Engineering topics
Lin, Hui
Publications and source records attributed to Lin, Hui.
Antimicrobial resistance and genomic characterization of Escherichia coli from pigs and chickens in Zhejiang, China
Escherichia coli is considered an opportunistic pathogen and an indicator for antimicrobial resistance (AMR) monitoring. Despite many reports on its AMR monitoring, studies based on genome-based analysis of AMR genes are still insufficient. Here, 181 E. coli strains were isolated from anal swab samples collected from pigs and chickens of animal farms located in Eastern China and sequenced through the Illumina platform. The results showed that 87.85% (159/181) of the E. coli isolates were multidrug-resistant (MDR). Ampicillin (AMP)- spectinomycin (SPT)- tetracycline (TET)- florfenicol (FFC)- sulfisoxazole (SF)- trimethoprim/sulfamethoxazole (SXT) was the predominant AMR pattern. By whole-genome sequencing, we found that ST10 (10.49%, 19/181) and ST48 (7.18%, 13/181) were major sequence types. IncFIB and IncX1 were the most prevalent plasmid replicons. The AMR genes bla NDM-5 (1.10%, 2/181), mcr -1 (1.10%, 2/181), tet (X4) (1.10%, 2/181), and cfr (6.08%, 11/181) were also found in these isolates. In addition, among the 169 virulence genes detected, we identified ast A (37.02%, 67/181), hly A (1.66%, 3/181), hly B (1.66%, 3/181) and hly D (1.66%, 3/181), which were closely related to heat-stable enterotoxin 1 and α-hemolysin. In addition, there were 33 virulence genes associated with the iron uptake system, and 46 were adhesion-related genes. Our study highlighted the need for routine surveillance of AMR with advanced genomic approaches, providing up-to-date data on the prevalence of AMR for the development and execution of antimicrobial stewardship policy.
A deep learning framework for layer-wise porosity prediction in metal powder bed fusion using thermal signatures
Abstract Part quality manufactured by the laser powder bed fusion process is significantly affected by porosity. Existing works of process–property relationships for porosity prediction require many experiments or computationally expensive simulations without considering environmental variations. While efforts that adopt real-time monitoring sensors can only detect porosity after its occurrence rather than predicting it ahead of time. In this study, a novel porosity detection-prediction framework is proposed based on deep learning that predicts porosity in the next layer based on thermal signatures of the previous layers. The proposed framework is validated in terms of its ability to accurately predict lack of fusion porosity using computerized tomography (CT) scans, which achieves a F1-score of 0.75. The framework presented in this work can be effectively applied to quality control in additive manufacturing. As a function of the predicted porosity positions, laser process parameters in the next layer can be adjusted to avoid more part porosity in the future or the existing porosity could be filled. If the predicted part porosity is not acceptable regardless of laser parameters, the building process can be stopped to minimize the loss.
Properties and reaction mechanism of phosphoric acid activated metakaolin geopolymer at varied curing temperatures
Reaction mechanism of phosphoric activated metakaolin is studied by techniques of calorimetry, ICP-OES, FTIR and NMR taking curing temperature and [H{sub 3}PO{sub 4}] as variables. A two-stage curing method including pre-curing at 40 °C for 24 h and second curing at 60/80 °C for another 24 h effectively mitigates thermal-cracking of the obtained silico-aluminate phosphate (SAP) samples, whose maximum compressive strength reaches 120 MPa. Dealumination of metakaolin in H{sub 3}PO{sub 4} solution produces low aluminate-containing silicate units and subsequently condensation of silicate tetrahedrons occurs. Higher temperature and H{sub 3}PO{sub 4} concentration accelerate the two processes. After complete reaction, A{sub VI} structure from metakaolin disappears and the dissolved Al preferably forms Al{sub VI}-O-P units. During reaction, metastable P-O-P intermediate appears in SAPs with higher P/Al ratio and finally transforms into Al-O-P structure upon PO{sub 4}{sup 3−} consumption. Phosphate units as P(OAl){sub x}(H{sub 2}O){sub 4-x} are connected with Si or Al structure units. Major structural units of the SAPs include Al-O-P, Si-O-P, Si-O-Si, and Si-O-Al.
Performance study of atomic tally methods for GPU-accelerated Monte Carlo dose calculation - 25352
Over the past several years, the graphics processing unit (GPU) technology has rapidly gained ground in scientific computing due to its outstanding performance and programmability. GPU implementation of Monte Carlo radiation transport for dose calculations has been reported by many investigators. The majority of these studies adopted single-precision floating point format because of the higher peak floating point operations per second (FLOPS) the GPUs can deliver than double-precision. It has been known that calculation using single-precision is more prone to numerical round-off errors, especially when a single tally data is accumulated 'atomically' and repeatedly by thousands of GPU threads. To mitigate this problem, the least intrusive solution in theory is to replace the single-precision atomic-add tally function with a double-precision version. However, the complexity lies in the fact that some GPUs (Nvidia GPUs prior to the Pascal generation; all current AMD GPUs) do not readily offer such double-precision function at hardware level, and that software emulation is too slow to use if not optimized properly. This paper discusses several atomic-add tally methods with reduced numerical errors used throughout ARCHER development. The original software-based compare-and-swap method (CAS) was shown to be inefficient due to high intra-warp thread contention, whereas the improved software-based warp-aggregated method (WAG) and Kahan summation method (KAS) eliminated the thread contention and performed very well on Kepler and Maxwell GPUs, being more than 13 times faster than CAS in our tests. The hardware-based (HB) double-precision atomic-add feature available on Pascal and Volta GPUs exceeded software emulation and offered the best performance universally, so did WIB, a combination of WAG and HB methods. It was also shown that in a single-precision dose engine, KAS managed to maintain high reliability when the single-precision atomic-add tally underestimated the dose by 25%. (authors)
Development of ARCHER towards clinical use: modeling and simulation of Varian Linac for radiation therapy dose calculations - 25449
Monte Carlo particle transport methods are well recognized as the most accurate approach to dose calculations for radiation therapy treatment planning. However, the lengthy calculation time has prevented Monte Carlo methods from being applied to dose calculations in the planning of radiation therapy. Recently, the emerging parallel computing hardware accelerators, such as general-purpose Graphics Processing Unit (GPU), have significantly boosted the performance of Monte Carlo codes. The accuracy of a clinical dose engine depends greatly on the accuracy of source term modeling and the methodology of dose calculations. Hence, in this study, an efficient and accurate source model of the Varian TrueBeam{sup R} Linac is developed and integrated with a fast photon-electron transport module of the recently developed high-performance Monte Carlo code, ARCHER. The validity of the source model and the particle transport physics are verified with established dose calculation codes such as EGSnrc and validated with experimental measurements. To demonstrate the capability of the platform in clinical applications, three clinical treatment plans (the lung, breast, and prostate) are simulated and analyzed. From the perspective of performance, the entire simulation of each clinical plan, starting from the source modeling to the end of particle transport within the patient phantom, can be finished in less than one minute using a single Titan X GPU card with 1% statistical error. In comparison, the same cases take the EGSnrc code hundreds of CPU hours to finish. The results suggest that this new version of ARCHER code has been successfully developed and tested as a clinically deployable dose engine for external photon beam IMRT plans in the clinical setting. (authors)
Self-Healing Attack-Resilient PMU Network for Power System Operation
In this paper, we propose a self-healing phasor measurement unit (PMU) network that exploits the features of dynamic and programmable configuration in a software-defined networking infrastructure to achieve resiliency against cyber-attacks. After a cyber-attack, the configuration of network switches is changed to isolate the compromised PMUs/phasor data concentrators to prevent further propagation of the attack; meanwhile, the disconnected yet uncompromised PMUs will be reconnected to the network to "self-heal" and thus restore the observability of the power system. Specifically, we formulate an integer linear programming model to minimize the overhead of the self-healing process (e.g., the recovery latency), while considering the constraints of power system observability, hardware resources, and network topology. We also propose a heuristic algorithm to decrease the computational complexity. Case studies of a PMU network based on the IEEE 30-bus and 118-bus systems are used to validate the effectiveness of the self-healing mechanism.
Contrasting Effects of Dissolved Organic Matter on Mercury Methylation by Geobacter sulfurreducens PCA and Desulfovibrio desulfuricans ND132
Not Available
Drp1 mediates compression-induced programmed necrosis of rat nucleus pulposus cells by promoting mitochondrial translocation of p53 and nuclear translocation of AIF
Compression-induced programmed cell death of nucleus pulposus (NP) cells is an important contributor to intervertebral disc degeneration (IDD). Dynamin-related protein 1 (Drp1), a crucial mitochondrial fission protein, triggers programmed necrosis upon cellular injury. However, limited information is available about the role of Drp1 in compression-induced programmed necrosis of NP cells. In the present study, we found that compression resulted in upregulation and mitochondrial translocation of Drp1. Inhibition of Drp1 by siRNA or mitochondrial division inhibitor 1 (mdivi-1) effectively prevented the programmed necrosis of NP cells treated with compression. Furthermore, Drp1 promoted mitochondrial translocation of p53 and nuclear translocation of apoptosis-inducing factor (AIF) in compression-treated NP cells. Inhibition of p53 mitochondrial translocation by pifithrin-μ (PFT-μ) and silencing of AIF expression by siRNA significantly alleviated compression-induced NP cell programmed necrosis. These data indicates that Drp1 mediates compression-induced programmed necrosis of NP cells by promoting mitochondrial translocation of p53 and nuclear translocation of AIF. - Highlights: • Compression increases the expression and mitochondrial translocation of Drp1 in NP cells. • Inhibition of Drp1 protects NP cells from compression-induced programmed necrosis. • p53 and AIF contribute to Drp1-mediated NP cell programmed necrosis.
Anthelminthic drug niclosamide sensitizes the responsiveness of cervical cancer cells to paclitaxel via oxidative stress-mediated mTOR inhibition
Drug repurposing represents an alternative therapeutic strategy to cancer treatment. The potent anti-cancer activities of a FDA-approved anthelminthic drug niclosamide have been demonstrated in various cancers. However, whether niclosamide is active against cervical cancer is unknown. In this study, we investigated the effects of niclosamide alone and its combination with paclitaxel in cervical cancer in vitro and in vivo. We found that niclosamide significantly inhibited proliferation and induced apoptosis of a panel of cervical cancer cell lines, regardless of their cellular origin and genetic pattern. Niclosamide also inhibited tumor growth in cervical cancer xenograft mouse model. Importantly, niclosamide significantly enhanced the responsiveness of cervical cancer cell to paclitaxel. We further found that niclosamide induced mitochondrial dysfunctions via inhibiting mitochondrial respiration, complex I activity and ATP generation, which led to oxidative stress. ROS scavenge agent N-acetyl-L-cysteine (NAC) completely reversed the effects of niclosamide in increasing cellular ROS, inhibiting proliferation and inducing apoptosis, suggesting that oxidative stress induction is the mechanism of action of niclosamide in cervical cancer cells. In addition, niclosamide significantly inhibited mammalian target of rapamycin (mTOR) signaling pathway in cervical cancer cells and its inhibitory effect on mTOR is modulated by oxidative stress. Our work suggests that niclosamide is a useful addition to the treatment armamentarium for cervical cancer and induction of oxidative stress may be a potential therapeutic strategy in cervical cancer. - Highlights: • Niclosamide is active against cervical cancer cells in vitro and in vivo. • Niclosamide sensitizes cervical cancer cell response to paclitaxel. • Niclosamide induces mitochondrial dysfunction and oxidative damage. • Niclosamide inhibits mTOR signaling in an oxidative stress-dependent manner.
Photochemical reactions between mercury (Hg) and dissolved organic matter decrease Hg bioavailability and methylation
Atmospheric deposition of mercury (Hg) to surface water is one of the dominant sources of Hg in aquatic environments and ultimately drives methylmercury (MeHg) toxin accumulation in fish. It is known that freshly deposited Hg is more readily methylated by microorganisms than aged or preexisting Hg; however the underlying mechanism of this process is unclear. Here we report that Hg bioavailability is decreased by photochemical reactions between Hg and dissolved organic matter (DOM) in water. Photo-irradiation of Hg-DOM complexes results in loss of Sn(II)-reducible (i.e. reactive) Hg and up to an 80% decrease in MeHg production by the methylating bacterium Geobacter sulfurreducens PCA. Loss of reactive Hg proceeded at a faster rate with a decrease in the Hg to DOM ratio and is attributed to the possible formation of mercury sulfide (HgS). Lastly, these results suggest a new pathway of abiotic photochemical formation of HgS in surface water and provide a mechanism whereby freshly deposited Hg is readily methylated but, over time, progressively becomes less available for microbial uptake and methylation.