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Sensitive and reliable methylation assay is important for oncogentic studies and clinical applications. Here, a new methylation assay was developed by the use of adapter-dependent adapter in library preparation. This new assay avoids the use of bisulfite and provides a simple and highly sensitive scanning of methylation spectra of circulating free DNA and genomic DNA.

The pairing mechanism in an antiferromagnetic (AFM) bosonic $t$-$J$ model is investigated via large-scale density matrix renormalization group calculations. In contrast to the competing orders in the fermionic $t$-$J$ model, we discover that a pair density wave (PDW) of tightly bound hole pairs coexists with the AFM order forming a ``supersolid'' at small doping in the bosonic model. The pairing order collapses at larger doping to a superfluid of single-boson condensation with the spin background polarized to a ferromagnetic (FM) order simultaneously. This pairing phase will disappear once a hidden quantum many-body Berry phase in the model is artificially switched off. Such a Berry phase, termed the phase string, introduces the sole ``sign problem'' in this bosonic model and imposes quantum phase frustration in the interference pattern between spin and charge degrees of freedom. Only via tightly pairing of doped holes, can such quantum frustration be most effectively erased in an AFM background. By contrast, the pairing vanishes as such a Berry phase trivializes in an FM background or is switched off by a sign-problem-free model (the Bose-Hubbard model at large $U$). The pairing mechanism proposed here is inherently quantum and many-body, stemming from exotic interference patterns caused by strong correlation effects, which is distinct from the semi-classical mechanisms based on bosonic fluctuations. Experimental schemes have been recently proposed to realize the bosonic $t$-$J$ model on ultracold Rydberg atom arrays, offering a useful platform to test the present unconventional pairing mechanism, which is also relevant to the fermionic case associated with high-temperature superconductors., Comment: 28 pages, 4+11 figures

Deep and low mass-ratio contact binaries (DLMCBs) are believed to be in the final stage of their contact phase, potentially leading to the formation of fast-rotating single stars such as FK Com-type stars and blue stragglers, as well as luminous red novae. These systems serve as an excellent laboratory for studying stellar coalescence and merging processes. Our search for DLMCBs began in 2004 and has since identified a group of such systems. Together with that collected from the literature, more than 100 DLMCBs have been detected so far. Half of them have had their periods investigated based on O-C curves. Some have shown period increases, while others have exhibited period decreases. Among them, more than half DLMCBs have cyclic variations, suggesting the possibility of the existence of a third body orbiting around the DLMCBs. Furthermore, with more data obtained extending the span of the O-C curve, more cyclic variations could be detected. The high proportion of signs of the presence of third bodies makes them an essential factor to consider when studying the merger of contact binaries., Comment: 8 pages, 3 figures, published in ASP Conference Series, Vol. 536, proceedings of the Twelfth Pacific Rim Conference on Stellar Astrophysics

The exclusive production of $J/\psi$ through Higgs boson radiative decay may serve a clean channel to extracting the charm quark Yukawa coupling. We calculate the two-loop QCD corrections to $H\rightarrow J/\psi(\Upsilon)+\gamma$ using an optimized nonrelativistic QCD (NRQCD) approach. We compute the ${\cal O}(\alpha_s^2)$ correction in the direct channel, where Higgs directly couples to $c\bar{c}$, as well as the ${\cal O}(\alpha_s)$ correction in the indirect channel, {\it viz.}, $H\to\gamma^*\gamma$ followed by the virtual photon fragmentation into $J/\psi$. Incorporating the destructive interference between the direct and indirect channels, we present to date the most accurate predictions for Higgs boson radiative decay into vector quarkonium, $\mathcal{B}(H\rightarrow J/\psi+\gamma) = 3.27_{-0.07}^{+0.30}{}^{+0.06}_{-0.06}{}_{-0.13}^{+0.13}\times 10^{-6}$, and $\mathcal{B}(H\rightarrow \Upsilon+\gamma)= 1.34_{-0.31}^{+0.75}{}^{+0.25}_{-0.20}{}^{+0.05}_{-0.05}\times 10^{-8}$., Comment: 12 pages, 4 figures, 3 tables

In recently years, a significant amount of research has been conducted on applying deep learning methods for glaucoma classification and detection. However, the explainability of those established machine learning models remains a big concern. In this research, in contrast, we learn from cognitive science concept and study how ophthalmologists judge glaucoma detection. Simulating experts' efforts, we propose a hierarchical decision making system, centered around a holistic set of carefully designed biomarker-oriented machine learning models. While biomarkers represent the key indicators of how ophthalmologists identify glaucoma, they usually exhibit latent inter-relations. We thus construct a time series model, named TRI-LSTM, capable of calculating and uncovering potential and latent relationships among various biomarkers of glaucoma. Our model is among the first efforts to explore the intrinsic connections among glaucoma biomarkers. We monitor temporal relationships in patients' disease states over time and to capture and retain the progression of disease-relevant clinical information from prior visits, thereby enriching biomarker's potential relationships. Extensive experiments over real-world dataset have demonstrated the effectiveness of the proposed model., Comment: 9 pages, 4 images

Due to the rapid growth of scientific publications, identifying all related reference articles in the literature has become increasingly challenging yet highly demanding. Existing methods primarily assess candidate publications from a static perspective, focusing on the content of articles and their structural information, such as citation relationships. There is a lack of research regarding how to account for the evolving impact among papers on their embeddings. Toward this goal, this paper introduces a temporal dimension to paper recommendation strategies. The core idea is to continuously update a paper's embedding when new citation relationships appear, enhancing its relevance for future recommendations. Whenever a citation relationship is added to the literature upon the publication of a paper, the embeddings of the two related papers are updated through a Temporal Graph Neural Network (TGN). A learnable memory update module based on a Recurrent Neural Network (RNN) is utilized to study the evolution of the embedding of a paper in order to predict its reference impact in a future timestamp. Such a TGN-based model learns a pattern of how people's views of the paper may evolve, aiming to guide paper recommendations more precisely. Extensive experiments on an open citation network dataset, including 313,278 articles from https://paperswithcode.com/about PaperWithCode, have demonstrated the effectiveness of the proposed approach., Comment: 10 pages, 4 figures, accepted by SDU@AAAI-2024. The AAAI Workshop on Scientific Document Understanding (2024)

It has been recently demonstrated that lightcone distribution amplitudes (LCDAs) for a heavy meson, defined in the heavy quark limit, can be extracted by simulating quasi-distribution amplitudes on the lattice with a large meson momentum $P^z$. This extraction involves a two-step procedure. In the first-step, the quasi-distribution amplitudes are matched onto the QCD LCDAs in the large $P^z$ limit. In the second step, the QCD LCDAs are matched onto the desired LCDAs defined in HQET. In this work, we present the $m_H^{2n}/(P^z)^{2n}$ and $\Lambda_\text{QCD}^2/(P^z)^2$ corrections in the first step with $m_H$ being the heavy meson mass. To account for $m_H^{2n}/(P^z)^{2n}$ corrections, we employ two methods: the moment relation that can provide mass corrections to all orders, and a leading-twist projector that gives the leading-order mass corrections. For the $\Lambda_\text{QCD}^2/(P^z)^2$ corrections, we employ a renormalon model that addresses the renormalon ambiguity stemming from the divergence of the perturbative series. We adopt two parametrizations for QCD LCDAs to conduct a numerical analysis. The results suggest that these corrections are typically smaller than 20\% in most regions, and should be included in a precision analysis. These findings will serve as a valuable guide for future studies on heavy meson LCDAs, particularly in the context of Lattice QCD, where accounting for such corrections is crucial for improving the accuracy and reliability of the results., Comment: 12 pages,7 figures

Hi-C sequencing is widely used for analyzing chromosomal interactions. In this study, we propose "superimposed Hi-C" which features paired EcoP15I sites in a linker to facilitate sticky-end ligation with target DNAs. Superimposed Hi-C overcomes Hi-C's technical limitations, enabling the identification of single cell's chromosomal interactions.

Vision-language models (VLMs) like CLIP have demonstrated impressive zero-shot ability in image classification tasks by aligning text and images but suffer inferior performance compared with task-specific expert models. On the contrary, expert models excel in their specialized domains but lack zero-shot ability for new tasks. How to obtain both the high performance of expert models and zero-shot ability is an important research direction. In this paper, we attempt to demonstrate that by constructing a model hub and aligning models with their functionalities using model labels, new tasks can be solved in a zero-shot manner by effectively selecting and reusing models in the hub. We introduce a novel paradigm, Model Label Learning (MLL), which bridges the gap between models and their functionalities through a Semantic Directed Acyclic Graph (SDAG) and leverages an algorithm, Classification Head Combination Optimization (CHCO), to select capable models for new tasks. Compared with the foundation model paradigm, it is less costly and more scalable, i.e., the zero-shot ability grows with the sizes of the model hub. Experiments on seven real-world datasets validate the effectiveness and efficiency of MLL, demonstrating that expert models can be effectively reused for zero-shot tasks. Our code will be released publicly.

We present the first calculation of next-to-leading order (NLO) factorized QED contributions to the short-distance hard coefficients of inclusive lepton-hadron deep inelastic scattering (DIS) in a joint QCD and QED factorization approach. We demonstrate how the joint factorization consistently factorize all perturbative collinear sensitivities of partonic scattering in both QCD and QED into corresponding universal hadron and lepton distribution functions without the need of any parameters other than the standard factorization scale. We discuss the necessary modification to DGLAP-type evolution of the parton and lepton distribution functions in this joint factorization approach. We also discuss the potential impact of this joint factorization approach on the extraction of partonic information from lepton-hadron DIS., Comment: 6 pages, 2 figures; contributed talk to DIS2024

Fine-tuning large language models (LLMs) with high parameter efficiency for downstream tasks has become a new paradigm. Low-Rank Adaptation (LoRA) significantly reduces the number of trainable parameters for fine-tuning. Although it has demonstrated commendable performance, updating parameters within a single scale may not be the optimal choice for complex downstream tasks.In this paper, we extend the LoRA to multiple scales, dubbed as LoRA$^2$. We first combine orthogonal projection theory to train a set of LoRAs in two mutually orthogonal planes. Then, we improve the importance score algorithm, which reduce parameter sensitivity score calculations by approximately 98.5\%. By pruning singular values with lower importance scores, thereby enhancing adaptability to various downstream tasks. Extensive experiments are conducted on two widely used pre-trained models to validate the effectiveness of LoRA$^2$. Results show that it significantly reduces the number of trainable parameters to just 0.72\% compared to full fine-tuning, while still delivering highly impressive performance. Even when the parameters are further reduced to 0.17M, it still achieves comparable results to the baseline with 8 times more parameters. Our code is available here: https://anonymous.4open.science/r/LoRA-2-5B4C

We theoretically demonstrate that carbon nanoscrolls -- spirally wrapped graphene layers with open endpoints -- can be characterized by a large positive magnetoconductance. We show that when a carbon nanoscroll is subject to an axial magnetic field of ~ 10T, the ballistic conductance at low carrier densities of the nanoscroll has an increase of about 200%. Importantly, we find that this positive magnetoconductance is not only preserved but can be even enhanced in the presence of on-site disorder. We prove that the positive magnetoconductance comes about the emergence of magnetic field-induced zero energy modes, specific of rolled-up geometries. Our results establish curved graphene systems as a new material platform displaying sizable magnetoresistive phenomena., Comment: 13 pages, 4 figures

Materials with flat bands can serve as a promising platform to investigate strongly interacting phenomena. However, experimental realization of ideal flat bands is mostly limited to artificial lattices or moir\'e systems. Here we report a general way to construct one-dimensional (1D) flat bands in phosphorene nanoribbons (PNRs) with pentagonal nature: penta-hexa-PNRs and penta-dodeca-PNRs, wherein the corresponding 1D flat bands are directly verified by using angle-resolved photoemission spectroscopy. We confirm that the observed 1D flat bands originate from the electronic 1D zigzag and Lieb lattices, respectively, as revealed by the combination of bond-resolved scanning tunneling microscopy, scanning tunneling spectroscopy, tight-binding models, and first-principles calculations. Our study demonstrates a general way to construct 1D flat bands in 1D solid materials system, which provides a robust platform to explore strongly interacting phases of matter., Comment: 13 pages, 4 figures

Symptom phenotypes are one of the key types of manifestations for diagnosis and treatment of various disease conditions. However, the diversity of symptom terminologies is one of the major obstacles hindering the analysis and knowledge sharing of various types of symptom-related medical data particularly in the fields of Traditional Chinese Medicine (TCM). Objective: This study aimed to construct an Integrated Ontology of symptom phenotypes (ISPO) to support the data mining of Chinese EMRs and real-world study in TCM field. Methods: To construct an integrated ontology of symptom phenotypes (ISPO), we manually annotated classical TCM textbooks and large-scale Chinese electronic medical records (EMRs) to collect symptom terms with support from a medical text annotation system. Furthermore, to facilitate the semantic interoperability between different terminologies, we incorporated public available biomedical vocabularies by manual mapping between Chinese terms and English terms with cross-references to source vocabularies. In addition, we evaluated the ISPO using independent clinical EMRs to provide a high-usable medical ontology for clinical data analysis. Results: By integrating 78,696 inpatient cases of EMRs, 5 biomedical vocabularies, 21 TCM books and dictionaries, ISPO provides 3,147 concepts, 23,475 terms, and 55,552 definition or contextual texts. Adhering to the taxonomical structure of the related anatomical systems of symptom phenotypes, ISPO provides 12 top-level categories and 79 middle-level sub-categories. The validation of data analysis showed the ISPO has a coverage rate of 95.35%, 98.53% and 92.66% for symptom terms with occurrence rates of 0.5% in additional three independent curated clinical datasets, which can demonstrate the significant value of ISPO in mapping clinical terms to ontologies., Comment: 39 pages, 6 figures, 6 tables

Due to the rapid advancements in multimodal large language models, evaluating their multimodal mathematical capabilities continues to receive wide attention. Despite the datasets like MathVista proposed benchmarks for assessing mathematical capabilities in multimodal scenarios, there is still a lack of corresponding evaluation tools and datasets for fine-grained assessment in the context of K12 education in Chinese language. To systematically evaluate the capability of multimodal large models in solving Chinese multimodal mathematical problems, we propose a Chinese Multi-modal Math Skill Evaluation Benchmark, named CMMaTH, contraining 23k multimodal K12 math related questions, forming the largest Chinese multimodal mathematical problem benchmark to date. CMMaTH questions from elementary to high school levels, provide increased diversity in problem types, solution objectives, visual elements, detailed knowledge points, and standard solution annotations. We have constructed an open-source tool GradeGPT integrated with the CMMaTH dataset, facilitating stable, rapid, and cost-free model evaluation. Our data and code are available.

The electric resistivity is examined in the constrained Hilbert space of a doped Mott insulator, which is dictated by a non-Ioffe-Larkin composition rule due to the underlying mutual Chern-Simons topological gauge structure. In the low-temperature pseudogap phase, where holons remain condensed while spinons proliferate, the charge transport is governed by a chiral spinon excitation, comprising a bosonic spin-$1/2$ at the core of a supercurrent vortex. It leads to a vanishing resistivity with the "confinement" of the spinons in the superconducting phase but a low-$T$ divergence of the resistivity once the spinon confinement is disrupted by external magnetic fields. In the latter, the chiral spinons will generate a Hall number $n_H =$ doping concentration $\delta$ and a Nernst effect to signal an underlying long-range entanglement between the charge and spin degrees of freedom. Their presence is further reflected in thermodynamic quantities such as specific heat and spin susceptibility. Finally, in the high-temperature spin-disordered phase, it is shown that the holons exhibit a linear-$T$ resistivity by scattering with the spinons acting as free local moments, which generate randomized gauge fluxes as perceived by the charge degree of freedom., Comment: 6+6 pages, 6 figures

We compute the structure of flux $h/(2e)$ vortices in a d-wave superconductor which emerges from a higher temperature pseudogap metal. Such a transition is described by a continuum theory of the Higgs condensation of 2 flavors of charge $e$ bosons which are fundamentals of an emergent SU(2) gauge field. Period-2 charge order is present near the vortex center. Upon coupling the electrons to the superconducting and charge order parameters, we find that the electronic local density of states does not have a zero-bias peak, in contrast to BCS theory. But there are sub-gap peaks at positive and negative bias, and these exhibit anti-phase periodic spatial modulations, similar to observations in scanning tunneling microscopy experiments in the underdoped cuprates (K. Matsuba et al., J. Phys. Soc. Jpn. 76, 063704 (2007))., Comment: 32 pages, 10 figures

Density functional theory (DFT) has been a cornerstone in computational chemistry, physics, and materials science for decades, benefiting from advancements in computational power and theoretical methods. This paper introduces a novel, cloud-native application, Accelerated DFT, which offers an order of magnitude acceleration in DFT simulations. By integrating state-of-the-art cloud infrastructure and redesigning algorithms for graphic processing units (GPUs), Accelerated DFT achieves high-speed calculations without sacrificing accuracy. It provides an accessible and scalable solution for the increasing demands of DFT calculations in scientific communities. The implementation details, examples, and benchmark results illustrate how Accelerated DFT can significantly expedite scientific discovery across various domains.

Giant resonances (GRs) provide crucial insights into nuclear physics and astrophysics. Exciting GRs using particles like electrons is effective, yet the angular momentum (AM) transfer of electrons, including both intrinsic spin and orbital degrees of freedom in inelastic scattering, has never been studied. Here, we investigate AM transfer in GRs excited by plane-wave and vortex electrons, developing a comprehensive AM-resolved inelastic electron scattering theory. We find that even plane-wave electrons can model-independently extract transition strengths of higher multipolarity by selecting specific AM states of scattered electrons. Additionally, relativistic vortex electrons with orbital angular momentum (OAM) $\pm1$ can be efficiently generated. Vortex electrons can also be used to extract GR transition strength as in the plane-wave case, regardless of the position of nucleus relative to the beam axis. Furthermore, relativistic vortex electrons with larger OAM can be generated for on-axis nuclei due to AM conservation. Our method offers new perspectives for nuclear structure research and paves the way for generating vortex particles.

Topological dislocation modes resulting from the interplay between spatial dislocations and momentum-space topology have recently attracted significant interest. Here, we theoretically and experimentally demonstrate time-dislocation topological modes which are induced by the interplay between temporal dislocations and Floquet-band topology. By utilizing an extra physical dimension to represent the frequency-space lattice, we implement a two-dimensional Floquet higher-order topological phase and observe time-dislocation induced $\pi$-mode topological corner modes in a three-dimensional circuit metamaterial. Intriguingly, the realized time-dislocation topological modes exhibit spatial localization at the temporal dislocation, despite homogeneous in-plane lattice couplings across it. Our study opens a new avenue to explore the topological phenomena enabled by the interplay between real-space, time-space and momentum-space topology., Comment: 9 pages, 4 figures

In this paper, we study the quasi-two-body decays $B\to P f_0(500)\to P\pi^+\pi^-$ [with $P=(\pi, K, \eta, \eta^{\prime})$] within framework of perturbative QCD (PQCD) factorization approach. With the help of $\pi$-$\pi$ distribution amplitude and scalar form factor $F_{\pi\pi}(\omega^2)$, we calculate the $CP$ averaged branching fraction and the $CP$ asymmetry for the quasi-two-body decays $B\to P f_0(500)\to P\pi^+\pi^-$. Taking the quasi-two-body decay $B^+ \to \pi^+ f_0(500) \to \pi^+ \pi^+ \pi^-$ as an explicit example, we present the behavior of differential branching fraction and direct $CP$ violation versus the $\pi$-$\pi$ invariant mass. The total branching fraction and direct $CP$ violation are $\mathcal{B}(B^+\to \pi^+ [\sigma\to]\pi^+\pi^-) = (1.78 \pm 0.41\pm 0.51) \times 10^{-6}$ and $\mathcal{A}_{CP}(B^+\to \pi^+ [\sigma\to]\pi^+\pi^-) = (29.8\pm 11.1\pm 13.0)\%$ respectively. Our results could be tested by further experiments., Comment: 15 pages, 3 figures, matches published version

Quantum heat engines and refrigerators are open quantum systems, whose dynamics can be well understood using a non-Hermitian formalism. A prominent feature of non-Hermiticity is the existence of exceptional points (EPs), which has no counterpart in closed quantum systems. It has been shown in classical systems that dynamical encirclement in the vicinity of an EP, whether the loop includes the EP or not, could lead to chiral mode conversion. Here, we show that this is valid also for quantum systems when dynamical encircling is performed in the vicinity of their Liouvillian EPs (LEPs) which include the effects of quantum jumps and associated noise - an important quantum feature not present in previous works. We demonstrate, using a Paul-trapped ultracold ion, the first chiral quantum heating and refrigeration by dynamically encircling a closed loop in the vicinity of an LEP. We witness the cycling direction to be associated with the chirality and heat release (absorption) of the quantum heat engine (quantum refrigerator). Our experiments have revealed that not only the adiabaticity-breakdown but also the Landau-Zener-St\"uckelberg process play an essential role during dynamic encircling, resulting in chiral thermodynamic cycles. Our observations contributes to further understanding of chiral and topological features in non-Hermitian systems and pave a way to exploring the relation between chirality and quantum thermodynamics., Comment: Accepted by Light: Science & Applications

Noncollinear antiferromagnets (nc-AFMs) have attracted increasing research attention in spintronics due to their unique spin structures and fascinating charge and spin transport properties. By using first-principles calculations, we comprehensively investigate the charge and spin Hall effects in representative noncollinear antiferromagnet Mn3Pt. Our study reveals that the Hall effects in nc-AFMs are critically dependent on the crystal facet orientation and temperature. For (001) orientated Mn3Pt, each charge and spin Hall conductivity element is comprised of both time reversal odd (T-odd) and even (T-even) contribution, associated with longitudinal conductivity, which leads to sizable and highly anisotropic Hall conductivity. The temperature dependence of charge and spin Hall conductivity has been elucidated by considering both phonon and spin disorder scattering. The scaling relations between Hall conductivity and longitudinal conductivity have also been investigated. The existence of prominent spin Hall effect in nc-AFMs may generate spin current with Sz spin polarization, which is advantageous for field free switching of perpendicular magnetization. Our work may provide unambiguous understanding on the charge and spin transport in noncollinear antiferromagnets and pave their way for applications in antiferromagnetic spintronics.