Miracle-dz/UniFAR-FTUs huggingface dataset:
Knowledge Aware Conversation Generation with Explainable Reasoning over Augmented Graphs

Two types of knowledge, triples from knowledge graphs and texts from documents, have been studied for knowledge aware open domain conversation generation, in which graph paths can narrow down vertex candidates for knowledge selection decision, and texts can provide rich information for response generation. Fusion of a knowledge graph and texts might yield mutually reinforcing advantages, but there is less study on that. To address this challenge, we propose a knowledge aware chatting machine with three components, an augmented knowledge graph with both triples and texts, knowledge selector, and knowledge aware response generator. For knowledge selection on the graph, we formulate it as a problem of multi-hop graph reasoning to effectively capture conversation flow, which is more explainable and flexible in comparison with previous works. To fully leverage long text information that differentiates our graph from others, we improve a state of the art reasoning algorithm with machine reading comprehension technology. We demonstrate the effectiveness of our system on two datasets in comparison with state-of-the-art models.
Supplementary data for 1 RNA m 1 A methylation regulates glycolysis of cancer cells through 2 modulating ATP 5 D 3 4

modulating ATP5D 3 4 Yingmin Wu1,2#, Zhuojia Chen3#, Guoyou Xie1 #, Haisheng Zhang1, Zhaotong Wang1, Jiawang 5 Zhou1, Feng Chen1, Jiexin Li1, Likun Chen3, Hongxin Niu4, Hongsheng Wang1* 6 7 1 Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of 8 Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; 9 2 School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, China ; 10 3 Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; 11 Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China 12 4 Department of General Practice, Zhujiang Hospital, Southern Medical University, 13 Guangzhou, China 14 15 # These authors contributed equally to this work. 16 * Corresponding author: Dr. Hongsheng Wang, Email: whongsh@mail.sysu. edu.cn, School 17 of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China. 18 19 20 21
'Causes of Widespread Foliar Damage from the June 2021 Pacific Northwest Heat Dome: More Heat than Drought'.

Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA; US Department of Agriculture, Forest Service, Pacific Northwest Region, State & Private Forestry, Forest Health Protection, Redmond, OR 97756, USA; Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; US Department of Agriculture, Forest Service, Pacific Northwest Research Station, Olympia, WA 98512, USA; Department of Forest Engineering, Resources, and Management, Oregon State University, Corvallis, OR 97331, USA; US Department of Agriculture, Forest Service, Pacific Northwest Research Station, Corvallis, OR 97331, USA; Oregon Climate Change Research Institute, College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR 97331, USA; PRISM Climate Group, Northwest Alliance for Computational Science and Engineering, Oregon State University, Corvallis, OR 97331, USA; Agronomy Department, University of Florida, Institute of Food and Agricultural Sciences, Gainesville, FL 32611, USA; Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, Western Australia 6983, Australia; CSIRO Land and Water, Private Bag 5, Wembley, Western Australia 6913, Australia; Corresponding author (chris.still@oregonstate.edu)
Positivity of $2\times 2$ block matrices of operators

We review some of the significant generalizations and applications of the celebrated Douglas theorem on the equivalence of factorization, range inclusion, and majorization of operators. We then apply it to find a characterization of the positivity of $2\times 2$ block matrices of operators in Hilbert spaces and finally describe the nature of such block matrices and provide several ways for showing their positivity.
Electronic and structural properties of SnO under pressure

Pressure-induced changes in the electronic and structural properties of tin monoxide are examined by means of ab initio density-functional calculations. Also, the pressure shifts of the A1g and Eg zone-center phonon modes are derived. The results are compared to recent experimental high-pressure data as well as to previous calculations for ambient conditions. In agreement with earlier findings we observe that the Sn-5s lone pair is not inert but hybridizes with the O-p states. Differences in that respect between SnO and PbO are shown to be a “relativistic dehybridization effect” caused by the large mass-velocity downshift of the Pb-6s states. SnO is a small-gap indirect semiconductor at ambient pressure, but an insulator-metal transition occurs as pressure is applied. The transition is estimated to occur around 5 GPa. The gap depends sensitively on the distance between the layers dEgap/ d lnc / a 21 eV.
Modeling of PDT kinetics in cell killing

Photodynamic therapy (PDT) provides an effective option for treatment of tumors and other diseases. In this work, we extended a previous rate-equation model in time domain with consideration of oxygen diffusion in a spherical cell model. Enhanced oxygen diffusion through cell membrane and non-PDT uptake of oxygen inside the cell have been investigated to study their effect on photobleaching and oxidization leading to cell killing within the context of PDT. We found that the improved PDT model can take into the account of the Michaelis-Menten uptake of the oxygen in addition to diffusion which allows quantitative modeling of photobleaching and cell killing.
Software-based neural network assisted movement compensation for nanoresolution piezo actuators

Micro- and nanoresolution applications are important part of functional material research, where imaging and observation of material interaction may go down to the molecular or even atomic level. Much of the nanometer range movement of scanning and manipulation instruments is made possible by usage of piezoelectric actuation systems. This paper presents a software based controller implementation utilizing neural networks for high precision positioning of a piezoelectric actuator. The controller developed can be used for controlling nanopositioning piezo actuators when sufficiently accurate feedback information is available. Piezo actuators exhibit complex hysteresis dynamics that need to be taken into account when designing an accurate control system. For inverse modelling purposes of the hysteresis related phenomena, a static hysteresis operator and a new developed dynamic creep operator are presented to be used in conjunction with a feed-forward type neural network. The controller utilizing the neural network inverse hybrid model is implemented as a software component for the existing Scalable Modular Control framework (SMC). Using the SMC framework and off-the-shelf components, a measurement and control system for the nanopositioning actuator is constructed and tested using two different capacitive sensors operating on y- and z-axes of the actuator. Using the developed controller, piezo actuator related hysteresis phenomena were successfully reduced making the nanometer range positioning of the actuator axes possible. Also, the effect of using a lower accuracy position sensor with more noise to control accuracy is briefly discussed.
Magneto-Optical Chirality in a Coherently Coupled Exciton–Plasmon System

Chirality is a fundamental asymmetry phenomenon, with chiral optical elements exhibiting asymmetric response in reflection or absorption of circularly polarized light. Recent realizations of such elements include nanoplasmonic systems with broken-mirror symmetry and polarization-contrasting optical absorption known as circular dichroism. An alternative route to circular dichroism is provided by spin-valley polarized excitons in atomically thin semiconductors. In the presence of magnetic fields, they exhibit an imbalanced coupling to circularly polarized photons and thus circular dichroism. Here, we demonstrate that polarization-contrasting optical transitions associated with excitons in monolayer WSe2 can be transferred to proximal plasmonic nanodisks by coherent coupling. The coupled exciton–plasmon system exhibits magneto-induced circular dichroism in a spectrally narrow window of Fano interference, which we model in a master equation framework. Our work motivates the use of exciton–plasmon interfaces as building blocks of chiral metasurfaces for applications in information processing, nonlinear optics, and sensing.
Multidimensional R2 gravity: the structure of constraints and canonical quantization

It is shown that curvature-squared gravity would be split into five essentially different variants at D)4. Every variant possesses its own number of physical degrees of freedom. The classification explicitly depends upon the dimension. The Dirac constrained canonical formalism is developed and its general structure is exhaustively studied. Explicit expressions of the first- and second-class constraints are specific for every variant of the theory.
A generalization of the logistic linear'model

Consider the logistic linear model, with some explanatory variables overlooked. Those explanatory variables may be quantitative or qualitative. In either case, the resulting true response variable is not a binomial or a beta-binomial but a sum of binomials. Hence, standard computer packages for logistic regression can be inappropriate even if an overdispersion factor is incorporated. Therefore, a discrete exponential family assumption is considered to broaden the class of sampling models. Likelihood and Bayesian analyses are discussed. Bayesian computation techniques such as Laplacian approximations and Markov chain simulations are used to compute posterior densities and moments. Approximate conditional distributions are derived and are shown to be accurate. The Markov chain simulations are performed effectively to calculate posterior moments by using the approximate conditional distributions. The methodology is applied to Keeler's hardness of winter wheat data for checking binomial assumptions and to Matsumura's Accounting exams data for detailed likelihood and Bayesian analyses.
Algorithms for Monte Carlo Simulations of the Ising Models on a Simple Cubic Lattice

The vectorized Monte Carlo algorithm by multi-spin coding is extended to the ±J Ising spin glass model on a simple cubic lattice in a magnetic field. Explicit logical expression is given for this algorithm. In addition, shorter logical expressions are found in some special cases.They are given for the heat-bath method under the general condition and for the Metropolis method under the condition, H = 0.
The DEAD-box protein Dbp6 is an ATPase and RNA annealase interacting with the peptidyl transferase center (PTC) of the ribosome

Abstract Ribosomes are ribozymes, hence correct folding of the rRNAs during ribosome biogenesis is crucial to ensure catalytic activity. RNA helicases, which can modulate RNA–RNA and RNA/protein interactions, are proposed to participate in rRNA tridimensional folding. Here, we analyze the biochemical properties of Dbp6, a DEAD-box RNA helicase required for the conversion of the initial 90S pre-ribosomal particle into the first pre-60S particle. We demonstrate that in vitro, Dbp6 shows ATPase as well as annealing and clamping activities negatively regulated by ATP. Mutations in Dbp6 core motifs involved in ATP binding and ATP hydrolysis are lethal and impair Dbp6 ATPase activity but increase its RNA binding and RNA annealing activities. These data suggest that correct regulation of these activities is important for Dbp6 function in vivo. Using in vivo cross-linking (CRAC) experiments, we show that Dbp6 interacts with 25S rRNA sequences located in the 5′ domain I and in the peptidyl transferase center (PTC), and also crosslinks to snoRNAs hybridizing to the immature PTC. We propose that the ATPase and RNA clamping/annealing activities of Dbp6 modulate interactions of snoRNAs with the immature PTC and/or contribute directly to the folding of this region.
Success rate and influencing factors of a balloon‐push technique: A new technique to remove side branch‐jailed struts under three‐dimensional optical coherence tomography guidance

Kissing balloon inflation with distal guide wire recross can cause severe stent deformation depending on the stent link location with respect to the carina. The balloon‐push technique, by which an inflated balloon is forced into the SB from the proximal main vessel (MV), is a feasible way to remove jailed struts without causing severe stent deformation.
The gyrfalcon (Falco rusticolus) genome

Abstract High-quality genome assemblies are characterized by high-sequence contiguity, completeness, and a low error rate, thus providing the basis for a wide array of studies focusing on natural species ecology, conservation, evolution, and population genomics. To provide this valuable resource for conservation projects and comparative genomics studies on gyrfalcon (Falco rusticolus), we sequenced and assembled the genome of this species using third-generation sequencing strategies and optical maps. Here, we describe a highly contiguous and complete genome assembly comprising 20 scaffolds and 13 contigs with a total size of 1.193 Gbp, including 8,064 complete Benchmarking Universal Single-Copy Orthologs (BUSCOs) of the total 8,338 BUSCO groups present in the library aves_odb10. Of these BUSCO genes, 96.7% were complete, 96.1% were present as a single copy, and 0.6% were duplicated. Furthermore, 0.8% of BUSCO genes were fragmented and 2.5% (210) were missing. A de novo search for transposable elements (TEs) identified 5,716 TEs that masked 7.61% of the F. rusticolus genome assembly when combined with publicly available TE collections. Long interspersed nuclear elements, in particular, the element Chicken-repeat 1 (CR1), were the most abundant TEs in the F. rusticolus genome. A de novo first-pass gene annotation was performed using 293,349 PacBio Iso-Seq transcripts and 496,195 transcripts derived from the assembly of 42,429,525 Illumina PE RNA-seq reads. In all, 19,602 putative genes, of which 59.31% were functionally characterized and associated with Gene Ontology terms, were annotated. A comparison of the gyrfalcon genome assembly with the publicly available assemblies of the domestic chicken (Gallus gallus), zebra finch (Taeniopygia guttata), and hummingbird (Calypte anna) revealed several genome rearrangements. In particular, nine putative chromosome fusions were identified in the gyrfalcon genome assembly compared with those in the G. gallus genome assembly. This genome assembly, its annotation for TEs and genes, and the comparative analyses presented, complement and strength the base of high-quality genome assemblies and associated resources available for comparative studies focusing on the evolution, ecology, and conservation of Aves.
Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5′-monophosphate as the biological substrate

Abstract Eukaryotic life benefits from—and ofttimes critically relies upon—the de novo biosynthesis and supply of vitamins and micronutrients from bacteria. The micronutrient queuosine (Q), derived from diet and/or the gut microbiome, is used as a source of the nucleobase queuine, which once incorporated into the anticodon of tRNA contributes to translational efficiency and accuracy. Here, we report high-resolution, substrate-bound crystal structures of the Sphaerobacter thermophilus queuine salvage protein Qng1 (formerly DUF2419) and of its human ortholog QNG1 (C9orf64), which together with biochemical and genetic evidence demonstrate its function as the hydrolase releasing queuine from queuosine-5′-monophosphate as the biological substrate. We also show that QNG1 is highly expressed in the liver, with implications for Q salvage and recycling. The essential role of this family of hydrolases in supplying queuine in eukaryotes places it at the nexus of numerous (patho)physiological processes associated with queuine deficiency, including altered metabolism, proliferation, differentiation and cancer progression.
Learning Invariant Rules from Data for Interpretable Anomaly Detection

In the research area of anomaly detection, novel and promising methods are frequently developed. However, most existing studies exclusively focus on the detection task only and ignore the interpretability of the underlying models as well as their detection results. Nevertheless, anomaly interpretation, which aims to provide explanation of why speciﬁc data instances are identiﬁed as anomalies, is an equally important task in many real-world applications. In this work, we propose a novel framework which synergizes several machine learning and data mining techniques to automatically learn invariant rules that are consistently satisﬁed in a given dataset. The learned invariant rules can provide explicit explanation of anomaly detection results in the inference phase and thus are extremely useful for subsequent decision-making regarding reported anomalies. Furthermore, our empirical evaluation shows that the proposed method can also achieve comparable or even better performance in terms of AUC and partial AUC on public benchmark datasets across various application domains compared with start-of-the-art anomaly detection models.
Generating corneal panoramic images from contact specular microscope images

: The contact specular microscope has a wider angle of view than that of the non-contact specular microscope but still cannot capture an image of the entire cornea. To obtain such an image, it is necessary to prepare ﬁlm on the parts of the image captured sequentially and combine them to create a complete image. This study proposes a framework to automatically generate an entire corneal image from videos captured using a contact specular microscope. Relatively focused images were extracted from the videos and panoramic compositing was performed. If an entire image can be generated, it is possible to detect guttae from the image and examine the extent of their presence. The system was implemented and the effectiveness of the proposed framework was examined. The system was implemented using custom-made composite software, Image Composite Software (ICS, K.I. Technology Co., Ltd., Japan, internal algorithms not disclosed), and a supervised learning model using U-Net was used for guttae detection. Several images were correctly synthesized when the constructed system was applied to 94 different corneal videos obtained from Fuchs endothelial corneal dystrophy (FECD) mouse model. The implementation and application of the method to the data in this study conﬁrmed its effectiveness. Owing to the minimal quantitative evaluation performed, such as accuracy with implementation, it may pose some limitations for future investigations.
On the choice of the most suitable indicator for the assembly state of dark matter haloes through cosmic time

The dynamical state and morphological features of galaxies and galaxy clusters, and their high-redshift precursors, are tightly connected with their assembly history, encoding crucial information about the formation and evolution of such cosmic structures. As a first step towards finding an optimal indicator of the assembly state of observed structures, we use a cosmological simulation of a moderate volume to critically examine the best definition of an indicator that is able to discriminate dark matter haloes undergoing mergers and/or strong accretion from haloes experimenting a relaxed evolution. Using a combination of centre offset, virial ratio, mean radial velocity, sparsity and ellipticity of the dark matter halo, we study how the thresholds on these parameters, as well as their relative weights, should evolve with redshift to provide the best classification possible. This allows us to split a sample of haloes in a totally relaxed, a marginally relaxed and an unrelaxed subsamples. The resulting classification strongly correlates with the merging activity obtained from the analysis of complete merger trees extracted from whole simulation data. The results on how the different indicators depend on redshift and halo mass, and their optimal combination to better match the true assembly history of haloes, could constitute relevant hints to find a suitable set of indicators applicable to observational data.
Review of Cookie Synchronization Detection Methods

The research community has deemed cookie synchronization detection an inherently challenging task. Studies aiming to identify cookie synchronizations often share high-level design choices, but deviate amongst low-level implementations. For example, the majority of studies label a cookie synchronization iff a user identifier is shared with a third party; however, there is a lack of consistency among implementations, such as party relations or identifier value definitions, or whether such definitions are even included. This review intends to provide a record of established methods and promote standardization of methods choice in future work.
The Colorado Ultraviolet Transit Experiment Mission Overview

Atmospheric escape is a fundamental process that affects the structure, composition, and evolution of many planets. The signatures of escape are detectable on close-in, gaseous exoplanets orbiting bright stars, owing to the high levels of extreme-ultraviolet irradiation from their parent stars. The Colorado Ultraviolet Transit Experiment (CUTE) is a CubeSat mission designed to take advantage of the near-ultraviolet stellar brightness distribution to conduct a survey of the extended atmospheres of nearby close-in planets. The CUTE payload is a magnifying near-ultraviolet (2479–3306 Å) spectrograph fed by a rectangular Cassegrain telescope (206 mm × 84 mm); the spectrogram is recorded on a back-illuminated, UV-enhanced CCD. The science payload is integrated into a 6U Blue Canyon Technology XB1 bus. CUTE was launched into a polar, low-Earth orbit on 2021 September 27 and has been conducting this transit spectroscopy survey following an on-orbit commissioning period. This paper presents the mission motivation, development path, and demonstrates the potential for small satellites to conduct this type of science by presenting initial on-orbit science observations. The primary science mission is being conducted in 2022–2023, with a publicly available data archive coming online in 2023.