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The complex and heterogeneous nature of the lignin macromolecule has presented a lasting barrier to its utilization. To achieve high lignin yield, the technical lignin extraction process usually severely modifies and condenses the native structure of lignin, which is a critical drawback for its utilization in conversion processes. In addition, there is no method capable of separating lignin from plant biomass with controlled structural properties. Here, we developed an N-heterocycle-based deep eutectic solvent formed between lactic acid and pyrazole (La-Py DES) with a binary hydrogen bonding functionality resulting in a high affinity toward lignin. Up to 93.7% of lignin was extracted from wheat straw biomass at varying conditions from 90 °C to 145 °C. Through careful selection of treatment conditions as well as lactic acid to pyrazole ratios, lignin with controlled levels of ether linkage content, hydroxyl group content, and average molecular weight can be generated. Under mild extraction conditions (90 °C to 120 °C), light-colored native-like lignin can be produced with up to 80% yield, whereas ether linkage-free lignin with low polydispersity can be obtained at 145 °C. Overall, this study offers a new strategy for native lignin extraction and generating lignin with controlled structural properties. [ABSTRACT FROM AUTHOR]

The influence of wall-corrugation-induced swirl flow on enhanced forced convection in wavy-plate-fin cores has been investigated. Three-dimensional computational simulations were carried out for steady-state periodically developed air flow (Pr ∼ 0.71; 50 ≤ Re ≤ 4000) with channel walls subject to constant-uniform temperature conditions. The recirculation that develops in the wall troughs and grows to have an axially helical character is scaled by the Swirl number Sw. As Sw increases with higher flowrate and/or corrugation severity, tornado-shaped vortices appear in the wave trough region midway of the interfin channel height, then extend longitudinally to encompass majority of the flow channel. The local wall-shear and heat transfer coefficient variations indicate that boundary-layer thinning upstream of the wave peak aids in intensifying momentum and heat transfer. However, the flow recirculation in wall trough impedes heat transfer at low Sw due to flow stagnation but promotes it at high Sw because of the vortices-induced augmented fluid mixing. The effects of this secondary flow are quantified by Φf(or j), which is seen to increase log-linearly as fin corrugation aspect ratio γ and/or fin spacing ratio ζ increases; the influence of cross section aspect ratio α is marginal. Moreover, the pressure drag penalty due to swirl critically affects overall pressure loss, and its proportion remains nearly constant when α varies, but grows as Sw, γ, and/or ζ increases and can be as much as 80% of the total pressure drop. [ABSTRACT FROM AUTHOR]

New generalized correlations for predicting the average fanning friction factor f and average Nusselt number Nu for laminar flow in plain plate-fin compact cores of rectangular cross section are presented. These are based on extended experimental data, as well as three-dimensional computational simulations, obtained for a broad range of fin density and geometrical attributes. The results indicate that while the fully developed forced convection scales only with the interfin channel cross-sectional ratio α (fin spacing by fin height), the entrance region hydrodynamic and thermal performance is additionally a function of the fin-core length L, flow Reynolds number Re, and fluid Prandtl number Pr. The developing flow and convection is further shown to scale as: (fRe)∼(L/dhRe)1/2⁠, and Nu ∼(L/dhRe)1/2Pr1/3ϕ(α)⁠, where f, Re, and Nu are all based on the hydraulic diameter dh of the interfin flow channel. Generalized correlations for both (fRe) and Nu are developed by the corresponding scaling of the forced convection behavior and asymptotic matching of the entrance or developing flow (short fin-core flow length) and the fully developed flow (large fin-core flow length) region performance. Finally, the predictions from these correlations are found to be within ±15% of all available experimental data for air, water, and glycol (0.71 ≤ Pr ≤ 10), and fin cores with 0 < α ≤ 1. [ABSTRACT FROM AUTHOR]

We have developed a passive long-wavelength infrared (LWIR) scattering-type scanning near-field optical microscope (s-SNOM) installed in a helium-free mechanically cooled cryostat, which facilitates cooling of an LWIR detector and optical elements to 4.5 K. To reduce mechanical vibration propagation from a compressor unit, we have introduced a metal bellows damper and a helium gas damper. These dampers ensure the performance of the s-SNOM to be free from mechanical vibration. Furthermore, we have introduced a solid immersion lens to improve the confocal microscope performance. To demonstrate the passive s-SNOM capability, we measured thermally excited surface evanescent waves on Au/SiO2 gratings. A near-field signal-to-noise ratio is 4.5 times the improvement with an acquisition time of 1 s/pixel. These improvements have made the passive s-SNOM a more convenient and higher-performance experimental tool with a higher signal-to-noise ratio for a shorter acquisition time of 0.1 s. [ABSTRACT FROM AUTHOR]

Three new series of catenar liquid crystals 1a-c derived from heterocyclic bisoxazoles and bisthiazoles exhibiting columnar phases were reported. All compounds 1a-c exhibited hexagonal columnar phases, which were confirmed by powder XRD diffractometer. Compounds 1a have a slightly wider temperature range of columnar phases than that of compounds 1b, which might be attributed to higher dipole polarized in 1a. A Ncell and Rar value equal to 2.54-2.76 and 19.99-20.45 Ų within a slice of 9.0 Å thick were obtained for three derivatives 1a-c (all ns=12), indicating that a single molecule was packed within columns in Colh phases. All derivatives showed good stabilities at temperature below T=408 °C on TGA. The PL spectra of all compounds 1a-c showed one intense peak at λmax=505-510 nm, and these photoluminescent emissions originated from quinoxaline moiety. [ABSTRACT FROM AUTHOR]

A wideband (0.8-6 GHz) receiver front-end (RFE) utilizing a shunt resistive feedback low-noise amplifier (LNA) and a micromixer is realized in 90 nm CMOS technology for software-defined radio (SDR) applications. With the shunt resistive feedback and series inductive peaking, the proposed LNA is able to achieve a wideband frequency response in input matching, power gain and noise figure (NF). A micromixer down converts the radio signal and performs single-to-differential transition. Measurements show the conversion gain higher than 17 dB and input matching (S11) better than -7.3 dB from 0.8 to 6 GHz. The IIP3 ranges from -7to -10 dBm, and the NF from 4.5 to 5.9 dB. This wideband receiver occupies 0.48 mm² and consumes 13 mW. [ABSTRACT FROM AUTHOR]

We investigate the dephasing rates in quasiballistic Aharonov-Bohm (AB) rings with local- and nonlocal-probe configurations by tuning the transmission through one arm of the ring. The dephasing rates are independent of the probe configuration while the transmissions through the ring paths are equal. In contrast, as AB interferometers are tuned to be strongly asymmetric, the dephasing rate of the local configuration becomes larger than that of the nonlocal configuration. We find that our observations can be qualitatively explained by voltage fluctuations from the measurement circuit, as proposed by G. Seelig, S. Pilgram, A. N. Jordan, and M. Btittiker [Phys. Rev. B 68, 161310(R) (2003)]. [ABSTRACT FROM AUTHOR]

Background and Purpose: During the development of atherosclerotic plaques, vascular smooth muscle cells (VSMCs) migrate from the media to the intima through the basement membrane and interstitial collagenous matrix, and proliferate to form neointima. Here, we investigate the mechanism of VSMC migration and proliferation caused by aggretin, a snake venom integrin alpha2beta1 agonist.Experimental Approach: Cultures of rat and human VSMCs were treated with aggretin and the signal transduction pathways induced by this agonist were examined by Western blotting, immunoprecipitation and electrophoretic mobility shift assay techniques.Key Results: Aggretin-induced VSMC proliferation was blocked by a monoclonal antibody (mAb) against integrin alpha2 (AII2E10) or against the platelet-derived growth factor receptor (PDGFR)-beta. Proliferation was also blocked by inhibition of the tyrosine kinase Src with PP2, phospholipase C (PLC) with U73122, extracellular signal-regulated kinase (ERK) with PD98059 or nuclear factor-kappa B (NF-kB) activation with pyrrolidine dithiocarbamate (PDTC). VSMC migration towards immobilized aggretin was increased in a modified Boyden chamber and this effect was blocked by alpha2beta1-Src-PLC-MAPK axis inhibitors, but not by PDTC, PDGFR-beta mAb, or a phosphoinositide-3 kinase inhibitor, LY294002. Aggretin stimulated the phosphorylation of PDGFR-beta, Src and ERK in a time-dependent manner. NF-kB translocation and platelet-derived growth factor (PDGF)-BB production were also observed. The ERK activation, NF-kB translocation and PDGF-BB production were blocked by PP2, U73122 and PD98059.Conclusions and Implications: Aggretin induces VSMC proliferation and migration mainly through binding to integrin alpha2beta1, and subsequently activates Src, PLC and ERK pathways, inducing NF-kB activation and PDGF production. [ABSTRACT FROM AUTHOR]

The characterization and scaling of the thermal-hydraulic performance in wavy plate-fin compact heat exchanger cores, based on the understanding of the physical phenomena and heat transfer enhancement mechanism is delineated. Experimental data are presented for forced convection in air (Pr = 0.71) with flow rates in the range 50 ≤ Re ≤ 4000. A variety of wavy-fin cores that span viable applications, with geometrical attributes described by the cross section aspect ratio α (ratio of fin spacing to height), fin corrugation aspect ratio γ (ratio of 2× corrugation amplitude to wave pitch), and fin spacing ratio ζ (ratio of fin spacing to wave pitch), are considered. To characterize and correlate the vortex-flow mixing in interfin spaces, a Swirl number Sw is introduced from the balance of viscous, inertial and centrifugal forces. It is shown that the laminar, transitional and turbulent flow regimes can be explicitly identified by this Swirl number. Based on the experimental results and extended analysis, new correlations for Fanning friction factor f and Colburn factor j are developed with Sw, α, γ, and ζ as scaling parameters. Requisite expressions are devised by a superposition of both enhancement components due to the corrugated surface area enlargement and induced swirl flow field, and they are combined to cover the laminar, transitional and turbulent regimes by the method of asymptotic matching. The resulting generalized correlations are further shown to predict all available experimental data for f and j factors to within ±20% and ±15%, respectively. [ABSTRACT FROM AUTHOR]

Hypoxia signaling is an ancient pathway by which animals can respond to low oxygen. Malfunction of this pathway disturbs hypoxic acclimation and can result in various diseases, including cancers. The role of hypoxia signaling in early embryogenesis remains unclear. Here, we show that in the blastula of the sea urchin Strongylocentrotus purpuratus, hypoxia-inducible factor α (HIFα), the downstream transcription factor of the hypoxia pathway, is localized and transcriptionally active on the future dorsal side. This asymmetric distribution is attributable to its oxygen-sensing ability. Manipulations of the HIFα level entrained the dorsoventral axis, as the side with the higher level of HIFα tends to develop into the dorsal side. Gene expression analyses revealed that HIFα restricts the expression of nodal to the ventral side and activates several genes encoding transcription factors on the dorsal side. We also observed that intrinsic hypoxic signals in the early embryos formed a gradient, which was disrupted under hypoxic conditions. Our results reveal an unprecedented role of the hypoxia pathway in animal development. [ABSTRACT FROM AUTHOR]

Hepatocellular carcinoma (HCC) is an aggressive tumor with a poor prognosis. Currently, only sorafenib is approved by the FDA for advanced HCC treatment; therefore, there is an urgent need to discover candidate therapeutic drugs for HCC. We hypothesized that if a drug signature could reverse, at least in part, the gene expression signature of HCC, it might have the potential to inhibit HCC-related pathways and thereby treat HCC. To test this hypothesis, we first built an integrative platform, the "Encyclopedia of Hepatocellular Carcinoma genes Online 2", dubbed EHCO2, to systematically collect, organize and compare the publicly available data from HCC studies. The resulting collection includes a total of 4,020 genes. To systematically query the Connectivity Map (CMap), which includes 6,100 drug-mediated expression profiles, we further designed various gene signature selection and enrichment methods, including a randomization technique, majority vote, and clique analysis. Subsequently, 28 out of 50 prioritized drugs, including tanespimycin, trichostatin A, thioguanosine, and several anti-psychotic drugs with anti-tumor activities, were validated via MTT cell viability assays and clonogenic assays in HCC cell lines. To accelerate their future clinical use, possibly through drug-repurposing, we selected two well-established drugs to test in mice, chlorpromazine and trifluoperazine. Both drugs inhibited orthotopic liver tumor growth. In conclusion, we successfully discovered and validated existing drugs for potential HCC therapeutic use with the pipeline of Connectivity Map analysis and lab verification, thereby suggesting the usefulness of this procedure to accelerate drug repurposing for HCC treatment. [ABSTRACT FROM AUTHOR]

Background: To automatically process large quantities of biological literature for knowledge discovery and information curation, text mining tools are becoming essential. Abbreviation recognition is related to NER and can be considered as a pair recognition task of a terminology and its corresponding abbreviation from free text. The successful identification of abbreviation and its corresponding definition is not only a prerequisite to index terms of text databases to produce articles of related interests, but also a building block to improve existing gene mention tagging and gene normalization tools. Results: Our approach to abbreviation recognition (AR) is based on machine-learning, which exploits a novel set of rich features to learn rules from training data. Tested on the AB3P corpus, our system demonstrated a F-score of 89.90% with 95.86% precision at 84.64% recall, higher than the result achieved by the existing best AR performance system. We also annotated a new corpus of 1200 PubMed abstracts which was derived from BioCreative II gene normalization corpus. On our annotated corpus, our system achieved a F-score of 86.20% with 93.52% precision at 79.95% recall, which also outperforms all tested systems. Conclusion: By applying our system to extract all short form-long form pairs from all available PubMed abstracts, we have constructed BIOADI. Mining BIOADI reveals many interesting trends of bio-medical research. Besides, we also provide an off-line AR software in the download section on http://bioagent.iis.sinica.edu.tw/BIOADI/. [ABSTRACT FROM AUTHOR]

Serine protease PRSS23 is a newly discovered protein that has been associated with tumor progression in various types of cancers. Interestingly, PRSS23 is coexpressed with estrogen receptor α (ERα), which is a prominent biomarker and therapeutic target for human breast cancer. Estrogen signaling through ERα is also known to affect cell proliferation, apoptosis, and survival, which promotes tumorigenesis by regulating the production of numerous downstream effector proteins. In the present study, we aimed to clarify the correlation between and functional implication of ERα and PRSS23 in breast cancer. Analysis of published breast cancer microarray datasets revealed that the gene expression correlation between ERa and PRSS23 is highly significant among all ERα-associated proteases in breast cancer. We then assessed PRSS23 expression in 56 primary breast cancer biopsies and 8 cancer cell lines. The results further confirmed the coexpression of PRSS23 and ERα and provided clinicopathological significance. In vitro assays in MCF-7 breast cancer cells demonstrated that PRSS23 expression is induced by 17β-estradiol-activated ERα through an interaction with an upstream promoter region of PRSS23 gene. In addition, PRSS23 knockdown may suppress estrogen-driven cell proliferation of MCF-7 cells. Our findings imply that PRSS23 might be a critical component of estrogen-mediated cell proliferation of ERα-positive breast cancer cells. In conclusion, the present study highlights the potential for PRSS23 to be a novel therapeutic target in breast cancer research. [ABSTRACT FROM AUTHOR]

Background: The significant advances in microarray and proteomics analyses have resulted in an exponential increase in potential new targets and have promised to shed light on the identification of disease markers and cellular pathways. We aim to collect and decipher the HCC-related genes at the systems level. Results: Here, we build an integrative platform, the Encyclopedia of Hepatocellular Carcinoma genes Online, dubbed EHCO http://ehco.iis.sinica.edu.tw, to systematically collect, organize and compare the pileup of unsorted HCC-related studies by using natural language processing and softbots. Among the eight gene set collections, ranging across PubMed, SAGE, microarray, and proteomics data, there are 2,906 genes in total; however, more than 77% genes are only included once, suggesting that tremendous efforts need to be exerted to characterize the relationship between HCC and these genes. Of these HCC inventories, protein binding represents the largest proportion (~25%) from Gene Ontology analysis. In fact, many differentially expressed gene sets in EHCO could form interaction networks (e.g. HBV-associated HCC network) by using available human protein-protein interaction datasets. To further highlight the potential new targets in the inferred network from EHCO, we combine comparative genomics and interactomics approaches to analyze 120 evolutionary conserved and overexpressed genes in HCC. 47 out of 120 queries can form a highly interactive network with 18 queries serving as hubs. [ABSTRACT FROM AUTHOR]