Object-oriented Neural Programming (OONP) for Document Understanding

We propose Object-oriented Neural Programming (OONP), a framework for semantically parsing documents in specific domains. Basically, OONP reads a document and parses it into a predesigned object-oriented data structure (referred to as ontology in this paper) that reflects the domain-specific semantics of the document. An OONP parser models semantic parsing as a decision process: a neural net-based Reader sequentially goes through the document, and during the process it builds and updates an intermediate ontology to summarize its partial understanding of the text it covers. OONP supports a rich family of operations (both symbolic and differentiable) for composing the ontology, and a big variety of forms (both symbolic and differentiable) for representing the state and the document. An OONP parser can be trained with supervision of different forms and strength, including supervised learning (SL) , reinforcement learning (RL) and hybrid of the two. Our experiments on both synthetic and real-world document parsing tasks have shown that OONP can learn to handle fairly complicated ontology with training data of modest sizes.Comment: accepted by ACL 201

Sculpting the maturation, softening and ethylene pathway: The influences of microRNAs on tomato fruits

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs), a ubiquitous class of short RNAs, play vital roles in physiological and biochemical processes in plants by mediating gene silencing at post-transcriptional (PTGS) level. Tomato is a model system to study molecular basis of fleshy fruit ripening and senescence, ethylene biosynthesis and signal transduction owing to its genetic and molecular tractability. To study the functions of miRNAs in tomato fruit ripening and senescence, and their possible roles in ethylene response, the next generation sequencing method was employed to identify miRNAs in tomato fruit. Bioinformatics and molecular biology approaches were combined to profile the miRNAs expression patterns at three different fruit ripening stages and by exogenous ethylene treatment.</p> <p>Results</p> <p>In addition to 7 novel miRNA families, 103 conserved miRNAs belonging to 24 families and 10 non-conserved miRNAs matching 9 families were identified in our libraries. The targets of many these miRNAs were predicted to be transcriptional factors. Other targets are known to play roles in the regulation of metabolic processes. Interestingly, some targets were predicted to be involved in fruit ripening and softening, such as Pectate Lyase, beta-galactosidase, while a few others were predicted to be involved in ethylene biosynthesis and signaling pathway, such as ACS, EIN2 and CTR1. The expression patterns of a number of such miRNAs at three ripening stages were confirmed by stem-loop RT-PCR, which showed a strong negative correlation with that of their targets. The regulation of exogenous ethylene on miRNAs expression profiles were analyzed simultaneously, and 3 down-regulated, 5 up-regulated miRNAs were found in this study.</p> <p>Conclusions</p> <p>A combination of high throughput sequencing and molecular biology approaches was used to explore the involvement of miRNAs during fruit ripening. Several miRNAs showed differential expression profiles during fruit ripening, and a number of miRNAs were influenced by ethylene treatment. The results suggest the importance of miRNAs in fruit ripening and ethylene response.</p

Synthesis and crystal structure of two dimensional network DB18-C-6 complex: [Na(DB 18-C-6)]₂[Pt(SCN)₆]

1415-1416A novel dibenzo-18-crown-6 (DB18-C-6) complex [Na(DB18-C-6)]2[Pt(SCN)6] (1) has been synthesized and characterized by elemental analysis, IR spectrum and X-ray diffraction analysis. The complex belongs to triclinic. space group P-1 with cell dimensions: a = 1.2500(3), b = 1.2825(3), c = 1.9342(4) nm, α =106.82(3) , β= 102.51(3),γ = 103.04(3)°, V = 2.7562nm3, Z=2, Dcalcd = 1.579 g/cm3, F(000) = 1316, R1 = 0.0364, wR2 = 0.0771. The complex shows a two-dimensional network structure of [Na(DB18-C-6)+ complex cations and [Pt(SCN)6]2- complex anion bridged by Na-N interactions between adjacent [Na(DB 18-C-6)+ and [pt(SCN)6]2- units

One-dimensional chain crown ether complexes: Synthesis and crystal structure of [Na(18-crown-6)]₂[M(mnt)₂](M = Zn, Cd)

327-330The reactions of IR-crown-6 with Na2[Zn(mnt)2] and Na2[Cd(mnt)2] have been studied and the complexes [Na(18-crown-6)]2[M(mnt)2](M = Zn, Cd), are characterized by elemental analysis, IR spectrum and X-ray diffraction analysis. 1 and 2 belong to monoclinic, space group c2/c with cell dimensions, 1: a = 2.2418(6), b = 1.1359(3), c = 1.9887(6) nm, β= 120.391 (4)o, V = 4.368(2), nm3, Z = 4, Dcalcd = 1.399 Mg/m3, F(000) = 1920, R1 = 0.0302, wR2 = 0.0560 and 2: a = 2.2547(6), b = 1.1412(3), c = 1.9938(6) nm, β=119.715(4)°, V = 4.455 nm3, Z = 4, Dcalcd = 1.442 Mg/m3 , F(000)= 1992, R1 = 0.0384, wR2 = 0.0575. Two complexes display a one-dimensional chain of [Na(18C6)]+(complex cations and [M(mnt)2]2- (M = Zn, Cd) complex anion bridged by Na-O interactions between adjacent&nbsp; [Na(18C6)]+ units respectively

MicroRNA profiling analysis throughout tomato fruit development and ripening reveals potential regulatory role of RIN on microRNAs accumulation

The development and ripening of tomato fruit are complex processes involving many gene regulatory pathways at the transcriptional and post-transcriptional level. Ripening inhibitor (RIN) is a vital transcription factor, which targets numerous ripening-related genes at the transcriptional level during tomato fruit ripening. MicroRNAs (miRNAs) are a class of short noncoding RNAs that play important roles in post-transcriptional gene regulation. To elucidate the potential regulatory relationship between rin and miRNAs during fruit development and ripening, we identified known miRNAs and profiled their expression in wild-type tomato and rin mutant using a deep sequencing approach combined with quantitative RT-PCR. A total of 33 known miRNA families were identified, of which 14 miRNA families were differently accumulated. Subsequent promoter analysis showed that possible RIN-binding motifs (CArG-box) tended to occur frequently in the promoter regions of partial differently expressed miRNAs. In addition, ethylene may participate in the regulation of miRNAs accumulation during tomato fruit ripening. Chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assay confirmed the direct binding of RIN to the promoter of MIR172a. Collectively, these results showed a close correlation between miRNA expression and RIN as well as ethylene, which further elucidated the regulatory roles of miRNAs during fruit development and ripening and enriched the regulatory network of RIN in tomato fruit