Discovery of Protein Phosphorylation Motifs through Exploratory Data Analysis

BACKGROUND: The need for efficient algorithms to uncover biologically relevant phosphorylation motifs has become very important with rapid expansion of the proteomic sequence database along with a plethora of new information on phosphorylation sites. Here we present a novel unsupervised method, called Motif Finder (in short, F-Motif) for identification of phosphorylation motifs. F-Motif uses clustering of sequence information represented by numerical features that exploit the statistical information hidden in some foreground data. Furthermore, these identified motifs are then filtered to find "actual" motifs with statistically significant motif scores. RESULTS AND DISCUSSION: We have applied F-Motif to several new and existing data sets and compared its performance with two well known state-of-the-art methods. In almost all cases F-Motif could identify all statistically significant motifs extracted by the state-of-the-art methods. More importantly, in addition to this, F-Motif uncovers several novel motifs. We have demonstrated using clues from the literature that most of these new motifs discovered by F-Motif are indeed novel. We have also found some interesting phenomena. For example, for CK2 kinase, the conserved sites appear only on the right side of S. However, for CDK kinase, the adjacent site on the right of S is conserved with residue P. In addition, three different encoding methods, including a novel position contrast matrix (PCM) and the simplest binary coding, are used and the ability of F-motif to discover motifs remains quite robust with respect to encoding schemes. CONCLUSIONS: An iterative algorithm proposed here uses exploratory data analysis to discover motifs from phosphorylated data. The effectiveness of F-Motif has been demonstrated using several real data sets as well as using a synthetic data set. The method is quite general in nature and can be used to find other types of motifs also. We have also provided a server for F-Motif at http://f-motif.classcloud.org/, http://bio.classcloud.org/f-motif/ or http://ymu.classcloud.org/f-motif/

Probing onset of strong localization and electron-electron interactions with the presence of direct insulator-quantum Hall transition

We have performed low-temperature transport measurements on a disordered two-dimensional electron system (2DES). Features of the strong localization leading to the quantum Hall effect are observed after the 2DES undergoes a direct insulator-quantum Hall transition with increasing the perpendicular magnetic field. However, such a transition does not correspond to the onset of strong localization. The temperature dependences of the Hall resistivity and Hall conductivity reveal the importance of the electron-electron interaction effects to the observed transition in our study.Comment: 9 pages, 4 figure

Snapshot Lifecycle Management -SLM

Abstract This paper sets forth "Snapshot Lifecycle Management", an innovative way to manage snapshot data rather than using Information Lifecycle Management. There are two major problems occurs in snapshot management by ILM: "inappropriate migration" and "redundancy". SLM manages snapshot data elaborately according to its characteristic to eliminate the twin problems. In addition, this paper also proposes "Snapshot Support for iLVM (Internet Logical Volume Management)", integrating SLM into iLVM. Use Copy-on-Write technique to update data between local site and remote site and replace the "Remote Region Time Parity" scheme in remote data checking

A delta-doped quantum well system with additional modulation doping

A delta-doped quantum well with additional modulation doping may have potential applications. Utilizing such a hybrid system, it is possible to experimentally realize an extremely high two-dimensional electron gas (2DEG) density without suffering inter-electronic-subband scattering. In this article, the authors report on transport measurements on a delta-doped quantum well system with extra modulation doping. We have observed a 0-10 direct insulator-quantum Hall (I-QH) transition where the numbers 0 and 10 correspond to the insulator and Landau level filling factor ν = 10 QH state, respectively. In situ titled-magnetic field measurements reveal that the observed direct I-QH transition depends on the magnetic component perpendicular to the quantum well, and the electron system within this structure is 2D in nature. Furthermore, transport measurements on the 2DEG of this study show that carrier density, resistance and mobility are approximately temperature (T)-independent over a wide range of T. Such results could be an advantage for applications in T-insensitive devices

Paradox of low field enhancement factor for field emission nanodiodes in relation to quantum screening effects

We put forward the quantum screening effect in field emission [FE] nanodiodes, explaining relatively low field enhancement factors due to the increased potential barrier that impedes the electron Fowler-Nordheim tunneling, which is usually observed in nanoscale FE experiments. We illustratively show this effect from the energy band diagram and experimentally verify it by performing the nanomanipulation FE measurement for a single P-silicon nanotip emitter (Φ = 4.94eV), with a scanning tungsten-probe anode (work function, Φ = 4.5eV) that constitutes a 75-nm vacuum nanogap. A macroscopic FE measurement for the arrays of emitters with a 17-μm vacuum microgap was also performed for a fair comparison

Effect of patient decision aids on choice between sugammadex and neostigmine in surgeries under general anesthesia: a multicenter randomized controlled trial

Background Shared decision making using patient decision aids (PtDAs) was established over a decade ago, but few studies have evaluated its efficacy in Asian countries. We therefore evaluated the application of PtDAs in a decision conflict between two muscle relaxant reversal agents, neostigmine and sugammadex, and sequentially analyzed the regional differences and operating room turnover rates. Methods This multicenter, outcome-assessor-blind, randomized controlled trial included 3,132 surgical patients from two medical centers admitted between March 2020 and August 2020. The patients were randomly divided into the classical and PtDA groups for pre-anesthesia consultations. Their clinicodemographic characteristics were analyzed to identify variables influencing the choice of reversal agent. On the day of the pre-anesthesia consultation, the patients completed the four SURE scale (sure of myself, understand information, risk-benefit ratio, encouragement) screening items. The operating turnover rates were also evaluated using anesthesia records. Results Compared with the classical group, the PtDA group felt more confident about receiving sufficient medical information (P < 0.001), felt better informed about the advantages and disadvantages of the medications (P < 0.001), exhibited a superior understanding of the benefits and risks of their options (P < 0.001), and felt surer about their choice (P < 0.001). Moreover, the PtDA group had a significantly greater tendency to choose sugammadex over neostigmine (P < 0.001). Conclusions PtDA interventions in pre-anesthesia consultations provided surgical patients with clear knowledge and better support. PtDAs should be made available in other medical fields to enhance shared clinical decision-making