GPCR-OKB: the G protein coupled receptor oligomer knowledge base

Rapid expansion of available data about G Protein Coupled Receptor (GPCR) dimers/oligomers over the past few years requires an effective system to organize this information electronically. Based on an ontology derived from a community dialog involving colleagues using experimental and computational methodologies, we developed the GPCR-Oligomerization Knowledge Base (GPCR-OKB). GPCR-OKB is a system that supports browsing and searching for GPCR oligomer data. Such data were manually derived from the literature. While focused on GPCR oligomers, GPCR-OKB is seamlessly connected to GPCRDB, facilitating the correlation of information about GPCR protomers and oligomers

Substring-based Machine Translation

Abstract Machine translation is traditionally formulated as the transduction of strings of words from the source to the target language. As a result, additional lexical processing steps such as morphological analysis, transliteration, and tokenization are required to process the internal structure of words to help cope with data-sparsity issues that occur when simply dividing words according to white spaces. In this paper, we take a different approach: not dividing lexical processing and translation into two steps, but simply viewing translation as a single transduction between character strings in the source and target languages. In particular, we demonstrate that the key to achieving accuracies on a par with word-based translation in the character-based framework is the use of a many-to-many alignment strategy that can accurately capture correspondences between arbitrary substrings. We build on the alignment method proposed in Neubig et al (2011), improving its efficiency and accuracy with a focus on character-based translation. Using a many-to-many aligner imbued with these improvements, we demonstrate that the traditional framework of phrase-based machine translation sees large gains in accuracy over character-based translation with more naive alignment methods, and achieves comparable results to word-based translation for two distant language pairs

Synthetic High-Resolution Line Spectra of Star-Forming Galaxies Below 1200A

We have generated a set of far-ultraviolet stellar libraries using spectra of OB and Wolf-Rayet stars in the Galaxy and the Large and Small Magellanic Cloud. The spectra were collected with the Far Ultraviolet Spectroscopic Explorer and cover a wavelength range from 1003.1 to 1182.7A at a resolution of 0.127A. The libraries extend from the earliest O- to late-O and early-B stars for the Magellanic Cloud and Galactic libraries, respectively. Attention is paid to the complex blending of stellar and interstellar lines, which can be significant, especially in models using Galactic stars. The most severe contamination is due to molecular hydrogen. Using a simple model for the H$_2$ line strength, we were able to remove the molecular hydrogen lines in a subset of Magellanic Cloud stars. Variations of the photospheric and wind features of CIII 1176, OVI 1032, 1038, PV 1118, 1128, and SIV 1063, 1073, 1074 are discussed as a function of temperature and luminosity class. The spectral libraries were implemented into the LavalSB and Starburst99 packages and used to compute a standard set of synthetic spectra of star-forming galaxies. Representative spectra are presented for various initial mass functions and star formation histories. The valid parameter space is confined to the youngest ages of less than 10 Myr for an instantaneous burst, prior to the age when incompleteness of spectral types in the libraries sets in. For a continuous burst at solar metallicity, the parameter space is not limited. The suite of models is useful for interpreting the restframe far-ultraviolet in local and high-redshift galaxies.Comment: 33 pages including 13 figures, accepted for publication in Ap

Under the microscope: Single molecule symposium at the University of Michigan, 2006

In recent years, a revolution has occurred in the basic sciences, which exploits novel single molecule detection and manipulation tools to track and analyze biopolymers in unprecedented detail. A recent Gordon Research Conference style meeting, hosted by the University of Michigan, highlighted current status and future perspectives of this rising field as researchers begin to integrate it with mainstream biology and nanotechnology. © 2006 Wiley Periodicals, Inc. Biopolymers 85:106–114, 2007Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55865/1/20621_ftp.pd

Bridging the Gap: A Survey on Integrating (Human) Feedback for Natural Language Generation

Many recent advances in natural language generation have been fueled by training large language models on internet-scale data. However, this paradigm can lead to models that generate toxic, inaccurate, and unhelpful content, and automatic evaluation metrics often fail to identify these behaviors. As models become more capable, human feedback is an invaluable signal for evaluating and improving models. This survey aims to provide an overview of the recent research that has leveraged human feedback to improve natural language generation. First, we introduce an encompassing formalization of feedback, and identify and organize existing research into a taxonomy following this formalization. Next, we discuss how feedback can be described by its format and objective, and cover the two approaches proposed to use feedback (either for training or decoding): directly using the feedback or training feedback models. We also discuss existing datasets for human-feedback data collection, and concerns surrounding feedback collection. Finally, we provide an overview of the nascent field of AI feedback, which exploits large language models to make judgments based on a set of principles and minimize the need for human intervention.Comment: Work in Progres

« La Tragédie du roi Christophe » du point de vue de l’histoire d’Haïti

This paper presents a multilingual study on, per single post of microblog text, (a) how much can be said, (b) how much is written in terms of characters and bytes, and (c) how much is said in terms of information content in posts by different organizations in different languages. Focusing on three different languages (English, Chinese, and Japanese), this research analyses Weibo and Twitter accounts of major embassies and news agencies. We first establish our criterion for quantifying \how much can be said" in a digital text based on the openly available Universal Declaration of Human Rights and the translated subtitles from TED talks. These parallel corpora allow us to determine the number of characters and bits needed to represent the same content in different languages and character encodings. We then derive the amount of information that is actually contained in microblog posts authored by selected accounts on Weibo and Twitter. Our results confirm that languages with larger character sets such as Chinese and Japanese contain more information per character than English, but the actual information content contained within a microblog text varies depending on both the type of organization and the language of the post. We conclude with a discussion on the design implications of microblog text limits for different languages

Neutrino Oscillations and the Supernova 1987A Signal

We study the impact of neutrino oscillations on the interpretation of the supernova (SN) 1987A neutrino signal by means of a maximum-likelihood analysis. We focus on oscillations between $\overline\nu_e$ with $\overline\nu_\mu$ or $\overline\nu_\tau$ with those mixing parameters that would solve the solar neutrino problem. For the small-angle MSW solution ($\Delta m^2\approx10^{-5}\,\rm eV^2$, $\sin^22\Theta_0\approx0.007$), there are no significant oscillation effects on the Kelvin-Helmholtz cooling signal; we confirm previous best-fit values for the neutron-star binding energy and average spectral $\overline\nu_e$ temperature. There is only marginal overlap between the upper end of the 95.4\% CL inferred range of $\langle E_{\overline\nu_e}\rangle$ and the lower end of the range of theoretical predictions. Any admixture of the stiffer $\overline\nu_\mu$ spectrum by oscillations aggravates the conflict between experimentally inferred and theoretically predicted spectral properties. For mixing parameters in the neighborhood of the large-angle MSW solution ($\Delta m^2\approx10^{-5}\,\rm eV^2$, $\sin^22\Theta_0\approx0.7$) the oscillations in the SN are adiabatic, but one needs to include the regeneration effect in the Earth which causes the Kamiokande and IMB detectors to observe different $\overline\nu_e$ spectra. For the solar vacuum solution ($\Delta m^2\approx10^{-10}\,\rm eV^2$, $\sin^22\Theta_0\approx1$) the oscillations in the SN are nonadiabatic; vacuum oscillations take place between the SN and the detector. If either of the large-angle solutions were borne out by the upcoming round of solar neutrino experiments, one would have to conclude that the SN~1987A $\overline\nu_\mu$ and/or $\overline\nu_e$ spectra had been much softer than predicted by currentComment: Final version with very minor wording changes, to be published in Phys. Rev.

Oral Ethanol Self-Administration in Rhesus Monkeys: Behavioral and Neurochemical Correlates

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66306/1/j.1530-0277.1999.tb04357.x.pd

RGS4 negatively modulates Nociceptin/Orphanin FQ opioid receptor signaling: implication for L-Dopa induced dyskinesia

Background and purpose Regulator of G-protein signal 4 (RGS4) is a signal transduction protein that accelerates intrinsic GTPase activity of Gαi/o and Gαq subunits, suppressing GPCR signaling. Here we investigate whether RGS4 modulates nociceptin/orphanin FQ (N/OFQ) opioid (NOP) receptor signaling and this modulation has relevance for L-Dopa-induced dyskinesia. Experimental approach HEK293T cells transfected with NOP, NOP/RGS4 or NOP/RGS19 were challenged with N/OFQ and the small molecule NOP agonist AT-403, using D1-stimulated cAMP levels as a readout. Primary rat striatal neurons and adult mouse striatal slices were challenged with N/OFQ or AT-403 in the presence of the experimental RGS4 chemical probe, CCG-203920, and D1-stimulated cAMP or phosphorylated extracellular signal regulated kinase 1/2 (pERK) responses were monitored. In vivo, CCG-203920 was co-administered with AT-403 and L-Dopa to 6-hydroxydopamine hemilesioned rats, and dyskinetic movements, striatal biochemical correlates of dyskinesia (pERK and pGluR1 levels) and striatal RGS4 levels were measured. Key results RGS4 expression reduced NOFQ and AT-403 potency and efficacy in HEK293T cells. CCG-203920 increased N/OFQ potency in primary rat striatal neurons, and potentiated AT-403 response in mouse striatal slices. CCG-203920 enhanced AT-403 mediated inhibition of dyskinesia and its biochemical correlates, without compromising its motor-improving effects. Unilateral dopamine depletion caused bilateral reduction of RGS4 levels, which was reversed by L-Dopa. L-Dopa acutely upregulated RGS4 in the lesioned striatum. Conclusions and Implications RGS4 physiologically inhibits NOP receptor signaling. CCG-203920 enhanced NOP responses and improved the antidyskinetic potential of NOP receptor agonists, mitigating the effects of striatal RGS4 upregulation occurring during dyskinesia expression