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Abstract Optical phonon engineering through nonlinear effects has been utilized in ultrafast control of material properties. However, nonlinear optical phonons typically exhibit rapid decay due to strong mode-mode couplings, limiting their effectiveness in temperature or frequency sensitive applications. Here we report the observation of long-lived nonlinear optical phonons through the spontaneous formation of phonon frequency combs in the van der Waals material CrXTe₃(X=Ge, Si) using high-resolution Raman scattering. Unlike conventional optical phonons, the highestA_gmode in CrGeTe₃splits into equidistant, sharp peaks forming a frequency comb that persists for hundreds of oscillations and survives up to 200K. These modes correspond to localized oscillations of Ge₂Te₆clusters, isolated from Cr hexagons, behaving as independent quantum oscillators. Introducing a cubic nonlinear term to the harmonic oscillator model, we simulate the phonon time evolution and successfully replicate the observed comb structure. Similar frequency comb behavior is observed in CrSiTe₃, demonstrating the generalizability of this phenomenon. Our findings demonstrate that Raman scattering effectively probes high-frequency nonlinear phonon modes, offering insight into the generation of long-lived, tunable phonon frequency combs with potential applications in ultrafast material control and phonon-based technologies. 

ABSTRACT ObjectiveEstuarine fishes experience significant diel and seasonal variations in their environments, with climate change introducing additional stressors, including altered salinity, temperatures, and water levels. American Eels Anguilla rostrata are present in Atlantic estuaries from Venezuela to Greenland. Despite their wide distribution and shrinking population, American Eels are understudied, in part because of the research challenges posed by their unusual catadromous life history. This study examines the spatial effects of changing estuarine water quality variables (water temperature, dissolved oxygen, and salinity) on the American Eel population in the Hudson River estuary (HRE). MethodsThe Hudson River Biological Monitoring Program, conducted from 1974 to 2017, consists of a suite of surveys recording fish abundance data and water quality variables. As the largest component of the Hudson River Biological Monitoring Program, the Long River Ichthyoplankton Survey contains 44 years of data on American Eels in the HRE. Using LRS catch data and Hudson River Biological Monitoring Program water quality measurements, we developed statistical models of American Eel population centers in the HRE. ResultsThe young-of-year and yearling-or-older population centers shifted downstream over the course of the Long River Ichthyoplankton Survey at average rates of approximately 1.1 and 0.41 km per year, respectively, despite higher temperatures and lower dissolved oxygen conditions closer to the estuary’s mouth. Mean water temperature and dissolved oxygen for the entire estuary have significant relationships with the population centers of both age-classes, although the eels were not apparently tracking stable conductivity or water temperature conditions; nor were the young of year tracking stable dissolved oxygen levels. ConclusionsThe downstream shift in HRE American Eel population centers over several decades and the relationship between this shift and changing environmental conditions indicate the need for improved understanding of the population dynamics of the globally distributed and declining species of the genus Anguilla. This knowledge is critical in the face of rapidly changing ecosystems. 

High-throughput sequencing (HTS) technologies have been instrumental in investigating biological questions at the bulk and single-cell levels. Comparative analysis of two HTS data sets often relies on testing the statistical significance for the difference of two negative binomial distributions (DOTNB). Although negative binomial distributions are well studied, the theoretical results for DOTNB remain largely unexplored. Here, we derive basic analytical results for DOTNB and examine its asymptotic properties. As a state-of-the-art application of DOTNB, we introduce DEGage, a computational method for detecting differentially expressed genes (DEGs) in scRNA-seq data. DEGage calculates the mean of the sample-wise differences of gene expression levels as the test statistic and determines significant differential expression by computing the P-value with DOTNB. Extensive validation using simulated and real scRNA-seq data sets demonstrates that DEGage outperforms five popular DEG analysis tools: DEGseq2, DEsingle, edgeR, Monocle3, and scDD. DEGage is robust against high dropout levels and exhibits superior sensitivity when applied to balanced and imbalanced data sets, even with small sample sizes. We utilize DEGage to analyze prostate cancer scRNA-seq data sets and identify marker genes for 17 cell types. Furthermore, we apply DEGage to scRNA-seq data sets of mouse neurons with and without fear memory and reveal eight potential memory-related genes overlooked in previous analyses. The theoretical results and supporting software for DOTNB can be widely applied to comparative analyses of dispersed count data in HTS and broad research questions. 

Abstract Heterochromatin is generally associated with the nuclear periphery, but how the spatial organization of heterochromatin is regulated to ensure epigenetic silencing remains unclear. Here we found that Sad1, an inner nuclear membrane SUN-family protein in fission yeast, interacts with histone H2A-H2B but not H3-H4. We solved the crystal structure of the histone binding motif (HBM) of Sad1 in complex with H2A-H2B, revealing the intimate contacts between Sad1_HBMand H2A-H2B. Structure-based mutagenesis studies revealed that the H2A-H2B-binding activity of Sad1 is required for the dynamic distribution of Sad1 throughout the nuclear envelope (NE). The Sad1-H2A-H2B complex mediates tethering telomeres and the mating-type locus to the NE. This complex is also important for heterochromatin silencing. Mechanistically, H2A-H2B enhances the interaction between Sad1 and HDACs, including Clr3 and Sir2, to maintain epigenetic identity of heterochromatin. Interestingly, our results suggest that Sad1 exhibits the histone-enhanced liquid-liquid phase separation property, which helps recruit heterochromatin factors to the NE. Our results uncover an unexpected role of SUN-family proteins in heterochromatin regulation and suggest a nucleosome-independent role of H2A-H2B in regulating Sad1’s functionality. 

Abstract In our previous study, we identified a shift in the synchrotron peak frequency of the blazar B2 1308+326 from 10^12.9to 10^14.8Hz during a flare, suggesting it could be a changing-look blazar (CLB). In this work, we investigate the changing-look behaviour of B2 1308+326 by analysing a newly acquired optical spectrum and comparing it with an archival spectrum. We find that between the two epochs, the continuum flux increased by a factor of ~4.4, while the Mgiiemission line flux decreased by a factor of 1.4 ± 0.2. Additionally, the equivalent width of the Mgiiline reduced from ~20 to ~3 Å, indicating an apparent shift from a flat-spectrum radio quasar (FSRQ) class to a BL Lacertae (BL Lac) class. Despite this apparent change, the ratio of accretion disk luminosity to Eddington luminosity remains >10⁻²during both epochs, indicating efficient accretion persists in B2 1308+326. The measured black hole mass remains consistent with an average $\log M_{\mathrm{BH}}=8.44$M_⊙. Our findings suggest that B2 1308+326 is not a genuine CLB but rather an intrinsic FSRQ that emerges as a BL Lac during high-flux states due to enhanced nonthermal emission. 

Abstract Single‐cell chromatin conformation capture (scHi‐C) techniques have evolved to provide significant insights into the structural organization and regulatory mechanisms in individual cells. Although many scHi‐C protocols have been developed, they often involve intricate procedures and the resulting data are sparse, leading to computational challenges for systematic data analysis and limited applicability. This review provides a comprehensive overview, quantitative evaluation of thirteen protocols and practical guidance on computational topics. It is first assessed the efficiency of these protocols based on the total number of contacts recovered per cell and thecis/transratio. It is then provided systematic considerations for scHi‐C quality control and data imputation. Additionally, the capabilities and implementations of various analysis methods, covering cell clustering, A/B compartment calling, topologically associating domain (TAD) calling, loop calling, 3D reconstruction, scHi‐C data simulation and differential interaction analysis is summarized. It is further highlighted key computational challenges associated with the specific complexities of scHi‐C data and propose potential solutions.