Miracle-dz/UniFAR-FTUs huggingface dataset:
SARS-CoV-2 Transmission from Human to Pet and Suspected Transmission from Pet to Human, Thailand

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been the cause of human pandemic infection since late 2019. SARS-CoV-2 infection in animals has also been reported both naturally and experimentally, rendering awareness about a potential source of infection for one health concern. ABSTRACT Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been the cause of human pandemic infection since late 2019. SARS-CoV-2 infection in animals has also been reported both naturally and experimentally, rendering awareness about a potential source of infection for one health concern. Here, we describe an epidemiological investigation of SARS-CoV-2 infection in 639 cats and 224 dogs throughout multiple waves of COVID-19 outbreaks in Thailand. To indicate the potential source of infection, we performed SARS-CoV-2 genomic sequencing of samples obtained from pets and contacted humans, combined with in-depth interviews to support the epidemiological investigation. In the tested animals, SARS-CoV-2 RNA was present in 23 cases (19 cats and 4 dogs). Whole-genome sequencing of selected samples showed various SARS-CoV-2 variants of concern, which included the original European lineage (B.1), Alpha (B.1.1.7), Delta (B.1.617), and Omicron (BA.2). Among SARS-CoV-2-positive pets, 34.78% had evidence of contact with infected humans. Together with genomic analysis and an overlapping timeline, we revealed evidence of viral transmission from infected humans as the primary source, which spread to household cats via an undefined mode of transmission and most likely circulated between cohoused cats and caretakers within the weeks before the investigation. The SARS-CoV-2 surface glycoprotein (spike gene) obtained from caretakers of individual cats contained sequence signatures found in the sequences of infected cats, indicating possible exposure to the virus excreted by cats. Although pet-to-human transmission of SARS-CoV-2 is considered relatively rare, our study provides suspected episodes of human infection from animals that were initially infected through contact with infected humans.
Multi-Regulation Computing: Examining the Legal and Policy Questions That Arise From Secure Multiparty Computation

This work examines privacy laws and regulations that limit disclosure of personal data, and explores whether and how these restrictions apply when participants use cryptographically secure multi-party computation (MPC). By protecting data during use, MPC offers the promise of conducting data science in a way that (in some use cases) meets or even exceeds most people's conceptions of data privacy. With MPC, it is possible to correlate individual records across multiple datasets without revealing the underlying records, to conduct aggregate analysis across datasets which parties are otherwise unwilling to share for competitive reasons, and to analyze aggregate statistics across datasets which no individual party may lawfully hold. However, most adoptions of MPC to date involve data that is not subject to privacy protection under the law. We posit that a major impediment to the adoption of MPC - on the data that society has deemed most worthy of protection - is the difficulty of mapping this new technology onto the design principles of data privacy laws. While a computer scientist might reasonably believe that transforming any data analysis into its privacy-protective variant using MPC is a clear win, we show in this work that the technological guarantees of MPC do not directly imply compliance with privacy laws. Specifically, a lawyer will likely want to ask several important questions about the pre-conditions that are necessary for MPC to succeed, the risk that data might inadvertently or maliciously be disclosed to someone other than the output party, and what recourse to take if this bad event occurs. We have two goals for this work: explaining why the privacy law questions are nuanced and that the lawyer is correct to proceed cautiously, and providing a framework that lawyers can use to reason systematically about whether and how MPC implicates data privacy laws in the context of a specific use case. Our framework revolves around three questions: a definitional question on whether the encodings still constitute 'personal data,' a process question about whether the act of executing MPC constitutes a data disclosure event, and a liability question about what happens if something goes wrong. We conclude by providing advice to regulators and suggestions to early adopters to spur uptake of MPC. It is our hope that this work provides the first step toward a methodology that organizations can use when contemplating the use of MPC.
Definitions of Esports: A Systematic Review and Thematic Analysis

The esports market has been growing exponentially has been growing exponentially with much interest from industry and academia. Perhaps because of this growth, there is a lack of agreement on what esports actually encompasses. We conducted a systematic review of 461 peer reviewed, full papers that provide a definition of esports. Findings highlighted the growth of the esports field across different domains, and increasing global interest in esports, but a lack of consensus regarding definition of the term. Through thematic analysis we identified nine dimensions across esports definitions. We critically assess these dimensions in terms of their representativeness and utility in describing the multifaceted nature of esports. Our work may help create a shared understanding of what esports is- and is not-capturing a diversity of experiences within organized competitive gaming and supporting continued research growth in this increasingly important domain.
Critical transverse forces in weakly pinned driven vortex systems

We present simulation results of the moving Bragg glass regime of a driven two-dimensional vortex system in the presence of a smoothly varying weak pinning potential. We study the critical transverse force and (i) demonstrate that it can be an order of magnitude larger than previous estimates and (ii) show that it is still observable when the system is driven along low higher-order lattice vectors. We confirm theoretical predictions that the critical transverse force is the order parameter of the so-called moving glass phase, and provide data to support experimentalists verifying the existence of a critical transverse force.
Values throughout the Game Space

Pro-social themes like empathy and wellbeing are gaining popularity within games to contrast the medium's stigmatised explorations of themes like violence, often to catalyse reflection or even change players' beliefs surrounding complex scenarios. These abstract themes can be classified as a game's "values": elements that are "useful or important" to game designers and their audience. Exploration of values in games was spearheaded by Values at Play, which described how values manifest in games and advocated for their explicit consideration within games and their discourse. Frameworks such as empathy, ethical, and anti-oppressive design all discuss similar values, but present ontological diversity that makes it difficult to collate games and frameworks under the values-conscious design umbrella. Such frameworks also often focus on design approaches and small-scale prototypes but pay less attention to how values influence aspects like publication and play. As such, the present research examines values within each stage of a game's lifecycle: design, development, publication, interaction, and reportage. Doing so provides an understanding of values in multiple game contexts. This provides new perspectives that form the basis of a taxonomy for values in games, which is then presented alongside practical questions for values-conscious designers, publishers, and players to guide its use.
Compilation of dynamic sparse tensor algebra

Many applications, from social network graph analytics to control flow analysis, compute on sparse data that evolves over the course of program execution. Such data can be represented as dynamic sparse tensors and efficiently stored in formats (data layouts) that utilize pointer-based data structures like block linked lists, binary search trees, B-trees, and C-trees among others. These specialized formats support fast in-place modification and are thus better suited than traditional, array-based data structures like CSR for storing dynamic sparse tensors. However, different dynamic sparse tensor formats have distinct benefits and drawbacks, and performing different computations on tensors that are stored in different formats can require vastly dissimilar code that are not straightforward to correctly implement and optimize. This paper shows how a compiler can generate efficient code to compute tensor algebra operations on dynamic sparse tensors that may be stored in a wide range of disparate formats. We propose a language for precisely specifying recursive, pointer-based data structures, and we show how this language can express many different dynamic data structures, including all the ones named above as well as many more. We then describe how, given high-level specifications of such dynamic data structures, a compiler can emit code to efficiently access and compute on dynamic sparse tensors that are stored in the aforementioned data structures. We evaluate our technique and find it generates efficient dynamic sparse tensor algebra kernels that have performance comparable to, if not better than, state-of-the-art libraries and frameworks such as PAM, Aspen, STINGER, and Terrace. At the same time, our technique supports a wider range of tensor algebra operations---such as those that simultaneously compute with static and dynamic sparse tensors---than Aspen, STINGER, and Terrace, while also achieving significantly better performance than PAM for those same operations.
MemoCraft: An Easy Design System for Interactive Edutainment

This article presents an easy design system, MemoCraft, for developing edutainment games. Teachers can visualize abstract and systematical knowledge as icons in embedded virtual spaces to build a digital game. Students learn knowledge and do quizzes by wandering and triggering icons with multi-modal interactions. User studies shows that MemoCraft enables common teachers to develop digital games easily, and motivates children to learn.
GDAP1 binds 4-hydroxynonenal, the toxic end-product of lipid peroxidation, using its GST-like binding pocket

GDAP1 (Ganglioside-induced differentiation-associated protein 1) is a novel member of the GST superfamily of detoxifying enzymes that is anchored to the outer mitochondrial membrane. GDAP1 mutations and changes in expression levels result in the inherited neuropathy Charcot-Marie-Tooth (CMT) disease, types 2K, 4A and 4H. GDAP1 activity has been associated with many mitochondrial functions however direct molecular interactions underpinning these connections have remained elusive. Here we establish that GDAP1 can bind 4-hydroxynonenal (4HNE), a toxic end-product of lipid peroxidation. 4HNE binding requires the α-loop, a large sequence motif that is inserted within the substrate recognition domain and is unique to GDAP1. In human cells, GDAP1 overexpression plays a cytoprotective role against oxidative stress. This effect is lost upon deletion of the α-loop. Lastly, we demonstrate that a CMT-causing mutant that destabilizes α-loop positioning also results in a decrease in 4HNE binding affinity. Together these results establish 4HNE as the biological ligand for GDAP1, provide mechanistic insight into 4HNE binding, and demonstrate that altered 4HNE recognition is the likely mechanism underlying CMT-causing mutants such as T157P near the 4HNE binding site.
Rotation, Convective Core Overshooting, and Period Changes in Classical Cepheid Stellar Evolution Models

Classical Cepheids are powerful probes of both stellar evolution and near-field cosmology thanks to their great luminosities, pulsations, and their adherence to the Leavitt (period–luminosity) Law. However, there still exist a number of questions regarding their evolution, such as the roles of rotation, convective core overshooting, and winds. ln particular, how do these processes impact Cepheid evolution and the predicted fundamental properties such as stellar mass? In this work, we compare a sample of Cepheids with measured rates of period change with new evolution models to test the impact of these first two processes. In our previous study we found that enhanced mass loss is crucial for describing the sample, and here we continue that analysis but for rotational mixing and core overshooting. We show that while rotation is important for stellar evolution studies, rotation itself is insufficient to model the distribution of period change rates from the observed sample. On the other hand, convective core overshooting is needed to explain the magnitude of the rates of period change, but does not explain the number of stars with positive and negative period change rates. In conclusion, we determine that convective core overshooting and stellar rotation alone are not enough to account for the observed distribution of Cepheid rates of period change and another mechanism, such as pulsation-driven mass loss, may be required.
Mining impactful discoveries from the biomedical literature

Motivation Literature-Based Discovery (LBD) aims to help researchers to identify relations between concepts which are worthy of further investigation by text-mining the biomedical literature. While the LBD literature is rich and the field is considered mature, standard practice in the evaluation of LBD methods is methodologically poor and has not progressed on par with the domain. The lack of properly designed and decent-sized benchmark dataset hinders the progress of the field and its development into applications usable by biomedical experts. Results This work presents a method for mining past discoveries from the biomedical literature. It leverages the impact made by a discovery, using descriptive statistics to detect surges in the prevalence of a relation across time. This method allows the collection of a large amount of time-stamped discoveries which can be used for LBD evaluation or other applications. The validity of the method is tested against a baseline representing the state of the art “time sliced” method. Availability The source data used in this article are publicly available. The implementation and the resulting data are published under open-source license: https://github.com/erwanm/medline-discoveries (code) https://zenodo.org/record/5888572 (datasets). An online exploration tool is also provided at https://brainmend.adaptcentre.ie/. Contact erwan.moreau@adaptcentre.ie
Entanglement generation between a charge qubit and its bosonic environment during pure dephasing: Dependence on the environment size

We study entanglement generated between a charge qubit and a bosonic bath due to their joint evolution which leads to pure dephasing of the qubit. We tune the parameters of the interaction, so that the decoherence is quantitatively independent of the number of bosonic modes taken into account and investigate, how the entanglement generated depends on the size of the environment. A second parameter of interest is the mixedness of the initial state of the environment which is controlled by temperature. We show analytically that for a pure initial state of the environment, entanglement does not depend on environment size. For mixed initial states of the environment, the generated entanglement decreases with the increase of environment size. This effect is stronger for larger temperatures, when the environment is initially more mixed, but in the limit of an infinitely large environment, no entanglement is created at any finite temperature.
DMD antisense oligonucleotide mediated exon skipping efficiency is affected by flanking intron retention time and target position within the exon

Mutations in the DMD gene are causative for Duchenne muscular dystrophy (DMD). Antisense oligonucleotide (AON) mediated exon skipping to restore disrupted dystrophin reading frame is a therapeutic approach that allows production of a shorter but functional protein. As DMD causing mutations can affect most of the 78 exons encoding dystrophin, a wide variety of AONs are needed to treat the patient population. Design of AONs is largely guided by trial-and-error, and it is yet unclear what defines the skippability of an exon. Here, we use a library of phosphorodiamidate morpholino oligomer (PMOs) AONs of similar physical properties to test the skippability of a large number of DMD exons. The DMD transcript is non-sequentially spliced, meaning that certain introns are retained longer in the transcript than downstream introns. We tested whether the relative intron retention time has a significant effect on AON efficiency, and found that targeting an exon flanked at its 5’ by an intron that is retained in the transcript longer (‘slow’ intron) leads to overall higher exon skipping efficiency than when the 5’ intron is ‘fast’. Regardless of splicing speed of flanking introns, we find that positioning an AON closer to the 5’ of the target exon leads to higher exon skipping efficiency opposed to targeting an exons 3’-end. The data enclosed herein can be of use to guide future target selection and preferential AON binding sites for both Duchenne and other disease amenable by exon skipping therapies.
Mapping the “missing” pathways of the anterior cingulate cortex in the human brain

The anterior cingulate cortex (ACC) is functionally closely related with the insula and the ventral lateral prefrontal cortex (vlPFC). Extensive work on their functional relationships has led to the salience network theory and advanced understanding of value-based learning and decision making. However, the anatomical connections between the ACC and the two regions remain unknown in the human brain. Despite the anatomical ground truth established by nonhuman primate (NHP) tract-tracing, diffusion magnetic resonance imaging (dMRI) has not seen success identifying homologous pathways in humans. In this study we show that the negative finding does not reflect a cross-species discrepancy but rather a technical issue. We used NHP dMRI as a bridge to compare the ground-truth pathways in NHPs and dMRI-derived pathways in humans. The insight from NHP data helped pinpoint a bias in fiber orientation distribution functions (fODFs) caused by the disproportion of anterior-posterior vs. medial-lateral fibers in the human brain. Guided by this information, we successfully recovered the ACC-insula and ACC-vlPFC pathways that followed the same trajectories as in the NHP dMRI and tract-tracing data. Our findings provide an anatomical basis for the functional interactions among the ACC, the insula and the vlPFC.
Early path dominance as a principle for neurodevelopment

We perform targeted attack, a systematic computational unlinking of the network, to analyze its effects on global communication across the network through its giant cluster. Across diffusion magnetic resonance images from individuals in the UK Biobank, Adolescent Brain Cognitive Development Study and Developing Human Connectome Project, we find that targeted attack procedures on increasing white matter tract lengths and densities are remarkably invariant to aging and disease. Time-reversing the attack computation suggests a mechanism for how brains develop, for which we derive an analytical equation using percolation theory. Based on a close match between theory and experiment, our results demonstrate that tracts are limited to emanate from regions already in the giant cluster and tracts that appear earliest in neurodevelopment are those that become the longest and densest. Significance As brains develop through neural growth and specialization, what mechanism ensures that new neurons are integrated into a fully connected brain, avoiding “bridges to nowhere”? Here, we study brain structure development from the perspective of percolation, a global measure of communication. Analyzing over 35,000 diffusion MRI scans on human individuals, from newborns to adults, we identify the following rules of brain neurogenesis through percolation theory: earlier tracts become longer and denser while maintaining a giant cluster. This signature, invariant to age or mental health, suggests a fundamental condition for the brain to function as an emergent whole.
Evaluating the topological charge density with the symmetric multi-probing method

We evaluated the topological charge density of SU(3) gauge fields on lattice by calculating the trace of overlap Dirac matrix employing symmetric multi-probing(SMP) method with 3 modes. Since the topological charge $Q$ for a given lattice configuration must be an integer number, it's easy to estimate the systematic error (the deviation of $Q$ to nearest integer). The results showed high efficiency and accuracy in calculating the trace of the inverse of a large sparse matrix with locality by using SMP sources, compared with that using point sources. We also showed the correlation between the errors and probing scheme parameter $r_{\mathrm{min}}$ as well as lattice volume $N_{L}$ and lattice spacing $a$. It was found that the computing time of calculating the trace by employing SMP sources is less dependent on $N_{L}$ than that by using point sources. Therefore the SMP method is very suitable for calculations on large lattices.
Q criterion for disc stability modified by external tidal field

The standard Q criterion (with Q > 1) describes the local stability of a disc supported by rotation and random motion. Most astrophysical discs, however, are under the influence of an external gravitational field which can affect their stability. A typical example is a galactic disc embedded in a dark matter halo. Here we do a linear perturbation analysis for a disc in an external field, and obtain a generalized dispersion relation and a modified stability criterion. An external field has two effects on the disc dynamics: first, it contributes to the unperturbed rotational field, and second, it adds a tidal field term in the stability parameter. A typical disruptive tidal field results in a higher modified Q value and hence leads to a more stable disc. We apply these results to the Milky Way, and to a low surface brightness galaxy UGC 7321. We find that in each case the stellar disc by itself is barely stable and it is the dark matter halo that stabilizes the disc against local, axisymmetric gravitational instabilities. This result has been largely missed so far because in practice the value for Q for a galactic disc is obtained in a hybrid fashion using the observed rotational field that is set by both the disc and the halo, and hence is higher than for a pure disc.