the current layer clusters, the impact of varying the latent dimension as well as having multiple bottleneck layers on the representational consistency.
A statistical study on the effects of IMF Bz and solar wind speed on auroral ion and electron precipitation

The variation in the average particle number and energy flux in the high-latitude region is determined as a function of the solar wind velocity, Vsw, and the z component of the interplanetary magnetic field, Bz. The study is made using the data from the SSJ/4 detectors on the satellites of the Defense Meteorological Satellite Program. In the study the high-latitude region is divided into spatial elements in magnetic local time and corrected geomagnetic latitude. One such matrix of spatial divisions is constructed for each of 30 paired ranges of values in Vsw and Bz. There are six divisions in Bz covering the range from −10 to +10 nT and five divisions in velocity covering the range from 200 to 800 km/s. Using approximately 34 million SSJ/4 spectra, the average electron and ion spectra are determined in each spatial element for each of the 30 paired values of Vsw and Bz. From the average spectra, the average integral energy and number fluxes for electrons and ions are calculated in each spatial bin. These values are then spatially integrated to give the average hemispheric inputs of the integral particle energy and number flux. Both quantities are found to vary in a simple and consistent manner with both Vsw and Bz. For both electrons and ions the variation with Bz tends to a minimum value for weak to moderately strong Bz positive. For decreasing values of Bz from the minimum, both quantities increase at a rate greater than linear. For increasing values of Bz from the minimum, both quantities tend to increase, least for the hemispheric electron energy flux and most for the hemispheric ion number flux. The variation in both quantities with Vsw for both electrons and ions is generally linear with the steepest slopes for the electron hemispheric energy flux. The variation with Bz and Vsw for all four quantities can be well fit by a simple quadratic equation either of the form ƒ(Bz, Vsw) = a(Bz − b)² + cVsw + d or ƒ(Bz, Vsw) = [a(Bz − b)² + 1][cVsw + d]. Either form indicates that the variation is no greater than quadratic in Bz and no more than linear in Vsw and that the variation is approximately symmetric for values above and below the minimum value of Bz, namely, b. This result is significantly different than either the half-wave rectifier or epsilon function for describing the solar-wind magnetospheric interaction.
RAREFACTION WAVES IN LIQUID AND GAS-LIQUID MEDIA

The thermodynamics of a substance in the critical state has been exten­ sively studied, and a strong dependence of the thermodynamic parameters on the temperature and pressure near the critical point has been revealed. However, processes such as heat exchange and finite-amplitude waves (shock waves) have not been as thoroughly investigated in the region of the critical point. In fact, the question of the dynamics of finite-amplitude perturbations of pressure, density, and temperature in the critical region has not been considered at all. One should mention just one study devoted to shock waves near the critical point, namely that by Zel'dovich (1946), who analyzed the entropy condition for shock-wave stability and theo­ retically the possible existence of rarefaction shock waves. The effect of the sign of (iJ2p/iJV2)s on the structure of compression and rarefaction waves was discussed by Thompson & Lambrakis (1973).
Hysteresis in the high pressure transformation of bcc‐ to hcp‐iron

The α‐Fe/e‐Fe phase transformation has been studied by the Mossbauer effect of 57Fe in a diamond anvil cell at hydrostatic pressures up to 24 GPa. The α/e composition is easily derived as a function of intermediate pressure. For rising pressures the transition onset is about 9 GPa and half of the α‐Fe is converted to e‐Fe by 15 GPa; for lowering pressures half of the e‐Fe is converted to α‐Fe by 9 GPa. The transition pressures, widths, and hysteresis widths are compared to those obtained by other techniques.
Computational Solutions of Unsteady Confined Viscous Flows With Variable Inflow Velocities for Unsteady Fluid-Structure Interaction Problems

This paper presents computational solutions of the unsteady viscous flows generated by the variation in time of the inflow velocities. These solutions are obtained using a specially developed time-accurate numerical method for the solution of the time-dependent Navier-Sokes equations. This method is applied to obtain solutions for the unsteady viscous flows past downstream-facing steps which are generated by harmonic variations in time of the inflow velocities. Complex flow separation patterns were found for these unsteady flows.Copyright © 2005 by ASME
Semiclassical quantization of billiards with mixed boundary conditions

The semiclassical theory for billiards with mixed boundary conditions is developed and explicit expressions for the smooth and the oscillatory parts of the spectral density are derived. The parametric dependence of the spectrum on the boundary condition is shown to be a very useful diagnostic tool in the semiclassical analysis of the spectrum of billiards. It is also used to check in detail some recently proposed parametric spectral statistics. The methods are illustrated in the analysis of the spectrum of the Sinai billiard and its parametric dependence on the boundary condition on the dispersing arc.