A symmetric systemic challenge elicits a right-biased response mediated by vasopressin signaling.
The 4 matches
- [1] § MATERIALS AND METHODS › Statistical analysis › Processing of physiological data › Stretching force ↔ force_measurement/report_SF_preprocess.Rmd, lines 21–44 · score 0.70 · stretching force measurements, loess smoothing, hind limbs, 0–10 mm, distance, WL
- [2] § MATERIALS AND METHODS › Statistical analysis › Processing of physiological data › Bayesian framework ↔ BayesianPValue.R, lines 1–50 · score 0.67 · Bayesian framework, RStan, interface, brms, emmeans
- [3] § MATERIALS AND METHODS › Statistical analysis › Processing of physiological data › Stretching force ↔ force_measurement/task_2/report_SF_AI.Rmd, lines 21–49 · score 0.64 · loess smoothing, stretching force measurements, hind limbs, 0–10 mm, distance, WL
- [4] § MATERIALS AND METHODS › Statistical analysis › Processing of physiological data › Bayesian framework ↔ force_measurement/task_1/report_SF_AI.Rmd, lines 95–143 · score 0.53 · student_t, Bayesian regression, brms, SD, chains, Predictors
Paper
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The authors' code
R Markdown · 466 lines · 12 KB · MIT · 1 match
- ---
- title: 'SF: Read and preprocess raw stretch force measurements 1 and 3'
- author: "Yaromir Kobikov <[email hidden]>"
- date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
- output:
- word_document: default
- html_document:
- toc: true
- toc_float:
- collapsed: false
- editor_options:
- chunk_output_type: inline
- ---
- ```{r setup, include=FALSE}
- source("../BayesianPValue.R")
- ```
- > **Stretch‑force experiments with symmetric WD groups.**
- > Force–distance curves from both hind limbs were recorded simultaneously after bilateral peptide injection.
- > Mechanical work for each limb (WL, WR) was obtained by integrating a loess‑smoothed force curve (span = 0.4, family = "symmetric") over 0–10 mm stretch.
- > Asymmetry was quantified as the work difference ΔW = WL − WR and the log‑ratio AI<sub>L/R</sub> = log₂(WL / WR).
- ## Read stretch force (SF) data
- Read raw sampled forces and match them with rat's descriptions
- ```{r config_vars, echo=FALSE}
- PATH_DIR_ROOT <- "../data"
- PATH_FOLDER_FORCE_MEASUREMENT <- "../data/Force-WD-20240513/"
- PATH_SF_DATA_CSV <- paste0(PATH_FOLDER_FORCE_MEASUREMENT, "sf_source_data_20260125.csv")
- FILE_NAME = '-ForceValues.xlsx'
- PATTERN = paste0('*', FILE_NAME)
- DESCRIPTION_FILE_NAME <- "WD_PA 25 12 26_1_v2.xlsx"
- SHEET <- "DATA_25 12 25" # for description
- TEST_NUM_FILES <- 55
- ```
- ```{r}
- correctDate <- Vectorize(function(date, pattern, sep="-") {
- dateSplit <- str_split(date, pattern)[[1]]
- return(paste0(dateSplit[1], sep, dateSplit[2], sep, dateSplit[3]))
- })
- read.StretchForce <- function(RatFile, show=TRUE) {
- ratName <- sub(FILE_NAME, "", basename(RatFile), fixed = TRUE)
- ratNum <- str_split(ratName, "SDU")[[1]][2]
- ratName <- paste0("SDU", "-", ratNum)
- sheetNames <- RatFile %>%
- excel_sheets() %>%
- as_tibble %>%
- filter(grepl(pattern = "F([0-9]+)", value))
- df <-
- map_df(
- .x = sheetNames$value,
- ~read_excel(path = RatFile, sheet = .x, range = cell_cols("A:C")),
- .id = "replication"
- ) %>%
- mutate(RatID = ratName) %>%
- relocate(RatID, .before = replication)
- if(show) print(paste0(ratName, " -> ", toString(count(sheetNames)$n), ", ", count(df)$n))
- return(df)
- }
- my.rwData <- function() {
- # if(file.exists(PATH_SF_DATA_CSV)) {
- # print(paste0("File ", " - ", PATH_SF_DATA_CSV, " - exists"))
- # return(read_csv(PATH_SF_DATA_CSV, show_col_types = FALSE))
- # }
- print("In process...")
- sf <-
- map_df(
- .x = list.files(path = PATH_FOLDER_FORCE_MEASUREMENT, pattern = PATTERN, full.names = TRUE),
- ~read.StretchForce(.x)
- )
- if(length(unique(sf$RatID)) == TEST_NUM_FILES) print(paste0(TEST_NUM_FILES, " - ", "OK"))
- # match rat's description with raw force measurements
- rats_description <-
- file.path(PATH_DIR_ROOT, DESCRIPTION_FILE_NAME) %>%
- read_excel(SHEET, .name_repair = "universal", na = c("", "NA", "NULL")) %>%
- rename(
- BW_pre = BW..pre.,
- BW_post = BW..post.
- # Measurement.1 = Measurement.1,
- # Measurement.3 = Measurement.3
- ) %>%
- select(
- RatID,
- Measurement1,
- Measurement3,
- BW_pre, BW_post,
- MP.1.1, MP.1.2, MP.1.3,
- MP.3.1, MP.3.2, MP.3.3
- ) %>%
- rename_with(
- ~ sub("^MP\\.(\\d+)\\.(\\d+)$", "PA\\1.\\2", .x),
- .cols = matches("^MP\\.(1|3)\\.(1|2|3)$")
- ) %>%
- mutate(RatID = factor(RatID),
- Trt1 = factor(Measurement1, c("24H WD", "Control 1")),
- Trt3 = factor(Measurement3, c("Sp", "Control 1", "Control 2", "Control 3", "SSR", "Conivaptan"))
- ) %>%
- filter(
- (!is.na(Trt1) & Trt1 != "") |
- (!is.na(Trt3) & Trt3 != "")
- )
- print(rats_description, n=100)
- #
- # print(rats_description %>%
- # count(Measurement3, sort = TRUE) %>%
- # filter(grepl("Coniv", Measurement3, ignore.case = TRUE)))
- sf <-
- merge(sf, rats_description, by = "RatID", all.x = TRUE, all.y = TRUE, sort = FALSE) %>%
- select(-`s"Time"`) %>%
- mutate(rep_i = as.integer(replication)) %>%
- # Decide which reps correspond to 24H and 2_3H based on rep count per RatID
- group_by(RatID) %>%
- mutate(
- n_rep = n_distinct(rep_i),
- # 24H always uses MP1.1-1.3 => reps 1:3 (if present)
- use_24H = rep_i %in% 1:3,
- # 2_3H uses MP3.1-3.3, but its rep positions depend on n_rep
- use_2_3H = case_when(
- n_rep %in% c(3, 6, 12) ~ FALSE, # no MP3.1-3.3
- n_rep %in% c(9, 14, 15) ~ rep_i %in% 7:9, # MP3.1-3.3
- n_rep >= 30 ~ rep_i %in% 13:15, # MP3.1-3.3
- # fallback for "other" counts (e.g., 18, 36, 37...):
- # if those reps exist, use them
- TRUE ~ case_when(
- all(13:15 %in% unique(rep_i)) ~ rep_i %in% 13:15,
- all(7:9 %in% unique(rep_i)) ~ rep_i %in% 7:9,
- TRUE ~ FALSE
- )
- ),
- Period = case_when(
- use_24H ~ "24H",
- use_2_3H ~ "2_3H",
- TRUE ~ NA_character_
- ),
- Period = factor(Period, levels = c("24H", "2_3H")),
- Trt = case_when(
- use_24H ~ Trt1,
- use_2_3H ~ Trt3,
- TRUE ~ NA
- )
- ) %>%
- ungroup() %>%
- # keep only selected reps
- filter(!is.na(Period)) %>%
- pivot_longer(
- cols = c("Left", "Right"),
- names_to = "Side",
- values_to = "SF"
- ) %>%
- mutate(SF = SF * (-1)) %>%
- # keep only rows where treatment exists for that period
- filter(!is.na(Trt), Trt != "")
- write_csv(x = sf, PATH_SF_DATA_CSV)
- return(sf)
- }
- ```
- ```{r input, results='hide'}
- myspan <- 0.4
- myname0 <- paste0("SF loess(symmetric span=", myspan, ")")
- data <- my.rwData()
- sf <-
- data %>%
- rename(repN = replication) %>%
- mutate(
- RatID = factor(RatID),
- # MS = factor(MS, c("Left", "Right"), c("L", "R")),
- # Later = factor(OperationSide == MS, c(FALSE, TRUE), c("Contra", "Ipsi")),
- # Trt = paste0(Trt, ".", OperationSide),
- Trt = factor(Trt),
- repN = factor(as.integer(repN))
- )
- # sf[!complete.cases(sf), c("RatID", "Trt", "repN", "SF")] # Any unmatched rats? Any unmeasured forces?
- ```
- The group sizes are (distinct rats only, same rats with different stimulation locations are counted as duplicates)
- ```{r dataset_n, echo=FALSE}
- d.sum <- sf %>%
- arrange(Trt, Period) %>%
- group_by(Trt, Period) %>%
- summarise(rats = length(unique(RatID))) %>%
- pivot_wider(names_from=c(Trt), values_from = rats)
- d.sum %>%
- flextable %>%
- fontsize(part = "header", size = 9) %>%
- autofit
- ```
- ## SF, 0-2 sec: Visual inspection of smoothing
- <!-- Filter 0-2 sec measurements, taking extra 0.5s for better smoothing. -->
- ```{r SF_combo_dta}
- mydta <- sf %>%
- filter(!is.na(SF)) %>%
- droplevels(.) %>%
- mutate(figName = paste0(RatID, ", ", Trt, ", replicate ", repN)) %>%
- select(figName, Period, Time, Side, Trt, SF) %>%
- # filter(figName == "SDU-115, 3h.BNI.L, replicate 12") %>%
- group_by(figName)
- ```
- Stretch force figure combining Contra, Ipsi and their difference.
- ```{r example_12_rep, echo=FALSE, fig.width=12, fig.height=8}
- myspan <- 0.4
- name_fig <- "SDU-005, 24H WD, replicate 1"
- name_plt <- paste0("raw ", name_fig)
- plt[[name_plt]] <-
- mydta %>%
- filter( figName == name_fig) %>%
- # pivot_wider(names_from = Later, values_from = SF) %>%
- # mutate(
- # "Contra - Ipsi" = Contra - Ipsi
- # ) %>%
- # pivot_longer(c("Contra", "Ipsi", "Contra - Ipsi"), names_to = "Limbs", values_to = "SF") %>%
- ggplot(aes(x = Time, y = SF, group = Side, col = Side)) +
- geom_line() +
- geom_smooth(
- formula = y ~ x,
- aes(col = paste0("loess ", myspan)),
- method ="loess",
- span = myspan,
- se = FALSE,
- method.args = list(family="symmetric")
- ) +
- labs(
- title = paste0(myname0, ", ", name_fig),
- x = "Time (sec)",
- y = "Stretching force (mg)"
- )
- print(plt[[name_plt]])
- ```
- ```{r}
- doc <- read_pptx()
- for(nm in names(plt)) {
- doc <- doc %>%
- add_slide(
- layout = "Title and Content",
- master = "Office Theme"
- ) %>%
- ph_with(
- value = rvg::dml(ggobj = plt[[nm]]),
- location = ph_location_type(
- type = "body"
- #, width=S_width,
- # height=S_height
- ),
- bg = "transparent"
- ) %>%
- ph_with(
- value = nm,
- location = ph_location_type(type = "title")
- )
- }
- doc %>% print(target = paste0("SF loess(symmetric span0.4)", ".pptx"))
- ```
- Visually check the smoothing by loess(), varying the "span" to see if alternatives are better than our choice.
- ```{r check_loess, include=FALSE}
- myspan.test <- 0.4
- junk <- mydta %>%
- group_map( ~{
- theName <- paste(.y)
- ggplot(data=.x, aes(y = SF, x = Time, group = Side, col = Side)) +
- geom_line() +
- geom_smooth(formula = y ~ x, aes(col = paste0(myspan.test + 0.1)), method="loess", span = myspan.test + 0.1, se=FALSE, method.args=list(family="symmetric")) +
- geom_smooth(formula = y ~ x, aes(col = paste0(myspan.test - 0.1)), method="loess", span = myspan.test - 0.1, se=FALSE, method.args=list(family="symmetric")) +
- geom_smooth(formula = y ~ x, aes(col = paste0(myspan.test)), method="loess", span=myspan.test, se=FALSE, method.args=list(family="symmetric")) +
- # theme(legend.position = "none") +
- labs(title=paste(myname0, theName), x="Time (sec)", y="Stretching force (mg)")
- } ) %>%
- setNames(unique(sort(mydta$figName)))
- mydta %>% n_groups()
- ```
- ```{r write_pptx_check_loess, echo=FALSE, fig.width=12, fig.height=8}
- for(nm in unique(mydta$figName)) {
- print(junk[[nm]])
- }
- doc <- read_pptx()
- for(nm in unique(mydta$figName)) {
- doc <- doc %>%
- add_slide(
- layout = "Title and Content",
- master = "Office Theme"
- ) %>%
- ph_with(
- value = rvg::dml(ggobj = junk[[nm]]),
- location = ph_location_type(
- type = "body"
- #, width=S_width,
- # height=S_height
- ),
- bg = "transparent"
- ) %>%
- ph_with(
- value = nm,
- location = ph_location_type(type = "title")
- )
- }
- doc %>% print(target = paste0(myname0, "_0.4_.pptx"))
- ```
- Define smoother for all Time points.
- ```{r smoother_W_AI}
- # 0-1 0.4-1 1-2 0-2 0.4-2
- smoother_W <- function(dta, ...) {
- # dtaF <- dta %>% filter(Time < 10.5, !is.na(SF))
- dtaF <- dta %>% filter(!is.na(SF))
- if(nrow(dtaF) < 1 | ncol(dtaF) < 2) {
- print(dta)
- return(data.frame())
- }
- my.sm <- loess(SF~Time, data=dtaF, family="symmetric", span=myspan)
- i_0_1 <- integrate(function(x) predict(my.sm, newdata=x), 0, 1)
- i_0_4_1 <- integrate(function(x) predict(my.sm, newdata=x), 0.4, 1)
- i_1_2 <- integrate(function(x) predict(my.sm, newdata=x), 1, 2)
- i_0_2 <- integrate(function(x) predict(my.sm, newdata=x), 0, 2)
- i_0_4_2 <- integrate(function(x) predict(my.sm, newdata=x), 0.4, 2)
- data.frame(
- dT = c(
- "T_0_1",
- "T_0.4_1",
- "T_1_2",
- "T_0_2",
- "T_0.4_2"
- ),
- W = c(
- i_0_1$value,
- i_0_4_1$value,
- i_1_2$value,
- i_0_2$value,
- i_0_4_2$value
- )
- )
- }
- ```
- Remove unneded columns from SF dataset
- ```{r clean_SF}
- sf_ai_dw <-
- sf %>%
- # filter(RatID == "TBI-250", Trt %in% c("UBI.R")) %>%
- select(Trt, Period, RatID, repN, Side, Time, SF) %>%
- ungroup %>%
- arrange(Trt, RatID, repN, Side, Time)
- ```
- Compute work (W) as integrals (0-1 sec, 0.4-1 sec, ...) of smoothed force measurements. dW = W_Left - W_Right
- ```{r compute_W_LR}
- sf_LR_dW <- sf_ai_dw %>%
- group_by(Trt, Period, RatID, repN) %>%
- pivot_wider(names_from = Side, values_from = SF) %>%
- # spread(MS, SF) %>%
- mutate( SF = Left - Right ) %>%
- group_modify(smoother_W) %>%
- ungroup %>%
- droplevels(.)
- ```
- Compute AI = log2(Left/Right) using integrals (0-1 sec, 0.4-1 sec, ...) of smoothed force measurements.
- ```{r compute_AI_LR}
- sf_LR_AI <- sf_ai_dw %>%
- group_by(Trt, Period, RatID, repN, Side) %>%
- group_modify(smoother_W) %>%
- ungroup %>%
- group_by(RatID, Trt, repN, dT) %>%
- pivot_wider(names_from = Side, values_from = W) %>%
- # spread(MS, W) %>%
- mutate( AI = log2( Left / Right ) ) %>%
- ungroup %>%
- droplevels(.)
- ```
- Save preprocessed SF
- ```{r smooth}
- myname <- paste0("SF Sp 0-1 0.4-1 1-2 0-2 0.4-2 loess(symmetric span", myspan, ")")
- save(sf_LR_dW, sf_LR_AI, sf, file=paste0(myname, "_rats.RData"))
- ```
report_SF_preprocess.Rmd at commit e5adf0d, under MIT · at the source
Overview
- Department of Pharmaceutical Biosciences Uppsala University Uppsala Sweden
- Department of Molecular Medicine University of Southern Denmark Odense M Denmark
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory Uppsala University Uppsala Sweden
- Neuronano Research Center, Department of Experimental Medical Science Lund University Lund Sweden
Abstract
Bilaterian animals exhibit functional asymmetry—population‐lev
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 4 matches between paragraphs and lines of code.
YaromirKo/biostatistics-wd
e5adf0d53cbc24f9a6c30099b0874064dcdb87ea, 31 August 2026Availability: 1 check, the latest on 26 September 2026: the link answers
- 26 September 2026: the link answers
25 files
- 1_task_mpa_pas_pa/
report_MPA_wd_vs_control , R, 433 lines.Rmd - 1_task_mpa_pas_pa/
report_PAS_wd_control.Rm , R, 417 linesd - 1_task_mpa_pas_pa/
report_Pa_wd_control.Rmd , R, 413 lines - 2_task_mpa_pas/
report_MPA_wd_ssr_coniva , R, 434 linesptan.Rmd - 2_task_mpa_pas/
report_MPA_wd_ssr_coniva , R, 434 linesptan_control_2_3.Rmd - 2_task_mpa_pas/
report_PAS_wd_ssr_coniva , R, 436 linesptan.Rmd - 2_task_mpa_pas/
report_PAS_wd_ssr_coniva , R, 436 linesptan_control_2_3.Rmd - 3_task_mpa_pas/
report_MPA_wd_sp.Rmd , R, 431 lines - 3_task_mpa_pas/
report_MPA_wd_sp_control , R, 431 lines_2_3.Rmd - 3_task_mpa_pas/
report_PAS_wd_sp.Rmd , R, 433 lines - 3_task_mpa_pas/
report_PAS_wd_sp_control , R, 434 lines_2_3.Rmd - BayesianPValue.R, R, 149 lines, 1 match
- force_measurement/
report_SF_preprocess.Rmd , R, 466 lines, 1 match - force_measurement/
task_1/ , R, 328 lines, 1 matchreport_SF_AI.Rmd - force_measurement/
task_1/ , R, 349 linesreport_SF_dw.Rmd - force_measurement/
task_2/ , R, 327 lines, 1 matchreport_SF_AI.Rmd - force_measurement/
task_2/ , R, 346 linesreport_SF_dw.Rmd - force_measurement/
task_2_2/ , R, 335 linesreport_SF_AI.Rmd - force_measurement/
task_2_2/ , R, 357 linesreport_SF_dw.Rmd - force_measurement/
task_3/ , R, 336 linesreport_SF_AI.Rmd - force_measurement/
task_3/ , R, 355 linesreport_SF_dw.Rmd - force_measurement/
task_3_2/ , R, 336 linesreport_SF_AI.Rmd - force_measurement/
task_3_2/ , R, 355 linesreport_SF_dw.Rmd - LICENSE, License, 21 lines
- README.md, Text, 187 lines
The paper's code and data availability statement is in the Data section.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 23 scripts, each with its path and the digest of its content;
- 4 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Data availability statement
The data that support the findings of this study are available on request from the corresponding author. Data supporting the findings of this study and all codes used for analysis are available within the article, its Supporting Information and on https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 3, 28 September 2026
- Publisher: n/a → Wiley
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 11 authors, 5 keywords, 15 MeSH terms, 2 funders, 66 references.
Cite
This paper
Watanabe, H., Kobikov, Y., Mohamed, S. Y., Rich, K., Sarkisyan, D., Nosova, O., Grönbladh, A., Hallberg, M., Schouenborg, J., Bakalkin, G., & Zhang, M. (2026). A symmetric systemic challenge elicits a right-biased response mediated by vasopressin signaling. Journal of neuroendocrinology, 38(9), e70257. https://
BibTeX
@article{watanabe2026sym
author = {Watanabe, Hiroyuki and Kobikov, Yaromir and Mohamed, Sara Yusuf and Rich, Karen and Sarkisyan, Daniil and Nosova, Olga and Grönbladh, Alfhild and Hallberg, Mathias and Schouenborg, Jens and Bakalkin, Georgy and Zhang, Mengliang},
title = {{A symmetric systemic challenge elicits a right-biased response mediated by vasopressin signaling}},
journal = {Journal of neuroendocrinology},
year = {2026},
month = sep,
volume = {38},
number = {9},
pages = {e70257},
publisher = {Wiley},
issn = {0953-8194},
doi = {10.1111/
url = {https://
pmid = {42702826},
pmcid = {PMC13547646}
}
RIS
TY - JOUR
AU - Watanabe, Hiroyuki
AU - Kobikov, Yaromir
AU - Mohamed, Sara Yusuf
AU - Rich, Karen
AU - Sarkisyan, Daniil
AU - Nosova, Olga
AU - Grönbladh, Alfhild
AU - Hallberg, Mathias
AU - Schouenborg, Jens
AU - Bakalkin, Georgy
AU - Zhang, Mengliang
TI - A symmetric systemic challenge elicits a right-biased response mediated by vasopressin signaling
T2 - Journal of neuroendocrinology
J2 - J Neuroendocrinol
PY - 2026
DA - 2026/
VL - 38
IS - 9
SP - e70257
SN - 0953-8194
PB - Wiley
DO - 10.1111/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1111/
"type": "article-journal",
"title": "A symmetric systemic challenge elicits a right-biased response mediated by vasopressin signaling",
"container-title": "Journal of neuroendocrinology",
"author": [
{
"family": "Watanabe",
"given": "Hiroyuki"
},
{
"family": "Kobikov",
"given": "Yaromir"
},
{
"family": "Mohamed",
"given": "Sara Yusuf"
},
{
"family": "Rich",
"given": "Karen"
},
{
"family": "Sarkisyan",
"given": "Daniil"
},
{
"family": "Nosova",
"given": "Olga"
},
{
"family": "Grönbladh",
"given": "Alfhild"
},
{
"family": "Hallberg",
"given": "Mathias"
},
{
"family": "Schouenborg",
"given": "Jens"
},
{
"family": "Bakalkin",
"given": "Georgy"
},
{
"family": "Zhang",
"given": "Mengliang"
}
],
"container-title-short":
"volume": "38",
"issue": "9",
"page": "e70257",
"DOI": "10.1111/
"PMID": "42702826",
"PMCID": "PMC13547646",
"ISSN": "0953-8194",
"publisher": "Wiley",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
9,
1
]
]
}
}
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