Engineering topics
Yang, Xi
Publications and source records attributed to Yang, Xi.
ST6GAL1 negatively regulates monocyte transendothelial migration and atherosclerosis development
Highlights: • ST6GAL1 expression is inversely related to atherosclerosis development. • Knockdown of ST6GAL1 in vascular endothelial cells directly promotes monocyte transendothelial migration. • ST6GAL1 overexpression inhibits TNFα-induced monocyte transendothelial migration. • β-catenin sialylation level is downregulated in inflammatory endothelial cells. Monocyte transendothelial migration is a critical step in the initial stage of atherosclerosis, in which the involvement of α-2,6 sialyltransferase 1 (ST6GAL1) has been confirmed by increasing evidence. But the direct relationship between ST6GAL1 and atherosclerosis remains incompletely uncertain. In this study, we demonstrated that the expression level of ST6GAL1 in vascular endothelium was significantly decreased in atherosclerosis development process, while obviously recovered after atherosclerosis regression. Further analysis showed that knockdown of ST6GAL1 by RNA interference in vascular endothelial cells EA. hy926 obviously promoted TNFα-triggered monocyte-transendothelial migration, whereas overexpression of ST6GAL1 strongly inhibited monocyte-transendothelial migration. Moreover, we firstly found β-catenin is a sialylated protein and its sialylation level is decreased in TNFα-treated EA. hy926 cells, suggesting that the function of ST6GAL1 in preventing both atherosclerosis development and monocyte transendothelial migration might result from the sialylation of β-catenin of endothelium. Our results suggested ST6GAL1 might be a potential target for atherosclerosis prevention and treatment.
Chitosan oligosaccharides enhance lipid droplets via down-regulation of PCSK9 gene expression in HepG2 cells
Highlights: • COS enhance lipid droplets in HepG2 cells. • COS down-regulate the expression of PCSK9 to maintain hepatic LDLR abundance and activity. • COS inhibit HNF1α and SREBP-2 activity leading to down-regulation of PCSK9. Chitosan oligosaccharides (COS), linear polymers of N-acetyl-D-glucosamine and deacetylated glucosamine, exhibit diverse pharmacological effects such as antimicrobial, antitumor, antioxidant and anti-inflammatory activities. Here, we explored their hypocholesterolemic effects in vivo and the molecular mechanisms of COS in hepatic cells. Our in vivo study of dyslipidemic ApoE{sup -/-} male mice showed that COS treatment of 500 mg kg{sup −1} d{sup −1} for 4 weeks clearly reduced the lipid deposits in the aorta and significantly decreased the hepatic proprotein convertase subtilisin/kexin type 9 (PCSK9) protein levels versus HFD groups (p < 0.05). To elucidate the mechanisms behind these effects, the HepG2 cell line was treated with COS. We found that COS (200 μg/ml) increased the amount of cell-surface low-density lipoprotein receptor (LDLR) and enhanced the lipid droplets in HepG2 cells (p < 0.05). The mRNA levels of LDLR and HMG-CoA protein levels were not altered, and the mRNA levels of PCSK9 were down-regulated by COS treatment for 24 h. We also observed that the expression levels of SREBP-2 (125 kD) and HNF-1α were increased in total cell lysates, but nuclear SREBP-2 (nSREBP-2, 68 kD, the active subunit of SREBP-2) levels were decreased and FOXO3a levels increased in nuclear lysates after COS treatment for 24 h. We demonstrated that one of the reasons for regulation of lipid transfer with COS is that FOXO3a levels are up-regulated by COS, leading to a reduction in the PCSK9 promoter binding capacity of HNF-1α and thus suppressing PCSK9 gene expression, up-regulating LDLR levels, and enhancing the lipid droplets in HepG2 cells. In addition, decreased expression of the PCSK9 gene was also contributed to by down-regulation of SREBP-2 by COS. We further confirmed the effect of suppression of PCSK9 expression by COS by utilizing RNA interference to silence HNF-1α and SREBP-2. Finally, to the best of our knowledge, we are the first to demonstrate that PCSK9 expression and LDLR activity are synergistically changed by a combination of HNF-1α and SREBP-2 after COS treatment. Our findings indicate that COS may regulate PCSK9 to modulate hepatic LDLR abundance and activity.
Investigation of composition, structure and bioactivity of extracellular polymeric substances from original and stress-induced strains of Thraustochytrium striatum
This paper was the first to study extracellular polymeric substances (EPSs) of Thraustochytrium striatum on composition, structure and bioactivities. Two strains of T. striatum including original (ori) and high-biomass (mut) strains (induced by high-nitrogen stress) were compared. The EPSs from both strains mainly contained polysaccharide (41–64%, w/w, dry basis) and protein (25–40%, w/w, dry basis), which was shown by the morphology study with an AFM. The monosaccharide profile of the EPS polysaccharide was consisted of glucose, galactose, arabinose, and trace amount of xylose. Glucose and arabinose took up to 82–90% (w/w, dry basis) of the total polysaccharide. The structure and functional groups of EPSs were determined by FTIR and NMR. The NMR results revealed that the major structural linkages of the polysaccharides of both ori and mut EPSs were 1 → 6-β-glucan and 1 → 4-α-galactan branched with l-α-arabinose. The EPSs were found to have anti-tumor activities against mouse melanoma B16-F0, human prostate carcinoma DU145, human cervical carcinoma HeLa, and human lung carcinoma A549. The EPSs also showed antioxidant and anti-inflammatory activities and antibacterial activity against Pseudomonas aeruginosa.
First Demonstration of the Transparent Fast-To-Slow Corrector Current Shift in the NSLS-II Storage Ring
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Development of New Operational Mode for NSLS-II Injector: Low-Energy 100MeV Linac-To-Booster Injection
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Improvements of NSLS-II X-ray Diagnostic Beamlines
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First demonstration of the fast-to-slow corrector current shift in the NSLS-II storage ring
In order to realize the full benefits of the high brightness and ultra-small beam sizes of NSLS-II, it is essential that the photon beams are exceedingly stable. In the circumstances of implementing local bumps, changing ID gaps, and long term drifting, the fast orbit feedback (FOFB) requires shifting the fast corrector strengths to the slow correctors to prevent the fast corrector saturation and to make the beam orbit stable in the sub-micron level. As the result, a reliable and precise technique of fast-to-slow corrector strength shift has been developed and tested at NSLS-II. This technique is based on the fast corrector response to the slow corrector change when the FOFB is on. In this article, the shift technique is described and the result of proof-of-principle experiment carried out at NSLS-II is presented. The maximum fast corrector current was reduced from greater than 0.45 A to less than 0.04 A with the orbit perturbation within ±1 μm.
Sun-Induced Chlorophyll Fluorescence, Photosynthesis, and Light Use Efficiency of a Soybean Field from Seasonally Continuous Measurements
Recent development of sun-induced chlorophyll fluorescence (SIF) technology is stimulating studies to remotely approximate canopy photosynthesis (measured as gross primary production, GPP). While multiple applications have advanced the empirical relationship between GPP and SIF, mechanistic understanding of this relationship is still limited. GPP:SIF relationship, using the standard light use efficiency framework, is determined by absorbed photosynthetically active radiation (APAR) and the relationship between photosynthetic light use efficiency (LUE) and fluorescence yield (SIF y ). While previous studies have found that APAR is the dominant factor of the GPP:SIF relationship, the LUE:SIF y relationship remains unclear. For a better understanding of the LUE:SIF y relationship, in this paper we deployed a ground-based system (FluoSpec2), with an eddy-covariance flux tower at a soybean field in the Midwestern U.S. during the 2016 growing season to collect SIF and GPP data simultaneously. With the measurements categorized by plant growth stages, light conditions, and time scales, we confirmed that a strong positive GPP:SIF relationship was dominated by an even stronger linear SIF:APAR relationship. By normalizing both GPP and SIF by APAR, we found that under sunny conditions our soybean field exhibited a clear positive SIF y :APAR relationship and a weak negative LUE:SIF y relationship, opposite to the positive LUE:SIF y relationship reported previously in other ecosystems. Our study provides a first continuous SIF record over multiple growth stages for agricultural systems and reveals a distinctive pattern related to the LUE:SIF y relationship compared with previous work. Finally, the observed positive relationship of SIF y :APAR at the soybean site provides new insights of the previous understanding on the SIF's physiological implications.
Resource Aware Intelligent Network Services (RAINS) Final Technical Report
The Resource Aware Intelligent Network Services (RAINS) project conducted research and developed technologies in the area of cyber infrastructure resource modeling and computation. The goal of this work was to provide a foundation to enable intelligent, software defined services which spanned the network AND the resources which connect to the network. A Multi-Resource Service Plane (MRSP) was defined, which allows resource owners/managers to locate and place themselves from a topology and service availability perspective within the dynamic networked cyberinfrastructure ecosystem. The MRSP enables the presentation of integrated topology views and computation results which can include resources across the spectrum of compute, storage, and networks. The RAINS project developed MSRP includes the following key components: i) Multi-Resource Service (MRS) Ontology/Multi-Resource Markup Language (MRML), ii) Resource Computation Engine (RCE), iii) Modular Driver Framework (to allow integration of a variety of external resources). The MRS/MRML is a general and extensible modeling framework that allows for resource owners to model, or describe, a wide variety of resource types. All resources are described using three categories of elements: Resources, Services, and Relationships between the elements. This modeling framework defines a common method for the transformation of cyber infrastructure resources into data in the form of MRML models. In order to realize this infrastructure datification, the RAINS project developed a model based computation system, i.e. “RAINS Computation Engine (RCE)”. The RCE has the ability to ingest, process, integrate, and compute based on automatically generated MRML models. The RCE interacts with the resources thru system drivers which are specific to the type of external network or resource controller. The RAINS project developed a modular and pluggable driver system which facilities a variety of resource controllers to automatically generate, maintain, and distribute MRML based resource descriptions. Once all of the resource topologies are absorbed by the RCE, a connected graph of the full distributed system topology is constructed, which forms the basis for computation and workflow processing. The RCE includes a Modular Computation Element (MCE) framework which allows for tailoring of the computation process to the specific set of resources under control, and the services desired. The input and output of an MCE are both model data based on MRS/MRML ontology and schema. Some of the RAINS project accomplishments include: Development of general and extensible multi-resource modeling framework; Design of a Resource Computation Engine (RCE) system which includes the following key capabilities; Absorb a variety of multi-resource model types and build integrated models; Novel architecture which uses model based communications across the full stack for all Flexible provision of abstract or intent based user facing interfaces; Workflow processing based on model descriptions; Release of the RCE as an open source software; Deployment of RCE in the University of Maryland/Mid-Atlantic Crossroad ScienceDMZ in prototype mode with a plan under way to transition to production; Deployment at the Argonne National Laboratory DTN Facility in prototype mode; Selection of RCE by the DOE SENSE (SDN for End-to-end Networked Science at the Exascale) project as the basis for their orchestration service.
BigData Express: Toward Schedulable, Predictable, and High-Performance Data Transfer
Big Data has emerged as a driving force for scientific discoveries. Large scientific instruments (e.g., colliders, and telescopes) generate exponentially increasing volumes of data. To enable scientific discovery, science data must be collected, indexed, archived, shared, and analyzed, typically in a widely distributed, highly collaborative manner. Data transfer is now an essential function for science discoveries, particularly within big data environments. Although significant improvements have been made in the area of bulk data transfer, the currently available data transfer tools and services can not successfully address the high-performance and time-constraint challenges of data transfer required by extreme-scale science applications for the following reasons: disjoint end-to-end data transfer loops, cross-interference between data transfers, and existing data transfer tools and services are oblivious to user requirements (deadline and QoS requirements). Fermilab has been working on the BigData Express project to address these problems. BigData Express seeks to provide a schedulable, predictable, and high-performance data transfer service for big data science. The BigData Express software is being deployed and evaluated at multiple research institutions, which include UMD, StarLight, FNAL, KISTI, KSTAR, SURFnet, Ciena, and other sites. Meanwhile, the BigData Express research team is collaborating with the StarLight International/National Communications Exchange Facility to deploy BigData Express at various research platforms, including Pacific Research Platform, National Research Platform, and Global Research Platform. It is envisioned that we are working toward building a high-performance data transfer federation for big data science.
On the Relationship Between Sub-Daily Instantaneous and Daily Total Gross Primary Production: Implications for Interpreting Satellite-Based SIF Retrievals
Spatially and temporally continuous estimation of plant photosynthetic carbon fixation (or gross primary production, GPP) is crucial to our understanding of the global carbon cycle and the impact of climate change. Besides spatial, seasonal and interannual variations, GPP also exhibits strong diurnal variations. Satellite retrieved solar-induced chlorophyll fluorescence (SIF) provides a spatially continuous, but temporally discrete measurement of plant photosynthesis, and has the potential to be used to estimate GPP at global scale. However, it remains unclear whether the seasonal time series of SIF snapshots taken at a fixed time of the day can be used to infer daily total GPP variation at spatial and seasonal scales. In this study, we first used GPP estimates from 135 eddy covariance flux sites, covering a wide range of geographic locations and biome types, to investigate the relationship between the instantaneous GPP (GPP(sub inst)) and daily GPP (GPP(sub daily)) on the seasonal course for different times of the day. Latitudinal and diurnal patterns were found to correspond to variations in photosynthetically active radiation (PAR) and light use efficiency (LUE), respectively. We then used the Soil-Canopy Observation Photosynthesis and Energy Balance (SCOPE) model and the FluxCom GPP product to investigate the instantaneous and daily SIF-GPP relationships at five flux tower sites along a latitudinal gradient and at a global scale for different biome types. The results showed that daily SIF had a stronger linear correlation with daily GPP than instantaneous SIF at the seasonal scale, with an instantaneous to daily SIF conversion factor following the latitudinal and seasonal pattern driven by PAR. Our study highlights the necessity to take the latitudinal and diurnal factors into consideration for SIF-GPP relationship analyses or for physiological phenology analyses based on SIF.
Optimizing the UED beam line design via ImpactT simulation
The high charge low energy compressor system developed at NSLS-II can generate 5MeV electron bunches with 50pC charge (10 -8 electrons) focusing to 30 micron beam size and bunch length of order of 100 fs. NSLS-II plans to build it as part of the existing instrument for the ultra-fast electron diffraction (UED) and ultra-fast electron microscope (UEM) experiments to be installed at ATF-II, BNL. The expected intensity will be several orders of magnitudes higher than achieved previously using current technology (~10 -4 -10 -5 electrons). This type of accelerator based MeV electron microscopes, taking advantage of strong interaction of electrons with matter and overcoming space charge problem, are complementary to XFEL, such as LCLS.
AC orbit bump method of local impedance measurement
A fast and precise technique of local impedance measurement has been developed and tested at NSLS-II. This technique is based on in-phase sine-wave (AC) excitation of four fast correctors adjacent to the vacuum chamber section, impedance of which is measured. The beam position is measured using synchronous detection. Use of the narrow-band sine-wave signal allows us to improve significantly the accuracy of the orbit bump method. Beam excitation by fast correctors results in elimination of the systematic error caused by hysteresis effect. The systematic error caused by orbit drift is also eliminated because the measured signal is not affected by the orbit motion outside the excitation frequency range. In this article, the measurement technique is described and the result of proof-of-principle experiment carried out at NSLS-II is presented.
Operation of the NSLS-II Injector with a Lower Booster Injection Energy
The NSLS-II injector consists of a 200 MeV linac and a 3 GeV full-energy booster synchrotron. The linac contains five traveling-wave S-band accelerating structures driven by two high-power klystrons. Optimization of the NSLS-II injector has continued since user operation started in October 2014. Beam losses have been minimized by the injector tuning and stabilization, and high level software has been developed to characterize the booster and injection parameters. However, due to the recently increased frequency of klystrons arcing which shortens the lifetime of the klystron, operation of the linac with lowered klystron output power would allow injection to be maintained with fewer trips and extended lifetime of klystrons. Apart from the energy difference, the low energy klystron operation is quite similar to the nominal 200 MeV operation. Injection trials were carried out with scaled magnet settings of the linac, linac-to- booster (LtB) transport line, and the booster. The beam was successfully injected into the booster on May 31, 2017 at the low energy mode of the 170 MeV LtB injection. Overall transfer efficiency from the linac to the storage ring is identical to the standard 200 MeV operation. The 170 MeV injection mode has been adopted in NSLS-II user operation ever since the beam study. In the most recent injector studies on June 28 and July 3, 2017, the booster injection energy was further decremented to the final target value of 100 MeV via applying the same method established in the 170 MeV operation. The ultimate value of 100 MeV is determined by the special requirement of operating the injector at single klystron while repairing the other klystron or with two klystrons with significantly reduced outputs for the purpose of maximizing klystron lifetimes.
Seasonal variations of leaf and canopy properties tracked by ground-based NDVI imagery in a temperate forest
Changes in plant phenology affect the carbon flux of terrestrial forest ecosystems due to the link between the growing season length and vegetation productivity. Digital camera imagery, which can be acquired frequently, has been used to monitor seasonal and annual changes in forest canopy phenology and track critical phenological events. However, quantitative assessment of the structural and biochemical controls of the phenological patterns in camera images has rarely been done. In this study, we used an NDVI (Normalized Difference Vegetation Index) camera to monitor daily variations of vegetation reflectance at visible and near-infrared (NIR) bands with high spatial and temporal resolutions, and found that the infrared camera based NDVI (camera-NDVI) agreed well with the leaf expansion process that was measured by independent manual observations at Harvard Forest, Massachusetts, USA. We also measured the seasonality of canopy structural (leaf area index, LAI) and biochemical properties (leaf chlorophyll and nitrogen content). Here we found significant linear relationships between camera-NDVI and leaf chlorophyll concentration, and between camera-NDVI and leaf nitrogen content, though weaker relationships between camera-NDVI and LAI. Therefore, we recommend ground-based camera-NDVI as a powerful tool for long-term, near surface observations to monitor canopy development and to estimate leaf chlorophyll, nitrogen status, and LAI.
NSLS-II Storage Ring BPM Calibration via LOCO
In the following, we describe a method of the beam based calibration of the beam position monitor (BPM) system in the NSLS-II storage ring (SR) via the LOCO (Linear Optics from Closed Orbits) technique. This method measures the orbit response matrix (ORM) and the dispersion function of the machine. The data are then fitted to a lattice model by adjusting parameters such as quadrupole and skew quadrupole strengths in the model, BPM gains and rolls, corrector gains and rolls of the measurement system. Therefore, BPM gains and rolls are obtained.