cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26977117.v1
title: Supplementary Material for: HLTF/SERPINE1 Axis Plays a Crucial Pro-oncogenic Role in the Progression from Cervical Precancerous Lesions to Cervical Carcinoma in Vitro

description: Objectives: Cervical carcinoma (CC) is prevalent among women worldwide with increasing risk. Finding effective methods for treating CC is of utmost importance. The aim of this study was to investigate the effect of SERPINE1 on the progression of cervical precancerous lesions to CC.
Design: Transcriptome sequencing and in vitro cell line studies.
Participants/Materials: Cervical precancerous lesions and CC samples and human cervical epithelial immortalized cell line H8, human CC cell lines HeLa and CaSki.
Setting and Methods: Next-generation sequencing was applied to identify 100 differentially expressed genes (DEGs) from cervical precancerous lesions and CC samples. With the application of the Search Tool for the Retrieval of Interacting Genes (STRING) database, we carried out the protein-protein interaction (PPI) network analysis, thus screening out serine protease inhibitor clade E member 1 (SERPINE1) with significant upregulation in CC cells. The helicase-like transcription factor (HLTF) was predicted as the upstream transcription factor using Human Transcription Factor Database (HumanTFDB). The chromatin immunoprecipitation (ChIP) experiment was conducted to validate the interaction between SERPINE1 and HLTF. The immunohistochemistry (IHC) was employed to determine the expression of SERPINE1 and HLTF in CC tissues. Following the upregulation or downregulation of SERPINE1 and HLTF, the Real-Time Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) was carried out to assess mRNA expression levels of SERPINE1 and HLTF in cells. Cell viability, migration, and invasion were evaluated using MTT assay, cell scratch assay, and Transwell assay, respectively. Western blot (WB) analysis was conducted to assess changes in the expression levels of matrix metalloproteinases and proteins related to epithelial-mesenchymal transition (EMT).
Results: The ChIP experiment confirmed the interaction between HLTF and SERPINE1. HLTF and SERPINE1 were upregulated in CC tissues and cells, and silencing SERPINE1 inhibited the EMT process and viability, migration, and invasion of CC cells. However, overexpression of SERPINE1 in CC cells showed the opposite trend. Rescue experiments demonstrated that silencing HLTF repressed CC cell viability, migration, and invasion, which could be restored by overexpressing SERPINE1.
Limitations: The effect of the HLTF/SERPINE1 axis on CC malignant progression has not been confirmed by in vivo experiments.
Conclusion: HLTF transcriptionally activates SERPINE1, promoting the progression from cervical precancerous lesions to CC.
DOI: 10.6084/m9.figshare.28226720.v1
title: Supplementary Material for: Development of macular atrophy after macular hole surgery in an eye with retinitis pigmentosa

description: Introduction
Macular hole is a rare complication that occurs in patients with retinitis pigmentosa, significantly reducing visual acuity. Although vitreous surgery for macular hole yields favorable outcomes, macular atrophy after surgery has been reported. We report the second case of retinitis pigmentosa in a patient who developed a 13-year progressive macular atrophy after macular hole surgery.
Case Presentation
A 64-year-old Japanese woman, who had been diagnosed with retinitis pigmentosa at 52 years of age, presented to our hospital with blurred vision in the left eye. Phacovitrectomy of the left eye was performed after a full-thickness macular hole was revealed by optical coherence tomography. We stained the internal limiting membrane during surgery using 0.05% indocyanine green and peeled it around the macular hole. Nevertheless, slight atrophy of the retinal pigment epithelium appeared in the left macula 17 days after surgery. The macular hole closed 1 year after surgery, and the macular atrophy gradually became more apparent and enlarged. Thirteen years later, atrophy had expanded to 2.5-disc diameters, and the left decimal best-corrected visual acuity was 0.1; no macular degeneration appeared in the right eye. Genetic examination revealed compound heterozygous variants in the EYS gene. 
Discussion　
Macular atrophy can develop after dye-assisted macular hole surgery for patients with retinitis pigmentosa. Potential risk factors for the development of postoperative macular atrophy include dye toxicity, light toxicity, surgical intervention in the macula, postoperative inflammation, and genotype. However, the exact cause of atrophy remains uncertain.
DOI: 10.17632/zgtryg9wvg
title: EEG MI-BCI Mouse Cursor Dataset

description: This dataset contains EEG recordings collected for research on brain-computer interface (BCI) applications, specifically for controlling a mouse cursor using motor imagery (MI). The data was recorded using an Emotiv Epoc+ 14 channel headset. Volounteers performed 1) left-hand movement, 2) right-hand movement and 3) break tasks. The data were recorded in Biomedical Instrumentation and Signal Processing Laboratory (BISPL) at Independent University, Bangladesh.
DOI: 10.17632/7fnsj6hhp5
title: KumbhPulse: Echoes of Emotion from the Divine Gathering

description: This Dataset comprises reviews and comments on the Kumbh Mela. It contains 49,425 multilingual end-user-generated posts gathered from social media websites X (then Twitter) and YouTube, across Kumbh Mela festivities from 2013-2025, Except 2014, 2015, and 2020. Every record has sentiment-labeled Hindi, English, Marathi, and other regional Indian dialects content normalized to English using Google Translate API. The comments were scraped with Selenium For X (Formerly Twitter ) and YouTube API, and annotated with the VADER sentiment analysis tool into Positive, Neutral, or Negative classes. Engagement metrics such as likes and timestamps are included for temporal and behavioral analysis.

Data is saved in structured .CSV files divided by year and contain anonymized user IDs, content of comments, likes, post date and time, and sentiment labels. This dataset can be used for sentiment trend analysis, tracking of public opinion, and multilingual NLP uses during major cultural events. With its status as one of the first open datasets on the emotional trace of the Kumbh Mela, it is an essential asset for scholars of digital sociology, AI, sentiment computing, and public engagement analysis.
DOI: 10.6084/m9.figshare.21803565.v2
title: Online Appendix

description: In online Appendix, we provide an example of simulated trajectories with known coefficient of habitat selection (time-varying) as well as the simulated habitat used for the movement simulation. <br> In Appendix_function, we provide multiples functions usefull to run time-varying HSA, and apply them on an example in Run_me.R file.
DOI: 10.6084/m9.figshare.24570104.v1
title: marine metaproteome

description: Data description:<br>ProteinSequence.zip contains 3 fasta files used for metaproteomic analysis: euk.db.fasta.gz: eukaryotic protein sequence predicted from metatranscriptomic assembly (&gt;0.8um) prok.db.fasta.gz: prokaryotic protein sequence predicted from metagenomic assembly (0.2-3um) euk.db.fasta.gz: viral protein sequence predicted from metagenomic assembly (&lt;0.2um)<br>KO_rel_abundance_table.zip contains 2 tables: ko.all.csv: relative abundance of KOs in metagenomic, metatranscriptomic and metaproteomic dataset ko.metaP.csv: relative abundance of KOs in metaproteomic dataset<br>MetaproteomicsResult.zip contains 5 files: 1_identifiedprotein.fasta: protein sequences identified in the analysis 2_taxonomy.csv: taxonomy classification of identified proteins 3_function.csv: functional annotation of identified proteins 4_abundance.csv: abundance (Peak area and NAAF value) of identified proteins in all samples. 5_metabolic_gene_annotation.csv annotation of metabolic genes involved in respiration, nitrification and denitrification
DOI: 10.17632/vxcv2dxscw
title: Seabed images and programs  for a Deep Learning training and testing on the MAR

description: 
1. Datasets.zip
This collection of images were part of that  used as training and testing datasets for a  a Deep Learning on the MAR in a paper that will published in Ocean Engineering recently.

2. Deep Learning programs.zip
This file includes the program and related modules of the ResNet network model used. The file named train.py can be used for training, extract image features, and finally output weight information. 
Resnet34.pth is the pre-training weight. predict.py can be used to classify seabed images.

3. Weights.zip 
This file is the weight information output after the training, where Data_set_M.pth is the result of this example data set, and Data_set_L.pth is the final result of this experiment.
DOI: 10.17632/wfzpdmc5vx
title: Banana_Leaf_Disease_Dataset_Bangladesh

description: The Banana leaf disease dataset dataset comprises 424 images of banana leaves collected in Noakhali, Rangamati and Bandarban,Chittagong, Bangladesh. The dataset’s primary directory is named "Banana_Leaf_Disease_Dataset_Bangladesh" across four classes Cordana, healthy (fresh), sigatoka, and pestalotiopsis. The raw images were initially captured in different formats (JPG, PNG, JPEG) and varied resolutions but were resized to a uniform 320x427 pixels at 72 dpi for model compatibility. The dataset was designed to support deep learning-based classification and detection models. Images were captured using a Xiaomi M2006C3MG mobile camera under natural lighting conditions to replicate real-world agricultural settings. The photographs vary in format, including JPG, PNG, and JPEG, with original dimensions of 320x500, 750x1000, and 2448x3264 pixels at a horizontal and vertical resolution of 96 dpi. To ensure consistency and model compatibility, all images were resized to 320x427 pixels at 72 dpi. Each image was checked for clarity, and samples were selected to represent variations in disease severity.
DOI: 10.17632/7h57yn2cwb
title: Data and analysis for: Abiotic characteristics and organic constituents of oviposition sites that attract gravid female stable flies, Stomoxys calcitrans, and induce oviposition

description: This dataset is supplementary to the manuscript "Abiotic characteristics and organic constituents of oviposition sites that attract gravid female stable flies, Stomoxys calcitrans, and induce oviposition." This manuscript investigated the attractiveness and oviposition induction ability of several substrates and aimed to determine the key constituent(s) of a highly effective one.

Prior to opening any subfolders, use the .Rproj file titled "Oviposition paper data publication.Rproj" to open RStudio and run all the subsequent .R files.

Included in this dataset are: 1) raw data for numbers of flies attracted to the various substrates in head-to-head comparisons, 2) raw data for the numbers of eggs laid on the various substrates, 3) the Rcode used to convert the count data into proportions which were then compared for each experiment, and in some cases, across experiments, as well as to generate figures 2-7 in the text, and 4) the resulting figures 2-7. The "Read me.txt" files in each subfolder contain more detailed information for each set of experiments.

Note: please refer to the "Read me.txt" file in the main folder for full descriptions of each subfolder.

Article Abstract:
"Gravid female stable flies, Stomoxys calcitrans (Linnaeus) (Diptera: Muscidae), oviposit in many types of organic substrates, including animal feces, but there is limited information as to which factors mediate attraction and oviposition. Here, we (1) tested effects of oviposition site moisture and odor on attraction and oviposition by flies, and (2) selected a highly effective oviposition site (fly rearing medium) to determine the key constituent(s) that mediate(s) attraction and oviposition. In moving- and still-air olfactometers as well as large laboratory rooms, we show that (i) odor and moisture of oviposition sites play distinguishable functional roles in the close range attraction of gravid female flies and their propensity to oviposit, (ii) rearing medium containing fish food, wheat bran, wood chips and a watery solution of ammonium bicarbonate (releasing NH3 and CO2) is a more appealing oviposition site to female flies than cow feces, (iii) ammonium bicarbonate in this medium is the key constituent for stable fly attraction and oviposition, (iv) NH3 alone or in combination with CO2, but not CO2 alone, attracts stable flies and induces oviposition, and (v) NH3/CO2 and fish food in combination are more attractive than NH3/CO2 or fish food alone. With fecal bacteria reportedly emitting NH3, and with stable fly larval development reportedly reliant on (fecal) microbes, it follows that gravid female flies may be guided by airborne microbe-derived cues originating from prospective oviposition sites. Isolating these microbes and identifying their odorants could enable the development of a synthetic odor blend which, coupled with NH3 and CO2, may prove highly effective as a trap lure to capture gravid female stable flies."
DOI: 10.17632/7hdbzkk672
title: Data for: The Formative Phase of the Helmand Civilization, Iran and Afghanistan: New Data from Compositional Analysis of Ceramics from Shahr-i Sokhta and Mundigak.

description: Ppm data from INAA of ceramics from the archaeological sites of Shahr-i Sokhta, Iran and Mundigak, Afghanistan.
DOI: 10.6084/m9.figshare.20056505.v1
title: PLoS One article supplementary data files

description: content-based image retrieval dataset supplementary files
DOI: 10.17632/jwsn7tfbrp
title: Concrete Crack Segmentation Dataset

description: The dataset includes 458 hi-res images together with their alpha maps (BW) indicating the crack presence. The ground truth for semantic segmentation has two classes to conduct binary pixelwise classification. The photos are captured in various buildings located in Middle East Technical University. You can access a larger dataset containing images with 227x227 px dimensions for classification which are produced from this dataset from http://dx.doi.org/10.17632/5y9wdsg2zt.1 .
DOI: 10.17632/37v2sbc8j4
title: Data sets on soil bacteria, enzyme activities, physical and chemical properties for different land use types and soil depths

description: The data contain three types of core indicators: 
(1) Soil physicochemical properties: including pH, bulk density (BD), soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), quick-acting phosphorus (AP), and quick-acting potassium (AK) were measured by potentiometric, ferrocyclic, and oxidative potassium dichromate methods, respectively;
(2) Enzyme activity data: six enzymes related to C/N/P cycling (α-glucosidase AG, β-glucosidase BG, etc.) were measured using microplate fluorescence; (3) Microbial community data: 16S rRNA genes VG, β-glucosidase BG, etc., were measured by Illumina PE300 platform. glucosidase AG, β-glucosidase BG, etc.), which were detected using the microtiter plate fluorescence method; 
(3) Bacterial community data: bacterial community composition and diversity data (e.g., relative abundance of phyla such as Chloroflexi, Actinobacteriota, etc.) were obtained by sequencing the V4-V5 region of the 16S rRNA gene via the Illumina PE300 platform.
The data collected were systematically analyzed through the above methodology to achieve the following objectives: (i) to study the effects of land use and soil depth on bacterial community composition and enzyme activities; (ii) to elucidate the relationship between soil physicochemical properties and bacterial communities as well as enzyme activities; and (iii) to explore the functional roles of enzymes in nutrient cycling and to predict bacterial functional profiles.
Redundancy and beta diversity analyses revealed that while the dominant bacterial phyla (Chloroflexi, Actinobacteriota, Acidobacteriota, and Proteobacteria) were consistent across land-use types, their relative abundances varied significantly. Cultivated lands exhibited higher bacterial diversity and species richness, along with enhanced functionality in C and N cycling. However, long-term tillage led to a decline in soil organic carbon (SOC), nutrient levels, and associated enzyme activities. Soil physicochemical properties, particularly total nitrogen (TN), SOC, and available phosphorus (AP), were identified as key drivers of bacterial community composition.
DOI: 10.15468/dl.6fjq6n
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Platytroctes Günther, 1878",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((17.9945 31.4042,17.9648 31.4107,17.9648 28.8496,26.9648 28.8496,26.9648 31.9498,25.9351 32.1234,25.521 32.0431,25.1292 32.4448,23.62 32.6843,23.2184 33.1274,22.2555 33.4227,21.6592 33.4362,20.3254 32.9854,19.735 32.5293,19.425 31.8208,19.6247 31.1033,19.1159 30.7686,17.9945 31.4042))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012966-250525065834625/datasets/export for details.
DOI: 10.17632/jr8z3c83fx
title: Hydrodynamic processes and extreme events recognized from the sedimentary records at ancient Port Shuomen in the Oujiang River mouth, Southeast China

description: Grain size, alkaline earth metals and eDNA data of sediment studies in Shuomen Ancient Port, Wenzhou
DOI: 10.6084/m9.figshare.22760468.v1
title: Data Set

description: Data Set
DOI: 10.15468/dl.w42qf3
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Oxalis enneaphylla Cav.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012965-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/jybm8hkp9y
title: PVRP-DC-SO instances

description: These are the 36 instances used in the article "The Periodic Vehicle Routing Problem with Driver Consistency and Service Time Optimization", written by Inmaculada Rodríguez-Martín and Hande Yaman, and published in …………….. These data files have the same format as the classical PVRP instances from the literature. We have kept this format, but in for the PVPR-DC-SO we skip some of the information in the files. The infomation we do not consider is: - The maximum duration of a route (denoted by D bellow) - The vehicles’capacity (denoted by Q bellow) - The service duration for each customer (denoter by d bellow) Taking this into account, the files are read in the following way: The first line contains the following information: type m n t where type = 1 (PVRP), m = number of vehicles, n = number of customers, t = number of days. The next t lines contain, for each day ,the following information: D Q where D = maximum duration of a route (0 means 'unbounded'), Q = maximum load of a vehicle. The next lines contain, for the depot and each customer, the following information: i x y d q f a list where i = customer number (0 corresponds to the depot), x = x coordinate, y = y coordinate, d = service duration, q = demand, f = frequency of visit, a = number of possible visit combinations, list = list of all possible visit combinations. Each visit combination is coded with the decimal equivalent of the corresponding binary bit string. For example, in a 5-day period, the code 10 which is equivalent to the bit string 01010 means that a customer is visited on days 2 and 4. (Days are numbered from left to right.)
DOI: 10.6084/m9.figshare.24201588.v1
title: Stranger Like Me Data Files

description: Dataset and files for analysis for the 2024, Journal of Avian Biology Paper by Dominguez et al.
DOI: 10.17632/3bs65nzpv2
title: Simulated ultrasonic pulse-echo well-integrity dataset

description: Pulse echo measurements are used to investigate the conditions on the outside of an oil or gas pipe by sending ultrasound pulses onto the pipe wall from a transducer inside of the pipe. These pulses reverberate within the pipe wall and the returned pulses are recorded at the transducer. A range of different algorithms are used today to analyse these recorded data and estimate pipe-wall thickness and impedance of the material behind the pipe, with the aim of determining the bonding of the material. To be able to develop current algorithms further it is crucial to understand currently used algorithms and their advantages and disadvantages.

The here presented data set is a collection of numerically simulated pulse-echo data for plate and pipe interfaces. This dataset contains pulse-echo trace data for a range of geometric and material variations together with their ground-truth values used to simulate the data. Hence, it allows to investigate the effects of variations like pipe diameter, thickness, bonding, and eccentring on the derived casing thickness and outer-material impedance.

The dataset was build using COMSOL Multiphysics simulations in 2.5D (axisymmetric) and 3D. Dimension of the models were chosen to fit typical pulse-echo set ups, with a transducer diameter of 25 mm and a distance between transducer and pipe/plate of 45 mm. The models were mainly carried out as time-explicit models with an absorbing layer surrounding the model domain to avoid domain boundary reflections. A Gaussian pulse with a 250 kHz centre frequency was used. Most of the models were carried out in 2.5D, as a good approximation of the 3D reality (Diez et. al, 2023). Geometry and material variations of the model include: pipe and plate walls, variations in wall thickness, pipe diameter, distance between transducer and pipe/plate, and variations for the materials inside and outside the pipe/plate. Further we included models with debonding between the pipe/plate and outer solid material, and eccentring between transducer and pipe/plate (3D models). All these variations are give in the Metadata_overview.csv file.
The data was exported from COMSOL as point measurements over the transducer surface (folder with text files). The data was then averaged over the transducer surface and saved together with the metadata allowing to reproduce the model domain as json files. For explanations regarding the json file metadata, please see the README_json.txt file.

The open-source Python toolbox Pyintegrity allows reading this json data into Python and analysing it using one of the implemented pulse-echo analysis algorithms.