cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/bb7tvwfss6
title: How social movements use religious creativity to address environmental crises in Indonesian local communities (1990-2022)

description: This dataset contains raw data and methodological explanations for a modified framework synthesis of 244 empirical studies (in English and Indonesian) on 208 environmental social movements operating in local communities in Indonesia from 1990 through 2022. 

The study resulted in a conceptual model showing how grassroots movements used lived religion to create new environmental practices and motivate environmental behavioural changes in diverse local communities. The study inventoried 571 examples of lived religious concepts, practices, rituals and systems that movements used to create environmental concepts and practices. 

This dataset includes four files:
 
Appendix A: Methods and data classification
This document provides further details about the methods and data classification used to conduct a modified synthesis framework.

Appendix B. Methods data
This Excel spreadsheet contains raw data for conducting the study with search logs, screening, and the classification of sources. Included sheets are:
• Search Logs: log of searches, count of summary data and chart
• Screening – Bibliographic Records: worksheet to screen 648 bibliographic sources
• Screening – Full-text sources: worksheet to screen 469 full-text sources
• Classification – Sources: classification sheet for 244 sources used in the study with descriptive characteristics
• Type of Sources: summary data and charts
• Language of Sources: summary data and charts

Appendix C. Results data 
This excel spreadsheet contains raw data on descriptive characteristics of the movements and the inventory of items used by movements. Included sheets are: 
• Inventory Content: Inventory of items used by movements to create new environmental concepts and practices.
• Classification – Movements: classification sheet for 208 movements by descriptive characteristics
• Date: summary data and charts
• Region: summary data and charts
• Province: summary data and charts
• District: summary data and charts
• Aims: summary data and charts
• Environmental Issues: summary data and charts
• Lived Religion: summary data and charts
• Religion and Other: summary data and charts

Appendix D. Movements and sources list 
This PDF file includes full bibliographic details of all 244 sources used in the study with a chart displaying which sources were used for each movement. 

Results of data analysis can be explored using interactive ArcGIS maps. 

Map of Environmental Social Movements in Indonesia 1990-2022 (ArcGIS): 
https://bit.ly/CRCS-map-movements

Map of Eco-religious Creativity (ArcGIS):
https://bit.ly/CRCS-map-content
DOI: 10.17632/pysgjrmbnv
title: Very low-field (0.05T) MR repeatability data 

description: Very low-field MR has emerged as a promising alternative to high-field MRI scanners, offering several advantages. The major benefits are that very low-field scanner are portable and affordability and low maintenance. However, challenges remain in integrating very low-field MRI into clinical practice and ensuring their widespread adoption in both high and low-resource settings. Some of the limitations include lower signal-to-noise ratio (SNR), low spatial resolution, and long scan time. Also, these systems are susceptible to environmental factors such as temperature, humidity, electromagnetic interference (EMI) and magnetic field inhomogeneity, and gradient heating. The repeatability data was acquired on in vitro phantom (ProMRI, ProProject, USA) at 0.05T from MultiWave Technologies, France.

The data was collected over 10 days (folders D1 to D10) with each folder containing 3 subfolders for 3 sessions (S1 to S3). Each session had a 3D TSE folder and two off-resonance (ΔB0) maps (before and after 3D TSE). The B0 folder had two 3D TSE sequences with an echo shift of 49μs between them. The Findf0 folder had f0 measurements before and after each scan to evaluate the effect of frequency drift on the image. We have also included phantom data acquired using Siemens 3T Skyra scanner with a 20-channel head and neck coil.
DOI: 10.17632/s5yvzkw4k3
title: Physical and biogenic complexity mediates ecosystem functions in urban sessile marine communities

description: Dataset associated with the paper "Physical and biogenic complexity mediates ecosystem functions in urban sessile marine communities" (2022) published in Journal of Applied Ecology.

Abstract:
 1 – The influence of habitat complexity on biodiversity is a central theme in ecology, with many studies reporting positive relationships. Reconciliation approaches in urbanised areas, such as eco-engineering, have increasingly focused on ‘re-building’ the complexity of degraded and/or homogenised habitats to support biodiversity. Yet the effects of increasing complexity and biodiversity on ecological functions are rarely measured. 
2 – We assessed how increasing the physical and/or biogenic complexity of habitats affects the net and gross primary productivity (NPP and GPP, respectively), community respiration and nutrient cycling (specifically dissolved inorganic phosphorus and nitrogen) of intertidal sessile marine communities at three sites. We manipulated physical complexity using two types of settlement tiles: ‘complex’, with crevices and ridges, and ‘flat’. We increased biogenic complexity on half the replicates of each tile type by seeding with oysters. 
3 – Increased physical and biogenic complexity resulted in greater sessile species richness at all sites. Although many variables assessed varied with sites and time of measurements, overall, GPP and NPP was greater on flat tiles than on complex ones.  These patterns were not explained by differences in the total surface area of tiles.. 
5 – Daily flux rates of Dissolved inorganic phosphorus had a significant positive relationship with biogenic complexity. There were no effects of biogenic or physical complexity on the net fluxes of dissolved inorganic nitrogen. 
6 – Effects of habitat complexity on the productivity and nutrient cycling of marine sessile communities were largely unrelated to diversity measures, such as richness or abundance of key taxa and functional groups. 

Synthesis and applications: Eco-engineering practices that manipulate habitat complexity might benefit from explicit functional targets that also consider associated ecosystem services, as we found that under some conditions there is a trade-off between biodiversity and functional targets. Our results suggest that increasing habitat complexity has a positive effect on sessile species richness, but not necessarily on productivity (GPP and NPP). The species pool available as well as light availability is likely to mediate effects of complexity on assemblages, so local environment needs to be a key consideration when designing interventions.
DOI: 10.6084/m9.figshare.1203566.v2
title: PONE-D-14-13172 Cell viability

description: Cell viability raw data about MS PONE-D-14-13172
DOI: 10.6084/m9.figshare.5202751.v1
title: The entropy value for driver fatigue detection

description: This is the four entropies of twelve healthy subjects for driver fatigue detection. Due to personal privacy, the digital number represents different participants. Each .mat file included five files, namely FE, SE, AE and PE described four entropy values in the training data and the corresponding label of class, which the number 1 represents the fatigue state and 0 represents the normal state in the process of driving.
DOI: 10.17632/8dpyj2wtsb
title: Data Files and Sample Solutions for “Scheduling Tugboats in a Seaport”

description: This folder contains data files of the problem instances that the authors have used in the computational experiments of the paper “Scheduling Tugboats in a Seaport.” It also contains a set of sample solutions.
DOI: 10.17632/cz3xt8mbpn
title: Synovial tissues histology from patients with end-stage osteoarthritis, soft tissue and traumatic injuries of the knee 

description: Cartilage degeneration is the hallmark of osteoarthritis (OA). The research hypothesis investigated was that the inflammatory response of synovium to different insults would vary both with the insult and with patient characteristics. We sought to determine which elements of synovial reactivity were linked to cartilage debris in OA patients. 

The data shows histopathology microimages of haematoxylin and eosin (HE)-stained knee synovial tissues from osteoarthritic total knee replacement and non-osteoarthritic soft tissue and trauma injury patients. Knee medial gutter synovial tissue samples were obtained from a cohort of 15 endstage primary osteoarthritis, and 17 patients with no clinical or radiological evidence of arthritis, 9 ligament tears and 8 tibial plateau fractures. Images show evidence of varying degrees of synovitis in the three different pathology groups. In addition, features such as cartilage debris and focal aggregations of inflammatory cells were noted.

The Mendeley data repository contains 32 individual patient folders containing the H&E-stained synovial tissue section images with identification grids and location maps. Each H&E folder holds a complete tissue section image labelled as HE_sample id_full, an image grids trail map labelled as HE_sample id_map, together with sequentially numbered image grids. Evidence of cartilage debris and inflammatory cells infiltration were most notable in the OA group.

Individual folder IDs can be linked to an anonymised set of individual patient’s data in the data in brief submission. Linked anonymised clinical data includes patient’s pathology, gender, age, body mass index (BMI), duration of symptoms, blood pressure, leukocytes count, C-reactive protein concentration, S100A8A9 protein level, ASA grade, cumulative illness rating scale (CIRS), WOMAC osteoarthritis index score, SF-12 physical component score and SF-12 mental component score. The holistic data can therefore inform of potential relationships between patient well-being, knee x-ray data, function and synovial tissue features.

The data were acquired following informed consent (Medical ethics approval reference: 15/NW/0661). All patients underwent knee surgery at the Liverpool University Hospitals NHS Foundation Trust, Liverpool. Exclusion criteria included RA patients and infection. Formalin fixed paraffin embedded synovial tissues were sectioned at 5μm and stained with haematoxylin and eosin. Images of all tissues were captured and anonymised and used to assess synovitis in all tissues according to the criteria of Krenn et al (2006). Histological microimages of each complete synovial tissue were captured at 20x and digitalised using an Aperio CS2 Digital Pathology Scanner.

These images can be utilised for further comparative characteristics of synovial tissue histology in the OA, arthroscopy and trauma groups to underpins the involvement of synovial tissues in OA pathogenesis.
DOI: 10.17632/j3kx2wtd2n
title: Long-term observation dataset of reactive oxidized nitrogen in the atmosphere of Mount Tai

description: This is the raw dataset for "Reactive oxidized nitrogen at a high mountain site in the North China Plain: Chemical speciation and temporalvariations during 2007-2023"
DOI: 10.6084/m9.figshare.26139184.v1
title: <b>Metagenome sequencing and 107 microbial genomes from across seamounts along in the Yap and Mariana trenches</b>

description: Microbes in the sediments across a series of seamounts along the island arc of the Yap and Mariana trenches were investigated by metagenome. In this study, we reconstructed 107metagenome-assembled genomes (MAGs), including 100bacteria and 7archaea. Of these MAGs, 26 (24.3%) were "near complete" (completeness &gt;90%), 50 (46.7%) were &gt;80% completeness, and 31 (29.0%) were &gt;75% completeness. Phylogenomic analysis revealed that over 85(n = 92) of these MAGs represented new taxa at different taxonomical levels. The species composition of these MAGs was most consistent with the previous reports, with the most abundant phyla being Proteobacteria (n = 39), Methylomirabilota (n = 27), and Nitrospirota (n = 7). These draft genomes provided novel data on species diversity and function in the seamountmicrobial community, which will provide reference data for extensive comparative genomic studies across crucial phylogenetic groups worldwide.
DOI: 10.6084/m9.figshare.25020908.v1
title: Gender Identity Stigma Teachers Acceptance and Parental Support as Predictors of Mental Health Among LGBT SHS Students.xlsx

description: The main purpose of the study was to investigate whether gender identity stigma, teachers’ acceptance, and parental support were predictors of mental health among LGBT senior high school students utilizing the predictive research design. A non-probability sampling, specifically the combination of convenience and snowball sampling was employed. A total of four hundred senior high school students participated in the study. Results revealed that the gender identity stigma, teachers’ acceptance, and parental support significantly predict the mental health of the respondents (F (3, 396) = 37.695, p&lt;.001. Specifically, Gender Identity Stigma (β = -.224, t = -4.542, p &lt; .001) negatively predicted Overall Mental Health while both Teachers’ Acceptance (β = .201, t = 4.493, p &lt; .001) and Parental Support (β = .253, t = 5.102, p &lt; .001) positively predicted the Overall Mental Health. The result of the study helped in developing intervention programs that will enhance the existing policy on gender and development in the education sector.
DOI: 10.17632/4w6krnywhn
title: Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples: Supplementary Data 1

description: Supplementary data for the study "Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples" by Reza Mirzazadeh, Zaneta Andrusivova and Ludvig Larsson et al. 

Spatially resolved transcriptomics (SRT) has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of unbiased SRT methods targeting the polyA tail of mRNA, relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available SRT assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present the RNA-Rescue Spatial Transcriptomics (RRST) workflow to improve mRNA recovery and robustness for fresh frozen (FF) specimens with moderate-to-low RNA quality. First, we benchmarked RRST against the standard Visium spatial gene expression protocol on high RNA quality samples. Then, we demonstrate the RRST to recover and rescue data from challenging samples including; human lung, colon, small intestine, childhood brain tumor, mouse brain and mouse bone/cartilage. Our results demonstrate RRST as a versatile, powerful, and reproducible protocol for FF specimens of different qualities and origins. 

Available data:
1. gene annotation files are available in the genes/ folder.
2. R objects containing spot annotations are available in the R_objects/ folder.
3. Sheets in .xlsx or .csv format containing sample meta data, annotations of mouse bone tissue and Visium FFPE probe set information are available in the sheets/ folder.
4. Tar archives containing spaceranger output files are available in the spaceranger_output/ folder.
5. High resolution H&E images are available in the images/ folder for colon, lung, mousebone, mousebrain, pediatric braun tumor and prostate cancer samples. Small intestine H&E images can be found in Supplementary Data 2 (see paper).
DOI: 10.17632/mcdfnhwjm9
title: Musculoskeletal Disorders in nursing workers

description: A systematic review of musculoskeletal disorders affecting nursing workers was carried out. Its factors, tasks and alternatives were identified to reduce the risks of suffering musculoskeletal disorders.
DOI: 10.6084/m9.figshare.24328660.v1
title: <b>MAPLES-DR: </b>MESSIDOR Anatomical and Pathological Labels for Explainable Screening of Diabetic Retinopathy

description: MAPLES-DR (MESSIDOR Anatomical and Pathological Labels for Explainable Screening of Diabetic Retinopathy), contains new diagnoses for DR and ME as well as new pixel-wise segmentation maps for 10 retinal structures on 198 images of the MESSIDOR public fundus dataset.4 Anatomical Structures: Optic Disc, Optic Cup, Macula, and Vessels;3 Bright Lesions: Exudates, Cotton Wool Spots, and Drusens;3 Red Lesions: Microaneurysms, Hemorrhages, and NeovesselsThe fundus images corresponding to the diagnostic labels and biomarker segmentation maps of MAPLES-DR are the property of the MESSIDOR consortium and are freely available from the Consortium's website.
DOI: 10.6084/m9.figshare.29104646.v1
title: Dataset for "Negative CO2 emissions to mitigate extremes in land hydrological cycle"

description: This dataset comprises the post‑processed data files and analysis scripts used in the study "Negative CO2 emissions to mitigate extremes in land hydrological cycle" by Shin et al. It includes model outputs from a nine‑member CESM2 ensemble simulation under both zero‑ and negative‑emissions scenarios. The full raw dataset is available upon request due to its large size.
DOI: 10.17632/tzgxsnfbdp
title: 2H-SIAM(1.0) for 2H-labeled Stable Isotope Assisted metabolomic

description: READ THE FILE "README.pdf" FIRSTLY.
2H-SIAM(V1.0).exe is a feature list-based algorithm (Win10, VB based) developed for tracking possible isotopologue pairs of stable isotope-labeled organic matters. With the help of this algorithm, we developed a 2H-labeled Stable Isotope Assisted metabolomic (2H-SIAM) pipeline which facilitate the screening of transformation products (TPs) of the substrates with high confidence. Additionally, our proposed 2H-SIAM pipeline is equipped with full GUI interface which contribute to lower the skill barriers of its application in research field. We provided example data and a step-by-step protocol for evaluation
DOI: 10.6084/m9.figshare.11316656.v3
title: Supplementary Files (Mitochondrial Genome Rearrangement in Amphibians)

description: <b>Additional file 1: Table S1. </b>Amphibian species with mt gene duplication or loss in this study. (XLSX 12 kb) <b>Additional file 2: Figure S1.</b><b> </b>Phylogenetic tree of all amphibians studied using ML method based on the nucleotide dataset of 13 mt PCGs. The number of species sampled for each lineage is shown in brackets. We marked the branches of the species with mt gene rearrangements and the names of species only involved with PCGs rearrangements in dark red, and a pale red background was set on the branch of neobatrachians, the group with the most intensive rearrangements. (PDF 542 kb) <b>Additional file 3: Figure S2.</b> Mitogenomic rearrangement patterns of all amphibian species investigated. The numbers in first column indicated the occurrence frequencies of patterns(a number less than three is defined as a rare rearrangement in this study). (PDF 119 kb) <b>Additional file 4: Word S1. </b>Amplification scheme and primers sequences for sequencing four mitochondrial genomes in this study.(DOCX 14.2kb) <b>Additional file 5: Text S1. </b>Multiple sequence alignment file (fasta format, an input file for constructing phylogenetic trees) based on nucleic acid sequences of 13 protein-coding genes from 233 species mitogenomes. (TXT 2899kb) <b>Additional file 6: Table S2. </b>List of best models for performing phylogenetic tree based on BI method in this study. (XLSX 10 kb)<b></b><br>
DOI: 10.6084/m9.figshare.21564780.v1
title: CattleGTEx-Gene expression data

description: The TPM values and counts for 8742 samples and 27607 genes （ARS-UCD1.2)
DOI: 10.17632/64sr8nwn64
title: Program and Data for "Asset holders' Consumption Risk and Tests of Conditional CCAPM"

description: The zipped folder contains the set of code and data necessary to replicate the results in the article "Asset holders' Consumption Risk and Tests of Conditional CCAPM" , forthcoming in the Journal of Financial Economics.
DOI: 10.17632/cnc2j4h26b
title: Facial Interlandmark distances on CT soft tissue models of 388 living persons

description: Averaged facial ILDs on CT-derived models and on ReFace approximations were reported by Simmons-Ehrhardt et al. [13] for 388 living subjects in the U.S.A.  These ILDs (Fig. 1) were defined by 12 standard anthropometric landmarks [22].  The CT database comprised both sexes and four ancestry groups, African female (n=50), African male (n=48), Asian female (n=48), Asian male (n=47), European female (n=49), European male (n=48), Hispanic female (n=49), and Hispanic male (n=49).   Each ReFace facial approximation was determined within the appropriate demographically related dataset, but from which data for each target was temporarily removed.  The approximations were compared with the known CT-derived 3D models, testing the verisimilitude of ReFace approximations by modeling a facial recognition system.
[13] T.L. Simmons-Ehrhardt, T. Flint, C.P. Saunders, K.L. Monson, Quantitative accuracy and 3D biometric matching of 388 statistically estimated facial approximations of live subjects, Forensic Img 21 (2020) 200377. doi:10.1016/j.fri.2020.200377.
[22] L.G. Farkas, Anthropometry of the Head and Face, 2nd ed., Raven Press, New York, 1994.
DOI: 10.6084/m9.figshare.27637749.v1
title: Supplementary Material for: Speech Perception Outcomes with the Anatomy-Based Fitting Map Among Experienced, Adult Cochlear Implant Users: A Longitudinal Study.

description: Introduction:
Anatomy-based fitting (ABF), a relatively new technique for cochlear implant programming, attempts to lessen the impact of the electrode insertion location-related frequency-to-place mismatch (FPM). This study aimed to compare vowels and consonant perception in quiet and in noise among experienced adult cochlear implant (CI) users using the ABF and the regular, conventional-based fitting (CBF) map (pre-ABF) over six months. 
Method:
Nine ears from eight experienced adult CI users were included in the experimental and longitudinal research. Using surgical planning software called Otoplan, post-operative computed CT scans were used to determine the locations of intracochlear electrodes and their angle of insertion. The anatomy-based frequency bands were produced by Maestro 9.0 CI fitting software using the Otoplan data. Nonsense syllables with consonant-vowel-consonant (CVC) recognition scores in quiet and noise (+5dB SNR) were compared at baseline, three, and six months after ABF. The vowels involved were /a, i, u/, while the consonants were voiced /b, d, g/ and voiceless /p, t, k/ plosives. Speech pieces were presented at 30 dB SL in a sound-treated room through a loudspeaker positioned at 0° azimuth. 
Results:
On average, the ABF maps shifted center frequency ranging from 0.46 semitones (0.04 octave) at (E12) to 23.94 semitones (1.99 octave) at (E1) as compared to the CBF maps. The mean vowel and consonant identification scores in quiet and in noise were significantly higher in ABF than in CBF (p&lt;0.05) with a large effect size and the trend of improvement was seen with time. Voiced consonants had better scores than the voiceless consonants. 
Conclusion:
The results demonstrated improved perception of vowels and consonants, particularly for sounds containing voicing cues after using the ABF maps. The results also suggested that ABF could be more effective for voice detection in noise. Overall, the findings indicate that correcting place mismatch with an ABF map may improve speech perception, at least among experienced adult cochlear implant users.