scholarly journals Supplemental Material: Volcanic carbon cycling in East Lake, Newberry Volcano, Oregon, USA

2021 ◽  
Author(s):  
Hilary Brumberg ◽  
Johan Varekamp ◽  
et al.

Details on the laboratory, data analysis, modeling methods, and equipment specifications, including methods and results of the two box models showing seasonal carbon cycling in East Lake, and raw data from the main text figures.<br>

2021 ◽  
Author(s):  
Hilary Brumberg ◽  
Johan Varekamp ◽  
et al.

Details on the laboratory, data analysis, modeling methods, and equipment specifications, including methods and results of the two box models showing seasonal carbon cycling in East Lake, and raw data from the main text figures.<br>


2016 ◽  
Author(s):  
Hilary Brumberg ◽  
◽  
Paula Tartell ◽  
Lena R. Capece ◽  
Johan C. Varekamp

2020 ◽  
Author(s):  
Alessandra Maciel Paz Milani ◽  
Fernando V. Paulovich ◽  
Isabel Harb Manssour

Analyzing and managing raw data are still a challenging part of the data analysis process, mainly regarding data preprocessing. Although we can find studies proposing design implications or recommendations for visualization solutions in the data analysis scope, they do not focus on challenges during the preprocessing phase. Likewise, the current Visual Analytics processes do not consider preprocessing an equally important stage in their process. Thus, with this study, we aim to contribute to the discussion of how we can use and combine methods of visualization and data mining to assist data analysts during the preprocessing activities. To achieve that, we introduce the Preprocessing Profiling Model for Visual Analytics, which contemplates a set of features to inspire the implementation of new solutions. In turn, these features were designed considering a list of insights we obtained during an interview study with thirteen data analysts. Our contributions can be summarized as offering resources to promote a shift to a visual preprocessing.


2021 ◽  
Author(s):  
Melanie Christine Föll ◽  
Veronika Volkmann ◽  
Kathrin Enderle-Ammour ◽  
Konrad Wilhelm ◽  
Dan Guo ◽  
...  

Background: Mass spectrometry imaging (MSI) derives spatial molecular distribution maps directly from clinical tissue specimens. This allows for spatial characterization of molecular compositions of different tissue types and tumor subtypes, which bears great potential for assisting pathologists with diagnostic decisions or personalized treatments. Unfortunately, progress in translational MSI is often hindered by insufficient quality control and lack of reproducible data analysis. Raw data and analysis scripts are rarely publicly shared. Here, we demonstrate the application of the Galaxy MSI tool set for the reproducible analysis of an urothelial carcinoma dataset. Methods: Tryptic peptides were imaged in a cohort of 39 formalin-fixed, paraffin-embedded human urothelial cancer tissue cores with a MALDI-TOF/TOF device. The complete data analysis was performed in a fully transparent and reproducible manner on the European Galaxy Server. Annotations of tumor and stroma were performed by a pathologist and transferred to the MSI data to allow for supervised classifications of tumor vs. stroma tissue areas as well as for muscle-infiltrating and non-muscle invasive urothelial carcinomas. For putative peptide identifications, m/z features were matched to the MSiMass list. Results: Rigorous quality control in combination with careful pre-processing enabled reduction of m/z shifts and intensity batch effects. High classification accuracy was found for both, tumor vs. stroma and muscle-infiltrating vs. non-muscle invasive tumors. Some of the most discriminative m/z features for each condition could be assigned a putative identity: Stromal tissue was characterized by collagen type I peptides and tumor tissue by histone and heat shock protein beta-1 peptides. Intermediate filaments such as cytokeratins and vimentin were discriminative between the tumors with different muscle-infiltration status. To make the study fully reproducible and to advocate the criteria of FAIR (findability, accessibility, interoperability, and reusability) research data, we share the raw data, spectra annotations as well as all Galaxy histories and workflows. Data are available via ProteomeXchange with identifier PXD026459 and Galaxy results via https://github.com/foellmelanie/Bladder_MSI_Manuscript_Galaxy_links. Conclusion: Here, we show that translational MSI data analysis in a fully transparent and reproducible manner is possible and we would like to encourage the community to join our efforts.


Author(s):  
Suranga C. H. Geekiyanage ◽  
Adrian Ambrus ◽  
Dan Sui

Abstract Conventional kick detection methods mainly include monitoring pit gains, surface flow data (flow in and flow out), surface and down-hole pressure variations, and outputs from physics-based models. Kick detection times depend on a driller’s individual ability to interpret these drilling measurements, symptoms and model predictions. Furthermore, testing a novel data-driven solution in a full-scale operation may induce non-productive time, safety risks and crew fatigue adding to false alarms that inevitably occur during testing. Therefore, the development of better, faster and less human intervention-dependent kick detection on a laboratory scale system is a valuable step before full-scale testing. We have generated a dataset containing seven typical drilling measurements and a sequence of gas kicks from experiments conducted in the laboratory scale. First, we employ data analysis tools following data pre-processing steps, data scaling, outlier detection, and natural feature selection. Next, we consider additional “engineered features” and apply different feature combinations to logistic regression with an ensemble method (boosting) for developing kick detection algorithms. In our data analysis, ‘Delta flow’ (difference between flow in and flow out of the well) and ‘Rate of change of delta flow’ designed features, combined with logistic regression and boosting, give promising results in detecting kicks. Finally, we propose an intelligent algorithm and alarm architecture for a complete kick alarm system, which draws from both data analysis and machine learning models developed in this work.


2016 ◽  
Vol 44 (3) ◽  
pp. 20150057
Author(s):  
Gokhan Kilic ◽  
Mehmet S. Unluturk

2017 ◽  
Vol 123 ◽  
pp. 816-819 ◽  
Author(s):  
D.E. Aguiam ◽  
A. Silva ◽  
V. Bobkov ◽  
P.J. Carvalho ◽  
P.F. Carvalho ◽  
...  

1972 ◽  
Vol 58 (2) ◽  
pp. 216-219 ◽  
Author(s):  
Ralph R. Grams ◽  
Eugene A. Johnson ◽  
Ellis S. Benson

ZOOTEC ◽  
2019 ◽  
Vol 40 (1) ◽  
pp. 12
Author(s):  
Sri Hardiastuti Yusuf ◽  
John E.G. Rompis ◽  
Meilani R. Tinangon ◽  
E.H.B. Sondakh

THE INFLUENCES OF DIFFERENT COOKING POT ON THE PHYSIC-CHEMICAL PROPERTIES OF THE TRADITIONAL “RINTEK WUUK (RW)” SEASONING CHICKEN. This research was done to evaluate the influence of cooking methods with different containers on physic-chemical properties (pH, water holding capacity, and cooking losses) of chicken meat seasoning traditional “rintek wuuk (RW)”. The research was conducted using complete random draft (CRD) through three container treatment (bamboo, ground and frying pan) using RW traditional seasoning. The physic-chemical properties were analyzed in animal science technology laboratory. Data analysis used analysis of variance (ANOVA). Results of this study showed that different cooking containers did not affect the physic-chemical properties of seasoning RW chicken meat. These results can be concluded that the use of different containers did not give a real influence on the physic-chemical properties of the seasoning RW chicken meat. Keywords: Chicken meat, cooking container, RW seasoning, Physic-chemical properties.        


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