Sequence‐based prediction of protein–peptide binding sites using support vector machine

Protein–peptide interactions are essential for all cellular processes including DNA repair, replication, gene‐expression, and metabolism. As most protein – peptide interactions are uncharacterized, it is cost effective to investigate them computationally as the first step. All existing approaches for predicting protein – peptide binding sites, however, are based on protein structures despite the fact that the structures for most proteins are not yet solved. This article proposes the first machine‐learning method called SPRINT to make Sequence‐based prediction of Protein – peptide Residue‐level Interactions. SPRINT yields a robust and consistent performance for 10‐fold cross validations and independent test. The most important feature is evolution‐generated sequence profiles. For the test set (1056 binding and non‐binding residues), it yields a Matthews’ Correlation Coefficient of 0.326 with a sensitivity of 64% and a specificity of 68%. This sequence‐based technique shows comparable or more accurate than structure‐based methods for peptide‐binding site prediction. SPRINT is available as an online server at: http://sparks-lab.org/ . © 2016 Wiley Periodicals, Inc.     

A scheme of access service recommendation for the Social Internet of Things

The rapid increase in the complexity and the extent of personalization of services in the Internet of Things (IoT) has led to a greater demand for frequent collaboration among heterogeneous devices. Moreover, with the inseparable relations between human and devices, the paradigm of Social IoT (SIoT) is gaining popularity in recent years. How to effectively facilitate the access to quality services and credible devices in large‐scale networks via defining, establishing, and managing social architectures among things has become a critical issue. In this paper, a scheme of access service recommendation for the SIoT is presented with the understanding of inherent constraints and factors that influence the security and stability of IoT networks. In which, timeliness properties are considered in each transaction for dynamic performance enhancements. With the benefits of promoting service discovery and composition, social relationships among things are introduced in the proposed scheme. An energy‐aware mechanism is also utilized as a restrictive factor in trustworthiness evaluation. Finally, the recommendation is based not only on the past performance but also on the social relationship and the energy status of nodes. Simulation experiments demonstrate the effectiveness and benefits of our scheme from three aspects including rating accuracy, dynamic behavior, and network stability. Copyright © 2015 John Wiley & Sons, Ltd.     

Design,Synthesis, and Versatile Processing of Indolo[3,2‐b]indole‐Based π‐Conjugated Molecules for High‐Performance Organic Field‐Effect Transistors

A series of indolo[3,2‐b]indole (IDID) derivatives comprising the core unit of N,N‐dihexyl‐IDID with different aromatic and aliphatic substituents at 2‐ and 7‐position are designed and synthesized to construct high‐performance organic semiconductors by different processing routes. Structure‐property relationship of the derivatives is comprehensively studied in terms of their photophysical, electrochemical, structural, and electrical characteristics. IDID derivatives are either evaporated in vacuum or dissolved in common organic solvents to ensure applicalbility in different processing routes toward outstanding p‐type semiconductor films. Among others, the excellently soluble compound 4H4TIDID (with 2‐ and 7‐substituents of 5‐hexyl‐2,2′‐bithiophene moiety, solubility >20 wt% in chloroform), shows the highest field‐effect hole mobility of 0.97 cm² V^?1 s^?1 in a device constructed by vacuum‐deposition and 0.18 cm² V^?1 s^?1 in device cosntructed by spin‐coating, respectively. The 2D grazing incidence X‐ray diffraction of 4H4TIDID films in both devices identically show the 2D molecular orientation favorable for the high transistor mobility.     

Determination of haloacetic acids in water using layered double hydroxides as a sorbent in dispersive solid‐phase extraction followed by liquid chromatography with tandem mass spectrometry

In the present study, highly efficient and simple dispersive solid‐phase extraction procedure for the determination of haloacetic acids in water samples has been established. Three different types of layered double hydroxides were synthesized and used as a sorbent in dispersive solid‐phase extraction. Due to the interesting behavior of layered double hydroxides in an acidic medium (pH?4), the analyte elution step was not needed; the layered double hydroxides are simply dissolved in acid immediately after extraction to release the analytes which are then directly introduced into a liquid chromatography with tandem mass spectrometry system for analysis. Several dispersive solid‐phase extraction parameters were optimized to increase the extraction efficiency of haloacetic acids such as temperature, extraction time and pH. Under optimum conditions, good linearity was achieved over the concentration range of 0.05–100 μg/L with detection limits in the range of 0.006–0.05 μg/L. The relative standard deviations were 0.33–3.64% (n = 6). The proposed method was applied to different water samples collected from a drinking water plant to determine the concentrations of haloacetic acids.     

Subsurface Space‐Charge Dopant Segregation to Compensate Surface Excess Charge in a Perovskite Oxide

Since the first prediction by Frenkel, many follow‐up studies have been carried out to show the presence of subsurface space‐charge layers having the opposite sign to that of the excess charge at the surface, producing overall neutrality in ionic crystals. However, no precise experimental evidence demonstrating how the aliovalent solutes segregate in the space‐charge region beneath the surface has been provided over the past several decades. By utilizing atomic‐scale imaging and chemical probing in a perovskite oxide, the origin of the surface excess charge at the topmost surface and the position of segregated dopants in the space‐charge region is precisely determined. The impact of the space‐charge contribution to the dopant distribution near the surface in oxide crystals is explored.     

Ultra fast symmetry and SIMD-based projection-backprojection (SSP) algorithm for 3-D PET image reconstruction

Remarkable progress in positron emission tomography (PET) development has occurred in recent years, in hardware, software, and computer implementation of image reconstruction. Recent development in PET scanners such as the high-resolution research tomograph (HRRT) developed by CTI (now Siemens) represents such a case and is capable of greatly enhanced resolution as well as sensitivity. In these PET scanners, the amount of coincidence line data collected contains more than 4.5 x 10(9) coincidence lines of response generated by as many nuclear detectors as 120 000. This formidable amount of data and the reconstruction of this data set pose a real problem in HRRT and have also been of the major bottle neck in further developments of high resolution PET scanners as well as their applications. In these classes of PET scanners, therefore, obtaining one set of reconstructed images often requires many hours of image reconstruction. For example, in HRRT with full data collection in a normal brain scan (using SPAN 3), the image reconstruction time is close to 80 min, making it practically impossible to attempt any list-mode-based dynamic imaging since the image reconstruction time would take many days (as much as 43 h or more for 32-frame dynamic image reconstruction). To remedy this data-handling problem in image reconstruction, we developed a new algorithm based on the symmetry properties of the projection and backprojection processes, especially in the 3-D OSEM algorithm where multiples of projection and back-projection are required. In addition, the single-instruction multiple-data (SIMD) technique also allowed us to successfully incorporate the symmetry properties mentioned above, thereby effectively reducing the total image reconstruction time to a few minutes. We refer to this technique as the symmetry and SIMD-based projection-backprojection (SSP) technique or algorithm and the details of the technique will be discussed and an example of the application of the technique to the HRRT's OSEM algorithm will be presented as a demonstration.     

Soluble and easily crystallized anthracene derivatives: precursors of solution-processable semiconducting molecules

New soluble anthracene derivatives containing thiophene and phenylenevinylene derivatives were synthesized via well-known synthetic routes. TIPS derivatives were added at the 9,10-positions of anthracene for the solubility and crystallinity. Both of the molecules were found to be promising for high charge mobility and stable organic semiconductors. The soluble anthracene core (TIPSAnt) is a potential precursor for the synthesis of novel semiconducting materials.