cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21205604
title: Supplementary Material for: Convolution Neural Networks and Targeted Fluorescent Nanoparticles to Detect and ICDAS Score Caries

description: Previous work has shown targeted fluorescent starch nanoparticles (TFSNs) can label the subsurface of carious lesions and assist dental professionals in the diagnostic process. In this study, we aimed to evaluate the potential of using artificial intelligence (AI) to detect and score carious lesions using the ICDAS in combination with fluorescent imaging following application of TFSNs on teeth with a range of lesion severities, using ICDAS-labeled images as the reference standard. A total of 130 extracted human teeth with ICDAS scores from 0 to 6 were selected by a calibrated cariologist according to ICDAS. Then, the same surface was imaged with a stereomicroscope under white-light illumination, and blue-light illumination with an orange filter following application of the TFSNs. Both sets of images were labeled by another blinded ICDAS-calibrated cariologist to demarcate lesion position and severity. Convolutional Neural Networks, state-of-the-art models in imaging AI, were trained to determine the presence, location, ICDAS score (severity), and lesion surface porosity (as an indicator of activity) of carious lesions, and tested by 30 k-fold validation for white-light, blue-light, and the combined image sets. The best models showed high performance for the detection of carious lesions (sensitivity 80.26%, PPV 76.36%) and potential for determining the severity via ICDAS scoring (accuracy 72%, SD 5.67%) and the detection of surface porosity as an indicator of the activity of the lesions (accuracy 90%, SD 7.00%). More broadly, the combination of targeted biopolymer nanoparticles with imaging AI is a promising combination of novel technologies that could be applied to many other applications.
DOI: 10.17632/s4dtmfmzxw.1
title: Semantic Coherence Dataset - SCD

description: Textual data are central to assess metrics built on top of language models. The dataset contains speech transcripts, which were arranged into two main classes, intended to experiment on intra-subject semantic coherence, and on inter-subject semantic coherence. Transcripts collected have been extracted from talks during almost 13 hours (overall 12:45:17) for the former class, and almost 30 hours (29:47:34) for the latter one.
Data delivered in this dataset have been employed to investigate whether the perplexity metric provides reliable results, both in within-subject condition and in across-subject condition. More specifically, perplexity is a measure originally conceived to assess the probabilistic inference properties of language models: it has been recently proved to be an appropriate device to categorize speech transcripts from healthy subjects vs. subjects suffering from Alzheimer Disease. This dataset has been employed to investigate the reliability of the perplexity metrics; data herein can be reused to conduct analysis on measures that rely on probabilistic models and that are aimed at analyzing the linguistic features of text documents.
DOI: 10.5281/zenodo.6822933
title: Chesapeake Bay Vertical Land Motions 2020

description: Global Positioning System (GPS) data from the 2020 campaign in the Chesapeake Bay region
DOI: 10.6084/m9.figshare.20301120
title: Supplementary Material for: Sulfatase-2 from cancer associated fibroblasts – an environmental target for hepatocellular carcinoma?

description: Introduction: Heparin sulfate proteoglycans in the liver tumour microenvironment (TME) are key regulators of cell signaling, modulated by Sulfatase-2 (SULF2). SULF2 overexpression occurs in hepatocellular carcinoma (HCC). Our aims were to define the nature and impact of SULF2 in the HCC TME. Methods: In liver biopsies from 60 patients with HCC, expression and localisation of SULF2 was analysed associated with clinical parameters and outcome. Functional and mechanistic impacts were assessed with immunohistochemistry (IHC), in silico using The Cancer Genome Atlas (TGCA), in primary isolated cancer activated fibroblasts, in monocultures, in 3D spheroids and in an independent cohort of 20 patients referred for sorafenib. IHC targets included αSMA, glypican-3, β-catenin, RelA-P-ser536, CD4, CD8, CD66b, CD45, CD68 and CD163. SULF2 impact of peripheral blood mononuclear cells was assessed by migration assays, with characterization of immune cells phenotype using fluorescent activated cell sorting. Results: We report that while SULF2 was expressed in tumour cells in 15% (9/60) of cases, associated with advanced tumour stage and type-2-diabetes, SULF2 was more commonly expressed in cancer associated fibroblasts (CAFs)(52%) and independently associated with shorter survival (7.2 versus 29.2 months, p=0.003). Stromal SULF2 modulated glypican-3/β-catenin signalling in-vitro, although in vivo associations suggested additional mechanisms underlying the CAF-SULF2 impact on prognosis. Stromal SULF2 was released by CAFS isolated from human HCC. It was induced by TGFβ1, promoted HCC proliferation and sorafenib resistance, with CAF-SULF2 linked to TGFβ1 and immune exhaustion in TGCA HCC patients. Autocrine activation of PDGFRβ/STAT3 signalling was evident in stromal cells, with release of the potent monocyte/macrophage chemoattractant CCL2 in vitro. In Human PBMCs, SULF2 preferentially induced migration of macrophage precursors (monocytes), inducing a phenotypic chance consistent with immune exhaustion. In human HCC tissues, CAF-SULF2 was associated with increased macrophage recruitment, with tumouroid studies showing stromal-derived SULF2 induced paracrine activation of the IKKβ/NF-κB pathway, tumour cell proliferation, invasion and sorafenib resistance. Conclusion: SULF2 derived from CAFs modulates glypican-3/β-catenin signalling, but also the HCC immune TME, associated with tumour progression and therapy resistance via activation of the TAK1/IKKβ/NF-κB pathway. It is an attractive target for combination therapies for patients with HCC.
DOI: 10.6084/m9.figshare.20418567
title: Supplementary Material for: Screening of Serum miRNAs as Diagnostic Biomarkers for Lung Cancer Using the Minimal-Redundancy-Maximal-Relevance Algorithm and Random Forest Classifier Based on a Public Database

description: <b><i>Background:</i></b> Lung cancer is one of the deadliest cancers, early diagnosis of which can efficiently enhance patient’s survival. We aimed to screening out the serum miRNAs as diagnostic biomarkers for patients with lung cancer. <b><i>Methods:</i></b> A total of 416 remarkably differentially expressed miRNAs were acquired using the limma package, and next feature ranking was derived by the minimal-redundancy-maximal-relevance method. An incremental feature selection algorithm of a random forest (RF) classifier was utilized to choose the top 5 miRNA combination with the optimum predictive performance. The performance of the RF classifier of top 5 miRNAs was analyzed using the receiver operator characteristic (ROC) curve. Afterward, the classification effect of the 5-miRNA combination was validated through principal component analysis and hierarchical clustering analysis. Analysis of top 5 miRNA expressions between lung cancer patients and normal people was performed based on GSE137140 dataset, and their expression was validated by qPCR. The hierarchical clustering analysis was used to analyze the similarity of 5 miRNAs expression profiles. ROC analysis was undertaken on each miRNA. <b><i>Results:</i></b> We acquired top 5 miRNAs finally, with the Matthews correlation coefficient value as 0.988 and the area under the curve (AUC) value as 0.996. The 5 feature miRNAs were capable of distinguishing most cancer patients and normal people. Furthermore, except for the lowly expressed miR-6875-5p in lung cancer tissue, the other 4 miRNAs all expressed highly in cancer patients. Performance analysis revealed that their AUC values were 0.92, 0.96, 0.94, 0.95, and 0.93, respectively. <b><i>Conclusion:</i></b> By and large, the 5 feature miRNAs screened here were anticipated to be effective biomarkers for lung cancer.
DOI: 10.6084/m9.figshare.21118888
title: Supplementary Material for: Diverse Parental Perspectives of the Social and Educational Needs for Expanding Newborn Screening through Genomic Sequencing

description: <b><i>Objective:</i></b> The aim of this study was to explore the parental views, attitudes, and preferences of expanded newborn screening (NBS) through genomic sequencing. <b><i>Study Design:</i></b> We conducted a semi-structured interview study with English and Spanish speaking mothers who had given birth within the USA in the past 5 years. The interviews explored opinions of expanding NBS, ethical and privacy concerns, and educational and social needs. <b><i>Results:</i></b> All participants were interested in some degree of NBS expansion. However, there were differing opinions about the characteristics of conditions that should be included with less consensus for conditions with low penetrance, those without approved treatment, or onset outside of early childhood. All parents endorsed potential medical utility but also nonmedical utility as a motivating factor including being able to prepare and not being surprised by health issues as they occurred. Most felt that it was important to have some choice about the conditions screened, and many expressed the importance of proper education to make an informed choice and a desire to receive this education in the prenatal period. Responses to the type of education and information needed to make an informed decision varied. <b><i>Conclusions:</i></b> Parents anticipate value in expanded NBS through genomic sequencing both for medical and nonmedical/personal utility. In order to successfully implement expanded NBS, prospective parents need more and earlier education about the process. These needs may differ by language and culture. Information needs to be easily accessible and to be curated by appropriate experts and stakeholders, including parents representative of the diversity of the USA.
DOI: 10.6084/m9.figshare.21369006
title: Supplementary Material for: Clinical Significance and Properties of IFN-γ<sup>+</sup>IL-17<sup>+</sup> Th17 Cells in Liver Injury Associated with Chronic Hepatitis B Virus Infection

description: <b><i>Introduction:</i></b> Our previous study demonstrated that intrahepatic Th17 cells exacerbated the progression of chronic hepatitis B virus (HBV) infection. Meanwhile, we found a small group of IFN-γ and IL-17 double-positive Th17 cells (IFN-γ<sup>+</sup>IL-17<sup>+</sup> Th17 cells) in liver tissues. This study aimed to investigate the clinical significance and properties of IFN-γ<sup>+</sup>IL-17<sup>+</sup> Th17 cells in liver injury associated with chronic HBV infection. <b><i>Methods:</i></b> The frequencies of CD4<sup>+</sup> Th cells, Tregs, and CD4<sup>+</sup> T cells expressing specific chemokine receptors in the blood and liver tissues were detected using flow cytometry. The chemotaxis of C C chemokine receptor 5 (CCR5) and C-X-C chemokine receptor 3 (CXCR3) toward IFN-γ<sup>+</sup>IL-17<sup>+</sup> Th17 cells and Tregs was evaluated by transwell chemotactic assay. Analyses of different variables were performed using GraphPad Prism v 5.01 and IBM SPSS Statistics 23.0. HBV-specific IFN-γ<sup>+</sup>IL-17<sup>+</sup> Th17 cells were investigated using a cell stimulation assay with HBV antigens in vitro. <b><i>Results:</i></b> The frequencies of IFN-γ<sup>+</sup>IL-17<sup>+</sup> Th17, Th17 cells, and Tregs in the blood were increased from normal controls to chronic hepatitis B (CHB) and acute-on-chronic liver failure (ACLF). The same trend could also be observed in CHB liver tissues compared to those in CHB blood specimens. Furthermore, the frequencies of IFN-γ<sup>+</sup>IL-17<sup>+</sup> Th17 cells were positively associated with Th17 cells, Th17 cell-related cytokines (IL-17 and IL-6), HBV DNA load, and the levels of HBsAg, HBeAg, and ALT. The ratios of IFN-γ<sup>+</sup>IL-17<sup>+</sup> Th17 cells to Tregs extremely decreased in ACLF blood specimens compared with those in CHB blood specimens. Additionally, CCR5 and CXCR3 were conducive to the recruitment of IFN-γ<sup>+</sup>IL-17<sup>+</sup> Th17 cells and Tregs to liver tissue. <b><i>Conclusions:</i></b> IFN-γ<sup>+</sup>IL-17<sup>+</sup> Th17 cells have Th17 cell-like properties in the progression of chronic HBV infection. CCR5 and CXCR3 facilitated the recruitment of IFN-γ<sup>+</sup>IL-17<sup>+</sup> Th17 cells and Tregs to the liver. Importantly, the ratio of IFN-γ<sup>+</sup>IL-17<sup>+</sup> Th17 cells to Tregs might be an effective assessment indicator of the severity of liver injury.
DOI: 10.5281/zenodo.6822832
title: Chesapeake Bay Vertical Land Motions 2019

description: Global Positioning System (GPS) data from 2019 campaign in the Chesapeake Bay region
DOI: 10.6084/m9.figshare.19588444
title: Supplementary Material for: The Effects of Consuming <b><i>Cannabis</i></b> Flower for Treatment of Fatigue

description: <b><i>Objectives:</i></b> We measure for the first time how commercially available <i>Cannabis</i> flower products affect feelings of fatigue. <b><i>Methods:</i></b> A total of 1,224 people recorded 3,922 <i>Cannabis</i> flower self-administration sessions between June 6, 2016, and August 7, 2019, using the Releaf App. Usage sessions included real-time subjective changes in fatigue intensity levels prior to and following <i>Cannabis</i> consumption, <i>Cannabis</i> flower characteristics (labeled phenotype, cannabinoid potency levels), combustion method, and any potential experienced side effects. <b><i>Results:</i></b> On average, 91.94% of people experienced decreased fatigue following consumption with an average symptom intensity reduction of 3.48 points on a 0–10 visual analog scale (SD = 2.70, <i>d</i> = 1.60, <i>p</i> &lt; 0.001). While labeled plant phenotypes (“<i>C. indica</i>,” “<i>C. sativa</i>,” or “hybrid”) did not differ in symptom relief, people that used joints to combust the flower reported greater symptom relief than pipe or vaporizer users. Across cannabinoid levels, tetrahydrocannabinol, and cannabidiol levels were generally not associated with changes in symptom intensity levels. <i>Cannabis</i> use was associated with several negative side effects that correspond to increased feelings of fatigue (e.g., feeling unmotivated, couch-locked) among a minority of users (&lt;24% of users), with slightly more users (up to 37%) experiencing a positive side effect that corresponds to increased energy (e.g., feeling active, energetic, frisky, or productive). <b><i>Conclusions:</i></b> The findings suggest that the majority of patients experience decreased fatigue from consumption of <i>Cannabis</i> flower consumed in vivo, although the magnitude of the effect and extent of side effects experienced likely vary with individuals’ metabolic states and the synergistic chemotypic properties of the plant.
DOI: 10.6084/m9.figshare.20226009
title: Supplementary Material for: Preliminary Study of Genome-Wide Association Identified Novel Susceptibility Genes for Hemorheological Indexes in a Chinese Population

description: <b><i>Background:</i></b> Genome-wide association studies for various hemorheological characteristics have not been reported. We aimed to identify genetic loci associated with hemorheological indexes in a cohort of healthy Chinese Han individuals. <b><i>Methods:</i></b> Genotyping was performed using Applied Biosystems Axiom™ Precision Medicine Diversity Array in 838 individuals, and 6,423,076 single nucleotide polymorphisms were available for genotyping. The relations were examined in an additive genetic model using mixed linear regression and combined with identical by descent matrix. <b><i>Results:</i></b> We identified 38 genetic loci (<i>p</i> &lt; 5 × 10<sup>−6</sup>) related to hemorheological traits. In which, <i>LOC102724502</i>-<i>OLIG2</i> rs28371438 was related to the levels of nd30 (<i>p</i> = 8.58 × 10<sup>−07</sup>), nd300 (<i>p</i> = 1.89 × 10<sup>−06</sup>), erythrocyte rigidity (<i>p</i> = 1.29 × 10<sup>−06</sup>), assigned viscosity (<i>p</i> = 6.20 × 10<sup>−08</sup>) and whole blood high cut relative (<i>p</i> = 7.30 × 10<sup>−08</sup>). The association of <i>STK32B</i> rs4689231 for nd30 (<i>p</i> = 3.85 × 10<sup>−06</sup>) and nd300 (<i>p</i> = 2.94 × 10<sup>−06</sup>) and <i>GTSCR1</i>-LINC01541 rs11661911 for erythrocyte rigidity (<i>p</i> = 9.93 × 10<sup>−09</sup>) and whole blood high cut relative (<i>p</i> = 2.09 × 10<sup>−07</sup>) was found. <i>USP25</i>-<i>MIR99AHG</i> rs1297329 was associated with erythrocyte rigidity (<i>p</i> = 1.81 × 10<sup>−06</sup>) and erythrocyte deformation (<i>p</i> = 1.14 × 10<sup>−06</sup>). Moreover, the association of <i>TMEM232</i>-<i>SLC25A46</i> rs3985087 and <i>LINC00470</i>-<i>METTL4</i> rs9966987 for fibrinogen (<i>p</i> = 1.31 × 10<sup>−06</sup> and <i>p</i> = 4.29 × 10<sup>−07</sup>) and plasma viscosity (<i>p</i> = 1.01 × 10<sup>−06</sup> and <i>p</i> = 4.59 × 10<sup>−07</sup>) was found. <b><i>Conclusion:</i></b> These findings may represent biological candidates for hemorheological indexes and contribute to hemorheological study.
DOI: 10.6084/m9.figshare.21162259
title: Supplementary Material for: Salivary Proteins as Dental Caries Biomarkers: A Systematic Review

description: Salivary proteins play an important role in repairing mechanisms of damaged tissues and the maintenance of oral health. However, there is a dearth of information in the literature regarding the concentrations of salivary proteins in caries-free (CF) and caries-active (CA) subjects. Hence, this systematic review was conducted to update our previous systematic review published in 2013 that aimed to assess the association between caries and salivary proteins by comparing CF and CA individuals. Thereby, evaluating the possibility of whether salivary proteins can be regarded as biomarkers for caries. An extensive search of studies was conducted using PubMed, EMBASE, Clarivate Analytics’ Web of Science, and Elsevier’s Scopus between July 2012 and January 2022, without any language restriction. Manual searching in Google Scholar and evaluation of bibliographies of the included studies were also undertaken. The Newcastle-Ottawa Scale was used to assess the risk of bias (RoB) within the included studies. Of 22 included studies, 1551 human subjects (range: 30 – 213 participants) were recruited, of which 848 (54.7%) were CA and 703 (45.3%) individuals were CF. Regarding the utilization of DMFT as the caries index, high variability was observed across different articles. A statistically significant increase in the salivary levels of alpha-amylase, acidic proline-rich protein-1, histatin-5, lactoperoxidase, and mucin-1 was found in CA patients, while the salivary levels of carbonic anhydrase 6, proteinase-3, and statherin were observed to be significantly increased in CF subjects. Conflicting results were found regarding the salivary levels of immunoglobulin-A and total proteins among CA and CF subjects. The included studies were categorized as low RoB (n=15), medium RoB (n=4), and high RoB (n=3). Due to significant heterogeneity among the included studies, no meta-analysis could be performed. In conclusion, salivary levels of protein(s) might be useful biomarker for caries diagnosis, especially alpha-amylase, acidic proline-rich protein-1, histatin-5, lactoperoxidase, mucin-1, carbonic anhydrase 6, proteinase-3, and statherin. However, their diagnostic value must be verified by large-scale prospective studies.
DOI: 10.6084/m9.figshare.21212912
title: Supplementary Material for: Knowledge and Attitudes about Privacy and Secondary Data Use among African-Americans Using Direct-to-Consumer Genetic Testing

description: <b><i>Introduction:</i></b> The rapidly expanding direct-to-consumer genetic testing (DTC GT) market is one area where narratives of underrepresented populations have not been explored extensively. This study describes African-American consumers’ personal experiences with and perceptions about DTC GT and explores similarities and differences between African-Americans and an earlier cohort of mostly European American consumers. <b><i>Methods:</i></b> Twenty semi-structured, qualitative interviews were held with individuals who self-identified as Black/African-American and completed DTC GT between February 2017 and February 2020. Interviews were transcribed and consensus-coded, using inductive content analysis. <b><i>Results:</i></b> Participants generally had positive regard for DTC GT. When considering secondary uses of their results or samples, most participants were aware this was a possibility but had little concrete knowledge about company practices. When prompted about potential uses, participants were generally comfortable with research uses but had mixed outlooks on other nonresearch uses such as law enforcement, cloning, and product development. Most participants expressed that consent should be required for any secondary use, with the option to opt out. The most common suggestion for companies was to improve transparency. Compared to European American participants, African-American participants expressed more trust in DTC GT companies compared to healthcare providers, more concerns about law enforcement uses of data, and a stronger expression of community considerations. <b><i>Discussion/Conclusion:</i></b> This study found that African-American consumers of DTC GT had a positive outlook about genetic testing and were open to research and some nonresearch uses, provided that they were able to give informed consent. Participants in this study had little knowledge of company practices regarding secondary uses. Compared to an earlier cohort of European American participants, African-American participants expressed more concerns about medical and law enforcement communities’ use of data and more reference to community engagement.
DOI: 10.6084/m9.figshare.21654983
title: Supplementary Material for: Potential Embolic Sources in Embolic Stroke of Undetermined Source Patients with Patent Foramen Ovale

description: <b><i>Introduction:</i></b> A patent foramen ovale (PFO) may coexist with other potential embolic sources (PESs) in patients with embolic stroke of undetermined source (ESUS), leading to difficulty in attributing the stroke to either the PFO or other PESs. We aimed to investigate the prevalence and predictors of concomitant PESs in ESUS patients with PFOs. <b><i>Methods:</i></b> A retrospective cohort study was conducted in a tertiary stroke centre. Consecutive patients with ESUS and a concomitant PFO admitted between 2012 and 2021 were included in the study. Baseline characteristics and investigations as a part of stroke workup including echocardiographic and neuroimaging data were collected. PESs were adjudicated by 2 independent neurologists after reviewing the relevant workup. <b><i>Results:</i></b> Out of 1,487 ESUS patients, a total of 309 patients who had a concomitant PFO with mean age of 48.8 ± 13.2 years were identified during the study period. The median Risk of Paradoxical Embolism (RoPE) score for the study cohort was 6 (IQR 5–7.5). Of the 309 patients, 154 (49.8%) only had PFO, 105 (34.0%) patients had 1 other PES, 34 (11.0%) had 2 PES, and 16 (5.2%) had 3 or more PES. The most common PESs were atrial cardiopathy (23.9%), left ventricular dysfunction (22.0%), and cardiac valve disease (12.9%). The presence of additional PESs was associated with age ≥60 years (<i>p</i> &lt; 0.001), RoPE score ≤6 (<i>p</i> <i>≤</i>0.001), and the presence of comorbidities including diabetes mellitus (<i>p</i> = 0.004), hypertension (<i>p</i>≤ 0.001), and ischaemic heart disease (<i>p</i> = 0.011). <b><i>Conclusion:</i></b> A large proportion of ESUS patients with PFOs had concomitant PESs. The presence of concomitant PESs was associated with older age and a lower RoPE score. Further, large cohort studies are warranted to investigate the significance of the PES and their overlap with PFOs in ESUS.