Showing papers by "Jing Guo published in 2022"

Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution

Abstract: Abstract Adaptation to cool climates has occurred several times in different angiosperm groups. Among them, Pooideae, the largest grass subfamily with ∼3,900 species including wheat and barley, have successfully occupied many temperate regions and play a prominent role in temperate ecosystems. To investigate possible factors contributing to Pooideae adaptive evolution to cooling climates, we performed phylogenetic reconstruction using five gene sets (with 1,234 nuclear genes and their subsets) from 157 transcriptomes/genomes representing all 15 tribes and 24 of 26 subtribes. Our phylogeny supports the monophyly of all tribes (except Diarrheneae) and all subtribes with at least two species, with strongly supported resolution of their relationships. Molecular dating suggests that Pooideae originated in the late Cretaceous, with subsequent divergences under cooling conditions first among many tribes from the early middle to late Eocene and again among genera in the middle Miocene and later periods. We identified a cluster of gene duplications (CGD5) shared by the core Pooideae (with 80% Pooideae species) near the Eocene–Oligocene transition, coinciding with the transition from closed to open habitat and an upshift of diversification rate. Molecular evolutionary analyses homologs of CBF for cold resistance uncovered tandem duplications during the core Pooideae history, dramatically increasing their copy number and possibly promoting adaptation to cold habitats. Moreover, duplication of AP1/FUL-like genes before the Pooideae origin might have facilitated the regulation of the vernalization pathway under cold environments. These and other results provide new insights into factors that likely have contributed to the successful adaptation of Pooideae members to temperate regions.

Low Colorectal Tumor Removal by E-Cadherin Destruction-Enabled Tumor Cell Dissociation.

Abstract: Treatments for low colorectal cancer (CRC) remain a great challenge due to the heavy physical and psychological burdens of colostomy, strong drug toxicity in chemotherapy, and myelosuppression-/chemoradiation-related gastrointestinal symptoms. In this study, a highly biosafe and effective tumor cell dissociation-based low CRC treatment modality has been verified on both PDOs in vitro and colorectal tumor models in vivo. Notably, controllable EDTA release at the tumor sites was achieved by the LDH degradation in response to a slightly acidic microenvironment of low CRC tumors. Resultantly, the intratumoral E-cadherin for intercellular junctions of low CRC tumors was effectively destroyed via Ca2+ depletion by released EDTA from the interlayers, initiating remarkable tumor cell dissociation and resultant tumor disaggregation/removal via defecation. Dissociated tumor cells were prevailingly enveloped by LDH/EDTA, which prevented them from readhering to adjacent tissues, providing an unprecedented, efficient and safe therapeutic modality for low CRC, which will benefit patients suffering low CRC.

Multiscale modeling of semimetal contact to two-dimensional transition metal dichalcogenide semiconductor

Abstract: A multiscale simulation approach is developed to simulate the contact transport properties between semimetal and a monolayer two-dimensional transition metal dichalcogenide (TMDC) semiconductor. The results elucidate the mechanisms for low contact resistance between semimetal and TMDC semiconductor contacts from a quantum transport perspective. The simulation results compare favorably with recent experiments. Furthermore, the results show that the contact resistance of a bismuth-MoS2 contact can be further reduced by engineering the dielectric environment and doping the TMDC material to [Formula: see text]. The quantum transport simulation indicates the possibility to achieve an ultrashort contact transfer length of ∼1 nm, which can allow aggressive scaling of the contact size.

Eradicating tumor in a recurrent cervical cancer patient with autologous tumor-infiltrating lymphocytes and a modified lymphodepleting regimen

Abstract: Tumor-infiltrating lymphocyte (TIL) therapy has shown promising results against several cancers. However, traditional lymphodepleting regimens are severe and represent a major limitation for a more widespread use of TIL. The modified pretreatment strategies may alleviate side effects and demonstrate the persistence of tumor-reactive T cells in the blood. Here, we report a case who was diagnosed recurrent cervical cancer with bladder metastasis. Omitting high dose of IL-2, she received intravenous dose of cyclophosphamide (20 mg/kg) for 3 days, approximately 48 hours before receiving the intravenous infusion of TILs. Half dosage (100 mg) of PD1 antibody was administered with purpose of neutralizing PD1 expressed on T cells surface. She achieved complete response 10 weeks after one-time TILs infusion. Adverse reactions were negligible and safely manageable in a general ward without the need for intervention from intensive care units. Time-course peripheral blood counts and TCR repertoire sequencing demonstrated a robust expansion and long-term persistence of the infused TILs. These results illustrated the potential value of modified lymphodepletion, followed by TILs for the treatment of patients with cervical cancer with local recurrence. Trial registration number, NCT04766320.

Dynamic immune ecosystem of dengue infection revealed by single‐cell sequencing

Abstract: Dengue is the most common human arboviral disease worldwide, which can result in severe complications. A dysfunctional immune response in dengue infective patients is a recurrent theme impacting symptoms and mortality, but the heterogeneity and dynamics of immune infiltrates during dengue infection remain poorly characterized. Here, we identified the immune cell types in scRNA‐seq data from 13127 cells of 10 dengue infective patients and discovered the dynamic immune ecosystems of dengue infection. Notably, genes that exhibited higher expression in specific cell types play important roles in response to virus infection in a module manner. Transcription factors (TFs) are the major regulators (i.e., PAX5, IRF7, KLF4, and IRF8) that can potentially regulate infection‐related genes. We demonstrated that the dynamic rewired regulatory network during dengue infection. Moreover, our data revealed the complex cell–cell communications from control to fever and severe dengue patients and prevalent cell–cell communication rewiring was observed. We further identified the IFN‐II and CXCL signaling pathways that medicated the communications and play important roles in dengue infection. Together, our comprehensive analysis of dynamic immune ecosystem of dengue infection provided novel insights for understanding the pathogenesis of and developing effective therapeutic strategies for dengue infection.

Computational Screening and Multiscale Simulation of Barrier-Free Contacts for 2D Semiconductor pFETs

Abstract: Low-resistance p-type contacts to two-dimensional (2D) semiconductors remains a critical challenge towards the industrial application of 2D channel materials in advanced logic technology. To address this challenge, we computationally screen and identify designs for ultralow-resistance p-type contacts to 2D semiconductors such as WSe2 by combining ab initio density-functional-theory (DFT) and quantum device simulations. Two new contact strategies, van der Waals metallic contact (such as 1H-NbS2), and bulk semimetallic contact (such as Co3 Sn2 S2), are identified as realistic pathways to achieving Schottky-barrier-free and low-contact-resistance p-type contacts for 2D semiconductor pFETs. Simulations of these new strategies suggest reduced metal-induced gap states, negligible Schottky barrier height and small contact resistance (down to ~20 Ω·μm). Preliminary experimental results in developing Co3 Sn2 S2 as a new semimetal contact material are also demonstrated.

An Angle-Compensating, Complex-Coefficient PI Controller Used for Decoupling Control of a Permanent-Magnet Synchronous Motor

Abstract: An asymmetric, cross-coupling effect, as well as digital control delays, in a permanent-magnet synchronous motor (PMSM) will deteriorate its current-control performance in the high-speed range, especially for electric motors used in electric vehicles (EVs) with features such as high-power density and a low carrier/modulation frequency ratio. In this paper, an angle-compensating, complex-coefficient, proportional-integrator (ACCC-PI) controller is proposed, which aims to provide an excellent decoupling performance even with considerable digital control delay. Firstly, the current open and closed loop complex-coefficient transfer functions were established in the synchronous rotation coordinate system. The proposed method, along with existing ones, were then evaluated and theoretically compared. On this basis, the parameter-tuning method of the ACCC-PI controller was presented. Finally, simulation and experimental results proved the correctness of the theoretical analysis and the proposed method.

Electroluminescence of atoms in a graphene nanogap

Abstract: Here, we report light emission from single atoms bridging a graphene nanogap that emit bright visible light based on fluorescence of ionized atoms. Oxygen atoms in the gap shows a peak emission wavelength of 569 nm with a full width at half maximum (FWHM) of 208 nm. The energy states produced by these ionized oxygen atoms bridging carbon atoms in the gap also produce a large negative differential resistance (NDR) in the transport across the gap with the highest peak-to-valley current ratio (PVR = 45) and highest peak current density (~90 kA/cm2) ever reported in a solid-state tunneling device. While tunneling transport has been previously observed in graphene nanogaps, the bridging of ionized oxygen observed here shows a low excess current, leading to the observed PVR. On the basis of the highly reproducible light emission and NDR from these structures, we demonstrate a 65,536-pixel light-emitting nanogap array.

Involvement of Cancer Stem Cells in Chemoresistant Relapse of Epithelial Ovarian Cancer Identified by Transcriptome Analysis

Abstract: Epithelial ovarian cancer (EOC) is the most lethal gynecological malignancy. Despite the initial resection and chemotherapeutic treatment, relapse is common, which leads to poor survival rates in patients. A primary cause of recurrence is the persistence of ovarian cancer stem cells (OCSCs) with high tumorigenicity and chemoresistance. To achieve a better therapeutic response in EOC relapse, the mechanisms underlying acquired chemoresistance associated with relapse-initiating OCSCs need to be studied. Transcriptomes of both chemosensitive primary and chemoresistant relapse EOC samples were obtained from ICGC OV-AU dataset for differential expression analysis. The upregulated genes were further studied using KEGG and GO analysis. Significantly increased expression of eighteen CSC-related genes was found in chemoresistant relapse EOC groups. Upregulation of the expression in four hub genes including WNT3A, SMAD3, KLF4, and PAX6 was verified in chemoresistant relapse samples via immunohistochemistry staining, which confirmed the existence and enrichment of OCSCs in chemoresistant relapse EOC. KEGG and GO enrichment analysis in microarray expression datasets of isolated OCSCs indicated that quiescent state, increased ability of drug efflux, and enhanced response to DNA damage may have caused the chemoresistance in relapse EOC patients. These findings demonstrated a correlation between OCSCs and acquired chemoresistance and illustrated potential underlying mechanisms of OCSC-initiated relapse in EOC patients. Meanwhile, the differentially expressed genes in OCSCs may serve as novel preventive or therapeutic targets against EOC recurrence in the future.

Inhibitory effect of Sparassis latifolia polysaccharides on cariogenic bacteria as studied in-vitro simulated oral processing

Abstract: ABSTRACT Growth inhibition of Streptococcus mutans (SM), Streptococcus salivarius (SS1), and Streptococcus sanguinis (SS2) were determined at different Sparassis latifolia polysaccharides (SLPs) concentrations (2%, 4%, 8%, 16%) mixed with artificial saliva (AS). Metabolomics was determined by the action of 4% SLPs and AS on each bacterium to obtain the bacteriostatic activity of SLPs on oral processing. The results showed that the 16% mixture could inhibit the growth of the oral bacteria S. mutans, S. salivarius, and S. sanguinis. The inhibitory effect on oral bacteria decreased with decreasing polysaccharide concentration. The metabolic pathways and metabolites analyses screened for active inhibitory substances against oral bacteria. These results implied that SLPs are potential new material for developing oral functional products.

Polynomial Estimation of Flux Linkage for Predictive Current Control in PMSM

Abstract: This article presents an automatic parameter identification method based on ordinary least square (OLS) algorithm for deadbeat predictive current control (DPCC) to fulfill the purpose of high steady and dynamic performance in permanent magnet synchronous motor (PMSM) drives. Different from the conventional model, a novel model based on the polynomial estimation of flux linkage is constructed which takes the cross-saturation effects into account. First, the conventional mathematical model of PMSM and the proposed model are presented, respectively, and the inverter considering nonideal factors is also analyzed. Then the parameter identification method is investigated, in which the measurement procedure is delimited in advance and the automatic identification method is developed. Furthermore, a voltage reconstruction algorithm is applied to solve the inverter nonlinearities and the digital time-delay effect, so as to improve the accuracy of the identified parameters. Accordingly, a novel DPCC algorithm is presented based on the proposed model to achieve better performance. Finally, based on the concept and principles mentioned before, a detailed comparison of the DPCC based on the classical model considering the parameters’ variation and the modified model of the proposed method is carried out on a laboratory prototype.

Concentration of Dimer for BCl3 and Rare Gas Atoms in the BCl3 Isotope Separation

Abstract: In the low temperature environment generated by supersonic flow in the process of laser assisted retardation of condensation of isotope separation for BCl3, the molecular isotopes BCl3 and carrier gas RG(RG=He,Ne,Ar,Kr,Xe) could form BCl3:RG dimer via contact collision process, the mechanism and relationship between dimer concentration and absolute temperature of dimer involving BCl3 molecules are of great significance to the regulation and selection of isotope separation parameters. In this work, based on the analytic description on the anharmonic interaction potential function of BCl3:RG, and considered the two-body and three-body collision induced association and dissociation of dimer, the concentration of BCl3:RG dimer is obtained with the absolute temperature in the range of 20~40K. The results show that the two-body collision dominates the formation of dimer in the low temperature region; with the initial molar fraction of BCl3 in the range of 0.01~0.1, the BCl3:RG dimer concentration changes approximately linearly with the initial molar fraction of BCl3, indicating that the initial molar fraction not only determines the theoretical upper limit of the dimer concentration, but also dominates the dimer concentration in the low temperature region. When the temperature of the supersonic flow chamber is about 20K, the concentration of BCl3:Kr dimer is the largest one, and the concentrations of other dimers are also presented. Furthermore, we explain the mechanism of laser assisted retardation of condensation in separation of isotopes using a simple model at the molecular scale by adjusting parameters of dissociation energy and stretching vibration frequency of the dimer.

Respiration and heart rates measurement using 77GHz FMCW radar with blind source separation algorithm

Abstract: This paper presents a blind source separation based signal processing method of measuring respiration and heartbeat rates using frequency modulated continues wave (FMCW) radar with working frequency range 77GHz-81GHz. To improve signal quality, complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) method is used in preprocessing stage to first decompose the phase signal into several intrinsic mode functions (IMFs) and then the phase signal is reconstructed by adding the selected IMFs. The accurate measurement results can be obtained by the proposed method both in separating respiratory and heartbeat signals of one person (the average deviations are 1.1 beat per minute and 6.8 beat per minute respectively), and in separating respiratory signals of two persons.

Performance Assessment of Quantum Processor Based on p-Type Semiconductor Quantum Dot Array

Abstract: A multiscale simulation method is developed to model and assess silicon- and germanium-hole-based quantum dot (QD) arrays for quantum processors. The multiscale process takes a bottom-up approach, which integrates device-level simulations into quantum circuit simulations for semiconductor QD array processors. This process allows essential device physics to be incorporated in the assessment of quantum circuit performance for a Si- or Ge-QD- based quantum processor. The results show that the Ge hole array provides a promising semiconductor platform to enhance entanglement between neighboring QDs for two-qubit quantum gates. Furthermore, a two-qubit quantum gate based on holes in Ge can achieve fast gate speed, and smaller device variability compared to its Si counterpart. Design and multiscale simulation of the Ge QD array processor shows its potential to achieve high fidelity in preparing the ansatz state of quantum chemistry simulations based on variational quantum eigensolver. The bottom-up, multiscale method developed here can allow the physical design and assessment of semiconductor-QD-based quantum processors from the physical properties of quantum gate devices and their underlying material properties.

Odd-Even Hash Algorithm: A Improvement of Cuckoo Hash Algorithm

Abstract: Hash-based data structures and algorithms are currently flourishing on the Internet. It is an effective way to store large amounts of information, especially for applications related to measurement, monitoring and security. At present, there are many hash table algorithms such as: Cuckoo Hash, Peacock Hash, Double Hash, Link Hash and D-left Hash algorithm. However, there are still some problems in these hash table algorithms, such as excessive memory space, long insertion and query operations, and insertion failures caused by infinite loops that require rehashing. This paper improves the kick-out mechanism of the Cuckoo Hash algorithm, and proposes a new hash table structure- Odd-Even Hash (OE Hash) algorithm. The experimental results show that OE Hash algorithm is more efficient than the existing Link Hash algorithm, Linear Hash algorithm, Cuckoo Hash algorithm, etc. OE Hash algorithm takes into account the performance of both query time and insertion time while occupying the least space, and there is no insertion failure that leads to rehashing, which is suitable for massive data storage.