Publications by authors named "Xiaofeng Wang"

871 Publications

Transverse and longitudinal coupling of LSPPs in isolated triangular Al-SiO-Al hybrid nanoplates for generation of local electromagnetic fields with enhanced intensity and increased decay time.

Nanotechnology 2021 Sep 16. Epub 2021 Sep 16.

National Center for Nanoscience and Nanotechnology, No 11,Beiyitiao 11,Zhongguancun, Beijing, 100190, CHINA.

Achieving a large enhancement of local electromagnetic fields in the ultraviolet waveband is desirable for some applications such as surface-enhanced Raman scattering and surface-enhanced fluorescence. In addition, it is more significant for some applications such as plasmon-enhanced harmonic generation to enhance the intensity of local electromagnetic fields and increase their decay time at the same time. In this paper, using the finite-difference time-domain method, we numerically demonstrate that using the linearly polarized light with a wavelength of 325 nm as the illumination light, an isolated triangular Al-SiO-Al hybrid nanoplate with optimized geometric parameters can produce a local electric field enhanced by a factor of about 108 at one of its top apexes, and produce two local electric fields enhanced by a factor of about 150 at two transverse dielectric/metal interfaces of one of its longitudinal side edges. Moreover, we also numerically demonstrate that the decay time of enhanced local electric fields produced by the isolated triangular Al-SiO-Al hybrid nanoplate is about 1.6 times as large as that of enhanced local electric fields produced by an isolated triangular Al nanoplate. These unique properties of the isolated triangular Al-SiO-Al hybrid nanoplate arise because of both the transverse coupling and the longitudinal coupling of localized surface plasmon polaritons (LSPPs) in this structure. Our findings make triangular Al-SiO-Al hybrid nanoplates very promising for application in many fields such as surface-enhanced Raman scattering and plasmon-enhanced harmonic generation.
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http://dx.doi.org/10.1088/1361-6528/ac2767DOI Listing
September 2021

Long non-coding RNA TUG1 knockdown prevents neurons from death to alleviate acute spinal cord injury via the microRNA-338/BIK axis.

Bioengineered 2021 Dec;12(1):5566-5582

Department of Orthopaedics, Huizhou City Center People's Hospital, Huizhou Guangdong, P.R. China.

Taurine up-regulated gene 1 (TUG1) is a cancer-associated long noncoding RNA (lncRNA) and engages in the development of spinal cord injury (SCI), a suffering neuropathological disorder. However, the regulatory role of TUG1 in acute SCI (ASCI) is still underdetermined. RT-qPCR and western blot analysis were applied to measure the expression of TUG1, microRNA-338 (miR-338), Bcl2-interacting killer (BIK), cleaved caspase 3 (c-caspase 3) and hypoxia-inducible factor-1 alpha (HIF-1α) in ASCI rats and hypoxic cells. Cell death was evaluated using flow cytometric analysis. The relationships among miR-338, TUG1 or BIK were confirmed by luciferase reporter assay, RNA immunoprecipitation and RNA pull-down. Accordingly, we monitored higher expression of TUG1 and BIK, but lower expression of miR-338 in ASCI rats and hypoxic cells. , hypoxia expedited cell death and c-caspase 3 levels. , ASCI rats were successfully developed as evidenced by diminished Basso-Beattie-Bresnahan (BBB) locomotor score and enhanced c-caspase 3 and HIF-1α expression. Nevertheless, TUG1 knockdown mitigated the cell death in ASCI rats and hypoxic cells. Mechanically, TUG1 interacted with miR-338 to regulate the BIK expression. Together, TUG1 silencing could alleviate the death in neurons and ASCI models via modulating the miR-338/BIK axis.
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http://dx.doi.org/10.1080/21655979.2021.1966258DOI Listing
December 2021

Computational identification of human ubiquitination sites using convolutional and recurrent neural networks.

Mol Omics 2021 Sep 13. Epub 2021 Sep 13.

College of Life Sciences, Shanxi Normal University, Linfen 041000, China.

Ubiquitination is a very important protein post-translational modification in humans, which is closely related to many human diseases such as cancers. Although some methods have been elegantly proposed to predict human ubiquitination sites, the accuracy of these methods is generally not very satisfactory. In order to improve the prediction accuracy of human ubiquitination sites, we propose a new ensemble method HUbipPred, which takes the binary encoding and physicochemical properties of amino acids as training features, and integrates two intensively trained convolutional neural networks and two recurrent neural networks to build the model. Finally, HUbiPred achieves AUC values of 0.852 and 0.844 in five-fold cross-validation and independent tests, respectively, which greatly improves the prediction accuracy compared to previous predictors. We also analyze the physicochemical properties of amino acids around ubiquitination sites, study the important roles of architectures (, convolution, long short-term memory (LSTM) and fully connected hidden layers) in the networks for prediction performance, and also predict potential ubiquitination sites in humans using HUbiPred. The training and test datasets, predicted human ubiquitination sites, and source codes of HUbiPred are publicly available at https://github.com/amituofo-xf/HUbiPred.
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http://dx.doi.org/10.1039/d0mo00183jDOI Listing
September 2021

Fabrication of Highly Interconnected Poly(ε-caprolactone)/cellulose Nanofiber Composite Foams by Microcellular Foaming and Leaching Processes.

ACS Omega 2021 Sep 25;6(35):22672-22680. Epub 2021 Aug 25.

School of Mechanics & Safety Engineering, National Center for International Joint research of Micro-Nano Molding Technology, Zhengzhou University, Zhengzhou 450001, China.

In this study, microcellular polycaprolactone (PCL)/sodium bicarbonate (NaHCO)/cellulose nanofiber (CNF) composite foams with highly interconnected porous structures were successfully fabricated by microcellular foaming and particle leaching processes. Supercritical CO (scCO) served as a physical foaming agent, NaHCO was chosen as a chemical foaming agent and porogen, and CNF acted as a heterogeneous nucleating agent. The effect of scCO, NaHCO, and CNF on pore structures and the cofoaming mechanism were investigated. The results indicated that the addition of NaHCO and CNF increased the melt strength of the PCL matrix significantly. During the foaming process, the presence of CNF can form a rigid network due to the hydrogen bonding or mechanical entanglement between individual nanofibers, improving the nucleating efficiency but slowing down the cell growth rate. Additionally, due to the interaction of "soft" PCL matrix and "hard" domains in a PCL-based composite during the foaming process, together with the NaHCO leaching process, highly interconnected cell structures appeared. The obtained PCL/NaHCO/CNF composite foams had a cell size of 15.8 μm and cell density of 6.3 × 10 cells/cm, as well as an open-cell content of 82%. The reported strategy in this paper may provide the guidelines and data supports for the fabrication of a PCL-based porous scaffold.
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http://dx.doi.org/10.1021/acsomega.1c02768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8427651PMC
September 2021

Ultrasonographic Features of Hypertrophic Interureteral Cristae in Transabdominal and Transrectal Ultrasonography.

Ultrasound Q 2021 Sep;37(3):244-247

Department of Ultrasound, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China.

Purpose: The aim of this study was to determine the value of transrectal ultrasound in the definitive diagnosis of hypertrophic interureteral cristae and to provide a definitive diagnostic basis for clinical treatment.

Materials And Methods: When the patient's bladder fills moderately, the ultrasound physician uses the transabdominal ultrasound probe to examine the patient's bladder and prostate carefully, focusing on bilateral ureterovesical portals, a cord-like hyperechoic structure visible between the bilateral ureterovesical portals. For further detailed observation, transrectal probe was used to measure the size of Hypertrophic Interureteral Cristae and describe the shape and internal echo. After the examination, the residual urine volume of bladder was measured after one-time urination.

Results: Hypertrophic interureteral cristae was a trilinear structure with a "high-low-high" echo. All the 33 patients had bladder wall thickening. In 9 cases of overfilling of bladder, there were slightly dilated ureterovesical portals at both ends of hypertrophic interureteral cristae. Thirty cases of benign prostatic hyperplasia, 11 patients who had undergone prostate hyperplasia surgery, 26 cases with different degrees trabecular and reticular hyperplasia of bladder wall, there were 9 cases with bladder diverticulum and 23 cases with mild hydronephrosis.

Conclusions: Transrectal ultrasound can confirm the diagnosis of Hypertrophic Interureteral Cristae.
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http://dx.doi.org/10.1097/RUQ.0000000000000481DOI Listing
September 2021

Insights from QM/MM-ONIOM calculations: the TADF phenomenon of phenanthro[9,10-]imidazole-anthraquinone in the solid state.

Phys Chem Chem Phys 2021 Sep 2. Epub 2021 Sep 2.

School of Chemical Engineering and Technology, Tianshui Normal University, Tianshui, Gansu 741001, China.

In this paper, we employed first-principles methods and the QM/MM technique to study the thermally activated delayed fluorescence (TADF) phenomenon of a near-infrared molecule (PIPAQ) in vacuum, solution, and the aggregation state. Our calculated results show that (1) the cluster can decrease the energy gap between the first singlet excited state (S) and the first triplet state (T) compared with the monomer, furthermore, the T state and S state in the cluster are energetically closer to each other, which implies that the energy gap is smaller in comparison with that in solution and can promote the intersystem crossing (ISC) process due to the surrounding effect; (2) the optimally tuned range-separated functional is applicable to simulation of excited states and the outcomes are in good agreement with experimental values; (3) the reorganization energies associated with ISC and the reverse intersystem crossing (RISC) processes between the S and T states are sensitive to the calculated methods and the environments, and thus the following calculated ISC and RISC rates vary dramatically according to different reorganization energies; (4) all radiative and nonradiative rates are insensitive to temperature, but sensitive to environments, all the radiative rates increase in the cluster while the nonradiative rates decrease, which enhances the fluorescence quantum efficiency and agrees with the observed value. The above results demonstrate that the surrounding effects are very important for modulating the photophysical properties of the PIPAQ compound. Finally, this studied conclusion can give a helpful insight into the TADF mechanism for the title compounds, by which novel TADF materials with excellent performance could be rationally designed.
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http://dx.doi.org/10.1039/d1cp00578bDOI Listing
September 2021

Complete genome sequencing and comparative analysis of Citrobacter koseri CKNJ, a strain isolated from patient with endogenous endophthalmitis.

Jpn J Infect Dis 2021 Aug 31. Epub 2021 Aug 31.

Department of Infectious Diseases, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, China.

Citrobacter koseri is an opportnistic pathogen can cause a variety of diseases. Though the mortality rate of C. koseri infections is high but there is a paucity of clinical information on them. Furthermore, the genomic features of this species are poorly studied. Herein, we presented a patient with endogenous endophthalmitis secondary to septicaemia, and collected a C. koseri isolate, CKNJ, from the blood of the patient. Whole genome sequencing revealed that the CKNJ harbors no plasmid and codes for 67 putative virulence factors. Whole genome SNP-based phylogenetic analysis revealed that strain CKNJ was close to the strains with same isolation sites. Compared to the other sequenced C. koseri chromosomes, CKNJ contains several strain-variable regions, including one prophage and two large genomic islands. The sequencing of the first complete genome of a clinical strain from China should reinforce our understanding of the genomic features and pathogenicity of this invasive infection-causing C. koseri with clinical significance.
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http://dx.doi.org/10.7883/yoken.JJID.2021.334DOI Listing
August 2021

Event-Triggered Control for Markov Jump Systems Subject to Mismatched Modes and Strict Dissipativity.

IEEE Trans Cybern 2021 Sep 1;PP. Epub 2021 Sep 1.

In order to save network resources of discrete-time Markov jump systems, an event-triggered control framework is employed in this article. The threshold parameter in the event-triggered mechanism is designed as a diagonal matrix in which all elements can be adjusted according to system performance requirements. The hidden Markov model is introduced to characterize the asynchronization between the controller and controlled system. The effect of randomly occurring gain fluctuations is taken into account during the controller design. For the purpose of guaranteeing that the closed-loop system is stochastically stable and satisfies the strictly (D₁,D₂,D₃)-ɣ-dissipative performance, sufficient conditions are constructed by employing the Lyapunov function and stochastic analysis. After linearization, the proposed controller gains are obtained by solving the linear matrix inequalities. Ultimately, a practical example of the dc motor device is used to illustrate the effectiveness of the proposed new design technique.
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http://dx.doi.org/10.1109/TCYB.2021.3105179DOI Listing
September 2021

The STING-IRF3 pathway contributes to paraquat-induced acute lung injury.

Toxicol Mech Methods 2021 Aug 29:1-40. Epub 2021 Aug 29.

Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.

Immune and inflammatory responses play significant roles in paraquat (PQ)-induced acute lung injury (ALI), but the specific mechanisms remain unclear. Our study aimed to investigate the action of STING-IRF3 signaling on PQ-induced ALI in mice. Following PQ administration, samples were collected at 2, 12, 24, and 48 h for in vivo studies, and 24 h for in vitro studies. Following PQ administration (30 mg/kg, i.p.), injury to mouse lungs was evaluated by H&E staining and wet/dry ratios, and lung oxidative damage was evaluated by MDA and SOD assays. The mRNA levels of , , and were detected by RT-PCR, the expression of STING and IRF3 were assessed by western blotting and IHC/IF, and the secretion of IFNβ was detected by ELISA. In vivo, PQ administration induced pathological changes and increased wet/dry ratios in lungs after 48 h. , , and mRNA levels in lung tissues, STING and pIRF3 protein levels in lung tissues, and IFNβ secretion in serum, were upregulated by PQ in a time-dependent manner. PQ administration promoted IRF3 nuclear translocation in lung tissues after 48 h. The above changes were all attenuated by dexamethasone treatment (5 mg/kg, i.p., qd). In vitro, PQ induced STING and IRF3 translocation. or silencing decreased the mRNA levels and supernatant secretion of IFNβ in PQ-treated RAW264.7 mouse macrophages. silencing also inhibited the protein and mRNA levels of IRF3 in vitro. Our study suggests that STING-IRF3 signaling contributes to PQ-induced ALI, providing new information for future treatment strategies.
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http://dx.doi.org/10.1080/15376516.2021.1974133DOI Listing
August 2021

Privacy-preserving genotype imputation in a trusted execution environment.

Cell Syst 2021 Aug 20. Epub 2021 Aug 20.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

Genotype imputation is an essential tool in genomics research, whereby missing genotypes are inferred using reference genomes to enhance downstream analyses. Recently, public imputation servers have allowed researchers to leverage large-scale genomic data resources for imputation. However, privacy concerns about uploading one's genetic data to a server limit the utility of these services. We introduce a secure hardware-based solution for privacy-preserving genotype imputation, which keeps the input genomes private by processing them within Intel SGX's trusted execution environment. Our solution features SMac, an efficient and secure imputation algorithm designed for Intel SGX, which employs a state-of-the-art imputation strategy also utilized by existing imputation servers. SMac achieves imputation accuracy equivalent to existing tools and provides protection against known side-channel attacks on SGX while maintaining scalability. We also show the necessity of our enhanced security by identifying vulnerabilities in existing imputation software. Our work represents a step toward privacy-preserving genomic analysis services.
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http://dx.doi.org/10.1016/j.cels.2021.08.001DOI Listing
August 2021

Duration of noninvasive ventilation is not a predictor of clinical outcomes in patients with acute exacerbation of COPD and respiratory failure.

Can J Respir Ther 2021 18;57:113-118. Epub 2021 Aug 18.

Respiratory Institute, Cleveland Clinic, Cleveland, OH, USA.

Purpose: Acute exacerbation of chronic obstructive pulmonary disease (COPD) is a major cause of mortality and morbidity. Noninvasive ventilation (NIV) is proven to be effective in the majority of patients with acute exacerbation COPD (AECOPD) complicated with respiratory failure. NIV could be lifesaving but also can delay mechanical ventilation if its efficacy is not assessed in a timely manner. In this study, we analyzed potential predictors of NIV failure in AECOPD in a tertiary medical intensive care unit (MICU). In particular, we wondered whether duration of NIV among those who eventually failed was associated with poor outcomes.

Methods: A retrospective review of consecutive patients with a primary diagnosis of AECOPD requiring NIV admitted to the MICU was conducted for the period between 2012 and 2017. Baseline data included demographics, APACHE III score, albumin level, blood lactate, and blood gas elements. Additional chart review was performed to collect NIV setting parameters on presentation to the MICU. Clinical outcome variables collected included outcome and duration of NIV, duration of invasive mechanical ventilation, MICU length of stay, hospital length of stay, and in-hospital mortality. Multivariate regression analysis was performed to determine independent variables associated with clinical outcomes.

Results: There were 370 patients who met the inclusion criteria; 53.2% were male. Mean age was 64.7 ± 11.2 years old. Mean baseline FEV was 34 ±17% of predicted. Patients had mean pH of 7.20 ± 0.54 and PCO of 70.3 ± 28.7 on presentation; 323 patients (87.3%) were successfully weaned off NIV; 47 patients (12.7%) failed NIV and required invasive mechanical ventilation. APACHE III score was higher among patients who failed NIV (68.3±18.9 versus 48.8± 15.2, < 0.001). In the subset of 47 patients who failed NIV requiring intubation, duration of NIV was 25.0 ± 58.8 h. Multivariate regression analysis yielded a model consisting of APACHE III score and body mass index as predictive variables for NIV failure (C-statistic = 0.809). Duration of NIV was not associated with worse clinical outcomes among patients who failed NIV.

Conclusions: NIV is successful in preventing invasive mechanical ventilation in majority of patients with acute respiratory failure due to COPD. Patients with worse clinical status at presentation are more likely to fail NIV and require mechanical ventilation. In the subgroup of patients who failed NIV, duration of NIV prior to intubation was not associated with poor clinical outcomes.
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http://dx.doi.org/10.29390/cjrt-2021-021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8372872PMC
August 2021

SAG-DTA: Prediction of Drug-Target Affinity Using Self-Attention Graph Network.

Int J Mol Sci 2021 Aug 20;22(16). Epub 2021 Aug 20.

College of Computer Science and Technology, Qingdao University, Qingdao 266071, China.

The prediction of drug-target affinity (DTA) is a crucial step for drug screening and discovery. In this study, a new graph-based prediction model named SAG-DTA (self-attention graph drug-target affinity) was implemented. Unlike previous graph-based methods, the proposed model utilized self-attention mechanisms on the drug molecular graph to obtain effective representations of drugs for DTA prediction. Features of each atom node in the molecular graph were weighted using an attention score before being aggregated as molecule representation. Various self-attention scoring methods were compared in this study. In addition, two pooing architectures, namely, global and hierarchical architectures, were presented and evaluated on benchmark datasets. Results of comparative experiments on both regression and binary classification tasks showed that SAG-DTA was superior to previous sequence-based or other graph-based methods and exhibited good generalization ability.
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http://dx.doi.org/10.3390/ijms22168993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8396496PMC
August 2021

MCN-CPI: Multiscale Convolutional Network for Compound-Protein Interaction Prediction.

Biomolecules 2021 07 29;11(8). Epub 2021 Jul 29.

College of Computer Science and Technology, Qingdao University, Qingdao 266071, China.

In the process of drug discovery, identifying the interaction between the protein and the novel compound plays an important role. With the development of technology, deep learning methods have shown excellent performance in various situations. However, the compound-protein interaction is complicated and the features extracted by most deep models are not comprehensive, which limits the performance to a certain extent. In this paper, we proposed a multiscale convolutional network that extracted the local and global features of the protein and the topological feature of the compound using different types of convolutional networks. The results showed that our model obtained the best performance compared with the existing deep learning methods.
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http://dx.doi.org/10.3390/biom11081119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8392217PMC
July 2021

An alternative start regimen with aripiprazole once-monthly in patients with schizophrenia: population pharmacokinetic analysis of a single-day, two-injection start with gluteal and/or deltoid intramuscular injection.

Curr Med Res Opin 2021 Aug 27:1-12. Epub 2021 Aug 27.

Otsuka Pharmaceutical Development & Commercialization, Inc, Princeton, NJ, USA.

Background: The single-injection start regimen for aripiprazole once-monthly 400 mg (AOM 400) in patients with schizophrenia requires a single intramuscular injection in the gluteal or deltoid site and 14 days of concurrent oral therapy. A simplified, single-day regimen of two injections at separate gluteal and/or deltoid injection sites, together with a single 20-mg dose of oral aripiprazole on the 1st day, was assessed.

Patients And Methods: A previously developed population-pharmacokinetic (popPK) model for characterizing aripiprazole PK following oral administration and gluteal intramuscular depot injection was expanded to include deltoid injection. Simulations were conducted to assess PK profiles following various (including two-injection) start regimens. Postmarketing data on patients who received higher-than-recommended AOM doses were used to assess overall safety/tolerability.

Results: The two-injection start regimen with a single concurrent oral dose displayed a comparable PK profile to the single-injection start regimen with concurrent 14-day oral administration in simulations. The safety assessment indicated the two-injection start regimen was unlikely to be associated with safety concerns beyond those expected with a single-injection start regimen.

Conclusion: These data support use of the two-injection start regimen in clinical practice to reduce reliance on daily oral administration and optimize the therapeutic benefits of AOM 400 in patients with schizophrenia.
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http://dx.doi.org/10.1080/03007995.2021.1965974DOI Listing
August 2021

Host GRXC6 restricts Tomato yellow leaf curl virus infection by inhibiting the nuclear export of the V2 protein.

PLoS Pathog 2021 Aug 16;17(8):e1009844. Epub 2021 Aug 16.

Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China.

Geminiviruses cause serious symptoms and devastating losses in crop plants. With a circular, single-stranded DNA genome, geminiviruses multiply their genomic DNA in the nucleus, requiring the nuclear shuttling of viral proteins and viral genomic DNAs. Many host factors, acting as proviral or antiviral factors, play key roles in geminivirus infections. Here, we report the roles of a tomato glutaredoxin (GRX), SlGRXC6, in the infection of Tomato yellow leaf curl virus (TYLCV), a single-component geminivirus. The V2 protein of TYLCV specifically and preferentially interacts with SlGRXC6 among the 55-member tomato GRX family that are broadly involved in oxidative stress responses, plant development, and pathogen responses. We show that overexpressed SlGRXC6 increases the nuclear accumulation of V2 by inhibiting its nuclear export and, in turn, inhibits trafficking of the V1 protein and viral genomic DNA. Conversely, the silenced expression of SlGRXC6 leads to an enhanced susceptibility to TYLCV. SlGRXC6 is also involved in symptom development as we observed a positive correlation where overexpression of SlGRXC6 promotes while knockdown of SlGRXC6 expression inhibits plant growth. We further showed that SlGRXC6 works with SlNTRC80, a tomato NADPH-dependent thioredoxin reductase, to regulate plant growth. V2 didn't interact with SlNTRC80 but competed with SlNTR80 for binding to SlGRXC6, suggesting that the V2-disrupted SlGRXC6-SlNTRC80 interaction is partially responsible for the virus-caused symptoms. These results suggest that SlGRXC6 functions as a host restriction factor that inhibits the nuclear trafficking of viral components and point out a new way to control TYLCV infection by targeting the V2-SlGRXC6 interaction.
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http://dx.doi.org/10.1371/journal.ppat.1009844DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8389846PMC
August 2021

Incorporation of quantitative MRI in a model to predict temporal lobe epilepsy surgery outcome.

Brain Commun 2021 16;3(3):fcab164. Epub 2021 Jul 16.

Department of Neurology, Epilepsy Center, Cleveland Clinic, Cleveland, OH, USA.

Quantitative volumetric brain MRI measurement is important in research applications, but translating it into patient care is challenging. We explore the incorporation of clinical automated quantitative MRI measurements in statistical models predicting outcomes of surgery for temporal lobe epilepsy. Four hundred and thirty-five patients with drug-resistant epilepsy who underwent temporal lobe surgery at Cleveland Clinic, Mayo Clinic and University of Campinas were studied. We obtained volumetric measurements from the pre-operative T1-weighted MRI using NeuroQuant, a Food and Drug Administration approved software package. We created sets of statistical models to predict the probability of complete seizure-freedom or an Engel score of I at the last follow-up. The cohort was randomly split into training and testing sets, with a ratio of 7:3. Model discrimination was assessed using the concordance statistic (C-statistic). We compared four sets of models and selected the one with the highest concordance index. Volumetric differences in pre-surgical MRI located predominantly in the frontocentral and temporal regions were associated with poorer outcomes. The addition of volumetric measurements to the model with clinical variables alone increased the model's C-statistic from 0.58 to 0.70 (right-sided surgery) and from 0.61 to 0.66 (left-sided surgery) for complete seizure freedom and from 0.62 to 0.67 (right-sided surgery) and from 0.68 to 0.73 (left-sided surgery) for an Engel I outcome score. 57% of patients with extra-temporal abnormalities were seizure-free at last follow-up, compared to 68% of those with no such abnormalities (-value = 0.02). Adding quantitative MRI data increases the performance of a model developed to predict post-operative seizure outcomes. The distribution of the regions of interest included in the final model supports the notion that focal epilepsies are network disorders and that subtle cortical volume loss outside the surgical site influences seizure outcome.
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http://dx.doi.org/10.1093/braincomms/fcab164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8361423PMC
July 2021

More metalwork removals in patients with olecranon fracture treated by tension band wiring than plate fixation-a propensity score matching analysis.

BMC Musculoskelet Disord 2021 Aug 13;22(1):692. Epub 2021 Aug 13.

Department of Traumatology and Orthopaedic Surgery, Institute of Orthopaedics, Huizhou Municipal Central Hospital, Huizhou, Guangdong, 516001, People's Republic of China.

Background: Traditional tension band wiring and plate fixation represent the commonest methods for treating olecranon fractures. However, there is no agreement on which method provides the best outcome. The aim of this retrospective study is to compare the outcomes of tension band wiring (TBW) and plate fixation (PF) for treating displaced olecranon fractures. This is the first study to use propensity score matching analysis to compare treatment methods for olecranon fracture.

Method: A total of 107 patients aged between 18 and 85 had acute isolated and displaced olecranon fractures. The patients were divided into either TBW (n = 49) or PF (n = 58) groups. To conduct propensity score matching for the treatment method (TBW versus PF), 58 patients were analyzed by logistic regression (29 patients in each group). Various demographic and treatment-related variables were examined and analyzed to determine their correlation.

Results: Functional effects between two groups are similar (in terms of Mayo Elbow Performance Score (MEPS), the patients' range of elbow motion (ROM) and forearm rotation (RFR), the time return to work (RTW)). The total adverse events rate and metalwork removal events rate are higher in TBW than that in PF. After propensity score matching analysis, similar primary treatment efficacy (indicated by MEPS> 90) in 2 groups and more primary adverse events (indicated by metalwork removal) were perceived in TBW than that in PF. Logistic regression analysis revealed that fracture type was an independent factor that affected the efficacy of a treatment (regression coefficient = - 1.24 < 0, P = 0.03), indicating that fracture severity was inversely proportional to the efficacy of a treatment for olecranon fracture. Furthermore, logistic regression analysis demonstrated that the treatment method was an independent factor that affected metalwork removal of olecranon fracture (regression coefficient 2.38 > 0, OR = 10.77, P < 0.01), indicating that the risk of metalwork removal in the TBW Group was 10.77 times that in the PF Group.

Conclusion: When initially discussing the surgical approach with patients, physicians should fully weigh the possibility that TBW may lead to a second surgery due to the higher risk of internal fixation removal and that TBW won't yield better functional outcomes than PF .
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http://dx.doi.org/10.1186/s12891-021-04559-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8364058PMC
August 2021

High Expression of Associates with Tumor Progression in Papillary Thyroid Cancer.

Cancer Biother Radiopharm 2021 Aug 12. Epub 2021 Aug 12.

Department of Breast and Thyroid Surgery, Dongying People's Hospital, Dongying, P.R. China.

(WW domain-containing E3 ubiquitin protein ligase 1) is increased in several kinds of carcinomas, but the influence of in papillary thyroid cancer (PTC) is not well understood. The expression of in PTC tissues and cells is detected by real-time reverse transcription PCR. The biological role of on PTC cell growth, apoptosis, migration, and invasion ability was assessed with the Cell Counting Kit-8, colony forming, flow cytometry, wound healing, and transwell assays, respectively. The expression of mRNA and protein is increased in PTC tissue samples and cells. There is closely correlation between the up expression of and clinical parameters, such as tumor size, TNM, and distant metastasis. Knockdown of blocks cell proliferation, migration, and invasion, causes cell cycle arrest, and induces apoptosis in PTC cells. Knockdown of increases PTEN level and reduces p-PI3K and p-Akt level in PTC cells. Knockdown of suppressed cell proliferation, migration, and invasion of PTC cell by downregulating the expression of p-PI3K and p-Akt, contributing to their understanding the pathogenesis of PTC.
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http://dx.doi.org/10.1089/cbr.2020.4148DOI Listing
August 2021

The regulation of long non-coding RNA 00958 (LINC00958) for oral squamous cell carcinoma (OSCC) cells death through absent in melanoma 2 (AIM2) depending on microRNA-4306 and Sirtuin1 (SIRT1) in vitro.

Bioengineered 2021 Dec;12(1):5085-5098

Department of Stomatology, The Second Affiliated Hospital of Harbin Medical University, Heilongjiang, China.

Long non-coding RNAs (lncRNAs) have been proposed as potential targets in OSCC gene therapy. Thus, the study aims to analyze how they exert functions in OSCC. LINC00958, AIM2, Gasdermin D (GSDMD) and tumor protein p53 (TP53) expression levels are analyzed by Quantitative Real-time PCR (qPCR) or Western blotting (WB) in OSCC cells lines. The roles of LINC00958 in cell proliferation, cell death, and GSDMD expression respectively were analyzed by Cell Counting Kit-8 (CCK8) assay, flow cytometry and Immunofluorescence (IF) assay. In addition, expressions of pyroptosis- and autophagy-related proteins are evaluated by WB detection. The targeted binding of LINC00958 and miR-4306 or AIM2 mRNA is predicted by bioinformatics analysis and detected by biodual luciferase system. RIP and qPCR assays analyze whether LINC00958 interacts with SIRT1. We found that LINC00958 showed upregulation in OSCC cells compared to normal oral epithelial cells. LINC00958 silencing significantly suppressed OSCC cell proliferation, induced cell death and reduced autophagy. LINC00958 regulated the levels of miR-4306 which binds to the 3'UTR of AIM2, and interacts with and modulates SIRT1 protein expression. LINC00958 regulated GSDMD and AIM2 levels, as well as p53 and SIRT1 levels. SIRT1 overexpression markedly reversed aforementioned effects of LINC00958. LINC00958 not only downregulated miR-4306 levels to activate the pyroptosis pathway mediated by AIM2 and promoted cancer cell survival but also induced a decrease in SIRT protein expression to further reduce p53 levels.
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http://dx.doi.org/10.1080/21655979.2021.1955561DOI Listing
December 2021

Measurement error and reliability of TMS metrics collected from biceps and triceps in individuals with chronic incomplete tetraplegia.

Exp Brain Res 2021 Aug 10. Epub 2021 Aug 10.

Plow Lab (ND 20), Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Ave, ND20, Cleveland, OH, 44195, USA.

Transcranial magnetic stimulation (TMS) is used to investigate corticomotor neurophysiology associated with functional recovery in individuals with spinal cord injury (SCI). There is insufficient evidence about test-retest measurement properties of TMS in SCI. Therefore, we investigated test-retest agreement and reliability of TMS metrics representing corticomotor excitability, output, gain, map (representation), and inhibition in individuals with cervical SCI. We collected TMS metrics from biceps and triceps muscles because of the relevance of this proximal muscle pair to the cervical SCI population. Twelve individuals with chronic C3-C6 SCI participated in two TMS sessions separated by ≥ 2 weeks. Measurement agreement was evaluated using t tests, Bland-Altman limits of agreement and relative standard error of measurement (SEM%), while reliability was investigated using intra-class correlation coefficient (ICC) and concordance correlation coefficient (CCC). We calculated the smallest detectable change for all TMS metrics. All TMS metrics except antero-posterior map coordinates and corticomotor inhibition were in agreement upon repeated measurement though limits of agreement were generally large. Measures of corticomotor excitability, output and medio-lateral map coordinates had superior agreement (SEM% < 10). Metrics representing corticomotor excitability, output, and inhibition had good-to-excellent reliability (ICC/CCC > 0.75). The smallest detectable change for TMS metrics was generally high for a single individual, but this value reduced substantially with increase in sample size. We recommend use of corticomotor excitability and recruitment curve area owing to their superior measurement properties. A modest group size (20 or above) yields more stable measurements, which may favor use of TMS metrics in group level modulation after SCI.
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http://dx.doi.org/10.1007/s00221-021-06160-2DOI Listing
August 2021

LINC01783 accelerated tongue squamous cell carcinoma progression via inhibiting miR-199b-5p.

J Cell Mol Med 2021 Sep 7;25(17):8140-8147. Epub 2021 Aug 7.

Jinan Stomatological Hospital, Jinan, China.

Growing studies illustrated that lncRNAs exert critical roles in development and occurrence of tumours including TSCC. In this research, we indicated that LINC01783 was up-regulated in TSCC cells (SCC1, Cal27, UM1 and SCC4) when compared to NHOK cell. RT-qPCR analysis indicated that LINC01783 was overexpressed in 22 TSCC cases (73.3%, 22/30) compared with no-tumour specimens. LINC01783 level was up-regulated in TSCC specimens when compared to no-tumour specimens. Ectopic expression of LINC01783 promoted TSCC cell cycle and growth and EMT progression in both TSCC cell SCC1 and Cal27. Overexpression of LINC01783 sponged miR-199b-5p in TSCC cell and elevated expression of LINC01783 inhibited miR-199b-5p expression. Moreover, we illustrated that miR-199b-5p was down-regulated in TSCC cells and specimen and LINC01783 level was up-regulated in TSCC specimens when compared to no-tumour specimens. Elevated expression of LINC01783 promoted TSCC cell growth, cycle and EMT progression by sponging miR-199b-5p. These data suggested that LINC01783 functioned as one oncogene and might be one treatment target for TSCC.
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http://dx.doi.org/10.1111/jcmm.16352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8419183PMC
September 2021

Circ_0025908 regulates cell vitality and proliferation via miR-137/HIPK2 axis of rheumatic arthritis.

J Orthop Surg Res 2021 Jul 30;16(1):472. Epub 2021 Jul 30.

Department of Traumatic Orthopedics, Institute of Orthopedics, Huizhou Central People's Hospital, No. 41, North E'ling Road, Huizhou, 516000, Guangdong Province, China.

Background: Rheumatic arthritis (RA) is an autoimmune disease with bad effects. Recent researches have shown that circular RNAs (circRNAs) could affect the progress of RA, but the mechanism still indistinct. In this work, we explored the roles of circ_0025908 in RA.

Methods: The levels of circ_0025908, microRNA-137 (miR-137), and mRNA of homeodomain-interacting protein kinase 2 (HIPK2) were detected by quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) in RA tissues. Meanwhile, the level of HIPK2 was quantified by Western blot analysis. Besides, the cell functions were examined by CCK8 assay, EdU assay, flow cytometry assay, ELISA, and Western blot. Furthermore, the interplay between miR-137 and circ_0025908 or HIPK2 was detected by dual-luciferase reporter assay.

Results: The levels of circ_0025908 and HIPK2 were upregulated, and the miR-137 level was decreased in RA tissues in contrast to that in normal tissues. For functional analysis, circ_0025908 deficiency inhibited cell vitality, cell mitotic cycle, cell proliferation, and immunoreaction in RA cells, whereas promoted cell apoptosis. Moreover, miR-137 was confirmed to repress the progression of RA cells by suppressing HIPK2. In mechanism, circ_0025908 acted as a miR-137 sponge to regulate the level of HIPK2.

Conclusion: Circ_0025908 facilitates the development of RA through increasing HIPK2 expression by regulating miR-137, which also offered an underlying targeted therapy for RA treatment.
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http://dx.doi.org/10.1186/s13018-021-02615-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8323297PMC
July 2021

Decreased levels of immune-regulatory cytokines in patients with immune thrombocytopenia and long-lasting overexpression of these cytokines in the splenectomized patients.

J Leukoc Biol 2021 08;110(2):335-341

Department of Hematology, Zhongshan Hospital, Qingpu Branch, Fudan University, Shanghai, China.

Immune thrombocytopenia (ITP) is an autoimmune-mediated disease characterized by decreased platelet counts. Cytokines play important roles in modulating the immune response and are involved in the pathogenesis of many autoimmune diseases. This study aimed at exploring the serum levels of a core set of cytokines that exert immune-regulatory functions in newly diagnosed ITP patients (both before and after treatment) and splenectomized ITP patients. Using the Bio-Plex suspension array system and ELISA, the serum levels of IL-10, IL-21, IL-27, IL-33, IL-35, IL-37, and TGF-β were detected. The data showed that the serum levels of the immune regulatory cytokines IL-10, IL-35, and TGF-β were significantly lower in newly diagnosed ITP patients. Decreased cytokine levels could be improved in patients with a complete response or a response after steroid-based treatment(s). The serum concentrations of TGF-β were positively correlated with the platelet counts both before and after treatment. All the detected immune-regulatory cytokines, except IL-37, showed significantly higher levels in splenectomized ITP patients than pretreatment ITP patients and healthy controls. In conclusion, these data suggest that lower levels of immune-regulatory cytokines are involved in the pathogenesis of ITP and that there is a long-lasting overexpression of immune-regulatory cytokines in ITP patients with splenectomy.
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http://dx.doi.org/10.1002/JLB.5AB0521-621RRDOI Listing
August 2021

Cognitive frailty predicting death and disability in Chinese elderly.

Neurol Res 2021 Jul 27:1-9. Epub 2021 Jul 27.

Department of Neurology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.

Objective: Cognitive frailty (CF) is associated with adverse health outcomes, but different CF models have been proposed in the literature. We explored whether cognitive impairment (CoI) assessed by the Revised Hasegawa dementia scale (HDS-R) and physical frailty (PF) assessed by the modified Frailty Phenotype can be combined to predict risks of adverse outcomes in elderly Chinese subjects.

Methods: The data collected in the Rugao Longevity and Aging Study were used. PF was assessed by the modified Frailty phenotype. CoI was defined as the lowest 20% of the HDS-R score. CF was defined as the co-existence of physical frailty and CoI, excluding those with severe CoI(HDR-S ≤ 10). The date and cause of death were acquired from the Death registry of Rugao's Civil Affairs Bureau. Disability was measured using the activities of daily living (ADL) scale.

Results: The prevalence of CF was 2.9% at baseline. During 3-year follow-up, 130 (8.1%) of the 1607 elderly subjects died. The highest mortality risk was observed among subjects with CF (hazard ratio [HR] = 2.94, 95% confidence interval [CI] = 1.28-6.78). Fully adjusted survival plots showed that CF was associated with the highest risk for 3-year mortality. The incidence of ADL disability was 6.0% after 3 years. Compared with the robust and non-CoI elderly, CF was associated with a 10.48-fold (95% CI 2.98-36.80) higher risk of ADL disability.

Conclusions: The CF model defined as a combination of HDS-R and Frail Phenotypes showed predictive validity for all-cause death and new-onset ADL disability 3 years later.
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http://dx.doi.org/10.1080/01616412.2021.1939235DOI Listing
July 2021

The Influence of Filler Size and Crosslinking Degree of Polymers on Mullins Effect in Filled NR/BR Composites.

Polymers (Basel) 2021 Jul 12;13(14). Epub 2021 Jul 12.

College of Chemistry, Jilin University, Changchun 130012, China.

Two factors, the crosslinking degree of the matrix () and the size of the filler (), have significant impact on the Mullins effect of filled elastomers. Herein, the result. of the two factors on Mullins effect is systematically investigated by adjusting the crosslinking degree of the matrix via adding maleic anhydride into a rubber matrix and controlling the particle size of the filler via ball milling. The dissipation ratios (the ratio of energy dissipation to input strain energy) of different filled natural rubber/butadiene rubber (NR/BR) elastomer composites are evaluated as a function of the maximum strain in cyclic loading (). The dissipation ratios show a linear relationship with the increase of within the test range, and they depend on the composite composition ( and ). With the increase of , the dissipation ratios decrease with similar slope, and this is compared with the dissipation ratios increase which more steeply with the increase in . This is further confirmed through a simulation that composites with larger particle size show a higher strain energy density when the strain level increases from 25% to 35%. The characteristic dependence of the dissipation ratios on and is expected to reflect the Mullins effect with mathematical expression to improve engineering performance or prevent failure of rubber products.
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http://dx.doi.org/10.3390/polym13142284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8309370PMC
July 2021

Modification of Threonine-825 of SlBRI1 Enlarges Cell Size to Enhance Fruit Yield by Regulating the Cooperation of BR-GA Signaling in Tomato.

Int J Mol Sci 2021 Jul 18;22(14). Epub 2021 Jul 18.

State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China.

Brassinosteroids (BRs) are growth-promoting phytohormones that can efficiently function by exogenous application at micromolar concentrations or by endogenous fine-tuning of BR-related gene expression, thus, precisely controlling BR signal strength is a key factor in exploring the agricultural potential of BRs. BRASSINOSTEROID INSENSITIVE1 (BRI1), a BR receptor, is the rate-limiting enzyme in BR signal transduction, and the phosphorylation of each phosphorylation site of SlBRI1 has a distinct effect on BR signal strength and botanic characteristics. We recently demonstrated that modifying the phosphorylation sites of tomato SlBRI1 could improve the agronomic traits of tomato to different extents; however, the associated agronomic potential of SlBRI1 phosphorylation sites in tomato has not been fully exploited. In this research, the biological functions of the phosphorylation site threonine-825 (Thr-825) of SlBRI1 in tomato were investigated. Phenotypic analysis showed that, compared with a tomato line harboring SlBRI1, transgenic tomato lines expressing SlBRI1 with a nonphosphorylated Thr-825 (T825A) exhibited a larger plant size due to a larger cell size and higher yield, including a greater plant height, thicker stems, longer internodal lengths, greater plant expansion, a heavier fruit weight, and larger fruits. Molecular analyses further indicated that the autophosphorylation level of SlBRI1, BR signaling, and gibberellic acid (GA) signaling were elevated when SlBRI1 was dephosphorylated at Thr-825. Taken together, the results demonstrated that dephosphorylation of Thr-825 can enhance the functions of SlBRI1 in BR signaling, which subsequently activates and cooperates with GA signaling to stimulate cell elongation and then leads to larger plants and higher yields per plant. These results also highlight the agricultural potential of SlBRI1 phosphorylation sites for breeding high-yielding tomato varieties through precise control of BR signaling.
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http://dx.doi.org/10.3390/ijms22147673DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8305552PMC
July 2021

A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation.

Cell 2021 08 7;184(17):4392-4400.e4. Epub 2021 Jul 7.

Department of Biomedical Sciences and Pathobiology, VA-MD Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA. Electronic address:

The coronavirus disease 2019 (COVID-19) pandemic underscores the need to better understand animal-to-human transmission of coronaviruses and adaptive evolution within new hosts. We scanned more than 182,000 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes for selective sweep signatures and found a distinct footprint of positive selection located around a non-synonymous change (A1114G; T372A) within the spike protein receptor-binding domain (RBD), predicted to remove glycosylation and increase binding to human ACE2 (hACE2), the cellular receptor. This change is present in all human SARS-CoV-2 sequences but not in closely related viruses from bats and pangolins. As predicted, T372A RBD bound hACE2 with higher affinity in experimental binding assays. We engineered the reversion mutant (A372T) and found that A372 (wild-type [WT]-SARS-CoV-2) enhanced replication in human lung cells relative to its putative ancestral variant (T372), an effect that was 20 times greater than the well-known D614G mutation. Our findings suggest that this mutation likely contributed to SARS-CoV-2 emergence from animal reservoirs or enabled sustained human-to-human transmission.
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http://dx.doi.org/10.1016/j.cell.2021.07.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8260498PMC
August 2021

Long-term decrease in Asian monsoon rainfall and abrupt climate change events over the past 6,700 years.

Proc Natl Acad Sci U S A 2021 Jul;118(30)

Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway

Asian summer monsoon (ASM) variability and its long-term ecological and societal impacts extending back to Neolithic times are poorly understood due to a lack of high-resolution climate proxy data. Here, we present a precisely dated and well-calibrated tree-ring stable isotope chronology from the Tibetan Plateau with 1- to 5-y resolution that reflects high- to low-frequency ASM variability from 4680 BCE to 2011 CE. Superimposed on a persistent drying trend since the mid-Holocene, a rapid decrease in moisture availability between ∼2000 and ∼1500 BCE caused a dry hydroclimatic regime from ∼1675 to ∼1185 BCE, with mean precipitation estimated at 42 ± 4% and 5 ± 2% lower than during the mid-Holocene and the instrumental period, respectively. This second-millennium-BCE megadrought marks the mid-to late Holocene transition, during which regional forests declined and enhanced aeolian activity affected northern Chinese ecosystems. We argue that this abrupt aridification starting ∼2000 BCE contributed to the shift of Neolithic cultures in northern China and likely triggered human migration and societal transformation.
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http://dx.doi.org/10.1073/pnas.2102007118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8325342PMC
July 2021

Genetic-algorithm-empowered metasurface design: simultaneous realization of high microwave frequency-selection and low infrared surface-emissivity.

Opt Express 2021 Jun;29(13):20150-20159

With the improvement of equipment integration, it is difficult to meet the increasing functional requirements with the function of a single spectrum. In this work, a multispectral functional metasurface (MFM) is designed to achieve multispectral compatibility between microwave and infrared using multi-optimization. For microwaves, a frequency selective surface (FSS) is designed to achieve frequency selectivity. And for infrared, a twice genetic algorithm (GA) is employed to further increase the metallic filling ratio, thus reducing the infrared emissivity while maintaining the performance of microwave FSS. In order to verify our design and method, the MFM is fabricated and measured, and all the results are consistent with the theoretical design. The performance of FSS can achieve 3dB bandwidth in 7.2-11.2GHz with low insertion losses and stability, and meanwhile the mean infrared emissivity has been reduced to 0.24 in 3-14μm. In summary, the designed multispectral compatible metasurface has wide application value in radome. What's more, the multi-optimization method for designing the multispectral metasurface can also be extended to other fields.
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http://dx.doi.org/10.1364/OE.427492DOI Listing
June 2021

Haplotype-based membership inference from summary genomic data.

Bioinformatics 2021 07;37(Suppl_1):i161-i168

Department of Informatics, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA.

Motivation: The availability of human genomic data, together with the enhanced capacity to process them, is leading to transformative technological advances in biomedical science and engineering. However, the public dissemination of such data has been difficult due to privacy concerns. Specifically, it has been shown that the presence of a human subject in a case group can be inferred from the shared summary statistics of the group, e.g. the allele frequencies, or even the presence/absence of genetic variants (e.g. shared by the Beacon project) in the group. These methods rely on the availability of the target's genome, i.e. the DNA profile of a target human subject, and thus are often referred to as the membership inference method.

Results: In this article, we demonstrate the haplotypes, i.e. the sequence of single nucleotide variations (SNVs) showing strong genetic linkages in human genome databases, may be inferred from the summary of genomic data without using a target's genome. Furthermore, novel haplotypes that did not appear in the database may be reconstructed solely from the allele frequencies from genomic datasets. These reconstructed haplotypes can be used for a haplotype-based membership inference algorithm to identify target subjects in a case group with greater power than existing methods based on SNVs.

Availability And Implementation: The implementation of the membership inference algorithms is available at https://github.com/diybu/Haplotype-based-membership-inferences.
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http://dx.doi.org/10.1093/bioinformatics/btab305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8275351PMC
July 2021
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