cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24998870.v1
title: Supplementary Material for: Accumulation of carbamylation-derived products in aneurysmal aorta

description: Introduction: Carbamylation is a nonenzymatic post-translational modification of proteins characterized by the binding of isocyanic acid to amino groups of proteins, which leads to the alteration of their properties. An increase of serum carbamylation-derived products, including homocitrulline (HCit), has been shown to be associated with the development of cardiovascular diseases. 
Methods: HCit was quantified by LC-MS/MS within extracts of aneurysmal and control human aortas. A mouse model of aortic aneurysm (ApoE-/- mice perfused with angiotensin II and fed with sodium cyanate) was used to evaluate the role of carbamylation in aneurysm development.
Results: HCit quantification showed a greater heterogeneity of values in aneurysmal aortas in comparison with control ones. At the maximum diameter of dilation, HCit values were significantly higher (+94%, p&lt;0.05) compared with less dilated areas. No differences was observed according to aneurysm size or when comparing ruptured and unruptured aneurysms. No significant effect of carbamylation on aneurysm development was observed using the animal model.
Conclusions: These results evidenced the accumulation of HCit within aneurysmal aortas but do not allow to conclude about the exact participation of protein carbamylation in the development of human abdominal aortic aneurysms.
DOI: 10.6084/m9.figshare.26535577.v2
title: Bubble dynamics manipulation in polymeric foaming

description: When pressure releasing a high-pressure-stable polymer/gas mixture, gas bubbles nucleate, grow and impinge to define the typical polyhedral cell structure of a foam. This is the case of a trivial pressure release to ambient pressure. We propose here the use of non-trivial pressure release, in fact, of pressure histories designed to manipulate the foaming process. In particular, by releasing the pressure to an intermediate pressure, it is possible to reduce the bubble growth and prevent impingement, thus gaining a tool for studying phenomena involved in polymer foaming and, more generally, in polymer physics. We studied the model PP/N2 system, and observed bubble growth, Ostwald ripening of close bubbles, bubble interaction causing shape change (from spherical to polyhedral and vice versa) up to coalescence, various bubble growth regimes, and bubble travel after periodic pressure histories. The proposed pressure treatment of nucleated polymer/gas systems allows manipulation of bubble dynamics and represents a powerful tool for characterizing polymers and polymer/gas systems and for validating and interrogating growth, impingement, and coalescence models.
DOI: 10.6084/m9.figshare.27143754.v2
title: Dataset of Intensity-specific and Posture-specific behaviour and health outcomes.

description: This dataset was used for the study with the aims to explore the compositional associations between intensity-specific and posture-specific behaviours and health outcomes in younger (M = 67.35 ± 2.03 years) and older (M = 75.73 ± 4.17 years) older adults. The study involved 309 older adults aged 65 and above from Czech Republic. Participants' intensity-specific behaviors, including sleep, SB, LPA and MVPA, and posture-specific behaviors, including lying, sitting, standing, moving, and walking, were measured using accelerometers. The data were analysed using compositional data analysis (CoDA). This dataset also include results of Timed up and Go test, Falls Efficacy Scale – International questionnaire, Short physical performance battery, usual gait speed and 5 times sit-to-stand test.
DOI: 10.17632/5yv963dhcs
title: Dataset - Co-Research with Children and Adolescents in the Digital Era

description: This dataset compiles empirical studies published between 2000 and 2025 that involved children and adolescents as active co-researchers using digital tools (e.g., apps, tablets, platforms) in qualitative, quantitative, or mixed-method research. The studies were selected based on predefined eligibility criteria and are presented in English or Spanish. Key variables include study objectives, main findings, digital tools used, study design, and the type of participation by children or adolescents. This dataset supports a systematic review exploring the methodological and ethical dimensions of participatory research with minors in digital contexts.
DOI: 10.6084/m9.figshare.12017724.v1
title: Supplementary Material for: Interactive Motion-Assisted Exposure Therapy for Veterans with Treatment-Resistant Posttraumatic Stress Disorder: A Randomized Controlled Trial

description: <b><i>Background:</i></b> Veterans with posttraumatic stress disorder (PTSD) tend to benefit less from evidence-based treatments than other PTSD populations. A novel virtual reality and motion-assisted exposure therapy, called 3MDR, provides treatment in an immersive, personalized and activating context. <b><i>Objective:</i></b> To study the efficacy of 3MDR for veterans with treatment-resistant PTSD. <b><i>Method:</i></b> In a randomized controlled trial (<i>n</i> = 43) 3MDR was compared to a non-specific treatment component control group. Primary outcome was clinician-rated PTSD symptoms at baseline, after 3MDR, and at the 12-week and 16-week follow-up (primary end point). Intention-to-treat analyses of covariance and mixed models were applied to study differences between groups at the end point and over the course of intervention, controlling for baseline scores. <b><i>Results:</i></b> The decrease in PTSD symptom severity from baseline to end point was significantly greater for 3MDR as compared to the control group, with a large effect size (<i>F</i>[1, 37] = 6.43, <i>p</i> = 0.016, <i>d</i> = 0.83). No significant between-group difference was detected in the course of PTSD symptoms during treatment when including all time points. The dropout rate was low (7%), and 45% of the patients in the 3MDR group improved clinically. The number needed to treat was 2.86. <b><i>Conclusions:</i></b> In this trial, 3MDR significantly decreased PTSD symptoms in veterans with, on average, a history of 4 unsuccessful treatments. The low dropout rate may be indicative of high engagement. However, a lack of significant differences on secondary outcomes limits conclusions that can be drawn on its efficacy and underlines the need for larger phase III trials. These data show emerging evidence for 3MDR and its potential to progress PTSD treatment for veterans (Dutch Trial Register Identifier: NL5126).
DOI: 10.6084/m9.figshare.28070483.v1
title: <b>Localised patterns of wild bee abundance indicate woodlands play multiple roles in supporting farmland populations</b> - datasets and code for full analysis

description: <b>Abstract</b>1. Higher woodland cover has been linked to increased wild bee abundance and diversity in temperate agricultural landscapes. However, our understanding of the roles played by the upper and lower strata of woodlands in supporting on-farm bees throughout the season is lacking.2. To explore these roles, we sampled bees (Anthophila) in woodland canopies and understories, and at field margins, from May to July, at 12 sites across agricultural landscapes in Norfolk, England.3. Relative abundance in woodland was generally higher before canopy closure. At this time, total trap catches between all three habitats were largely equivalent, and woodland canopies with flowering <i>Acer pseudoplatanus </i>L. supported more bees. However, throughout the season, open-habitat bee abundance was consistently higher closer to woodlands. After canopy closure, more open areas within woodlands were linked to greater bee abundance, except during a spike in temperatures when understory relative abundance was also at its highest.4. These results indicate that woods on farmland provide floral resources to bees before canopy closure, which can be augmented with nectar-producing canopy trees. They also indicate that more open woodlands likely extend the availability of understory floral resources; and that farmland woods, regardless of management, may continue to provide non-floral resources – including respite from hot weather – throughout the season.
DOI: 10.25403/upresearchdata.20291454.v1
title: Decolonization in archaeology collections

description: The dataset contains narrative notes from the participants and their interpretations. The interviews and questionnaires were employed to collect the data. The content analysis technique was used to interpret the data. With this, the researcher was able to track down, record, and interpret the appearance of concepts from different literature. The supplementary data underpin the study titled 'Towards a decolonised archeology collection: a case study of the National Museum of Namibia'.
DOI: 10.6084/m9.figshare.24470620.v1
title: Annotations and associated frequency signals

description: Labelled industry datasets are the most valuable asset in prognostics and health management (PHM) research. However, creating labelled industry datasets is both difficult and expensive, making publicly available industry datasets rare at best. While labels are generally unavailable, many industry datasets contain annotations, maintenance work orders, or logbooks, with free-form text containing technical language descriptions of component properties, valuable information for any PHM model. Alas, publicly available annotated industry datasets are also scarce, in particular ones with associated signals available. Therefore, we release data from an annotated process industry dataset, consisting of 21090 pairs of signals and annotations from one year of kraftliner production.The annotations are written, in Swedish, by on-site Swedish experts, and the signals consist of accelerometer vibration measurements from two large (80x10x10m) paper machines. The data is cleaned and structured so that each annotation is associated with ten days of signal measurements leading up to the annotation date, where one signal measurement consists of 8192 samples over 6.4 seconds, which becomes 3200 samples stretching over 500 Hz in the frequency domain. The associated annotations are attached to each signal sample, so that the list of annotations is as long as the list of signals. In total, there are 43 unique annotations, though most are associated with multiple signals from different machines due to commonalities in fault descriptions. The language data is pre-processed so that all letters are lower case, numbers are removed, and names are replaced with the Swedish word "egennamn", meaning "name of a person" in English.Also included are pre-computed embeddings, which facilitates faster and easier testing for researchers wanting to easily investigate training signal encoders supervised through technical language supervision. The data presented here was used in the article "Technical Language Supervision for Intelligent Fault Diagnosis in Process Industry" (https://papers.phmsociety.org/index.php/ijphm/article/view/3137). Please cite this article if you use this dataset.To use this dataset without understanding Swedish, please consult "Processing of Condition Monitoring Annotations with BERT and Technical Language Substitution: A Case Study" (https://www.papers.phmsociety.org/index.php/phme/article/view/3356) on how to augment the technical data to facilitate easier language model translations to other languages, and don't hesitate to contact me if you have questions regarding the data.Accessing the data is simple; all you need to do to load spectra and annotation pairs is:import pandas as pdspectra_note_df = pd.read_pickle("TL_spectra_note_df_big.pkl")all_spectra = TL_spectra_note_df['Spectra']all_annotations = TL_spectra_note_df['Notes']Pre-computed embeddings can be accessed through:all_embeddings = TL_spectra_note_df['Embeddings']
DOI: 10.6084/m9.figshare.28296383.v1
title: DNA files of all substrate proteins produced and described in Ryan et al., "A signaling inspired synthetic toolkit for efficient production of tyrosine phosphorylated proteins"

description: Tyrosine phosphorylation is an important post-translational modification that regulates many biochemical signaling networks in multicellular organisms. To date, 46,000 tyrosines have been observed in human proteins, but relatively little is known about the function and regulation of most of these sites. A major challenge has been producing recombinant phosphoproteins in order to test the effects of phosphorylation. Mutagenesis to acidic amino acids often fails to replicate the size and charge of a phosphorylated tyrosine residue and synthetic amino acid incorporation has high cost with relatively low yield. Here, we demonstrate an approach, inspired by how native tyrosine kinases find targets in cells -- through a secondary targeting interaction, augmenting innate catalytic specificity of a tyrosine kinase, without overriding it. We engineered complementary vector systems for multiple approaches to producing high yields of phosphoprotein products in E. coli. Here, we test phosphorylation as a function of the targeting interaction (an SH3-polyproline sequence) affinity, different reaction methods across kinases of different specificity. This system presents an inexpensive and tractable system to producing phosphoproteins and phosphopeptides and we demonstrate how it can be used for testing antibody specificity on targets of EGFR and PD-1. This methodology is a generalizable approach for enhancing the enzymatic action on a recombinant protein via the flexibility of in vitro reactions and co-expression approaches. We refer to this as SISA-KiT, for Signaling Inspired Synthetically Augmented Kinase Toolkit. <br>Described in detail at "A signaling inspired synthetic toolkit for efficient production of tyrosine phosphorylated proteins" Margaret M. Ryan, Reagan Portelance, Graham F. Newman, Gabrielle Martinez, Swathi Shekharan, Anqi Wu, Savannah Angel, Katherine E. Schaberg, Petra Gilmore, Robert Sprung, Reid Townsend, Kristen M. Naegle bioRxiv 2024.12.22.629992; doi: https://doi.org/10.1101/2024.12.22.629992
DOI: 10.6084/m9.figshare.5718487.v1
title: Physiological Responses of Slow-Growing Chickens under Diurnally Cycling Temperature in a Hot Environment

description: ABSTRACT Free-range chicken production has significantly increased in recent years and it often entails exposing birds to cyclic environmental conditions. The objective of the current study was to investigate the effect of bird strain and sex, and rearing system on the physiological responses of Potchefstroom Koekoek (PK), Ovambo (OV) and Naked Neck (NN) chickens reared in a hot environment. Body weight (BW), rectal temperature (RT), respiratory rate (RR) and heart rate (HR) were determined weekly for 4 weeks, in 3 slow-growing chicken strains under cyclic environmental conditions. A total of 288, 20-week old Potchefstroom Koekoek (PK), Ovambo (OV) and Naked Neck (NN) chickens were separated by sex and allocated to extensive and intensive rearing systems. Ambient temperature and relative humidity (RH) were used to compute a temperature humidity index (THI). A Proc MIXED model was used to analyze fixed effects and a linear regression model was fitted to test the relationship between THI and response parameters. All factors studied influenced (p&lt;0.05) BW while none affected (p&gt;0.05) RT. Higher BW (p&lt;0.05) were obtained with OV in both rearing systems. Sex influenced (p=0.0021) HR but not RR (p&gt;0.05). Week and rearing system affected (p&gt;0.05) RR. THI showed significant correlation with RR and HR. THI was higher in intensive than extensive rearing. Physiological responses of PK, OV and NN are comparable under similar rearing conditions.
DOI: 10.6084/m9.figshare.17111420.v1
title: Supplementary Material for: Lower Serum Potassium Levels at Admission are Associated with the Risk of Recurrent Stroke in Patients with Acute Ischemic Stroke or Transient Ischemic Attack

description: <b><i>Introduction:</i></b> Serum potassium abnormality is a risk factor of incident stroke, but whether it is associated with recurrent stroke in patients with acute ischemic stroke (AIS) or transient ischemic attack (TIA) remains unknown. This study aimed to investigate the association of serum potassium with the risk of recurrent stroke in patients with AIS or TIA. <b><i>Methods:</i></b> We included 12,425 patients from the China National Stroke Registry III. Patients were classified into 3 groups according to tertiles of potassium. The outcomes were recurrence of stroke and combined vascular events at 1 year. Cox proportional hazards regression was adopted to explore the associations by calculating hazard ratios (HRs) and their 95% confidence intervals (CIs). <b><i>Results:</i></b> Among 12,425 enrolled patients, the median (interquartile range) of potassium was 3.92 (3.68–4.19) mmol/L. Compared with the highest tertile, after adjusted for confounding factors, the lowest tertile potassium was associated with increased risk of recurrent stroke at 1 year. The adjusted HR with 95% CI was 1.21 (1.04–1.41). There was an independent, linear association between serum potassium and stroke recurrence. Per 1 mmol/L decrease of potassium was associated with 19% higher risk of recurrent stroke (HR, 1.19; 95% CI, 1.04–1.37). Similar trends were found in ischemic stroke and combined vascular events. <b><i>Conclusions:</i></b> Lower serum potassium level was independently associated with elevated risk of recurrent stroke in patients with AIS or TIA. The finding suggested that monitoring serum potassium may help physicians to identify patients at high risk of recurrent stroke and to stratify risk for optimal management.
DOI: 10.6084/m9.figshare.7159967.v1
title: Supplementary Material for: How Long Non-Coding RNAs and MicroRNAs Mediate the Endogenous RNA Network of Head and Neck Squamous Cell Carcinoma: a Comprehensive Analysis

description: <b><i>Background/Aims:</i></b> Long non-coding RNAs (lncRNAs) act as competing endogenous RNAs (ceRNAs) to compete for microRNAs (miRNAs) in cancer metastasis. Head and neck squamous cell carcinoma (HNSCC) is one of the most common human cancers and rare biomarkers could predict the clinical prognosis of this disease and its therapeutic effect. <b><i>Methods:</i></b> Weighted gene co-expression network analysis (WGCNA) was performed to identify differentially expressed mRNAs (DEmRNAs) that might be key genes. GO enrichment and protein–protein interaction (PPI) analyses were performed to identify the principal functions of the DEmRNAs. An lncRNA-miRNA-mRNA network was constructed to understand the regulatory mechanisms in HNSCC. The prognostic signatures of mRNAs, miRNAs, and lncRNAs were determined by Gene Expression Profiling Interactive Analysis (GEPIA) and using Kaplan–Meier survival curves for patients with lung squamous cell carcinoma. <b><i>Results:</i></b> We identified 2,023 DEmRNAs, 1,048 differentially expressed lncRNAs (DElncRNAs), and 82 differentially expressed miRNAs (DEmiRNAs). We found that eight DEmRNAs, 53 DElncRNAs, and 16 DEmiRNAs interacted in the ceRNA network. Three ceRNAs (HCG22, LINC00460 and STC2) were significantly correlated with survival. STC2 transcript levels were significantly higher in tumour tissues than in normal tissues, and the STC2 expression was slightly upregulated at different stages of HNSCC. <b><i>Conclusion:</i></b> LINC00460, HCG22 and STC2 exhibited aberrant levels of expression and may participate in the pathogenesis of HNSCC.
DOI: 10.6084/m9.figshare.16866292.v1
title: Supplementary Material for: Molecular detection of parvovirus in Manchurian chipmunks (Tamias sibiricus asiaticus) captured in Korea

description: Cross-species transmission of viral diseases alarms our global community for its potential of novel pandemic events. Of various viral pathogens noted recently, parvoviruses have posed public health threats not only to humans but to wild animals. To investigate the prevalence of parvoviruses in wild Manchurian chipmunks, here we detected genetic fragments of the nonstructural protein of parvovirus by polymerase chain reaction in wild Manchurian chipmunk specimens captured in the central and southern regions of South Korea and compared their sequence homology with references. Of a total of 348 specimens examined, chipmunk parvovirus (ChpPV)-specific gene fragments were detected with a 31.32 % rate (109 chipmunks of 348) in their kidney, liver, lung, and spleen samples, and the chipmunks captured in Gangwon Province exhibited the highest positive rate (45.37%), followed by Gyeongsang (35.29%), Gyeonggi (31.03%), Chungcheong (20.00%), and Jeolla (19.70%). When compared with the reference sequences registered in GenBank, a partial ChpPV sequence showed 97.70% identity to the previously reported Korean strain at the nucleic acid level. In the phylogenetic analysis, ChpPV exhibited closer relationship to primate parvoviruses, erythroviruses, and bovine parvovirus than to adeno-associated viruses. Despite limited sample size and genetic sequences examined in this study, our results underline the prevalence of ChpPV in Korea and emphasize the need of close surveillance of parvoviruses in wild animals.
DOI: 10.6084/m9.figshare.23586384.v1
title: Bitterling eggs and embryos NCN

description: This is dataset used to come to conclusion of large-scale sampling of bitterling prevalence and abundance in freshwater mussels across polish water bodies.
DOI: 10.17632/t2b9httjsm
title: MATLAB code for: Scour effects on lateral behavior of pile groups in sands

description: MATLAB codes for laterally loaded pile group analysis under scoured conditions using the proposed method as described in the manuscript title "Scour effects on lateral behavior of pile groups in sands"
DOI: 10.6084/m9.figshare.5125825.v1
title: Supplementary Material for: Emotions and Memory in Borderline Personality Disorder

description: Memory processes such as encoding, storage, and retrieval of information are influenced by emotional content. Because patients with borderline personality disorder (BPD) are particularly susceptible to emotional information, it is relevant to understand whether such memory processes are altered in this patient group. This systematic literature review collects current evidence on this issue. Research suggests that emotional information interferes more strongly with information processing and learning in BPD patients than in healthy controls. In general, BPD patients do not seem to differ from healthy control subjects in their ability to memorize emotional information, but they tend to have specific difficulties forgetting negative information. Also, BPD patients seem to recall autobiographical, particularly negative events with stronger arousal than healthy controls, while BPD patients also show specific temporo-prefrontal alterations in neural correlates. No substantial evidence was found that the current affective state influences learning and memory in BPD patients any differently than in healthy control subjects. In general, a depressive mood seems to both deteriorate and negatively bias information processing and memories, while there is evidence that dissociative symptoms impair learning and memory independently of stimulus valence. This review discusses methodological challenges of studies on memory and emotions in BPD and makes suggestions for future research and clinical implications.
DOI: 10.17632/mhnksdw8jn
title: Protein-level mutant p53 reporters identify druggable low-frequency precancerous clones in noncancerous tissues

description: Protein-level mutant p53 reporters identify druggable low-frequency precancerous clones in noncancerous tissues
DOI: 10.5281/zenodo.15314459
title: PyTomography SPECT Tutorial data

description: This data set contains raw SPECT projection data acquired on a variety of scanners and for a variety of isotopes. The data is used in the official PyTomography SPECT tutorials at this website.
DOI: 10.5281/zenodo.15314460
title: PyTomography SPECT Tutorial data

description: This data set contains raw SPECT projection data acquired on a variety of scanners and for a variety of isotopes. The data is used in the official PyTomography SPECT tutorials at this website.