High Redundant Data Research Articles

Multiview Subspace Clustering via Low-Rank Symmetric Affinity Graph.

Multiview subspace clustering (MVSC) has been used to explore the internal structure of multiview datasets by revealing unique information from different views. Most existing methods ignore the consistent information and angular information of different views. In this article, we propose a novel MVSC via low-rank symmetric affinity graph (LSGMC) to tackle these problems. Specifically, considering the consistent information, we pursue a consistent low-rank structure across views by decomposing the coefficient matrix into three factors. Then, the symmetry constraint is utilized to guarantee weight consistency for each pair of data samples. In addition, considering the angular information, we utilize the fusion mechanism to capture the inherent structure of data. Furthermore, to alleviate the effect brought by the noise and the high redundant data, the Schatten p-norm is employed to obtain a low-rank coefficient matrix. Finally, an adaptive information reduction strategy is designed to generate a high-quality similarity matrix for spectral clustering. Experimental results on 11 datasets demonstrate the superiority of LSGMC in clustering performance compared with ten state-of-the-art multiview clustering methods.

Scaling and merging macromolecular diffuse scattering with mdx2.

Diffuse scattering is a promising method to gain additional insight into protein dynamics from macromolecular crystallography experiments. Bragg intensities yield the average electron density, while the diffuse scattering can be processed to obtain a three-dimensional reciprocal-space map that is further analyzed todetermine correlated motion. To make diffuse scattering techniques more accessible, software for data processing called mdx2 has been created that is both convenient to use and simple to extend and modify. mdx2 is written in Python, and it interfaces with DIALS to implement self-contained data-reduction workflows. Data are stored in NeXus format for software interchange and convenient visualization. mdx2 can be run on the command line or imported as a package, for instance to encapsulate a complete workflow in a Jupyter notebook for reproducible computing and education. Here, mdx2 version 1.0 is described, a new release incorporating state-of-the-art techniques for data reduction. The implementation of a complete multi-crystal scaling and merging workflow is described, and the methods are tested using a high-redundancy data set from cubic insulin. It is shown that redundancy can be leveraged during scaling to correct systematic errors and obtain accurate and reproducible measurements of weak diffuse signals.

Crowdsourcing Analysis of Twitter Data on Climate Change: Paid Workers vs. Volunteers

Web based crowdsourcing has become an important method of environmental data processing. Two alternatives are widely used today by researchers in various fields: paid data processing mediated by for-profit businesses such as Amazon’s Mechanical Turk, and volunteer data processing conducted by amateur citizen-scientists. While the first option delivers results much faster, it is not quite clear how it compares with volunteer processing in terms of quality. This study compares volunteer and paid processing of social media data originating from climate change discussions on Twitter. The same sample of Twitter messages discussing climate change was offered for processing to the volunteer workers through the Climate Tweet project, and to the paid workers through the Amazon MTurk platform. We found that paid crowdsourcing required the employment of a high redundancy data processing design to obtain quality that was comparable with volunteered processing. Among the methods applied to improve data processing accuracy, limiting the geographical locations of the paid workers appeared the most productive. Conversely, we did not find significant geographical differences in the accuracy of data processed by volunteer workers. We suggest that the main driver of the found pattern is the differences in familiarity of the paid workers with the research topic.

Importance of multiple diffraction avoidance for charge density observation

It might not be well recognized, most reflections are contaminated by multiple diffractions (MD). Therefore high redundancy data could not coincide with high accuracy data when MDs are not avoided. We collected both data set of MD-avoided and no MD-avoided ones and investigated its effectiveness in electron density measurement. For data collection, four-circle diffractometer at KEK-PF BL14A (Tsukuba, Japan) was used. In MD-avoided measurement, each reflection is collected at angle setting of least of MD contamination which calculated by psi-scan simulation software MDC [1]. In no MD-avoided measurement, usual bisect setting were used. In no MD-avoided measurement, intensities of forbidden reflections of YMn2O5 are more than 10 times largely observed than for MD-avoided one, and resulting residual density map is also highly contaminated reflecting the tendency of Fo>>Fc which is typical for reflections of weak intensity. Figure 1 shows this situation. Figure 2 is the deformation density of YTiO3 for MD-avoided data. Where model density of without Ti-3d1 valence electrons is subtracted from experimentally observed electron density. In the figure, quenching of angular momentum of Ti-3d1 electron is clearly observed. Although Rint could not be an ideal indicator of data accuracy since it cannot perceive Fo>>Fc, Rint(F) of MD-avoided measurement for YTiO3 is significantly reduced to ~0.5%. For no MD-avoided one, Rint(F) is ~1.2%. Since accuracy of MD-avoidance technique is confirmed, the next step is to exploit informations of only a few numbers of valence electrons among F(000) electrons. To accomplish this, wave function based refinement such as XAO [2] should be applied and studied.

The role of wavelength and source in the search for sulfur-atom positions evaluated in two case studies: lysozyme at room temperature and cryo apocrustacyanin A1

Synchrotron radiation beamlines offer automated data collection with faster and larger detectors, a choice of wavelength(s), intense beams and fine collimation. An increasing output of protein crystal structures sustains an interest in streamlining data collection protocols. Thus, more and more investigators are looking into the use of the anomalous signal from sulfur to obtain initial phase information for medium-size proteins. This type of experiment ideally requires the use of synchrotron radiation, softer X-rays and cryocooling of the sample. Here the results are reported of an investigation into locating the weak,i.e.sulfur, anomalous scatterers in lysozyme using rotating anode or synchrotron radiation data recorded at room temperature. It was indeed possible to locate the sulfur atoms from a lysozyme crystal at room temperature. Accurate selection of images during scaling was needed where radiation damage effects were detected. Most interestingly, comparisons are provided of high-redundancy data sets recorded with synchrotron radiation at λ = 2.0 and 1.488 Å, and with CuKα and MoKα radiation. Apocrustacyanin A1 was also investigated; from the results of a very high redundancy data collection using softer synchrotron X-rays and a cryo-cooled crystal, it was possible to find the sulfur atoms.

Ab initio crystallographic structure determination of insulin from protein to electron density without crystal handling.

Insulin crystals suitable for cryogenic data collection and structure determination by single-wavelength anomalous scattering (SAS) were obtained by a self-optimization screening process in a single capillary tube without manipulation of the crystals at any time. Using the counter-diffusion crystallization technique, screening for optimal conditions for crystal growth, incorporation of a strong anomalous scattering halide and cryogenic solution took place simultaneously in a single capillary tube. The crystals in the capillaries can be placed directly in the cryostream for data collection using a conventional home-laboratory X-ray source. High-redundancy data were used to obtain a Patterson solution from the anomalous signal of iodine. As a result, the anomalous scattering-atom position was determined and the phase calculated, giving rise to an initial electron-density map at 2.4 A resolution. This entire procedure from crystal growth to the determination of an initial structure was performed within four weeks.

Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.

The structure of a tetragonal crystal form of thiostrepton has been solved using the anomalous dispersive effects of five S atoms from high-redundancy data collected to 1.33 A resolution at the Cu Kalpha wavelength. Data measured to 1.02 A resolution with a synchrotron source were used for refinement. Details of the molecular structure, intramolecular and intermolecular interactions are given.