The various performance criteria applied in this analysis include the probability of reaching the ultimate target, the costs, elapsed times and system vulnerability resulting from any intrusion. This Excel file contains all the logical, probabilistic and statistical data entered by a user, and required for the evaluation of the criteria. It also reports the results of all the computations.

Time-Series Matrix (TSMx): A visualization tool for plotting multiscale temporal trends TSMx is an R script that was developed to facilitate multi-temporal-scale visualizations of time-series data. The script requires only a two-column CSV of years and values to plot the slope of the linear regression line for all possible year combinations from the supplied temporal range. The outputs include a time-series matrix showing slope direction based on the linear regression, slope values plotted with colors indicating magnitude, and results of a Mann-Kendall test. The start year is indicated on the y-axis and the end year is indicated on the x-axis. In the example below, the cell in the top-right corner is the direction of the slope for the temporal range 2001–2019. The red line corresponds with the temporal range 2010–2019 and an arrow is drawn from the cell that represents that range. One cell is highlighted with a black border to demonstrate how to read the chart—that cell represents the slope for the temporal range 2004–2014. This publication entry also includes an excel template that produces the same visualizations without a need to interact with any code, though minor modifications will need to be made to accommodate year ranges other than what is provided. TSMx for R was developed by Georgios Boumis; TSMx was originally conceptualized and created by Brad G. Peter in Microsoft Excel. Please refer to the associated publication: Peter, B.G., Messina, J.P., Breeze, V., Fung, C.Y., Kapoor, A. and Fan, P., 2024. Perspectives on modifiable spatiotemporal unit problems in remote sensing of agriculture: evaluating rice production in Vietnam and tools for analysis. Frontiers in Remote Sensing, 5, p.1042624. https://www.frontiersin.org/journals/remote-sensing/articles/10.3389/frsen.2024.1042624 TSMx sample chart from the supplied Excel template. Data represent the productivity of rice agriculture in Vietnam as measured via EVI (enhanced vegetation index) from the NASA MODIS data product (MOD13Q1.V006). TSMx R script: # import packages library(dplyr) library(readr) library(ggplot2) library(tibble) library(tidyr) library(forcats) library(Kendall) options(warn = -1) # disable warnings # read data (.csv file with "Year" and "Value" columns) data <- read_csv("EVI.csv") # prepare row/column names for output matrices years <- data %>% pull("Year") r.names <- years[-length(years)] c.names <- years[-1] years <- years[-length(years)] # initialize output matrices sign.matrix <- matrix(data = NA, nrow = length(years), ncol = length(years)) pval.matrix <- matrix(data = NA, nrow = length(years), ncol = length(years)) slope.matrix <- matrix(data = NA, nrow = length(years), ncol = length(years)) # function to return remaining years given a start year getRemain <- function(start.year) { years <- data %>% pull("Year") start.ind <- which(data[["Year"]] == start.year) + 1 remain <- years[start.ind:length(years)] return (remain) } # function to subset data for a start/end year combination splitData <- function(end.year, start.year) { keep <- which(data[['Year']] >= start.year & data[['Year']] <= end.year) batch <- data[keep,] return(batch) } # function to fit linear regression and return slope direction fitReg <- function(batch) { trend <- lm(Value ~ Year, data = batch) slope <- coefficients(trend)[[2]] return(sign(slope)) } # function to fit linear regression and return slope magnitude fitRegv2 <- function(batch) { trend <- lm(Value ~ Year, data = batch) slope <- coefficients(trend)[[2]] return(slope) } # function to implement Mann-Kendall (MK) trend test and return significance # the test is implemented only for n>=8 getMann <- function(batch) { if (nrow(batch) >= 8) { mk <- MannKendall(batch[['Value']]) pval <- mk[['sl']] } else { pval <- NA } return(pval) } # function to return slope direction for all combinations given a start year getSign <- function(start.year) { remaining <- getRemain(start.year) combs <- lapply(remaining, splitData, start.year = start.year) signs <- lapply(combs, fitReg) return(signs) } # function to return MK significance for all combinations given a start year getPval <- function(start.year) { remaining <- getRemain(start.year) combs <- lapply(remaining, splitData, start.year = start.year) pvals <- lapply(combs, getMann) return(pvals) } # function to return slope magnitude for all combinations given a start year getMagn <- function(start.year) { remaining <- getRemain(start.year) combs <- lapply(remaining, splitData, start.year = start.year) magns <- lapply(combs, fitRegv2) return(magns) } # retrieve slope direction, MK significance, and slope magnitude signs <- lapply(years, getSign) pvals <- lapply(years, getPval) magns <- lapply(years, getMagn) # fill-in output matrices dimension <- nrow(sign.matrix) for (i in 1:dimension) { sign.matrix[i, i:dimension] <- unlist(signs[i]) pval.matrix[i, i:dimension] <- unlist(pvals[i]) slope.matrix[i, i:dimension] <- unlist(magns[i]) } sign.matrix <-...

Excel spreadsheets by species (4 letter code is abbreviation for genus and species used in study, year 2010 or 2011 is year data collected, SH indicates data for Science Hub, date is date of file preparation). The data in a file are described in a read me file which is the first worksheet in each file. Each row in a species spreadsheet is for one plot (plant). The data themselves are in the data worksheet. One file includes a read me description of the column in the date set for chemical analysis. In this file one row is an herbicide treatment and sample for chemical analysis (if taken). This dataset is associated with the following publication: Olszyk , D., T. Pfleeger, T. Shiroyama, M. Blakely-Smith, E. Lee , and M. Plocher. Plant reproduction is altered by simulated herbicide drift toconstructed plant communities. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 36(10): 2799-2813, (2017).

Excel spreadsheet containing, in separate sheets, the underlying numerical data for figure panels 2B–2D, 3B–3D, 3F–3F, 4B–4C, 5B, 5D, S2, S3A–S3E, S3G–S3I, S4A–S4D, S5A–S5B, S5E–S5G, S6A–S6D, S7B, S7D, S7F–S7G, S8C, S9B, S9D, S10B–S10C, S11B–S11C, S11E–S11F, S12A–S12H, S13A–S13B, S14, S15. (XLSX)

Mobile Application Coverage: The 30% Curse and Ways Forward## Purpose In this artifact, we provide the information about our benchmarks used for manual and tool exploration. We include coverage results achieved by tools and human analysts as well as plots of the coverage progression over time for analysts. We further provide manual analysis results for our case study, more specifically extracted reasons for unreachability for the case study apps and extracted code-level properties, which constitute a ground truth for future work in coverage explainability. Finally, we identify a list of beyond-GUI exploration tools and categorize them for future work to take inspiration from. We are claiming available and reusable badges; the artifact is fully aligned with the results described in our paper and comprehensively documented.## ProvenanceThe paper preprint is available here: https://people.ece.ubc.ca/mjulia/publications/Mobile_Application_Coverage_ICSE2025.pdf## Data The artifact submission is organized into five parts:- 'BenchInfo' excel sheet describing our experiment dataset- 'Coverage' folder containing coverage results for tools and analysts (RQ1) - 'Reasons' excel sheet describing our manually extracted reasons for unreachability (RQ2)- 'ActivationProperties' excel sheet describing our manually extracted code properties of unreached activities (RQ3)- 'ActivationProperties-Graph' pdf which presents combinations of the extracted code properties in a graph format.- 'BeyondGUI' folder containing information about identified techniques which go beyond GUI exploration.The artifact requires about 15MB of storage.### Dataset: 'BenchInfo.xlsx'This file list the full application dataset used for experiments into three tabs: 'BenchNotGP' (apps from AndroTest dataset which are not on Google Play), 'BenchGP' (apps from AndroTest which are also on Google Play) and 'TopGP' (top ranked free apps from Google Play). Each tab contains the following information:- Application Name- Package Name- Version Used (Latest)- Original Version- # Activities- Minimum SDK- Target SDK- # Permissions (in Manifest)- List of Permissions (in Manifest)- # Features (in Manifest)- List of Features (in Manifest)The 'TopGP' sheet also includes Google-Play-specific information, namely:- Category (one of 32 app categories)- Downloads- Popularity RankThe 'BenchGP' and 'BenchNotGP' sheets also include the original version (included in the AndroTest benchmark) and the source (one of F-Droid, Github or Google Code Archives).### RQ1: 'Coverage'The 'Coverage' folder includes coverage results for tools and analysts, and is structured as follows:- 'CoverageResults.xlsx": An excel sheet containing the coverage results achieved by each human analysts and tool. - The first tab described the results over all apps for analysts combined, tools combined, and analysts + tools, which map to Table II in the paper. - Each of the following 42 tab, one per app in TopGP, marks the activities reached by Analyst 1, Analyst 2, Tool 1 (ape) and Tool 2 (fastbot), with an 'x' in the corresponding column to indicate that the activity was reached by the given agent.- 'Plots': A folder containing plots of the progressive coverage over time of analysts, split into one folder for 'Analyst1' and one for 'Analyst2'. - Each of the analysts' folder includes a subfolder per benchmark ('BenchNotGP', 'BenchGP' and 'TopGP'), containing as many png files as applications in the benchmark (respectively 47, 14 and 42 image files) named 'ANALYST_[X]_[APP_PACKAGE_NAME]'.png.### RQ2: 'Reasons.xslx'This file contains the extracted reasons for unreachability for the 11 apps manually analyzed. - The 'Summary' tab provides an overview of unreached activities per reasons over all apps and per app, which corresponds to Table III in the paper. - The following 11 tabs, each corresponding to and named after a single application, describe the reasons associated with each activity of that application. Each column corresponds to a single reason and 'x' indicates that the activity is unreached due to the reason in that column. The top row sums up the total number of activities unreached due to a given reason in each column.- The activities at the bottom which are greyed out correspond to activities that were reached during exploration, and are thus excluded from the reason extraction.### RQ3: 'ActivationProperties.xslx'This file contains the full list of activation properties extracted for each of the 185 activities analyzed for RQ2.The first half of the columns (columns C-M) correspond to the reasons (excluding Transitive, Inconclusive and No Caller) and the second half (columns N-AD) correspond to properties described in Figure 5 in the paper, namely:- Exported- Activation Location: - Code: GUI/lifecycle, Other Android or App-specific - Manifest- Activation Guards: - Enforcement: In Code or In Resources - Restriction: Mandatory or Discretionary- Data: - Type: Parameters, Execution Dependencies - Format: Primitive, Strings, ObjectsThe rows are grouped by applications, and each row correspond to an activity of that application. 'x' in a given column indicates the presence of the property in that column within the analyzed path to the activity. The third and fourth rows sums up the numbers and percentages for each property, as reported in Figure 5.### RQ3: 'ActivationProperties-Graph.pdf'This file shows combinations of the individual properties listed in 'ActivationProperties.xlsx' in a graph format, extending the combinations described in Table IV with data (types and format) and reasons for unreachability.### BeyondGUIThis folder includes:- 'ToolInfo.xlsx': an excel sheet listing the identified 22 beyond-GUI papers, the date of publication, availability, invasiveness (Source code, Bytecode, framework, OS) and their targeting strategy (None, Manual or Automated).- ToolClassification.pdf': a pdf file describing our paper selection methodology as well as a classication of the techniques in terms of Invocation Strategy, Navigation Strategy, Value Generation Strategy, and Value Generation Types. We fully introduced these categories in the pdf file.## Requirements & technology skills assumed by the reviewer evaluating the artifactThe artifact entirely consists of Excel sheets which can be opened with common Excel visualization software, i.e., Microsoft Excel, coverage plots as PNG files and PDF files. It requires about 15MB of storage in total.No other specific technology skills are required of the reviewer evaluating the artifact.

The Rcs (regulator of capsule synthesis) phosphorelay is a conserved cell envelope stress response mechanism in enterobacteria. It responds to perturbations at the cell surface and the peptidoglycan layer from a variety of sources, including antimicrobial peptides, beta-lactams, and changes in osmolarity. RcsF, an outer membrane lipoprotein, is the sensor for this pathway and activates the phosphorelay by interacting with an inner membrane protein IgaA. IgaA is essential; it negatively regulates the signaling by interacting with the phosphotransferase RcsD. We previously showed that RcsF-dependent signaling does not require the periplasmic domain of the histidine kinase RcsC and identified a dominant negative mutant of RcsD that can block signaling via increased interactions with IgaA. However, how the inducing signals are sensed and how signal is transduced to activate the transcription of the Rcs regulon remains unclear. In this study, we investigated how the Rcs cascade functions without its only known sensor, RcsF, and characterized the underlying mechanisms for three distinct RcsF-independent inducers. Previous reports showed that Rcs activity can be induced in the absence of RcsF by a loss of function mutation in the periplasmic oxidoreductase DsbA or by overexpression of the DnaK cochaperone DjlA. We identified an inner membrane protein, DrpB, as a multicopy RcsF-independent Rcs activator in E. coli. The loss of the periplasmic oxidoreductase DsbA and the overexpression of the DnaK cochaperone DjlA each trigger the Rcs cascade in the absence of RcsF by weakening IgaA-RcsD interactions in different ways. In contrast, the cell-division associated protein DrpB uniquely requires the RcsC periplasmic domain for activation; this domain is not needed for RcsF-dependent signaling. This suggests the possibility that the RcsC periplasmic domain acts as a sensor for some Rcs signals. Overall, the results add new understanding to how this complex phosphorelay can be activated by diverse mechanisms.