Exploiting the performance of dictionary-based bio-entity name recognition in biomedical literature

Bio-entity name recognition is the key step for information extraction from biomedical literature. This paper presents a dictionary-based bio-entity name recognition approach. The approach expands the bio-entity name dictionary via the Abbreviation Definitions identifying algorithm, improves the recall rate through the improved edit distance algorithm and adopts some post-processing methods including Pre-keyword and Post-keyword expansion, Part of Speech expansion, merge of adjacent bio-entity names and the exploitation of the contextual cues to further improve the performance. Experiment results show that with this approach even an internal dictionary-based system could achieve a fairly good performance.     

High throughput tryptic digestion via poly (acrylamide-co-methylenebisacrylamide) monolith based immobilized enzyme reactor

A poly (acrylamide-co-methylenebisacrylamide) (poly (AAm-co-MBA)) monolith was prepared by thermal polymerization in the 100 or 250 μm i.d. capillary. The monolithic support was activated by ethylenediamine followed by glutaraldehyde. Trypsin was then introduced to form an immobilized enzyme reactor (IMER). The prepared IMER showed a reliable mechanical stability and permeability (permeability constant K = 2.65 × 10⁻¹³ m²). With BSA as the model protein, efficient digestion was completed within 20 s, yielding the sequence coverage of 57%, better than that obtained from the traditional in-solution digestion (42%), which took about 12 h. Moreover, BSA down to femtomole was efficiently digested by the IMER and positively identified by matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). To test the applicability of IMER for complex sample profiling, proteins extracted from Escherichia coli were digested by the IMER and further analyzed by nanoreversed phase liquid chromatography-electrospray ionization-mass spectrometry (nanoRPLC-ESI-MS/MS). In comparison to in-solution digestion, despite slightly fewer proteins were positively identified at a false discovery rate (FDR) of ∼1% (333 vs 411), the digestion time used was largely shortened (20 s vs 24 h), implying superior digestion performance for the high throughput analysis of complex samples.     

Photoelectron imaging and theoretical studies of silver monohalides AgX- (X = Cl, Br, I) and AuCl-

Photodetachment of AgX(-) (X = Cl, Br, I) and AuCl(-) is studied by a photoelectron velocity map imaging technique and theoretical calculations. Photoelectron spectra (PES) and photoelectron angular distributions (PADs) were obtained. The vibrationally resolved spectra provided approximately equal electron affinities (EAs) for AgX: 1.593(22) eV for AgCl, 1.623(21) eV for AgBr, and 1.603(22) eV for AgI, respectively. Franck-Condon simulations of these spectra gave the equilibrium bond lengths and vibrational frequencies of the title anions. Relativistic density functional theory (DFT) calculations using BLYP, PW91, PBE, and BP86 functionals have been performed to predict the EAs of the AgX (X = Cl, Br, I) molecules. The computed EAs at the BP86 level of theory are in good agreement with the experimental values. Energy partitioning analyses (EPA) at the BP86(ZORA)/QZ4P level of theory of both anions and their neutrals were reported.     

Studies of iridoid glycosides using liquid chromatography/electrospray ionization tandem mass spectrometry

Fragmentation pathways of five iridoid glycosides have been studied by using electrospray ionization multi-stage tandem mass spectrometry (ESI-MS(n)). The first-stage MS data of the five iridoid glycosides were compared. The MS spectra showed that the adduct ions of iridoid glycosides and the formate anion were diagnostic ions to distinguish iridoid glycosides with a carboxyl group at the C-4 position or an ester group at the C-4 position. The MS fragmentation pathways of the five iridoid glycosides were also studied. Analyzing the product ion spectra of iridoid glycosides, some neutral losses were observed, such as H(2)O, CO(2) and glucose residues, which were very useful for the identification of the functional groups in the structures of iridoid glycosides. Furthermore, specific loss of one molecule of methyl 3-oxopropanoate or 3-oxopropanic acid was firstly discussed, which corresponded to the isomerization of the hemiacetal group in the structure of iridoid aglycone. According to the fragmentation mechanisms and HPLC/MS(n) data, the structures of five iridoid glycosides in a crude extract of Gardenia jasminoisdes fruit have been identified. Three compounds were compared with standards and the other two were identified as shanzhiside and genipin gentibioside by their MS(n) data without standard compounds. In order to further validate the veracity of the deduction, genipin gentiobioside was isolated from the extract of Gardenia jasminoisdes fruit using Purification Factory and was further identified by C- and H-NMR.     

Effects of chromium ion on sulfur removal during pyrolysis and hydropyrolysis of coal

The effects of impregnated Cr³⁺ on sulfur removal during pyrolysis and hydropyrolysis of coal were investigated by loading CrCl₃ into raw, demineralized and pyrite removed coal, respectively. The results indicate that Cr has no effect on the removal of pyrite. Cr affects the removal of total sulfur by forming Cr₇S₈ and affecting the removal of organic sulfur. Cr acts as the sulfur removing agent by promoting the decomposition of the unstable organic sulfur at low temperature. However, it behaves to be sulfur fixing agent between 400 and 700 °C so as to inhibit the evolution of H₂S, even in hydropyrolysis. With the increase of temperature from 700 to 1050 °C, a certain ratio of Cr₇S₈ is converted into organic sulfur during pyrolysis; however, almost all the Cr₇S₈ is reduced into Cr at 1050 °C during hydropyrolysis. And Cr significantly promotes the removal of organic sulfur at high temperature within reducing atmosphere. The XPS results indicate that the sulfur is enriched on coke surface by Cr, which is attributable to the formation of Cr₇S₈ as well as the transfer of organic sulfur from bulk to surface during pyrolysis and hydropyrolysis.     

Long-term super-resolution imaging of mitochondrial dynamics

Monitoring dynamics of mitochondria has become an essential approach to explore the function of mitochondria in living cells with the emergence of super-resolution fluorescence microscopy. However, long-term super-resolution imaging of mitochondria is still challenging due to the lack of photostable fluorescent probes and stable mitochondria-specific markers which are not affected by the changes of mitochondrial membrane potential. Here, we introduce a method for long-term imaging mitochondrial dynamic through the SNAP-tag fluorogenic probe based on 4-azetidinyl-naphthalimide derivatives. Using structured illumination microscopy (SIM), we observed the fusion and fission of mitochondria over a course of 16 min at 109 nm resolution. Furthermore, the interactions as well as fusion between mitochondria and lysosomes were studied during mitophagy at the nanoscale. Convincingly, the combination of SNAP-tag fluorogenic probes and super-resolution fluorescence microscopy will offer a new way to monitor dynamic mitochondria in living cells.     

分子反应动力学如何走向21世纪

分子反应动力学领域正在发展之中,还远未进入成熟期。有些课题,如涉及对化学反应性基本理解方面的飞秒化学、立体化学动力学、态一态化学、选模化学以及有关新反应类型方面的团簇化学动力学、自由基反应动力学、气一固表面反应动力学等皆处于它们发展的中间阶段。另外有些课题,如激光控制化学反应,则仅处于初创阶段。它们如何进入21世纪呢?我们建议将来应该研究如下课题:(1)飞秒化学及立体态一态动力学;(2)激光控制化学反应;(3)团簇形成规律、结构及动力学;(4)分子高振动激发态光谱、自由基光谱及动力学;(5)理论研究。本文对上述课题给予简要的讨论。     

Determination of the molecular weight of polyoxypropylenepolyols by <Superscript>1</Superscript>H NMR spectroscopy

Commercial and laboratory samples of polyoxypropylenepolyols were studied by ¹H NMR spectroscopy at operating frequencies of 100 and 500 MHz. Various methods depending on the solvent used were suggested for determining the equivalent weight (molecular weight of the polyether per terminal hydroxy group). The ¹H NMR data are compared to the data obtained by chemical methods and gel permeation chromatography.     

A Surface Femtosecond Two-Photon Photoemission Spectrometer for Excited Electron Dynamics and Time-Dependent Photochemical Kinetics

A surface femtosecond two-photon photoemission (2PPE) spectrometer devoted to the study of ultrafast excited electron dynamics and photochemical kinetics on metal and metal oxide surfaces has been constructed. Low energy photoelectrons are measured using a hemispheri-cal electron energy analyzer with an imaging detector that allows us to detect the energy and the angular distributions of the photoelectrons simultaneously. A Mach-Zehnder interferom-eter was built for the time-resolved 2PPE (TR-2PPE) measurement to study ultrafast surface excited electron dynamics, which was demonstrated on the Cu(111) surface. A scheme for measuring time-dependent 2PPE (TD-2PPE) spectra has also been developed for studies of surface photochemistry. This technique has been applied to a preliminary study on the photochemical kinetics on ethanol/TiO₂(110). We have also shown that the ultrafast dy-namics of photoinduced surface excited resonances can be investigated in a reliable way by combining the TR-2PPE and TD-2PPE techniques.