Modular Synthesis of Sketches Using Models

One problem with the constraint-based approaches to synthesis that have become popular over the last few years is that they only scale to relatively small routines, on the order of a few dozen lines of code. This paper presents a mechanism for modular reasoning that allows us to break larger synthesis problems into small manageable pieces. The approach builds on previous work in the verification community of using high-level specifications and partially interpreted functions (we call them models) in place of more complex pieces of code in order to make the analysis modular. The main contribution of this paper is to show how to combine these techniques with the counterexample guided synthesis approaches used to efficiently solve synthesis problems. Specifically, we show two new algorithms; one to efficiently synthesize functions that use models, and another one to synthesize functions while ensuring that the behavior of the resulting function will be in the set of behaviors allowed by the model. We have implemented our approach on top of the open-source Sketch synthesis system, and we demonstrate its effectiveness on several Sketch benchmark problems.National Science Foundation (U.S.) (Grant NSF-1116362)National Science Foundation (U.S.) (Grant NSF-1139056)United States. Dept. of Energy (Grant DE-SC0005372

Human-Computer Music Performance: From Synchronized Accompaniment to Musical Partner

Live music performance with computers has motivated many research projects in science, engineering, and the arts. In spite of decades of work, it is surprising that there is not more technology for, and a better understanding of the computer as music performer. We review the development of techniques for live music performance and outline our efforts to establish a new direction, Human-Computer Music Performance (HCMP), as a framework for a variety of coordinated studies. Our work in this area spans performance analysis, synchronization techniques, and interactive performance systems. Our goal is to enable musicians to ncorporate computers into performances easily and effectively through a better understanding of requirements, new techniques, and practical, performance-worthy implementations. We conclude with directions for future work

Exact Histogram Specification Optimized for Structural Similarity

An exact histogram specification (EHS) method modifies its input image to have a specified histogram. Applications of EHS include image (contrast) enhancement (e.g., by histogram equalization) and histogram watermarking. Performing EHS on an image, however, reduces its visual quality. Starting from the output of a generic EHS method, we maximize the structural similarity index (SSIM) between the original image (before EHS) and the result of EHS iteratively. Essential in this process is the computationally simple and accurate formula we derive for SSIM gradient. As it is based on gradient ascent, the proposed EHS always converges. Experimental results confirm that while obtaining the histogram exactly as specified, the proposed method invariably outperforms the existing methods in terms of visual quality of the result. The computational complexity of the proposed method is shown to be of the same order as that of the existing methods. Index terms: histogram modification, histogram equalization, optimization for perceptual visual quality, structural similarity gradient ascent, histogram watermarking, contrast enhancement

Structural insights into how Prp5 proofreads the pre-mRNA branch site

During the splicing of introns from precursor messenger RNAs (pre-mRNAs), the U2 small nuclear ribonucleoprotein (snRNP) must undergo stable integration into the spliceosomal A complex-a poorly understood, multistep process that is facilitated by the DEAD-box helicase Prp5 (refs. 1-4). During this process, the U2 small nuclear RNA (snRNA) forms an RNA duplex with the pre-mRNA branch site (the U2-BS helix), which is proofread by Prp5 at this stage through an unclear mechanism5. Here, by deleting the branch-site adenosine (BS-A) or mutating the branch-site sequence of an actin pre-mRNA, we stall the assembly of spliceosomes in extracts from the yeast Saccharomyces cerevisiae directly before the A complex is formed. We then determine the three-dimensional structure of this newly identified assembly intermediate by cryo-electron microscopy. Our structure indicates that the U2-BS helix has formed in this pre-A complex, but is not yet clamped by the HEAT domain of the Hsh155 protein (Hsh155HEAT), which exhibits an open conformation. The structure further reveals a large-scale remodelling/repositioning of the U1 and U2 snRNPs during the formation of the A complex that is required to allow subsequent binding of the U4/U6.U5 tri-snRNP, but that this repositioning is blocked in the pre-A complex by the presence of Prp5. Our data suggest that binding of Hsh155HEAT to the bulged BS-A of the U2-BS helix triggers closure of Hsh155HEAT, which in turn destabilizes Prp5 binding. Thus, Prp5 proofreads the branch site indirectly, hindering spliceosome assembly if branch-site mutations prevent the remodelling of Hsh155HEAT. Our data provide structural insights into how a spliceosomal helicase enhances the fidelity of pre-mRNA splicing

Deuterated species in extragalactic star-forming regions

We present a theoretical study of the deuterated species detectability in various types of extragalactic star-forming regions based on our predictions of chemical abundances. This work is motivated by the past and current attempts at observing deuterated species in external galaxies such as NGC~253, IC~342 and the LMC. Here, we investigate the influence of the density, the temperature, the FUV radiation field, the cosmic ray ionisation, and the metallicity on the fractional abundances and D/H abundance ratios of about 20 deuterated species. Without modelling any particular source, we determined how the deuterium chemistry behaves in different physical environments such as starburst, cosmic-rays enhanced environments, low metallicity and high redshift galaxies. In general, our predicted column densities seem in good agreement with those derived from the current limited dataset of observations in external galaxies. We provide, for the first time, a list of key deuterated species whose abundances are high enough to be possibly detectable by the Atacama Large Millimeter Array (ALMA) and Herschel, as a function of galactic nuclear activity and redshift.Comment: 19 pages, 6 figures, 5 tables, In press in Ap

Matching experiments across species using expression values and textual information

Motivation: With the vast increase in the number of gene expression datasets deposited in public databases, novel techniques are required to analyze and mine this wealth of data. Similar to the way BLAST enables cross-species comparison of sequence data, tools that enable cross-species expression comparison will allow us to better utilize these datasets: cross-species expression comparison enables us to address questions in evolution and development, and further allows the identification of disease-related genes and pathways that play similar roles in humans and model organisms. Unlike sequence, which is static, expression data changes over time and under different conditions. Thus, a prerequisite for performing cross-species analysis is the ability to match experiments across species

Effective index of refraction, optical rotation, and circular dichroism in isotropic chiral liquid crystals

This paper concerns optical properties of the isotropic phase above the isotropic-cholesteric transition and of the blue phase BP III. We introduce an effective index, which describes spatial dispersion effects such as optical rotation, circular dichroism, and the modification of the average index due to the fluctuations. We derive the wavelength dependance of these spatial dispersion effects quite generally without relying on an expansion in powers of the chirality and without assuming that the pitch of the cholesteric $P$ is much shorter than the wavelength of the light $\lambda$, an approximation which has been made in previous studies of this problem. The theoretical predictions are supported by comparing them with experimental spectra of the optical activity in the BP III phase.Comment: 15 pages and 7 figures. Submitted to PR

Parties, promiscuity and politicisation: business-political networks in Poland

Research on post-communist political economy has begun to focus on the interface between business and politics. It is widely agreed that informal networks rather than business associations dominate this interface, but there has been very little systematic research in this area. The literature tends to assume that a politicised economy entails business-political networks that are structured by parties. Theoretically, this article distinguishes politicisation from party politicisation and argues that the two are unlikely to be found together in a post-communist context. Empirically, elite survey data and qualitative interviews are used to explore networks of businesspeople and politicians in Poland. Substantial evidence is found against the popular idea that Polish politicians have business clienteles clearly separated from each other according to party loyalties. Instead, it is argued that these politicians and businesspeople are promiscuous. Since there seems to be little that is unusual about the Polish case, this conclusion has theoretical, methodological, substantive and policy implications for other post-communist countries

Multiple tumor suppressors regulate a HIF-dependent negative feedback loop via ISGF3 in human clear cell renal cancer.

Whereas VHL inactivation is a primary event in clear cell renal cell carcinoma (ccRCC), the precise mechanism(s) of how this interacts with the secondary mutations in tumor suppressor genes, including PBRM1, KDM5C/JARID1C, SETD2, and/or BAP1, remains unclear. Gene expression analyses reveal that VHL, PBRM1, or KDM5C share a common regulation of interferon response expression signature. Loss of HIF2α, PBRM1, or KDM5C in VHL-/-cells reduces the expression of interferon stimulated gene factor 3 (ISGF3), a transcription factor that regulates the interferon signature. Moreover, loss of SETD2 or BAP1 also reduces the ISGF3 level. Finally, ISGF3 is strongly tumor-suppressive in a xenograft model as its loss significantly enhances tumor growth. Conversely, reactivation of ISGF3 retards tumor growth by PBRM1-deficient ccRCC cells. Thus after VHL inactivation, HIF induces ISGF3, which is reversed by the loss of secondary tumor suppressors, suggesting that this is a key negative feedback loop in ccRCC. © 2018, Liao et al

Scattering of particles by neutron stars: Time-evolutions for axial perturbations

The excitation of the axial quasi-normal modes of a relativistic star by scattered particles is studied by evolving the time dependent perturbation equations. This work is the first step towards the understanding of more complicated perturbative processes, like the capture or the scattering of particles by rotating stars. In addition, it may serve as a test for the results of the full nonlinear evolution of binary systems.Comment: 7 pages, 5 figures, Phys. Rev. D in pres