DEEPAligner: Deep encoding of pathways to align epigenetic signatures

Background and objectiveRecently, differential DNA Methylation is known to affect the regulatory mechanism of biological pathways. A pathway encompasses a set of interacting genes or gene products that altogether perform a given biological function. Pathways often encode strong methylation signatures that are capable of distinguishing biologically distinct subtypes. Even though Next Generation Sequencing techniques such as MeDIP-seq and MBD-isolated genome sequencing (MiGS) allow for genome-wide identification of clinical and biological subtypes, there is a pressing need for computational methods to compare epigenetic signatures across pathways.MethodsA novel alignment method, called DEEPAligner (Deep Encoded Epigenetic Pathway Aligner), is proposed in this paper that finds functionally consistent and topologically sound alignments of epigenetic signatures from pathway networks. A deep embedding framework is used to obtain epigenetic signatures from pathways which are then aligned for functional consistency and local topological similarity.ResultsExperiments on four benchmark cancer datasets reveal epigenetic signatures that are conserved in cancer-specific and across-cancer subtypes.ConclusionThe proposed deep embedding framework obtains highly coherent signatures that are aligned for biological as well as structural orthology. Comparison with state-of-the-art network alignment methods clearly suggest that the proposed method obtains topologically and functionally more consistent alignments.Availabilityhttp://bdbl.nitc.ac.in/DEEPAligner     

Two pairs of new alkaloid enantiomers with a spiro [benzofuranone-benzazepine] skeleton from the bark of Juglans mandshurica

(±)-Juglanaloid A (1) and B (2), two pairs of novel naturally occurring alkaloid enantiomers bearing an unprecedented spiro [benzofuranone-benzazepine] skeleton, were isolated from the bark of Juglans mandshurica Maxim. The unusual 6, 5, 7, 6-cyclic system with a rare spiro cyclic center at C-4 was determined on the basis of spectroscopic data. Chiral separation of 1 and 2 yielded two pairs of enantiomers, 1a/1b and 2a/2b. The absolute configurations were established by comparing the experimental and calculated electronic circular dichroism spectra. The potential anti-AD properties of 1a/1b and 2a/2b were evaluated by the Thioflavin T assay.     

Different substrate materials effect on structure of ta-C films by Raman spectroscopy for magnetic recording sliders

Raman spectra, using visible (514 nm) and ultraviolet (244 nm) excitation, of tetrahedral amorphous carbon (ta-C) films of thickness of 5 nm have been studied as a function of different substrates materials. These materials are Fe-Co (Fe: 67 at.%, Co: 33 at.%) alloy, Fe-Ni alloy (Fe: 18 at.%, Ni: 82 at.%), Au and Al₂O₃-TiC (Al₂O₃: 64 at.%, TiC: 36 at.%), which are mainly used in magnetic recording sliders. The spectra show that the films deposited on Al₂O₃-TiC contain the highest sp³ content, with a lower sp³ content observed in films deposited to Fe-Co and Fe-Ni alloys. The lowest sp³ content was observed in films on the Au substrate. The results also indicate that the anti-wear performance of ta-C film on different substrates varies as Al₂O₃-TiC (the best) > Fe-Co and Fe-Ni alloy > Au (the worst). Also mechanisms are proposed to explain the effect of substrate material on these thin film properties.     

Seed-mediated synthesis of uniform ZnO nanorods in the presence of polyethylene glycol

Large quantities of ZnO nanorods have been synthesized by the seed-mediated method in the presence of polyethylene glycol at 90 °C. The products are characterized using X-ray diffraction, scanning electron microscopy, transmission electron microscopy and high-resolution transmission electron microscopy. The as-grown ZnO nanorods are uniform with a diameter of 40–70 nm and length about 2 μm. The nanorods grew along the [0 0 1] direction. Possible roles of ZnO seeds and polymer in the growth of ZnO nanorods are also discussed.     

EXAFS study of mechanical-milling-induced solid-state amorphization of Se

Complete solid-state amorphization has been realized in elemental selenium by means of mechanical milling of crystalline Se powder. Extended X-ray-absorption fine-structure measurements (EXAFS) indicated that the amorphization process of crystalline Se was accompanied with a decrease of the nearest neighboring coordination number and the bond length, and the increase of the Debye-Waller factor. Combined with the previous study, we conclude that the mechanical milling results in the strengthening of intra-chain and weakening of inter-chain interactions of Se during amorphization. Compared to the structure of the as-quenched amorphous Se, the first nearest neighbor coordination number of the as-milled amorphous Se becomes smaller, while the Debye-Waller factor is larger, which is caused by the milling process.     

Fault diagnosis for a class of nonlinear uncertain hybrid systems

This paper presents a fault diagnosis architecture for a class of hybrid systems with nonlinear uncertain time-driven dynamics, measurement noise, and autonomous and controlled mode transitions. The proposed approach features a hybrid estimator based on a modified hybrid automaton framework. The fault detection scheme employs a filtering approach that attenuates the effect of the measurement noise and allows tighter mode-dependent thresholds for the detection of both discrete and parametric faults while guaranteeing no false alarms due to modeling uncertainty and mode mismatches. Both the hybrid estimator and the fault detection scheme are linked with an autonomous guard events identification (AGEI) scheme that handles the effects of mode mismatches due to autonomous mode transitions and allows effective mode estimation. Finally, the fault isolation scheme anticipates which fault events may have occurred and dynamically employs the appropriate isolation estimators for isolating the fault by calculating suitable thresholds and estimating the parametric fault magnitude through adaptive approximation methods. Simulation results from a five-tank hybrid system illustrate the effectiveness of the proposed approach.     

Antitumor-promoting constituents from Chaenomeles sinensis KOEHNE and their activities in JB6 mouse epidermal cells

Primary screening of antitumor-promoting activity using soft agar colony assays with JB6 cells was employed to isolate 22 compounds from Chaenomeles sinensis KOEHNE. These compounds were lyoniresinol-2a-O-alpha-L-rhamnopyranoside (1), lyoniresinol-2a-O-beta-D-glucopyranoside (2), aviculin (3), betulinic acid (4), betulin (5), 3-O-(E)-p-coumaroylbetulin (6), 3-O-(E)-caffeoylbetulin (7), 3-O-(Z)-p-coumaroylbetulin (8), 3-O-(E)-caffeoyllupeol (9), alphitolic acid (10), sorbikortal II (11), tormentic acid (12), euscaphic acid (13), corosolic acid (14), maslinic acid (15), erythrodiol (16), 1-beta-D-glucopyranosyloxy-3,4,5-trimethoxybenzene (17), avicularin (18), 7-O-beta-D-glucopyranosylkaempferol (19), 5-O-beta-D-glucopyranosylgenistein (20), 7-O-beta-D-glucopyranosylgenistein (21), epicatechin (22), and beta-sitosterol (23) and were identified using spectral data such as MS, (1)H- and (13)C-NMR. Compound 1, having a rhamnosyl group, showed greater activity than 2, having a glucosyl group, and 3, which was a bis-demethoxy derivative of 1. Betulinic acid (4), having a C-28 carboxyl group, 3-O-(E)-caffeoylbetulin (7), and tormentic acid (12) showed more potent activity than betulin (5), which has a C-28 hydroxymethyl group.     

Development of an HPLC Fingerprint for Quality Control of Radix Semiaquilegiae

A simple and accurate fingerprinting method using LC with photodiode-array detection (HPLC–DAD) has been developed for quality control of the roots of Semiaquilegia adoxoides (DC.) Makino (Chinese name “Tian-Kui-Zi”), a traditional Chinese medicine with much important biological activity. For the first time, HPLC fingerprints were investigated and used for evaluation of Tiankuizi collected from different locations. Many unusual reference samples were separated and assigned, but most were complicated epimers. Remarkable effects of the ratio of mobile-phase components on the elution of these epimers were also observed.     

Study on the bioavailability of nateglinide-hydroxypropyl-beta-cyclodextrin complex capsule in rabbits by liquid chromatographic-tandem mass spectrometry

To evaluate the bioavailability of nateglinide-hydroxypropyl-beta-cyclodextrin (HPCD) complex, a rapid and specific liquid chromatographic-tandem mass spectrometric method was developed and validated to determine nateglinide in rabbit serum. The analyte was extracted from serum samples by liquid-liquid extraction, separated on a Zorbax C(18) column and detected by tandem mass spectrometry with an atmospheric pressure chemical ionization interface. Daidzein was used as the internal standard. The method has a lower limit of quantitation of 0.25 mg/L using 200 micro L serum. The intra- and inter-day relative standard deviations calculated from quality control (QC) samples were below 4%. The inter-day relative error was within 1%. Nateglinide serum concentrations in rabbits given nateglinide-hydroxypropyl-beta-cyclodextrin complex were much higher than those given the free drug. Significant difference was observed in main pharmacokinetic parameters of t(max) and C(max) but not AUC(0-t) between the complex and free drug. It was concluded that the absorption rate of nateglinide-HPCD complex was enhanced, compared with that of nateglinide free drug.     

Impact of silicon doping on the magnetocaloric effect of MnFeP0.35As0.65 powder

The magnetocaloric effect in the MnFeP_0.35As_0.65−xSi_x intermetallic compounds, prepared via solid-state sintering was studied. Adiabatic temperature and magnetic entropy changes were obtained in order to characterize these compounds. The substitution of silicon for arsenic leads to a significant enhancement of the magnetocaloric effect for silicon amount x = 0.11. The adiabatic temperature change increased from 2.3 to 3.3 K for the magnetic field change from 0 to 1.7 T. This improvement has been correlated with the increase of crystalline cell volume and change of lattice constants. Additionally, the structure of pure MnFeP_0.33As_0.67 has been modeled in order to check the spin alignment within the framework of ferromagnetic collinear model.