THE ROLE OF PKS1 MEDIATED SECONDARY METABOLISM IN HOST PENETRATION AND COLONIZATION DURING RICE BLAST DISEASE

Ph.DDOCTOR OF PHILOSOPH

AFDM-SCMA: A Promising Waveform for Massive Connectivity over High Mobility Channels

This paper studies the affine frequency division multiplexing (AFDM)-empowered sparse code multiple access (SCMA) system, referred to as AFDM-SCMA, for supporting massive connectivity in high-mobility environments. First, by placing the sparse codewords on the AFDM chirp subcarriers, the input-output (I/O) relation of AFDM-SCMA systems is presented. Next, we delve into the generalized receiver design, chirp rate selection, and error rate performance of the proposed AFDM-SCMA The proposed AFDM-SCMA is shown to provide a general framework and subsume the existing OFDM-SCMA as a special case. Third, for efficient transceiver design, we further propose a class of sparse codebooks for simplifying the I/O relation, referred to as I/O relation-inspired codebook design in this paper. Building upon these codebooks, we propose a novel iterative detection and decoding scheme with linear minimum mean square error (LMMSE) estimator for both downlink and uplink channels based on orthogonal approximate message passing principles. Our numerical results demonstrate the superiority of the proposed AFDM-SCMA systems over OFDM-SCMA systems in terms of the error rate performance. We show that the proposed receiver can significantly enhance the error rate performance while reducing the detection complexity

A Versatile Method of Engineering the Electron Wavefunction of Hybrid Quantum Devices

With the development of quantum technology, hybrid devices that combine superconductors (S) and semiconductors (Sm) have attracted great attention due to the possibility of engineering structures that benefit from the integration of the properties of both materials. However, until now, none of the experiments have reported good control of band alignment at the interface, which determines the strength of S-Sm coupling and the proximitized superconducting gap. Here, we fabricate hybrid devices in a generic way with argon milling to modify the interface while maintaining its high quality. First, after the milling the atomically connected S-Sm interfaces appear, resulting in a large induced gap, as well as the ballistic transport revealed by the multiple Andreev reflections and quantized above-gap conductance plateaus. Second, by comparing transport measurement with Schr\"odinger-Poisson (SP) calculations, we demonstrate that argon milling is capable of varying the band bending strength in the semiconducting wire as the electrons tend to accumulate on the etched surface for longer milling time. Finally, we perform nonlocal measurements on advanced devices to demonstrate the coexistence and tunability of crossed Andreev reflection (CAR) and elastic co-tunneling (ECT) -- key ingredients for building the prototype setup for realization of Kitaev chain and quantum entanglement probing. Such a versatile method, compatible with the standard fabrication process and accompanied by the well-controlled modification of the interface, will definitely boost the creation of more sophisticated hybrid devices for exploring physics in solid-state systems.Comment: 18 pages, 9 figure

A Conserved Mechanism for Control of Human and Mouse Embryonic Stem Cell Pluripotency and Differentiation by Shp2 Tyrosine Phosphatase

Recent studies have suggested distinctive biological properties and signaling mechanisms between human and mouse embryonic stem cells (hESCs and mESCs). Herein we report that Shp2, a protein tyrosine phosphatase with two SH2 domains, has a conserved role in orchestration of intracellular signaling cascades resulting in initiation of differentiation in both hESCs and mESCs. Homozygous deletion of Shp2 in mESCs inhibited differentiation into all three germ layers, and siRNA-mediated knockdown of Shp2 expression in hESCs led to a similar phenotype of impaired differentiation. A small molecule inhibitor of Shp2 enzyme suppressed both hESC and mESC differentiation capacity. Shp2 modulates Erk, Stat3 and Smad pathways in ES cells and, in particular, Shp2 regulates BMP4-Smad pathway bi-directionally in mESCs and hESCs. These results reveal a common signaling mechanism shared by human and mouse ESCs via Shp2 modulation of overlapping and divergent pathways

DeepSeek LLM: Scaling Open-Source Language Models with Longtermism

The rapid development of open-source large language models (LLMs) has been truly remarkable. However, the scaling law described in previous literature presents varying conclusions, which casts a dark cloud over scaling LLMs. We delve into the study of scaling laws and present our distinctive findings that facilitate scaling of large scale models in two commonly used open-source configurations, 7B and 67B. Guided by the scaling laws, we introduce DeepSeek LLM, a project dedicated to advancing open-source language models with a long-term perspective. To support the pre-training phase, we have developed a dataset that currently consists of 2 trillion tokens and is continuously expanding. We further conduct supervised fine-tuning (SFT) and Direct Preference Optimization (DPO) on DeepSeek LLM Base models, resulting in the creation of DeepSeek Chat models. Our evaluation results demonstrate that DeepSeek LLM 67B surpasses LLaMA-2 70B on various benchmarks, particularly in the domains of code, mathematics, and reasoning. Furthermore, open-ended evaluations reveal that DeepSeek LLM 67B Chat exhibits superior performance compared to GPT-3.5

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

The role of snx41-based pexophagy in magnaporthe development.

Pexophagy, the degradation of peroxisomes via selective autophagy, depends on Atg20/Snx42 function in Saccharomyces cerevisiae. Besides its role in selective autophagy, Atg20/Snx42 is also involved in an autophagy-independent endosomal retrieval trafficking, in cooperation with two other sorting nexins, Snx41 and Snx4. Recently, we reported that the sorting nexin MoSnx41, which showed high sequence similarity to yeast Snx41 and Snx42/Atg20 proteins, regulates the gamma-glutamyl cycle and GSH production and is essential for conidiation and pathogenicity in Magnaporthe oryzae. Pexophagy was also found to be defective in Mosnx41Δ mutant. These findings indicate that MoSnx41 likely serves combined functions of Snx42/Atg20 and Snx41 in M. oryzae.. In this study, we performed complementation analyses and demonstrate that MoSnx41 alone serves the dual function of protein sorting (ScSnx41) and pexophagy (ScSnx42/Atg20). To study the potential biological function of pexophagy in fungal pathogenic life cycle, we created deletion mutants of potential pexophagy-specific genes, and characterized them in terms of pexophagy, conidiation and pathogenesis. We identified Pex14 as an essential protein for pexophagy in M. oryzae. Overall, our results show that pexophagy per se is not essential for asexual development or virulence in M. oryzae

Role of Macroautophagy in Nutrient Homeostasis During Fungal Development and Pathogenesis

Macroautophagy is a non-selective, bulk degradation process conserved in eukaryotes. Response to starvation stress and/or regulation of nutrient breakdown/utilization is the major intracellular function of macroautophagy. Recent studies have revealed requirement for autophagy in diverse functions such as nutrient homeostasis, organelle degradation and programmed cell death in filamentous fungal pathogens, for proper morphogenesis and differentiation during critical steps of infection. In this review, we aim to summarize the physiological functions of autophagy in fungal virulence, with an emphasis on nutrient homeostasis in opportunistic human fungal pathogens and in the rice-blast fungus, Magnaporthe oryzae. We briefly summarize the role of autophagy on the host side: for resistance to, or subversion by, the pathogens

Traffic Flow Modeling of Freeway Variable Speed Limit Control Based on the Big Data of Driving Behavior

Variable speed limit (VSL) control is a flexible restriction on the rate at which motorists can drive on a given stretch of road. Effective VSL control can increase safety and provide clear guidance for motorists. Previous traffic flow models of VSL control were mostly based on the influence of VSL on average speed (macro) or driver’s expected speed (micro). Few models considered the influence of VSL on driver’s actual driving behavior. In this paper, we first briefly introduce the big traffic data involved in this study and explain the mapping relationship between the data and driving behavior. Then, we analyze the driver’s actual driving behavior under the VSL control. Then, an improved single-lane cellular automaton model is established based on the driving behavior characteristics under VSL control. After that, we calibrate the parameters of the single-lane cellular automaton model with the left lane as the calibration object. Finally, this paper uses the proposed single-lane cellular automaton model to simulate the traffic flow characteristics under VSL control. The numerical simulation results show that the simulation of the variable speed limit in different density intervals presents different results, but these results are consistent with the actual situation of variable speed limit control, which verifies the validity of the proposed model