cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15852420
title: Codes and key processed files for Xie et al. manuscript

description: Codes and scripts used in Xie et al. manuscript

 

IMPORTANT NOTE: the biomarkers and algorithms in this repo are protected by multiple patents. The codes could only be used for academic evaluations, distributed under the [CC BY-NC-ND 4.0](https://creativecommons.org/licenses/by-nc-nd/4.0/ "CC BY-NC-ND") license. Please contact Dr. Kun Sun (sunkun@szbl.ac.cn) for enquiries about commercial usages.

 

Our programs/codes were developed on a CentOS v7.5 (64-bit, kernal version v3.10.0) machine with the following software and packages:

- Ktrim v1.6.0;

- Bowtie2 v2.3.5.1;

- Bedtools v2.29.2;

- R v4.1.2, requires "ggplot2", "ggpubr", "ggprism", "reshape2", "forcats", "ggbeeswarm", "dplyr", "cowplot", "tidyverse", "verification", "gbm", "caret", "foreach", "doParallel", "binom", and "pROC" packages.

 

CfDNA data processing

For raw cfDNA read processing, including preprocessing, alignment, and duplicate removal, please refer to Liu et al. STAR Protocols 2025 (https://www.sciencedirect.com/science/article/pii/S2666166725001637) and this https://github.com/hellosunking/STAR-Protocol-cfDNA-end-selection.

 

CfDNA feature extractions

1. For size, end selection and motif features, please refer to Ju et al. Cell Reports Methods 2024 (https://www.sciencedirect.com/science/article/pii/S2667237524002601), Liu et al. STAR Protocols 2025 (https://www.sciencedirect.com/science/article/pii/S2666166725001637), and this https://github.com/hellosunking/STAR-Protocol-cfDNA-end-selection.

2. For E-index, please refer to An et al. Nature Communications 2023 (https://www.nature.com/articles/s41467-023-35959-6) and https://github.com/hellosunking/STAR-Protocol-cfDNA-end-selection.

3. Programs for copy number analysis, including extracting mean and s.d. values from the reference panel, calculating read counts per bin and converting to Z-scores, are provided in `Copy.number` directory. We first analyzed the referece panel to calculcate mean and sd values for each 5Mb genomic bin using `1.calc.mean.sd.in.reference/process.reference.sh`, and generated `1.calc.mean.sd.in.reference/Prostate.reference.bin5M.mean.sd` file; then we calculated the Z-scores for each sample per bin using `2.calc.z.score/calc.Zscore.sh`.

4. Programs for analyzing AR-specific binding regions, including region definition and extracting cfDNA signals, are provided in `AR-specific.binding.regions` directory. You need to prepare a `bed.list` file and then run `2.profile.cfDNA/profile.cfDNA.sh` to get the features.

5. Programs for calculating RSD (relative sequencing depth) values for TEs are provided in `RSD` directory. You need to prepare a `bed.list` file and then run `calc.RSD.sh` to get the features.

 

Building PROTECTOR and PROTECTOR+ models

Programs and feature matrices for building PROTECTOR and PROTECTOR+ models are provided in `PROTECTOR.model` directory. Run `build.PROTECTOR.models.sh` to build the models and plot ROC curves.
DOI: 10.5285/5b29d98e-28b6-4ca7-89b3-57174d6b404a
title: Topography, orthoimagery, topographic change, predicted hydraulic flow, and bedload transport rates of the Bislak River, the Philippines

description: For the Bislak River, the Philippines,  this dataset contains: (i) topography and orthoimagery in 2019 and 2020; (ii) Digital Elevation Models (DEMs) of Difference; (iii) predicted depth, velocity and shear stress from HEC-RAS two-dimensional hydraulic model simulations for 10, 50 and 100 year return period flood scenarios; and (iv) calculated bedload transport for 10, 50 and 100 year return period flood scenarios.

Shear stress predictions were combined with median (D50) grain size observations to compute bedload transport rates for four different river patterns (meandering, wandering, braided, deltaic). For the 50 year return period flood event, bedload transport rates were also calculated for the D16 and D84 grain size. Geomorphic change detection was used to identify geomorphic change which took place between 2014-2019 and 2019-2020. All geospatial data are in WGS 1984 UTM Zone 51N.

This data was created as part of a numerical, two-dimensional hydraulic modelling investigation to predict patterns of flood inundation and bedload transport for the Bislak River Philippines under different flood scenarios (10-, 50- 100-year flood events).
description: An initial airborne LiDAR topographic survey of the Bislak River was completed in 2014, as reported by Rubio-Paringit and Parangit (2015). Subsequent airborne LiDAR topographic surveys were commissioned in 2019 and 2020 to provide repeat datasets. The Bislak DEMs were formed from a fusion of topographic data collected from different survey techniques (e.g. LiDAR, echo sounding and spectrally based depth mapping). HEC-RAS 2D software was used to predict inundation patterns (depth, velocity, shear stress). 

Bislak River Bedload transport rate predictions were generated using the shear stress rasters exported from HEC-RAS. Shear stress rasters were split into river morphology types (meandering, wandering, braided, deltaic).
DOI: 10.11588/duerer.online.69808bae91c04
title: Nürnberg - Dürer-Grab auf dem St. Johannisfriedhof, 193627
DOI: 10.25420/britishmuseum.31170958.v1
title: Sheep shearing

description: The audio features an interview with Petar Taukci, related to his story of sheep raising and presents the process of shearing sheep and collecting wool as raw material for the production of woolen yarn for weaving.
DOI: 10.25420/britishmuseum.31170958
title: Sheep shearing

description: The audio features an interview with Petar Taukci, related to his story of sheep raising and presents the process of shearing sheep and collecting wool as raw material for the production of woolen yarn for weaving.
DOI: 10.25420/britishmuseum.31170964
title: Field record from the interview with Peotr Taucchi

description: The field notes present the principal investigator's comments regarding the interview with Petar Taukci related to his story of sheep herding and present comments on the process of sheep shearing and wool collection as raw material for the production of woolen yarn for weaving.
DOI: 10.25420/britishmuseum.31170964.v1
title: Field record from the interview with Peotr Taucchi

description: The field notes present the principal investigator's comments regarding the interview with Petar Taukci related to his story of sheep herding and present comments on the process of sheep shearing and wool collection as raw material for the production of woolen yarn for weaving.
DOI: 10.6084/m9.figshare.30948518
title: WWTP-QA: A dataset for question answering in wastewater treatment plants in China

description: Under qa/, the policy qa/ directory contains train.json, val.json, and test.json with 19,074, 2,119, and 2,355 policy QA samples, respectively. The knowledge qa/ directory contains the same three files, with 12,168, 1,513, and 1,578 knowledge QA samples. All QA samples follow an Alpaca-style instruction-tuning format and are stored as JSON objects with three fields: instruction, input, and output. Here, instruction corresponds to the question, output corresponds to the answer, and input provides optional supplementary context (set to the empty string "" for all samples in this dataset).
DOI: 10.6084/m9.figshare.30948518.v2
title: WWTP-QA: A dataset for question answering in wastewater treatment plants in China

description: Under qa/, the policy qa/ directory contains train.json, val.json, and test.json with 19,074, 2,119, and 2,355 policy QA samples, respectively. The knowledge qa/ directory contains the same three files, with 12,168, 1,513, and 1,578 knowledge QA samples. All QA samples follow an Alpaca-style instruction-tuning format and are stored as JSON objects with three fields: instruction, input, and output. Here, instruction corresponds to the question, output corresponds to the answer, and input provides optional supplementary context (set to the empty string "" for all samples in this dataset).
DOI: 10.6084/m9.figshare.30948518.v1
title: WWTP-HDQA: A dataset for hazard detection and question answering in wastewater treatment plants in China

description: At the top level, the dataset is organized into two folders: hazard detection/ and qa/. Each folder contains subdirectories organized by individual subsets. Under hazard detection/, the secondary clarifier/ and confined space/ directories share the same file structure, each containing images.zip, labels.zip, train.txt, test.txt, and classes.txt. In secondary clarifier/, images.zip contains 1,600 secondary clarifier images and labels.zip contains the correspond?ing 1,600 YOLO-format annotation files (.txt). The files train.txt and test.txt list the image paths for the training and test sets, respectively. In confined space/, images.zip contains 3,500 confined space images and labels.zip contains the cor?responding annotations. train.txt and test.txt similarly list the image paths for the training and test sets. In both directories, classes.txt provides the label map by listing class names in the order of their numeric IDs.Under qa/, the policy qa/ directory contains train.json, val.json, and test.json with 19,074, 2,119, and 2,355 policy QA samples, respectively. The knowledge qa/ directory contains the same three files, with 12,168, 1,513, and 1,578 knowledge QA samples. All QA samples follow an Alpaca-style instruction-tuning format and are stored as JSON objects with three fields: instruction, input, and output. Here, instruction corresponds to the question, output corresponds to the answer, and input provides optional supplementary context (set to the empty string "" for all samples in this dataset).
DOI: 10.25420/britishmuseum.31171222
title: Wool cleaning

description: Audio recording of the process of documenting the process of cleaning sheep wool from various contaminants, realized by Dr. Marina Miron, the principal investigator of the project.
DOI: 10.25420/britishmuseum.31171222.v1
title: Wool cleaning

description: Audio recording of the process of documenting the process of cleaning sheep wool from various contaminants, realized by Dr. Marina Miron, the principal investigator of the project.
DOI: 10.25420/britishmuseum.31171303
title: Wool scalding

description: Audio recording of the process of documenting the process of scalding sheep wool, realized by Dr. Viorel Miron, assistant to the principal investigator.
DOI: 10.25420/britishmuseum.31171303.v1
title: Wool scalding

description: Audio recording of the process of documenting the process of scalding sheep wool, realized by Dr. Viorel Miron, assistant to the principal investigator.
DOI: 10.25420/britishmuseum.31171387
title: Wool carding

description: Documenting the wool carding process together with the women who participate in the implementation of the project stages.
DOI: 10.25420/britishmuseum.31171387.v1
title: Wool carding

description: Documenting the wool carding process together with the women who participate in the implementation of the project stages.
DOI: 10.25420/britishmuseum.31171576
title: Wool combing

description: Documenting the process of combing wool together with the women who participate in the implementation of the project stages.
DOI: 10.25420/britishmuseum.31171576.v1
title: Wool combing

description: Documenting the process of combing wool together with the women who participate in the implementation of the project stages.
DOI: 10.5284/1113005
title: HS2 Phase One: Heritage GIS Digital Archive - Raster Data

description: This collection comprises the GIS raster generated from the HS2 Phase One historic environment programme.
DOI: 10.25420/britishmuseum.31171699
title: Wool spinning

description: Documenting the spinning process of the already combed wool together with the women who participate in the implementation of the project stages.
DOI: 10.25420/britishmuseum.31171699.v1
title: Wool spinning

description: Documenting the spinning process of the already combed wool together with the women who participate in the implementation of the project stages.
DOI: 10.25420/britishmuseum.31171753
title: Passing the threads

description: Documenting the process of passing spun woolen threads from the spindle to the reel, used to form "heads" that are considered when preparing everything needed for weaving a carpet.
DOI: 10.25420/britishmuseum.31171753.v1
title: Passing the threads

description: Documenting the process of passing spun woolen threads from the spindle to the reel, used to form "heads" that are considered when preparing everything needed for weaving a carpet.
DOI: 10.25420/britishmuseum.31171792
title: Dyeing the threads

description: Documenting the process of dyeing woolen yarn with natural dyes derived from grapes, walnut leaves and beets.
DOI: 10.25420/britishmuseum.31171792.v1
title: Dyeing the threads

description: Documenting the process of dyeing woolen yarn with natural dyes derived from grapes, walnut leaves and beets.
DOI: 10.25420/britishmuseum.31171885
title: Installation of the loom

description: Audio recording of the installation of the loom with an explanation of the assembly process. Demonstration of the elements of the loom with their names. The loom was made of linden and fir wood by craftsman Dorin Onici from Tudora village, Stefan Voda district.
DOI: 10.25420/britishmuseum.31172083
title: Preparation of the warp

description: Audio recording of the process of preparing the warp for carpet weaving. Knowledge bearers demonstrate the tools and how to place them for warping the bases for carpet weaving
DOI: 10.25420/britishmuseum.31172083.v1
title: Preparation of the warp

description: Audio recording of the process of preparing the warp for carpet weaving. Knowledge bearers demonstrate the tools and how to place them for warping the bases for carpet weaving
DOI: 10.25420/britishmuseum.31172263
title: Installation of the warp

description: Audio recording of the process of passing the warp threads through the heddles, which allow the threads to be raised and lowered to create the necessary opening for weaving. After the threads are passed through the heddles, they are passed through the spaces of the comb (the heddle), which helps to keep the warp threads in the correct position and at the appropriate distances. The ends of the warp threads are tied to the weft bar of the warp (the winding roll).
DOI: 10.25420/britishmuseum.31172263.v1
title: Installation of the warp

description: Audio recording of the process of passing the warp threads through the heddles, which allow the threads to be raised and lowered to create the necessary opening for weaving. After the threads are passed through the heddles, they are passed through the spaces of the comb (the heddle), which helps to keep the warp threads in the correct position and at the appropriate distances. The ends of the warp threads are tied to the weft bar of the warp (the winding roll).
DOI: 10.5284/1113006
title: HS2 Phase One: Heritage GIS Digital Archive

description: This collection contains the GIS spatial datasets generated from the HS2 Phase One historic environment programme which, according to the HS2 Historic Environment Research and Delivery Strategy (HERDS), are the key elements in the delivery of historic environment digital data.
DOI: 10.5281/zenodo.18456717
title: Data Source for article Knitting RFID Yarns Towards Smart Fabrics for Motion Sensing and Identification
DOI: 10.5281/zenodo.18456718
title: Data Source for article Knitting RFID Yarns Towards Smart Fabrics for Motion Sensing and Identification
DOI: 10.5517/ccdc.csd.cc27zqgf
title: CCDC 2085105: Experimental Crystal Structure Determination

description: Related Article: Marek Król, Grzegorz Ślifirski, Jerzy Kleps, Piotr Podsadni, Ilona Materek, Anna E. Kozioł, Franciszek Herold
|2023|Int.J.Mol.Sci.|24|517|doi:10.3390/ijms24010517
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.31229755
title: <b>Distinct circulating microRNA signatures in female patients with central precocious puberty</b>

description: Supplementary material included in the manuscript entitled "<b>Distinct circulating microRNA signatures in female patients with central precocious puberty</b>".
DOI: 10.6084/m9.figshare.31229755.v1
title: <b>Distinct circulating microRNA signatures in female patients with central precocious puberty</b>

description: Supplementary material included in the manuscript entitled "<b>Distinct circulating microRNA signatures in female patients with central precocious puberty</b>".
DOI: 10.25420/britishmuseum.31173019
title: Winding the threads into balls

description: Audio recording of the process of winding the threads on the balls using a roundabout, a special authentic tool made of wood, old spindles are placed, which hold the tension of the threads divided into "heads". The holders of weaving knowledge from the village of Stoianovca participate in the process.
DOI: 10.25420/britishmuseum.31173019.v1
title: Winding the threads into balls

description: Audio recording of the process of winding the threads on the balls using a roundabout, a special authentic tool made of wood, old spindles are placed, which hold the tension of the threads divided into "heads". The holders of weaving knowledge from the village of Stoianovca participate in the process.
DOI: 10.25824/redu/owvwpq
title: Data for hexagonal boron nitride/graphite heterostructures studied by low energy cathodoluminescence spectroscopy

description: This dataset contains experimental data acquired during the work developed for the Master’s dissertation “Hexagonal Boron Nitride/Graphite heterostructures studied by Low Energy Cathodoluminescence Spectroscopy”. The data include scanning tunneling microscopy (STM) and atomic force microscopy (AFM) images, as well as cathodoluminescence spectra acquired in an STM-based setup. The datasets comprise raw and processed data obtained under different experimental conditions, such as variations in temperature, bias voltage, beam current, acquisition time, and spatial position. STM and AFM images can be opened using Gwyddion. Spectral data are provided in plain text (.txt) format and can be opened and analyzed using standard data analysis software, such as Origin. The data support the figures, analyses, and discussions presented in the dissertation. Detailed acquisition parameters and data processing information are provided in the accompanying README files.
DOI: 10.25420/britishmuseum.31173079
title: Winding the threads onto reels

description: Audio recording of the process of winding the threads on bobbins using a winch, a special authentic tool made of wood, 3-4 "bobbins" cut from reeds are placed in a row, on which the threads of the ball are sequentially wound. The holders of weaving knowledge from the village of Stoianovca participate in the process.
DOI: 10.25420/britishmuseum.31173079.v1
title: Winding the threads onto reels

description: Audio recording of the process of winding the threads on bobbins using a winch, a special authentic tool made of wood, 3-4 "bobbins" cut from reeds are placed in a row, on which the threads of the ball are sequentially wound. The holders of weaving knowledge from the village of Stoianovca participate in the process.
DOI: 10.25420/britishmuseum.31173136
title: First stage of weaving

description: Audio recording of the process of initial weaving of the carpet using a shuttle and threads cut from old cotton clothes. Women demonstrate the process of weaving "ribbons" with a shuttle, how the colors are combined in one "pitka". The bearers of weaving knowledge from the village of Stoianovca participate in the process.
DOI: 10.25420/britishmuseum.31173136.v1
title: First stage of weaving

description: Audio recording of the process of initial weaving of the carpet using a shuttle and threads cut from old cotton clothes. Women demonstrate the process of weaving "ribbons" with a shuttle, how the colors are combined in one "pitka". The bearers of weaving knowledge from the village of Stoianovca participate in the process.
DOI: 10.25420/britishmuseum.31173154
title: Bobbins ”kanuri” for weaving

description: Audio recording of the process of winding the skein, a dialect name, in literary language - "kanuri", which is used when weaving an ornament, which is "picked by fingers", without a shuttle. The bearers of weaving knowledge from the village of Stoianovca participate in the process.
DOI: 10.25420/britishmuseum.31173154.v1
title: Bobbins ”kanuri” for weaving

description: Audio recording of the process of winding the skein, a dialect name, in literary language - "kanuri", which is used when weaving an ornament, which is "picked by fingers", without a shuttle. The bearers of weaving knowledge from the village of Stoianovca participate in the process.
DOI: 10.25420/britishmuseum.31185574
title: Second stage of weaving

description: Audio recording of the process of weaving the ornament in the "siluchano" technique or "picked by fingers" technique, using threads in the same colors that were used in weaving "ribbons" with the shuttle. In the process of weaving the ornament, the threads are connected to prevent holes from forming in the carpet. The bearers of weaving knowledge from the village of Stoianovca participate in the process.
DOI: 10.25420/britishmuseum.31185574.v1
title: Second stage of weaving

description: Audio recording of the process of weaving the ornament in the "siluchano" technique or "picked by fingers" technique, using threads in the same colors that were used in weaving "ribbons" with the shuttle. In the process of weaving the ornament, the threads are connected to prevent holes from forming in the carpet. The bearers of weaving knowledge from the village of Stoianovca participate in the process.
DOI: 10.25420/britishmuseum.31185586
title: Finishing the carpet weaving

description: Audio recording of the process of completing the weaving of the carpet and cutting the carpet from the base. In the process of cutting the carpet, the threads are connected three by three, so as not to unravel the carpet. The bearers of weaving knowledge from the village of Stoianovca participate in the process.
DOI: 10.25420/britishmuseum.31185586.v1
title: Finishing the carpet weaving

description: Audio recording of the process of completing the weaving of the carpet and cutting the carpet from the base. In the process of cutting the carpet, the threads are connected three by three, so as not to unravel the carpet. The bearers of weaving knowledge from the village of Stoianovca participate in the process.