scholarly journals A Multi-dimensional Integrative Scoring Framework for Predicting Functional Regions in the Human Genome

2021 ◽  
Author(s):  
Xihao Li ◽  
Godwin Yung ◽  
Hufeng Zhou ◽  
Ryan Sun ◽  
Zilin Li ◽  
...  
Keyword(s):  
Mixed Model ◽  
Model Framework ◽  
Functional Roles ◽  
Genomic Epidemiology ◽  
Functional Regions ◽  
Functional Variants ◽  
Dna Elements ◽  
Diverse Origin ◽  
Functional Dna ◽  
Different Characteristics

Attempts to identify and prioritize functional DNA elements in coding and noncoding regions, particularly through use of in silico functional annotation data, continue to increase in popularity. However, specific functional roles may vary widely from one variant to another, making it challenging to summarize different aspects of variant function. Here we propose Multi-dimensional Annotation Class Integrative Estimation (MACIE), an unsupervised multivariate mixed model framework capable of integrating annotations of diverse origin to assess multi-dimensional functional roles for both coding and noncoding variants. Unlike existing one-dimensional scoring methods, MACIE views variant functionality as a composite attribute encompassing multiple different characteristics, and estimates the joint posterior functional probability vector of each genomic position, a quantity that offers richer and more interpretable information in the presence of multiple aspects of functionality. Applied to a variety of independent coding and non-coding datasets, MACIE demonstrates powerful and robust performance in discriminating between functional and non-functional variants. We also show an application of MACIE to fine-mapping using lipids GWAS summary statistics data from the European Network for Genetic and Genomic Epidemiology Consortium.

Hierarchical Modelling of Facial Perceptions: A Secondary Analysis of Aggressiveness Ratings

2020 ◽  
Author(s):  
Mark Christopher Adkins ◽  
Nataly Beribisky ◽  
Stephan Bonfield ◽  
Linda Farmus
Keyword(s):  
Factor Analysis ◽  
Mixed Model ◽  
Structural Information ◽  
Secondary Analysis ◽  
Specific Factor ◽  
Primary Analysis ◽  
Model Framework ◽  
Psychological Science ◽  
Individual Traits ◽  
Confirmatory Factor

The Psychological Science Accelerator’s (PSA) primary project tested for latent structure using exploratory factor analysis and confirmatory factor analysis but we decided to diverge from this approach and model individual traits separately. Our interest mainly was in examining the interplay between “stimulus ethnicity” and “stimulus sex” to discover how differing levels of these criterion differ across region, country, lab etc. While the necessary and prerequisite hierarchical structural information about each trait could certainly be found within the primary project’s dataset, we did not assume that any specific factor structure from the PSA’s primary analysis would necessarily hold, therefore we based our decision to model the data from each trait separately using a mixed model framework.

Impact of Chatbot in Transforming the Face of Retailing- An Empirical Model of Antecedents and Outcomes

2019 ◽  
Vol 12 ◽  
Author(s):  
Kumari Anshu ◽  
Loveleen Gaur ◽  
Arun Solanki
Keyword(s):  
Research Work ◽  
Shopping Behavior ◽  
Model Framework ◽  
Shopping Experience ◽  
The Face ◽  
Strongly Agree ◽  
Different Characteristics ◽  
Work Done ◽  
The Impact ◽  
Self Administered Questionnaire

Chatbot has emerged as a significant resolution to the swiftly growing customer caredemands in recent times. Chatbot has emerged as one of the biggest technological disruption. Simply speaking, it is a software agent facilitating interaction between computers and humans in natural language. So basically, it is a simulated, intellectual dialogue agent functional in a range of consumer engagement circumstances. It is the easiest and simplest means enable interaction between the retailers and the customers. </p><p> • Purpose- Most of the research work done in this field is concerned with their technical aspects. The recent research on chatbot pay little attention to the impact it is creating on users’ experience. Through this work, author is making an effort to know the customer-oriented impact that the chatbot bear on the shoppers. The purpose of this study is to develop and empirically test a framework that identify the customer oriented attributes of chatbot and impact of these attributes on customers. </p><p> • Objectives- The study intends to bridge the gap between concepts and actual attributes and applications on the subject of Chatbot. The following research objectives can address the various aspects of Chatbot affecting the different characteristics of consumers shopping behaviors: a) Identify the various attributes of chatbot that bears an impression on consumer shopping behavior. b) Evaluate the impact of chatbot on consumer shopping behavior that leads to the development of chatbot usage and adoption among the customer. </p><p> • Design/Methodology/Approach – For the purpose of analysis, author has administered Factor analysis and Multiple regression using SPSS version 23 for identification of various attributes of Chatbot and knowing their impact on shoppers. A self-administered questionnaire from the review of literature is developed. Industry experts in the field of retailing and academician evaluate the questionnaire. Primary information from the respondents is gathered using this questionnaire. The questionnaire comprises of Likert scale on a scale of 1 to 5 where 1 stands for strongly disagree and 5 stands for strongly agree. Data is collected from 126 respondents, out of which 111 respondents were finally considered for study and analysis purpose. </p><p> • Findings – The empirical results show that the study identifies various attributes of chatbot like Trust, Usefulness, Satisfaction, Readiness to Use and Accessibility. It is also found that chatbot is really influencing the customers in providing them with shopping experience, which can be very helpful to the businesses for increasing the sales and creating repurchase intention among the customers. </p><p> • Originality/value – The recent research on chatbot pay little attention to the impact it is creating on customers who are actually interacting with it on regular basis. The research paper extends information for understanding and appreciating the customer oriented attributes of artificially intelligent Chatbot. In this regard, the author has developed a model framework and proposed the attributes identified. Through the work, author is also making an effort to test empirically the impact of the identified attributes on the shoppers.

scholarly journals Functional equivalency and diversity of cis-acting elements among yeast replication origins.

1997 ◽  
Vol 17 (9) ◽  
pp. 5473-5484 ◽  
Author(s):  
S Lin ◽  
D Kowalski
Keyword(s):  
Origin Recognition Complex ◽  
Common Mechanism ◽  
Dna Unwinding ◽  
Replication Origins ◽  
Yeast Saccharomyces Cerevisiae ◽  
Autonomously Replicating Sequence ◽  
Cis Acting ◽  
Dna Elements ◽  
Functional Dna ◽  
Dna Replication Origins

The DNA replication origins of the yeast Saccharomyces cerevisiae require several short functional elements, most of which are not conserved in sequence. To better characterize ARS305, a replicator from a chromosomal origin, we swapped functional DNA elements of ARS305 with defined elements of ARS1. ARS305 contains elements that are functionally exchangeable with ARS1 A and B1 elements, which are known to bind the origin recognition complex; however, the ARS1 A element differs in that it does not require a 3' box adjacent to the essential autonomously replicating sequence consensus. At the position corresponding to ARS1 B3, ARS305 has a novel element, B4, that can functionally substitute for every type of short element (B1, B2, and B3) in the B domain. Unexpectedly, the replacement of element B4 by ARS1 B3, which binds ABF1p and is known as a replication enhancer, inhibited ARS305 function. ARS305 has no short functional element at or near positions corresponding to the B2 elements in ARS1 and ARS307 but contains an easily unwound region whose functional importance was supported by a broad G+C-rich substitution mutation. Surprisingly, the easily unwound region can functionally substitute for the ARS1 B2 element, even though ARS1 B2 was found to possess a distinct DNA sequence requirement. The functionally conserved B2 element in ARS307 contains a known sequence requirement, and helical stability analysis of linker and minilinker mutations suggested that B2 also contains a DNA unwinding element (DUE). Our findings suggest that yeast replication origins employ a B2 element or a DUE to mediate a common function, DNA unwinding during initiation, although not necessarily through a common mechanism.

Grass-fed vs. grain-fed beef systems: performance, economic, and environmental trade-offs

2021 ◽  
Author(s):  
S C Klopatek ◽  
E Marvinney ◽  
T Duarte ◽  
A Kendall ◽  
X Yang ◽  
...  
Keyword(s):  
Environmental Impacts ◽  
Mixed Model ◽  
Cropping Systems ◽  
Carcass Quality ◽  
Marbling Score ◽  
Model Framework ◽  
Land Occupation ◽  
Final Body Weight ◽  
Systems Model ◽  
Trade Offs

Abstract Between increasing public concerns over climate change and heightened interest of niche market beef on social media, the demand for grass-fed beef has increased considerably. However, the demand increase for grass-fed beef has raised many producers' and consumers' concerns regarding product quality, economic viability, and environmental impacts that have thus far gone unanswered. Therefore, using a holistic approach, we investigated the performance, carcass quality, financial outcomes, and environmental impacts of four grass-fed and grain-fed beef systems currently being performed by ranchers in California. The treatments included: 1) steers stocked on pasture and feedyard finished for 128 days (CON); 2) steers grass-fed for 20 months (GF20); 3) steers grass-fed for 20 months with a 45-day grain finish (GR45); and 4) steers grass-fed for 25 months (GF25). The data were analyzed using a mixed model procedure in R with differences between treatments determined by Tukey HSD. Using carcass and performance data from these systems, a weaning-to-harvest life cycle assessment (LCA) was developed in the Scalable, Process-based, Agronomically Responsive Cropping Systems model framework, to determine global warming potential (GWP), consumable water use, energy, smog, and land occupation footprints. Final body weight varied significantly between treatments (P &lt;0.001) with the CON cattle finishing at 632 kg, followed by GF25 at 570 kg, GR45 at 551 kg, and GF20 478 kg. Dressing percentage (DP) differed significantly between all treatments (P &lt; 0.001). The DP was 61.8% for CON followed by GR45 at 57.5%, GF25 at 53.4%, and GF20 had the lowest DP of 50.3%. Marbling scores were significantly greater for CON compared to all other treatments (P &lt; 0.001) with CON marbling score averaging 421 (low-choice ≥ 400). Breakeven costs with harvesting and marketing for the CON, GF20, GR45, and GF25 were $6.01, $8.98, $8.02, and $8.33 per kg hot carcass weight (HCW), respectively. The GWP for the CON, GF20, GR45, and GF25 were 4.79, 6.74, 6.65 and 8.31 CO2e/kg HCW, respectively. Water consumptive use for CON, GF20, GR45, and GF25 were 933, 465, 678 and 1250 L /kg HCW, respectively. Energy use for CON, GF20, GR45, and GF25 were 18.7, 7.65, 13.8 and 8.85 MJ /kg HCW, respectively. Our results indicated that grass-fed beef systems differ in both animal performance and carcass quality resulting in environmental and economic sustainability tradeoffs with no system having absolute superiority.

Phylogenetic Footprinting to Find Functional DNA Elements

2007 ◽  
pp. 367-380
Author(s):  
Austen R. D. Ganley ◽  
Takehiko Kobayashi
Keyword(s):  
Phylogenetic Footprinting ◽  
Dna Elements ◽  
Functional Dna

scholarly journals A Novel Approach to the Design and Analysis of Field Experiments to Study Variation in the Tolerance and Resistance of Cultivars to Root Lesion Nematodes (Pratylenchus spp.)

2020 ◽  
Vol 110 (10) ◽  
pp. 1623-1631
Author(s):  
Karyn L. Reeves ◽  
Clayton R. Forknall ◽  
Alison M. Kelly ◽  
Kirsty J. Owen ◽  
Joshua Fanning ◽  
...  
Keyword(s):  
Mixed Model ◽  
Field Experiments ◽  
Linear Mixed Model ◽  
Random Regression ◽  
Yield Response ◽  
Response Curves ◽  
Model Framework ◽  
Management Options ◽  
Nematode Reproduction ◽  
Yield Response Curves

The root lesion nematode (RLN) species Pratylenchus thornei and P. neglectus are widely distributed within cropping regions of Australia and have been shown to limit grain production. Field experiments conducted to compare the performance of cultivars in the presence of RLNs investigate management options for growers by identifying cultivars with resistance, by limiting nematode reproduction, and tolerance, by yielding well in the presence of nematodes. A novel experimental design approach for RLN experiments is proposed where the observed RLN density, measured prior to sowing, is used to condition the randomization of cultivars to field plots. This approach ensured that all cultivars were exposed to consistent ranges of RLN in order to derive valid assessments of relative cultivar tolerance and resistance. Using data from a field experiment designed using the conditioned randomization approach and conducted in Formartin, Australia, the analysis of tolerance and resistance was undertaken in a linear mixed model framework. Yield response curves were derived using a random regression approach and curves modeling change in RLN densities between sowing and harvest were derived using splines to account for nonlinearity. Groups of cultivars sharing similar resistance levels could be identified. A comparison of slopes of yield response curves of cultivars belonging to the same resistance class identified differing tolerance levels for cultivars with equivalent exposures to both presowing and postharvest RLN densities. As such, the proposed design and analysis approach allowed tolerance to be assessed independently of resistance.

scholarly journals Modeling Relations between Compacted and Uncompacted Crown Ratio for the Northern United States

2019 ◽  
Vol 65 (5) ◽  
pp. 593-601
Author(s):  
James A Westfall ◽  
Megan B E Westfall ◽  
KaDonna C Randolph
Keyword(s):  
United States ◽  
Random Effects ◽  
Goodness Of Fit ◽  
Tree Mortality ◽  
Mixed Model ◽  
The United States ◽  
Repeated Measurements ◽  
Growth Potential ◽  
Model Framework ◽  
Northern United States

Abstract Tree crown ratio is useful in various applications such as prediction of tree mortality probabilities, growth potential, and fire behavior. Crown ratio is commonly assessed in two ways: (1) compacted crown ratio (CCR—lower branches visually moved upwards to fill missing foliage gaps) and (2) uncompacted crown ratio (UNCR—no missing foliage adjustment). The national forest inventory of the United States measures CCR on all trees, whereas only a subset of trees also are assessed for UNCR. Models for 27 species groups are presented to predict UNCR for the northern United States. The model formulation is consistent with those developed for other US regions while also accounting for the presence of repeated measurements and heterogeneous variance in a mixed-model framework. Ignoring random-effects parameters, the fit index values ranged from 0.43 to 0.78, and root mean squared error spanned 0.08–0.15; considerable improvements in both goodness-of-fit statistics were realized via inclusion of the random effects. Comparison of UNCR predictions with models developed for the southern United States exhibited close agreement, whereas comparisons with models used in Forest Vegetation Simulator variants indicated poor association. The models provide additional analytical flexibility for using the breadth of northern region data in applications where UNCR is the appropriate crown characteristic.

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