scholarly journals Exploring the Cooccurrence Patterns of Multiple Sets of Genomic Intervals

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Hao Wu ◽  
Zhaohui S. Qin
Keyword(s):  
Spatial Relationship ◽  
Pairwise Comparison ◽  
Software Tool ◽  
Real Data ◽  
R Package ◽  
Genomic Research ◽  
Model Parameters ◽  
Sufficient Statistics ◽  
Relationship Of ◽  
The Relationship

Background. Exploring the spatial relationship of different genomic features has been of great interest since the early days of genomic research. The relationship sometimes provides useful information for understanding certain biological processes. Recent advances in high-throughput technologies such as ChIP-seq produce large amount of data in the form of genomic intervals. Most of the existing methods for assessing spatial relationships among the intervals are designed for pairwise comparison and cannot be easily scaled up.Results. We present a statistical method and software tool to characterize the cooccurrence patterns of multiple sets of genomic intervals. The occurrences of genomic intervals are described by a simple finite mixture model, where each component represents a distinct cooccurrence pattern. The model parameters are estimated via an EM algorithm and can be viewed as sufficient statistics of the cooccurrence patterns. Simulation and real data results show that the model can accurately capture the patterns and provide biologically meaningful results. The method is implemented in a freely available R packagegiClust.Conclusions. The method and the software provide a convenient way for biologists to explore the cooccurrence patterns among a relatively large number of sets of genomic intervals.

Organization of electricity and capacity supplies: experience and practice of reforms in a particular region

2021 ◽  
pp. 92-103
Author(s):  
Alexandra Vasilyevna Yashchenko
Keyword(s):  
Power Supply ◽  
Electric Power Industry ◽  
Real Data ◽  
General Concept ◽  
Network Problems ◽  
Market Transformation ◽  
Separate Region ◽  
Supply Industry ◽  
Relationship Of ◽  
The Relationship

The article examines the process of formation of the power supply industry in the 2000s using the example of a separate region. The market transformation of RAO UES was carried out under the slogan of increasing the efficiency and reliability of interaction between the economy and the energy sector. However, in practice, the creation of the energy market faced many problems, the specifics of the “special product” electricity, network problems, institutional and other problems. On the example of the Altai Territory, the genesis of the territorial power supply system is shown within the framework of the general concept of market reform of the electric power industry. On the basis of real data of the supplier of last resort and the real consumer of electricity and capacity, a retrospective of the relationship of these entities in practice is shown. The dynamics of the average price for electricity is calculated and its quite significant growth is shown for the entire post-reform period of observations.

Study on Theoretical Elasticity and Plasticity Model of the Stock Price Based on Material Distortion Theory

2011 ◽  
Vol 138-139 ◽  
pp. 1274-1279
Author(s):  
Su Zhang ◽  
Zuo Quan Zhang ◽  
Xuan Wu ◽  
Xiao Yue Li ◽  
Rong Zhu
Keyword(s):  
Stock Price ◽  
Trading Volume ◽  
Share Price ◽  
Model Parameters ◽  
Plasticity Model ◽  
Scientific Result ◽  
Volume Relationship ◽  
New Ideas ◽  
Relationship Of ◽  
The Relationship

According to the price volume relationship of the stock, with the help of the elasticity and plasticity theory in the physics, some new ideas like stock equilibrium price, share price elasticity, and share price plasticity are put forward. Then elasticity and plasticity model of the stock price are built on account of the relationship between share price and trading volume, and model parameters are tested by a kind of software calling Eviews from econometrics. In the end, we get relatively scientific result.

scholarly journals PEMODELAN ANGKA KEMATIAN IBU DI INDONESIA DENGAN PENDEKATAN GEOGRAPHICALLY WEIGHTED POISSON REGRESSION

2017 ◽  
Vol 18 (2) ◽  
pp. 76-94
Author(s):  
Rivan Destyanugraha ◽  
Robert Kurniawan
Keyword(s):  
Sustainable Development ◽  
Poisson Regression ◽  
Sustainable Development Goals ◽  
Model Parameters ◽  
Health Development ◽  
Maternal Deaths ◽  
Development Goals ◽  
Estimation Of Model Parameters ◽  
Relationship Of ◽  
The Relationship

Maternal Mortality Rate (MMR) is one of the important indicators of a country's health development and is one of the targets of achieving Sustainable Development Goals (SDGs). This study aims to develop a model on the relationship of MMR with provincial health development variables using the Geographically Weighted Poisson Regression (GWPR) method; as well as mapping the model to the provincial map. Estimation of model parameters using PODES data for 2011 and the projected health and projection profile of 2010-2013. The obtained model consists of four variables that influence the number of maternal deaths: (1)  the ratio of health facilities, (2) the ratio of midwives, (3) the percentage of deliveries assisted by health personnel, and (4) the percentage of pregnant women received Fe tablets. The mapping of the four variables into the provincial map yields three groups of regions with different levels of significance of variables. The AIC value and the GWPR model deviance are lower than Poisson regression, indicated that the AKI model with GWPR is better than Poisson regression.   Angka Kematian Ibu (AKI) merupakan salah satu indikator penting pembangunan kesehatan suatu negara danmenjadi salah satu target pencapaian Sustainable Development Goals (SDGs). Penelitian ini bertujuan menyusun model hubungan AKI dengan variabel-variabel pembangunan kesehatan provinsi menggunakan metode Geographically Weighted Poisson Regression (GWPR) dan memetakan model tersebut kedalam peta provinsi. Estimasi parameter model menggunakan data PODES tahun 2011 dan profil kesehatan dan proyeksi penduduk tahun 2010-2013. Model yang diperoleh terdiri dari empat variabel yang mempengaruhi jumlah kematian ibu yaitu rasio sarana kesehatan, rasio bidan, persentase persalinan ditolong tenaga kesehatan, dan persentase ibu hamil mendapat tablet Fe. Pemetaan empat variabel tersebut ke dalam peta provinsi menghasilkan tiga kelompok wilayah dengan tingkat signifikansi variabel yang berbeda-beda. Nilai AIC dan deviance model GWPR lebih rendah dari regresi Poisson menunjukkan bahwa model AKI dengan GWPR lebih baikdari regresi Poisson.

Research on Method of Confirming Typical SWMM Water Quality Parameters

2011 ◽  
Vol 243-249 ◽  
pp. 5308-5313 ◽  
Author(s):  
Hai Yan Li ◽  
Li Tao Yue
Keyword(s):  
Water Quality ◽  
Rate Constant ◽  
Quality Parameters ◽  
Water Quality Parameters ◽  
Model Parameters ◽  
Rainfall Runoff ◽  
Relationship Of ◽  
The Relationship ◽  
Swmm Model ◽  
Buildup Rate

Taking a roof in Shanghai for example, through the comparison of the relationship of rainfall and SS load in a single rainfall runoff obtained by experiment and SWMM simulation, typical water SWMM model parameters (maximum buildup possible C1, buildup rate constant C2, washoff coefficient S1 and washoff exponent S2) could be obtained. With this method, other cities’ water quality parameters for SWMM simulation could be confirmed, so as to provide basis for simulating water quality by SWMM.

scholarly journals Genetic Characterization of Escherichia coli Populations from Host Sources of Fecal Pollution by Using DNA Fingerprinting

2003 ◽  
Vol 69 (5) ◽  
pp. 2587-2594 ◽  
Author(s):  
Sandra L. McLellan ◽  
Annette D. Daniels ◽  
Alissa K. Salmore
Keyword(s):  
Escherichia Coli ◽  
Pairwise Comparison ◽  
Fecal Pollution ◽  
Host Animal ◽  
Host Group ◽  
E Coli ◽  
Single Host ◽  
Relationship Of ◽  
The Relationship

ABSTRACT Escherichia coli isolates were obtained from common host sources of fecal pollution and characterized by using repetitive extragenic palindromic (REP) PCR fingerprinting. The genetic relationship of strains within each host group was assessed as was the relationship of strains among different host groups. Multiple isolates from a single host animal (gull, human, or dog) were found to be identical; however, in some of the animals, additional strains occurred at a lower frequency. REP PCR fingerprint patterns of isolates from sewage (n = 180), gulls (n = 133), and dairy cattle (n = 121) were diverse; within a host group, pairwise comparison similarity indices ranged from 98% to as low as 15%. A composite dendrogram of E. coli fingerprint patterns did not cluster the isolates into distinct host groups but rather produced numerous subclusters (approximately >80% similarity scores calculated with the cosine coefficient) that were nearly exclusive for a host group. Approximately 65% of the isolates analyzed were arranged into host-specific groups. Comparable results were obtained by using enterobacterial repetitive intergenic consensus PCR and pulsed-field gel electrophoresis (PFGE), where PFGE gave a higher differentiation of closely related strains than both PCR techniques. These results demonstrate that environmental studies with genetic comparisons to detect sources of E. coli contamination will require extensive isolation of strains to encompass E. coli strain diversity found in host sources of contamination. These findings will assist in the development of approaches to determine sources of fecal pollution, an effort important for protecting water resources and public health.

scholarly journals multiMarker: software for modelling and prediction of continuous food intake using multiple biomarkers measurements

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Silvia D’Angelo ◽  
Isobel Claire Gormley ◽  
Aoife E. McNamara ◽  
Lorraine Brennan
Keyword(s):  
Food Intake ◽  
Web Application ◽  
Real Data ◽  
R Package ◽  
Great Sensitivity ◽  
Web Based ◽  
Ongoing Research ◽  
Multiple Biomarkers ◽  
The Relationship ◽  
The Web

Abstract Background Metabolomic biomarkers offer potential for objective and reliable food intake assessment, and there is growing interest in using biomarkers in place of or with traditional self-reported approaches. Ongoing research suggests that multiple biomarkers are associated with single foods, offering great sensitivity and specificity. However, currently there is a dearth of methods to model the relationship between multiple biomarkers and single food intake measurements. Results Here, we introduce multiMarker, a web-based application based on the homonymous R package, that enables one to infer the relationship between food intake and two or more metabolomic biomarkers. Furthermore, multiMarker allows prediction of food intake from biomarker data alone. multiMarker differs from previous approaches by providing distributions of predicted intakes, directly accounting for uncertainty in food intake quantification. Usage of both the R package and the web application is demonstrated using real data concerning three biomarkers for orange intake. Further, example data is pre-loaded in the web application to enable users to examine multiMarker’s functionality. Conclusion The proposed software advance the field of Food Intake Biomarkers providing researchers with a novel tool to perform continuous food intake quantification, and to assess its associated uncertainty, from multiple biomarkers. To facilitate widespread use of the framework, multiMarker has been implemented as an R package and a Shiny web application.

Interaction screening by Kendall’s partial correlation for ultrahigh-dimensional data with survival trait

2020 ◽  
Vol 36 (9) ◽  
pp. 2763-2769
Author(s):  
Jie-Huei Wang ◽  
Yi-Hau Chen
Keyword(s):  
Partial Correlation ◽  
Association Studies ◽  
B Cell Lymphoma ◽  
Real Data ◽  
R Package ◽  
Supplementary Information ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Interaction Screening ◽  
Relationship Of

Abstract Motivation In gene expression and genome-wide association studies, the identification of interaction effects is an important and challenging issue owing to its ultrahigh-dimensional nature. In particular, contaminated data and right-censored survival outcome make the associated feature screening even challenging. Results In this article, we propose an inverse probability-of-censoring weighted Kendall’s tau statistic to measure association of a survival trait with biomarkers, as well as a Kendall’s partial correlation statistic to measure the relationship of a survival trait with an interaction variable conditional on the main effects. The Kendall’s partial correlation is then used to conduct interaction screening. Simulation studies under various scenarios are performed to compare the performance of our proposal with some commonly available methods. In the real data application, we utilize our proposed method to identify epistasis associated with the clinical survival outcomes of non-small-cell lung cancer, diffuse large B-cell lymphoma and lung adenocarcinoma patients. Both simulation and real data studies demonstrate that our method performs well and outperforms existing methods in identifying main and interaction biomarkers. Availability and implementation R-package ‘IPCWK’ is available to implement this method, together with a reference manual describing how to perform the ‘IPCWK’ package. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals THE LAST TIME ANALYSIS OF THE FOLLOWING FAMILY IN AL-QUR'AN PERSPECTIVE

2020 ◽  
Vol 2 (2) ◽  
pp. 18-20
Author(s):  
Rona Dwi Rahmah
Keyword(s):  
Natural Disasters ◽  
Correlation Coefficient ◽  
Real Data ◽  
Least Square Method ◽  
Least Square ◽  
Single Word ◽  
Time Analysis ◽  
The Earth ◽  
Relationship Of ◽  
The Relationship

Abstract. Earthquakes are natural disasters caused by shocks on the earth due to faults and the sudden movement of tectonic rocks that make up the earth's crust. This study of earthquakes will be interesting if explored further from the perspective of the Qur'an because in the Qur'an there are many verses that speak of earthquakes. As explained in the Qur'an Al-Zalzalah verses 1-8. On February 14 2016 to February 23 2016 aftershocks occurred in the Klagon Village Area, Saradan District, Madiun. To analyze when the end of aftershocks ends by using the Least Square Method and the relationship of frequency of aftershocks to times that include the Omori, Omogi 1, Omogi 2 and Utsu methods. The conclusion of this study is the Omogi 2 method which has obtained the correlation coefficient r = 0.195 from the correlation value -1 ≤ r ≤ 1, with the aftershocks ending on day 464 and from the comparison of aftershock frequency corresponding to the graph between the results data calculations with real data (actual data) namely the Omogi 2 method. And basically the term earthquake in the Qur'an can still be said not to make the verses interpreted as a single word containing the meaning of the earthquake as a brief explanation of aftershocks in the perspective of the Qur'an.

scholarly journals Hypotheses about the relationship of cognition with psychopathology should be tested by embedding them into empirical priors

2018 ◽  
Author(s):  
Michael Moutoussis ◽  
Alexandra Kathryn Hopkins ◽  
Raymond J Dolan
Keyword(s):  
Computational Models ◽  
Point Of View ◽  
Model Parameters ◽  
Parameter Inference ◽  
Cross Domain ◽  
Empirical Priors ◽  
Relationship Of ◽  
The Relationship ◽  
The Brain ◽  
Decision Making Biases

Mechanistic hypotheses about psychiatric disorders are increasingly formalized as computational models of information-processing in the brain. Model parameters, characterizing for example decision-making biases, are hypothesized to correlate with clinical constructs. This is promising, but here we draw attention to some techniques used to minimize noise in parameter estimation which are in common use but may be unhelpful. Namely, the use of empirical priors that do not incorporate relationships between psychopathology and modelled processes will suppress the very relationships of interest. This is because the variability associated with psychopathology will be indistinguishable from that due to noise from the point of view of the hierarchical, or random-effects, fit that used the empirical priors in question. We advocate incorporating cross-domain, e.g. psychopathology-cognition relationships into the parameter inference itself.

scholarly journals Otolith Morphometrics of Selar Crumenophthalmus From Kema Strait

2018 ◽  
Vol 6 (1) ◽  
pp. 98
Author(s):  
Rofino Taliawo ◽  
Fransine B Manginsela ◽  
Nego E. Bataragoa
Keyword(s):  
Aspect Ratio ◽  
Linear Relationship ◽  
R Package ◽  
The Body ◽  
Fish Length ◽  
R Program ◽  
Area And Perimeter ◽  
Length Width ◽  
Relationship Of ◽  
The Relationship

Otolith or ear stone of fish,  known as a result of biomineralization which takes place in the body of the fish. In some studies, otolith used to estimate age and stock structure of the fish.  The otolith  was categorized into three  types called sagitta, lagena and utrikulus and  the most widely studied. This study was designed to describe the characteristics  of the otolith of S. crumenophthalmus  by implementing  six index form descriptors.Tthe  study also dimed at determinition the relationship of fish length and otolith length as well as otolith width .  Linear regression approch was used to analyse the relationship of fish length and whole characteristics otolith . Those parameters were analysed using Excel and application R program  ( the package the FSA ). The results  show that otolith S.crumenophthalmus  sagitta has 6 descriptor indicees thatt are as follow: 1) the irregular surface (from factor < 1), 2) comparison against a full round (roundness ≠ 1), no 3) (full circle-shaped circularity: 21), 4) do not form a perfect square (R ≠ 1) and 5 axis) changes of 28-29 and 6) form a somewhat elongated (aspect ratio > 1). The value index  otolith form is showed ellipse.Based on the results of the analysis, the otolith left and right (length, width, perimeter, and area) otolith males S. crumenophthalmus has no different. Same alsois found on the case of males otolith, left and on right (long) females otolith S. crumenophthalmus does not differ except the width of the otolith, the area and perimeter size of a different otolith real. The relationship between  the length size and width dimensions of otolith with the total length of the fish has a linear relationship. The second parameter of the linear relationship is marked by the determination coefficient values on otolith length varies between 0,56-0,62 and its width ranged from 0.49 to 0.69. For female fish, otolith lenght detemination coefficient varies between 0.27 and 0.25 to its width ranges from 0.15 to 0.19.Key words: S.crumenophthalmus, otolith Morfometrik, Gulf of Kema AbstrakOtolit atau batu telinga ikan dikenal sebagai hasil dari biomineralisasi yang berlangsung dalam  tubuh  ikan. Pada beberapa studi, otolit digunakan  untuk mengestimasi umur ikan serta struktur stok. Dari tiga (3) organ otolit (sagitta, utrikulus dan lagena), yang paling banyak diteliti adalah otolit sagitta.Penelitian yang dilakukan bertujuan untuk mendeskripsikan karakter otolit ikan Selar crumenophthalmus (yang  mengunakan   6 deskriptor indeks bentuk) dan menentukan hubungan panjang tubuh ikan dengan panjang otolit serta lebarnya.Hubungan ukuran otolit terhadap panjang total ikan dianalis mengunakan persamaan regresi linier sederhana. Alat yang digunakan untuk menganalisis bentuk serta hubungan otolit menggunakan aplikasi Excel serta program R package FSA.Dari hasil analisis, otolit sagitta ikan Selar crumenophthalmus memiliki 6 deskriptor indeks yang hasilnya adalah : 1) permukaan yang tidak teratur (from factor < 1), 2) perbandingan terhadap bulat penuh (roundness ≠1), 3) tidak berbentuk  lingkaran penuh (circularity: 21), 4) tidak membentuk persegi sempurna (R≠1) dan 5) perubahan sumbu sebesar 28-29 serta 6) bentuk agak memanjang (aspect ratio >1). Dari nilai indeks bentuk tersebut, otolit Selar crumenophthalmus menunjukan bentuk yang elips.Berdasarkan hasil analisis, otolit kiri dan kanan (panjang, lebar, , perimeter area /luas) otolit jantan Selar crumenophthalmus tidak berbeda nyata. Sama halnya dengan otolit jantan, kiri dan kanan (panjang) otolit betina Selar crumenophthalmus tidak berbeda nyata, namun lebar otolit, area serta perimeter otolit berbeda nyata.Hubungan antara dimensi ukuran panjang dan lebar otolit dengan  panjang total  ikan memiliki hubungan linier. Hubungan linear kedua parameter tersebut ditandai dengan nilai koefisien determinasi pada panjang otolit ikan jantan  bervariasi antara 0, 56- 0, 62 dan lebarnya berkisar antara 0,49 sampai 0,69. Untuk ikan betina, koefisien deteminasi panjang otolit bervariasi antara 0,25 sampai 0,27 dan lebarnya berkisar antara 0,15 sampai 0,19.Kata kunci: Selar crumenophthalmus,  Morfometrik otolit, Teluk Kema

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