Abstract–Definitive screening designs permit the study of many quantitative factors in a few runs more than twice the number of factors. In practical applications, researchers often require a design for m quantitative factors, construct a definitive screening design for more than m factors and drop the superfluous columns. This is done when the number of runs in the standard m-factor definitive screening design is considered too limited or when no standard definitive screening design (sDSD) exists for m factors. In these cases, it is common practice to arbitrarily drop the last columns of the larger design. In this article, we show that certain statistical properties of the resulting experimental design depend on the exact columns dropped and that other properties are insensitive to these columns. We perform a complete search for the best sets of 1–8 columns to drop from sDSDs with up to 24 factors. We observed the largest differences in statistical properties when dropping four columns from 8- and 10-factor definitive screening designs. In other cases, the differences are small, or even nonexistent.

Categorical scatterplots with R for biologists: a step-by-step guide

Benjamin Petre1, Aurore Coince2, Sophien Kamoun1

1 The Sainsbury Laboratory, Norwich, UK; 2 Earlham Institute, Norwich, UK

Weissgerber and colleagues (2015) recently stated that ‘as scientists, we urgently need to change our practices for presenting continuous data in small sample size studies’. They called for more scatterplot and boxplot representations in scientific papers, which ‘allow readers to critically evaluate continuous data’ (Weissgerber et al., 2015). In the Kamoun Lab at The Sainsbury Laboratory, we recently implemented a protocol to generate categorical scatterplots (Petre et al., 2016; Dagdas et al., 2016). Here we describe the three steps of this protocol: 1) formatting of the data set in a .csv file, 2) execution of the R script to generate the graph, and 3) export of the graph as a .pdf file.

Protocol

• Step 1: format the data set as a .csv file. Store the data in a three-column excel file as shown in Powerpoint slide. The first column ‘Replicate’ indicates the biological replicates. In the example, the month and year during which the replicate was performed is indicated. The second column ‘Condition’ indicates the conditions of the experiment (in the example, a wild type and two mutants called A and B). The third column ‘Value’ contains continuous values. Save the Excel file as a .csv file (File -> Save as -> in ‘File Format’, select .csv). This .csv file is the input file to import in R.

• Step 2: execute the R script (see Notes 1 and 2). Copy the script shown in Powerpoint slide and paste it in the R console. Execute the script. In the dialog box, select the input .csv file from step 1. The categorical scatterplot will appear in a separate window. Dots represent the values for each sample; colors indicate replicates. Boxplots are superimposed; black dots indicate outliers.

• Step 3: save the graph as a .pdf file. Shape the window at your convenience and save the graph as a .pdf file (File -> Save as). See Powerpoint slide for an example.

Notes

• Note 1: install the ggplot2 package. The R script requires the package ‘ggplot2’ to be installed. To install it, Packages & Data -> Package Installer -> enter ‘ggplot2’ in the Package Search space and click on ‘Get List’. Select ‘ggplot2’ in the Package column and click on ‘Install Selected’. Install all dependencies as well.

• Note 2: use a log scale for the y-axis. To use a log scale for the y-axis of the graph, use the command line below in place of command line #7 in the script.

7 Display the graph in a separate window. Dot colors indicate

replicates

graph + geom_boxplot(outlier.colour='black', colour='black') + geom_jitter(aes(col=Replicate)) + scale_y_log10() + theme_bw()

References

Dagdas YF, Belhaj K, Maqbool A, Chaparro-Garcia A, Pandey P, Petre B, et al. (2016) An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor. eLife 5:e10856.

Petre B, Saunders DGO, Sklenar J, Lorrain C, Krasileva KV, Win J, et al. (2016) Heterologous Expression Screens in Nicotiana benthamiana Identify a Candidate Effector of the Wheat Yellow Rust Pathogen that Associates with Processing Bodies. PLoS ONE 11(2):e0149035

Weissgerber TL, Milic NM, Winham SJ, Garovic VD (2015) Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm. PLoS Biol 13(4):e1002128

https://cran.r-project.org/

http://ggplot2.org/

This dataset contains all the data and code needed to reproduce the analyses in the manuscript: Penn, H. J., & Read, Q. D. (2023). Stem borer herbivory dependent on interactions of sugarcane variety, associated traits, and presence of prior borer damage. Pest Management Science. https://doi.org/10.1002/ps.7843 Included are two .Rmd notebooks containing all code required to reproduce the analyses in the manuscript, two .html file of rendered notebook output, three .csv data files that are loaded and analyzed, and a .zip file of intermediate R objects that are generated during the model fitting and variable selection process. Notebook files 01_boring_analysis.Rmd: This RMarkdown notebook contains R code to read and process the raw data, create exploratory data visualizations and tables, fit a Bayesian generalized linear mixed model, extract output from the statistical model, and create graphs and tables summarizing the model output including marginal means for different varieties and contrasts between crop years. 02_trait_covariate_analysis.Rmd: This RMarkdown notebook contains R code to read raw variety-level trait data, perform feature selection based on correlations between traits, fit another generalized linear mixed model using traits as predictors, and create graphs and tables from that model output including marginal means by categorical trait and marginal trends by continuous trait. HTML files These HTML files contain the rendered output of the two RMarkdown notebooks. They were generated by Quentin Read on 2023-08-30 and 2023-08-15. 01_boring_analysis.html 02_trait_covariate_analysis.html CSV data files These files contain the raw data. To recreate the notebook output the CSV files should be at the file path project/data/ relative to where the notebook is run. Columns are described below. BoredInternodes_26April2022_no format.csv: primary data file with sugarcane borer (SCB) damage Columns A-C are the year, date, and location. All location values are the same. Column D identifies which experiment the data point was collected from. Column E, Stubble, indicates the crop year (plant cane or first stubble) Column F indicates the variety Column G indicates the plot (integer ID) Column H indicates the stalk within each plot (integer ID) Column I, # Internodes, indicates how many internodes were on the stalk Columns J-AM are numbered 1-30 and indicate whether SCB damage was observed on that internode (0 if no, 1 if yes, blank cell if that internode was not present on the stalk) Column AN indicates the experimental treatment for those rows that are part of a manipulative experiment Column AO contains notes variety_lookup.csv: summary information for the 16 varieties analyzed in this study Column A is the variety name Column B is the total number of stalks assessed for SCB damage for that variety across all years Column C is the number of years that variety is present in the data Column D, Stubble, indicates which crop years were sampled for that variety ("PC" if only plant cane, "PC, 1S" if there are data for both plant cane and first stubble crop years) Column E, SCB resistance, is a categorical designation with four values: susceptible, moderately susceptible, moderately resistant, resistant Column F is the literature reference for the SCB resistance value Select_variety_traits_12Dec2022.csv: variety-level traits for the 16 varieties analyzed in this study Column A is the variety name Column B is the SCB resistance designation as an integer Column C is the categorical SCB resistance designation (see above) Columns D-I are continuous traits from year 1 (plant cane), including sugar (Mg/ha), biomass or aboveground cane production (Mg/ha), TRS or theoretically recoverable sugar (g/kg), stalk weight of individual stalks (kg), stalk population density (stalks/ha), and fiber content of stalk (percent). Columns J-O are the same continuous traits from year 2 (first stubble) Columns P-V are categorical traits (in some cases continuous traits binned into categories): maturity timing, amount of stalk wax, amount of leaf sheath wax, amount of leaf sheath hair, tightness of leaf sheath, whether leaf sheath becomes necrotic with age, and amount of collar hair. ZIP file of intermediate R objects To recreate the notebook output without having to run computationally intensive steps, unzip the archive. The fitted model objects should be at the file path project/ relative to where the notebook is run. intermediate_R_objects.zip: This file contains intermediate R objects that are generated during the model fitting and variable selection process. You may use the R objects in the .zip file if you would like to reproduce final output including figures and tables without having to refit the computationally intensive statistical models. binom_fit_intxns_updated_only5yrs.rds: fitted brms model object for the main statistical model binom_fit_reduced.rds: fitted brms model object for the trait covariate analysis marginal_trends.RData: calculated values of the estimated marginal trends with respect to year and previous damage marginal_trend_trs.rds: calculated values of the estimated marginal trend with respect to TRS marginal_trend_fib.rds: calculated values of the estimated marginal trend with respect to fiber content Resources in this dataset:Resource Title: Sugarcane borer damage data by internode, 1993-2021. File Name: BoredInternodes_26April2022_no format.csvResource Title: Summary information for the 16 sugarcane varieties analyzed. File Name: variety_lookup.csvResource Title: Variety-level traits for the 16 sugarcane varieties analyzed. File Name: Select_variety_traits_12Dec2022.csvResource Title: RMarkdown notebook 2: trait covariate analysis. File Name: 02_trait_covariate_analysis.RmdResource Title: Rendered HTML output of notebook 2. File Name: 02_trait_covariate_analysis.htmlResource Title: RMarkdown notebook 1: main analysis. File Name: 01_boring_analysis.RmdResource Title: Rendered HTML output of notebook 1. File Name: 01_boring_analysis.htmlResource Title: Intermediate R objects. File Name: intermediate_R_objects.zip

Introduction

Welcome to the Cyclistic bike-share analysis case study! In this case study, you will perform many real-world tasks of a junior data analyst. You will work for a fictional company, Cyclistic, and meet different characters and team members. In order to answer the key business questions, you will follow the steps of the data analysis process: ask, prepare, process, analyze, share, and act. Along the way, the Case Study Roadmap tables — including guiding questions and key tasks — will help you stay on the right path.

Scenario

You are a junior data analyst working in the marketing analyst team at Cyclistic, a bike-share company in Chicago. The director of marketing believes the company’s future success depends on maximizing the number of annual memberships. Therefore, your team wants to understand how casual riders and annual members use Cyclistic bikes differently. From these insights, your team will design a new marketing strategy to convert casual riders into annual members. But first, Cyclistic executives must approve your recommendations, so they must be backed up with compelling data insights and professional data visualizations.

Ask

How do annual members and casual riders use Cyclistic bikes differently?

Guiding Question:

What is the problem you are trying to solve?
  How do annual members and casual riders use Cyclistic bikes differently?
How can your insights drive business decisions?
  The insight will help the marketing team to make a strategy for casual riders

Prepare

Guiding Question:

Where is your data located?
  Data located in Cyclistic organization data.

How is data organized?
  Dataset are in csv format for each month wise from Financial year 22.

Are there issues with bias or credibility in this data? Does your data ROCCC? 
  It is good it is ROCCC because data collected in from Cyclistic organization.

How are you addressing licensing, privacy, security, and accessibility?
  The company has their own license over the dataset. Dataset does not have any personal information about the riders.

How did you verify the data’s integrity?
  All the files have consistent columns and each column has the correct type of data.

How does it help you answer your questions?
  Insights always hidden in the data. We have the interpret with data to find the insights.

Are there any problems with the data?
  Yes, starting station names, ending station names have null values.

Process

Guiding Question:

What tools are you choosing and why?
  I used R studio for the cleaning and transforming the data for analysis phase because of large dataset and to gather experience in the language.

Have you ensured the data’s integrity?
 Yes, the data is consistent throughout the columns.

What steps have you taken to ensure that your data is clean?
  First duplicates, null values are removed then added new columns for analysis.

How can you verify that your data is clean and ready to analyze? 
 Make sure the column names are consistent thorough out all data sets by using the “bind row” function.

Make sure column data types are consistent throughout all the dataset by using the “compare_df_col” from the “janitor” package.
Combine the all dataset into single data frame to make consistent throught the analysis.
Removed the column start_lat, start_lng, end_lat, end_lng from the dataframe because those columns not required for analysis.
Create new columns day, date, month, year, from the started_at column this will provide additional opportunities to aggregate the data
Create the “ride_length” column from the started_at and ended_at column to find the average duration of the ride by the riders.
Removed the null rows from the dataset by using the “na.omit function”
Have you documented your cleaning process so you can review and share those results? 
  Yes, the cleaning process is documented clearly.

Analyze Phase:

Guiding Questions:

How should you organize your data to perform analysis on it? The data has been organized in one single dataframe by using the read csv function in R Has your data been properly formatted? Yes, all the columns have their correct data type.

What surprises did you discover in the data?
  Casual member ride duration is higher than the annual members
  Causal member widely uses docked bike than the annual members
What trends or relationships did you find in the data?
  Annual members are used mainly for commute purpose
  Casual member are preferred the docked bikes
  Annual members are preferred the electric or classic bikes
How will these insights help answer your business questions?
  This insights helps to build a profile for members

Share

Guiding Quesions:

Were you able to answer the question of how ...

Various water column variables, including salinity, dissolved inorganic nutrients, pH, total alkalinity, dissolved inorganic carbon, radio-carbon isotopes were measured in samples collected using a Niskin-bottle rosette at selected depths from sites offshore of California and Oregon from October to November 2019 during NOAA Ship Lasker R-19-05 (USGS field activity 2019-672-FA). CTD (Conductivity Temperature Depth) data were also collected at each depth that a Niskin-bottle sample was collected and are presented along with the water sample data. This data release supersedes version 1.0, published in August 2020 at https://doi.org/10.5066/P9ZS1JX8. Versioning details are documented in the accompanying VersionHistory_P9JKYWQU.txt file.

Petition subject: Execution case Original: http://nrs.harvard.edu/urn-3:FHCL:12233039 Date of creation: (unknown) Petition location: Uxbridge Selected signatures:Luther RistSusan R. UsherHarriett N. Moury Total signatures: 175 Legal voter signatures (males not identified as non-legal): 64 Female signatures: 84 Unidentified signatures: 27 Female only signatures: No Identifications of signatories: inhabitants, [females] Prayer format was printed vs. manuscript: Manuscript Signatory column format: not column separated Additional non-petition or unrelated documents available at archive: additional documents available Additional archivist notes: Leander Thompson Location of the petition at the Massachusetts Archives of the Commonwealth: Governor Council Files, April 17, 1847, Case of Leander Thompson Acknowledgements: Supported by the National Endowment for the Humanities (PW-5105612), Massachusetts Archives of the Commonwealth, Radcliffe Institute for Advanced Study at Harvard University, Center for American Political Studies at Harvard University, Institutional Development Initiative at Harvard University, and Harvard University Library.

Attached is the complete raw data from Vaughan and Dixson 2021 ‘Assessing the impact of static and fluctuating ocean acidification on the behavior of Amphiprion percula’.

Data collected from the behavioral lateralization trials has been inputted into the file ‘Vaughan_2020_Lateralization_Raw’. Column A indicate the CO₂ treatment group, where “SPD” = Static Present Day, “SFD” = Static Future Day, “FPD” = Fluctuating Present Day, and “FFD” = Fluctuating Future Day. Each individual fish used from each treatment group (n=30) is displayed in Column B. Column C shows the binary results, in order, of each fish’s turns in the T-maze, and was scored as 0 (right turn) or 1 (left turn) for a total of 10 turns. The total number of turns to the right and left are provided in Column D-E. The relative lateralization (L_R) of each fish was calculated {L_R = [(Turn to the right – Turn to the left)/(Turn to the right + Turn to the left)] ∗ 100} in Column F. Absolute lateralization (L_A) is provided in Column G.

Chemosensory response data has been inputted into the file ‘Vaughan_2020_Chemosensory_Raw’. Column A and B display treatment group and fish ID (n=20) as outlined above. The cue used in trial of either Tang (nonpredator) or Cod (predator) is provided in Column C, and the control in Column D. Numbers in these are used solely for the purpose of data analysis. The side of the cue in the flume is provided in Column E, and corresponds with the cue labelled in Column C. Buckets containing either the cue or control were placed above the flume and color coded as “BS” (blue side) and “RS” (red side), as the person scoring the trials was blinded. This also helped account for the switch (from one side of the flume to the other) that occurs halfway through each trial. Columns F-G represent results from the first 2min recording period, and Columns H-I represent results from the second 2min recording period. The total tallies from each fish are provided in Column J; the totals from each side are calculated in Columns K-L, and then sorted by either cue or control in Columns M-N. Proportions and percentages in cue and control are calculated and provided in Columns O-P and Q-R, respectively.

Carbonate chemistry data is compiled and provided in the ‘Vaughan_2020_Carbonate_Chemistry’. Measurements were taken each week (Column A) of each treatment group (as stated above, Column B). Column C reflects the time recordings were taken in the fluctuating treatments to hit the high, mid and low CO₂ points at “6:30”, “12:30” and “18:30”. Measurements of static treatment groups were taken at randomly selected times to get the reflection of the carbonate chemistry of these treatments, but for the purpose of clarity in this document they are listed as “Static”. Measurements were taken from a subset of tanks each that rotated each week (Column D). Our target pH_NBS values (i.e. what was programmed into the APEX System) are listed in Column E. Columns F-H displayed pH_NBS (taken with APEX probes), temperature °C (taken with a portable Mettler Toledo probe) and salinity (taken with a refractometer). Water samples were analyzed spectrophotometrically to provide pH_T and dissolved inorganic carbon, with values provided in Columns I-J. Using the program CO2SYS, total alkalinity and pCO₂ were calculated, with values provided in Columns K-L.

One of the methods for the separation of stable isotopes is the thermal diffusion column. The advantages of this method include small-scale operations because of apparatus simplicity and a small inventory, especially in gas phase operations. These features attract attention to the tritium and noble gas separation system. In this research, the R cascade was used for designing and determining the number of columns. Moreover, the square cascade was adopted for the final design because of its flexibility. Calculations were performed as an example for the separation of 20Ne and 22Ne isotopes. Accordingly, all R cascades that have enriched Ne isotopes to more than 99% were investigated, and the number of columns was determined. Also, using the specified columns, the square cascade parameters were optimized. A calculation code entitled ''RSQ_CASCADE'' was developed in this regard. The unit separation factor of 3 was considered, and the number of stages was studied in the range of 10 to 20. The results showed that the column separation power, the relative total flow rate, and the required columns were linearly related to the number of stages. The separation power and relative total flow decreased with the increase of stage number while the number of columns increased. Therefore, the cascade of 85 columns was recommended to separate the Ne stable isotopes. These calculations resulted in the 17-stage square cascade, with five columns in each stage. By changing the stages cut, feed point, and cascade feed flow rate, the best parameters of square cascade were determined according to the cascade separation power and column separation power. As the column separation power had the maximum value in the cascade feed 50, it was selected for separating Ne isotopes.

Introduction

This is a case study called Capstone Project from the Google Data Analytics Certificate.

In this case study, I am working as a junior data analyst at a fictitious bike-share company in Chicago called Cyclistic.

Cyclistic is a bike-share program that features more than 5,800 bicycles and 600 docking stations. Cyclistic sets itself apart by also offering reclining bikes, hand tricycles, and cargo bikes, making bike-share more inclusive to people with disabilities and riders who can’t use a standard two-wheeled bike.

Scenario

The director of marketing believes the company’s future success depends on maximizing the number of annual memberships. Therefore, your team wants to understand how casual riders and annual members use Cyclistic bikes differently. From these insights, our team will design a new marketing strategy to convert casual riders into annual members.

****Primary Stakeholders:****

1: Cyclistic Executive Team

2: Lily Moreno, Director of Marketing and Manager

ASK

1. How do annual members and casual riders use Cyclistic bikes differently?
2. Why would casual riders buy Cyclistic annual memberships?
3. How can Cyclistic use digital media to influence casual riders to become members?

# Prepare

The last four quarters were selected for analysis which cover April 01, 2019 - March 31, 2020. These are the datasets used:

Divvy_Trips_2019_Q2
Divvy_Trips_2019_Q3
Divvy_Trips_2019_Q4
Divvy_Trips_2020_Q1

The data is stored in CSV files. Each file contains one month data for a total of 12 .csv files.

Data appears to be reliable with no bias. It also appears to be original, current and cited.

I used Cyclistic’s historical trip data found here: https://divvy-tripdata.s3.amazonaws.com/index.html

The data has been made available by Motivate International Inc. under this license: https://ride.divvybikes.com/data-license-agreement

Limitations

Financial information is not available.

Process

Used R to analyze and clean data

• After installing the R packages, data was collected, wrangled and combined into a single file.
• Columns were renamed.
• Looked for incongruencies in the dataframes and converted some columns to character type, so they can stack correctly.
• Combined all quarters into one big data frame.
• Removed unnecessary columns

Analyze

• Inspected new data table to ensure column names were correctly assigned.
• Formatted columns to ensure proper data types were assigned (numeric, character, etc).
• Consolidated the member_casual column.
• Added day, month and year columns to aggregate data.
• Added ride-length column to the entire dataframe for consistency.
• Deleted trip duration rides that showed as negative and bikes out of circulation for quality control.
• Replaced the word "member" with "Subscriber" and also replaced the word "casual" with "Customer".
• Aggregated data, compared average rides between members and casual users.

Share

After analysis, visuals were created as shown below with R.

Act

Conclusion:

• Data appears to show that casual riders and members use bike share differently.
• Casual riders' average ride length is more than twice of that of members.
• Members use bike share for commuting, casual riders use it for leisure and mostly on the weekends.
• Unfortunately, there's no financial data available to determine which of the two (casual or member) is spending more money.

Recommendations

• Offer casual riders a membership package with promotions and discounts.

Feedback: Mukharbek Organokov organokov.m@gmail.com

Context

Sloan Digital Sky Survey current DR16 Server Data release with Galaxies, Stars and Quasars.

License: Creative Commons Attribution license (CC-BY) More datailes here. Find more here.

Content

The table results from a query which joins two tables:
- "PhotoObj" which contains photometric data
- "SpecObj" which contains spectral data.

16 variables (double) and 1 additional variable (char) 'class'. A class object can be predicted from the other 16 variables.

Variables description:
objid = Object Identifier
ra = J2000 Right Ascension (r-band)
dec = J2000 Declination (r-band)
u = better of deV/Exp magnitude fit (u-band)
g = better of deV/Exp magnitude fit (g-band)
r = better of deV/Exp magnitude fit (r-band)
i = better of deV/Exp magnitude fit (i-band)
z = better of deV/Exp magnitude fit (z-band)
run = Run Number
rerun = Rerun Number
camcol = Camera column
field = Field number
specobjid = Object Identifier
class = object class (galaxy, star or quasar object)
redshift = Final Redshift
plate = plate number
mjd = MJD of observation
fiberid = fiberID

Comments

• A four-color UVGR intermediate-band photometric system (Thuan-Gunn astronomic magnitude system) is discussed in [1]. The Sloan Digital Sky Survey (SDSS) photometric system, a new five-color (u′ g′ r′ i′ z′) wide-band CCD system is described in [2]
• The variables 'run', 'rerun', 'camcol' and 'field' features which describe a field within an image taken by the SDSS. A field is basically a part of the entire image corresponding to 2048 by 1489 pixels. A field can be identified by: - run number, which identifies the specific scan, - the camera column, or "camcol," a number from 1 to 6, identifying the scanline within the run, and the field number. The field number typically starts at 11 (after an initial rampup time), and can be as large as 800 for particularly long runs. - An additional number, rerun, specifies how the image was processed.
• The variable 'class' identifies an object to be either a galaxy (GALAXY), star (STAR) or quasar (QSO).
  ####References:
  [1] Thuan & Gunn (1976, PASP, 88,543)
  [2] Fukugita, M. et al, Astronomical J. v.111, p.1748

Data server

Data can be obtained using SkyServer SQL Search with the command below:
-- This query does a table JOIN between the imaging (PhotoObj) and spectra
-- (SpecObj) tables and includes the necessary columns in the SELECT to upload
-- the results to the SAS (Science Archive Server) for FITS file retrieval.
SELECT TOP 100000
p.objid,p.ra,p.dec,p.u,p.g,p.r,p.i,p.z,
p.run, p.rerun, p.camcol, p.field,
s.specobjid, s.class, s.z as redshift,
s.plate, s.mjd, s.fiberid
FROM PhotoObj AS p
JOIN SpecObj AS s ON s.bestobjid = p.objid
WHERE
p.u BETWEEN 0 AND 19.6
AND g BETWEEN 0 AND 20

Learn how to. Some examples. Full SQL Tutorial.

Or perform a complicated, CPU-intensive query of SDSS catalog data using CasJobs, SQL-based interface to the CAS.

Acknowledgements

SDSS collaboration.

Inspiration

The Sloan Digital Sky Survey has created the most detailed three-dimensional maps of the Universe ever made, with deep multi-color images of one-third of the sky, and spectra for more than three million astronomical objects. It allows to learn and explore all phases and surveys - past, present, and future - of the SDSS.

Petition subject: Against railroad discrimination with focus on white passengers Original: http://nrs.harvard.edu/urn-3:FHCL:10956457 Date of creation: (unknown) Petition location: Sudbury Legislator, committee, or address that the petition was sent to: Francis R. Gourgas, Concord Selected signatures:J.H. BrownSally BrownLoring Eaton Total signatures: 76 Legal voter signatures (males not identified as non-legal): 31 Female signatures: 37 Unidentified signatures: 8 Female only signatures: No Identifications of signatories: inhabitants, [females] Prayer format was printed vs. manuscript: Printed Signatory column format: not column separated Additional non-petition or unrelated documents available at archive: no additional documents Additional archivist notes: 11057/4 written on back Location of the petition at the Massachusetts Archives of the Commonwealth: House Unpassed 1842, Docket 1153 Acknowledgements: Supported by the National Endowment for the Humanities (PW-5105612), Massachusetts Archives of the Commonwealth, Radcliffe Institute for Advanced Study at Harvard University, Center for American Political Studies at Harvard University, Institutional Development Initiative at Harvard University, and Harvard University Library.

Walking and running are mechanically and energetically different locomotion modes. For selecting one or another, speed is a parameter of paramount importance. Yet, both are likely controlled by similar low-dimensional neuronal networks that reflect in patterned muscle activations called muscle synergies. Here, we investigated how humans synergistically activate muscles during locomotion at different submaximal and maximal speeds. We analysed the duration and complexity (or irregularity) over time of motor primitives, the temporal components of muscle synergies. We found that the challenge imposed by controlling high-speed locomotion forces the central nervous system to produce muscle activation patterns that are wider and less complex relative to the duration of the gait cycle. The motor modules, or time-independent coefficients, were redistributed as locomotion speed changed. These outcomes show that robust locomotion control at challenging speeds is achieved by modulating the relative contribution of muscle activations and producing less complex and wider control signals, whereas slow speeds allow for more irregular control.

In this supplementary data set we made available: a) the metadata with anonymized participant information, b) the raw EMG, c) the touchdown and lift-off timings of the recorded limb, d) the filtered and time-normalized EMG, e) the muscle synergies extracted via NMF and f) the code to process the data, including the scripts to calculate the Higuchi's fractal dimension (HFD) of motor primitives. In total, 180 trials from 30 participants are included in the supplementary data set.

The file “metadata.dat” is available in ASCII and RData format and contains:

• Code: the participant’s code
• Group: the experimental group in which the participant was involved (G1 = walking and submaximal running; G2 = submaximal and maximal running)
• Sex: the participant’s sex (M or F)
• Speeds: the type of locomotion (W for walking or R for running) and speed at which the recordings were conducted in 10*[m/s]
• Age: the participant’s age in years
• Height: the participant’s height in [cm]
• Mass: the participant’s body mass in [kg]
• PB: 100 m-personal best time (for G2).

The files containing the gait cycle breakdown are available in RData format, in the file named “CYCLE_TIMES.RData”. The files are structured as data frames with as many rows as the available number of gait cycles and two columns. The first column named “touchdown” contains the touchdown incremental times in seconds. The second column named “stance” contains the duration of each stance phase of the right foot in seconds. Each trial is saved as an element of a single R list. Trials are named like “CYCLE_TIMES_P20_R_20,” where the characters “CYCLE_TIMES” indicate that the trial contains the gait cycle breakdown times, the characters “P20” indicate the participant number (in this example the 20th), the character “R” indicate the locomotion type (W=walking, R=running), and the numbers “20” indicate the locomotion speed in 10*m/s (in this case the speed is 2.0 m/s). Please note that the following trials include less than 30 gait cycles (the actual number shown between parentheses): P16_R_83 (20), P16_R_95 (25), P17_R_28 (28), P17_R_83 (24), P17_R_95 (13), P18_R_95 (23), P19_R_95 (18), P20_R_28 (25), P20_R_42 (27), P20_R_95 (25), P22_R_28 (23), P23_R_28(29), P24_R_28 (28), P24_R_42 (29), P25_R_28 (29), P25_R_95 (28), P26_R_28 (29), P26_R_95 (28), P27_R_28 (28), P27_R_42 (29), P27_R_95 (24), P28_R_28 (29), P29_R_95 (17).

The files containing the raw, filtered and the normalized EMG data are available in RData format, in the files named “RAW_EMG.RData” and “FILT_EMG.RData”. The raw EMG files are structured as data frames with as many rows as the amount of recorded data points and 13 columns. The first column named “time” contains the incremental time in seconds. The remaining 12 columns contain the raw EMG data, named with muscle abbreviations that follow those reported above. Each trial is saved as an element of a single R list. Trials are named like “RAW_EMG_P03_R_30”, where the characters “RAW_EMG” indicate that the trial contains raw emg data, the characters “P03” indicate the participant number (in this example the 3rd), the character “R” indicate the locomotion type (see above), and the numbers “30” indicate the locomotion speed (see above). The filtered and time-normalized emg data is named, following the same rules, like “FILT_EMG_P03_R_30”.

The files containing the muscle synergies extracted from the filtered and normalized EMG data are available in RData format, in the files named “SYNS_H.RData” and “SYNS_W.RData”. The muscle synergies files are divided in motor primitives and motor modules and are presented as direct output of the factorisation and not in any functional order. Motor primitives are data frames with 6000 rows and a number of columns equal to the number of synergies (which might differ from trial to trial) plus one. The rows contain the time-dependent coefficients (motor primitives), one column for each synergy plus the time points (columns are named e.g. “time, Syn1, Syn2, Syn3”, where “Syn” is the abbreviation for “synergy”). Each gait cycle contains 200 data points, 100 for the stance and 100 for the swing phase which, multiplied by the 30 recorded cycles, result in 6000 data points distributed in as many rows. This output is transposed as compared to the one discussed in the methods section to improve user readability. Each set of motor primitives is saved as an element of a single R list. Trials are named like “SYNS_H_P12_W_07”, where the characters “SYNS_H” indicate that the trial contains motor primitive data, the characters “P12” indicate the participant number (in this example the 12th), the character “W” indicate the locomotion type (see above), and the numbers “07” indicate the speed (see above). Motor modules are data frames with 12 rows (number of recorded muscles) and a number of columns equal to the number of synergies (which might differ from trial to trial). The rows, named with muscle abbreviations that follow those reported above, contain the time-independent coefficients (motor modules), one for each synergy and for each muscle. Each set of motor modules relative to one synergy is saved as an element of a single R list. Trials are named like “SYNS_W_P22_R_20”, where the characters “SYNS_W” indicate that the trial contains motor module data, the characters “P22” indicate the participant number (in this example the 22nd), the character “W” indicates the locomotion type (see above), and the numbers “20” indicate the speed (see above). Given the nature of the NMF algorithm for the extraction of muscle synergies, the supplementary data set might show non-significant differences as compared to the one used for obtaining the results of this paper.

The files containing the HFD calculated from motor primitives are available in RData format, in the file named “HFD.RData”. HFD results are presented in a list of lists containing, for each trial, 1) the HFD, and 2) the interval time k used for the calculations. HFDs are presented as one number (mean HFD of the primitives for that trial), as are the interval times k. Trials are named like “HFD_P01_R_95”, where the characters “HFD” indicate that the trial contains HFD data, the characters “P01” indicate the participant number (in this example the 1st), the character “R” indicates the locomotion type (see above), and the numbers “95” indicate the speed (see above).

All the code used for the pre-processing of EMG data, the extraction of muscle synergies and the calculation of HFD is available in R format. Explanatory comments are profusely present throughout the script “muscle_synergies.R”.

GOLD daytime disk scan (DAY) measurements are used to derive the ratio of the column abundance of thermospheric O relative to N2, conventionally referred to as O/N2 or ΣO/N2, but abbreviated to ON2 for the GOLD data product. ON2 is derived from dayside Level 1C data after binning pixels 2x2 for approximately 68 disk scan measurements performed per day by GOLD in nominal operation.

Algorithm heritage

The disk ON2 retrieval algorithm was originally developed by Computational Physics, Inc. (CPI) for use with GUVI and SSUSI radiance images (Strickland et al., 1995). The GOLD implementation of this algorithm takes advantage of GOLD's ability to transmit the full spectrum to maximize the signal-to-noise ratio and eliminate atomic emission lines that contaminate the N2 LBH bands (e.g., N I 149.3 nm). This algorithm has been extensively documented and applied over the past several decades (e.g., Evans et al. [1995]; Christensen et al. [2003]; Strickland et al. [2004]) and Correira et al. [2021] describe the implementation used for the GOLD data.

Algorithm theoretical basis

The geophysical parameter retrieved, O/N2, is the ratio of the vertical column density of O relative to N2, defined at a standard reference N2 depth of 1017 cm-2, which is chosen to minimize uncertainty in the derived O/N2. It is retrieved directly from the ratio of the O I 135.6 nm and N2 LBH band intensities measured by GOLD on the dayside disk (DAY measurement mode). The AURIC atmospheric radiance model (Strickland et al. [1999]) is used to derive this relationship as a function of solar zenith angle and to create the look-up table (LUT) used by the algorithm.

References

Christensen, A. B., et al. (2003), Initial observations with the Global Ultraviolet Imager (GUVI) in the NASA TIMED satellite mission, J. Geophys. Res., vol. 108, NO. A12, 1451, doi:10.1029/2003JA009918.

Correira, J., Evans, J. S., Lumpe, J. D., Krywonos, A., Daniell, R., Veibell, V., et al. (2021). Thermospheric composition and solar EUV flux from the Globalscale Observations of the Limb and Disk (GOLD) mission. Journal of Geophysical Research: Space Physics, 126, e2021JA029517. https://doi.org/10.1029/2021JA029517

Evans, J. S., D. J. Strickland and R. E. Huffman (1995), Satellite remote sensing of thermospheric O/N2 and solar EUV: 2. Data analysis, J. Geophys. Res., vol. 100, NO. A7, pages 12,227-12,233.

Strickland, D. J., R. R. Meier, R. L. Walterscheid, J. D. Craven, A. B. Christensen, L. J. Paxton, D. Morrison, and G. Crowley (2004), Quiet-time seasonal behavior of the thermosphere seen in the far ultraviolet dayglow, J. Geophys. Res., vol. 109, A01302, doi:10.1029/2003JA010220.

Strickland, D.J., J. Bishop, J.S. Evans, T. Majeed, P.M. Shen, R.J. Cox, R. Link, and R.E. Huffman (1999), Atmospheric Ultraviolet Radiance Integrated Code (AURIC): theory, software architecture, inputs and selected results, JQSRT, 62, 689-742.

Strickland, D. J., J. S. Evans, and L. J. Paxton (1995), Satellite remote sensing of thermospheric O/N2 and solar EUV: 1. Theory, J. Geophys. Res., 110, A7, pages 12,217-12,226.

In comparison to proteomics, the application of two-dimensional liquid chromatography (2D LC) in the field of metabolomics is still premature. One reason might be the elevated chemical complexity and the associated challenge of selecting proper separation conditions in each dimension. As orthogonality of dimensions is a major issue, the present study aimed for the identification of successful stationary phase combinations. To determine the degree of orthogonality, first, six different metrics, namely, Pearson’s correlation coefficient (1 – |R|), the nearest-neighbor distances (H̅NND), the “asterisk equations” (AO), and surface coverage by bins (SCG), convex hulls (SCCH), and α-convex hulls (SCαH), were critically assessed by 15 artificial 2D data sets, and a systematic parameter optimization of α-convex hulls was conducted. SGG, SCαH with α = 0.1, and H̅NND generated valid results with sensitivity toward space utilization and data distribution and, therefore, were applied to pairs of experimental retention time sets obtained for >350 metabolites, selected to represent the chemical space of human urine. Normalized retention data were obtained for 23 chromatographic setups, comprising reversed-phase (RP), hydrophilic interaction liquid chromatography (HILIC), and mixed-mode separation systems with an ion exchange (IEX) contribution. As expected, no single LC setting provided separation of all considered analytes, but while conventional RP×HILIC combinations appeared rather complementary than orthogonal, the incorporation of IEX properties into the RP dimension substantially increased the 2D potential. Eventually, one of the most promising column combinations was implemented for an offline 2D LC time-of-flight mass spectrometry analysis of a lyophilized urine sample. Targeted screening resulted in a total of 164 detected metabolites and confirmed the outstanding coverage of the 2D retention space.

Petition subject: To abolish slavery in Washington D.C. and against the admission of Florida and slave states Original: http://nrs.harvard.edu/urn-3:FHCL:11857942 Date of creation: 1838-12-19 Petition location: Boston Legislator, committee, or address that the petition was sent to: George Bradburn, Nantucket Selected signatures:Samuel E. SewallCharles R. PettengillJames C. OdiornePerez GillJoseph NoyesOrin CarpenterJohn T. HiltonRobert MorrisCatherine BarbadoesChloe A. LeeWilliam C. NellEunice R. DavisPeter GrayHenry WeedenJoel W. Lewis Total signatures: 162 Legal voter signatures (males not identified as non-legal): 133 Female signatures: 12 Unidentified signatures: 17 Female only signatures: No Identifications of signatories: citizens, [females], [males of color], [females of color] Prayer format was printed vs. manuscript: Printed Signatory column format: not column separated Additional non-petition or unrelated documents available at archive: no additional documents Additional archivist notes: Appears that only the bottom two sections include females Location of the petition at the Massachusetts Archives of the Commonwealth: Senate Unpassed 1839, Docket 10525 Acknowledgements: Supported by the National Endowment for the Humanities (PW-5105612), Massachusetts Archives of the Commonwealth, Radcliffe Institute for Advanced Study at Harvard University, Center for American Political Studies at Harvard University, Institutional Development Initiative at Harvard University, and Harvard University Library.

The collection of datasets published contain the input parameters and output simulations from a single column 1D radiative transfer simulations using the Rapid Radiative Transfer Model for General Circulation Model (GCM) applications (RRTMG).

The simulations are focused on a selected case study of low-level-stratus clouds during the PS106 research cruise conducted in 2017 in the Central Arctic. The simulations are based on remote sensing observations, which were synergistically used with the Cloudnet algorithm to derive macro and microphysical properties of clouds. The atmospheric profiles of temperature, pressure, and ozone are from ERA5 (European Centre for Medium-Range Weather Forecasts (ECMWF) Re-Analysis) and values of surface albedo from CERES (Clouds and the Earth's Radiant Energy System) SYN1deg Ed. 4.1.