Assessing the effects of symmetry on motif disovery and modeling

BACKGROUND: Identifying the DNA binding sites for transcription factors is a key task in modeling the gene regulatory network of a cell. Predicting DNA binding sites computationally suffers from high false positives and false negatives due to various contributing factors, including the inaccurate models for transcription factor specificity. One source of inaccuracy in the specificity models is the assumption of asymmetry for symmetric models. METHODOLOGY/PRINCIPAL FINDINGS: Using simulation studies, so that the correct binding site model is known and various parameters of the process can be systematically controlled, we test different motif finding algorithms on both symmetric and asymmetric binding site data. We show that if the true binding site is asymmetric the results are unambiguous and the asymmetric model is clearly superior to the symmetric model. But if the true binding specificity is symmetric commonly used methods can infer, incorrectly, that the motif is asymmetric. The resulting inaccurate motifs lead to lower sensitivity and specificity than would the correct, symmetric models. We also show how the correct model can be obtained by the use of appropriate measures of statistical significance. CONCLUSIONS/SIGNIFICANCE: This study demonstrates that the most commonly used motif-finding approaches usually model symmetric motifs incorrectly, which leads to higher than necessary false prediction errors. It also demonstrates how alternative motif-finding methods can correct the problem, providing more accurate motif models and reducing the errors. Furthermore, it provides criteria for determining whether a symmetric or asymmetric model is the most appropriate for any experimental dataset

Gene variants with suicidal risk in a sample of subjects with chronic migraine and affective temperamental dysregulation

BACKGROUND: Risk factors for suicide are at least partially heritable and functional polymorphisms of targeted genes have been suggested to be implicated in the pathogenesis of this phenomenon. However, other studies examining the association between specific gene variants and suicide revealed inconsistent findings. We aims to evaluate the possible association between MAO-A3, CYP1A2*1F and GNB3 gene variants, hopelessness and suicidal risk in a sample of subjects with chronic migraine and affective temperamental dysregulation. METHODS: 56 women were genotyped for MAO-A3, CYP1A2*1F and GNB3 gene variants. Participants were also assessed using Beck Hopelessness Scale (BHS), the Temperament Evaluation of the Memphis, Pisa, Paris and San Diego-Autoquestionnaire (TEMPS-A), and the Suicidal History Self-Rating Screening Scale (SHSS). RESULTS: Patients with higher total scores on affective dysregulated temperaments are more likely to have higher BHS (11.27 +/- 5.54 vs. 5.73 +/- 3.81; t19.20 = -3.57; p = 9 indicating high levels of hopelessness. No association was found between MAO-A3, CYP1A2*1F and GNB3 gene variants and suicidal risk as assessed by BHS and SHSS. CONCLUSIONS: This study did not sustain the association between MAO-A3, CYP1A2*1F and GNB3 gene variants and increased suicidal risk in patients with chronic migraine and affective temperamental dysregulation. Further studies investigating the gene-environment interaction or focusing on other genetic risk factors involved in suicidal behaviour are needed

A fault-tolerant multiprocessor architecture for aircraft, volume 1

A fault-tolerant multiprocessor architecture is reported. This architecture, together with a comprehensive information system architecture, has important potential for future aircraft applications. A preliminary definition and assessment of a suitable multiprocessor architecture for such applications is developed

A STOCHASTIC MODELING FOR THE UNSTABLE FINANCIAL MARKETS

Considering the present economic context, the measurement of performances has become a permanent preoccupation for organizations, since the whole process is based on it, offering the necessary feedback to identify both the positive actions which have led to favorable results for the organization, and the negative ones, in order to correct them in the future. To do this, we have to measure what is most importantly to measure. Starting from these considerations, the present paper approaches from a theoretical and practical point of view the economic rate of return as the indicator which synthesizes best an organization’s financial-economic performance. We have calculated and analyzed the economic rate of return for a group of Ten Romanian Firms in the food industry, through different calculation relations, pointing out the advantages/disadvantages of each calculation method.belated integral, forward-backward stochastic equations, pathwise uniqueness, financial modeling.

The Analysis of the Companies Profitability Level Either Before or After the Merger (Case Study Upon 7 Open Companies in 2012)

This study aims to analyze the profitability of companies before and after merger. The study of the population is the registered companies in Indonesia Stock Exchange in 2012. Having applied technical purposive sampling, finally this study has selected 7 companies as the research samples. The level of profitability of companies assessed using the Return On Asset (ROA), Return On Investment (ROI), Return On Equit (ROE), Earning Per Share (EPS). Observation period of this study is one year before and one year after merger. Statistic test used is normality one sample test. The result determined that there had not been any increasing of the ROA of the companies happened after the merger. However, the ROE, ROI and EPS had been increased

Laju Konversi Lahan Sawah Menjadi Perkebunan Sawit dan Faktor-faktor yang Mempengaruhinya Serta Dampaknya terhadap Produksi Padi di Kabupaten Kampar, Riau

Conversion Rate of Rice Field to Palm Oil Plantation, the Affected Factors and Its Impact to Rice Production in Kampar District, Riau. Kampar district is a center of rice production area in Riau Province and since ten years ago had been being conversed to palm oil plantation. This study aimed: (1) to identify the rate of land conversion, (2) to analyze factors that influence the conversion of paddy fields at the farm level, (3) to identify impact of paddy field conversion on rice production. The study was conducted in Kampar district from April to December 2013 using survey design and involving 60 farmers as respondent that consisted of 30 paddy farmers in Kampar Sub District and 30 farmers in Tambang Sub District who undertook paddy field conversion to palm oil plantations. Analyzing the data used multiple linear regressions. The results of landsat analysis from 2002 to 2010 showed a decreased occurred paddy field area by 1955.79 ha (21.77%) (from 8,984 ha to 7028.21 acres). The factors which significantly influenced paddy field conversion were: (1) reduction in paddy farming income, (2) an increase in palm oil farming income, (3) irrigation constraints, and (4) the lack of knowledge regarding the regulation of paddy field. Paddy field conversion during the period of 2002-2010 was estimated on causing the loss of 9,192 t of grain, which was, equivalent to 5,767 t of rice per years. Key words: Land conversion, palm oil, paddy field, Kampar District Kabupaten Kampar merupakan sentra produksi beras di Provinsi Riau yang dalam kurun waktu sepuluh tahun terakhir terjadi konversi lahan sawah. Penelitian ini bertujuan: (1) mengidentifikasi laju konversi lahan sawah, (2) menganalisis faktor-faktor yang mempengaruhi konversi lahan sawah di tingkat petani, (3) mengidentifikasi dampak konversi lahan sawah terhadap ketahanan pangan. Penelitian dilaksanakan di Kabupaten Kampar Provinsi Riau dari bulan April hingga Desember 2013 menggunakan rancangan survey yang melibatkan 60 petani responden, terdiri dari 30 petani padi di Kecamatan Kampar dan 30 petani yang melakukan konversi lahan sawah ke perkebunan kelapa sawit di Kecamatan Tambang. Analisis data mengggunakan regresi linear berganda. Hasil interpretasi data citra landsat 2002-2010 menunjukkan terjadi penyusutan lahan sawah seluas 1.955,79 ha (21,77%) dari 8.984 ha menjadi 7.028,21 ha. Faktor-faktor yang diduga secara signifikan mempengaruhi konversi lahan sawah di tingkat petani adalah: (1) penurunan pendapatan USAhatani padi, (2) peningkatan pendapatan USAhatani kelapa sawit, (3) kendala irigasi dan (4) kurangnya pengetahuan tentang kebijakan larangan konversi lahan sawah. Konversi lahan sawah selama periode 2002 - 2010 diperkirakan telah menyebabkan hilangnya 9.192 t gabah kering giling atau setara dengan 5.767 t beras/tahun

Advanced information processing system: The Army fault tolerant architecture conceptual study. Volume 2: Army fault tolerant architecture design and analysis

Described here is the Army Fault Tolerant Architecture (AFTA) hardware architecture and components and the operating system. The architectural and operational theory of the AFTA Fault Tolerant Data Bus is discussed. The test and maintenance strategy developed for use in fielded AFTA installations is presented. An approach to be used in reducing the probability of AFTA failure due to common mode faults is described. Analytical models for AFTA performance, reliability, availability, life cycle cost, weight, power, and volume are developed. An approach is presented for using VHSIC Hardware Description Language (VHDL) to describe and design AFTA's developmental hardware. A plan is described for verifying and validating key AFTA concepts during the Dem/Val phase. Analytical models and partial mission requirements are used to generate AFTA configurations for the TF/TA/NOE and Ground Vehicle missions

Phase transition and scaling behavior of topological charged black holes in Horava-Lifshitz gravity

Gravity can be thought as an emergent phenomenon and it has a nice "thermodynamic" structure. In this context, it is then possible to study the thermodynamics without knowing the details of the underlying microscopic degrees of freedom. Here, based on the ordinary thermodynamics, we investigate the phase transition of the static, spherically symmetric charged black hole solution with arbitrary scalar curvature $2k$ in Ho\v{r}ava-Lifshitz gravity at the Lifshitz point $z=3$. The analysis is done using the canonical ensemble frame work; i.e. the charge is kept fixed. We find (a) for both $k=0$ and $k=1$, there is no phase transition, (b) while $k=-1$ case exhibits the second order phase transition within the {\it physical region} of the black hole. The critical point of second order phase transition is obtained by the divergence of the heat capacity at constant charge. Near the critical point, we find the various critical exponents. It is also observed that they satisfy the usual thermodynamic scaling laws.Comment: Minor corrections, refs. added, to appear in Class. Quant. Grav. arXiv admin note: text overlap with arXiv:1111.0973 by other author

Advanced information processing system: The Army fault tolerant architecture conceptual study. Volume 1: Army fault tolerant architecture overview

Digital computing systems needed for Army programs such as the Computer-Aided Low Altitude Helicopter Flight Program and the Armored Systems Modernization (ASM) vehicles may be characterized by high computational throughput and input/output bandwidth, hard real-time response, high reliability and availability, and maintainability, testability, and producibility requirements. In addition, such a system should be affordable to produce, procure, maintain, and upgrade. To address these needs, the Army Fault Tolerant Architecture (AFTA) is being designed and constructed under a three-year program comprised of a conceptual study, detailed design and fabrication, and demonstration and validation phases. Described here are the results of the conceptual study phase of the AFTA development. Given here is an introduction to the AFTA program, its objectives, and key elements of its technical approach. A format is designed for representing mission requirements in a manner suitable for first order AFTA sizing and analysis, followed by a discussion of the current state of mission requirements acquisition for the targeted Army missions. An overview is given of AFTA's architectural theory of operation