Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient, out-of-memory sparse MTTKRP on massively parallel architectures

Tensor decomposition (TD) is an important method for extracting latent information from high-dimensional (multi-modal) sparse data. This study presents a novel framework for accelerating fundamental TD operations on massively parallel GPU architectures. In contrast to prior work, the proposed Blocked Linearized Coordinate (BLCO) format enables efficient out-of-memory computation of tensor algorithms using a unified implementation that works on a single tensor copy. Our adaptive blocking and linearization strategies not only meet the resource constraints of GPU devices, but also accelerate data indexing, eliminate control-flow and memory-access irregularities, and reduce kernel launching overhead. To address the substantial synchronization cost on GPUs, we introduce an opportunistic conflict resolution algorithm, in which threads collaborate instead of contending on memory access to discover and resolve their conflicting updates on-the-fly, without keeping any auxiliary information or storing non-zero elements in specific mode orientations. As a result, our framework delivers superior in-memory performance compared to prior state-of-the-art, and is the only framework capable of processing out-of-memory tensors. On the latest Intel and NVIDIA GPUs, BLCO achieves 2.12 -- 2.6X geometric-mean speedup (with up to 33.35X speedup) over the state-of-the-art mixed-mode compressed sparse fiber (MM-CSF) on a range of real-world sparse tensors.
Curvature identities for Einstein manifolds of dimensions 5 and 6

Patterson discussed the curvature identities on Riemannian manifolds in [14], and a curvature identity for any 6-dimensional Riemannian manifold was independently derived from the Chern-Gauss-Bonnet Theorem [8]. In this paper, we provide the explicit formulae of Patterson’s curvature identity that holds on 5-dimensional and 6-dimensional Einstein manifolds. We confirm that the curvature identities on the Einstein manifold from the previous work [8] are the same as the curvature identities deduced from Patterson’s result. We also provide examples that support the theorems.
SMGRL: A Scalable Multi-resolution Graph Representation Learning Framework

Graph convolutional networks (GCNs) allow us to learn topologically-aware node embeddings, which can be useful for classiﬁcation or link prediction. However, by construction, they lack positional awareness and are unable to capture long-range dependencies without adding additional layers—which in turn leads to over-smoothing and increased time and space complexity. Further, the complex dependencies between nodes make mini-batching challenging, limiting their applicability to large graphs. This paper proposes a Scalable Multi-resolution Graph Representation Learning (SMGRL) framework that enables us to learn multi-resolution node embeddings efﬁciently. Our framework is model-agnostic and can be applied to any existing GCN model. We dramatically reduce training costs by training only on a reduced-dimension coarsening of the original graph, then exploit self-similarity to apply the resulting algorithm at multiple resolutions. Inference of these multi-resolution embeddings can be distributed across multiple machines to reduce computational and memory requirements further. The resulting multi-resolution embeddings can be aggregated to yield high-quality node embeddings that capture both long-and short-range dependencies between nodes. Our experiments show that this leads to improved classiﬁcation accuracy, without incurring high computational costs.
Attenuation of turbulence in a periodic cube by finite-size spherical solid particles

Abstract To investigate the attenuation of turbulence in a periodic cube due to the addition of spherical solid particles, we conduct direct numerical simulations using an immersed boundary method with resolving flow around each particle. Numerical results with systematically changing particle diameters and Stokes numbers for a fixed volume fraction $\varLambda$ show that the additional energy dissipation rate in the wake of particles determines the degree of the attenuation of turbulent kinetic energy. On the basis of this observation, we propose formulae describing the condition and degree of the attenuation of turbulence intensity. We conclude that particles with size proportional to $\lambda /\sqrt {\gamma }$, where $\lambda$ and $\gamma$ are the Taylor length and the mass density ratio between particles and fluid, most significantly reduce the intensity of developed turbulence under the condition that $\gamma$ and $\varLambda$ are fixed.
E/B mode decomposition of HSC-Y1 cosmic shear using COSEBIs: Cosmological constraints and comparison with other two-point statistics

We perform a cosmic shear analysis of Hyper Suprime-Cam Subaru Strategic Program first-year data (HSC-Y1) using complete orthogonal sets of E/B-integrals (COSEBIs) to derive cosmological constraints. We compute E/B-mode COSEBIs from cosmic shear two-point correlation functions measured on an angular range of 4′ < θ < 180′. We perform a standard Bayesian likelihood analysis for cosmological inference from the measured E-mode COSEBIs, including contributions from intrinsic alignments of galaxies as well as systematic effects from point spread function model errors, shear calibration uncertainties, and source redshift distribution errors. We adopt a covariance matrix derived from realistic mock catalogs constructed from full-sky gravitational lensing simulations that fully take account of the survey geometry and measurement noise. For a flat Λ cold dark matter model, we find $S\,_8 \equiv \sigma _8\sqrt{\Omega _{\rm m}/0.3}=0. 809_{-0.026}^{+0.036}$. We carefully check the robustness of the cosmological results against astrophysical modeling uncertainties and systematic uncertainties in measurements, and find that none of them has a significant impact on the cosmological constraints. We also find that the measured B-mode COSEBIs are consistent with zero. We examine, using mock HSC-Y1 data, the consistency of our S8 constraints with those derived from the other cosmic shear two-point statistics, the power spectrum analysis by Hikage et al. (2019, PASJ, 71, 43) and the two-point correlation function analysis by Hamana et al. (2020, PASJ, 72, 16), which adopt the same HSC-Y1 shape catalog, and find that all the S8 constraints are consistent with each other, although the expected correlations between derived S8 constraints are weak.
Collision of two interacting electrons on a mesoscopic beam splitter: Exact solution in the classical limit

Experiments on collisions of isolated electrons guided along the edges in quantum Hall setups can mimic mixing of photons with the important distinction that electrons are charged fermions. In the so-called electronic Hong-Ou-Mandel (HOM) setup uncorrelated pairs of electrons are injected towards a beamsplitter. If the two electron wave packets were identical, Fermi statistics would force the electrons to scatter to different detectors, yet this quantum antibunching may be confounded by Coulomb repulsion. Here we model an electronic HOM experiment using a quadratic 2D saddle point potential for the beamsplitter and unscreened Coulomb interaction between the two injected electrons subjected to a strong out-of-plane magnetic field. We show that classical equations of motion for the drift dynamics of electrons' guiding centers take on the form of Hamilton equations for canonically conjugated variables subject to the saddle point potential and the Coulomb potential where the dynamics of the center-of-mass coordinate and the relative coordinate separate. We use these equations to determine collision outcomes in terms of a few experimentally tuneable parameters: the initial energies of the uncorrelated electrons, relative time delay of injection and the shape of the saddle point potential. A universal phase diagram of deterministic bunching and antibunching scattering outcomes is presented with a single energy scale characterizing the increase of the effective barrier height due to interaction of coincident electrons. We suggest clear-cut experimental strategies to detect the predicted effects and give analytical estimates of conditions when the classical dynamics is expected to dominate over quantum effects.
Fully self-consistent optimized effective potentials from a convex minimization problem

The optimized effective potential method is formulated as a convex minimization problem. This formulation does not require assumptions about v-representability nor functional differentiability. The formulation provides a natural framework for fully self-consistent calculations, where both a Kohn–Sham system with a non-local potential and an additional system with a local potential are jointly optimized. The formulation is also well suited for extensions to other flavors of densityfunctional theory, e.g., current-density functional theory, where additional potentials besides the electrostatic potential are added.
Inductive Matrix Completion: No Bad Local Minima and a Fast Algorithm

The inductive matrix completion (IMC) problem is to recover a low rank matrix from few observed entries while incorporating prior knowledge about its row and column subspaces. In this work, we make three contributions to the IMC problem: (i) we prove that under suitable conditions, the IMC optimization landscape has no bad local minima; (ii) we derive a simple scheme with theoretical guarantees to estimate the rank of the unknown matrix; and (iii) we propose GNIMC, a simple Gauss-Newton based method to solve the IMC problem, analyze its runtime and derive recovery guarantees for it. The guarantees for GNIMC are sharper in several aspects than those available for other methods, including a quadratic convergence rate, fewer required observed entries and stability to errors or deviations from low-rank. Empirically, given entries observed uniformly at random, GNIMC recovers the underlying matrix substantially faster than several competing methods.
The Study on a Propulsion System by Fin Stroke:(The Development of Fin Ship)

The purpose of this paper is to study the problem which a propulsion method by fin stroke like fish and dolphins is practically applied to the propulsive system of ships. The Fin Ship, which mounts a dolphin-style oscillating wing apparatus under the bottom of the ship, is made for trial and a feasibility test from the engineering stand-point is carried out.The Fin Ship has the following merits; it is free from rolling and pitching of the ship; the danger of one being involved into the rotating screw can be eliminated; contamination of water resulting from the screw stirring up water can be prevented; the propulsive efficiency which gives about 66% in low frequency range is high compared with that of conventional small propellers.It is found that this new propulsion system has great possibility to be applied for low speed ships.
Co-administration of Favipiravir and the Remdesivir Metabolite GS-441524 Effectively Reduces SARS-CoV-2 Replication in the Lungs of the Syrian Hamster Model

During a pandemic, repurposing drugs that are approved for other diseases is a quick and realistic treatment option. In this study, we found that co-administration of favipiravir and the remdesivir metabolite GS-441524 more effectively blocked SARS-CoV-2 replication in the lungs of Syrian hamsters than either favipiravir or GS-441524 alone as part of a prophylactic or therapeutic regimen. ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide since December 2019, causing coronavirus disease 2019 (COVID-19). Although vaccines for this virus have been developed rapidly, repurposing drugs approved to treat other diseases remains an invaluable treatment strategy. Here, we evaluated the inhibitory effects of drugs on SARS-CoV-2 replication in a hamster infection model and in in vitro assays. Favipiravir significantly suppressed virus replication in hamster lungs. Remdesivir inhibited virus replication in vitro, but was not effective in the hamster model. However, GS-441524, a metabolite of remdesivir, effectively suppressed virus replication in hamsters. Co-administration of favipiravir and GS-441524 more efficiently reduced virus load in hamster lungs than did single administration of either drug for both the prophylactic and therapeutic regimens; prophylactic co-administration also efficiently inhibited lung inflammation in the infected animals. Furthermore, pretreatment of hamsters with favipiravir and GS-441524 effectively protected them from virus transmission via respiratory droplets upon exposure to infected hamsters. Repurposing and co-administration of antiviral drugs may help combat COVID-19. IMPORTANCE During a pandemic, repurposing drugs that are approved for other diseases is a quick and realistic treatment option. In this study, we found that co-administration of favipiravir and the remdesivir metabolite GS-441524 more effectively blocked SARS-CoV-2 replication in the lungs of Syrian hamsters than either favipiravir or GS-441524 alone as part of a prophylactic or therapeutic regimen. Prophylactic co-administration also reduced the severity of lung inflammation. Moreover, co-administration of these drugs to naive hamsters efficiently protected them from airborne transmission of the virus from infected animals. Since both drugs are nucleotide analogs that interfere with the RNA-dependent RNA polymerases of many RNA viruses, these findings may also help encourage co-administration of antivirals to combat future pandemics.
The Staphylococcus aureus CidA and LrgA Proteins Are Functional Holins Involved in the Transport of By-Products of Carbohydrate Metabolism

The Staphylococcus aureus cidABC and lrgAB operons represent the founding members of a large, highly conserved family of genes that span multiple kingdoms of life. Despite the fact that they have been shown to be involved in bacterial PCD during biofilm development, very little is known about the molecular/biochemical functions of the proteins they encode. ABSTRACT The Staphylococcus aureus cidABC and lrgAB operons encode members of a well-conserved family of proteins thought to be involved in programmed cell death (PCD). Based on the structural similarities that CidA and LrgA share with bacteriophage holins, we have hypothesized that these proteins function by forming pores within the cytoplasmic membrane. To test this, we utilized a “lysis cassette” system that demonstrated the abilities of the cidA and lrgA genes to support bacteriophage endolysin-induced cell lysis. Typical of holins, CidA- and LrgA-induced lysis was dependent on the coexpression of endolysin, consistent with the proposed holin-like functions of these proteins. In addition, the CidA and LrgA proteins were shown to localize to the surface of membrane vesicles and cause leakage of small molecules, providing direct evidence of their hole-forming potential. Consistent with recent reports demonstrating a role for the lrgAB homologues in other bacterial and plant species in the transport of by-products of carbohydrate metabolism, we also show that lrgAB is important for S. aureus to utilize pyruvate during microaerobic and anaerobic growth, by promoting the uptake of pyruvate under these conditions. Combined, these data reveal that the CidA and LrgA membrane proteins possess holin-like properties that play an important role in the transport of small by-products of carbohydrate metabolism. IMPORTANCE The Staphylococcus aureus cidABC and lrgAB operons represent the founding members of a large, highly conserved family of genes that span multiple kingdoms of life. Despite the fact that they have been shown to be involved in bacterial PCD, very little is known about the molecular/biochemical functions of the proteins they encode. The results presented in this study reveal that the cidA and lrgA genes encode proteins with bacteriophage holin-like functions, consistent with their roles in cell death. However, these studies also demonstrate that these operons are involved in the transport of small metabolic by-products of carbohydrate metabolism, suggesting an intriguing link between these two seemingly disparate processes.
An Analysis of the Novel Fluorocycline TP-6076 Bound to Both the Ribosome and Multidrug Efflux Pump AdeJ from Acinetobacter baumannii

Treatment of antibiotic-resistant organisms such as A. baumannii represents an ongoing issue for modern medicine. The multidrug efflux pump AdeJ serves as a major resistance determinant in A. baumannii through its action of extruding antibiotics from the cell. ABSTRACT Antibiotic resistance among bacterial pathogens continues to pose a serious global health threat. Multidrug-resistant (MDR) strains of the Gram-negative organism Acinetobacter baumannii utilize a number of resistance determinants to evade current antibiotics. One of the major resistance mechanisms employed by these pathogens is the use of multidrug efflux pumps. These pumps extrude xenobiotics directly out of bacterial cells, resulting in treatment failures when common antibiotics are administered. Here, the structure of the novel tetracycline antibiotic TP-6076, bound to both the Acinetobacter drug efflux pump AdeJ and the ribosome from Acinetobacter baumannii, using single-particle cryo-electron microscopy (cryo-EM), is elucidated. In this work, the structure of the AdeJ–TP-6076 complex is solved, and we show that AdeJ utilizes a network of hydrophobic interactions to recognize this fluorocycline. Concomitant with this, we elucidate three structures of TP-6076 bound to the A. baumannii ribosome and determine that its binding is stabilized largely by electrostatic interactions. We then compare the differences in binding modes between TP-6076 and the related tetracycline antibiotic eravacycline in both targets. These differences suggest that modifications to the tetracycline core may be able to alter AdeJ binding while maintaining interactions with the ribosome. Together, this work highlights how different mechanisms are used to stabilize the binding of tetracycline-based compounds to unique bacterial targets and provides guidance for the future clinical development of tetracycline antibiotics. IMPORTANCE Treatment of antibiotic-resistant organisms such as A. baumannii represents an ongoing issue for modern medicine. The multidrug efflux pump AdeJ serves as a major resistance determinant in A. baumannii through its action of extruding antibiotics from the cell. In this work, we use cryo-EM to show how AdeJ recognizes the experimental tetracycline antibiotic TP-6076 and prevents this drug from interacting with the A. baumannii ribosome. Since AdeJ and the ribosome use different binding modes to stabilize interactions with TP-6076, exploiting these differences may guide future drug development for combating antibiotic-resistant A. baumannii and potentially other strains of MDR bacteria.
Maintaining a focus on opportunities at work: The interplay between age, job complexity, and the use of selection, optimization, and compensation strategies

The concept of focus on opportunities describes how many new goals, options, and possibilities employees believe to have in their personal future at work. This study investigated the specific and shared effects of age, job complexity, and the use of successful aging strategies called selection, optimization, and compensation (SOC) in predicting focus on opportunities. Results of data collected from 133 employees of one company (mean age = 38 years, SD = 13, range 16–65 years) showed that age was negatively, and job complexity and use of SOC strategies were positively related to focus on opportunities. In addition, older employees in high-complexity jobs and older employees in low-complexity jobs with high use of SOC strategies were better able to maintain a focus on opportunities than older employees in low-complexity jobs with low use of SOC strategies.
Shining a Light on the Shadows: Endogenous Trade Structure and the Growth of an Online Illegal Market

How do illegal markets grow and develop? Using unique transaction-level data on 7,205 market actors and 16,847 illegal drug exchanges on a “darknet” drug market, the authors evaluate the network processes that shape online illegal drug trade and promote the growth of online illegal drug markets. Contrary to past research on online markets, the authors argue that the high-risk context of illegal trade enhances market actors’ reliance on social relationships that emerge endogenously from transaction networks. The findings reveal a highly structured trade network characterized by dense clustering and frequent recurrent drug exchange. Dynamic network models reveal that both embeddedness and closure in exchange structure increase the hazard rate of illegal drug trade, with effect sizes comparable to formal reputations. These effects are pronounced in the early stages of market development but wane once the market reaches maturity. These findings demonstrate the powerful, temporally contingent, influence of transaction networks on illegal trade in online markets and reveal how endogenous networks of economic relations can promote risky exchange under conditions of relative anonymity and illegality.
The Spatial Separation of Callistopteris baldwinii (Hymenophyllaceae) Sporophytes and Gametophytes Along Elevational Gradients in Hawai‘i

Abstract. Ferns and lycophytes are unique among land plants in having two independent life stages, the haploid gametophyte generation and the diploid sporophyte generation. While in most species the sporophyte is the dominant, long-lived portion of the life cycle, in some ferns the gametophyte is capable of sustained vegetative growth, and a number of species produce sporophytes only in parts of their geographic range (a pattern known as the separation of generations). One such species is the Hawaiian filmy fern Callistopteris baldwinii, whose growth form varies across elevational gradients. This species occurs as independent gametophytes near sea level, produces dwarfed sporophytes at mid elevations, and at the highest elevations—where precipitation is greatest due to the orographic uplift of trade winds—it grows as large, mature sporophytes. We measured temperature, relative humidity, and precipitation for several populations of this fern on the island of O‘ahu in Hawai‘i to determine whether these environmental factors may influence the spatial separation of generations exhibited by C. baldwinii on the island. Our results indicate that temperature and precipitation vary across life stages of C. baldwinii, underscoring the key role environmental conditions play in the completion of the fern life cycle.
More on the Spread of Nonnative Ferns in Georgia and the Southeastern United States

Abstract. Relative to other vascular plants, ferns have been overlooked with respect to the potential for nonnatives to spread into natural areas and potentially displace native species. An unusual site in the Piedmont of northeast Georgia was found to harbor two species of nonnative ferns that have clearly become naturalized. A third species at the site represents the appearance in a natural setting of another nonnative fern species whose cultivars and hybrids are being more widely planted as ornamentals. Examination of herbarium specimens from Georgia and the Southeastern United States clarified the status of some earlier records and some overlooked records, based on misidentifications or questionable status as naturalized. The species involved (Arachniodes simplicior, Polystichum polyblepharum, and Anisocampium niponicum (=Athyrium niponicum)) are all introductions from temperate regions in East Asia and probably represent escapes from cultivation via spores. The appearance of these species in natural communities raises questions about their potential to spread farther and to become pests by crowding out native flora. The invasive potential of these three species and five other species discussed in a previous paper is evaluated based on field observations as well as information about their status as an epiphyte or ground dweller, reproductive plasticity, ecological requirements, and popularity as horticultural ornamentals.