scholarly journals Inferring phage-bacteria infection networks from time series data

2016 ◽  
Author(s):  
Luis F. Jover ◽  
Justin Romberg ◽  
Joshua S. Weitz
Keyword(s):  
Time Series ◽  
Time Course ◽  
Community Dynamics ◽  
Time Series Data ◽  
Plaque Assay ◽  
Interaction Network ◽  
Series Data ◽  
Factors Affecting ◽  
Evolutionary Changes

In communities with bacterial viruses (phage) and bacteria, the phage-bacteria infection network establishes which virus types infects which host types. The structure of the infection network is a key element in understanding community dynamics. Yet, this infection network is often difficult to ascertain. Introduced over 60 years ago, the plaque assay remains the gold-standard for establishing who infects whom in a community. This culture-based approach does not scale to environmental samples with increased levels of phage and bacterial diversity, much of which is currently unculturable. Here, we propose an alternative method of inferring phage-bacteria infection networks. This method uses time series data of fluctuating population densities to estimate the complete interaction network without having to test each phage-bacteria pair individually. We use in silico experiments to analyze the factors affecting the quality of network reconstruction and find robust regimes where accurate reconstructions are possible. In addition, we present a multi-experiment approach where time series from different experiments are combined to improve estimates of the infection network and mitigate against the possibility of evolutionary changes to infection during the time-course of measurement.

scholarly journals Inferring phage–bacteria infection networks from time-series data

2016 ◽  
Vol 3 (11) ◽  
pp. 160654 ◽  
Author(s):  
Luis F. Jover ◽  
Justin Romberg ◽  
Joshua S. Weitz
Keyword(s):  
Time Series ◽  
Time Course ◽  
Community Dynamics ◽  
Time Series Data ◽  
Plaque Assay ◽  
Interaction Network ◽  
Series Data ◽  
Factors Affecting ◽  
Evolutionary Changes

In communities with bacterial viruses (phage) and bacteria, the phage–bacteria infection network establishes which virus types infect which host types. The structure of the infection network is a key element in understanding community dynamics. Yet, this infection network is often difficult to ascertain. Introduced over 60 years ago, the plaque assay remains the gold standard for establishing who infects whom in a community. This culture-based approach does not scale to environmental samples with increased levels of phage and bacterial diversity, much of which is currently unculturable. Here, we propose an alternative method of inferring phage–bacteria infection networks. This method uses time-series data of fluctuating population densities to estimate the complete interaction network without having to test each phage–bacteria pair individually. We use in silico experiments to analyse the factors affecting the quality of network reconstruction and find robust regimes where accurate reconstructions are possible. In addition, we present a multi-experiment approach where time series from different experiments are combined to improve estimates of the infection network. This approach also mitigates against the possibility of evolutionary changes to relevant phenotypes during the time course of measurement.

scholarly journals Jonckheere–Terpstra–Kendall-based non-parametric analysis of temporal differential gene expression

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Hitoshi Iuchi ◽  
Michiaki Hamada
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
Time Course ◽  
Time Series Data ◽  
Expression Patterns ◽  
Detection Methods ◽  
Series Data ◽  
Expression Levels ◽  
Over Time ◽  
Non Parametric

Abstract Time-course experiments using parallel sequencers have the potential to uncover gradual changes in cells over time that cannot be observed in a two-point comparison. An essential step in time-series data analysis is the identification of temporal differentially expressed genes (TEGs) under two conditions (e.g. control versus case). Model-based approaches, which are typical TEG detection methods, often set one parameter (e.g. degree or degree of freedom) for one dataset. This approach risks modeling of linearly increasing genes with higher-order functions, or fitting of cyclic gene expression with linear functions, thereby leading to false positives/negatives. Here, we present a Jonckheere–Terpstra–Kendall (JTK)-based non-parametric algorithm for TEG detection. Benchmarks, using simulation data, show that the JTK-based approach outperforms existing methods, especially in long time-series experiments. Additionally, application of JTK in the analysis of time-series RNA-seq data from seven tissue types, across developmental stages in mouse and rat, suggested that the wave pattern contributes to the TEG identification of JTK, not the difference in expression levels. This result suggests that JTK is a suitable algorithm when focusing on expression patterns over time rather than expression levels, such as comparisons between different species. These results show that JTK is an excellent candidate for TEG detection.

scholarly journals Uncertainty quantification of the effects of biotic interactions on community dynamics from nonlinear time-series data

2018 ◽  
Vol 15 (147) ◽  
pp. 20180695 ◽  
Author(s):  
Simone Cenci ◽  
Serguei Saavedra
Keyword(s):  
Time Series ◽  
Community Dynamics ◽  
Time Series Data ◽  
Multivariate Time Series ◽  
Model Averaging ◽  
Biotic Interactions ◽  
Series Data ◽  
Time Intervals ◽  
Novel Approach ◽  
Data Generating Process

Biotic interactions are expected to play a major role in shaping the dynamics of ecological systems. Yet, quantifying the effects of biotic interactions has been challenging due to a lack of appropriate methods to extract accurate measurements of interaction parameters from experimental data. One of the main limitations of existing methods is that the parameters inferred from noisy, sparsely sampled, nonlinear data are seldom uniquely identifiable. That is, many different parameters can be compatible with the same dataset and can generalize to independent data equally well. Hence, it is difficult to justify conclusive assertions about the effect of biotic interactions without information about their associated uncertainty. Here, we develop an ensemble method based on model averaging to quantify the uncertainty associated with the effect of biotic interactions on community dynamics from non-equilibrium ecological time-series data. Our method is able to detect the most informative time intervals for each biotic interaction within a multivariate time series and can be easily adapted to different regression schemes. Overall, this novel approach can be used to associate a time-dependent uncertainty with the effect of biotic interactions. Moreover, because we quantify uncertainty with minimal assumptions about the data-generating process, our approach can be applied to any data for which interactions among variables strongly affect the overall dynamics of the system.

scholarly journals Faktor-Faktor yang Mempengaruhi Alih Fungsi Lahan Sawah di Kabupaten Aceh Besar

2018 ◽  
Vol 3 (4) ◽  
pp. 525-533
Author(s):  
Raudhatul Husna ◽  
Azhar Azhar ◽  
Edy Marsudi
Keyword(s):  
Time Series ◽  
Population Density ◽  
Rice Field ◽  
Time Series Data ◽  
Statistical Tests ◽  
Secondary Data ◽  
Series Data ◽  
Factors Affecting ◽  
Rice Productivity ◽  
Negative Impacts

Abstrak. Alih fungsi lahan atau lazimnya disebut sebagai konversi lahan adalah  perubahan fungsi sebagian atau seluruh kawasan lahan dari fungsinya semula (seperti yang direncanakan) menjadi fungsi lain yang membawa dampak negatif terhadap lingkungan dan potensi lahan itu sendiri. Penelitian ini bertujuan untuk mengetahui apakah harga lahan, kepadatan penduduk, produktivitas padi dan jumlah PDRB dapat mempengaruhi alih fungsi lahan sawah di Kabupaten Aceh Besar. Data yang digunakan dalam penelitian ini adalah data sekunder. Data yang dikumpulkan adalah data time series dengan range tahun 2002 sampai 2016. Penelitian ini menggunakan metode analisis  regresi linier berganda. hasil penelitian dan pembahasan serta pengujian SPSS menunjukkan bahwa harga lahan, kepadatan penduduk, dan produktivitas padi berpengaruh nyata terhadap alih fungsi lahan sawah di Kabupaten Aceh Besar. sedangkan jumlah PDRB tidak berpengaruh terhadap alih fungsi lahan sawah. Hal ini ditunjukkan oleh koefisien regresi untuk variabel jumlah PDRB sebesar 0,00015. Hasil pengujian statistik menunjukkan nilai t hitung untuk jumlah PDRB sebesar 1,315 dengan nilai signifikan sebesar 0,218. Sedangkan nilai t tabel sebesar 1,782 yang berarti nilai t hitung t tabel (1,315 1,782).  Factors Affecting The Conversion Of Paddy Fields In Kabupaten Aceh Besar Abstract. Land use change or commonly referred to as land conversion is a change in the function of part or all of the land area from its original function (as planned) into other functions that bring negative impacts to the environment and the potential of the land itself. This study aims to find out whether the price of land, population density, rice productivity and the amount of GRDP can affect the conversion of rice field functions in Aceh Besar District. The data used in this research is secondary data. The data collected is time series data with range of year 2002 until 2016. This research use multiple linier regression analysis method. the results of research and discussion and testing of SPSS showed that land price, population density, and rice productivity significantly affected the conversion of wetland in Aceh Besar district. while the number of GDP does not affect the conversion of wetland. This is indicated by the regression coefficient for the GRDP variable of 0.00015. The results of statistical tests show the value of t arithmetic for the amount of GRDP by 1.315 with a significant value of 0.218. While the value of t table of 1.782 which means the value of t arithmetic t table (1,315 1.782).

P–368 Dynamic metabolomic profiling during early implantation period

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
Y Zhang ◽  
Y W Zhao ◽  
C C Wang ◽  
T C Li
Keyword(s):  
Mass Spectrometry ◽  
Time Series ◽  
Embryo Transfer ◽  
Study Design ◽  
Empirical Bayes ◽  
Time Course ◽  
Time Series Data ◽  
Series Data ◽  
Metabolomic Profiling ◽  
Implantation Period

Abstract Study question To investigate the different metabolomic profiling in serum between pregnant and non-pregnant women during early implantation period. Summary answer Metabolomics of progesterone-related hormones enhances from ET day3 for pregnancy women compared with non-pregnancy women. What is known already Metabolomics is based on high-throughput analytical methods to identify and quantify metabolites. Compared to other omics study, metabolomics is the closest one to the phenotype, allowing the observation of dynamic changes in phenotype at specific timepoints. So far there is no published work about the metabolomics profile in human early implantation period. Study design, size, duration: Study design: comparative study. Size: 14 pregnancy women and 14 non-pregnancy women. duration: time-course. Participants/materials, setting, methods Participants: pregnancy women and unpregnancy women after embryo transfer (ET). Setting: university-based study. Methods: Peripheral blood were collected at ET day0, 3, 6 and 9. metabolomic profiling in serum by platforms of capillary electrophoresis-mass spectrometry (CE-MS) and liquid chromatography–mass spectrometry (LC-MS). Main results and the role of chance There were no statistical difference of the age, BMI, basal FSH level, endometrium thickness on the day of embryo transfer, distribution of primary and secondary fertility, embryo transfer cycle as well as the infertile types between the two groups. After deleting those with over 50% missing data, we finally have 310 metabolites into statistical analysis. Among the 310 metabolite, lipid metabolites account the largest percentage, nearly half of all metabolites. The second biggest class of metabolites in our data was organic acids. Combined results in repeated measurement ANOVA (RM-ANOVA) and ANOVA-simultaneous component analysis (ASCA) as well as multivariate empirical Bayes time-series analysis (MEBA), we finally found that progesterone-related hormones were the most important metabolites for the whole time-series data. Those significant metabolites showed a significant down regulation from ET day0 to ET day3 and up regulation from ET day3 to ET day9. Limitations, reasons for caution we have limited sample size for this study and further validation is necessary for confirmation. Wider implications of the findings: The phenomenon of upregulation of progesterone-related hormones from day3 in pregnancy group might be related to the embryo-originated hcg. Because the embryo has entered into endometrium at day3 and produced cytokines, hcg and other interaction with endometrium. Trial registration number NA

Use of ordered logit model with time series data for determining the factors affecting the milk yield of Holstein Friesians

2019 ◽  
Author(s):  
Özge Akkuş ◽  
Volkan Sevinç
Keyword(s):  
Time Series ◽  
Milk Yield ◽  
Logit Model ◽  
Time Series Data ◽  
Series Data ◽  
Ordered Logit ◽  
Factors Affecting ◽  
Ordered Logit Model ◽  
Lactation Length ◽  
Cattle Breeders

This article aims to introduce the use of ordered logit model with time series data in milk productivity studies and determine the important factor levels affecting the milk yield of Holstein Friesians. The data consists of 2002 records collected for the years 2009-2015 from the reports of the Cattle Breeders’ Association of Turkey (CBAT) in Muðla province in Turkey. The direct and marginal effects of the variables: parity, lactation length and year of calving on milk yield are investigated and the probabilities regarding the milk yield production for a given specific parity, lactation length and calving year are calculated. The results show that milk yield slightly increases on the 4th parity of cows. As far as the years concerned, although there had mostly been a steady amount of milk production between 2009 and 2015 years, there was a significant decrease in 2011 and increase in 2014.

scholarly journals Persepsi Kualitas Mahasiswa Program Studi DIII Akuntansi Polines Selama Praktek Kerja Lapangan (PKL) di Industri

2018 ◽  
Vol 1 (1) ◽  
Author(s):  
Moh.Hasanudin Marliyati ◽  
Sri Murtini ◽  
Resi Yudhaningsih ◽  
Retno Retno
Keyword(s):  
Information Technology ◽  
Time Series ◽  
Communication Skills ◽  
Time Series Data ◽  
Soft Skills ◽  
Series Data ◽  
Central Java ◽  
Hard Skills ◽  
Main Components

<p>This research aimed at exploring the quality of accounting diploma <br />students during their internship program in industries. The term of student’s <br />quality described in this research isexplained using 5 main components as follows: (1) communication skills (2) teamwork (3) independence (4) creativity (5) accounting and information technology (IT)-related skills. The research’s sample is industries where students of Diploma in Accounting of State Polytechnic of Semarang (SPS) took their intership and the students themselves whom have completed their internship program for three months in various institutions such as private enterprises, state owned enterprises, local government offices spread out around Central Java. The data on this research is time series data taken from 2015 to 2016 and was collected using questionnaires from the corresponding industries about the students competencies both hard skills and soft skills. <br />Data was scored using Likert scale, ranges from Poor (1) to Excellent (5) and <br />analyzed using statistic descriptive. The result showed that average students’ <br />quality during their internship was good. Among the 5 skills observed, the <br />corresponding industries ranked teamwork skills as the highest, followed by <br />independence, creativity, communication skills and the accounting and IT -related skills. It is expected that the result can be used for future development of Accounting Program Study of SPS.</p>

scholarly journals Estimating Elasticities for Multi-Modal Public Transport Demand: A Time Series Approach

2010 ◽  
Author(s):  
Konstantina Gkritza ◽  
Ioannis Golias ◽  
Matthew G. Karlaftis
Keyword(s):  
Time Series ◽  
Public Transport ◽  
Public Transportation ◽  
Time Series Data ◽  
Transportation Systems ◽  
Seemingly Unrelated Regression ◽  
Series Data ◽  
Factors Affecting ◽  
Use Of Time ◽  
Time Series Approach

Research on the demand side of public transportation systems with the use of time series data frequently shows conflicting results with respect to fare elasticities and the factors affecting it. In this analysis we complement prior research by developing seemingly unrelated regression equation models with monthly data for a city served by three different modes of public transportation. The results indicate that, as expected, urban public transport demand in Athens, Greece, is inelastic with respect to fares but, surprisingly, highly inelastic with respect to automobile fuel cost. Further, different transit modes have significantly different fare elasticities, a finding with important practical implications.

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