Incremental Skip-gram Model with Negative Sampling

This paper explores an incremental training strategy for the skip-gram model with negative sampling (SGNS) from both empirical and theoretical perspectives. Existing methods of neural word embeddings, including SGNS, are multi-pass algorithms and thus cannot perform incremental model update. To address this problem, we present a simple incremental extension of SGNS and provide a thorough theoretical analysis to demonstrate its validity. Empirical experiments demonstrated the correctness of the theoretical analysis as well as the practical usefulness of the incremental algorithm

Predicting Causes of Reformulation in Intelligent Assistants

Intelligent assistants (IAs) such as Siri and Cortana conversationally interact with users and execute a wide range of actions (e.g., searching the Web, setting alarms, and chatting). IAs can support these actions through the combination of various components such as automatic speech recognition, natural language understanding, and language generation. However, the complexity of these components hinders developers from determining which component causes an error. To remove this hindrance, we focus on reformulation, which is a useful signal of user dissatisfaction, and propose a method to predict the reformulation causes. We evaluate the method using the user logs of a commercial IA. The experimental results have demonstrated that features designed to detect the error of a specific component improve the performance of reformulation cause detection.Comment: 11 pages, 2 figures, accepted as a long paper for SIGDIAL 201

The role of GTP in transient splitting of 70S ribosomes by RRF (ribosome recycling factor) and EF-G (elongation factor G).

Ribosome recycling factor (RRF), elongation factor G (EF-G) and GTP split 70S ribosomes into subunits. Here, we demonstrated that the splitting was transient and the exhaustion of GTP resulted in re-association of the split subunits into 70S ribosomes unless IF3 (initiation factor 3) was present. However, the splitting was observed with sucrose density gradient centrifugation (SDGC) without IF3 if RRF, EF-G and GTP were present in the SDGC buffer. The splitting of 70S ribosomes causes the decrease of light scattering by ribosomes. Kinetic constants obtained from the light scattering studies are sufficient to account for the splitting of 70S ribosomes by RRF and EF-G/GTP during the lag phase for activation of ribosomes for the log phase. As the amount of 70S ribosomes increased, more RRF, EF-G and GTP were necessary to split 70S ribosomes. In the presence of a physiological amount of polyamines, GTP and factors, even 0.6 microM 70S ribosomes (12 times higher than the 70S ribosomes for routine assay) were split. Spermidine (2 mM) completely inhibited anti-association activity of IF3, and the RRF/EF-G/GTP-dependent splitting of 70S ribosomes

The ribosome-recycling step: consensus or controversy?

Ribosome recycling, the last step in translation, is now accepted as an essential process for prokaryotes. In 2005, three laboratories showed that ribosome-recycling factor (RRF) and elongation factor G (EF-G) cause dissociation of ribosomes into subunits, solving the long-standing problem of how this essential step of translation occurs. However, there remains ongoing controversy regarding the other actions of RRF and EF-G during ribosome recycling. We propose that the available data are consistent with the notion that RRF and EF-G not only split ribosomes into subunits but also participate directly in the release of deacylated tRNA and mRNA for the next round of translation

Structural insights into initial and intermediate steps of the ribosome-recycling process

The ribosome recycling factor (RRF) and elongation factor G (EF-G) disassemble the 70S post-termination complex (PoTC) into mRNA, tRNA, and two ribosomal subunits. We have determined cryo-EM structures of the PoTC•RRF complex, with and without EF-G. We find that domain II of RRF initially interacts with universally conserved residues of the 23S rRNA helices 43 and 95, and protein L11 within the 50S ribosomal subunit. Upon EF-G binding, both RRF and tRNA are driven toward the tRNA-exit (E) site, with a large rotational movement of domain II of RRF toward the 30S ribosomal subunit. During this intermediate step of the recycling process, domain II of RRF and domain IV of EF-G adapt unusual conformations. Furthermore, binding of EF-G to the PoTC•RRF complex reverts the ribosome from ratcheted to unratcheted state. These results suggest that (i) the ribosomal intersubunit reorganizations upon RRF binding and subsequent EF-G binding could be instrumental in destabilizing the PoTC, and (ii) the modes of action of EF-G during tRNA translocation and ribosome recycling steps are markedly different

Protein synthesis factors (RF1, RF2, RF3, RRF, and tmRNA) and peptidyl-tRNA hydrolase rescue stalled ribosomes at sense codons.

During translation, ribosomes stall on mRNA when the aminoacyl-tRNA to be read is not readily available. The stalled ribosomes are deleterious to the cell and should be rescued to maintain its viability. To investigate the contribution of some of the cellular translation factors on ribosome rescuing, we provoked stalling at AGA codons in mutants that affected the factors and then analyzed the accumulation of oligopeptidyl (peptides of up to 6 amino acid residues, oligopep-)-tRNA or polypeptidyl (peptides of more than 300 amino acids in length, polypep-)-tRNA associated with ribosomes. Stalling was achieved by starvation for aminoacyl-tRNA(Arg4) upon induced expression of engineered lacZ (β-galactosidase) reporter gene harboring contiguous AGA codons close to the initiation codon or at internal codon positions together with minigene ATGAGATAA accompanied by reduced peptidyl-tRNA hydrolase (Pth). Our results showed accumulations of peptidyl-tRNA associated with ribosomes in mutants for release factors (RF1, RF2, and RF3), ribosome recycling factor (RRF), Pth, and transfer-messenger RNA (tmRNA), implying that each of these factors cooperate in rescuing stalled ribosomes. The role of these factors in ribosome releasing from the stalled complex may vary depending on the length of the peptide in the peptidyl-tRNA. RF3 and RRF rescue stalled ribosomes by drop-off of peptidyl-tRNA, while RF1, RF2 (in the absence of termination codon), or Pth may rescue by hydrolyzing the associated peptidyl-tRNA. This is followed by the disassembly of the ribosomal complex of tRNA and mRNA by RRF and elongation factor G

HASC2011corpus: Towards the Common Ground of Human Activity Recognition

UbiComp '11 Proceedings of the 13th international conference on Ubiquitous computing, September 17-21, 2011, Beijing, ChinaHuman activity recognition through the wearable sensor will enable a next-generation human-oriented biquitous computing. However, most of research on human activity recognition so far is based on small number of subjects, and non-public data. To overcome the situation, we have gathered 4897 accelerometer data with 116 subjects and compose them as HASC2011corpus. In the field of pattern recognition, it is very important to evaluate and to improve the recognition methods by using the same dataset as a common ground. We make the HASC2011corpus into public for the research community to use it as a common ground of the Human Activity Recognition. We also show several facts and results of obtained from the corpus

TDP-43 regulates cholesterol biosynthesis by inhibiting sterol regulatory element-binding protein 2

Dyslipidemia is considered an essential component of the pathological process of amyotrophic lateral sclerosis (ALS), a fatal motor neuron disease. Although TAR DNA Binding Protein 43 kDa (TDP-43) links both familial and sporadic forms of ALS and cytoplasmic aggregates are a hallmark of most cases of ALS, the molecular mechanism and the in vivo relation of ALS dyslipidemia with TDP-43 have been unclear. To analyze the dyslipidemia-related gene expression by TDP-43, we performed expression microarray and RNA deep sequencing (RNA-Seq) using cell lines expressing high levels of TDP-43 and identified 434 significantly altered genes including sterol regulatory element-binding protein 2 (SREBP2), a master regulator of cholesterol homeostasis and its downstream genes. Elevated TDP-43 impaired SREBP2 transcriptional activity, leading to inhibition of cholesterol biosynthesis. The amount of cholesterol was significantly decreased in the spinal cords of TDP-43-overexpressed ALS model mice and in the cerebrospinal fluids of ALS patients. These results suggested that TDP-43 could play an essential role in cholesterol biosynthesis in relation to ALS dyslipidemia