FKRR-MVSF: A Fuzzy Kernel Ridge Regression Model for Identifying DNA-Binding Proteins by Multi-View Sequence Features via Chou\u27s Five-Step Rule

DNA-binding proteins play an important role in cell metabolism. In biological laboratories, the detection methods of DNA-binding proteins includes yeast one-hybrid methods, bacterial singles and X-ray crystallography methods and others, but these methods involve a lot of labor, material and time. In recent years, many computation-based approachs have been proposed to detect DNA-binding proteins. In this paper, a machine learning-based method, which is called the Fuzzy Kernel Ridge Regression model based on Multi-View Sequence Features (FKRR-MVSF), is proposed to identifying DNA-binding proteins. First of all, multi-view sequence features are extracted from protein sequences. Next, a Multiple Kernel Learning (MKL) algorithm is employed to combine multiple features. Finally, a Fuzzy Kernel Ridge Regression (FKRR) model is built to detect DNA-binding proteins. Compared with other methods, our model achieves good results. Our method obtains an accuracy of 83.26% and 81.72% on two benchmark datasets (PDB1075 and compared with PDB186), respectively

Sinusoidal Obstruction Syndrome

Sinusoidal obstructive syndrome (SOS) is a fibrous occlusive disease of hepatic sinusoids or hepatic venules. Small hepatic blood vessel damage, especially hepatic sinusoidal endothelial cell damage, is its main feature. Based on etiology, SOS is mainly classified into pyrrolidine alkaloids-related SOS, hematopoietic stem cell transplantation-related SOS, and SOS of unknown etiology. In recent years, the incidence of SOS has been increasing. However, due to the complexity of the etiology, the lack of specificity in clinical manifestations, the difficulty of early diagnosis, and the limited treatment options, it often leads to poor treatment effects and even death. This chapter aims to analyze and organize the pathogenesis, pathological characteristics, diagnosis, treatment, and prognosis of different types of SOS, to provide certain references for the prevention and treatment of the disease

FKRR-MVSF: A Fuzzy Kernel Ridge Regression Model for Identifying DNA-Binding Proteins by Multi-View Sequence Features via Chou\u27s Five-Step Rule

DNA-binding proteins play an important role in cell metabolism. In biological laboratories, the detection methods of DNA-binding proteins includes yeast one-hybrid methods, bacterial singles and X-ray crystallography methods and others, but these methods involve a lot of labor, material and time. In recent years, many computation-based approachs have been proposed to detect DNA-binding proteins. In this paper, a machine learning-based method, which is called the Fuzzy Kernel Ridge Regression model based on Multi-View Sequence Features (FKRR-MVSF), is proposed to identifying DNA-binding proteins. First of all, multi-view sequence features are extracted from protein sequences. Next, a Multiple Kernel Learning (MKL) algorithm is employed to combine multiple features. Finally, a Fuzzy Kernel Ridge Regression (FKRR) model is built to detect DNA-binding proteins. Compared with other methods, our model achieves good results. Our method obtains an accuracy of 83.26% and 81.72% on two benchmark datasets (PDB1075 and compared with PDB186), respectively

Notch1 is required for hypoxia-induced proliferation, invasion and chemoresistance of T-cell acute lymphoblastic leukemia cells

Background Notch1 is a potent regulator known to play an oncogenic role in many malignancies including T-cell acute lymphoblastic leukemia (T-ALL). Tumor hypoxia and increased hypoxia-inducible factor-1α (HIF-1α) activity can act as major stimuli for tumor aggressiveness and progression. Although hypoxia-mediated activation of the Notch1 pathway plays an important role in tumor cell survival and invasiveness, the interaction between HIF-1α and Notch1 has not yet been identified in T-ALL. This study was designed to investigate whether hypoxia activates Notch1 signalling through HIF-1α stabilization and to determine the contribution of hypoxia and HIF-1α to proliferation, invasion and chemoresistance in T-ALL. Methods T-ALL cell lines (Jurkat, Sup-T1) transfected with HIF-1α or Notch1 small interference RNA (siRNA) were incubated in normoxic or hypoxic conditions. Their potential for proliferation and invasion was measured by WST-8 and transwell assays. Flow cytometry was used to detect apoptosis and assess cell cycle regulation. Expression and regulation of components of the HIF-1α and Notch1 pathways and of genes related to proliferation, invasion and apoptosis were assessed by quantitative real-time PCR or Western blot. Results Hypoxia potentiated Notch1 signalling via stabilization and activation of the transcription factor HIF-1α. Hypoxia/HIF-1α-activated Notch1 signalling altered expression of cell cycle regulatory proteins and accelerated cell proliferation. Hypoxia-induced Notch1 activation increased the expression of matrix metalloproteinase-2 (MMP2) and MMP9, which increased invasiveness. Of greater clinical significance, knockdown of Notch1 prevented the protective effect of hypoxia/HIF-1α against dexamethasone-induced apoptosis. This sensitization correlated with losing the effect of hypoxia/HIF-1α on Bcl-2 and Bcl-xL expression. Conclusions Notch1 signalling is required for hypoxia/HIF-1α-induced proliferation, invasion and chemoresistance in T-ALL. Pharmacological inhibitors of HIF-1α or Notch1 signalling may be attractive interventions for T-ALL treatment

Physical Properties of H II Regions in M51 from Spectroscopic Observations

M51 and NGC 5195 is an interacting system that can be explored in great details with ground-based telescopes. The H II regions in M51 were observed using the 2.16 m telescope of the National Astronomical Observatories of the Chinese Academy of Sciences and the 6.5 m Multiple Mirror Telescope with spatial resolution of less than $\sim100$ pc. We obtain a total of 113 spectra across the galaxy and combine the literature data of Croxall et al. to derive a series of physical properties, including the gas-phase extinction, stellar population age, star formation rate (SFR) surface density, and oxygen abundance. The spatial distributions and radial profiles of these properties are investigated in order to study the characteristics of M51 and the clues to the formation and evolution of this galaxy. M51 presents a mild radial extinction gradient. The lower gas-phase extinction in the north spiral arms compared to the south arms are possibly caused by the past encounters with the companion galaxy of NGC 5195. A number of H II regions have the stellar age between 50 and 500 Myr, consistent with the recent interaction history by simulations in the literatures. The SFR surface density presents a mild radial gradient, which is ubiquitous in spiral galaxies. There is a negative metallicity gradient of $-0.08$ dex $R_{e}^{-1}$ in the disk region, which is also commonly found in many spiral galaxies. It is supported by the "inside-out" scenario of galaxy formation. We find a positive abundance gradient of 0.26 dex $R_{e}^{-1}$ in the inner region. There are possible reasons causing the positive gradient, including the freezing of the chemical enrichment due to the star-forming quenching in the bulge and the gas infall and dilution due to the pseudobulge growth and/or galactic interaction.Comment: 20 pages, 8 figures, 1 appendix, Accepted for publication in PASP. Comments and suggestions are welcom

Wheat gluten proteins phosphorylated with sodium tripolyphosphate : changes in structure to improve functional properties for expanding applications

Poor solubility of wheat gluten proteins (WG) has negative impact on functional attributes such as gelation and emulsification, which limits it use in the food industry. In this study, WG underwent different degrees of phosphorylation using sodium tripolyphosphate (STP). Phosphoric acid groups were successfully incorporated in the WG via covalent bonding (C–N–P and C–O–P) involving hydroxyl and primary amino groups from WG. The introduction of phosphoric acid groups increased the negative charge of phosphorylation-WG, which caused the enhancement of electrostatic repulsion between proteins and reduced the droplet size in emulsions, thereby allowing proteins to be more efficiently dispersed in the solution system. The change of structure induced with phosphorylation improved hydration of protein, making the WG with higher solubility, thereby resulting in the improvement of its emulsification, foaming, thermal stability, and rheological properties. Therefore, WG can be modified by phosphorylation which caused an overall improvement of functional properties, thus facilitating the expansion of WG applications

Teleost TRAF7, a protein functions in the host antiviral responses via NF-κB and IRF3/7 mediated signaling

Tumor necrosis factor receptor-associated factors (TRAFs) play vital roles in tumor necrosis factor receptor (TNF-R) and interleukin-1 receptor/Toll-like receptor (IL-1R/TLR) mediated signaling pathway. However, the role that TRAF7 plays in the host immune responses is largely unknown in comparison to the extensive and in-depth research that has been conducted on other members of the TRAF family. Notably, Lc-TRAF7, a cloned TRAF7 ortholog, was discovered in the large yellow croaker (Larimichthys crocea) in the current study, which has an open reading frame (ORF) of 1,962 base pairs and encodes a protein of 653 amino acids (aa). Lc-TRAF7 is consisted of a RING finger domain, a coiled-coil domain, and seven WD40 domains, with the genomic organization consisted of 20 exons and 19 introns. According to the expression analysis, Lc-TRAF7 was presented in a wide range of detected organs and tissues of the healthy fish, and was able to significantly induced by stimulations of poly I:C, LPS, PGN, and Pseudomonas plecoglossicida infection. Subcellular distribution analysis revealed that Lc-TRAF7 was a cytoplasmic protein, with the RING finger and coiled-coil domain function importantly in its subcellular localization. Luciferase assays demonstrated that Lc-TRAF7 overexpression significantly induced the activation of NF-κB, IRF3, IRF7, and IFN1 promoters. In addition, the WD40 domains play a pivotal role in the NF-κB promoter activation, whereas the RING finger and coiled-coil domain were essential in the IRF3, IRF7, and IFN1 promoter activation. Notably, Lc-TRAF7 overexpression could suppress SVCV proliferation in EPC cells, and the expression levels of IRF3, IRF7, ISG15, ISG56, RSAD2, and TNF-α were up-regulated under Lc-TRAF7 overexpression in LYCMS cells. These findings collectively implied that Lc-TRAF7 may function as an important regulator in the host antiviral responses via the NF-κB as well as IRF3/7 involved signaling pathways

The LAMOST Survey of Background Quasars in the Vicinity of the Andromeda and Triangulum Galaxies -- II. Results from the Commissioning Observations and the Pilot Surveys

We present new quasars discovered in the vicinity of the Andromeda and Triangulum galaxies with the LAMOST during the 2010 and 2011 observational seasons. Quasar candidates are selected based on the available SDSS, KPNO 4 m telescope, XSTPS optical, and WISE near infrared photometric data. We present 509 new quasars discovered in a stripe of ~135 sq. deg from M31 to M33 along the Giant Stellar Stream in the 2011 pilot survey datasets, and also 17 new quasars discovered in an area of ~100 sq. deg that covers the central region and the southeastern halo of M31 in the 2010 commissioning datasets. These 526 new quasars have i magnitudes ranging from 15.5 to 20.0, redshifts from 0.1 to 3.2. They represent a significant increase of the number of identified quasars in the vicinity of M31 and M33. There are now 26, 62 and 139 known quasars in this region of the sky with i magnitudes brighter than 17.0, 17.5 and 18.0 respectively, of which 5, 20 and 75 are newly-discovered. These bright quasars provide an invaluable collection with which to probe the kinematics and chemistry of the ISM/IGM in the Local Group of galaxies. A total of 93 quasars are now known with locations within 2.5 deg of M31, of which 73 are newly discovered. Tens of quasars are now known to be located behind the Giant Stellar Stream, and hundreds behind the extended halo and its associated substructures of M31. The much enlarged sample of known quasars in the vicinity of M31 and M33 can potentially be utilized to construct a perfect astrometric reference frame to measure the minute PMs of M31 and M33, along with the PMs of substructures associated with the Local Group of galaxies. Those PMs are some of the most fundamental properties of the Local Group.Comment: 26 pages, 6 figures, AJ accepte

A Boiling‐Water‐Stable, Tunable White‐Emitting Metal–Organic Framework from Soft‐Imprint Synthesis

A new avenue for making porous frameworks has been developed by borrowing an idea from molecularly imprinted polymers (MIPs). In lieu of the small molecules commonly used as templates in MIPs, soft metal components, such as CuI, are used to orient the molecular linker and to leverage the formation of the network. Specifically, a linear dicarboxylate linker with thioether side groups reacted simultaneously with Ln3+ ions and CuI, leading to a bimetallic net featuring strong, chemically hard Eu3+–carboxylate links, as well as soft, thioether‐bound Cu2I2 clusters. The CuI block imparts water stability to the host; with the tunable luminescence from the lanthanide ions, this creates the first white‐emitting MOF that is stable in boiling water. The Cu2I2 block also readily reacts with H2S, and enables sensitive colorimetric detection while the host net remains intact.White light/white heat: A porous metal–organic framework, inspired by conceptually crosscutting the molecular imprint of polymers and the template of zeolites, emits white light in boiling water. The MOF incorporates an effective hard‐and‐soft divide, in which the EuIII–carboxylate framework holds up the primary grid, whereas the imbedded soft CuI block, like a template, can be dislodged (e.g., by reacting with H2S) from the surrounding sulfur donors while the host net remains intact.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137455/1/chem201504941-sup-0001-misc_information.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/137455/2/chem201504941.pd

Cortex phellodendri

Cortex phellodendri is used to reduce fever and remove dampness and toxin. Berberine is an active ingredient of C. phellodendri. Berberine from Argemone ochroleuca can relax airway smooth muscle (ASM); however, whether the nonberberine component of C. phellodendri has similar relaxant action was unclear. An n-butyl alcohol extract of C. phellodendri (NBAECP, nonberberine component) was prepared, which completely inhibits high K+- and acetylcholine- (ACH-) induced precontraction of airway smooth muscle in tracheal rings and lung slices from control and asthmatic mice, respectively. The contraction induced by high K+ was also blocked by nifedipine, a selective blocker of L-type Ca2+ channels. The ACH-induced contraction was partially inhibited by nifedipine and pyrazole 3, an inhibitor of TRPC3 and STIM/Orai channels. Taken together, our data demonstrate that NBAECP can relax ASM by inhibiting L-type Ca2+ channels and TRPC3 and/or STIM/Orai channels, suggesting that NBAECP could be developed to a new drug for relieving bronchospasm