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A bstract Non-simply connected Calabi-Yau threefolds play a central role in the study of string compactifications. Such manifolds are usually described by quotienting a simply connected Calabi-Yau variety by a freely acting discrete symmetry. For the Calabi-Yau threefolds described as complete intersections in products of projective spaces, a classification of such symmetries descending from linear actions on the ambient spaces of the varieties has been given in [ 16 ]. However, which symmetries can be described in this manner depends upon the description that is being used to represent the manifold. In [ 24 ] new, favorable, descriptions were given of this data set of Calabi-Yau threefolds. In this paper, we perform a classification of cyclic symmetries that descend from linear actions on the ambient spaces of these new favorable descriptions. We present a list of 129 symmetries/non-simply connected Calabi-Yau threefolds. Of these, at least 33, and potentially many more, are topologically new varieties.

Despite having key functions in terrestrial ecosystems, information on the dominant soil fungi and their ecological preferences at the global scale is lacking. To fill this knowledge gap, we surveyed 235 soils from across the globe. Our findings indicate that 83 phylotypes (<0.1% of the retrieved fungi), mostly belonging to wind dispersed, generalist Ascomycota, dominate soils globally. We identify patterns and ecological drivers of dominant soil fungal taxa occurrence, and present a map of their distribution in soils worldwide. Whole-genome comparisons with less dominant, generalist fungi point at a significantly higher number of genes related to stress-tolerance and resource uptake in the dominant fungi, suggesting that they might be better in colonising a wide range of environments. Our findings constitute a major advance in our understanding of the ecology of fungi, and have implications for the development of strategies to preserve them and the ecosystem functions they provide.

A bstract We study two aspects of the physics of heterotic Line Bundle Standard Models on smooth Calabi-Yau threefolds. First, we investigate to what degree modern moduli stabilization scenarios can affect the standard model spectrum in such compactifications. Specifically, we look at the case where some of the complex structure moduli are fixed by a choice of hidden sector bundle. In this context, we study the frequency with which the system tends to be forced to a point in moduli space where the cohomology groups determining the spectrum in the standard model sector jump in dimension. Second, we investigate to what degree couplings, that are permitted by all of the obvious symmetries of the theory, actually vanish due to certain topological constraints associated to their higher dimensional origins. We find that both effects are prevalent within the data set of heterotic Line Bundle Standard Models studied.

Early detection and intervention are very important for the diagnosis and treatment of Parkinson’s disease. Firstly, according to the characteristics of dysarthria and abnormal sensitivity to the pronunciation of words such as ‘[pɑ˥’, ‘pjɑʊ˥’, ‘ pən˥’, and ‘pjɛn˥’ in patients with early Parkinson’s disease, a Chinese tongue twister “[pɑ˥ paɪ⇃ pjɑʊ˥ pɪŋ˥ pən˥ peɪ⇃ pʰo˥, pʰɑʊ˥ ˩pɪŋ˥ pɪŋ˥ pʰaɪ↿ peɪ⇃ pjɛn˥ pʰɑʊ⇃” was designed. The original recordings of Parkinson’s suspected patients were collected in a hospital geriatrics clinic to construct a tongue twister speech database. Secondly, Hilbert transform is introduced to process audio data to obtain the instantaneous amplitude signal of speech, the peak value, peak position, peak width and peak area of each syllable corresponding to the instantaneous amplitude and the total speech length, are extracted to construct the machine learning speech feature data set. Finally, SVM is introduced to train and evaluate the speech features of Parkinson’s disease suspected patients, its performance is compared with those of BP and LSTM models. The results show that the recognition accuracy of the three machine learning models is 92.10%, 88.94% and 90.18%, respectively, which indicates that the speech features extracted in this paper are effective. Combined with instantaneous amplitude features of speech and SVM model, a computer-aided diagnosis system for Parkinson’s disease is built. The clinical trial results show that the recognition accuracy of the system for Parkinson’s disease patients can reach 91.43%, and the system has fast response speed and strong anti-interference ability, which can fully assist doctors in making real-time and remote selections of patients with Parkinson’s disease.

We investigate the proposed holographic duality between the TsT transformation of IIB string theory on AdS 3 ×$$\\mathcal{N}$$with NS-NS flux and a single-trace$$T\\overline{T }$$deformation of the symmetric orbifold CFT. We present a non-perturbative calculation of two-point correlation functions using string theory and demonstrate their consistency with those of the$$T\\overline{T }$$deformation. The two-point correlation function of the deformed theory on the plane, written in momentum space, is obtained from that of the undeformed theory by replacing h with$$h+2\\frac{\\widetilde{\\lambda }}{w}p\\overline{p }$$, where h is the spacetime conformal weight,$$\\widetilde{\\lambda }$$is a deformation parameter, p and$$\\overline{p }$$are the momenta, and w labels the twisted sectors in the deformed symmetric product. At w = 1, the non-perturbative result satisfies the Callan-Symanzik equation for double-trace$$T\\overline{T }$$deformed CFT derived in [1]. We also perform conformal perturbations on both the worldsheet CFT and the symmetric orbifold CFT as a sanity check. The perturbative and non-perturbative matching between results on the two sides provides further evidence of the conjectured$${\\text{TsT}}/T\\overline{T }$$correspondence.

The organization of chromatin into self-interacting domains is universal among eukaryotic genomes, though how and why they form varies considerably. Here we report a chromosome-scale reference genome assembly of pepper ( Capsicum annuum ) and explore its 3D organization through integrating high-resolution Hi-C maps with epigenomic, transcriptomic, and genetic variation data. Chromatin folding domains in pepper are as prominent as TADs in mammals but exhibit unique characteristics. They tend to coincide with heterochromatic regions enriched with retrotransposons and are frequently embedded in loops, which may correlate with transcription factories. Their boundaries are hotspots for chromosome rearrangements but are otherwise depleted for genetic variation. While chromatin conformation broadly affects transcription variance, it does not predict differential gene expression between tissues. Our results suggest that pepper genome organization is explained by a model of heterochromatin-driven folding promoted by transcription factories and that such spatial architecture is under structural and functional constraints. The organization of chromatin into self-interacting domains is universal among eukaryotic genomes. Here, the authors report a reference-grade pepper genome assembly and use this reference to help describe the relationship among 3D chromatin conformation, chromatin function, and gene expression.

Simulating physical dynamics to solve hard combinatorial optimization has proven effective for medium- to large-scale problems. The dynamics of such systems is continuous, with no guarantee of finding optimal solutions of the original discrete problem. We investigate the open question of when simulated physical solvers solve discrete optimizations correctly, with a focus on coherent Ising machines (CIMs). Having established the existence of an exact mapping between CIM dynamics and discrete Ising optimization, we report two fundamentally distinct bifurcation behaviors of the Ising dynamics at the first bifurcation point: either all nodal states simultaneously deviate from zero (synchronized bifurcation) or undergo a cascade of such deviations (retarded bifurcation). For synchronized bifurcation, we prove that when the nodal states are uniformly bounded away from the origin, they contain sufficient information for exactly solving the Ising problem. When the exact mapping conditions are violated, subsequent bifurcations become necessary and often cause slow convergence. Inspired by those findings, we devise a trapping-and-correction (TAC) technique to accelerate dynamics-based Ising solvers, including CIMs and simulated bifurcation. TAC takes advantage of early bifurcated “trapped nodes” which maintain their sign throughout the Ising dynamics to reduce computation time effectively. Using problem instances from open benchmark and random Ising models, we validate the superior convergence and accuracy of TAC. Physical and physics-inspired computation is emerging as a new paradigm for tackling hard optimization problems. In this work, the authors establish rigorous mathematical conditions together with new design principles for physical as well as simulated dynamical systems to solve general Ising models.

This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 702057 (CLIMIFUN). M.D.-B. was supported by a Ramón y Cajal grant from the Spanish Ministry of Science and Innovation (RYC2018-025483-I). M.D-B. is also supported by a project from the Spanish Ministry of Science and Innovation (PID2020-115813RA-I00), and a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014-2020 Objetivo temático “01 - Refuerzo de la investigación, el desarrollo tecnológico y la innovación”) associated with the research project P20_00879 (ANDABIOMA). S.L. was supported by the National Natural Science Foundation of China (grant no. 32101491) and fellowship of China Postdoctoral Science Foundation (2021M701968). P.G.-P. was supported by a grant from the Spanish Ministry of Science and Innovation (DUALSOM, PID2020-113021RA-I00). E.G. is supported by the European Research Council grant agreement 647038 (BIODESERT) and the Consellería de Educación, Cultura y Deporte de la Generalitat Valenciana, and the European Social Fund (APOSTD/2021/188).

Antifreeze agents play a critical role in various fields including tissue engineering, gene therapy, therapeutic protein production, and transplantation. Commonly used antifreeze agents such as DMSO and other organic substances are known to have cytotoxic effects. Antifreeze proteins sourced from cold-adapted organisms offer a promising solution by inhibiting ice crystal formation; however, their effectiveness is hindered by a dynamic ice-shaping (DIS) effect and thermal hysteresis (TH) properties. In response to these limitations, antifreeze peptides (AFPs) have been developed as alternatives to antifreeze proteins, providing similar antifreeze properties without the associated drawbacks. This review explores the methods for acquiring AFPs, with a particular emphasis on chemical synthesis. It aims to offer valuable insights and practical implications to drive the realm of sub-zero storage.

Background The basic helix–loop–helix (bHLH) transcription factors (TFs) serve crucial roles in regulating plant growth and development and typically participate in biological processes by interacting with other TFs. Capsorubin and capsaicinoids are found only in Capsicum , which has high nutritional and economic value. However, whether bHLH family genes regulate capsorubin and capsaicinoid biosynthesis and participate in these processes by interacting with other TFs remains unknown. Results In this study, a total of 107 CabHLHs were identified from the Capsicum annuum genome. Phylogenetic tree analysis revealed that these CabHLH proteins were classified into 15 groups by comparing the CabHLH proteins with Arabidopsis thaliana bHLH proteins. The analysis showed that the expression profiles of CabHLH009 , CabHLH032 , CabHLH048 , CabHLH095 and CabHLH100 found in clusters C1, C2, and C3 were similar to the profile of carotenoid biosynthesis in pericarp, including zeaxanthin, lutein and capsorubin, whereas the expression profiles of CabHLH007 , CabHLH009 , CabHLH026 , CabHLH063 and CabHLH086 found in clusters L5, L6 and L9 were consistent with the profile of capsaicinoid accumulation in the placenta. Moreover, CabHLH007 , CabHLH009 , CabHLH026 and CabHLH086 also might be involved in temperature-mediated capsaicinoid biosynthesis. Yeast two-hybrid (Y2H) assays demonstrated that CabHLH007 , CabHLH009 , CabHLH026 , CabHLH063 and CabHLH086 could interact with MYB31, a master regulator of capsaicinoid biosynthesis. Conclusions The comprehensive and systematic analysis of CabHLH TFs provides useful information that contributes to further investigation of CabHLHs in carotenoid and capsaicinoid biosynthesis.