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Chen, Feng

Publications and source records attributed to Chen, Feng.

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Electronic friction in interacting systems

We consider the effects of strong light-matter interaction on electronic friction in molecular junctions within the generic model of a single molecule nanocavity junction. Results of the Hubbard nonequilibrium Green function (NEGF) simulations are compared with mean-field NEGF and generalized Head-Gordon and Tully (HGT) approaches. Mean-field NEGF is shown to fail qualitatively at strong intrasystem interactions, while accuracy of the generalized HGT results is restricted to situations of well separated intramolecular excitations when bath induced coherences are negligible. Numerical results show effects of bias and cavity mode pumping on electronic friction. Here, we demonstrate nonmonotonic behavior of the friction on the bias and intensity of the pumping field and indicate possibility of engineering friction control in single molecule junctions.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2019

Near-Optimal and Practical Algorithms for Graph Scan Statistics with Connectivity Constraints

One fundamental task in network analysis is detecting “hotspots” or “anomalies” in the network; that is, detecting subgraphs where there is significantly more activity than one would expect given historical data or some baseline process. Scan statistics is one popular approach used for anomalous subgraph detection. This methodology involves maximizing a score function over all connected subgraphs, which is a challenging computational problem. A number of heuristics have been proposed for these problems, but they do not provide any quality guarantees. Here, we propose a framework for designing algorithms for optimizing a large class of scan statistics for networks, subject to connectivity constraints. Our algorithms run in time that scales linearly on the size of the graph and depends on a parameter we call the “effective solution size,” while providing rigorous approximation guarantees. In contrast, most prior methods have super-linear running times in terms of graph size. Extensive empirical evidence demonstrates the effectiveness and efficiency of our proposed algorithms in comparison with state-of-the-art methods. Our approach improves on the performance relative to all prior methods, giving up to over 25% increase in the score. Further, our algorithms scale to networks with up to a million nodes, which is 1–2 orders of magnitude larger than all prior applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Roux, Simon↗
DOE OSTI2018

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background: Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods: Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results: . Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions: PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Roux, Simon↗
DOE OSTI2018

Current-Induced Forces for Nonadiabatic Molecular Dynamics

We present general first-principles derivation of the expression for current-induced forces. The expression is applicable in nonequilibrium molecular systems with arbitrary intramolecular interactions and for any electron-nuclei coupling. It provides a controlled consistent way to account for quantum effects of nuclear motion around a classical trajectory, accounts for electronic non-Markov character of the friction tensor, and suggests a method for treatment beyond strictly adiabatic approximation. Lastly, we show the connection of the expression with previous studies and discuss effective ways to evaluate the friction tensor.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Integrative omics analyses broaden treatment targets in human cancer

Although large-scale, next-generation sequencing (NGS) studies of cancers hold promise for enabling precision oncology, challenges remain in integrating NGS with clinically validated biomarkers. To overcome such challenges, we utilized the Database of Evidence for Precision Oncology (DEPO) to link druggability to genomic, transcriptomic, and proteomic biomarkers. Using a pan-cancer cohort of 6570 tumors, we identified tumors with potentially druggable biomarkers consisting of drug-associated mutations, mRNA expression outliers, and protein/phosphoprotein expression outliers identified by DEPO. As a result, within the pan-cancer cohort of 6570 tumors, we found that 3% are druggable based on FDA-approved drug-mutation interactions in specific cancer types. However, mRNA/phosphoprotein/protein expression outliers and drug repurposing across cancer types suggest potential druggability in up to 16% of tumors. The percentage of potential drug-associated tumors can increase to 48% if we consider preclinical evidence. Further, our analyses showed co-occurring potentially druggable multi-omics alterations in 32% of tumors, indicating a role for individualized combinational therapy, with evidence supporting mTOR/PI3K/ESR1 co-inhibition and BRAF/AKT co-inhibition in 1.6 and 0.8% of tumors, respectively. We experimentally validated a subset of putative druggable mutations in BRAF identified by a protein structure-based computational tool. Finally, analysis of a large-scale drug screening dataset lent further evidence supporting repurposing of drugs across cancer types and the use of expression outliers for inferring druggability. Finally, our results suggest that an integrated analysis platform can nominate multi-omics alterations as biomarkers of druggability and aid ongoing efforts to bring precision oncology to patients.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Effects of oral and subcutaneous administration of HSP60 on myeloid-derived suppressor cells and atherosclerosis in ApoE−/− mice

HSP60 has been proved to be closely related to atherosclerosis due to its antigenicity. To determine this antigenicity effect, the ApoE−/− mice were fed with western-type diet and HSP60 was administrated orally or subcutaneously (SC) for potential vaccine against atherosclerosis. Here, we observed the ApoE−/− mice with oral HSP60 administration group showed a significant reduction in plaque size at the aortic root; accompanied by increased MSDCs (CD11b{sup +}Gr1{sup +}) in peripheral blood and spleen which was mostly composed of M-MDSCs (CD11b{sup +}LY6G{sup −}LY6C{sup high}), and increased plasma IL-10 and splenic Foxp3, Arg1, iNOS mRNA as well as decreased plasma IFN-γ and splenic T-bet mRNA compared to control group. Surprisingly, ApoE−/− mice with subcutaneous HSP60 administration group showed contrary results and their MDSCs were mostly composed of G-MDSCs (CD11b{sup +}LY6G{sup +}LY6C{sup low}). As expected, both PBS-oral and PBS-SC groups showed no significant effects on both the immune response and atherosclerotic plaque formation. In contrast, subcutaneous administration of HSP60 causes the opposite response. Thus, we propose the proper method for administering HSP60 as a new immunologic agent for prevention and treatment of atherosclerosis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared to missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Finally, our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Up-regulated miR-548k promotes esophageal squamous cell carcinoma progression via targeting long noncoding RNA-LET

Highlights: • miR-548k is significantly upregulated in ESCC and indicates poor prognosis. • miR-548k promotes the proliferation and migration of ESCC cells. • miR-548k directly targets and represses long noncoding RNA-LET (lncRNA-LET). • lncRNA-LET inhibits the proliferation and migration of ESCC cells. • The roles of miR-548k on ESCC are dependent on the negative regulation of lncRNA-LET. Dysregulated noncoding RNAs have been observed in diverse cancers. MIR458K is frequently amplified in esophageal squamous cell carcinoma (ESCC). However, the expression, clinical significances, and action mechanisms of miR-548k in ESCC are still unclear. In this study, we found that miR-548k is significantly up-regulated in ESCC tissues and cell lines. Up-regulated miR-548k expression is significantly correlated with advanced invasion depth, lymph node metastasis, advanced TNM stage, and poor overall survival. Gain-of- and loss-of-function assays demonstrated that miR-548k promotes the proliferation and migration of ESCC cells in vitro and tumor growth in vivo. Mechanistically, we found that miR-548k directly targets and represses the expression of long noncoding RNA-LET (lncRNA-LET), and further down-regulates p53 and up-regulates NF90. In addition, we found that lncRNA-LET is down-regulated and inversely correlated with miR-548k in ESCC. Down-regulated lncRNA-LET also indicated poor overall survival of ESCC patients. Functional assays demonstrated that lncRNA-LET inhibits the proliferation and migration of ESCC cells, and the effects of miR-548k on ESCC are dependent on the negative regulation of lncRNA-LET. In summary, our data revealed the critical roles of miR-548k-lncRNA-LET regulation axis in ESCC and suggested that the miR-548k-lncRNA-LET regulation axis may be promising prognostic biomarkers and therapeutic targets for ESCC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome

The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Emergence of Magnetic Flux Generated in a Solar Convective Dynamo. I. The Formation of Sunspots and Active Regions, and The Origin of Their Asymmetries

We present a realistic numerical model of sunspot and active region formation based on the emergence of flux bundles generated in a solar convective dynamo. To this end, we use the magnetic and velocity fields in a horizontal layer near the top boundary of the solar convective dynamo simulation to drive realistic radiative-magnetohydrodynamic simulations of the uppermost layers of the convection zone. The main results are as follows. (1) The emerging flux bundles rise with the mean speed of convective upflows and fragment into small-scale magnetic elements that further rise to the photosphere, where bipolar sunspot pairs are formed through the coalescence of the small-scale magnetic elements. (2) Filamentary penumbral structures form when the sunspot is still growing through ongoing flux emergence. In contrast to the classical Evershed effect, the inflow seems to prevail over the outflow in a large part of the penumbra. (3) A well-formed sunspot is a mostly monolithic magnetic structure that is anchored in a persistent deep-seated downdraft lane. The flow field outside the spot shows a giant vortex ring that comprises an inflow below 15 Mm depth and an outflow above 15 Mm depth. (4) The sunspots successfully reproduce the fundamental properties of the observed solar active regions, including the more coherent leading spots with a stronger field strength, and the correct tilts of bipolar sunspot pairs. These asymmetries can be linked to the intrinsic asymmetries in the magnetic and flow fields adapted from the convective dynamo simulation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Mimicking the Bioactivity of Fibroblast Growth Factor-2 Using Supramolecular Nanoribbons

Fibroblast growth factor (FGF-2) is a multifunctional growth factor that has pleiotropic effects in different tissues and organs. In particular, FGF-2 has a special role in angiogenesis, an important process in development, wound healing, cell survival, and differentiation. Therefore, incorporating biological agents like FGF-2 within therapeutic biomaterials is a potential strategy to create angiogenic bioactivity for the repair of damaged tissue caused by trauma or complications that arise from age and/or disease. However, the use of growth factors as therapeutic agents can be costly and does not always bring about efficient tissue repair due to rapid clearance from the targeted site. An alternative would be a stable supramolecular nanostructure with the capacity to activate the FGF-2 receptor that can also assemble into a scaffold deliverable to tissue. We report here on peptide amphiphiles that incorporate a peptide known to activate the FGF-2 receptor and peptide domains that drive its self-assembly into supramolecular nanoribbons. These FGF2-PA nanoribbons displayed the ability to increase the proliferation and migration of the human umbilical vein endothelial cells (HUVECs) in vitro to the same extent as the native FGF-2 protein at certain concentrations. We confirmed that this activity was specific to the FGFR1 signaling pathway by tracking the phosphorylation of downstream signaling effectors such ERK1/2 and pH3. These results indicated the specificity of FGF2-PA nanoribbons in activating the FGF-2 signaling pathway and its potential application as a supramolecular scaffold that can be used in vivo as an alternative to the encapsulation and delivery of the native FGF-2 protein.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Sulfated glycopeptide nanostructures for multipotent protein activation

Biological systems have evolved to utilize numerous proteins with capacity to bind polysaccharides for the purpose of optimizing their function. A well-known subset of these proteins with binding domains for the highly diverse sulfated polysaccharides are important growth factors involved in biological development and tissue repair. Here, we report on supramolecular sulfated glycopeptide nanostructures, which display a trisulfated monosaccharide on their surfaces and bind five critical proteins with very different polysaccharide binding domains. Binding does not disrupt the filamentous shape of the nanostructures or their internal β-sheet backbone, but must involve accessible adaptive configurations to interact with such different proteins. The glycopeptide nanostructures amplified signaling of bone morphogenetic protein 2 significantly more than the natural sulfated polysaccharide heparin, and promoted regeneration of bone in the spine with a protein dose that is 100-fold lower than expected. These super-bioactive nanostructures may enable many therapies in the horizon involving proteins.

36 MATERIALS SCIENCE↗