ConSole: using modularity of contact maps to locate solenoid domains in protein structures.

BackgroundPeriodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms have been developed for the detection and analysis of structures of periodic proteins.ResultsConSole recognizes modularity in protein contact maps, allowing for precise identification of repeats in solenoid protein structures, an important subgroup of periodic proteins. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool. As a next step of ConSole analysis, we show how detection of solenoid repeats in structures can be used to improve sequence recognition of these motifs and to detect subtle irregularities of repeat lengths in three solenoid protein families.ConclusionsThe ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure. ConSole is available as a web-based, interactive server and is available for download at http://console.sanfordburnham.org

Dusty space plasma diagnosis using temporal behavior of polar mesospheric summer echoes during active modification

The objective of this paper is to study the effect of different plasma and dust parameters on Polar Mesospheric Summer Echoes (PMSE) temporal behavior after turn-on and turn-off of radio wave heating and to use these responses to diagnose the properties of the dust layer. The threshold radar frequency and dust parameters for the enhancement or suppression of radar echoes after radio wave heating turn-on are investigated for measured mesospheric plasma parameters. The effect of parameters such as the electron temperature enhancement during heating, dust density, dust charge polarity, ion-neutral collision frequency, electron density and dust radius on the temporal evolution of electron irregularities associated with PMSE are investigated. The possible diagnostic information for various charged dust and background plasma quantities using the temporal behavior of backscattered radar power in active experiments is discussed. The computational results are used to make predictions for PMSE active modification experiments at 7.9, 56, 139, 224 and 930MHz corresponding to existing radar facilities. Data from a 2009 VHF (224 MHz) experiment at EISCAT is compared with the computational model to obtain dust parameters in the PMSE

Exploring Application Performance on Emerging Hybrid-Memory Supercomputers

Next-generation supercomputers will feature more hierarchical and heterogeneous memory systems with different memory technologies working side-by-side. A critical question is whether at large scale existing HPC applications and emerging data-analytics workloads will have performance improvement or degradation on these systems. We propose a systematic and fair methodology to identify the trend of application performance on emerging hybrid-memory systems. We model the memory system of next-generation supercomputers as a combination of "fast" and "slow" memories. We then analyze performance and dynamic execution characteristics of a variety of workloads, from traditional scientific applications to emerging data analytics to compare traditional and hybrid-memory systems. Our results show that data analytics applications can clearly benefit from the new system design, especially at large scale. Moreover, hybrid-memory systems do not penalize traditional scientific applications, which may also show performance improvement.Comment: 18th International Conference on High Performance Computing and Communications, IEEE, 201

Salivary inflammatory biomarkers during initial orthodontic tooth movement

BACKGROUND: Orthodontic tooth movement is a complex process involving a number of inflammatory and anabolic/catabolic pathways. Further, successful treatment depends on proper timing of orthodontic measures with regard to patient’s growth spurt. Saliva analysis has emerged as a non-invasive collection method to track biomarkers relevant to both tooth movement biology and growth prediction. The aim of the present study was to analyze changes in tooth movement and assess relationships with salivary levels of alkaline phosphatase, IGF-1, TGF-β1, testosterone, BMP-2, BMP-4, and BMP-9t. METHODS: Twenty seven healthy patients (17 females, 10 males) with a mean age of 13.3 years, undergoing orthodontic treatment with a non-extraction treatment plan were selected for the study. Height, weight, and other demographic features were recorded; maxillary and mandibular alginate impressions were obtained, and 10 mL saliva samples were taken at the initial visit (T0), after 4 weeks (T1), 3 months (T2), and then at 3-month intervals (T3, T4, T5). Casts were made from alginate impressions. Little’s Irregularity Index, intercanine widths, intermolar widths, arch lengths, and tooth widths were measured. Saliva samples were analyzed for the concentrations of alkaline phosphatase, IGF-1, TGF-β1, testosterone, BMP-2, BMP-4, and BMP-9 by multiplex immunoassay and/or ELISA. Data were analyzed using correlation coefficients and ANOVA. RESULTS: Over the six timepoints, there were statistically significant changes in the level of testosterone (p < 0.05) and Little’s Irregularity Index (p < 0.01), with the most significant changes occurring at the beginning of treatment (T0 to T1). Statistically significant correlations (p < 0.05) were observed between testosterone and height/weight, intercanine width and intermolar width, BMP-4 and intercanine/intermolar width, alkaline phosphatase and testosterone, alkaline phosphatase and TGF-β1, and among the BMPs. CONCLUSION: The changes in Little’s Irregularity Index reflects successful progress of the orthodontic treatment. The correlations observed among the various salivary concentrations suggest a number of further directions for study